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1. Manufacturers Sensors Instruments and Calibrations SPECCHIO defines Manufacturers Sensors Instruments and Calibrations which each have their own table in the database Manufacturer A manufacturer of spectroradiometric instruments The list of possible Manufacturers is a fixed table in SPECCHIO Users cannot add to it change it or even view it If you require a new Manufacturer to be added you must contact your System Administrator The table as released with this version of SPECCHIO can be found in Appendix B Predefined Manufacturer Table of this document Each Manufacturer is assigned an integer Manufacturer ID Sensor A description of a physical setup of a Sensor or a model of a spectroradiometric Instrument A Sensor is usually identified by a Sensor type designator also referred to as a Instrument type or Instrument model which is generally defined by the manufacturer Each Sensor has a fixed number of bands average wavelengths and FWHM Full Width at Half Maximum per channel and a Sensor type number usually a numeric code given by the manufacturer Each Sensor Type is defined only once in the database As released SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 20 of 134 SPECCHIO Instrument Calibration Example Manufacturer G E R Manufacturer ID Name URL Short Name User Guide SPECCHIO has a standard set of Sensors already defined in its database The table a
2. SPECCHIO Metadata selection tabs C Metadata editor VIN Order by Le Hierarchy Tree Browser i on Example Order By Indicator t Ji GER Example User Guide Metadata Spectrum Metadata display area Group selection area Campaign Metadata pamp ng Date v Generic Target Properties Vegetation example J Thumination J Instrument J Instrument Settngs J Instrumentaten J Keywords Figure 39 Metadata editor dialog Hierarchy Tree Browser Order By Indicator Refresh button Update button Reset button Metadata selection tabs Metadata display area Spectrum Metadata Group selection area Shows the Campaigns present in the database and allows selecting of Campaigns sub trees and Spectra Select the sort order to use for Spectra in the left hand Campaign navigation window Click this button to update the Campaign Tree Navigator after making changes which affect it Click this button to write all changed Metadata back into the database Click this button to ignore all changes made since the last time the Update button was clicked and redisplay the Metadata panel from the database Select either Campaign to display and edit Campaign related Metadata or Metadata to display and edit Spectrum related Metadata This will show the Metadata selected by the Metadata selection tab Click on these checkboxes to display or suppress the various Groups of Spectru
3. 2009 The Spectral Database SPECCHIO for Improved Long Term Ssability and Data Sharing Computers amp Geosciences 35 3 pp 557 565 Hueni A Rey S Schl pfer D Schopfer J amp Kneubuehler M 2009 Visualisation Processing and Storage of Spectrodirectional Data Based on the Spectral Database SPECCHIO IGARSS 09 Cape Town South Africa Hueni A Schopfer J Schl pfer D Kneubuehler M amp Nieke J 2008 Pre processing of Dual view FIGOS data Towards Operational BRDF Retrieval Proceedings ISPRS Beijing China Landgrebe D 1997 On Information Extraction Principles for Hyperspectral Data West Lafayette IN Purdue University Oracle Technology Network 2013 Java Regular Expressions Tutorial Retrieved June 21 2013 from http docs oracle com javase tutorial essential regex index html SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 128 of 134 SPECCHIO User Guide Schaepman Strub G Schaepman M amp al e 2006 Reflectance Quantities in Optical Remote Sensing Definitions and Case Studies Remote Sensing of Environment 103 27 42 Schopfer J 2008 Spectrodirectional Ground based Remote Sensing Using Dual view Goniometry Zurich Remote Sensing Laboratories Schopfer J Dangel S amp al e 2007 Dual Field of View Goniometer System FIGOS 10th Intl Symposium on Physical Measurements and Spectral Signatures in Remote Sensing Davos Switzerland Wikipedia
4. 3 Band Average Wavelength nm Full Width at Half the Maximum FWHM nm 350 351 352 353 354 355 356 357 358 359 Figure 98 Part of a Sensor definition file being edited in Excel CW ON Om fF WMH PO Ph Mh PhS PM PS PS PO PS fo oh A text file view of the same file Note that the tab positions do not appear to line up when displayed this way Name Description Company Type no no of channels ASD FSFR ASD Fieldspec FR ASD 4 2151 Band Average Wavelength nm Full width at Half the Maximum FWHM nm 1 350 2 2 351 2 3 352 2 4 353 2 5 354 2 6 355 2 7 356 2 8 357 2 9 358 2 10 359 2 11 360 2 12 361 2 13 362 2 14 363 2 15 364 2 16 365 2 17 366 2 18 367 2 19 368 2 20 369 2 21 370 2 Instrument Administration Any user can open the Instrument Administration dialogs but only Administrators can save changes to the database For each Instrument in the SPECCHIO database the following fields are stored Field name Instrument Text string This name will appear in the name dropdown list of Instruments Instrument Selected from dropdown list of This Institute list is created in the owner Institutes Create new user account dialog See section 3 2 User Accounts SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 117 of 134 SPECCHIO User Guide Serial Text string The Instrument s physical serial number number Sensor Selected from dropdown list of Defines the Instrument type or model Senso
5. A new query is performed every time any change is made in any Metadata entry box Initially no query is active so the Matching Spectra box is empty The searching follows these rules e A search condition is created by making the search conditions for a Metadata Attribute non empty Empty fields do not trigger any search conditions e Initially all Metadata query fields are empty Even the data time fields are empty but the date time dialog displays the current date and time in this case e Once a date time selection field is modified it cannot be made empty again Therefore searching will be done on this date time until the dialog box is closed This applies independently to the start and end date times e Anew query is performed every time any field is changed Even if only one character is typed or removed a new query is performed For date time fields a new query is performed each time the date time picker is closed e To be selected a Spectrum must satisfy all search criteria entered SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 86 of 134 SPECCHIO User Guide e The minima and maxima search conditions for a numeric or date time Metadata Attribute are independent That is it is valid to enter just a minimum or just a maximum value e Numeric and date time search ranges are inclusive That is if you enter a minimum Spectrum Number of 20 Spectra with Spectrum Number greater or equal to 20 will be selected
6. click on that O timen Spectrum here triticaa 011 triticaa 012 tritcasa 0135 triticaa 014 triticaa 015 triticas 016 Refresh To see the Reference Spectrum for a selection of Target Spectra enter an SQL search string to select them in this box Filename restriction Figure 33 Viewing Target Spectra and their related Reference Spectra Use this Hierarchy tree browser to select one or more Spectra Enter an SQL matching string in the Filename restriction control to restrict the Target Spectra selected See section 4 8 SQL Matching Strings This control does not affect the display of the Spectra in the hierarchy tree browser display It only reduces the effectively selected Spectra to those that also match the SQL matching string The File Names of all Reference Spectra linked to the selected Spectra will be shown in the Linked references box If you select the Campaign node and clear the Filename restriction control all linked Reference Spectra in the Campaign will be displayed If any Target Spectrum is displayed in the Linked References box a link has been set up in the wrong direction Because each Target Spectrum should not be linked to more than one Reference Spectrum the number of Reference Spectra displayed should be less than the number of Target Spectra selected Right hand side Use this side of this dialog to select Reference Spectra and show their related Target Spectra It operates in t
7. is stored in the SPECCHIO database Refer to section 4 6 Changing your User Details for more information 3 3 Administrator Access Certain SPECCHIO functions such as uploading Instrument definitions and Calibrations require administrator permission For normal Users these menu operations are greyed out When the SPECCHIO database is created it has an Administrator account defined The User Name and Password for this account are not generally advertised See your SPECCHIO Administrator if you require access to these administration functions 3 4 Campaigns SPECCHIO organises the Spectra for each new sampling experiment into Campaigns The Spectral data in each Campaign can be viewed and operated on together Campaigns can contain Spectra measured with different instruments and sensors including instruments of different Sensor types and measurements done at different times using an Instrument which has been calibrated one or more times between these measurements 3 5 Campaign Hierarchy Structure On your computer the Spectral data files for a Campaign must be placed into a sub folder structure which organises the Spectra according to their context or sampling design SPECCHIO does not impose any restrictions on the complexity of Campaign and sub folder hierarchies SPECCHIO does not enforce any particular way of using this hierarchical structure The hierarchy tree structure can have any number of levels and can be unbalanced if des
8. pdf Version 3 1 05 03 2014 User Guide Horizon Name Alpha string Horizon Number Integer Each of the following measurements has two Metadata Attributes the measurement itself and a description field which holds an alpha string describing the method used to determine that measurement The table below lists the expected measurement unit and gives a brief explanation where the name is not self explanatory Air Dry Water Content g g Water content of air dried soil Available P Available phosphorus Bulk Density g cm2 Carbon CEC cmol Kg Clay Coarse Sand Electrical Conductivity Deci Siemens Metre Exchangeable Acidity cmol Kg Exchangeable Ca cmol Kg Exchangeable K cmol Kg Exchangeable Mg cmol Kg Exchangeable Na cmol Kg Extractable Fe mg Kg Fine Sand Geothite Gibsite Hematite Illite Kaolinite Montmorillonite pH CaCl2 pH Page 45 of 134 SPECCHIO User Guide DH Water pH Silt Smectite Total K Total N Total P Water Content 0_1 Bar cm2 cm2 Water Holding Capacity 15 Bar 3 14 21 Vegetation Biophysical Variables Crown Cover Percentage Tree Crown Cover Percentage Approx Crown Metres Estimated tree crown diameter Diameter Chlorophyll Content ugrams cm2 Chlorophyll content of the collected vegetation sample rns We wen oe clea vegeaton anoe Water Content Grams cm2 Wa
9. section 3 15 Spaces Space Factory and Data Processing using the Space Network Pressing the Process button in the Data Hierarchy Browser or Query Builder starts this processing tool The window below appears Querv Builder 000 Space Network Processor Browser Query c 0 M Show only my data Type Sensor instrument Space gt 3 mona test Campaign D 2151 gt test byte arr Campaign gt 0 Soil and Water Experiment Campa Y lagos_artificial_turf Campaign v lagos_artificial_turf Y f hem_a_20 gt EE gt i reference gt Q hem_b_30 gt hem c 40 gt 0 FEK4B Andys Spectra Campaign gt I mfr Campaign gt Q sdb_admin_test Campaign Number of resulting rows gt 0 Avalanche Study Campaign gt ithe new test Campaign 66 gt B Overcast_sky Campaign Vectors 66 S ee Se Se Se lc eS E S a S O O gt Gi test_envi_lib Campaign Show report Fileexport Process gt 9 DiY_slbs Campaign M M gt i todays test campaign Campaign gt rsl instruments Campaign a gt ii test_after_load_fiddling Campaign X Figure 60 Space Network Processor interface with the Query Builder in the background A number of spaces are placed on the processing plane of the Space Network Processor depending on the query built in Query Builder Figure 60 shows a space containing 66 Spectra created based on a selection in the Query Builder Figure 61 shows the common elements o
10. 1 05 03 2014 Page 73 of 134 SPECCHIO User Guide and Shift keys The operations in the preceding section will then apply to all selected Spectra Similarly it is possible to select multiple nodes in the Campaign hierarchy and operate on all Spectra in those nodes Warning Do not select multiple Spectra or nodes across different Campaigns and then update all selected Spectra to share the same Metadata values If subsequent users select the Apply to all spectra button when editing Metadata it will change the Metadata across both Campaigns which is a very unexpected and confusing result 4 17 Uploading Metadata from Excel files SPECCHIO supports uploading Metadata to your Campaign from Excel spreadsheet files saved as an XLS file It does not support loading form CSV XLSX or other Excel file formats Nominated 5l B c D E F Matching E File Name I emperature Latitude Longitude Elevation Location Column 2 triticaa 001 23 2 35 222 140 02 264 2 Highfield Forest 3 triticaa 002 23 3 35 232 140 02 264 2 Highfield Forest 4 triticaa 003 23 4 35 242 140 02 264 2 Highfield Forest 5 triticaa 004 23 5 35 252 140 02 264 2 Highfield Forest DaO 6 triticaa 005 264 2 Highfiel amp Forest one triticag OC i 4 C Spectrum 23 8 35 28 23 9 35 292 24 35 302 24 1 35 312 24 2 35 322 24 3 35 332 When the the row data are Matches Matching copied to that Q TD Column Spectru
11. 18 Sampling Geometry Group cccscscscscscssvensvencesecesecesecesecusuarsuarsrensrareraseras 42 3 14 19 Scientific References Group cccccccsesceteeceeeeeseueurerseseseceeueueerersenenesueaearens 44 3 14 20 Soil Parameters Group ccscscscscscsescnenscensnensenecenecesecusesusucasrausransvarsraneras 44 3 14 21 Vegetation Biophysical Variables ccccscecscseceeseeeeeeeeeeeeeeeeeeeesenesenenenenees 46 3 15 Spaces Space Factory and Data Processing using the Space Network 0006 46 A SPECCHIO Basic Operation wcisisissstccswccsicscisavcessnsacsacrwawssteanedennsseanaccuns 49 ek Mac Operaio sssrinin ania Ea 49 ta WII OD aO a T 49 o Mah WINGON derriera Ereuna Ea 50 4 4 Logging In and Connecting to a Database s sssssssssssrssrnnnnrnnrnsrnrnsnnsrnrnsnnrnnne 51 Aa MONG OUR einn E E E eet E E tent 52 4 6 Changing your User Details ssssssussnsusnannnnannnnnnnnnnnnnnnnsnnnnnnannannnnnsnnnnnnnnnnnnnnn 52 4 7 Browsing the Hierarchy Tree s asssssssannnnansnannnnannnnnnnnnnnnnnnnnnnnnnnnnnannnnnsnnnnnnnnnnnnnnn 52 Ao SOL MatCNINO SUING Sst snnadecsesctensanederte naaa Aoii 54 4 9 Entering Dates and TIMes ssssssussunnnnusnannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnsnnnnnnnnnnnnnnn 54 4 10 Overview of SPECCHIO Data Loading ssssesssneresrsnnrnnrernrnnrsrnrnsnnrnrnennrnrnrnnne 54 4 11 Creating a new Campaign cc0 c cccccceeeececesececesccececeeccesesecensenessssessceeesreeeeeeeeers 55 4 12 Load
12. 254 0 98 0 02 255 0 981 0 02 256 0 98 0 02 257 0 98 0 02 258 0 98 0 02 259 0 981 0 02 260 0 98 0 02 261 0 98 0 02 262 0 978 0 02 263 0 979 0 02 Before loading a calibration file a Sensor definition fitting the wavelengths of the calibration must be present in the database In the case of Spectralon reference panels the Sensor definition is the Perkin Elmer Lambda 19 Sensor To add a new place marker Calibration e Select the correct Reference Panel to display its data e Right click anywhere within the Calibrations box A menu is displayed e Select Add calibration from this menu A new Calibration with empty information is immediately loaded to the database and displayed e Enter the required Calibration identification parameters You cannot enter the actual calibrated values e Click Update to write the new Calibration information back to the database To add a new complete Calibration from a file e Select the correct Reference Panel to display its data e Right click anywhere within the Calibrations box A menu is displayed e Select Add calibration from file from this menu A file selection dialog is displayed e Select the Calibration file you wish to upload To remove a Calibration e Right click anywhere over the Calibration you wish to remove from this Instrument s information A menu is displayed e Select Remove calibration from this menu The Calibration information is immediately removed from the databa
13. ASD calibration files cannot be loaded as SPECCHIO calibration files The Spectra from these Instruments are adjusted according to the calibration within the ASD Instrument itself and so there is no requirement to load them here SPECCHIO reads the centre wavelengths of the Instrument bands from these files but ignores the Spectrum values when reading these files as Calibration files In normal operations the same file which is used to load an Instrument Calibration would also be read by the general Campaign Spectra load process see 4 10 Overview of SPECCHIO Data Loading Note Other file formats which also store centre wavelengths of bands such as Ocean Optics UniSpec single beam GER 3700 or APOGEE are not yet supported by SPECCHIO for Calibration file reading Attempting to use these file formats may lead to unpredictable results SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 120 of 134 SPECCHIO User Guide To add a new place marker Calibration e Select the correct Instrument to display its data e Right click anywhere within the Calibrations box A menu is displayed e Select Add calibration from this menu A new Calibration with empty information is immediately loaded to the database and displayed e Enter the required Calibration identification parameters You cannot enter the actual calibrated values e Click Update to write the new Calibration information back to the database To add a new complete Calibration
14. Bah mixed instr_INR ASD_calil_BODY csv Bal mixed instr_INR ASD_cali_HDR csv Bal mixed instr_RSL ASD 1_BODY csv Bah mixed instr_RSL ASD 1_HDR csv Bal mixed instr_RSL GER 3700_BODY csv Bah mixed instr_RSL GER 3700_HDR csv 5 4 1 CSV Spectrum Export Format Multiple Spectra are written into a single CSV file with the data for each Spectrum in a separate column If the Split header and body option is selected then the header and body are written into separate CSV files Otherwise they are written into a single CSV file header first The header contains as many lines as there are Metadata Attributes defined in all of the selected Spectra The first column of each row is the Metadata Attribute name The body contains one row for each wavelength The first column is the wavelength in nanometres and the subsequent columns are the values at those wavelengths for each selected Spectrum The following figure shows an Excel view of a CSV file created with three Spectra and the header and body written into the same file ojo N On e Go ho a 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 Pp oA UB Number Comment Capture date Loading date Filename Internal no of avg Is reference Latitude Longitude Altitude Location Campaign name Campaign desc Landcover Cloud cover octas Ambient temp C Air pressure Rel humidity Wind direction Wind speed
15. Data Browser window will open e Using the Hierarchy Browser select a Hierarchy node or a selection of Spectra The Spectra IDs will appear in the Matching Spectra box e Right click in the Matching Spectra box A menu will appear e Select Copy R ready query to clipboard from the menu e Switch to the R application and paste the query from the clipboard as you require References for a list of academic articles related to SPECCHIO and its use SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 7 of 134 SPECCHIO 2 Glossary User Guide The explanations of words and terms in this glossary include both those terms which may not be familiar to some readers and those which have a specific meaning in the context of SPECCHIO or this document Calibration Client server FOR Codes HTTP HTTPS Instrument Type Australian National Data Service This body hosts the Research Data Australia RDA service SPECCHIO supports publishing research data to this service See http www ands org au and Chapter 7 Publishing Data to ANDS The process of linking an Instrument s response to a defined physical input for example assigning the correct wavelengths to a band or assigning factors that describe the relationship between radiance and recorded digital numbers Refers to an activity during which Spectral samples were acquired A Campaign is defined in a contextual sense It is not restricted by any temporal or spatial prop
16. It will overwrite any previous results SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 83 of 134 SPECCHIO User Guide Data Query and Output The Spectrum Browser The SPECCHIO Spectrum Browser allows users to browse the Campaign hierarchy to locate Spectral data and then to launch operations on the selected data Those operations are selected by clicking the one of the row of six buttons in the right hand panel The operations of these buttons is explained in sections with those names in this chapter Select Data Processing amp Output Browse data hierarchy from the Main Window to see the following window Data Browser V3 dE _X d isualisations Gonio Example Vegetation example GER Example 1 en S Splitting rules for file export and plotting Split spaces by sensor Split spaces by sensor and unit Split spaces by sensor instrument calibration_no and unit Figure 51 The main Browse data hierarchy window Visualisations This menu item displays a drop down list of graphic visualisation options which you can apply to the Spectra listed in the Matching Spectra box These options match those listed in section 8 5 Visualisation Modules Depending on the option and Spectra selected some of these Visualisation options may take several minutes to process Show only my data Set this check box to restrict the display in the Hierarchy Tree browser to Campaigns
17. Note that when using a UNIX system you may have to enter a dot as filename see section 4 2 Unix Operation Base name Enter a character string which will be prefixed to the file name This name should contain only characters that are allowed in filenames depends on your operating system The base name is used to build the real filenames according to one of the following patterns lt base name gt _ lt sensor_name gt lt file extension gt lt base name gt _ lt instrument_name gt cal lt calibration sequence number gt lt file extension gt The actual choice of naming pattern depends on the selection made in the Splitting rules for exporting and plotting question in the previous Query builder dialog or Data browser dialog If no Instrument has been defined the Sensor name will be used Split header and body Applies to CSV files only The Spectra data will be split into two separate CSV files The body file will have the string _Bopy appended to the file name and _Hpr is appended to the file name for the header file ENVI SLB files are always split into header and body The data are also split according to the selection made on the Splitting rules for file export and plotting question in the Query Builder or Spectrum Browser dialogs See comment below about file naming Time format Select your desired time format Selecting milliseconds makes it easier to use the timestamp as an X axis value in Excel plotting The data file names
18. Open on terra a Figure 18 Specifying a pathname under UNIX using the dot as entry in the Enter file name box Depending on the UNIX windowing system some of the dialogs are not properly displayed unless they are maximized 4 3 Main Window SPECCHIO s Main Window opens when the application is started It is used to launch all of SPECCHIO s functions Main Menu Progress Report Database Panel Connection Info 4 SPECCHIO V3_ Database Data Input Data Processing amp Output Data Maintenance Special Functions Help Database connection status Connected as PRobert to https gsw 1 dc 10 dev vm intersect org au 8 18 1 specchio_service Figure 19 Main window Main menu Select the SPECCHIO functions you wish to run from here SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 50 of 134 SPECCHIO User Guide Progress Report Panel Displays the database connection information and information about the progress of many of SPECCHIO s processes e g file loading Database Connection Status This information is displayed in the Progress Report Panel and shows the User Name you are logged in as and the database you are logged in to The panel on the left side of this window is not used in this version of SPECCHIO 4 4 Logging In and Connecting to a Database Because the user account details are kept in the database connecting to the SPECCHIO database and logging in are performed as one operation
19. Page 101 of 134 SPECCHIO User Guide 8 4 3 Reference Data Reference name RSL Field Spectralon 10 RSL 003 SRT 99 100 KH Show Reference Info Figure 68 Reference panel setting in the Metadata Editor If no calibration data can be found a warning is displayed and the module creates no output space Figure 69 shows a processing chain that selects the panel correction factors and plots using a Spectral line plot Figure 70 0 Proc module Get Panel Correction Factors 1 Ref panel com factors Vis module Spectral Line Plot Type Sensor instrument Space Settings Type Spectral Space Settings D 2151 is d D 2251 Waiting for data Status Waiting for data Vectors 66 ahis Vectors 1 Figure 69 Processing chain selecting the correction factors and plotting them as a Spectrum Reflectance p oO 0 1000 2000 3000 Wavelength nm Figure 70 Reference panel correction factors Correct for Reference Panel Non Idealness This module applies calibration factors to correct Spectra for the reference panel non idealness These correction factors are selected from the database using the Reference Panel Correction Factors module The module requires two inputs the Spectra to be corrected and the correction factors The input space selection dialog offers the according choices Figure 71 _ Input Space Selection Primary Spectra Correction Factors Co a 0 1 1 2 C Cance
20. Preconfigured information for your database and the log in accounts you have created on your computer is stored in the db config txt file on your computer See section 3 2 User Accounts for instructions on creating a User Account To log in to a SPECCHIO Server e Start the SPECCHIO Application See the instructions specific to your computer in the Release Notes e Select the Database and Connect to database menu items from SPECCHIO s Main Window to display the following dialog box eo Connect to database Known connections https AHueni2 v473 vanager de 8181 specchio_service jdbc specchio_test Web Application Server v473 vanager de Port 8181 Application Path specchio_service Data Source Name jdbc specchio_test Username AHueni Password eeeee Connect Cancel Figure 20 Connect to Database dialog e From the Known connections dropdown list select the connection with your User Name following the https characters The User Name will be a contraction of your own First and Last Names e Inspect the values which are updated in the dialog box It should not be necessary to change anything unless specifically requested by your database administrator e Click on Connect The dialog box will close and there will be short delay while the database is read The details of your database and log in account will be displayed in the right hand panel of the Main Window and the sub menu items for SPECCHIO functions will
21. Report Reports are generated by clicking on the Show report button in the Query Builder or Spectrum Browser It operates on all Spectra which are selected at the time this button is clicked Reports are shown in a window in the following form SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 87 of 134 SPECCHIO User Guide x BRAR 1 0 185 Wavelength nm 1 of 40 spectra V Instrument Settings V Personnel v Data Portal Instrumentation Pictures V Environmental Conditions V Keywords V Processing V General V Location Sampling Geometry J Generic Target Properties V Names J Scientific References Illumination V Optics J Soil Parameters Instrument J PDFs J Vegetation Biophysical Variables V Select All Select None Campaign Details Data Portal Environmental Conditions General Acquisition Time 2005 08 30 21 32 57 File Comments File Format GER Signature File File Name GROS3005 080 Loading Time 2013 06 19 11 04 17 Measurement Unit Radiance Spectrum Number 80 Generic Target Properties a i a Close Figure 54 Spectrum report frame Just below the Spectrum graph the number of Spectra graphs in the report is shown with a control to allow you to select which Spectrum graph you wish to display 1 of 10 spectra Figure 55 Spectrum Graph selection control Click on the up and down arrows to cause the Spectrum graph display to cycle through the available Spec
22. SUN ANGIES cccceccceeeeeeeeeeeceeaeaeeesaeaeeesaeaeseeaeaeeesasaesesaeaesnseeaes 81 4 19 Calculation of Goniometer ANGIeS ccccceceeceeeeeeeeeeeaeeeeeeaesesasaeaeesaeeeeaeaeeesenaes 82 5 Data Query and QUPU wicceatessirinestaeinssansieiseriiasctieneienatsdienisessiemanae 84 S1 INe Spectrum BROWSED ccdsuc suacsentecaanessaswsaatnss mawaaeineiauencanaiannantaiasaietenessaemieniaueeun 84 eZ OUR BO raaa suet aaeacaaiedantedenuraanaenemietancneneasacusaaceneinus 85 Da NOW RDO oaa E A EEE 87 DA FC EDON iaaa AE E E E EAE vent 90 IAL CSV Spectrum EXPO FORME across a A 92 Da PO E E A A sea uaewsiee ania 92 D CUA NO aaa E EE AEE 93 S7 RRC a A 93 Da PUDS COIC CUO iin a E E E E A eee err tre 93 6 HeD FUN CUONS osinon EE 94 6 1 List available Metadata Elements cccecececeeseeeeeeeeeeeeeeseeeeeeeeeeeseeeeeseneeeneneaeges 94 O ADU eacttens cars eniveteusaeieeu seeeaeaaineu en s seeeweusanatevedeatasieiaaneseusssucieton screen ssianws 94 7 Publishing Data to ANDS ssssssssnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn 95 8 Interactive Processing using Space NetworkS sssssssnsnnnnnnnnnnnnnnnnnn 98 8 1 Graphical Representations of Spaces and Modules ccscscsceeeeeeeeeeeeseeeeeeeeneeenenens 99 8 2 Adding Modules and linking with Spaces cccccceceeeeeeeeeeeeeeeeeeeeeaeaeaeeeeeeeeaeaeaes 100 83 Configuration OF MOGUICS a pascasiensisscnsaccnensnnniirsenenmunsaanesasrenenannsconanssesianaveanmniw
23. Sensor zenith Sensor azimuth lIlumination zenith lIlumination azimuth Sensor distance Illumination distance Measurement unit Measurement type llumination source Sampling environment Spectrum names Target types 350 351 352 353 354 355 4 2005 09 11 23 09 50 2005 09 11 23 09 54 2005 09 11 23 09 58 2006 12 11 18 23 03 2006 12 11 18 23 03 2006 12 11 16 23 03 bfern 001 10 false 40 3849 175 622 52 Vegetation Example Deciduous forest 0 18 calm 0 47 7073 21 975 Reflectance Single Sun Field 0 0251693 0 026092373 0 026704056 0 026676136 0 025368243 0 02532748 2 bfern 002 10 false 40 3849 175 622 54 2 Vegetation Example Deciduous forest 47 7025 21 9535 Reflectance 0 02180227 0 022058768 0 02304296 0 023551108 0 022222875 0 022796206 bfern 003 false Vegetation Example Deciduous forest calm Reflectance Single Sun Field 10 40 3849 175 621 49 2 0 47 6981 21 9333 1 Blackfern Common Cyathea medullaris Latin Tree 100 Figure 58 CSV file example loaded into Excel 5 5 Process 0 021688519 0 021206077 0 022523083 0 023339724 0 021277064 0 022375558 A separate chapter of this Use Guide is devoted to this topic Please see Chapter 8 Interactive Processing using Space Networks SPECCHIO _UserGuide pdf Version 3 1 05 03 2014 Page 92 of 134 SPECCHIO User Guide 5 6 Spectral plot Using this option p
24. Spectra Suite Supported Ocean Optics Spectra Suite text files Formats Comments The required file extension is csv although the files are not comma separated Example file SpectraSuite Data File AEF EAFAFEEFAFLEFAEEAFEELAFAE EEE HEHE Date wed Sep 15 19 14 15 CEST 2010 User telerilevamento Dark Spectrum Present No Reference Spectrum Present No Number of Sampled Component Spectra 1 Spectrometers HR4C1076 Integration Time usec 1000000 CHR4C1076 SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 27 of 134 SPECCHIO User Guide Spectra Averaged 10 CHR4C1076 Boxcar Smoothing O CHR4C1076 Correct for Electrical Dark No CHR4C1076 Strobe Lamp Enabled No CHR4C1076 Correct for Detector Non linearity No CHR4C1076 Correct for Stray Light No HR4C1076 Number of Pixels in Processed Spectrum 3648 gt gt gt gt gt Begin Processed Spectral Data lt lt lt lt lt Wavelength nm radiance w m 2 sr 1 nm 1 717 00000 0 17904775 717 02000 0 17878146 717 04000 0 17849983 717 06000 0 17820124 3 11 8 HDF5 Files containing FGI goniometer measurements Standard or Finnish Geodetic Institute proprietary format Format Owner Devices ASD in combination with the FIGIFIGO goniometer Supported HDF5 files and XML files containing measurement data from FGI Finish Formats Geodetic Institute goniometer measurements The newest data structure version with a coupled xml file containing all the Metadata is
25. You can do this by highlighting multiple Spectra or by highlighting a hierarchy node as shown in Figure 38 above If required refine your selection by entering an SQL matching string in the related Filename restriction control See section 4 8 SQL Matching Strings Using the right hand side References hierarchy tree browser locate and select the Reference Spectra you wish to link You can do this by highlighting multiple Spectra or by highlighting a hierarchy node as shown in Figure 38 above If required refine your selection by entering an SQL matching string in the related Filename restriction control See section 4 8 SQL Matching Strings Verify that the correct Target and Reference Spectra are displayed in the central Target Spectra and Reference Spectra boxes respectively Ensure that they are also each in the correct box and not reversed Click Link to create the links according to the method described above 4 16 Displaying and Editing Metadata The SPECCHIO Metadata Editor allows you to enter and modify both Campaign and Spectrum Metadata Refer to sections 3 13 and 3 14 for detailed information about Metadata stored by SPECCHIO Metadata is most easily displayed using SPECCHIO s Metadata editor To open the Metadata Editor select Data Input and Edit metadata from SPECCHIO s Main Window menu The following Metadata Editor window is displayed SPECCHIO_ UserGuide pdf Version 3 1 05 03 2014 Page 67 of 134
26. a special character so must be used to escape it so matches the in the file name 0 matches any number of 0 characters 5 matches 5 and the forces the match to complete at the end of the string Note If a value in the DB Va ue column matches more than one row in the XLS file no matching row will be shown in the Table Value column and no Spectrum will be updated Using preconfigured column information If you often load Metadata from XLS files you can pre configure the XLS column mappings you want to use This will be more efficient and reduce your chance of making a mistake Create an extra XLS spreadsheet which lists the Column Names you ve used in your spreadsheet along with the matching names SPECCHIO uses for these fields SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 79 of 134 SPECCHIO User Guide Put XLS Column A header row must Put corresponding heading names in be present but is SPECCHIO first column not used Attribute names in second column 1 xts Column Name Specchio Name Location Location Name Temperature 4 Latitude File Name Ambient Temperature Latitude File Name Longitude Elevation Figure 47 Setup up pre defined column allocations The table must be in the first datasheet of the spreadsheet Each SPECCHIO Metadata Attribute name must be on the same row as its matching XLS column name The names in both columns are case sensitive Leading
27. and trailing spaces must be avoided There must be a header row but it is skipped over The rows do not need to be sorted into any sequence The file must be saved as an XLS file CSV XLSX or other Excel file formats are not Supported To use a pre configured column matching spreadsheet Select Data input and Get metadata from XLS from the menus on the SPECCHIO Main Window The following dialog will be displayed Only those Campaigns to which you have write permission will be displayed Select the Campaign hierarchy node or Spectra to which you want the Metadata to be uploaded Select Fi e and Open file from the menu bar on this screen Browse to the XLS Metadata file you have previously prepared and Open it Select File and Open Column Element Matching File from the menu bar on this screen Browse to the column mappings XLS file and open it The name of file you have opened will be shown in the Element Column Auto Matching control Element Column Auto Matching Matching File Column Matches xls Apply Auto Matching Click on the Apply Auto Matching button The information from the column SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 80 of 134 SPECCHIO User Guide matching XLS file will be read and the drop down boxes in the second two rows of the Matching amp Element Assignment Control box will be updated e In the column that you wish to use as the Matching Column in the top ro
28. change Minutes and Seconds do as for Hours e Clicking on the required Date closes the dialog box but only if the date is not already highlighted e If you do not want to change the date click on the down triangle in the data input field to close the date picker 4 10 Overview of SPECCHIO Data Loading The process of loading data into SPECCHIO involves a number of steps Depending on your acquisition device some of these steps may not be needed because the information is recorded by your device and uploaded with the Spectral data Create a Campaign This establishes a name for your Campaign and sets up structures in the SPECCHIO database to receive the Campaign Spectra and other information See section 4 11 Creating a new Campaign SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 54 of 134 SPECCHIO User Guide Load Campaign Data This examines the format of the Spectral data on your hard disk parses its content from your hard disk and inserts into the SPECCHIO database See section 4 12 Loading Campaign Spectral Data Correct Acquisition Times to UTC SPECCHIO expects Acquisition Times to be UTC but many devices record a local time SPECCHIO provides a function to change local times to UTC See section 4 14 UTC Time Correction Add Target Reference Links For acquisition devices which do not put this information into the Spectral files you will need to enter this information manually See section 4 15 Managing Target Referen
29. e If a search condition for a Metadata Attribute is present Spectra without that Metadata Attribute will never be selected e When matching text strings SPECCHIO uses a MySQL Query LIKE clause Therefore the following are supported Matches zero or more characters Matches exactly one character Causes the next character to be matched That is will match a sign and _ will match an underscore character e For dropdown lists the test is not performed if Nil is set Otherwise only those Spectra with exactly that value will be selected Notes Text Metadata Attributes which are present but empty can be selected by using but not by _ Text Metadata Attributes which contain only a single space can be selected by using _ Or a Space It is common for some Spectrum file formats to have a File Comment field which contains only a space This is not so for other Metadata Attributes Warning There is no option to search by Campaign Name except for the Campaign Name in the Spectrum related Metadata Group Campaign Details This is NOT the Campaign s name and will generally not be present See section 3 14 Spectrum related Metadata for more information on the Spectrum related Campaign Details Group of Metadata Attributes After you have entered search criteria for the Spectra you wish to operate on click one of the six action buttons See the following sections for details of the operation of these buttons 5 3 Show
30. from a file e Select the correct Instrument to display its data e Right click anywhere within the Calibrations box A menu is displayed e Select Add calibration from file from this menu A file selection dialog is displayed e Select the Calibration file Unispec SPU file or SpectraVista SIG file you wish to upload To remove a Calibration e Right click anywhere over the Calibration you wish to remove from this Instrument s information A menu is displayed e Select Remove calibration from this menu The Calibration information is immediately removed from the database and remove from the display in the Calibrations box Reference Panel Administration In order to change or remove Reference Panel information you must be logged in as an Administrator SPECCHIO stores a table of Reference Panel information The Reference Panels in this list appear in the dropdown list for the Reference Metadata Attribute in the Instrumentation Group This Metadata Attribute is used in some functions of the Space Processing Netowok described in Chapter 8 Interactive Processing using Space Networks and in particular during the reference panel correction procedure as described in sections 8 4 2 and 8 4 3 Each Reference Panel record holds the following information Field name Reference Text string This name will appear in the dropdown list name of Reference Panels which is used to set the Reference Metadata Attribute in the Instrumentatio
31. identify the Spectra in this Collection by searching for it using SPECCHIO s Query Builder Each Spectrum will have one ANDS Collection Key Metadata value for each Collection in which it has been included When data are published SPECCHIO reformats the Metadata from the selected Spectra into the RIF CS format which is an XML format involving two files It then places those files in a discoverable location on the server On a regular basis currently daily the RDA service inspects this location If there are any RIF CS files present it copies them validates them and if they pass validation publishes the Collection description on RDA for general access Information about the RIF CS format can be found on the ANDS website referred to at the start of this Chapter SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 95 of 134 SPECCHIO User Guide Note The RIF CS file is a logical reference to your Spectral data so it s important to ensure that this data remains valid and accessible in the SPECCHIO database This will ensure that it can be provided at a later time to those that request it based on the Published ANDS information In the Publication step the following Metadata are copied from SPECCHIO to the files which are sent to ANDS The values of the Metadata are taken from the Spectrum with the highest Spectrum ID which will be the one from your Collection that was the last to be loaded into SPECCHIO If these Metadata Attribu
32. log in to SPECCHIO as you To create a User account e Start the SPECCHIO Client Application on your local computer See the instructions specific to your computer in the Release Notes e Select the Database and Create new user account menu items to display the following dialog box SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 12 of 134 SPECCHIO eno Create user account Server Details Port Connect Application Path Data Source Name User Account Details Cancel Figure 2 Create User Account dialog User Guide e Enter the Web Application Server Port Application Path and Data Source Name strings specified in the SPECCHIO Release Notes or that have been supplied to you by your database administrator e Click on Connect The remaining fields on the screen will become active If ANDS Publishing is supported for your database ANDS related fields will appear in the dialog box as shown below See Chapter 7 Publishing Data to ANDS for more information about the ANDS service and its operation If the server you are connecting requires a license agreement an according checkbox short license explanation and link to the actual license are provided SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 13 of 134 SPECCHIO User Guide 00 Create user account Server Details Web Application Server specchio uow edu au Port 443 Connect Application Path _ specchio_servi
33. or Version data capture software Gain SWIR1 Integer ASD specific gain Instrument Channel Alpha string Channel designation for multi channel instruments e g irradiance and reflected radiance channels Integration Time ms Integration time Number of Internal Integer Number of Spectra recorded internally and averaged Scans over by the Instrument Gain SWIR2 Integer ASD specific gain Offset SWIR1 Integer ASD specific offset SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 37 of 134 SPECCHIO User Guide Offset SWIR2 Integer ASD specific offset Time since last DC Integer Seconds since last dark current measurement Not currently filled even if it s in the input file UniSpec Spectral Alpha string UniSpec specific setting indicates if the Resampling resampling was ON or OFF If SPECCHIO loads this value from the input Spectrum file it will set one of the values ON or OFF 3 14 9 Instrumentation Group These attributes describe the Instrumentation used at the time the Spectrum was acquired For some file formats particularly HDF files the following Instrumentation settings are read from the Spectrum input file and set into the Spectrum Metadata For other formats it must be set manually Azimuth Alpha string Sensor name used to measure the azimuth on a Sensor Type goniometric facility Contact Probe Drop down list Contact probe instrumentation name usually includes a l
34. permit you to store values which are outside the valid range which can be misleading or lead to unpredictable results later 4 16 1 Displaying and Editing Campaign Metadata See section 3 13 Campaign related Metadata for detailed information about individual Campaign Metadata fields their meanings and operation To edit a Campaign s Campaign related Metadata e Click on the Campaign tab to highlight it and display Campaign related Metadata e In the Campaign Tree Navigator click on the Campaign for which you wish to edit the Metadata or click on anything in that Campaign s sub tree The Metadata for that Campaign will be read from the database and displayed in the Metadata display area e Modify the Metadata Attribute values as you require e Click on Update to cause these changes to be written to the database You can now click on another Campaign name and repeat this procedure Clicking on Metadata Group names in the Spectrum Metadata selection area does not affect the Campaign editing tab If you change the Campaign Name Attribute click on the Refresh button to cause that change to be shown in the Campaign Tree Navigator 4 16 2 Displaying and Editing Spectrum Metadata See section 3 14 Spectrum related Metadata for detailed information about individual Campaign Metadata fields the way they are organised into Metadata groups their meanings and operation In order to understand the operation of this Editor it is h
35. rectangular boxes but their contents are quite different SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 99 of 134 SPECCHIO User Guide Proc module Radiance to Reflectance settings Automatic selection from DB Status Waiting for data Figure 63 Examples of the graphical representation of a space left and a processing module right Figure 64 Examples of the graphical representation of a space left and a processing module right Proc module A module name Settings Information about the configuration if applicable Status The current processing status text and progress bar During processing the progress is shown by the progress bar Spaces and modules can be rearranged by dragging with the mouse The edges are updated automatically A group of elements can be moved as single block Select the elements by dragging a box around them using the mouse then drag the selection Figure 65 Ref panel cor factors Type Spectral Space D 2251 Vectors 1 Proc module Get Panel Correction Factors Settings 0 Type Sensor Instrument Space D 2151 Vectors 1 Status Waiting for data Proc module Waveband filtering L Settings Status Waiting for data Proc module Correct for Panel Settings Automatic selection from DB he Status Waiting for data 3 Type Spectral Space D 2151 Vectors 1 a Ref Panel cor Re
36. researchers SPECCHIO was then further enhanced through a project run by the University of Wollongong in 2012 2013 2014 This project was supported by the Australian National Data Service ANDS ANDS is supported by the Australian Government through the National Collaborative Research Infrastructure Strategy Program and the Education Investment Fund EIF Super Science Initiative Specchio is an Italian word meaning mirror or looking glass It can also be used to refer to a table of data or a scoreboard Document scope SPECCHIO uses a Client Server architecture This User Guide details operation of the Client component of SPECCHIO This document focuses on the Windows operation of SPECCHIO for most of its descriptions screen shots and examples The operation of the SPECCHIO on Mac and Linux is equivalent and can be inferred from the Windows descriptions Intended audience This document assumes that readers are familiar with e remote sensing and the disciplines and processes related to it e the general operation of their own computer e the general concept of a client server architecture SPECCHIO ownership and access SPECCHIO was originally built by the Remote Sensing Laboratories at the University of Zurich and extended by Intersect for the School of Earth and Environmental Sciences at the University of Wollongong Copyright and licensing SPECCHIO is licensed under the Creative Commons Attribution Share
37. setl 8224 8224 8224 8224 8224 8224 8224 8224 8224 8224 8224 8224 8224 8224 8224 8224 external data set2 8224 8224 8224 8224 8224 8224 8224 8224 8224 8224 8224 8224 8224 8224 8224 8224 SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 25 of 134 SPECCHIO User Guide external data dark 0 0 0 0 0 0 0 0 external data mask 0 optic LENS 4 LENS 4 temp 36 21 9 08 5 30 36 45 9 08 5 37 battery 7 5 7 4 error 0 O units Radiance Radiance time 8 9 10 10 49 47 AM 8 9 10 10 52 36 AM longitude 01116 9879 E 01116 9933 E latitude 4806 4988 N 4806 5075 N gpstime 084748 000 085034 000 comm memory slot 0 0 factors data 350 6 127369 73 4658 17 3 66 352 1 130962 30 4815 39 3 68 353 7 132239 65 4916 35 3 72 355 3 128726 40 4836 48 3 76 356 8 124030 10 4677 99 3 77 358 4 123421 08 4677 13 3 79 359 9 130810 10 4966 42 3 80 3 11 5 Apogee Files Standard or Apogee Instruments Format Owner Supported Apogee text files restricted to one tested file format only see Formats example below Comments The SPECCHIO Apogee file loader was added to SPECCHIO for one special case That is the only Apogee file example that has been available for testing Therefore this file reader has not been well tested It is provided as is and should be used with caution Example of supported Apogee format text file File cachimbalito2 p5_2 TRM TRANS gt Wave 733 53
38. string abc only abcd or aabc will not be matched 1 abcd 2 will match any combination of the characters a b c or d which occurs between the digits 1 and 2 C C will match either or will match any run of periods 0 9 will match any integer number 0 9 0 9 will match any number with a decimal point Page 132 of 134 SPECCHIO User Guide Appendix B Predefined Manufacturer Table manufacturer_id name GER YES Beckman Labsphere Inc APOGEE Spectra Vista Ocean Optics MULL On oUW Dp WN Analytical Spe www www asdi com NULL NULL www labsphere com www apogee inst com www spectravista com www oceanoptics com NULL short_name ASD GER YES BECKMAN LABSPHERE APOGEE SVC OceanOptics HULL SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 133 of 134 SPECCHIO User Guide Appendix C Predefined Sensor Table sensor_id name description response_type sensor_type_no no_of_channels manufacturer_id 3 ASD FS FR 3 ASD FieldSpec FR or FieldSpec3 type HULL 4 2151 1 GER 3700 GER 3700 HULL 3700 647 2 6 MFR 7 MFR 7 Rotating Shadowband Radiometer NULL 7 7 3 7 Beckman UV 5240 Beckman UV 5240 HULL 5240 826 9 USGS Beckman UV 5240 Beckman UV 5240 ULL 5240 420 10 SVC HR 1024 Spectra Vista HR 1024 PULL 1024 1024 7 SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 134 of 134
39. support viewing them Multiple values for non image Attributes can be added from Excel files See section 4 17 Uploading Metadata from Excel files The Metadata Attribute tables below indicate those Attributes which are permitted to take multiple values All others are limited to a single value Users cannot enter Metadata except into these already defined fields If new Metadata Attributes are required they can generally be defined easily Contact your System Administrator with a detailed description of the Metadata field you need added and a specification for the data that it can contain Also see section 6 1 List available Metadata Elements for instructions for producing a machine readable list of Spectrum related Metadata Attributes A number of the Metadata Attributes below take an element of a dropdown list for their value The definition of these lists is either taken from user managed SPECCHIO tables such as Sensor or Instrument lists or the definition is parameterised within the SPECCHIO database Such parameterised lists can generally be changed See your SPECCHIO system administrator if you require a change in any of these lists The source of the dropdown list is explained for each relevant Metadata Attribute 3 14 1 Campaign Details Group Note Some formats for Spectrum files contain Campaign related information particularly HDF formatted files When Spectrum files of these formats are loaded the Campaign related Metadata
40. that they contain is loaded into these Attributes for each Spectrum This allows you to review it and if necessary manually transfer it to the Campaign related Metadata fields described in section 3 13 Campaign related Metadata The fields in this Group can store different values for each Spectrum in a Campaign It is not recommended to enter Campaign Metadata into these Spectrum related Metadata fields Instead use the Campaign Metadata fields described in section 3 13 Campaign related Metadata Alpha string Agency identifier of entity involved in the sample collection Copied from the Agency Code field if it is set in the related input Spectrum file when it is loaded SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 32 of 134 SPECCHIO User Guide Campaign Alpha string Further specification of a particular Campaign Mainly used Name where a SPECCHIO Campaign comprises several original sampling Campaigns Copied from the Campaign Name field if it is set in the related Spectrum file particularly HDF files when it is loaded Project ID Alpha string Any project identification applying to this Campaign Copied from the Project ID field if it is set in the related input Spectrum file when it is loaded 3 14 2 Data Portal Group These Metadata Attributes relate to the Publishing of the Spectrum on the Australian National Data Service ANDS See Chapter 7 Publishing Data to ANDS for more information about the use of
41. 114 9 4 Definition of new Sensors sssssssnsannnnnnnnnnnannnnanannanennnnanannnnanannnnnnnnnsnnnnnnnnnnnnn 115 9 5 Instrument Administration ssssssesssssrsrssrsrnsnnnnrnnnnnnnnnnnrnrnnnnrnnnnnnnnnnnnnnnnnnnnnnni 117 g5 Instirdmnent CallDratonS cenis nae a a 120 9 6 Reference Panel Administration s sssssssnnnsnnnnnanannnnennnnnnannanannnnnnnnnnnsnnnnnnnnnnnnn 121 9 6 1 Reference Panel Calibrations s sssssunanannnnannnnsnsnnnnnnnnnnannnnnnanannnnanannnnsnnnnnn 123 10 Matlab Integration ccccscscssseeceeeseseseeeeceeeneneeeeeeeeaeneseneesesenenenenss 125 11 R TACO AU ON sirni 127 12 REICKONGCES crura E E 128 ES Document HISTOIY van necnauetvacscenmensartncdsavieunniensesiwinteacsiestiutuntniueieneseus 130 Appendix A Regular Expressions Tutorial cscscsessseseeseseseesesensnenenes 131 Appendix B Predefined Manufacturer Table cssscssseseseneseneseneneness 133 Appendix C Predefined Sensor Table scssscsesesesnseeneneseneeeesenenenenes 134 SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 5 of 134 SPECCHIO User Guide 1 1 1 1 2 1 3 1 4 1 5 Introduction SPECCHIO is a database for storing spectral data acquired by spectroradiometers and their associated metadata combined with a user friendly interface SPECCHIO was first developed at the Remote Sensing Labs at the Geography Department University of Zurich to support long term usability and data sharing between
42. 134 SPECCHIO User Guide Applying this function twice is safe as the calculated sun angles will always be the same Spectra which do not have Latitude and Longitude values will not have sun angles calculated for them If the Latitude or Longitude is outside of the normal ranges for example a Latitude value of 115 degrees sun angles will be calculated but they will not be meaningful If UTC times are during the night sun angles below the horizon will be calculated 4 19 Calculation of Goniometer Angles If a set of Spectra has been captured in a standard way using a supported goniometer the Sensor Zenith and Sensor Azimuth Metadata Attributes for these Spectra can be computed and assigned using this function The supported goniometers are those that use the following measurement pattern Figure 49 Data capture sequence of the RSL FIGOS LAGOS system A full directional set consists of 66 Spectra These Spectra must be grouped under a single node in the Data Hierarchy Tree To calculate goniometer angles for a set of Spectra e Select Special Functions and Gonio angle calculation from the menus in the Main Window i Gonio Example Vegetation example GER Example SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 82 of 134 SPECCHIO User Guide Figure 50 Goniometer angle calculation dialog In the data hierarchy browser of the Metadata Editor select the node that contains the spectrodirec
43. 134 SPECCHIO User Guide GPS device A Dory O52 Ds gt Reflectance Spectral data Radiance Radiance DN gt Data fie amp metadata a nem sy I Sy a ll Rees oY Field object Spectroradiometer Field laptop Lab computer SPECCHIO DB Figure 9 Dataflow and involved hardware Typically the operations carried out for each Campaign are e Creation of anew Campaign in SPECCHIO and linking it to the sub folder of Spectra on your computer s disk e Uploading of Spectra data from your local disk to the SPECCHIO database e Entering of Metadata into the SPECCHIO database for the uploaded Spectra e Repeated data query visualisation processing and file output based on the uploaded data 3 7 Research Groups and Accessing SPECCHIO Campaigns When you upload data for a Campaign to SPECCHIO all Users of your SPECCHIO database can access your Campaign However only you can modify or delete your Campaign unless you specifically allow others to have write access to it This access is controlled by setting a Research Group of Users for each Campaign that you upload Just as you can add other Users to the Campaign s Research Group so you can remove them too The membership of each Research Group is stored as Metadata for the Campaign Each Research Group applies only to one Campaign See 3 13 Campaign related Metadata for more information about Metadata and 4 16 1 Displaying and Editing Campaign Metadata for i
44. 2013 Regular Expression Description Retrieved June 21 2013 from http en wikipedia org wiki Regular_expression SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 129 of 134 SPECCHIO User Guide 13 Document History Version Date Author s Remark esses First document version 15 12 2006 14 02 2007 Bug fixes and added features 1 1 18 10 2007 A Hueni Added txt file reader multi user capabilities db_config txt file Admin functions 1 2 29 05 2008 A Hueni Added Spectral plot Campaign export Metadata editor enhancements 15 06 2008 Added Campaign import function 2 0 12 03 2009 A Hueni Major update Added reference panel handling processing extension Instrument and reference panel tools Updated export import 2 1 02 09 2010 A Hueni Added Instrument settings Metadata enhancements time selection SVC HR1024 Instrument Instrument calibration Apogee support 2 2 0 02 05 2012 A Hueni Added FGI HDF file support generic Metadata target reference link improvements Metadata P Deen Els editor enhancements ASD binary file format Metadata date time selection beam geometries 2 2 1 A Hueni Upgrade direct irradiance calculation for MFR 7 D Kuekenbrink GUErY builder hierarchy browser split space processing improvements mixed folder data loading UniSpec file loader SPECPR file loader 3 0 21 06 2013 Peter Roberts UOW Intersect overhaul Database now Intersect referenced via HTTP f
45. 4283 0 02092695 0 02092695 0 02129602 0 02499968 0 02648243 0 02222193 0 01759 22 370 0 0251672 0 02068911 0 0205066 0 02143872 0 0251672 0 02609931 0 02255335 0 01752 23 371 0 0253656 0 02216616 0 02066827 0 02160774 0 0253656 0 02630507 0 02404509 0 01635 24 372 0 02585498 0 02256722 0 02115348 0 02209378 0 02632185 0 02726215 0 02444782 0 01735 4 4 gt hi bfern_from_SNP_INR ASD_ASDFSF J Figure 14 Top left corner of example Spectrum spreadsheet 3 11 14 TXT Space Formatted Text Files Note TXT files are deprecated except in the case where Reference Panel calibrations are loaded as Spectra Please use the Excel file format instead Standard or Format Owner Devices Supported Formats Comments N A IDL Interactive Data Language or ENVI text file output White space separated text files as produced by IDL programs or ENVI when writing Spectral data to text files TXT Spectrum files can be created or viewed with a text editor Each file can hold one or more Spectra Values in each line are white space separated Tabs are OK Starting each line with whitespace is optional The first line of the file is a heading line The first value on this heading line must be wvl Its subsequent values are used as the File name Metadata Attribute values for the Spectra in SPECCHIO Spectrum names cannot include spaces All values on subsequent lines must be numeric The first column is SPECCHIO_U
46. 4296 0 02252308 0 02251576 0 02670406 0 02827833 0 02461723 0 01780 a 353 0 02667814 0 02355111 0 02333972 0 02272015 0 02667814 0 02855144 0 02542441 6 354 0 02536824 0 02222287 0 02127706 0 02212023 0 02536824 0 02651935 0 02337398 0 0179 E 355 0 02532748 0 02279621 0 02237556 0 02216154 0 02469282 0 02765212 0 02385152 0 01794 8 356 68 1 0 02306737 0 02242806 0 02232398 0 02476973 0 02838261 0 02413042 9 357 0 02465166 0 02250804 0 02036442 0 02250804 0 02572347 0 0278671 0 02357985 i 10 358 0 02545843 0 02255876 0 02116152 0 02255876 0 02578144 0 0279299 0 02363299 0 01826 3591 0 02576228 0 022542 0 02189644 0 022542 0 02619015 0 02790914 0 0240433 12 360 0 02555094 0 02234399 0 02223933 0 02234399 0 02661992 0 0276889 0 02448195 13 361 0 02452836 0 02135697 0 02051422 0 02135697 0 02558549 0 02664262 0 02347123 0 016714 14 362 0 02585315 0 02275078 0 02171665 0 02223371 0 02637022 0 02740434 0 02430196 0 01706 15 363 0 02699409 0 02397205 0 0229647 0 02276041 0 0267898 0 02800144 0 02477511 16 364 0 02560426 0 022661 0 02167992 0 02079489 0 02471923 0 02658534 0 02275706 0 017656 17 365 0 0261002 0 02264477 0 02168531 0 02130286 0 02571776 0 02705967 0 02264477 0 01784 18 366 0 02609165 0 02289031 0 0216651 0 0216651 0 02665815 0 02760011 0 02289031 0 017614 19 367 0 02506964 0 02321263 0 02135562 0 02135562 0 02692665 0 02785515 0 02321263 0 01671 20 368 0 02430984 0 02181487 0 02125899 0 02125899 0 02551208 0 02708275 0 02246123 0 01728 21 369 0 0244
47. 7 The wavelength text field below is reflecting the wavelength of the chosen band Selecting a band triggers a re plotting of both hemispherical plot and Spectral plot 1 431 861 1291 1721 2151 Wvi nm 1342 0 Figure 87 Band selection slider and wavelength text field Band The sampling points plot shows the sampling point positions projected onto a 2d Cartesian coordinate system Figure 88 One of these points is always selected indicated by the little square around it Information about the selected point is shown in the text fields on the right of the plot filename of the respective Spectrum azimuth and zenith angles of the observation geometry Changing the selected sampling point by clicking the mouse on another point changes the Spectrum displayed in the Spectrum plot automatically The azimuth angle is measured relative to the solar principal plane i e 0 principal plane opposite of the illumination source Goniometer Sampling points Sampling Point Information Filename hem_a 001 Azimuth 0 Zenith 75 Figure 88 Sampling point position plot and information about the selected sampling point SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 109 of 134 SPECCHIO User Guide The Spectral plot component displays the Spectrum of the selected sampling point Figure 89 A red vertical line indicates the current wavelength as selected by the band selection slider The text fields on the righ
48. Alike 3 0 Unported Licence Therefore its source is readily available for inspection and development It can be found in LICENCE html and at http creativecommons org licenses by sa 3 0 For Further Information Please refer to the following documents for more information about SPECCHIO Unless otherwise stated they can be found in the SPECCHIO Installation kit SPECCHIO_ReleaseNotes pdf can be found in each Installation Kit and provides installation instructions for the SPECCHIO Client SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 6 of 134 SPECCHIO User Guide SPECCHIO_Tutorial pdf provides instruction in the operation of key areas of the SPECCHIO Client SPECCHIO_ServerlInstallation pdf provides system administrators with information to assist in managing and maintaining a SPECCHIO Server System SPECCHIO Web Site www specchio ch General information about SPECCHIO Some of this information may be related to other non UOW versions of SPECCHIO SPECCHIO UoW https specchio uow edu au Installation kits for University of Wollongong version of the SPECCHIO Client and documentation for that version SPECCHIO GitHub https github com IntersectAustralia dc10 Source code for the University of Wollongong version of SPECCHIO See also Chapter 0 To extract R Java code for a R query from the SPECCHIO client e Select Data Processing amp Output and Browse data hierarchy from the menu on the Main Window The
49. CHIO Note E3 HR Instrument Test Campaign Ca HR Instrument radiances i targets HR O71710 0017 sig HR O71710 0018 sig E references HR 071710 0017 sig HR 071710 0018 sig E reflectances HR 0O71710 0017 sig HR 0O71710 0018 sig User Guide Figure 13 Automatically generated hierarchy for HR 1024 files For SPECCCHIO version pre 3 1 It is highly recommended to enter the Instrument into the database and load a wavelengths calibration The wavelengths between instruments differ quite a lot and the standard Sensor definition pre stored in SPECCHIO is only a poor representation of the real wavelengths Example files Spectra Vista HR 1024 name My Documents HR1024_Data HR 071710 0017 sig instrument HR 0761008 integration 2 22 20 12 50 30 scan time 1 1 optic LENS14 LENS14 temp 31 29 0 41 5 71 31 53 0 41 5 77 battery 7 7 7 7 error 0 O units Radiance Radiance time 7 18 10 9 47 09 AM 7 18 10 9 47 31 AM longitude 11121 2335 w 11121 2324 w latitude 5330 5955 N 5330 5964 N gpstime 154336 000 154356 000 comm memory slot 0 0 factors data 344 2 56023 55 4381 86 7 82 345 8 54418 00 4186 00 7 69 347 3 56037 65 4365 57 7 79 348 9 59474 63 4568 75 7 68 Spectra Vista SIG Data name My Documents HR1024_Data HR 080910 0010 sig instrument HR 0971030 integration 20 19 2 30 200 60 30 scan time 3 3 scan settings AD AI AD AI external data
50. Radiance 11 00 13 00 15 00 17 00 Time Figure 91 Time Line Explorer window The example given in Figure 91 is using MFR sunphotometer data A removal of the broadband channel is needed for the Spectral plot to work properly The according processing chain is shown in Figure 92 0 Proc module Broadband filtering Type Sensor instrument Space Settings Filtering 1 bands Type Spectral Space D 7 a D 6 Status for data Vectors 554 Vectors 554 Vis module Time Line Explorer Settings Status Waiting for data Figure 92 Processing chain for the exploration of the narrowband MFR channels in the Time Line Explorer 8 6 File Export Module File export modules can be attached to any space and do not generate an output space but write the data to a file A file export module must be configured using its configuration dialog Figure 93 The dialog is identical to the one described in 5 4 e000 File output i File format CSV HH Target directory Browse Basename J Options C Split header and body Time format yyyy MM dd HH mm ss O Milliseconds since 1st Jan 1970 00 00 00 OK Cancel Figure 93 File export configuration SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 111 of 134 SPECCHIO User Guide The Spectral data written to the file reflects the data content of the space The Metadata is however mainly read from the database and may sh
51. SPECCHIO User Guide FCHIO User Guide Version 3 1 Date 05 03 2014 Authors P Roberts Intersect A Hueni amp D Kuekenbrink Remote Sensing Laboratories University of Zurich File SPECCHIO_UserGuide pdf Pages 134 measurements products policy SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 1 of 134 SPECCHIO User Guide Table of Contents Table OF Contents conina NE 2 1 MOUCHO raen EE 6 LiL DOCUMENT SCODS seriinin aA aai Aai Arii 6 L2 ImendegaudieNCE csiiirviderricriiniannidr i iii 6 1 3 SPECCHIO ownership and ACCESS uu cccceceveceveneverevevavevavsvaessaessseneseseneneneueseuesseensass 6 1 4 Copyright and lic nsing ccccccccceneeeececeeeeneecereeoncncnensoeeeoeoncneneasasssseoesneneneneas 6 LS For UI UOT OU sicescet ocete cies irnastorc ante E EEE EEE 6 2 GIOSSAEV sonics AEEA 8 3 SPECCHIO COnCCDUS cicsroidnissn danaa a 11 Bet BATON E E 12 Se U TAOM arra EE E O 12 33 AAMINStatOr ACCESS ac ecereteattenteenateramatenaniieesnenisasnncianeaensoneniniancretararanendeebaeds 16 BG CAIN PONG INS cierren eE EEE EEE EEEE E EEEE 16 3 5 Campaign Hierarchy Structure ssssssssssnnnnsnnunnnsnnsnunnunnunnusnnnnnnnnnnunnunnnnnnnnnnnnnnnn 16 36 Operational Daal OW a4 dc ncutassasnscdemectansventesessseucrsaneneaeneseuesaneiensasmnenenesientieasian 18 3 7 Research Groups and Accessing SPECCHIO Campaigns ccccccceeeeeeeeeeeeaeaeeees 19 SO TIN Pela retro sonarus tc te conten E EE E E E
52. TS TS Targetspectrum Referencing in the database via datalink RS Reference panel spectrum Figure 37 Referencing of reference panel Spectra by target Spectra based on timeline information This function is useful for campaigns where Target and Reference Spectra are collected in separate Spectral files for example when using the ASD spectroradiometer in radiance mode Note that this method is a trivial solution for more scientific results consider writing your own routine in a higher level language e g calculating the mean and standard deviations of the reference panel readings and using these to interpolate over time to estimate the irradiance for each measured target spectrum SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 66 of 134 SPECCHIO User Guide Target Reference Lin Show existing links Create new links Target spectra ltriticaa 001 ID 1294 triticaa 066 ID 1293 triticaa 014 ID 1306 iticaa 015 ID 1307 triticaa 016 ID 1308 ltriticaa 017 ID 1309 iticaa 019 ID 1310 iticaa 020 ID 1311 triticaa 021 ID 1312 triticaa 022 ID 1313 triticaa 023 ID 1314 igure 38 Creating multiple new T arget Reference Spectra links To create links between multiple targets and references Using the left hand side 7argets hierarchy tree browser locate and select the Target Spectra you wish to link
53. Waiting for data 5 Delta 4 Ref Panel com Reflactance Vis module Spectral Line Plot Type Spectral Space Type Spectral Space Settings D 2151 D 2151 j Status Waiting for data Vectors 1 Vectors 1 Vis module Spectral Line Plot Settings Status Waiting for data Figure 74 Space Processing Network for the panel correction and delta calculation J _ T J J mo i ror f T 1000 2 1000 2000 1000 2000 Wavelength nm Wavelength nm Wavelength nm Figure 75 Spectral plots of input Spectrum left panel corrected Spectrum middle and delta Spectrum left 8 4 5 Waveband Filter Waveband filtering is used to cut wavelengths regions from Spectra A typical example is the removal of noisy wavebands caused by water vapour absorption The wavebands are freely configurable The Configure menu brings up the Filter configuration dialog Figure 76 e00 Filter configuration Filter regions nm New Cancel 11400 0 1500 0 5 Mo d Ty Remove Figure 76 Filter configuration window SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 104 of 134 SPECCHIO User Guide To add a new filter region click New and enter the upper and lower wavelengths in nanometres in the Filter Definition dialog Figure 77 OO Filter Definition Lower wvl nm 1700 OK Upper wvl nm 1800 Cancel Figure 77 Filter defin
54. adata Displaying Metadata values is done using the Metadata Editor window To display a single Spectrum s Metadata Using the hierarchy browser select the Spectrum for which you wish to display the Metadata values Click on the Metadata tab to display Spectrum Metadata G Metadata Editor V Campaign Metadata Campaign Details a D rs General Acquisition Time 2005 05 31 22 19 48 v File Comments File Format ASD Binary File Name cabbage 000 Loading Time 2013 06 19 09 45 23 w Measurement Unit Reflectance w Spectrum Number 0 Generic Target Properties Instrument Instrument INR ASD v C Lo x Campaign Details Data Portal V Environmental Conditions General Generic Target Properties _ Ww Illumination v Instrument Instrument Settings v Instrumentation J Keywords Location v Names v Optics V PDFs V Personne v Pictures Processing Sampling Geometry Scientific References Soil Parameters Vegetation Biophysical Variables Sensor ASD FS FR 3 J Select All Select None Figure 40 Metadata editor dialog e Select or de select the check boxes for the Metadata Groups The check boxes are displayed on the right in the Spectrum Metadata Group selection area e Scroll to the required Metadata Group to see the values of the Metadata Attribute in that Group Note Only Metadata Attributes which have values for the sele
55. al Conditions Group These Metadata describe the environmental conditions at the time the Spectrum measurements were taken SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 33 of 134 SPECCHIO User Guide hPa Ambient air pressure Ambient Degrees Celsius Ambient air temperature Temperature Cloud Cover Percentage Cloud cover as a percentage of the hemisphere Relative Humidity Percentage Relative air humidity Sampling Drop down list Describes where data were spectrally acquired Environment i e Field or laboratory Weather Conditions Alpha string Description of weather conditions Wind Direction Degrees Direction where wind is coming from Enter a bearing that is clockwise from North Wind Speed Metres second Speed of the wind 3 14 4 General Group This Metadata Group collects together information about the Spectrum s file Acquisition Date Time 24h UTC time when Spectrum was measured rime If the acquisition system s time was not set to UTC then adjust the time to UTC using the Special functions Correct local time to UTC function described in section 4 14 UTC Time Correction File Alpha string Comments about Spectrum Comments SPECCHIO sets any comments entered when capturing the Spectrum into this field on Spectrum upload Only some input file formats support this feature for example ASD s R3 capturing software File Format Selected from dropdown list The format of the file from which thi
56. an web site at http www Modtran5 com 3 11 13 Excel files Standard or Microsoft Excel Spreadsheet files Format Owner Supported XLS files only CSV XLSX etc are not supported Formats CSV files may be erroneously read as Ocean Optics SpectraSuite Data Files See section 3 11 7 Ocean Optics SpectraSuite Data Files Comments The first column of the Excel file must contain the Wavelength values in increasing order with a heading in the first row Each of the second and subsequent columns contains the data for a single Spectrum The first row is the name of the Spectrum Subsequent rows in the column contain the Spectrum values for the wavelengths specified in the first column The Spectra s File name Metadata Attribute values are constructed from the Excel file name and the Spectrum name in the first row of the Ww a spreadsheet separated with a character SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 29 of 134 SPECCHIO User Guide There can be no other data in the spreadsheet and the table of data must be rectangular with no gaps Excel formatting is ignored Only the first datasheet is read Example file B G D E F G H 1 Wvl bfern1 bfern2 bfern3 bfern4 bfernS bfern6 bfern7 bfern8 2 350 0 0251693 0 02180227 0 02168852 0 0208316 0 0251693 0 0272244 0 0228867 0 01638 3 351 0 02609237 0 02205877 0 02120608 0 02185116 0 02609237 0 02736029 0 02311907 0 01675 4 352 0 02670406 0 0230
57. any node except the specchio root node Selecting a Campaign node is valid SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 113 of 134 SPECCHIO User Guide e Click the Remove button All data that is below the selected node or nodes will be deleted For example if a Campaign is selected then all hierarchies and Spectra belonging to this Campaign will be deleted In addition all Metadata that has been entered for the deleted objects will be removed along with the objects e Close the dialog box by clicking on Close Warning There is no further prompt to warn you The data are deleted as soon as you click the Remove button This action cannot be undone Removing data can take a long time A progress bar shows which hierarchy is currently being removed 9 2 Campaign Export The Campaign export functionality writes all data of a Campaign to a single XML file which retains the hierarchy and Metadata structure of the Campaign The information from the Sensors Instruments and Calibrations used by the Campaign is also copied into the XML file These XML files can be used to import the Campaign into another SPECCHIO database instance The exported XML file will be named with the Campaign name date and time of export To export a Campaign e Select Data Maintenance and Export campaign from the menu of the Main Window 7 Campaign Export All relational data of this campaign will be exported to an xml file Target dir
58. are constructed using the following components Campaign name The Campaign name is always used in the output file name It is not recommended to export data from multiple Campaigns at one time The results are undefined Sensor name The Sensor name is always used in the output file name There will be separate files for each Sensor Unit type If you select Split spaces by sensor and unit or Split spaces by sensor instrument calibration_no and units there will be separate files for each value of the Unit Metadata Attribute Calibration number If you select Split spaces by sensor instrument calibration_no and units there will also be separate files for each Calibration for each Sensor and Unit combination Example Consider a Campaign containing Spectra captured with the following three Instruments e An ASD Instrument belonging to the Institute of Natural Resources Massey University named INR ASD with calibration sequence number 1 e An ASD Instrument belonging to the Remote Sensing Laboratories University of Zurich named RSL ASD 1 with no calibrations entered in the database e AGER 3700 Instrument belonging to the Remote Sensing Laboratories University of Zurich named RSL GER 3700 with no calibrations entered in the database A CSV file output of this Campaign with the option Split header and body results in the following files SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 91 of 134 SPECCHIO User Guide
59. ata Group e Right click on the name of the field you wish to delete A Delete button will appear SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 71 of 134 SPECCHIO User Guide e Click on this Delete button The Metadata field will disappear from the display and the Update button will become active e Click on the Update button to write the change back to the database If the Metadata is shared by other Spectra the dialog in Figure 41 will be displayed Select your desired action and click OK To add a new Metadata value e Display the Metadata Attribute values for the required Spectrum as described in the previous sub section e Ensure that the check box for the required Metadata Group is ticked and scroll to that Metadata Group e Right click on any blank space within the Metadata Group s display box A menu of Metadata items that can be added for that Group will be displayed e Click on the menu entry for the Metadata item you wish to add A data entry field for the Metadata entry will be displayed e Enter the value you require for this Metadata field e Click on the Update button to write this change back to the database 4 16 2 3 Editing Metadata for All Spectra in a Sub tree of the Campaign tree SPECCHIO allows for simultaneous updating of Metadata for multiple Spectra This feature is typically used when multiple Spectra have just been uploaded and a selection of their Metadata items shares the sa
60. ata will be loaded Note Do not add additional Spectra to files that hold multiple Spectra such as TXT and XLS files The loading process checks for existing data at the file level so the existing file will be detected and not loaded missing the new data After uploading new data you may need to set the Metadata for the new data Depending on your Campaign Hierarchy design the new data may be interspersed with your existing data Take care not to delete or corrupt the Metadata on your existing data by ensuring that you select only your new Spectra when you update the Metadata 4 13 2 Uploading Additional Spectral Data from a Second Computer SPECCHIO permits multiple Paths to be stored against each Campaign This permits the same data to be managed and augmented from multiple computers To upload from a second computer e On the second computer make an exact copy of the entire Campaign folder tree as SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 58 of 134 SPECCHIO User Guide it was uploaded from the first computer It does not have to be in the same location as it was on the first computer but the sub folder structure sub folder names and file names must be identical e Add the new hierarchy sub folders and files into the existing sub folder structure e Select Data Input and Load campaign data from the menu on the Main Window e From the drop down list for the Campaign name control select the name of the Campaign
61. ated by a comma Marks Select the way you want the data points represented on the graph X Y Ticks Place specific labels along the X and Y axes For example entering Threshold 450 3 Maximum 670 23 will place the string Threshold at the point 450 3 along the axis and Maximum at 670 23 Grid If checked the graph will include a grid Stems If checked each data point will be joined to the X axis by a straight line Connect If checked the data points will be joined by straight lines If you check this option it is probably best to select the option None for the Marks question in order to show a thin clean line Use Color If checked the various data lines on the graph will be given different colours If not checked they will all be black Use Line Styles If checked the data points will be connected with dashed lines This option has no effect unless Connect is checked These details are not remembered once you move away from viewing this graph Page 89 of 134 SPECCHIO User Guide SPECCHIO scales the graph s Y Axis for Spectra with Measurement unit set to Reflectance to display correctly even when there is strong atmospheric noise in the usual regions of 1350 1440nm 1790 1980nm and 2360 2500nm For these graphs the maximum Y value is set by calculating the mean and standard deviation in the wavelength region 300 1200nm and then setting Max Y Axis value Mean 3 StdDev When Spectra havi
62. ave been transported to a separate measuring facility and the Sample taken from the Target at that facility Typically for each Campaign there should be PDF uploaded to the Experimental Design Metadata item in the PDFs Metadata Group to explain the Target and Sample structure and the reasons for that structure Sample Date Time 24h Time when the original sample was collected in the Collection Date field This will generally be a different from the time it was measured The time zone is not specified Note that the Special functions Correct local time to UTC function does not operate on this time SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 35 of 134 SPECCHIO User Guide Sample alpha string Identification of the sample as collected Number This will not in general match the Spectrum Number or Spectrum ID A Sample Number may be common to a variety of Spectra Site ID alpha string Identification of the site from which the sample was collected Target alpha string Description of the Target Description Target ID alpha string Identification of the Target that was collected 3 14 6 Illumination Group Polarization alpha string Description of illumination polarisation typically Horizontal or Vertical but other comments may be used as well Polarization Degrees Polarisation direction usually measured clockwise from Angle vertical 3 14 7 Instrument Group This Group of Attributes descr
63. case sensitive 3 14 11 Location Group This Group collects information about the capturing location WGS84 World Geodetic System of 1984 should be used as the reference Geoid for these measurements Altitude Metres Altitude of spatial position Latitude Degrees Latitude of spatial position Northern hemisphere coordinates are positive southern hemisphere coordinates are negative Coordinates are entered as floating point numbers for degrees and fractions of degrees Longitude Degrees Longitude of spatial position Locations west of Greenwich are positive east of Greenwich are negative That is longitudes in Australia are negative Coordinates are entered as floating point numbers for degrees and fractions of degrees Location Alpha string Usual name of the spatial position where the sampling took Name place State alpha string Identifier of the State in which the observations were made To avoid confusion in searching later it is suggested to use the standard abbreviation for the state for example in Australia use NSW Qld Vic Do not use periods leading embedded or trailing spaces in the field Searching is not case sensitive 3 14 12 Names Group This Group collects the possible names for the species or objects in the Spectrum sample Common alpha string Common name given to target applies particularly to plants ENVI alpha string Name extracted from ENVI header Header When ENVI Fi
64. ce Data Source Name jdbc specchio User Account Details Title First name Last name Institute RSL University of Zurich Add new institute Description __ I already have an ANDS party identifier ANDS Party Identifier Figure 3 Create User Account dialog for ANDS users 800 Create user account Server Details Web Application Server v473 vanager de Connect Application Path specchio_service Data Source Name jdbc specchio_test User Account Details Title First name Last name Institute RSL University of Zurich Add new institute Description Create Cancel YOU ACKNOWLEDGE THAT YOU HAVE READ THE PROGRAM LICENSE AGREEMENT UNDERSTAND IT AND AGREE TO BE BOUND BY ITS TERMS AND CONDITIONS YOU FURTHER AGREE THAT IT IS THE COMPLETE AND EXCLUSIVE STATEMENT OF THE AGREEMENT BETWEEN YOU AND UNIVERSITY OF ZURICH WHICH SUPERSEDES ANY PROPOSAL OR PRIOR AGREEMENT ORAL OR WRITTEN AND ANY OTHER COMMUNICATIONS RELATING TO THE SUBJECT MATTER OF THIS AGREEMENT Data License http specchio ch SPECCHIO UZH License V1l pdf Figure 4 Create User Account dialog for non ANDS users with specific server license agreement SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 14 of 134 SPECCHIO User Guide e Select your Title and enter your First name and Last Name These will be used to identify the data which you uploa
65. ce Links Complete Metadata upload The Spectral Metadata that was not included in the Spectral files must be uploaded either from an Excel file or manually entered using SPECCHIO s Metadata editor See sections 4 16 Displaying and Editing Metadata and 4 17 Uploading Metadata from Excel files Calculate Sun Angles SPECCHIO provides a function to calculate sun angles based on the UTC date and time of the Spectrum acquisition and the latitude and longitude of the acquisition location and to write them into the Spectra Metadata See section 4 18 Calculation of Sun Angles Calculate Goniometer Angles If you have used a supported goniometer and collected the Spectra in the correct sequence SPECCHIO provides a function to calculate the Sensor orientation parameters and write them into the Spectra Metadata See section 4 19 Calculation of Goniometer Angles After these steps your Campaign s Spectral data is complete and ready for use exporting or publishing to ANDS 4 11 Creating a new Campaign e Select Data Input and Create new campaign from the Main Window menus This brings up the new Campaign dialog Create new campaign Campaign name Main directory Create Create amp Load Cancel Figure 24 New Campaign dialog e Enter the name you have selected for this Campaign The maximum length is 45 characters e To set the Main directory field select the Browse button to display a folder tree Th
66. cessing module applied to Spectrum Multiple Processing Module Attribute values may be added to each Spectrum This Metadata Attribute is provided to permit non SPECCHIO programmatic processes to keep track of the level or amount of processing which they have performed on the related Spectrum SPECCHIO does not use this value Alpha string Name of file that provided the original data This applies if data is processed outside of SPECCHIO This Metadata Attribute is provided to permit non SPECCHIO programmatic processes to keep track of the level or amount of processing which they have performed on the related Spectrum SPECCHIO does not use this value Alpha string This records the time shift processing that was applied to the Spectrum using the Special functions Correct local time to UTC operation See 4 14 UTC Time Correction for more information on changing the times Multiple Time Shift fields will be added if the Time Shift function is applied multiple times 3 14 18 Sampling Geometry Group Numbers in this Group can all be entered as floating point numbers Beam Geometry Drop down list SPECCHIO supports the nine fundamental beam geometry types describing the incoming and reflected beams For further information about the beam geometry types please refer to Schaepman Strub Schaepman amp al 2006 and Figure 15 below Illumination Degrees Absolute illumination source azimuth angle measured Azimuth
67. cle Technology Network 2013 for more information A Sample taken from a Target and measured often at some later time under controlled conditions A sample will generally have a collection date time and a measurement date time which will be different Sensor See Instrument Type Spectralon A particular brand of reflective reference panel produced by LabSphere Spectralon panels are available in various configurations ranging from pure white to greyish and almost black See Reference Panel SQL Structured Query Language sometimes pronounced sequel A special purpose programming language designed for managing data held in a relational database management system RDBMS Target Spectrum acquired by measuring the target where the target is the Spectrum object of interest TCP IP Transmission Control Protocol Internet Protocol The common designator to refer to the protocols used for internet communication SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 9 of 134 SPECCHIO User Guide White A Spectrum acquired over a reference panel that has a reflectance of Reference close to 100 Spectrum SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 10 of 134 3 SPECCHIO User Guide SPECCHIO Concepts SPECCHIO is a distributed client server system The client which operates on the user s computer has been written using Java No SPECCHIO data is stored locally on the client computer The serv
68. clockwise from geographic North SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 42 of 134 SPECCHIO User Guide Illumination Metres Distance between the illumination source and target for Distance artificial illumination Illumination Degrees Illumination source zenith Zenith angle measured from nadir This angle will always be between 0 and 90 degrees If the Illumination is directly over the target the value will be zero Sensor Degrees Sensor azimuth angle relative Azimuth to the illumination angle The angle is measured clockwise from the Illumination Azimuth A negative angle implies an anti clockwise measurement direction A position opposite the sun is 0 forward scattering while the backward scattering position in the solar principle plain lies at 180 Sandmeier Muller et al 1998 In this example the Sensor Azimuth is approximately 110 Note that some datasets in the database may have different definitions if in doubt consult the relevant literature Sensor Metres Distance of Sensor from the target Distance Sensor Degrees Sensor zenith angle measured Zenith from nadir This angle will always be between 0 and 90 degrees If the Sensor is directly over the target the value will be zero SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 43 of 134 SPECCHIO User Guide Incoming Reflected Directional Conical Hemispherical Directional Bidirectional Di
69. cted Spectrum are displayed 4 16 2 2 Editing Metadata for a Single Spectrum In each of the processes in this section after you change or delete any Metadata value click Update to write your change back into the database If that Metadata value is Shared by another unselected Spectrum the following dialog will be displayed SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 70 of 134 SPECCHIO User Guide Update shared record The data in the fields listed below are referred to by multiple records You can update metadata for all of these records or only the records selected in the navigator Gain_SWIR 1 shared by 64 records Apply to all spectra Selected spectra only Cancel Figure 41 Shared data operation selector dialog The second sentence in the dialog box will change to You can de ete metadata for all records if you have deleted the Metadata value rather than changed it This dialog allows you to select how you want the Entity Attribute Value table to be updated The exact choice of options will depend on whether you performed a change or a delete Apply to all spectra The shared record in the Entity Attribute Value table will be updated or deleted and therefore all Spectra which share this Metadata value will be affected by this change Understand how widely the shared record is referenced when you use this option It is possible for the value to be used for any other Spectrum in the
70. d sequence There should be no other Spectra in that folder The goniometer angle calculation has been designed for the use of the FIGOS and LAGOS goniometers system RSL University of Zurich New Spectra can be added to ongoing Campaigns by first adding the files for those Spectra into the existing Campaign sub folder data structure on your computer s disk and then invoking the SPECCHIO load operation for the entire Campaign again Only new Spectra discovered in the sub folder hierarchy will be added to the database Existing Spectra will not be duplicated Example Multiple sites for each species In this example each species is sampled at a number of sample sites The sites are numbered in the order of sampling At each site several readings are taken to capture the variation exhibited by the specimen in question A site therefore contains a number of Spectra This leads to the following hierarchical folder structure Spectrum 1 Spectrum 2 Spectum 1 Spectrum 2 Spectrum 1 Spectrum 2 Spectrum n Spectrum n Spectrum n Figure 6 Hierarchical folder structure Although the term species is used it essentially represents the different classes found in a study These classes can either be assigned according to already existing classification systems e g for plants or minerals In other cases a hypothesis might exist that a number of objects can be separated into classes If so the setup of the experiment
71. d to SPECCHIO to other SPECCHIO users e Select the name of your Institute from the dropdown list If the name of your Institute is not present in the list click on Add new institute This will cause the following dialog box to appear r mA Create new institute ss Department Institute Street Number Street City Post Office Code Country WWW Figure 5 Create new institute dialog Fill out all the details of your Institute After checking it is complete and correct click Create This will create an entry for your Institute on the SPECCHIO server e Enter your email address a URL which other SPECCHIO users can use to contact you and access information about you and a short user description The URL is an optional field e If your server s database supports ANDS Publishing and you already have an ANDS Party Identifier set the checkbox and enter your ANDS Party Identifier in the relevant field Take care when entering this field You cannot change it later If you do not have an ANDS Party Identifier leave the checkbox unchecked and SPECCHIO will create one for you e If your server s database requires you to agree to a specific license please read the license and click the checkbox e Click on Create The dialog box will close Warning Take care to enter the details for a new Institute correctly There is no function to change an Institute record nor to remove an Institute record from
72. e 8 5 1 Spectral Line Plot Use this plot to display one or more Spectra as continuous curves Spectra are plotted with an automatic colour shift from red to blue for easier interpretation 1 0 Reflectance 0 5 0 0 0 1000 2000 3000 Wavelength nm Figure 82 Spectral line plot of snow avalanche reflectance Spectra 8 5 2 Spectral Scatter Plot Use this plot to display values per Spectral band as singular points This is useful to plot e g data of sensors with just one band e g MFR broadband as single values cannot be visualized as line plots Scatter plots are also useful to show the variation of the values per band Figure 83 shows an example of the variation per channel for several MFR sunphotometer readings Note the generation of scatter plots of several Spectra with high dimensionality tends to be quite slow Radiance 400 600 800 1000 Wavelength nm Figure 83 Scatterplot showing the variation per channel for several MFR sunphotometer readings SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 107 of 134 SPECCHIO User Guide 8 5 3 Gonio Sampling Points Plot Use this plot to visualise the sampling positions of directional measurements acquired by a goniometer system The plot is not expecting any specific number of points or particular geometry The sampling points are projected from their angular definition zenith azimuth onto a 2d Cartesian coordinate system Figure 84 Goniometer Sampl
73. e 8 of 134 SPECCHIO User Guide MySQL The world s most widely used relational database management system RDMS according to Wikipedia It is the RDMS used by the SPECCHIO Server See SQL Research Data Australia Australian National Data Service s ANDS flagship service which provides a comprehensive window into the Australian Research Data Commons It is an Internet based discovery service designed to provide rich connections between data projects researchers and institutions and promote visibility of Australian research data collections in search engines See http researchdata ands org au Reference A calibrated reflective panel with known reflectance properties It is Panel usually white but may be grey or even close to black A Reference Panel can be measured under the same lighting conditions as a target Sample in order to get an approximation of the Spectrum of the solar irradiance or to collect data for the conversion of a target radiance to reflectance factors Reference A Spectrum acquired over a Reference Panel Spectrum Regular In computing a regular expression often abbreviated regex or Expression regexp is a sequence of text characters some of which are understood to be metacharacters with symbolic meaning and some of which have their literal meaning that together can be used by a regular expression processor to identify textual material of a given pattern See Wikipedia 2013 and Ora
74. e Instrument Calibration List to select the most appropriate calibration to use This value is used if there is insufficient information available to use the dates For some Spectrum file formats this value is set automatically on Spectrum loading Otherwise it can be set manually Extended alpha string Instrument name Instrument Name This field can be used to further describe the Instrument used to capture this Spectrum especially if the Instrument is not shown in the dropdown list of Instruments Instrument alpha string Serial number of the Instrument Serial Number As for Extended Instrument Name above enter this value if the specific Instrument is not shown in the drop down lists 3 14 8 Instrument Settings Group These attributes describe the settings of the Instrument at the time the Spectrum was acquired For some Instruments and file formats the following Instrument settings are read from the Spectrum input file and set into the Spectrum Metadata For others these values must be recorded manually Automatic Dark Alpha string Indicates if Dark current has been compensated Current Correction for by the Instrument If SPECCHIO loads this value from the input Spectrum file it will set one of the values ON or OFF Capturing Software Alpha string Name of the Instrument operation software or Name data capture software Capturing Software Alpha string Version of the Instrument operation software
75. e Main directory path is a file system pathname pointing to the folder that contains all hierarchies and Spectra for this Campaign When you load Spectral data it will be loaded from this folder Navigate to the required path on your hard disk When using a UNIX system you may have to enter a dot as filename see SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 55 of 134 SPECCHIO User Guide Note 4 12 section 4 2 Unix Operation e Click Create to create the new empty Campaign in the database e A message box will appear once the Campaign has been successfully created Click OK to close it e Click Cancel to close the Campaign creation dialog It is not advisable to have two Campaigns with the same name There is no check for the existence of a Campaign of the same name so please check the names of the existing Campaigns before you create your own in order to avoid multiple Campaigns with identical or confusing names The Campaign is now ready to receive uploads of Spectral data It is also possible to use the Create and Load button to combine the operations of creating the Campaign and uploading the data Read the next section before using this combined operation Loading Campaign Spectral Data All Spectral data in the sub folder tree at the disk location you specify will be loaded from your computer to the database as a single operation On your local disk drive prepare a sub folder structure which reflec
76. e automatically added to known instruments if differences in centre wavelengths are encountered during data loading Instrument ar l Joe s GER Calibration History Sensor 3700 GER 3700 Instrument Number Sensor ID Name Calibration 3 Name Owning Institute Description Serial Number Date Manufacturer ID sensor ID Calibration Number Type No Picture Comments No of Bands Measured wavelength Wavelength at at each band each band Figure 10 Relationship between an Instrument its Calibrations Sensor and Manufacturer Consider the example above of Joe s GER 3700 Instrument This Instrument is an instance of a GER 3700 Sensor The Sensor defines the average wavelength per band In turn the Sensor has a reference to the Manufacturer record for that Sensor s Manufacturer As long as no Calibration for the Instrument has been entered into the database the channels defined in the Sensor will be used for plotting and exporting Spectral data When wavelength Calibrations are entered for Instruments the calibrated wavelengths SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 21 of 134 SPECCHIO User Guide override the Sensor specifications For further information please refer to HUni amp Kneubuhler SPECCHIO A System for Storing and Sharing Spectroradiometer Data 2007 3 11 Supported Input Spectrum File Formats The following Spectrum file types are supported for loading into SPECCHIO Campaig
77. ectory Cancel Figure 95 Campaign Export Dialog e Select the Campaign you wish to export from the Campaign name dropdown list e Click the Browse button to open a file dialog box e Select the folder into which you want the XML file to be written and close the dialog box e Click Export The Campaign Export dialog box will close and a progress box will appear When the export is complete it will close 9 3 Campaign Import Note In order to use this option you must be logged in as an Administrator The import function reads an XML file that was created by the SPECCHIO Export campaign function The import will create an exact copy of the exported Campaign It will also add any Sensor Instrument or Calibration information that is referenced by this Campaign if it does not already appear in this database To import a Campaign e Select Data Maintenance and Import campaign from the menu of the Main Window SPECCHIO _UserGuide pdf Version 3 1 05 03 2014 Page 114 of 134 SPECCHIO User Guide Notes 9 4 Warning Campaign Import Import source file SPECCHIO Administrator Nicholas Sheppard Peter Roberts Karl Hermann Vincent Tran Karlos Herrmannos Campaign owner Figure 96 Campaign Import Dialog e Click the Browse button to open a file dialog box e Select the XML file that you want to import into your current SPECCHIO database and close the dialog box e Inthe Campaign Owner bo
78. ectra if all Spectra which share this value are to be changed Click SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 72 of 134 SPECCHIO User Guide on Selected spectra only if only the Spectra under this node are to have the Metadata Attribute value changed To delete a Metadata value from all Spectra under a node e Navigate to the correct Campaign hierarchy node and click on it to highlight it e Ensure that the check box for the required Metadata Group is ticked and scroll to that Metadata Group e Right click on the name of the field you wish to delete A Delete button will appear e Click on this Delete button The Metadata field will disappear from the display and the Update button will become valid e Click on the Update button to write the change back to the database e If the Metadata value is shared with other Spectra not under the scope of this node the dialog in Figure 41 will be displayed Click on either Apply to all spectra if all Spectra which share this value are to have it deleted Click on Selected spectra only if only the Spectra under this node are to have the Metadata Attribute value deleted Warning If you delete a Metadata Attribute which shows multiple values in the current view all values of this Metadata Attribute will be deleted from a selected Spectra even if some Spectra have multiple values of the Attribute To reset a specific Metadata item for all Spectra u
79. ectroradiometer Data Retrieved 2007 from SPIE Newsroom http spie org x18220 xml Huni A Nieke J Schopfer J Kneubuhler M amp Itten K 2007 2nd Generation of RSL s Spectrum Database SPECCHIO ISMPSRS Davos Switzerland Huni A Nieke J Schopfer J Kneubuhler M amp Itten K 2007 Metadata of Spectral Data Collections 5th EARSeL Workshop on Imaging Spectroscopy Bruges Belgium Hueni A 2006 Field Spectroradiometer Data Acquisition Organisation Processing and Analysis on the Example of New Zealand Native Plants Palmerston North Massey University Institute of Natural Resources Hueni A amp Kneubuehler M 2009 SPECCHIO A Free Spectral Data Management and Processing System SPIE Optics and Photonics San Diego CA Hueni A amp Tuohy M 2006 Spectroradiometer Data Structuring Pre Processing and Analysis An IT Based Approach Journal of Spatial Science 51 2 93 102 Hueni A Kneubuehler M amp Schaepman M 2010 International Geoscience and Remote Sensing Symposium Hawaii USA Hueni A Kneubuehler M Nieke J amp Itten K 2009 Processing Extension for the Spectral Database SPECCHIO Proceedings EARSeL SIG IS Tel Aviv Israel Hueni A Malthus T Kneubuehler M amp Schaepman M 2011 Data Exchange Between Distributed Spectral Databases Computers amp Geosciences 37 861 873 Hueni A Nieke J Schopfer J Kneub hler M amp Itten K
80. ectrum load functions has not been tested and may not work 3 11 2 GER Signature Files Standard or Spectra Vista Corporation Format Owner SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 22 of 134 SPECCHIO User Guide Supported GER 3700 signature text files Formats Files produced by other GER instruments are untested Comments These files hold two Spectral measurements at once the Target Spectrum and the white Reference Spectrum When read two sub folders named targets and references are created The input file name is used as both the Target Spectrum s name in the targets folder and the Reference Spectrum s name in the references folder A data link is created linking the Target Spectrum to the Reference Spectrum SEEGER targets GR053005 078 references GR0353005 078 Figure 11 Automatically created hierarchies for GER files 3 11 3 MFR OUT Files Standard or Format Owner Devices MFR Sun Photometer Supported MFR Photometer OUT files Formats MER 7 Comments These files contain the capture time the sun zenith angle and the Spectral data for total diffuse and direct irradiance The sun angle and the direct irradiance data are discarded and only the total and diffuse Spectra are stored When read two sub folders named tota and diffuse are created The input file name is used as both the name of the total Spectrum s name in the tota folder and the diffuse Spectrum s name in the diffuse
81. eference links Select Special Functions and Target references links from the menu of the Main Window Click on the Create new links tab in the centre panel to display the following dialog You can switch back and forth between the Create new links and Show existing links tabs at any time gt Target Reference Links Show existing links Create new links Target spectra triticaa 010 ID 1302 Reference spectra triticaa 006 ID 1288 Gonio_example Notes H triticaa 001 H triticaa 002 triticaa 003 H triticaa 004 H triticaa 005 H triticaa 007 H triticaa 008 H triticaa 009 E a triticaa 010 H triticaa 011 H triticaa 012 H triticaa 013 H triticaa 014 H triticaa 015 triticaa 016 reference y target p triticaa 000 E He UEAN H triticaa 018 triticaa 030 H triticaa 042 H triticaa 054 i triticaa 066 ad target H Vegetation example fH GER Example Figure 36 Creating a single new Target Reference Spectra link The left and right sides of this dialog do not operate independently unlike the dialog which displays links in the previous section The positions of the Target Spectra and Reference Spectra boxes in the central panel are reversed when compared with the position of these boxes in the previous section To link a single Target and Reference Spectrum e Us
82. elpful to understand how Spectrum Metadata are stored by SPECCHIO There are two storage methods Mandatory Metadata The following attributes are stored for all Spectra and are always displayed Measurement unit File format Sensor Instrument and Reference If they are not relevant or no data is available set them to Nil EAV Metadata So that space is optimised for all other Metadata Attributes SPECCHIO stores only those values which are set They are stored in an Entity Attribute Value table where one Metadata value is stored in SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 69 of 134 SPECCHIO User Guide each row of the table as an Attribute Value pair such as Latitude 35 33943 or Ambient Temp 23 5 The Entity field in that row stores a list of Spectra which are associated with this particular Attribute and Value Note SPECCHIO allows changing of most Metadata fields but for some Metadata Attributes it does not make sense It could often be confusing and should not be done except in unusual circumstances For example changing the File Name or File Format for a Spectrum does not make sense and may case unexpected results in subsequent Spectrum upload operations Changing the Spectrum Number is also rarely meaningful and could often be confusing Changing the automatically set Acquisition Time and Loading Time values will generally be confusing There are other cases too 4 16 2 1 Displaying a Single Spectrum s Met
83. ensor Definition File dialog e Click Browse navigate to the Sensor definition file and open it e Click OK to read the file and insert the new Sensor into the database SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 115 of 134 SPECCHIO User Guide Sensor definition files are a proprietary format tab separated text file that can be edited in a text editor or in Excel The file format is as follows the tab positions have been lined up for clarity Name Description Company Type no no of channels lt sensor name gt lt sensor descr gt lt company name gt lt type number gt lt no of channels gt Band Average Wavelength nm FWHM nm lt band number gt lt wavelength gt lt fwhm gt lt band number gt lt wavelength gt lt fwhm gt lt band number gt lt wavelength gt lt fwhm gt The first two rows define basic parameters of this Sensor the first row being the names of the five parameters which are required and the second row being their values These parameters must be provided in the given sequence The names in the first row are required and must be correct lt sensor name gt The name by which this new Sensor will be known to SPECCHIO It will appear in the Sensor Metadata Attribute s dropdown list lt sensor descr gt A short description of this Sensor lt company name gt The name of the company which manufactures this Sensor It must exactly match the value in the short_name column for one of the ma
84. entire database although it is usually just shared by other Spectra in the same Campaign Selected spectra only Only the selected Spectrum will be affected To achieve this SPECCHIO will create a new entry in the Entity Attribute Value table and link only the selected Spectrum to it For a delete operation only the reference to the current Spectrum will be removed from the Entity list No other Spectrum will be affected Cancel Your change or delete request will be discarded and no changes for this Metadata value will be made You should then click on Reset to cause the original database values to be redisplayed To modify a Metadata value e Display the Metadata Attribute values for the required Spectrum as described in the previous sub section e Ensure that the check box for the required Metadata Group is ticked and scroll to that Metadata Group e Click in the field and type in the required value When the field contains a valid value the Update button will become valid e Click on the Update button to write the modified value back to the database If the Metadata is shared by more than one Spectrum the dialog in Figure 41 will be displayed Select your desired action and click OK To delete a Metadata value e Display the Metadata Attribute values for the required Spectrum as described in the previous sub section e Ensure that the check box for the required Metadata Group is ticked and scroll to that Metad
85. er uses MySQL to manage its database Communication between the client and the server is done over an intranet or the internet using the HTTPS protocol This system architecture allows for multiple servers each with their own database but each client will generally access only a single server User A s Computer SPECCHIO User Application Web Application Server SPECCHIO Web 41s Application eee OE VEr Intranet User A s or Campaign Data _ _ Internet SPECCHIO MySQL Database Nien aAbaAuaAnn p Data uploaded for User A s Campaign data SPECCHIO User Application Data uploaded for y User B s Campaign p data User B s Campaign Data Campaign data kept in both locations after uploading Figure 1 The SPECCHIO distributed processing model Each User identifies the database they are accessing using the following three fields Web Application Server A URL string which indicates the computer on which the SPECCHIO database server is running Port The TCP IP port number on which the Web Application Server must be accessed Application Path The path of the application on the Web Application Server SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 11 of 134 SPECCHIO User Guide 3 1 3 2 Notes To find out the values of these three fields for your site you should check the SPECCHIO release notes for the version of SPECCHIO which you have installed or you should contact your site s databa
86. ersion 3 1 05 03 2014 Page 126 of 134 SPECCHIO User Guide 11 R Integration R integration uses the rJava package For more information please see www specchio ch To extract R Java code for a R query from the SPECCHIO client e Select Data Processing amp Output and Browse data hierarchy from the menu on the Main Window The Data Browser window will open e Using the Hierarchy Browser select a Hierarchy node or a selection of Spectra The Spectra IDs will appear in the Matching Spectra box e Right click in the Matching Spectra box A menu will appear e Select Copy R ready query to clipboard from the menu e Switch to the R application and paste the query from the clipboard as you require SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 127 of 134 SPECCHIO User Guide 12 References Astronomical Applications Department of the U S Naval Observatory 2003 Universal Time Retrieved May 1 2013 from Astronomical Information Center http aa usno navy mil fag docs UT php Australian Research Council 2008 Australian and New Zealand Standard Research Classification ANZSRC Australia Bureau of Statistics Retrieved May 2013 from http www abs gov au ausstats abs nsf mf 1297 0 CSIRO 2011 The Australian Soil Classification Retrieved June 21 2013 from http www clw csiro au aclep asc_re_on_line soilhome htm Huni A amp Kneubuhler M 2007 December SPECCHIO A System for Storing and Sharing Sp
87. erties A commonly used networked computer architecture which involves a server which hosts a main computing facility such as a database or computation facility and a number of clients which access the server using a network such as an intranet or the internet SPECCHIO uses this architecture Field of Research Codes This coding system was designed and developed by the Australian Research Council http www arc gov au to categorise areas of research FOR Codes are widely used across Australian research bodies such as universities and the CSIRO and government departments such as the Bureau of Census and Statistics Lists of FOR Codes can be found at sites such as http www abs gov au ausstats abs nsf Products 6BB427AB9696C22 5CA2574180004463E 0pendocument Hypertext Transfer Protocol HTTP is a very widely used network protocol which is also used by SPECCHIO Clients to communicate with the SPECCHIO Server HTTPS is the secure version of this protocol In the context of this document an individual spectroradiometric Instrument Such an Instrument will have a serial number and an owner A model or type of spectroradiometric Instrument It will be described by a model number and manufacturer In this document and the SPECCHIO client this term is used interchangeably with the terms Instrument Model Sensor and Sensor Type SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Pag
88. eter is configured to acquire radiances the irradiance will commonly be characterised indirectly by measuring the radiance reflected by a reference panel This may be preferable to the direct acquisition of reflectance data as information about the irradiance can be retrieved from the dataset The structure must therefore hold target and the related reference radiance Spectra in adjacent folders v ref target example v Planta plant_a 000 plant_a 001 plant_a 002 gt Plant B gt Plant C v B Reference ref 000 ref 001 ref 002 Figure 8 A possible structure for the storage of target and reference radiance Spectra In this example the Reference sub folder holds the reference Spectra which relate to the Spectra in the plant A Plant B and Plant c sub folders 3 6 Operational Dataflow A typical dataflow is illustrated in Figure 9 A spectroradiometer is used to capture the radiance of field objects Optionally a GPS connected to the field laptop where Supported by the capturing software records the spatial position of the field object This is a recommended setup as the spatial position can later be automatically loaded into the database Spectra and Metadata are saved on the field laptop These files are transferred to a laboratory computer where they are read by the SPECCHIO application and stored in the relevant tables in the Spectral database SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 18 of
89. eview carefully that you have selected the correct Spectra Important do not Skip this step because you cannot retract once you have Published e Click onthe Publish button The following dialog which shows all members of the Research Group is displayed SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 96 of 134 SPECCHIO User Guide Publish Collection Please select the principal investigator Peter Roberts e Select the principal investigator from the list by clicking on the name e Click Submit If the Collection Metadata is successfully validated the Publication will proceed and a dialog box will be displayed showing the ANDS Collection Key that was assigned to this Publication If validation is not successful an error dialog will be displayed e Click Close to close the ANDS Collection Key dialog Alternatively you can select Build query instead of Browse data hierarchy in the above process and build a query to select the Spectra you want included in your Collection If any mistake in the Metadata is detected for the Spectra in your Collection SPECCHIO will display an error dialog and Publication process will not proceed Correct the error and retry the Publication process SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 97 of 134 SPECCHIO User Guide 8 Interactive Processing using Space Networks For an introduction to the concept of the Space Processing Network please refer to
90. f the Space Network Processor processing plane spaces edges context sensitive menu of the processing plane and the Run button SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 98 of 134 SPECCHIO User Guide Context sensitive menu of the Space Edge Processing plane Processing plane 000 Swace Network Processor 0 Type Sensor instrument Space D 2151 Vectors 66 Proc module Radiance to Reflectance Settings Automatic selection from DB 9 Add Module Status Waiting for data ooo Run Type Spectral Space D 2151 Vectors 66 m e ll ll ll A EE EE I l l Ml i i i i i i lt Figure 61 Elements of the Space Network Processor 4 gt ce 8 1 Graphical Representations of Spaces and Modules Spaces are depicted as rectangular boxes as shown here 0 Type Sensor Instrument Space D 2151 Vectors 17 Figure 62 Examples of the graphical representation of a space left and a processing module right Each space displays the following information Integer A unique number zero in the example below Type A space type which can be Sensor Instrument Space if loaded from the database or Spectral Space if generated by a processing module D A dimension D which is equal to the number of Spectral bands of the Spectra held by this space Vectors A number of vectors which is equal to the number of Spectra held by this space Modules are also depicted as
91. flectance Type Spectral Space D 2151 Vectors 1 Figure 65 Multiple selection of elements after dragging a box around them 8 2 Adding Modules and linking with Spaces To add a module click the mouse menu button over some empty area of the processing plane This brings up the context sensitive menu shown in Figure 61 Select Add Module and a selection of the available modules will appear Figure 66 Select one of the modules click OK and a new module will be added to the processing plane To connect the module with an input space click the menu button over the module This displays the popup menu of the module Figure 67 Select Set Input Spaces and in the Input Space Selection dialog select the number of the space to connect and click OK Figure 67 Note that all spaces are given a unique number which is located on the top left of each space Connecting an input space automatically generates an output space which is added to the processing plane and connected with the module SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 100 of 134 SPECCHIO User Guide 8 3 8 4 8 4 1 8 4 2 AO Module Selection Modules Radiance to Reflectance Transformation Ref Panel Corr Factors Correct for Ref Panel Delta Waveband Filter Broadband Filter Cancel Narrowband Filter Visualisation Module File Export Module Proof of Concept Figure 66 Module selection dialog Input S
92. folder SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 23 of 134 SPECCHIO User Guide small_MFR_set Campaign Small MFR Set total 2005 08 17 11 21 59 2005 08 17 11 22 59 2005 08 17 11 23 59 2005 08 17 11 24 59 2005 08 17 11 25 59 2005 08 17 11 26 59 2005 08 17 11 27 59 2005 08 17 11 28 59 2005 08 17 11 30 00 use 2005 08 17 11 21 59 2005 08 17 11 22 59 2005 08 17 11 23 59 2005 08 17 11 24 59 2005 08 17 11 25 59 2005 08 17 11 26 59 2005 08 17 11 27 59 2005 08 17 11 28 59 2005 08 17 11 30 00 Figure 12 Automatically created hierarchies for MFR data a a a Ti an an as as 88 8 6 3 11 4 SVC HR 1024 Files Standard or Spectra Vista Corporation Format Owner Supported SVC HR 1024 files captured using a PDA Formats Files acquired with a laptop are a different file format and are not recognised by the current file loading routine Comments The HR 1024 stores radiances of reflectance panel target and the computed target reflectance During the data loading SPECCHIO generates a hierarchical structure to store these files see Figure 13 setting up data links that connect the reflectance to the target radiance and connecting the target radiance to the reference radiance If the Instrument was set to acquire radiances only i e no white reference taken then no special structure will be created SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 24 of 134 SPEC
93. g the extra time shift processing messages is more difficult As date time fields are stored in milliseconds the time shift is implemented as SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 61 of 134 SPECCHIO User Guide 4 15 Note Date_time_in_milliseconds Date_time_in_milliseconds hours_east_of_gmt mi11liseconds_per_hour Therefore if a time shift happens across midnight the calendar date of the capture time will also be shifted back or forth depending on whether hours_east_of_gmt is positive or negative For example for a local capture time around 10am in Oceania a time shift of around 12 hours East of GMT is needed The UTC time will then be 10pm the previous day A Time Shift Metadata Attribute value in the Processing Metadata Group is added to each Spectrum that has its Acquisition Time adjusted by this function JE ip Processing Capture time was shifted by 9 Time Shift 0 hours East using the SPECCHI O timeshift function Sampling Geometry ADD Figure 31 Time Shift Metadata Attribute after applying a UTC Time Shift Managing Target Reference Links You will need to add links from your target Spectra to the related reference Spectra if you want to use some of the Processing options of SPECCHIO The dialog boxes for viewing existing links and adding new links appear similar but there are important differences Please compare the two dialog boxes carefully in the following sections In the
94. ge of this Campaign i e the User defining and loading the Campaign This field is filled automatically and cannot be changed Path The file system path pointing to the main folder from which this Campaign was uploaded Multiple paths can be defined to support uploading of subsequent Spectral data from multiple computers This is intended to assist when further data is uploaded for this Campaign Research Group Members A list of Users of this SPECCHIO database who have permission to modify this Campaign Each of these Users must be registered with a SPECCHIO User account SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 31 of 134 SPECCHIO User Guide 3 14 Spectrum related Metadata For more information on the Metadata parameters supported by SPECCHIO please refer to Huni amp Kneubuhler SPECCHIO A System for Storing and Sharing Spectroradiometer Data 2007 When Spectra are uploaded to a Campaign the SPECCHIO upload process identifies Metadata found in the Spectrum files and copies it into SPECCHIO Spectrum Metadata fields for each Spectrum it uploads Once uploaded this Metadata can be viewed edited removed or added to Similar Metadata Attributes are grouped into named sections to facilitate management A few Metadata Attributes are permitted to take multiple values such as Keywords or Processing Group Attributes The SPECCHIO s Metadata Editor does not support addition of more than a single value but does
95. h lists all of the Metadata Attributes which are supported by the connected database It shows the Metadata Groups the Attributes in each Group and the data type for each Attribute The data type values and their meanings are binary_val The value is a binary stream of data representing an image such as a JPEG image file datetime_val The value is selected from a date and time picker double_val A floating point value int_val An integer value string_val An alphanumeric string or a PDF file taxonomy_id The value is chosen from a drop down list About This function shows the version of the SPECCHIO Client that you are running and provides a link to the SPECCHIO web site SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 94 of 134 SPECCHIO User Guide 7 Publishing Data to ANDS Data from SPECCHIO can be published to the Research Data Australia RDA service of the Australian National Data Service ANDS From the ANDS website Research Data Australia the flagship service of the Australian National Data Service ANDS provides a comprehensive window into the Australian Research Data Commons Research Data Australia is an Internet based discovery service designed to provide rich connections between data projects researchers and institutions and promote visibility of Australian research data collections in search engines ANDS is partnering with research institutions and data producing agencies to bring about four
96. he same way as the left hand side but views the links in the reverse direction SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 63 of 134 SPECCHIO User Guide These Target Spectra duplicates are removed from this list although there shouldn t be any link to These Reference Spectra triticaa 004 ID 1297 triticaa 005 ID 1298 triticaa 007 ID 1299 triticaa 008 ID 1300 triticaa 009 ID 1301 triticaa 010 ID 1302 triticaa 011 ID 1303 To see the Target Spectra for just one Reference Spectrum click on that Spectrum here There can be more than one linked Target Spectrum triticaa 012 ID 1304 triticaa 013 ID 1305 triticaa 014 ID 1306 triticaa 015 ID 1307 triticaa 016 ID 1308 triticaa 017 ID 1309 triticaa 019 ID 1310 triticaa 020 ID 1311 triticaa 021 ID 1312 triticaa 022 ID 1313 triticaa 023 ID 1314 To see the Target Spectra for a selection of Reference Spectra enter an SQL search string to select them in this hox F Figure 34 Viewing Reference Spectra and their related Target Spectra If you select the Campaign node on the right hand side and clear the Filename restriction control all Target Spectra with Reference Spectra links will be displayed If any Reference Spectrum is displayed in the Linked targets box a link has been set up in the wrong direction Because each Reference Spectrum can be linked from many Target Spectra the numbe
97. hese controls to check that the upload is set up correctly before proceeding Assignment Details Number of assignable columns 0 Number of assigned columns 5 triticaa 000 ltriticaa 006 ltriticaa 018 triticaa 030 ltriticaa 042 ltriticaa 054 triticaa 066 itriticaa 001 ltriticaa 001 ltriticaa 002 triticaa 002 triticaa 003 ltriticaa 003 ltriticaa 004 ltriticaa 004 triticaa 005 triticaa 005 Itriticaa 007 ltriticaa 007 triticaa 008 triticaa 008 ltriticaa 009 ltriticaa 009 itriticaa 010 triticaa 0 10 triticaa O11 triticaa 011 ltriticaa 012 triticaa 013 ltriticaa 012 itriticaa 013 ltriticaa 014 itriticaa 015 triticaa 016 ltriticaa 017 triticaa 019 To upload Metadata ltriticaa 020 Number of assignable columns The number of columns in the XLS file which remain unused Number of assigned columns The number of columns in the XLS file which will be copied into Metadata Attributes Number of spectra The number of Spectra selected in the hierarchy tree browser see below Number of matches The number of selected Spectra which match data in the Matching Column of the XLS file Spectrum First column The Spectrum IDs of all selected Spectra DB Value Second column The value from the SPECCHIO database of the Metadata Attribute wh
98. ibes the specific spectroradiographic Instrument which was used to measure this Spectrum Instrument Dropdown list The name of the specific Instrument used to take these measurements The drop down list is a list of Instruments which is created and maintained using the Data maintenance Instrument admin function This Attribute is always present and cannot be deleted It should be set if known If no data is available set it to Nil This Attribute is generally set when Spectra are loaded but should be checked to ensure that SPECCHIO determined it correctly Sensor Dropdown list The name of the Sensor used in the specific Instrument used to take these measurements ist is a list of Sensors which is created and maintained using the Data maintenance Load sensor definition function If the Instrument Attribute above is set this Sensor Attribute is ignored and the value stored in the Instrument record is used instead This Attribute is always present and cannot be deleted If not required it can be set to Nil This Attribute is generally set when Spectra are loaded but should be checked to ensure that SPECCHIO has determined it correctly SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 36 of 134 SPECCHIO User Guide Calibration integer Calibration number of the most recent calibration for the Number Instrument at the time the measurements were taken Generally the Acquisition Time is compared against the Calibration Time in th
99. icaa 010 triticaa 011 triticaa 012 triticaa 013 _Insert Selected Metadata Figure 44 Metadata upload dialog after file open e Set up the dropdown boxes in the Matching amp Element Assignment Control according to the instructions under Column selection operation above In the case given above it will be as follows SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 77 of 134 SPECCHIO User Guide Assignment Details Number of assignable columns 3 Number of assigned columns 2 Matching Details Number of spectra 70 Number of matches 12 Spectru DBValue Table Va LJ Ju rutaaa vvu di v 1291 ltriticaa 042 1292 triticaa 054 1293 triticaa 066 1294 triticaa 001 triticaa 001 1295 ltriticaa 002 triticaa 002 1296 _ triticaa 003 triticaa 003 Figure 45 Metadata upload dialog after setting parameters e Verify that the Matching amp Assignment Control is set up correctly by checking the contents of the Assignment Details and Matching Details boxes e Click onthe Insert selected metadata button in the left panel to cause the Metadata to be loaded If SPECCHIO finds a Metadata Attribute already exists for any Spectrum SPECCHIO will ask how you wish to proceed by displaying the foll
100. ich you have identified in the Matching Column Table Value Third column The matched value from the Matching Column of the XLS file The data in this row will be loaded into the Metadata for this Spectrum You must already have an Excel file containing the Metadata to upload e Select Data input and Get metadata from XLS from the menus on the SPECCHIO Main Window The following dialog will be displayed Only those Campaigns to SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 76 of 134 SPECCHIO User Guide which you have write permission will be displayed Metadata Augmentation from Tabular Data Vegetation example Figure 43 Metadata upload initiation dialog e Select the Campaign hierarchy node or Spectra to which you want the Metadata to be uploaded e Select File and Open file from the menu bar on this screen A standard file selection dialog will be displayed Browse to the XLS file you have previously prepared and Open it The file will be read and the dialog will be augmented and appear similar to the following la 4s Metadata Augmentation from Tabular Data c Co LLX REGEX Matching amp Element Assignment Control REGEX start REGEX end REGEX example Element Column Auto Matching Matching File NIL PM Gonio Example Vegetation example E GER Example triticaa 001 triticaa 002 triticaa 003 triticaa 004 itriticaa 005 triticaa 007 triticaa 008 triticaa 009 trit
101. ight source and provides optical input to the spectrometer Drop down list Goniometer name Illumination Drop down list Illumination source name e g Sun or Hg lamp Sources Integrating Drop down list Integrating sphere name Sphere Light Source Alpha string Settings of artificial light source Parameters Reference Drop down list Selected from the list of References defined in the SPECCHIO database This Attribute is mandatory and cannot be deleted If it is not relevant or no data is available set it to V White Alpha string Name of the white Reference Panel Reference Users do not have permission to add to SPECCHIO s Reference Panel Panel Name table When a Spectrum is being loaded and the Reference Panel it refers to is not in SPECCHIO s Reference Panel table then the name of the Reference Panel will be written into this field This provides the information needed for the user to resolve the Reference Panel link information after the Spectrum load is completed 3 14 10 Keywords Group Keywords can be used to search for particular Spectra in the SPECCHIO s Spectrum Query function SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 38 of 134 SPECCHIO User Guide Keyword Alpha string Freely chosen keyword that describes a Spectrum or a Spectral collection Multiple permitted Take care with spelling and avoid leading or trailing spaces to avoid confusion when searching Keyword searching is not
102. ing Campaign Spectral Data ssssssssnssnnnnnnnsnnnrnrrsnnrrnnnnnnsnnnnnnnrnernrnnrnnne 56 4 13 Loading Additional Spectral Data sssssssenssnnnnnnnnnnsrnnnsnnrnnrnnnnnrnrnnnnrnnrnrnnnnnne 58 4 13 1 Uploading Addition Spectral Data from the Same Computer sssssesssssssesenn 58 4 13 2 Uploading Additional Spectral Data from a Second Computer s ssesssssssesssn 58 4 13 3 Uploading Additional Spectral Data in a New Data Hierarchy cceeeeeeees 59 414 UIC IMS CorrecUohnsisriniiscnanrernnisnci e a aa 61 4 15 Managing Target Reference LINKS cccccccceceeeeeeeeeeeaeeeeeeaeseeeaeaeeeaeeeseeaeeeseeaes 62 4 15 1 Viewing or deleting existing Target Reference IiNKS ccccceeeeeeeeeeeeeeeeeeaes 62 4 15 2 Deleting Existing Target Reference LINKS cccccceceeeeeeeeeeeeeeeeaeeeeeeaeeeeeeaes 64 4 15 3 Adding new Target Reference linkS cccccsesececseaeeeeeeaeaeeeeeeanseeaeansesaeanees 65 SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 3 of 134 SPECCHIO User Guide 4 16 Displaying and Editing Metadata cccccccce cece ee eeeeeeesa sees eeeeeeeeasaeaeseseeesesaeas 67 4 16 1 Displaying and Editing Campaign Metadata ccccecececeeeeeeeeeeeeeeeeeeeeeaeees 69 4 16 2 Displaying and Editing Spectrum Metadata ccceccceeeeeeeeeeeeeeeeseeaeeeaeenes 69 4 17 Uploading Metadata from Excel fileS ccccceccececeeeeeeeeeeeeeeeeeeaeeeeeeaeeeseeaesesaeaes 74 4 18 Calculation Of
103. ing points Figure 84 Goniometer sampling point positions 8 5 4 Gonio Hemisphere Explorer The Hemisphere Explorer allows the interactive exploration of a spectrodirectional dataset typically acquired by a goniometer system Figure 85 shows an explorer window displaying a LAGOS Laboratory goniometer system dataset Schopfer 2008 e800 Gonio Hemisphere Explorer Space no 0 Hemispherical Radiance Plot Spectral plot Spectrum Statistics Mean 0 00409 Min 0 Max 0 00844 Stddev 0 064 Sampling Point Information Filename hem_a 001 Azimuth 0 Zenith 75 J rr Band 1 431 861 1291 1721 2151 Wvi nm 628 0 Figure 85 Gonio Hemisphere Explorer window The explorer window comprises a number of components interacting with each other as described hereafter SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 108 of 134 SPECCHIO User Guide The hemispherical plot Figure 86 displays an interpolated surface of a specific wavelength Clicking the icon in the top left of the plot brings up a control panel for plot adjustments rotations A Hemispherical Radiance Plot Aa Rotate Chart Rotation Control Y A Z Axis 34 0 a v v X Axis lt gt 41 Light Le amp gt lt gt 100 Figure 86 Interpolated 3D plot for a chosen wavelength left and rotation toolbox to manipulate the 3D plot Use the band selection slider to select a Spectral band for display Figure 8
104. ing the left hand side Targets hierarchy tree browser locate and select the Target Spectrum you wish to link Its name will be displayed in the Target Spectra box SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 65 of 134 SPECCHIO User Guide e Using the right hand side References hierarchy tree browser locate and select the Reference Spectrum you wish to link Its name will be displayed in the Reference Spectra box e Verify that the correct Target and Reference Spectra are displayed in the central Target Spectra and Reference Spectra boxes respectively Ensure that they are also each in the correct box and not reversed e Click Link to create the link Warnings Do not click the Link button twice This will add the link twice even though it is still displayed only once Duplicated links generally do not cause problems in later processing but may cause confusion if you later attempt to delete a duplicated link Before creating any link check that the link does not already exist so you do not duplicate it It is also possible to create multiple links simultaneously by selecting multiple Target Spectra In addition if multiple Reference Spectra are highlighted as each Target Spectrum is processed the Reference Spectrum with the closest Acquisition time Metadata Attribute is selected for linking Reference panel spectra timeline o o po e c LL Target spectra timeline TS TS TS TS TSs
105. ing to one or more repetitions of the previous character Strings enclosed within square brackets will match any one of the characters within the brackets Use between to match one of range of characters mp1 will match the string example at the fourth character Aexa Will match example but Axa will not le will match example but p1 will not a c will match abc aac adc a7c and a c but it will not match ac Or abbc ab c will match ac abc abbc or abbbc but will not match a7c or ahc It will match aac at the second character and acc at the first character because there are zero characters between the a and c in those strings ab c will match abc abbc or abbbc but will not match ac a 123 b will match alb a2b or a3b only It will not match ab or any other substring 0 9 matches any digit a z matches any letter a z0 9 matches any digit or letter Page 131 of 134 SPECCHIO Escape character Combinations SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 In order to match a special character precede it with the backslash character Special characters are VA 1 0O 3 Putting before other characters often has a special meaning so should be avoided Any of the above search methods can be combined User Guide will match will match will match C will match A c will match any string with c as its second character Aabc will match the
106. ired This sub folder structure will be replicated in the SPECCHIO database when the Campaign data are uploaded The concept of a hierarchical data structure that is used in SPECCHIO has been adapted from SpectraProc Hueni A Field Spectroradiometer Data Acquisition Organisation Processing and Analysis on the Example of New Zealand Native Plants 2006 which was built on a fixed hierarchy of three levels However SPECCHIO supports hierarchies of arbitrary shape and number of levels Preferably the design of sampling experiments should include hierarchical data structuring from the beginning However existing data can be re arranged to meet these requirements There are some specific restrictions on the Campaign hierarchy tree structure SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 16 of 134 SPECCHIO User Guide e No other files can be in the sub folder tree except Spectral files Keep images PDF files and other files in a separate folder probably next to the top level folder of your tree hierarchy structure e All of the files in a folder must be of the same data format and version although the sub folders of a folder may have files with a different data format For FGI HDF files it is possible to have an h5 file as well aS a xm1 file in one folder e To conveniently use SPECCHIO s goniometer angle calculation all of the Spectra measured at the different angles should be put in one folder and observed in the define
107. iting for data Vis module Spectral Line Plot 2 Settings Type Spectral Space Status Waiting for data D 1 Vectors 1 Vis module Spectral Scatter Plot Settings Status Waiting for data Figure 79 A space processing network demonstrating the function of broad and narrowband filters The plot shown in Figure 78 was generated by the Spectral Line Plot of space number 0 Figure 80 shows the plots of space 2 Broadband value as a scatter plot and space 3 Narrowband channels as a Spectral curve 1 0 1000 0 8 0 6 g 0 4 0 2 0 0 400 600 800 1000 0 200 600 800 Wavelength nm Figure 80 Plots of the narrowband channels left and of the broadband channel right 8 5 Visualisation Modules Visualisation modules can be attached to any space and do not generate an output space but display a new window containing the respective plot or data explorer A visualisation module can be configured to produce a number of plots explorers as listed in the following sections Data explorers are graphical components that allow interactive data exploration The titles of the plot windows do contain information about the plot type and the space the data was read from Figure 81 Gonio Sampling Points Plot Space no 0 Goniometer Sampling points Figure 81 Information displayed in the window title SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 106 of 134 SPECCHIO User Guid
108. ition dialog To remove an existing filter region select the region in the list and click Remove 8 4 6 Broadband and Narrowband Filters The filters act on the element type of Sensor elements They are useful to process data of sensors that contain bands widely differing Spectral resolutions An example is the MFR sunphotometer which features one panchromatic band and 6 narrower bands The value ranges of the broad and narrow bands are very different and even a simple plot cannot be created satisfactorily see Figure 78 The broadband channel has been placed at the likely centre wavelength of 673nm As the bands of the MFR are defined in the order of the broadband followed by the narrowbands in the database the plot shows two Spectral lines Mixing broad and narrowbands should not be done from a physical point of view 400 600 800 1000 Wavelength nm Figure 78 Spectral plot of broad and narrowband MFR channels Figure 79 shows a space processing network that illustrates the function of broad and narrowband filters SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 105 of 134 SPECCHIO User Guide 0 Proc module Broadband filtering 1 TYPe SeScr nsrUMenT Spoon Settings Filtering 1 bands Type Spectral Space tatus Waiting for data Vectors 1 va Vectors 1 Proc module Narrowband filtering Settings Filtering 6 bands Vis module Spectral Line Plot Settings Status Waiting for data Status Wa
109. l Figure 71 Input space selection for the Correct for Panel module Note that the dimensions of the spaces holding the Spectra and correction factors must be identical a check on the wavelengths is not carried out In the example shown in Figure 72 a waveband filtering is applied to the correction factors as these were measured with a larger wavelength range SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 102 of 134 SPECCHIO User Guide 0 Proc module Get Panel Correction Factors 1 Ref panel con factors Type Sensor instrument Space Settings Type Spectral Space D 2151 7 ee j D 2251 Status Waiting for data Vectors 1 Vectors 1 2 Proc module Waveband filtering Type Spectral Space Settings D iid Status Waiting for data Vectors 1 Correct for Pane 3 Ref Pane corr Refl Type Spectral Space D 2151 Vectors 1 Proc module Settings Automatic selection from DB Status Waiting for data Figure 72 Space Processing Network for reference panel correction The panel correction can be applied to radiance or reflectance values However correcting radiances for the panel will only make sense if followed by a radiance to reflectance conversion such that p L p D ref Lre The correction procedure can handle multiple reference panels and multiple calibration coefficients and will apply the correct coefficients to the appropriate Spectra 8 4 4 De
110. les are loaded see 3 11 6 ENVI Spectral Library Files the content of the Spectrum Names tag is copied here if it is set in the input file alpha string Latin or scientific name given to target 3 14 13 Optics Group This Group permits describing specific optics which are attached to the recording Instrument SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 39 of 134 SPECCHIO User Guide FOV Integer degrees Field of view of the Instrument used for the sampling This may vary as a result of using a special foreoptic Optics alpha string Designator given to the optics attached to the Instrument Name 3 14 14 PDFs Group SPECCHIO supports uploading of up to two PDF files for each Spectrum To optimise storage in the database select all Spectra that a PDF file applies to and upload just once Depending on your internet access speed uploading large PDF files may be slow Experimental Attached PDF Document describing the experimental design and Design the scientific reasons for doing so Field Protocol Attached PDF Copy of the field protocol filled in during data capture 3 14 15 Personnel Group Investigator Alpha string Investigator s name Multiple It is not necessarily related to any SPECCHIO User s name and is not permitted checked against the list of Users names Nor is this field checked against the Investigator field provided in the Campaign Metadata This Metadata Attribute is supported
111. lick Add picture from this menu A file selection dialog box is displayed e Select the image file you wish to upload The image will appear in the Pictures box with a space for a caption below it e Click within the caption entry control and type in your required image caption e Click the Update button to load the image and caption to the database Larger images may take a short while to upload If you decide against uploading your new selected image click the Reset button Do not right click and select Remove Image This may not yield the desired result when Update is clicked To remove a picture from the currently displayed Instrument definition e Right click on the image you wish to remove A menu will be displayed e Click Remove picture from this menu The picture and its caption will disappear from the Pictures box e Click Update to write this change to the database SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 119 of 134 SPECCHIO User Guide 9 5 1 Instrument Calibrations Each Instrument has an optional Calibration History with one or more Calibrations When Spectra from an Instrument are processed the Instrument s Calibration History is searched for the most recent Calibration at the time each Spectrum was acquired If there is no Calibration History or the acquisition time precedes the date of the first Calibration the Instrument s Sensor definition is used instead For each Calibrati
112. lots of all currently selected Spectra are displayed Separate plots are created based on the setting of the Splitting rules for file export and plotting question in the Query Builder or Spectrum Browser dialogs This example shows six Spectra plotted on a single graph Spectral Plot T T T 1 L 1 4 1 6 wavelength nm Figure 59 Spectral plot graph The four plot options that are described on page 88 in the section 5 3 Show Report are also available for the Spectral Plot option They relate to the four buttons shown at the top right of the above window 5 7 Refli calc This function is the same as Process except that if you have a set of Spectra selected which all have Data Links to white Reference Spectra it will set up a transformation from Radiance to Reflectance for those Spectra as default operations in the Process window Refer to Chapter 8 Interactive Processing using Space Networks for further information 5 8 Publish Collection A separate chapter of this User Guide is devoted to this topic Please see Chapter 7 Publishing Data to ANDS SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 93 of 134 SPECCHIO User Guide 6 6 1 6 2 Help Functions The Info functions do not affect your data or the SPECCHIO Database They are selected from the menu on the Main Window List available Metadata Elements This function will launch your computer s default text editor and open a text file whic
113. lta This module calculates a delta value i e the difference between two inputs A and B Delta A B where A B MxN matrix of M Spectra of dimensionality N Thus a delta vector is calculated by d b where m 1 M This implies that the input spaces must have identical number of vectors and dimensionalities The delta module takes two input spaces Figure 73 Input Space Selection Spectra A Spectra B 0 Cancel o 0 1 3 4 x a Figure 73 Input space selection for the Delta module SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 103 of 134 SPECCHIO User Guide A possible use is the calculation of the difference between recorded reflectance and reference panel corrected reflectance Figure 74 shows a processing network for this purpose and Figure 75 shows the according Spectral plots generated by the network 1 Ref panel corr factors 0 Proc module Get Panel Correction Factors Type Sensor instrument Space Settings Type Spectral Space D 2151 5 j D 2251 Status Waiting for data Vectors 1 Vectors 1 Vis module Spectral Line Plot a l Proc module Waveband filtering Type Spectral Space Settings Status Waiting for data Settings Status Waiting for data D 2151 Vectors 1 Proc module Delta Proc module Correct for Panel Settings Delta A B Settings Automatic selection from DB Status Waiting for data Status
114. m Metadata Se ect All displays them all and Se ect None hides them all In this editor whenever changes are made to any Metadata entries they are saved in an action list They are not written immediately to the database When the Update button is clicked the action list is processed and the database is updated When the Reset button is clicked the action list is discarded without being processed and the content of the Metadata display area is redisplayed from the database SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 68 of 134 SPECCHIO User Guide Warning Click on Update after every change to a Metadata item If you make multiple changes before clicking Update these changes are written to the database but not necessarily in the order in which you made them This can yield unexpected results as the last change you made may not be the last one to be written Metadata entry fields are of various types including integer floating point alpha string date times or special lists Generally the editor restricts you to entering values which are consistent with the data type However the editor does not perform validation checks on entered data For example while you must enter a valid number for the Relative Humidity the editor will not reject negative values or values greater than 100 Warning Take care to enter numbers which are within the valid range for the Metadata Attribute you are entering The editor will
115. m s Metadata matches Radiante ON a OQ O Ambient Temperature 23 6 Acquisition Time 2006 06 24 19 42 36 Fir Comments File F mat ASD Binary v Fie Name triticaa 005 Loading Time 2013 05 28 12 10 06 w Measurement Unit Radiance Spectrum Number 5 ff Locaton 7 Altitude m 264 2 Latitude Degrees 35 26 Location Name Highfi ya Forest A Longitude Degrees 140 02 The operation of this process can be tailored as described below SPECCHIO _UserGuide pdf Version 3 1 05 03 2014 Page 74 of 134 SPECCHIO User Guide Input XLS file format Metadata Excel files must conform to the following conventions in order to be loaded correctly e Only the first data sheet is loaded e The first row must contain column headings It will be displayed and referenced during the upload process but it will not be uploaded The column headings do not need to match Metadata Attribute names e Each row holds data which is uploaded to one Spectrum e The rows do not need to be sorted e One column identified at upload time is used as the Matching Column It identifies which Spectrum will receive the data from each row e If a Spectrum is selected in the Matching Column in more than one row all of these rows are ignored e Other columns contain the Metadata that will be uploaded e You can select to ignore some columns during the upload process Column selection operation After you have
116. m the menu on the Main Window e From the drop down list for the Campaign name control select the name of the Campaign you are uploading to The list of paths in the Path box will change to be those defined for the selected Campaign Load Spectral Data Campaign name GER Ex C Users Peter Desktop Intersect DC 10 Specchio Example Data ger_example GER_example Spectral data of the selected campaign will be loaded from the selected directory load Canca Figure 29 File upload dialog showing multiple paths SPECCHIO stores every path name that has been used to upload data to this Campaign However in this box it will only display those paths which point to locations which exist on your computer If the original data upload was done from this computer it is likely that the original data upload path will be shown e Click on New Path A file selection dialog will open e Navigate to the folder that you created with the second data hierarchy and select it This new path will be added to the list of paths in the Path box Be sure to select SPECCHIO _UserGuide pdf Version 3 1 05 03 2014 Page 60 of 134 SPECCHIO User Guide the correct folder level e Click Load The dialog box will close and progress messages will be shown in the right hand part of the Main Window indicating the total number of files that have been found and the number of new Spectra which have been loaded 4 14 UTC Time Correc
117. me values This is a common scenario as Metadata of Spectra are often highly redundant especially when multiple measurements of the same object were acquired When multiple Spectra are selected either by selecting a node in the Campaign Tree or by selecting multiple Spectra individually the Metadata values that are common across all selected Spectra are displayed For any Metadata Attribute for which even one Spectrum has a different value or is missing that Attribute the string Multiple Values is displayed For Metadata Attributes which are selected from dropdown lists the value Vi is shown if the values are not the same for all Spectra To change a specific Metadata item for all Spectra under a node This method requires that the Metadata Attribute has the same value for all Spectra See the next procedure if that is not the case e Navigate to the correct Campaign hierarchy node and click on it to highlight it e Ensure that the check box for the required Metadata Group is ticked and scroll to that Metadata Group e Click in the field to be changed and type in the required new value When the field contains a valid value the Update button will become valid e Click on the Update button to write the change back to the database for all Spectra for this node e If the Metadata value is shared with other Spectra not under the scope of this node the dialog in Figure 41 will be displayed Click on either Apply to all sp
118. n Group SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 121 of 134 SPECCHIO User Guide Reference Selected from dropdown This Institute list is created in the Create owner list of Institutes new user account dialog See section 3 2 User Accounts Serial Text string The Reference Panel s physical serial number number Reference Selected from predefined There is presently only one brand brand dropdown list Spectralon defined in SPECCHIO If you require further brands to be added speak to your System Administrator Pictures JPEG image on some Multiple pictures of the Reference Panel users computers PNG may be uploaded to each Reference Panel GIF or TIFF may also be definition supported Calibrations See section 9 6 1 Multiple Calibrations make up the Reference Panel Calibration history for each Reference Calibrations Panel When the SPECCHIO database is installed the table of Reference Panels is empty To open the Reference Panel Administration dialog e Select Data Maintenance and Instrumentation Admin from the menu on the Main Window e Click in the Reference Data tab Instrument Selector a Cate 2005 0 1 30 00 00 00 CalibraSon number 1 BRAE Calibration information and graphs will be shown here Figure 100 Reference Data Editor Wavetenoth inmi xt o cs WS The operation of the Reference Panel dialog is analogous to that for Instruments Refer to section 9 5 Instrumen
119. naneains 101 8 4 Processing Module Descriptions cccccceeecee eee ee cess eeeeeea eens ee eeeeeeaeaeaeeeseeeeeeaeaeaes 101 8 4 1 Radiance to Reflectance Transformation ccccceceeeeeeceeeeeeeeeeeeeeeeeeeeeeeeeaees 101 8 4 2 Reference Panel Correction Factors cccsceceeeeseceseeeeeeeeeseeeeeeseseevaeseseneneeas 101 8 4 3 Correct for Reference Panel Non Idealness ccccecccceceeeeeeeeeeeeeeeeeaeeeeeaees 102 ey DRaa T E EEE aedeiainarenan aauateua osenneanaue 103 SA Wave DSC ll GCP sairaana E Aa EE S 104 8 4 6 Broadband and Narrowband Filters ccecececeeeeeeeeeeeeeeeeseeeseeeeeseeeseeeeeeseeenees 105 8 5b VISUAISAHONM MOGUICS norssi roninai nua a a a a 106 Sek PE a ENO POE adasa EE EEEE 107 2 Spectral Scatter POl sinudantciunicoaranavuhonaenasetesoivuenaeiensocosmaciatecotmeraanes 107 8 53 Gono Samping POMS PIGE siventenacaceqacasentengeeceatnoctiasmenceeceadeersmeneeeneeoateciaten 108 8 5 4 Gonio Hemisphere Explorer ss essssssssssnunnusnusnunnnnnnnnunnnsnnnnnnnnnnnnnnsnnnnnnnnnnnnnnn 108 Gao HO LNE RPO One a AA 110 B50 TME ENE EON E anani iii AEEA EEA 110 BO Fe EXOT MNOGU arusini Ea a E EA 111 SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 4 of 134 SPECCHIO User Guide 9 Data AAMINIStratiOn ccccceceeeeseeeeceeeeeeeeseeeeueaeeuaueneeeueueueueaeauenseseannas 113 91 Removing CAC cesses ce see Gee E E een dace 113 OZ AMID ON EXODO aonana AE EEA aanananentadeea 114 23 CamMmpgn IMPO anaE E A E
120. ndard deviation Calibrations can be added from a file or manually entered If added from a file they are complete Calibrations If added manually they are place markers only and do not contain enough information to be used as a Calibration They should be replaced with a Calibration uploaded from a file when that information is available Calibrations do not need to be loaded in chronological order but they will be used according to their dates The Calibration file supplies the Wavelength Rho Sigma table The Calibration date Calibration number and comments must be manually updated after the table is loaded This file is formatted as follows e A tab separated text file usually with TXT extension e The first line must be a heading line Its first value must be exactly wvl and there must be a heading for the Rho column e The entry for each wavelength is on a new line e The values on each line are in the sequence Wavelength Rho and Sigma e The Sigma value is optional However if it is present it must be present on all lines and there must also be a heading for it in the first line of the file Note For Spectralon calibration files as provided by LabSphere if required uncertainty information must be added by the user to the file before loading SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 123 of 134 SPECCHIO User Guide Example wvl rho sigma 250 0 98 0 02 251 0 98 0 02 252 0 981 0 02 253 0 98 0 02
121. ndatory and cannot be deleted This Attribute is set automatically depending on the file format being read However for some formats it is not known and is therefore set to Nil If it is not set or is set incorrectly plotting may not be correct Spectrum Integer Some recording devices and file formats apply a number Number which is recorded in the Spectrum file If a Spectrum is loaded from such a file format the number will be placed into this Metadata field If the file does not define a Spectrum Number this Metadata Attribute remains unset Some file loaders may generate an artificial number This behaviour is deprecated and should not be relied upon Note that this number is not the Spectrum ID and usually does not hold the same value as the Spectrum ID The integer numbers which are displayed when Spectra are selected in the Query Builder or when a Spectrum is highlighted in the Hierarchy Viewer are Spectrum IDs Spectrum Numbers can be changed in the Metadata Editor but probably shouldn t be Spectrum IDs cannot be changed 3 14 5 Generic Target Properties Group The Generic Target Properties Group holds data related to a Target or Sample It could apply to both soil and vegetation studies In this context a Sample is regarded as a sample taken from the Target and measured Multiple Samples can be taken from any Target and measured independently They may have been taken from the Target in the field or the Target may h
122. nder a node to have the same value e Navigate to the correct Campaign hierarchy node and click on it to highlight it e Ensure that the check box for the required Metadata Group is ticked and scroll to that Metadata Group The value displayed in the Metadata field should be Multiple Values to indicate that the values are not the same for all Spectra e Right click on the Metadata field name to show a Delete button Click on the Delete button The Metadata field will disappear from the screen e Click the Update button to write this change into the database This step is critical don t skip it e Right click within the Metadata Group box to display a menu of Metadata Attributes that can be added to this Metadata Group Click on the Metadata Attribute to be added back e Enter the value you require for this Metadata Attribute e Click on the Update button to write this change back to the database 4 16 2 4 Editing Metadata for Multiple Unrelated Spectra The operations in the preceding section can be applied to multiple unrelated Spectra It is possible to select multiple Spectra by holding the Control key while clicking on each additional Spectrum to be selected It is also possible to select a range of Spectra by selecting the first Spectrum and then holding the Shift key while you click on the last Spectrum in the range This is consistent with common Windows usage of the Control SPECCHIO_UserGuide pdf Version 3
123. ng no Sensor definition are plotted the X axis will represent bands and not frequency For sensors comprising broad and narrow band elements e g MFR only the narrow bands will be plotted 5 4 File Export Files are exported by clicking on the File export button in the Query Builder or Spectrum Browser It operates on all Spectra which are selected at the time this button is clicked The following window will open File output File format Target directory Split header and body Time format yyyy MM dd HH mm ss Milliseconds since 1st Jan 1970 00 00 00 Figure 57 File output dialog Controls are as follows File format Select from the drop down list CSV Data is written to a text file in comma separated value format This file type can be read into Excel A full description of the way CSV files are used can be found below at section 5 4 1 CSV Spectrum Export Format ENVI SLB ENVI Spectral library file consisting of two files a header file lt file_name gt hdr and a body file lt file_name gt slb Spectral data are written as floating point values either 32 bit or 64 bit depending on the architecture of the machine The datatype field in the header file is set accordingly datatype 4 or 5 respectively SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 90 of 134 SPECCHIO User Guide Target folder Click on Browse to select the folder into which the output files will be written
124. ng on it This effectively selects all Spectra under this node Select a second node or Spectrum by holding the Control key and clicking on it or equivalent Mac mouse action Select a range of Spectra by clicking on the first Spectrum to select it holding the Shift key and clicking on the last Spectrum or equivalent Mac mouse action Change your selection by clicking on the new item you want to select without Control or Shift keys In addition there are two options Order by Use the drop down menu to choose the sort order for Spectra within each node The options are Sampling date The Spectra are sorted in increasing order of the date and time in the Acquisition Time Metadata Attribute Filename The Spectra are sorted in increasing alphabetical order of the string in the Filename Metadata Attribute Insert order The Spectra are sorted in increasing order of the date and time in the Loading Time Metadata Attribute Often these three orders are the same or at least similar So you may not notice any change of sequence Refresh Click this button to cause the Hierarchy Tree to be reloaded from the database Use this button if the operation you have just performed some background operation or some other user has changed the database since this dialog box was opened SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 53 of 134 SPECCHIO User Guide 4 8 Note 4 9 SQL Matching Strings When matching te
125. ning If the message box advising successful completion does not appear the upload did not complete normally Check the count of uploaded Spectra to determine how much was completed See below for information on recovering from upload errors If a folder contains unknown file types mixed file types or files with invalid data the loading process will stop A dialog box will generally appear indicating the offending file and the cause of the problem You should check the cause of the problem rectify it and attempt the upload again Spectra which successfully uploaded the first time will not be uploaded again 4 13 Loading Additional Spectral Data If further Spectral data becomes available for your Campaign it is possible to conveniently add it to your existing SPECCHIO Campaign There are a number of different scenarios which may apply 4 13 1 Uploading Addition Spectral Data from the Same Computer In this case add the new Spectral data to the existing sub folder structure on your computer s disk from which you uploaded the original Spectral data e Do not add any files other than Spectral data and ensure that all files within each sub folder have the same file format e Do not change the file names of any of the original files e Do not change or rename the sub folders but you may add new sub folders To upload the new Spectral data follow the process described in section 4 12 Loading Campaign Spectral Data Only the new d
126. nm P1x 1050 val 25 767 Time 23ms Avg 7 Sm 0 Sg 0 Tc on Xt 1 chl 400 00 1 102E 000 400 50 1 131E 000 401 00 1 205E 000 401 50 1 257E 000 402 00 1 260E 000 402 50 1 336E 000 403 00 1 341E amp 000 403 50 1 418E 000 404 00 1 451E 000 404 50 1 444E 000 405 00 1 488E 000 SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 26 of 134 SPECCHIO User Guide 3 11 6 ENVI Spectral Library Files Standard or Exelis Visual Information Systems Format Owner ENVI Software Library Supported ENVI Spectral library files SLB and SLI Formats Comments The import routine reads each hdr file in the folder Each hdr file refers to either an s1lb or s1i file for the body of the Spectrum data That is Spectrum data are stored in pairs of files For example my_spectra hdr my_spectra slb Or my_spectra hdr my_spectra sli Both slb and s1i files can be mixed in the one sub folder Each file pair can contain more than one Spectrum If present Spectrum names are read from the header file and stored in the database in the Filename Metadata Attribute The File Type Metadata Attribute is set to ENVI Har The Sensor definition i e central wavelengths is not read from the ENVI header file You should define the correct Sensor using the Data Maintenance Load sensor definition menu functions See 9 4 Definition of new Sensors 3 11 7 Ocean Optics SpectraSuite Data Files Standard or Ocean Optics Format Owner Ocean Optics
127. now be active You can repeat this process at any time and log in as a different User or even log in again as the same User SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 51 of 134 SPECCHIO User Guide 4 5 4 6 4 7 Logging Out There is no specific log out function for SPECCHIO Closing the Main Window will close your database session If you restart SPECCHIO you will need to log in again If you select Database and Connect to database from the SPECCHIO Main Window menus while you are logged in SPECCHIO will log you out before logging in again as the new User Changing your User Details After you have logged in and connected to your database you can adjust your User Information To edit your User Information e Select Database and Edit user information from the menu items from the main SPECCHIO screen The following dialog box will be displayed showing your current User information s a Edit user account User Account Details Title M v Firstname Peter Lastname Roberts Institute Software Development Intersect Add new institute E mail enquiries intersect org au WWW http www intersect org au ANDS Party Identifier uow edu au PTY SL 03 Figure 21 User Information update dialog e Update the information as required You cannot change the ANDS Party Identifier e Clink on Update to cause the changes to be written back into the database This process doe
128. ns Each of the 14 file categories listed below is read by a separate file loader Once the file type in a folder has been determined the related file loader is activated and it reads all files in that folder Therefore you must not place the files of more than one file type in any input folder Note that ASD Binary and ASD Indico 7 are different files types and cannot be mixed Similarly UniSpec and UniSpec SPU are different file types and cannot be mixed 3 11 1 ASD Binary Files Standard or Analytical Spectral Devices Format Owner ASD FieldSpecPro FS3 spectroradiometers Supported Old file format ASD FS3 ASD FS PRO and ASD FSVNIR binary files Formats cause an error Comments Indico Version 7 files are read by a different file reader and so cannot be mixed in the same folder as ASD binary files ASD Calibration files raw as stored on ASD laptops can also be loaded using SPECCHIO s Spectrum load functions This permits advanced users to explore the information content of the Calibrations they describe In the current release loading ILL REF files will 3 11 1 ASD Indico Version 7 Files Standard or Analytical Spectral Devices Format Owner Indico Pro Software Supported New file format Indico Version 7 Formats Comments ASD Binary files are read by a different file reader and so cannot be mixed in the same folder as Indico 7 format files Loading of ASD Calibration files of this version using the Sp
129. nstructions for updating it When you add another SPECCHIO User to the Research Group for your Campaign that User gets all the rights that you have for that Campaign That is they can modify the data add to it or remove it They can also change the membership of the Research Group It is not possible to remove the original uploader of the Campaign from the list of Users in the Research group 3 8 Time Data SPECCHIO expects acquisition times for Spectra acquisition to be in UTC Coordinated Universal Time For practical purposes UTC is considered equivalent to GMT However the term UTC is recommended for technical contexts Astronomical Applications Department of the U S Naval Observatory 2003 The above implies that all computers capturing data for use in SPECCHIO should have their time zone set to GMT and their system time adjusted to UTC However this is not usual so the Spectrum acquisition date time can be modified in the database if a time different from UTC was used SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 19 of 134 SPECCHIO User Guide 3 9 Note Warning 3 10 Other times such as Spectra upload times and calibration times are usually stored in local time Data Links For some calculations on Spectra such as the conversion of a Radiance Spectrum to a Reflectance Factor Spectrum SPECCHIO needs to know the related White Reference Spectrum for each Target Spectrum Data links are used to define
130. nufacturers in SPECCHIO s predefined manufacturer s table See Appendix B Predefined Manufacturer Table for the list of manufacturers and their short_name values lt type number gt SPECCHIO will attempt to match this integer number to the Instrument Type number in Spectrum files when they are read This is used to automatically set the Sensor in the Spectrum s Metadata lt no of channels gt The number of frequency channels measured by this Sensor This must be the same as the number of lines in the Band Table in this file The third row must have the headings of the parameters for each band Rows 4 to 3 lt no of channels gt must have three numeric values on each line lt band number gt An integer number starting at 1 and incrementing for each band in the Band Table lt wavelength gt The central wavelength of this band in nanometers lt fwhm gt The Full Width at Half the Maximum value for this band The value is difference of the upper and lower frequencies in nanometers This value is presently ignored It is included for possible later new features Notes on the file format e There must be exactly one tab character between each field e The lines must not start with a tab character Example An Excel view of a Sensor Definition File SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 116 of 134 SPECCHIO User Guide 9 5 Note Company Type no no of channels 2 ASD FSFR ASD Fieldspec FR ASD 4 2151
131. o Matching Matching File NIL Matching Column Genera Assignment Details File Name s if Concatenated to form a Number of assignable columns 5 regular expression Number of assigned columns 0 ae 1 2 2 2 Matching Dets Atriti 3 J triticaa 0 5 abria A z Number of matches 12 gt 5 2 lata 7 2 roe tru DB Value Table Va 8 J 285 ltriticaa 000 a 9 J 286 ltriticaa 006 10 287 triticaa 018 ll 7 288 itriticaa 030 12 2 289 itriticaa 042 13 2 1290 itriticaa 054 291 itriticaa 066 The regular expression 418 triticaa 001 1 matches this DB Value i z 420 triticaa 003 3 so this Spectrum is the 1 lriticaa 004 14 one that will receive the 422 ltriticaa 005 5 new Metadata values 423 itriticaa 007 7 424 itritcaa 008 8 425 triticaa 009 19 426 ltriticaa 010 10 427 itriticaa O11 11 428 triticaa 012 12 429 itritcaa 013 13 430 _ _ triticaa 014 43 1 itriticaa 0 15 432 itriticaa 016 433 triticaa 017 434 itriticaa 019 435 triticaa 020 Figure 46 Using Regular Expressions for selecting Spectra For each row of the XLS file the data in the Matching Column is concatenated with the REGEX start and REGEX end contents to form a Regular Expression The matching process is then performed using Regular Expressions See Appendix A Regular Expressions Tutorial In the above example the 4 forces the matching to start at the beginning of the string is
132. o select one or more Spectra based on their Metadata and then perform operations on all of these selected Spectra The operations which can be performed on the selected Spectra are the same as for the Spectrum Browser and are explained in the later sections of this Chapter To Launch the Query Builder select Data Processing amp Output Build query from the menu on SPECCHIO s Main Window Data Usage Policy Digital Object Identifier Number of results ee eee Show report File export Process Spectral Plot Refi Calc Publish Collection Splitting rules for file export and plotting 5 Split spaces by sensor Split spaces by sensor and unit 5 Split spaces by sensor instrument calibration_no and unit Measurement Unit NIL X Acquisition Time 2013 06 19 14 09 03 2013 06 19 14 09 03 w File Comments Figure 52 The main Query Builder window Matching Spectra 15419 15421 Copy Matlab ready query to clipboard Copy R ready query to clipboard SPECCHIO _UserGuide pdf Version 3 1 05 03 2014 Page 85 of 134 SPECCHIO User Guide Figure 53 Popup menu to copy the query statements as Matlab or R script The parts of this window are Visualisations This menu item displays a drop down list of graphic visualisation options which you can apply to the Spectra listed in the Matching Spectra box These options match those listed in section 8 5 Visualisation Modules Depending
133. on the following information can be stored Field ame pormat comment OO Calibration Date time The date on which this Calibration was performed date selected by Where possible SPECCHIO will use the Calibration with date picker the most recent date and time which is prior to the Acquisition date time of the Spectrum being processed Calibration Integer The sequence number of this Calibration If there is number insufficient date information and a Calibration Number is given in the Spectrum s Metadata SPECCHIO will attempt to select a Calibration based on this Calibration sequence number It usually starts at 0 and is incremented for each new Calibration However this is not a SPECCHIO requirement Text String A comment about this Calibration Calibration Floating Table of wavelengths of the centre of each band The wavelengths point array number of entries in this table must match the number of entries in the Sensor definition for this Instrument Calibrations can be added from a file or manually entered If added from a file they are complete Calibrations If added manually they are place markers only and do not contain enough information to be used as a Calibration They should be replaced with a Calibration uploaded from a file when that information is available SPECCHIO supports the following formats for loading Instrument Calibrations e Unispec SPU files e SpectraVista SIG files Only HR 1024 has been tested Note
134. on the option and Spectra selected some of these Visualisation options may take several minutes to process Left panel There is one box for each SPECCHIO Spectrum related Metadata Group and within each box all of the Metadata Attributes for that Group are listed with a data entry box Matching Spectra The Spectrum IDs of the matching Spectra are listed in this box Clicking the menu mouse button over this text box brings up a menu that copies the query statement in Matlab or R syntax into the clipboard Number of results The number of Spectra IDs listed in the Matching Spectra box is shown in this box Six action buttons The six action buttons Show report File export Process Spectral plot Refl calc and Publish Collection will become active when you have selected one or more Spectra The operations they imply will be performed on the selected Spectra Each of these buttons has a section in this Chapter Splitting rules for file export and plotting Click on the radio buttons to select one of the options Split spaces by sensor Split spaces by sensor and unit or Split spaces by sensor instrument calibration_no and units This selection will affect the operation if you select the Process Spectral Plot or File export buttons See the relevant option description section in this chapter for more information Queries are created by entering selection criteria into the Metadata Attribute controls in the left panel
135. ouse click patterns Left Click The normal selection or activation click Right Click Context menu display Control Left Click Adding a single item to the selection Control Click adds the item clicked to any already selected items Shift Left Click Adding a range of items to the selection Shift Click adds the item clicked plus any items between the last selected item and the currently selected item to any already selected items There are a variety of Mac mouse types which can be used and also a variety of settings for configuring the Mac mouse The Mac user is advised to consider their mouse button settings prior to starting SPECCHIO operation so all of the above functions are accessible 4 2 Unix Operation As described under Mac Operation above Unix users should also consider how to access on their computer the various mouse click combinations that are described in this document The functionality of the GUI is generally consistent across all tested operating systems However there is a difference in the selection of folder pathnames under UNIX As a filename is required in the Open dialog enter a dot in the Enter file name box Figure 18 Alternatively on some UNIX machines just click the folder but do not double click in this fashion the folder will be selected and no has to be inserted in the Enter file name box SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 49 of 134 SPECCHIO User Guide
136. ow some contradictions to the State of the space SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 112 of 134 SPECCHIO User Guide 9 Data Administration The Data Administration functions are useful for managing the integrity of the SPECCHIO database The following functions are restricted to users with Administrator permission Menuitem Operations Restricted to Administrators Removing data belonging to other users Import campaign All functions Load sensor definition All functions Instrument Changing adding or deleting any Instrument or Reference administration Panel information 9 1 Removing data Spectra hierarchies or entire Campaigns can be removed from the database using the Data Remover Users can only remove data from the database if they are a member of the Campaign s Research Group see 3 7 Research Groups and Accessing SPECCHIO Campaigns A user with Administrator permissions can remove all datasets irrespective of their owner To remove data e Select Data Maintenance and Remove data from the Main Window menus The following window is displayed Only the Campaigns which you have permission to remove will be displayed Gonio Example Vegetation example Figure 94 Data Remover dialog e Use the Spectral data browser to select the nodes or Spectra that you wish to remove Multiple Spectra and nodes can be selected by using the Shift and Control keys You can select
137. owing dialog box which lists the Metadata Attribute name that already exists in this example File Comments Insert of existing metaparameter File Comments 0 You are about to insert a new metaparameter of the type File Comments Some of the selected records already feature a metaparameter of the type File Comments Please select one of the following actions Select one of these three options from the dropdown list Skip this parameter No data from this column of the XLS file will be loaded into the SPECCHIO database Insert anyway Add another value for this Metadata Attribute This option is not supported for some Metadata Attributes For example adding a second File Name or Spectrum Number is not permitted Delete existing and insert new values The Metadata values in the XLS file will replace those in the Spectra Click OK to continue processing using the action you have selected Click Cancel to skip processing of this column This has the same result as selecting Skip this parameter Adjusting the matching strings If the data in the Matching Column of the XLS file is a partial match to the Metadata Attribute values in the database you can use the REGEX box to assist in the match SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 78 of 134 SPECCHIO User Guide Start and end markers always used Matching amp Element Assignment Control REGEX example triticaa 0 1 Element Column Aut
138. pace S Input Space 0 1l Eeancet 3 K Confioure mam ee id Set Input Spaces N Rampuvi l gt JZ Figure 67 Popup menu of a module left and the input space selection dialog right Configuration of Modules Some modules may need configuration To display the configuration dialog of a module click menu over the module and select Configure The possible configuration settings of each module are detailed in the respective module description Processing Module Descriptions Radiance to Reflectance Transformation The module Radiance to Reflectance is building ratios of target and reference panel radiances Leg As a prerequisite datalinks of the type Spectralon must exist between the target Spectra and the corresponding reference Spectra For an explanation of how such links are created please refer to 4 15 Managing Target Reference Links Reference Panel Correction Factors This module retrieves the correction factors for all reference panels that were used during data acquisition of the Spectra contained by the input space As prerequisites a reference panel must be set for the input Spectra using the Metadata Editor Figure 68 and calibration data for the panel must have been loaded to the database Calibration data loading is a task of the system administrator For details on the reference panel administration see 9 5 SPECCHIO_UserGuide pdf Version 3 1 05 03 2014
139. pace by a processing module Processing modules are effecting a transformation on a space i e the Spectral data vectors of the input space are transformed to an output space The algorithm of the processing module defines the dimensionality of the resulting space This is illustrated in Figure 17 with an input space of dimensionality N being transformed into another discrete space of dimensionality M Although processing modules tend to have singular SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 47 of 134 SPECCHIO User Guide input output in most cases they may have multiple inputs and generate multiple outputs SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 48 of 134 SPECCHIO User Guide 4 SPECCHIO Basic Operation SPECCHIO has been setup to comply as much as possible with the look and feel of the operating system on which it is running The screenshots provided in the following sections have been taken mostly on Windows Vista Depending on your operating system the windows and widgets may look a little different 4 1 Mac Operation On Mac systems the SPECCHIO client application menus do not appear at the top of the screen as is common for Mac applications Instead they appear at the top of the SPECCHIO Main Window in a similar way to the Windows screen shots in this document SPECCHIO uses the following mouse click combinations on Windows This document describes SPECCHIO operation in terms of these Windows m
140. pectral Data Campaign name GER Ex C Users Peter Desktop Intersect DC 10 Specchio Example Data ger_example GER_example Spectral data of the selected campaign will be loaded from the selected directory Load Cancel Figure 25 Load Spectral Data dialog e From the list of Campaign names in the dropdown box select the name of the Campaign into which you want to load data e Highlight the Path name which contains the Campaign data sub folder tree on your computer If the path name is not in the list click on New Path navigate to the path on your computer and select it It will now be highlighted e Click the Load button The dialog box closes and the loading progress is shown in the right panel of the Main Window A message box will appear once all data has been loaded to the system Do not perform other operations on this Campaign until the load has completed e Click OK to clear the message box After uploading your Spectral data to SPECCHIO do not change the sub folder structure on the hard disk that you set up and used You will need this again if you wish to upload further Spectral data to this Campaign in the future Instrument and Sensor selection SPECCHIO searches the existing Sensor and Instrument definitions in the database to find a match for the Spectrum data loaded It sets the Instrument and Sensor Metadata Attrinutes for the Spectrum to the one it chooses If SPECCHIO does not find a ma
141. pectrum File Formats cccccceceseceeeeeeeeeeeeeeavseseeneneaeaeenenes 31 3 13 Campaign related Metadata ssusssnnsnunnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn 31 3 14 Spectrum related Metadata ssassssssnannannnanuasnusannnasseanannsanannanaaanannansnnannnannnnnua 32 3 14 1 Campaign Details Group ccccececscecececeeeseeeeeeeeeeeeeseeeeeaeenaestanetanatatatatanas 32 SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 2 of 134 SPECCHIO User Guide D142 Data POM AL GROW cannes saawanarcennstaneciananaina oaeiai 33 3 14 3 Environmental Conditions Group ccccecececeeseeeeeeeeeeeeeeeeeeeeeeeeeenenesenenenens 33 DAA GWE Fal OU peneda E AAA EA 34 3 14 5 Generic Target Properties GroOUD s sssessssessnsnnesnnanonnnnennunanennanennnnonannenonannen 35 Selo MEMNANON GLOU beindi ea aa E E Ea 36 DAG MOUMEN G OUD n E E EE 36 3 14 8 Instrument Settings Group ssessssssssssssssnsnnnnnnnnsrnsrnnnnnnnnrnnrnernnrnnnnnrnennnnnan 37 3 14 9 Instrumentation Group sssesessssanennnsanennoeannesonansannnenonnenennnnonennnsanunnonannenena 38 FARIT KYW TOUD eana aa E EEE EEN 38 aA LOCION GOUD asrnane ET 39 Sette NIMES GOUD crrr E a E 39 JAAS ODUCS GOUD uieii ennn E EAEE AEE E 39 r POPS TOU ia E EE swoneae ceueaieyew 40 SG US Personnel GlOUD cancctsacmensianen ios saseraahaidnmadiners tutadndeantaeahendndeuebeeatecanneientionss 40 ered UCTS CG OUD a E A A E 40 SAL Proce Smo OUD eenid E E E 41 3 14
142. r of Spectra shown in the Linked targets box can be many more than the number of selected Spectra 4 15 2 Deleting Existing Target Reference Links The option to delete existing links works simultaneously but independently on the two halves of the Show existing links dialog When the Delete selected links button is clicked all links to and from the Spectra highlighted in the Linked references and Linked targets boxes will be deleted It is possible to highlight Spectra in one of these boxes only After deleting the Linked references and Linked targets boxes will be updated This may take a little time SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 64 of 134 SPECCHIO User Guide The two halves of this dialog still operate independently In this example the two selected Campaigns are not even the same Target Reference Links q plinked targets GR083005 080 ID 1505 NI getation example GR083005 083 ID 1511 i Jya GR083005 084 ID 1513 i References erences GR083005 080 GR083005 081 GR083005 082 GR083005 083 GR083005 084 GR083005 085 GR083005 086 GR083005 087 GR083005 088 GR083005 089 amp Targets triticaa 054 ID 1292 triticas 066 ID 1293 GR083005 087 ID 1519 1GR083005 088 ID 1521 GROS3005 089 ID 1523 from these highlighted Spectra will be deleted Figure 35 Deleting Target Reference Spectra links 4 15 3 Adding new Target R
143. re are often cases when a new set of Spectra is required to be uploaded and this new set does not relate to the existing Spectra in the Campaign In this case a new folder structure can be created at the top level of the Campaign SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 59 of 134 SPECCHIO User Guide we spetu Nu di GER Example GER_example References 4 Targets LLN Canin Examnia Figure 27 Data Hierarchy of GER example after initial load In the above example there is one sub folder in the GER Example If the user has performed a second largely independent part of the experiment its results may be loaded as a new top level folder in the Campaign Main GER 50 GER Examole Original GER Example Campaign gt i GER upload top level folder which Example oS Sse relates to original upload path Campaign t Sree folder Sd pm rarte Second GER Example Campaign upload top level folder which Targets M Mania amp 2 2 relates to a new upload path Figure 28 Data Hierarchy of GER example after loading second part To upload a new data hierarchy to an existing Campaign e Prepare the second upload folder tree of Spectra on your computer and ensure it has a different name from the first one It does not need to be in the same folder as the first one owned by the same user as the first one or even on the same computer as the first one e Select Data Input and Load campaign data fro
144. rectional conical Directional hemispherical CASE 1 CASE 2 CASE 3 Conical Conical directional Biconical Conical hemispherical CASE 4 CASE 5 CASE 6 Y DY WHE _ J gt JE J JA Hemispherical Hemispherical directional Hemispherical conical Bihemispherical CASE 7 CASE 8 CASE 9 s Ee Figure 15 The nine beam geometry cases A 3 14 19 Scientific References Group Citation Alpha string Publication to be cited when using these Spectral Multiple data permitted Publication Alpha string Publication relevant to these Spectral data Multiple permitted 3 14 20 Soil Parameters Group The Attributes in this Group have been provided to allow specification of the soil type according to the Australian Soil Classification The table below shows the list of Metadata Attributes provided by SPECCHIO and the type of data they hold Please refer to the documents defining that classification system to see a detailed explanation of the meaning of each item At the time of writing this document an explanation of this classification system can be found at CSIRO 2011 Australian Soil ASC Order Alpha string Classification parameters ASC Sub Order Alpha string Sampling Lower Depth Metres Sampling Upper Depth Metres Horizon Desig Master Alpha string Horizon Desig Sub Alpha string Division SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 44 of 134 SPECCHIO Measurements SPECCHIO_UserGuide
145. ront end ANDS Collection export 05 03 2014 Added calibration support and automatic sensor instrument definition SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 130 of 134 SPECCHIO Appendix A User Guide Regular Expressions Tutorial Regular expressions are widely used across the computer industry when text string matching is required They permit a rich array of sophisticated matching functionality A complete explanation of regular expressions is beyond the scope of this tutorial Readers with a desire to see a complete list of all options should see the Java tutorial at http docs oracle com javase tutorial essential regex index html The following is a quick summary of the most useful regular expression functions for SPECCHIO Users Simple string Start of string End of string Any character Repeated character Repeated characters Alternate characters Character ranges A L L SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 A simple string containing no special characters will match those characters in a target string regardless of where within the target string they Occurs The character will match the beginning of the target string The character will match the end of the text string The period character will match any character Asterisk causes the matching to zero or more repetitions of the preceding character The plus sign causes the match
146. rs defined in database for this particular Instrument Pictures JPEG image on some users Multiple pictures of the Instrument computers PNG GIF or TIFF may be uploaded to each Instrument may also be supported definition Calibrations See section 9 5 1 Instrument Multiple Calibrations make up the Calibrations Calibration history for each Instrument To open the Instrument Administration dialog e Select Data Maintenance and Instrumentation Admin from the menu on the Main Window e Click in the Instrument Data tab Instrument Selector bersect HR 3024 istumert Dots Reset Ociete nsrument Calibration information and graphs will be shown here Figure 99 Instrument Data Editor The various parts of this dialog and their operation are explained in the following table Instrument Selector This dropdown list includes all Instruments in the SPECCHIO Instrument Table Use this to select which Instrument you wish to view or edit Instrument Data There are two related boxes with this title One shows the data for the Instrument Selected by the Instrument Selector You can modifiy the data displayed in this box The other has two buttons Reset Click this button to reset the display in the Instrument Data box with information re read from the database SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 118 of 134 SPECCHIO User Guide Note Update Click this button to write any updated da
147. s Spectrum was uploaded This Attribute is always present and is generally set by SPECCHIO when the Spectrum is read If no data is available it should be set to Nil Although this value can be changed it is not advised All Spectra are stored internally in the database in SPECCHIO s internal Spectrum format File Name alpha string The name of the file from which this Spectrum was uploaded In the case of input file formats which support multiple Spectra per file such as XLS or TXT the name of the Spectrum within the file is appended to this file name Although this value can be changed it is not advised Changing it may result in duplicate Spectra when a subsequent Spectrum upload is performed for this Campaign alpha string Version of the input file format SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 34 of 134 SPECCHIO User Guide Loading Time Date Time 24h The system time when the Spectrum was loaded into database This value is automatically set to the SPECCHIO server s system time when the Spectrum is uploaded to SPECCHIO Note that this may not be the same as the client s system time The Special functions Correct local time to UTC function does not operate on this time Measurement Selected from dropdown list Describes the nature of the measurement Unit select from Reflectance Radiance Transmission Absorbance DNS Irradiance Mueller10 Mueller20 and Wavelength This Attribute is ma
148. s flag can be set to exclude specific Spectra from processing However negative tests cannot be performed by the Query Builder so this is intended for automated processing control For manual management Spectra which are not intended for processing should be placed in specific sub folders There are currently no SPECCHIO processes which test this flag It is generally intended for use by non SPECCHIO processes such as processes written using Matlab SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 41 of 134 SPECCHIO Processing Algorithm Multiple permitted Processing Level Processing Module Multiple permitted Source File Multiple permitted Time Shift Multiple permitted User Guide Alpha string Description of processing algorithm applied to Spectrum Multiple Processing Algorithm fields may be added to each Spectrum Each process which modifies a Spectrum should set an informative message into a new Metadata Attribute of this type for each Spectrum it modifies There are currently no SPECCHIO processes which set this flag It is generally intended for use by non SPECCHIO processes Floating point Numeric designator of a specific processing level This Metadata Attribute is provided to permit non SPECCHIO programmatic processes to keep track of the level or amount of processing which they have performed on the related Spectrum SPECCHIO does not use this value Alpha string Name of pro
149. s not change your User Name or Password so there is no requirement to modify anything in the db_config txt file Browsing the Hierarchy Tree There are many places in the SPECCHIO operation when a Campaign Hierarchy browse control such as the one below is displayed as part of an operation dialog SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 52 of 134 SPECCHIO User Guide Windows Mac Order by Sampling Date w Order by Sampling Date di specchio E specchio I D GER Example v GER Example di GER_example di Vegetation_example gt i Vegetation example v E GER_example v E References GR083005 080 7 GR083005 081 7 GR083005 082 7 GR083005 083 GR083005 084 7 GR083005 085 7 GR083005 086 7 GR083005 087 7 GR083005 088 7 GR083005 089 gt Targets gt Gonio Example i References GRO83005 080 GRO83005 081 GRO83005 082 GRO83005 083 amp GRO83005 084 amp GRO83005 085 GRO83005 086 amp GRO83005 087 GRO83005 088 GRO83005 089 di Targets Gonio Example Vegetation example Refresh Refresh Figure 22 Campaign Hierarchy browse controls for Windows and Mac This browse control operates much like a normal folder and file browser Click on the and icons or or for Mac to cause the hierarchy levels to be expanded or collapsed Select an individual Spectrum by clicking on it Select a node in the hierarchy by clicki
150. s released with this version of SPECCHIO can be found in Appendix C Predefined Sensor Table of this document However new Sensors can be added to this list As of V3 1 of SPECCHIO new sensors are automatically generated if no appropriate sensor is found during the loading of spectral input files Each Sensor is assigned a unique integer Sensor ID by SPECCHIO An instance of a certain Sensor Type There can be several different Instruments that are all of one Sensor Type Each Instrument has a defined owner Each Instrument record in the Instrument Table refers to its related entry in the Sensor table so that its standard Sensor technical details can be accessed As of V3 1 of SPECCHIO new instruments are automatically added to the database when no matching instrument can be identified during data loading Each Instrument is assigned a unique integer Instrument Number Instruments optionally have a history of Calibrations There are generally multiple Calibrations in that history each Calibration being identified by either a date and or a Calibration Number which is a sequence number incremented each time the Instrument is sent for calibration Calibration Numbers are unique for an Instrument An Instrument Calibration defines an updated set of average wavelengths per band When a Calibration is available its information overrides the information in the Sensor record for the Instrument As of V3 1 of SPECCHIO new wavelength calibrations ar
151. se administrator Before You Start Please check the Release Notes that were included in the SPECCHIO Installation Kit The Release Notes detail e the system pre requisites you will need to run the SPECCHIO Client e the SPECCHIO installation process e the SPECCHIO URL Port Number Application path and data source path you must use and e any specific instructions or limitations related to the version you have installed User Accounts In order to log in to a SPECCHIO server database you will need a User Name and Password These are assigned automatically so anyone who has downloaded the SPECCHIO Application and knows the URL Port Number Data Source and Application Path for a SPECCHIO database server can create a User Name and Password for that database All data that you upload to SPECCHIO will be tagged with your User Name User Accounts are not intended to be secure It is assumed that SPECCHIO will be run from computers in safe environments There is nothing preventing anyone who knows the Web Application Server s URL Port Data Source and Path from creating a User Account and accessing all of the data in that Server s database However they will not be able to remove or change any data except the data which they upload User Names and Passwords are stored locally on the user s computer in plain text in the db config txt file to Support convenient logging in Therefore anyone with access to your computer can easily
152. se and remove from the display in the Calibrations box SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 124 of 134 SPECCHIO User Guide 10 Matlab Integration The Matlab environment is a well established tool in engineering research and science Matlab includes a Java Virtual Machine and thus allows the use of Java classes within Matlab code To extract Java code for a Matlab query from the SPECCHIO client e Select Data Processing amp Output and Browse data hierarchy from the menu on the Main Window The Data Browser window will open e Using the Hierarchy Browser select a Hierarchy node or a selection of Spectra The Spectra IDs will appear in the Matching Spectra box e Right click in the Matching Spectra box A menu will appear e Select Copy Matlab ready query to clipboard from the menu e Switch to the Matlab application and paste the query from the clipboard as you require It is also possible to use Build query instead of Browse data hierarchy in the process above See sections Chapter 5 Data Query and Output for more information about using these tools For more details on using Matlab with SPECCHIO data please refer to the SPECCHIO MATLAB Guide SPECCHIO_MatlabGuide pdf Example Matlab ready query from Data Hierarchy Browser The following is an example of what is placed on the clipboard by the above process when the data hierarchy browser is used query Query spectrum query setQueryType Quer
153. se dialogs users with Administrator permission can view and change any data Other users can view and operate on only the Campaigns they uploaded or for which they are in the Research Group 4 15 1 Viewing or deleting existing Target Reference links Select Special Functions and Target references links from the menu of the Main Window The following dialog will be displayed Ensure that the Show existing links tab is selected in the centre panel a Target Reference Links e Show existing links Create new links Linked references GER Example Figure 32 Viewing Target Reference links Selecting and expanding nodes within these data hierarchy browsers requires many database accesses and so can take a little time to complete SPECCHIO _UserGuide pdf Version 3 1 05 03 2014 Page 62 of 134 SPECCHIO User Guide There are two halves to this dialog which function completely independently Left hand side Use this side to select Target Spectra and see their related Reference Spectra 4 Target Reference Links Targets These Target Spectra Show existing links Create new links Order by Samping Date v e link to specchio a a Gonio Ex norton These Reference Spectra d ampie 2 jp Gonio_example I witicaa F duplicates are removed Hi reference ID 12 ete k yapab an from this list To see the Reference Spectrum for just one Target Spectrum
154. se nena E 19 2 A EMMIS icici cece ersnecice s seyerees E E E a E a 20 3 10 Manufacturers Sensors Instruments and Calibrations cccccceceeveceeeaveneevaeenas 20 3 11 Supported Input Spectrum File Formats ccccecesececeseeeeeeeeeeeeeeeeeaeeeaeeeenaenatass 22 Sele A DBD FHE ennen a anaes euwanaaeaenmane S 22 Selick ASD INGICO VEISION 7 PUGS iervesniinia a a 22 3dl2 GER Signature FICS assinar mairan ikain nE EEEN PENARE EEE N EARE a 22 ILLS MER OUT TNC ee chenescs neinuseaatbetecios tenn dsandaaneusionnseneautcnanelerts enunienebeaesusmnniesiawass 23 ILA SVC R024 FICS ciceoatasuaia abeeaetesmonanasanauticensonnaniaeeteais chun dueceeeetnemeubiaaeant 24 SILS Apogee FOG serr a ee ener ee ee ee eee ee 26 JLO ENVI Spectral LIDFary Fil S asiscccastcvsansrevasuectatiaierattseamatnraciescutaeaesaxoneneaendeenen 27 3 11 7 Ocean Optics SpectraSuite Data Files ccccceceseseseceeeeeeeeeeeaeeeaeseaeaeaeenseanes 27 3 11 8 HDF5 Files containing FGI goniometer measurements s sssssssssssrnsrernsnns 28 3 11 9 UniSpec Single Channel sssssisresiovirirnanoni iine teaneceuehieaee seoececueb out eawee 28 3 11 10 UniSpec Double Channel SPU sssssessesssnnsnnnnnunnusnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnne 28 ALLE SPEC PR err a A E A adeneuscoenemvasenneseceness 29 Stbl MOTIT ADEA TFI cerra aa E E EEE 29 S EXCES A ES 29 3 11 14 TXT Space Formatted Text Files ccscsesesesescseserescueseneneuenseensecesecenecesesass 30 3 12 Supported Output S
155. selected the XLS file to upload the following control is displayed as part of a larger dialog Matching Bement Asag ment Control 1 t Row Select one Matching Column 2 Row Select Metadata Group 3 4 Row Select Metadata Attribute Entire contents of selected XLS file displayed for reference Figure 42 Matching amp Element Assignment Control This control shows the contents of the XLS file you have opened and allows you to select how it will be used The three rows of dropdown boxes are used as follows SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 75 of 134 SPECCHIO Second Row User Guide Selecting the Matching Column In one of the columns only select Matching Column from NIL the drop down list This indicates the column that will be used to search for the Spectrum to receive the Metadata for each row Selecting the Metadata Group In all columns that you want to use select the Metadata Group that contains the Metadata Attribute which is listed in that column Campaign Details Environmental Conditions kl General Generic Target Properties Selecting the Metadata Attribute In all columns that you want to use select the Metadata Attribute which is listed in that column After you have set up these three rows of selection parameters the Assignment Details and Matching Details controls will show how the XLS data will be uploaded Use t
156. serGuide pdf Version 3 1 05 03 2014 Page 30 of 134 SPECCHIO User Guide the wavelength in nanometres Subsequent columns are the Spectrum values for each Spectrum at that wavelength Example The following TXT Spectrum file example defines two Spectra named mean_090499 and mean_020599 They each have observations at wavelengths from 350nm to 361inm wv mean_090499 mean_020599 350 000 0 0246756 0 0229771 351 000 0 0246917 0 0228430 352 000 0 0247316 0 0229652 353 000 0 0248502 0 0231014 354 000 0 0250081 0 0232272 355 000 0 0250736 0 0232273 356 000 0 0249883 0 0233005 357 000 0 0249174 0 0233962 358 000 0 0250481 0 0234734 359 000 0 0252141 0 0235376 360 000 0 0253346 0 0236057 361 000 0 0253806 0 0236832 3 12 Supported Output Spectrum File Formats Spectrum data can be written in two data formats e CSV Comma Separated Values for subsequent import into various 3 party applications like spreadsheets or statistical packages e ENVI Spectral Library SLB 3 13 Campaign related Metadata SPECCHIO allows Users to store Metadata about the Spectral data they have uploaded into SPECCHIO Campaigns It is stored at two levels Campaign related Metadata and Spectrum related Metadata The following Metadata Attributes can be set independently for each Campaign Campaign name The name under which the Campaign is stored in the SPECCHIO database A free format description of the Campaign Investigator The person in char
157. should mirror this hypothesis If no such assumption exists all objects can be put into the same class i e species and the identification of classes could then be carried out by a technique such as cluster analysis Figure 7 shows an example of a folder structure containing ASD Spectral files The main folder vegetation_example holds all species sub folders for the study This main folder is the folder that needs to be specified in the Main directory in the Campaign Creation dialog See section 4 11 Creating a new Campaign The three species folders contain their related site sub folders The site sub folders contain all Spectral files collected at these sites for that species SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 17 of 134 SPECCHIO User Guide The Spectral files are auto numbered by the ASD capturing software within each site folder Folders x Name Size Type Vegetation_example El cabbage 000 9KB 000 File Blackfern fi cabbage 001 9KB O01 File sitet E cabbage 002 9KB 002 File Cabbage_tree E cabbage 003 9KB 003 File sitet E cabbage 004 9KB O04 File site2 E cabbage 005 9KB 005 File gt Lemonwood E cabbage 006 9KB 006 File sitet E cabbage 007 9KB 007 File site2 E cabbage 008 9KB 008 File site3 Ej cabbage 009 9KB 009 File Figure 7 Example of a folder structures holding Spectral files Example Reference and Target Spectra If a spectroradiom
158. still experimental and is not yet not fully supported Comments As there is more than one Spectrum per file each Spectrum is saved separately The name of each Spectrum is constructed from the Campaign name the beam geometry if HDRF or BRF a data structure identifier and an auto numbered identifier e g Snow7 HDRF ib2 14 3 11 9 UniSpec Single Channel Standard or PP Systems Format Owner Supported UniSpec Single Beam text files Formats Comments Note that UniSpec and UniSpec SPU files are read by different file readers and so cannot be mixed in the same input Spectrum folder 3 11 10 UniSpec Double Channel SPU Standard or PP Systems Format Owner Supported UniSpec Dual Beam text files SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 28 of 134 SPECCHIO User Guide me Comments Note that UniSpec and UniSpec SPU files are read by different file readers and so cannot be mixed in the same input Spectrum folder 3 11 11 SPECPR Standard or U S Geological Survey Format Owner USGS PRISM softwar Supported SPECPR Formats Comments Search for more information about PRISM software and the SPECPR file format from the U S Geological web site 3 11 12 Modtran Albedo File Standard or Spectral Sciences Inc and U S Air Force Research Laboratory Format Owner Modtran5 atmospheric radiative transfer model software Supported Modtran Albedo files Formats Comments More information can be found on the Modtr
159. t Administration and use the instructions in that section and its sub section on Calibrations to understand the operation of Reference Panel viewing and maintenance SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 122 of 134 SPECCHIO User Guide 9 6 1 Reference Panel Calibrations Each Reference Panel can have one or more Calibrations defined For each Calibration the following information can be stored Feld name Format comment Calibration Date time The date on which this Calibration was performed date selected by Where possible SPECCHIO will use the Calibration with date picker the most recent date and time which is prior to the Acquisition date time of the Spectrum being processed Calibration Integer The sequence number of this Calibration If there is number insufficient date information and a Calibration Number is given in the Spectrum s Metadata SPECCHIO will attempt to select a Calibration based on this Calibration sequence number It usually starts at 0 and is incremented for each new Calibration However this is not a SPECCHIO requirement Text String A comment about this Calibration Calibration A table of calibration values at various wavelengths with table the following fields Wavelength The wavelength in nanometres at which the Calibration values apply Rho The reflectance factor of the panel at this wavelength in the range 0 to 1 Sigma The uncertainty estimate of the Rho value expressed as a sta
160. t of the plot display Spectral statistics of the current Spectrum Spectral plot Spectrum Statistics Mean 0 00409 Min O0 Max 0 00844 Stddev 0 064 1000 2000 3000 W nm favelength Figure 89 Spectral plot component with wavelength indicator and Spectrum statistic information 8 5 5 Time Line Plot Use a time line plot to plot a Spectral band versus time Figure 90 shows showing the direct irradiance over time for an MFR sunphotometer band with centre wavelength 496 4nm The channel to be plotted can be chosen in the list below the plot Time information is retrieved from the sampling time of the Spectra ANDO Time Line Plot Space no 0 7 Temporal Spectral Plot 11 00 13 00 15 00 17 00 Time Instrument Channels 673 413 7 0 496 4 a 612 7 Figure 90 Time Line Plot showing the direct irradiance over time for centre wavelength 496 4nm 8 5 6 Time Line Explorer The time line explorer consists of a time line plot and a Spectral plot Figure 91 The red bar in the time plot indicates what Spectrum is plotted in the Spectral plot i e the Spectral plot shows the Spectrum taken at a certain time The red bar in the Spectral plot shows the currently selected Instrument channel which is plotted versus time in the time line plot SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 110 of 134 SPECCHIO User Guide OOO Time Line Explorer Space no 1 l Temporal Spectral Plot Spectral plot
161. ta entered into the fields in the Instrument Data box back to the database This button is only active for users with Administration permission Pictures Any picture of the Instrument uploaded to the database is displayed in this box Calibrations This box shows all Calibrations which have been uploaded for this Instrument Insert new instrument Click this button to create a new Instrument in the database Set the correct details for this new Instrument in the Instrument Data fields and then click Update to write this new data back into the database This button is only active if you have Administrator permissions Delete instrument Click this button to delete the currently displayed Instrument You must click OK in a confirmation dialog box which is displayed before the Instrument is deleted from the database This button is only active if you have Administrator permissions An Instrument cannot be deleted while still referenced by one or more Spectra in the database Each Instrument can have one or more pictures loaded JPEG images are supported on all platforms On some computer systems GIF PNG and TIFF may also be supported It is recommended not to load large images to avoid lengthy upload times Images should generally be re sampled to be about 400 to 500 pixels high or wide To add a picture to the currently displayed Instrument definition e Right click anywhere within the Pictures box A menu will be displayed e C
162. tch in its Instrument and Sensor tables it will create an Instrument record and set the Spectrum s Instrument Metadata Attribute to refer to it The Sensor Metadata Attribute will be set to Nil After uploading Spectra always use the Metadata Editor to check the settings of the Instrument and Sensor Type which SPECCHIO has tried to determine from the input Spectra characteristics If they are not set or not correct use the Metadata Editor to correct them See 4 16 Displaying and Editing Metadata for more information on the Metadata Editor Reference Panel selection SPECCHIO searches its Reference Panel table and attempts to find a match for any Reference Panel specified in the input Spectrum Currently no commercial file format do include reference panel information If SPECCHIO does not find a match for the Reference Panel in its tables it will set the Reference Panel Metadata Attribute value to Vi and attempt to store the Reference Panel name in the White Reference Panel Name Metadata Attribute SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 57 of 134 SPECCHIO User Guide Note After uploading Spectra use the Metadata Editor to check the setting of the Reference Panel which SPECCHIO has tried to determine from the input Spectra If it is not set or not correct use the Metadata Editor to correct it See 4 16 Displaying and Editing Metadata for more information on the Metadata Editor Handling Spectrum upload errors War
163. ter content of the collected vegetation sample Wet Weight Grams Wet weight of the collected vegetation sample 3 15 Spaces Space Factory and Data Processing using the Space Network SPECCHIO offers interactive configurable data processing The concept is based on the feature spaces Landgrebe 1997 and complex process flows can be realised by building networks consisting of spaces and processing modules For detailed information please refer to Hueni A Kneubuehler Nieke amp Itten 2009 Spaces are used throughout the system for processing visualisation and file output In all these cases vector data must be related to Spectral dimensions and this information is held by the space Moreover a space can hold only Spectra that are of the same dimension SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 46 of 134 SPECCHIO User Guide The Space Factory is a conceptual central component of the SPECCHIO system It creates new spaces based on given inputs and contains the logic to form non mixed Spaces Assume the use case of displaying Spectral plots of a number of Spectra In a first step the user will select the Spectra to be plotted by effecting a subspace projection Huni Nieke Schopfer Kneubuhler amp Itten 2nd Generation of RSL s Spectrum Database SPECCHIO 2007 Internally this will yield a number of record IDs that are matching the user s selection These IDs are now handed to the Space Factory In
164. ternally spaces are created for all existing combinations of the respective sensors instruments calibrations and measurement units associated with the Spectra see Figure 16 Space list User defined subspace projection ID list Space 1 Space User search conditions Factory Query builder or Data Hierarchy Browser Group by sensor instrument calibration measurement unit Space 2 Figure 16 Building spaces based on user defined subspace projections The Space Factory returns a list of the created spaces Each space can now in turn be used as an input argument of a plotting class instance Utilizing the Space Factory ensures that all Spectra contained by a space have a common wavelength per band and the same measurement unit i e the following processing modules do not need to carry out uniformity checks but can apply their algorithms directly e g plotting of Spectral vectors against the common wavelengths of the space Interactive flexible and configurable data processing is based on the concept of the Space Network Such networks consist of processing modules and data sinks sources connected by directed edges we ew ew ew em ee em eK KH HLLULUllCU PR eeeencthanemeweerkinnrllllO OO eww ww www wr KK 4 Space transformation p b p b i Processing l l i x _ pb Module x _ p b pbx aby Meee eee ee eee eee Figure 17 Transformation into a new s
165. tes have multiple values for that last Spectrum only the first Metadata Attribute value is used e Description Campaign related Metadata e Citation Scientific References Metadata Group e Publication Scientific References Metadata Group e Data use policy Data Portal Metadata Group e FOR Code Data Portal Metadata Group e Digital Object Identifier Data Portal Metadata Group e Location Name Location Metadata Group e Acquisition Time General Metadata Group The Acquisition Times for all Spectra in the Collection are scanned and the maximum and minimum times are written to the RIF CS file In addition User Information for the nominated Principal Investigator is copied to the published files The User Information for the User doing the SPECCHIO publication operation is not used unless of course it s the same User Values copied include the following e Title and Name e Email address e Department and Institute Name e ANDS Party Identifier Refer to 3 2 User Accounts for more information especially information on the ANDS Party Identifier To Publish a Collection to ANDS e Ensure that all Spectra to be included in the Collection have their Metadata set correctly as described above e Select Data Processing amp Output then Browse data hierarchy from the menu on the Main Window e Set the Show only my data option e Select the Spectra to be included in the Collection in the Data hierarchy browser e R
166. the Attributes in this Group ANDS Alpha string The ANDS Collection Keys under which this Spectrum has Collection been Published Key This Metadata Attribute is only available when accessing a SPECCHIO Multiple Server which is ANDS enabled permitted This Attribute supports multiple values with a new additional value written each time the Spectrum is part of a Collection which is Published to ANDS It is possible to edit this Metadata Attribute but it is strongly recommended not to Data Usage Alpha string String that defines the usage policy for example Please Policy cite XXX et al or Inform the principal investigator The value of this Attribute is copied to the Published Collection when this Spectrum is published to ANDS FOR Code Dropdown List SPECCHIO supports selection from a small relevant subset of the Field of Research codes defined by the Australian Bureau of Statistics Australian Research Council 2008 This Metadata Attribute is only available when accessing a SPECCHIO Server which is ANDS enabled The value of this Attribute is copied to the Published Collection when this Spectrum is published to ANDS Multiple permitted Digital Object Alpha string A digital object identifier DOI See http www doi org Identifier for further information about DOIs The value of this Attribute is copied to the Published Collection when this Spectrum is published to ANDS 3 14 3 Environment
167. the SPECCHIO server If there is a need to change or remove an Institute record you will need to request your database administrator to do it for you It is also possible to create a totally blank institute record The process above will generate the following additional information and store it in the server database s User list along with the information that was entered User Name A short unique name constructed from your own name which will be used to identify you when you log into the SPECCHIO server Password A password that is required when you log into the SPECCHIO server SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 15 of 134 SPECCHIO User Guide ANDS Party Identifier If your database supports ANDS Publishing this string is generated It identifies data which you Publish to ANDS To view your ANDS Party Identifier follow the procedure shown below for editing your User Account details A line is also added to the db config txt file on your computer This line holds sufficient information for you to log into your database If you edit this file you can add other known accounts to it The account which appears as the first non comment line is the default account in the login dialog Follow the instructions in the comment lines in the file if you wish to make manual changes See section 4 4 Logging In and Connecting to a Database When you are logged on to SPECCHIO you can edit the User Account information which
168. these relationships A data link is a reference from a Target Spectrum to its related Reference Spectrum There are two types of calculation for which SPECCHIO uses Reference Spectra The type is selected automatically based on Target Spectrum s Metadata Attributes White Reference The linked Spectrum is the Radiance Spectrum of a white Reference Panel such as a Spectralon panel in the same illumination conditions If a Target Spectrum has its Measurement Unit Metadata Attribute set to Radiance the link will be created as a White Reference link Cosine The linked Spectrum is an Irradiance Spectrum usually acquired with a cosine receptor If a Target Spectrum has its Measurement Unit Metadata Attribute set to Radiance then a Cosine link will be created In some cases data links are set up automatically during Campaign data loading For example GER signature files include the Spectra of both target and white reference Data links do not make sense for Target Spectra with Measurement Units other than Radiance and for Reference Spectra other than Radiance or Irradiance In other cases the results are undefined and they should not be set The Data Link type is set up when the link is created If the Spectrum measurement type is changed after the Data Links are set up then the Data Links will not be correct and incorrect calculations could result The Data Links should be deleted and set up again in order for calculations to be correct
169. tion This tool is provided to adjust the capture time in cases when it was recorded in local time instead of UTC It applies a time shift to the Acquisition Date Metadata Attribute based on the number of hours entered by the user If times are not correct in UTC the calculation of sun angles will be wrong To adjust local times to UTC e Select Special Functions and Correct local time to UTC from the menu in the Main Window r UTC Time Correction ol Ji specchio Gonio Example Vegetation example GER Example Selected hierarchy No of spectra Hours East of GMT Figure 30 UTC Time Correction dialog e Select the hierarchy node containing the Spectra that need to be time shifted or select the individual Spectra files The first selected hierarchy name and the number of Spectra are shown on the right in read only fields e Enter the number of hours to adjust in the Hours East of GMT field Use positive numbers for longitudes East of GMT that is the number for Australia will be positive e Click onthe Apply button e Close the dialog using the Close button Warning Do not click the UTC dialog s Apply button a second time This will cause the time shift to be applied a second time and a second Time shift processing message to be added to each Spectrum You can time shift back by applying a third time shift with a negated time shift value but removin
170. tional measurement Spectra for which you wish to calculate the Sensor directions Gonio Angle Calculation der by Sampling Date a specchio di Gonio Example di Gonio_example reference h triticaa 001 I triticaa 002 triticaa 003 i triticaa 004 triticaa 005 triticaa 007 triticaa 008 triticaa 009 a beiti c If you have selected a valid node SPECCHIO will scan the Spectra to extract the required information It will take a few seconds Valid nodes have 66 or fewer ASD Binary Radiance Spectra You cannot select the Spectra directly If there are fewer than 66 Spectra enter the sequence numbers of the missing Spectra separated by commas in the Gaps field Click the Calculate button This will fill the Spectra dummes box with the total number of Spectra after the gaps are inserted It should be exactly 66 It will also fill the calculation box with the Spectra names sequence numbers and angles For example 1 0 75 triticaa 001 where the gonio sequence of triticaa 001 is 1 its Sensor Azimuth is 0 and its Sensor Zenith is 75 Review the results in these boxes carefully to see that they are correct If not you can repeat any of the steps above and click again on Calculate When the results in this box are correct click Apply and the results will be written to the database Click Close to close this dialog box It is OK to repeat this process
171. to receive the Investigator name which is provided in some Spectrum file formats for example some HDF files Users are generally encouraged to rely on the Campaign Metadata either the Investigator Research Group Members or Description fields for this function 3 14 16 Pictures Group SPECCHIO supports uploading of up to four images for each Spectrum To optimise storage in the database select all Spectra that an image applies to and upload it just once Depending on your internet access speed uploading large images may be slow The supported uploadable image formats may vary between PC Linux and Mac JPEG is supported on all operating systems GIF PNG or TIFF may also be supported on some users computers When uploaded all image formats are converted and stored as JPEG images These images can be viewed directly on the Metadata Editor screen Note Pictures should be reduced in size before loading to the database An appropriate size is around 400 to 500 pixels width or height Sampling Uploaded image file Picture showing the general sampling Environment Picture environment in vicinity of the target Multiple permitted Sampling Setup Uploaded image file Picture showing the positions of Sensor Picture and illumination in relation to the target SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 40 of 134 SPECCHIO User Guide Sky Picture Uploaded image file Picture of the sky ideally taken hemispherically M
172. tra The selected graph is displayed after a short processing delay Click on the Metadata Group check boxes to enable or disable display of the respective Metadata Group Click on the Close button to close this window There are four action buttons at the top of this window Click on this button to Print the graph The Metadata are not printed It is recommended that you set the plot parameters first using the eT button to add a title and identifying information to your printed graph K Reset Click on this button to reset the graph to its originally displayed form le Set plot Click on this button to change the display parameters for the parameters graph The following Dialog is displayed SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 88 of 134 SPECCHIO SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 User Guide Set plot format Figure 56 Title Grid Stems Connect Use Color Wavelength nm Use Line Styles Reflectance 360 75 2489 25 0 0 1 483973883777404 various bigdots pixels Cancel File output dialog Enter the Title you want to appear at the top of the printed page Caption Enter text that you want to appear under the graph X Y Label Enter the labels that you want to use to label the X and Y axes X Y Range Enter the lowest and highest values that you want to appear on the X and Y axes The two values in each question must be separ
173. transformations to data unmanaged to managed disconnected to connected invisible to findable and single use to reusable that will enable Australia s research data to become a national strategic resource to support better more efficient and defensible research and improved policy input ANDS is funded by the Australian Government through the National Collaborative Research Infrastructure Strategy NCRIS and the Education Investment Fund EIF Super Science Initiative See http www ands org au and https researchdata ands org au for more information on ANDS and this service In SPECCHIO you can only Publish data for which you are the owner or a member of the Research Group Publication from SPECCHIO involves these key steps 1 Decide on the Spectra to be grouped together and published as a Collection The Spectra can be all of a Campaign part of a Campaign or even be selected from multiple Campaigns 2 Ensure that the Spectra in the Collection are complete and meet the minimum Metadata requirements for Publishing including their Campaign Metadata 3 Decide on the Principal Investigator and ensure their SPECCHIO User information is correct and up to date Publish the Collection indicating the Principal Investigator SPECCHIO generates an ANDS Collection Key for this Collection and writes it to all Spectra in the Collection key Metadata Attribute in the Data Portal Group The ANDS Collection Key can be used to
174. ts the hierarchy you require for your data in SPECCHIO and put your Spectrum data files into this structure See section 3 5 Campaign Hierarchy Structure for more information on designing this structure The entire sub folder tree must contain only Spectrum files and each sub folder within the tree must contain only files of one Spectrum file format When you start the Spectrum load process SPECCHIO will process all sub folders and files within this sub folder tree and create a matching structure for your Campaign in the database For each sub folder it will use the various Spectrum File loaders listed in section 3 11 Supported Input Spectrum File Formats until one reports that it can read a file in the sub folder It then processes all files in that sub folder using that file loader If any file cannot be read it will report an error giving the name of the file that failed Correct the offending file either by removing it if it is not a Spectrum file sorting it into a sub folder with similarly formatted files or finding an uncorrupted version of the file Then restart the upload process Those Spectra which have already been successfully uploaded will not be processed a second time To upload Campaign Spectral data e Select Data Input and Load campaign data from the SPECCHIO Main Window The following dialog is displayed SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 56 of 134 SPECCHIO User Guide Note Note Load S
175. ultiple permitted Target Picture Uploaded image file Picture showing the target Multiple permitted 3 14 17 Processing Group These Attributes describe processing which has been performed on the Spectrum These Attributes are added or set when that processing is done This processing may be done by SPECCHIO or it may be processing done by some other function connecting to the SPECCHIO database This may be a Matlab program a Java program or a program written using any other tool or language While it is possible generally these Attributes should not be edited manually Data Alpha string Notes produced by the data ingestion module during data Ingestion loading into SPECCHIO Notes Multiple Data Ingestion Notes may be added to each Spectrum Multiple permitted Integer Designates this Spectrum as a dark current Spectrum The Metadata Attribute s value should be either 0 indicating False or 1 indicating True If the Metadata Attribute does not exist this implies False Garbage Integer Designates this Spectrum is not intended for inclusion in the Flag main experimental evaluation The Metadata Attribute s value should be either 0 indicating False or 1 indicating True If the Metadata Attribute does not exist this implies False If you create a node named Garbage all Spectra in the sub tree below this node will have this flag set to 1 when they are loaded The test for the node name is case sensitive Thi
176. w dropdown box select Matching Column e Carefully review the information shown in the Assignment Details and Matching Details boxes and ensure it is correct e Click onthe Insert Selected Metadata button 4 18 Calculation of Sun Angles The sun angles can be stored for each Spectrum as Metadata in the Illumination Group as Illumination Zenith and Illumination Azimuth Sun angles can be calculated for a Spectrum if the spatial position in Latitude and Longitude and the capture time in UTC are known and stored in the Spectrum s Metadata To Calculate Spectra s Sun Angles e Ensure that the Acquisition Time has been correctly adjusted to UTC for all Spectra e Ensure that the Spectra s locations are correctly set in the Location Group s Latitude and Longitude Metadata Attributes e Select Special Functions and Sun angle calculations from the menu in the Main Window A Hierarchy Tree Browser is displayed p Sun Angle Calculatio xX Order by specchio Gonio Example Vegetation example GER Example Figure 48 Sun Angle Calculation dialog e Select the Spectra to be processed A single Spectrum or multiple Spectra can be selected The Number of Selected Spectra field will be updated e Click on Apply to calculate the sun angles and write them into the Spectra s Metadata e Click Close to close the dialog SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 81 of
177. which were uploaded by you or Campaigns for which you have been added to the Research Group Browse hierarchy tree The hierarchy tree is displayed and various Campaigns nodes or Spectra can be selected See 4 7 Browsing the Hierarchy Tree for information on using this control Matching Spectra The Spectrum IDs of the Spectra which are highlighted in the browse panel are listed in this box Number of results The number of Spectra IDs listed in the Matching Spectra box is shown in this box Six action buttons Of these six action buttons Show report File export Process Spectral plot and Refl calc will become active when you have selected one or more Spectra SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 84 of 134 SPECCHIO User Guide The Publish Collection button is only present if you are accessing an ANDS enabled SPECCHIO Server and is only active if you have selected Show only my data The operations these buttons initiate will be performed on the selected Spectra Each of these buttons has a section in this chapter Splitting rules for file export and plotting Click on the radio buttons to select one of the options Split spaces by sensor Split spaces by sensor and unit or Split spaces by sensor instrument calibration_no and units This selection will affect the operation if you select the Process Spectral Plot or File export buttons 5 2 Query Builder SPECCHIO s Query Builder provides a way t
178. x select the name of the Researcher who will be the imported Campaign s owner e Click Import When the import is complete the Campaign Import dialog will close The Export and Import database versions must be the same SPECCHIO does not check this If they are not the same the new Campaign will not be readable and the database may give unpredictable results The name of the imported Campaign will be identical to the name of the exported Campaign If you import into the same database you exported from you will have two identically named Campaigns To avoid confusion it would be advisable to rename the newly imported one using the Metadata Editor to change the Campaign Metadata s Campaign Name value Definition of new Sensors A new Sensor can be defined by loading a Sensor definition file Once defined it will appear in the dropdown list of Sensor names which appears at several places within SPECCHIO Take care when defining new sensors There is no method of editing or inspecting Sensor information using the SPECCHIO Client Therefore there is no method of confirming that your data was entered correctly so prepare your input Sensor definition file very carefully To load a Sensor Definition file e Select Data Maintenance and Load sensor definition from the menu on SPECCHIO s Main Window The following dialog is displayed Read Sensor Defintion File Si efinition gt Figure 97 Read S
179. xt strings SPECCHIO uses the LIKE clause on the MySQL Query This SQL clause supports wildcard characters for matching variable strings Therefore the following are supported in most SPECCHIO searching or matching strings Matches zero or more characters Matches exactly one character Causes the next character to be matched That is will match a sign and _ will match an underscore character There is just one case where Regular Expressions are used by SPECCHIO instead of SQL Matching Strings This case is described separately Entering Dates and Times SPECCHIO uses a Date and Time selection dialog which is similar to many others Here are a few tips for using it Down triangular arrow in the data xample Acquisition Time 20 2 06 t f S 4 Jun 2006 input field U Sun Mon Tue Wed Thu Fe Sat Lees med 3 t f tr O 6 7 8s 9 10 y 4 12 13 14 15 16 17 t 18 19 20 21 22 23 24 e 25 26 27 28 29 3 Time selector up and down triangular arrows 7 40 11 PM Figure 23 Date and Time picker dialog e Select the Time first Because selecting the Date closes the dialog e To change the Hours click on the hour number in the Date and Time Picker it will not be highlighted and the cursor will not move but trust me and then click on the time selector up and down triangles to adjust the number You cannot type in the number directly e To
180. y SELECT_QUERY query addcolumn spectrum_id cond QueryConditionoObject spectrum spectrum_id id_array 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 ids_list java util ArrayListQ for 1 1 size id_array 2 ids_list add id_array 1 end cond setValue ids_list cond setOperator in query add_condition cond ids specchio_client getSpectrumIdsMatchingQuery query Example Matlab ready query from Query Builder The following is an example of what is placed on the clipboard by the above process when the query builder is used query Query spectrum query setQueryType Query SELECT_QUERY query addcolumn spectrum_id cond SpectrumQueryCondition C spectrum measurement_unit_id cond setvalue 0 cond setOperator SPECCHIO_UserGuide pdf Version 3 1 05 03 2014 Page 125 of 134 SPECCHIO User Guide query add_condition cond cond EAVQueryConditionObject C eav spectrum_x_eav File Name string_val cond setValueC triti cond setOperator like query add_condition cond cond SpectrumQueryCondition C spectrum sensor_id cond setValue 0 cond setOperator query add_condition cond cond SpectrumQueryCondition spectrum instrument_id cond setValue 0 cond setOperator query add_condition cond ids specchio_client getSpectrumIdsMatchingQuery query SPECCHIO_UserGuide pdf V
181. you are uploading to The list of paths in the Path box will change to be those defined for the selected Campaign Load Spectral Data Campaign name GER Ex Spectral data of the selected campaign will be loaded from the selected directory Load Cancel Figure 26 File upload dialog showing no paths SPECCHIO stores every path name that has been used to upload data to this Campaign However in this box it will only display those paths which point to locations which exist on your computer In this scenario it is likely that no existing paths will be valid on your computer and so no paths will be shown in this dialog box for the Campaign in question e Click on New Path A file selection dialog will open e Navigate to the folder that you copied to your computer and select it This new path will be added to the list of paths in the Path box Be sure to select the right level folder e Click Load The dialog box will close and progress messages will be shown in the right hand part of the Main Window indicating the total number of files that have been found and the number of new Spectra which have been loaded Warning If you select the folder above or below the one selected when the Campaign was first loaded it will not be recognised as the same folder and will cause all of the existing data to be duplicated in your SPECCHIO Campaign 4 13 3 Uploading Additional Spectral Data in a New Data Hierarchy The

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