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WebGR User`s manual

1. After completion click Back 7 3 3 Further preparation For further steps see the chapters for editing protocols page 46 and editing expertises page 47 Page 56 WebGR users manual v1 0a 8 FAQ S Pictures are of low quality on my screen difficult to see rings did you try zooming For Image Q1 17_1 nothing happens if press copy WS two things can cause this For the first there are no annotations made in the reference and for the second the annotations where exactly at the same positions as your annotations But there is also a bug for some situations the program makes automatically a annotation at the point 0 0 How do I return to the main page after finishing N click My CE Search gives error message Nothing found There are no results for your search Try less filters What does a certain input field mean Please ask the administrator about the definition of the meta data What happens if press Save as There is no option to define any name so why is the button Save not available we assume that save is only to save an existing annotation and save as is meant to save a new annotation Why do we need two buttons In both cases we overwrite an annotation an empty one or a filled If this can be combined in one button this would be nice save as means save as new annotation and save means update the current annotation N What happens when using the refresh all annotation
2. Image CEis running stop calibration exercise FISH Calibration exercise name EJO1 Description My CE u li An Figure 46 start stop state in calib Protocol m e ha mml KIA JE ration exercise _ iaa weka el If a calibration exercise is started it is not possible to delete the calibration exercise If a calibration exercise is stopped it is not possible to make annotations However the reading of annotations is possible Page 53 WebGR users manual v1 0a 7 Administrator The administrator can parametrise the application to the institutions needs It is possible to add attributes add and edit value lists that are used for the search and edit forms within the application 7 1 Preface For security reasons the BACK BUTTON OF BROWSER isn t allowed in all forms 7 2 Login and logout Click on any menu item to login Login with your username e mail address and personal password The password is stored encrypted so it s not possible to read out only to reset Click on Logout below the menu items to logout 7 3 Preparation 7 3 1 Edit user To set a new role to a user you have to edit the user Click Search user if necessary enter filter criteria Search button click edit in designated user row choose role in role select and click Save button Choose data manager or ws manager If necessary click BACK BUTTON OF BROWSER twice and repeat 7 3 2 Edit at
3. 6 2 2 Shown attributes Select the attribute you want to show in the annotation module Click the Add attribute to list button To remove a certain attribute again click Remove attribute next to the designated attribute 6 2 3 Participants To add edit or remove participants click Edit participants Page 50 WebGR users manual v1 0a Calibration exercise EJ01 ID 1 Assign values T Expertise level Please select y I Stock assessment T Assign values form T Role Please select Applyto selected List of participants Norman rauthe re de Trainee Ingmar pforr 7 Trainee Coordinator 7 Moksness Erlend moksness r gt gt Coordinator 7 Quincoces I aki iquincoces gt Coordinator Ernesto ernestof ik Si Coordinator Hansson maria hanssol nggi ihe aa Trainee Cardador F tima cardador amp v e 0 Trainee Sj berg Rajlie rajlie sjoberg u 2 2 Intermediate Reader Anastasopoulou Katerina kanast e ir lt Trainee Reader kelig mahe ou Trainee Reader murenu mmurenu 2 Trainee Reader Ulrich Ulrich bertth 7 Trainee Reader Pi eiro Carmen carmen pineiro o 20 Trainee Reader de Boois Ingeborg ingeborg deboois s Trainee McCurdy william wilie mecurdy s tri gt 7 Trainee Reader Francesca francesca vale it ta Trainee etherton mark etherton 1 7 Trainee Check all Uncheck all Remove from participants Reset search user s to add Back Figu
4. OTO 4 jpg NA Q1 SL3 OTO 4 1280 960 IVA Q1 SL3 OTO 5 jpg VA Q1 SL30TO5 1280 960 NA Q1 SL3 OTO 7 jpg IVA Q1 SL3 OTO 7 1280 960 Figure 45 List of images images already assigned have readonly check mark 1 Select fish or image attribute and click Add attribute to list button Enter or select value s for the attribute In the case of simple number fields integer decimal you are able to enter FROM and TO value for ranges with larger than equal and smaller than equal For the exact value enter the same value in the FROM and TO field Click Save button to save the imageset attribute settings In case you want to have more attributes combined repeat 1 3 Page 52 WebGR users manual v1 0a 5 Click add images to add images for the now defined imageset 6 Check the boxes next to the images in the designated image rows 7 Click add images button Click remove next to the image you want to remove from the imageset again This function is not available for images that have annotations already Click remove attribute next to the attribute you want to remove from the imageset attributes again 6 2 5 Calibration exercise final notes Please make sure you set key expertise comparable and imageset to your needs Calibration Exercises with incomplete settings will not be shown The workshop manager CE coordinator can start and stop calibration exercises Calibration exercise EJ01 ID 1
5. Start new worksho e Edit attributes Download attribute CSV User name pforr zadi de User role admin Logout SOME RIGHTS RESERUED ORGANS Imprint Funded by EC DGMARE Figure 21 Workshop list 4 8 My Calibration exercises By clicking on My calibration exercises you see a list with all calibration exercises you are invited in or all your training exercises you started before Click annotate to start the annotation interface See Annotations Click browse annotations to show the already available annotations See Browse annotations 4 9 Calibration exercise statistics Click on statistics in the designated calibration exercise row to view the statistical tables The statistical reports include e annotations e list of the participants e list of the images and the connected fish data e definition of the calibration exercise Within the statistical tables click download as CSV file to download a Comma Separated Values file to process with Spreadsheet software like Calc or Excel or statistical software Page 23 WebGR users manual v1 0a The statistical table of the annotation shows all readers and images involved in the calibration exercise Main menu RC1 annotations o Register new user show all e My user data show only trainees e Forgot password show only intermediates Help show only experts A sho
6. WebGR users manual v1 0a Upload images Upload image s C Dokumente und Einst Durchsuchen Durchsuchen Durchsuchen Durchsuchen Fish Sample Code ftesta71 111 RESOLUTION dpi ao Subject otolith y IMAGE_COMMENT just comment MAGNIFICATION 30 PREPARATION_METHOD method TYPE_OF_STRUCTURE otolith x Figure 32 Upload images In the form all active image attributes are available to fill out Type in the existing fish sample code exactly as you used it before Or type in a new fish sample code Select the image files you want to upload You can add several files at once Select the subject and type of structure of the image If you need more subjects subjects can be added over the attribute descriptor Fill out the other image attributes If you need more attributes they can be added over the attribute descriptor Please give as much information as you and others would need for searching and finding the image later Click the Save button If the fish sample code is not in the database you will be prompted to add a new fish see Figure 33 Page 35 WebGR users manual v1 0a LENGTH mern WEIGHT g STOCK ARCHIVING_CODE AREA CAPTURE_DATE GEAR FISH_COMMENT SPECIES Please selet y SAMPLING_DATE OBSERVED_MATURITY_STAGE SAMPLING_INSTITUTE ARCHIVING_ INSTITUTE RESPONSABLE SCIENTIST SAMPLING SOURCE Please select y LONGTITUDE G geo signed LA
7. and after the result rows actions like edit or delete can be shown as clickable links The Figure 18 shows the result list for calibration exercises In the first column you see the available actions that depend on the object and your authorisation in WebGR The shown workshop name is clickable and gets you to the workshop details The protocol is also clickable and opens the protocol file Page 20 WebGR users manual v1 0a Main menu RC1 List of images ister ser My user data Forgot password Help My calibration exercises e My workshops Start new training calibration exercise IVA Q1 SL1 OTO 5 jpg IVA Q1 SL1 OTO 5 1280 960 IVA Q1 SL1 OTO 6 jpg IVA Q1 SL1 OTO 6 1280 960 Search Browse annotation by image and fish Show attributes IVA Q1 SL1 OTO 8jpg IVA Q1 SL1 OTO 8 1280 960 IVA Q1 SL2 OTO 6 jpg IVA Q1 SL2 OTO B 1280 960 Image upload Batch im uploa Edit protocols Edit expertises Edit attributes Download attribute CSV User name pforr zadi de User role admin Logout SOME RIGHTS RESERUED egative commons Imprint Funded by EC DGMARE IVA Q1 SL2 OTO 8 jpg IVA Q1 SL2 OTO8 1280 960 IVA Q1 SL3 OTO 2 jpg IVA Q1 SL3 OTO 2 1280 960 IVA Q1 SL3 OTO 4 jpg IVA Q1 SL3 OTO 4 1280 960 IVA Q1 SL3 OTO 5 jpg IVA Q1 SL3OTOS 1280 960 IVA Q1 SL3 OTO 7 jpg IVA Q1 SL3 OTO 7 1280 960 Figure 19 Search result list for images Figure 19 Shows the result list for images The thumbn
8. copy button in this row All settings are loaded now Modify the annotation and click Save to create a new annotation Go back to tab Annotation to see that you have a new annotation All this functions are available in the standard calibration exercises too Note If you want to discuss or compare with other users you must join a group more about this at chapter User 4 4 Leave the training Click Exit If you leave the training your exercises will be saved and you can start it the next time by clicking on my calibration exercises This list contains all your exercises All your data and Workshops are available at the start screen too see Figure 10 Page 13 WebGR users manual v1 0a 4 5 My user data You can check your personal expertises here Click the expertises and then click Submit The data manager or administrator can add expertises at any time and will do so in order to create new calibration exercises for new expertises Please return to here to update your knowledge skills Main menu RC1 e Register new user e My user data Forgot password e Help e My calibration exercises e My workshops e Start new trainin calibration exercise e Search Browse annotation b image and fish e Show attributes e Image upload Batch image upload e Edit protocols e Edit expertises e Start new worksho e Edit attributes Download attribute CSV User name p
9. itimens Recursos n Biol gicos Imprint IPIMAR Funded by L Portugal EC DEN AR E E rajie sjoberg dfiskeriverket se ws manager Rajlie Sj berg rajlie sjoberg fiskeriverket se Swedish edit Board of U L Figure 20 Search result list for users In case you use a search in context of an action like add participants radio buttons or check boxes are available in front of each row With the check boxes you can select certain objects and execute an action for all selected objects like adding the users to the participants list of a calilbration exercise see Figure 20 4 7 Workshop list You can search for workshops with My workshops and Search List all workshops To show the information about a workshop click info in the designated workshop row Page 22 WebGR users manual v1 0a Main menu RC1 e Register new user e My user data workshop list e Forgot password info Sukarrieta EJ 2009 11 11 2009 11 12 ernesto ipimar pt e Hel edit delete not available e My calibration exercises RAW DELETE e My workshops info Test Bonn WKMSSPDF2010 2010 01 01 2010 01 09 ingeborg deboois wur nl Start new trainin edit Calibration exercise delete not available RAW DELETE Search E e Browse annotation b image and fish e Show attributes e Image upload Batch image upload e Edit protocols e Edit expertises e
10. protocol NA redfish v Add protocol Please select 7 Add attribute to list Expertise image 15 all y Add expertise Show comparable other user group annotationsireferences Please select y Add attribute to list Vv Allow adding images to image set at random Vv Save IVA Q1 SL1 OTO 5 jpg IVA Q1 SL1 OTO Sjpg IVA Q1 SL1 OTO 6 jpg IVA Q1 SL1 OTO 8 jpg IVA Q1 SL2 OTO 8 jpg IVA Q1 SL2 OTO 8 jpg IVA Q1 SL3 OTO 2 jpg wittrip127_9 jpg remove Number of images add atrandorn add images replicate current calibration exercise Remove attribute Remove attribute ARCHIVING_CODE Remove attribute SEX Remove attribute AREA Remove attribute CAPTURE_DATE Remove attribute SPECIES Remove attribute Please select Participants Number of participants 17 Edit participants Figure 43 Edit calibration exercise form Add attribute to list Choose an existing protocol or add a new protocol See edit protocol Choose an existing expertise or add a new expertise See edit expertise e Check Show comparable other user group annotations references if you want to show the other users annotations in the annotation interface or do not check if it s a blind test e Check Allow adding images to image set at random if you want to be able to add images to the image set at random e After completion click Save button
11. same key amp reference for image expertise as CE in CE Q WebGR WebGR reference of image with 0 1 same key amp expertise as this CE Group Group references of CEs within 0 n this workshop with same key amp Group expertise as this CE Make workshop Workshop WS reference of CEs within 0 1 WS ref reference for image workshop with same key amp for this key amp expertise as this CE Speise WebGR WebGR reference of image with 0 1 same key amp expertise as this CE Workshop Workshop references of image 0 n Group with same key amp expertise as WebGR Make WebGR thisCE reference for image ref WebGR WebGR reference of image 0 1 Page 27 WebGR users manual v1 0a 4 11 Browse annotations Annotation Compare Images Image vti_osf_cod_40907506_005_008 jpg Zoom 55 ee MAX refresh Fish vti_osf_cod_40907506_005_008 a 7 2727 yi 174 54 Read Coun Age Acceptance pm 3 15 0 copy SOME RIGHTS RESERUED Figure 24 Browse annotations Click Browse annotations to load a set of images with annotations into the annotation interface You can only show images and annotations but you can not create new annotations or change existing annotations Page 28 WebGR users manual v1 0a 5 Data manager The data manager succeeds all rights from reader Additional functions are upload edit and delete own images files and fish data edit own fish and image parameter and also administrate
12. 0a Main menu RC1 Calibration exercise list Register new user My user data Forgot password Help browse annotations Plaice fecundity macroscopic WKMSSPDF2010 Test area 51 Test species prowse annotations WEMSSPOF cut annotate ffnen von import csy x az My calibration exercises statistics e My workshops details Sie m chten folgende Datei herunterladen e Start new training FA import csv calibration exercise E Yom Typ Microsoft Office Excel Comma Separated Values File Yon http athen webgr zadi de e Search e Browse annotation by wie soll Firefox mit dieser Datei verfahren image and fish ffnen mit Mozila Firefox y Mozilla Firefox e Image upload P F r Dateien q Batch image upload Andere e Edit protocols e Edit expertises L Figure 28 Operating system dialog Open file A dialog box opens Select other in open with selectbox xi _ Sie m chten folgende Datei herunterladen EE import csv Vom Typ Microsoft CUA x Yon http fathen we pill Microsoft Office Excel Separated Yalues File Wie soll Firefox mit dieser E3 impork csy ffnen mit and Diesen Eintrag senden an Datei speichern cog he F r Dateien dieses Lis Y Durchsuchen x Figure 29 Operating system dialog Select help application To open the file with OpenOffice Calc select scalc exe and click OK Click OK OpenOffice
13. 1 Register and login You have to click Register a new user to create a new account see Figure 1 After filling the form click Submit The system sends an e mail to the given e mail address You have to click the link inside the mail for a confirmation After the confirmation click any function on the menu e g My user data and log in into WebGR with your new account see Figure 2 Click on My user data to change your personal settings and password if you want to Page 6 WebGR users manual v1 0a 4 Reader Quick start Training exercise Every confirmed user gets the status Reader Now you can be invited to calibration exercises In the meantime you can search the database for fishes and images and run training calibration exercises D welcome to WebGR Main menu RC1 WebGR is an European project that aims to develop Open Source software for supporting studies of fish growth and reproduction e Register new user In particular it promotes the usage of online services to organize calibration workshops e My user data e Forgot password Calibration workshops are carried out for a long time between scientists reading otoliths to identify individual age so that all e Hel scientists tune their interpretation of the ageing protocols It has recently being extended to also cover identification of maturity gen stages with gonads In general it can be applied to all situations where distinct scientists h
14. HTS RESERUED show imageset definition Figure 5 The annotation interface with explanations You start your annotations with choosing annotation and just clicking on the image You will see a red cross See Figure 6 The number of dots you make is counted see Figure 5 textual input Page 10 WebGR users manual v1 0a coer ee a 2 l mn us por Fish 4 1 087 27 y 347 27 Count Age Acceptance la 0 Attribute Brightness K 0 Exit E m ess Lalal Contrast 77 S 0 Role Coordinator Reset Color N B a Meera Delete Group subject otolith WS Ref PR WebGR Ref show imageset definition Figure 6 Make an annotation You can change brightness contrast and color to see more details see Figure 7 Brightness Ly 10 Exit lt gt Pl Contrast Fe 4 Role Coordinator BEER Color EN lt _ 2 Specie Hake mn Area all Group subject otolith Jomar comes WS Ref SOME RIGHTS RESERLED show imageset definition dab SL Figure 7 Changing brightness contrast and color Type in the age and comments see Figure 8 Page 11 WebGR users manual v1 0a lt lt Own annotations list Ji Brightness 7 10 Exit we gt maan Lalan Contrast Fe Ve 49 Role Coordinator Reset Color 227 Area all u show imageset definition WebGR Ref Figure 8 Saved annotation Specie Hake 1 sub
15. TITUDE G geo signed SEX female C male undefined Fish Sample Code ftesta71111 Save Figure 33 Add edit fish form Please give as much information as you and others would need for searching and finding the fish later Page 36 WebGR users manual v1 0a 5 4 Batch image upload import With the import functionality you can import fish data image data and image files at once You can create data in the system without using the forms This batch import could need preparation of your existing data This basically means reformating the data in a spread sheet e g e renaming of headers to match the system e deleting of unit or percent signs in the value cells e adding required columns and data The import procedure contains e creation of CSV file e upload of CSV file and images e before import check import of data and image files after import check 5 4 1 Upload Select file s for upload Wahlen Sie die zu ladenden Dateien von Zuletzt verwendete D Desktop Eigene Dateien sr Arbeitsplatz mm a a Dateiname import csv BD jpg i52 jpg i53 jpg BA p Y bung Dateityp JImportfiles y Abbrechen A Add file s Remove file s Figure 34 Select files screen from operating system here Windows 1 Generate the files see below Page 37 WebGR users manual v1 0a 2 click batch import to start the procedure 3 Click Add file s 4 Opera
16. Test key Hake Otoliths test3 attripute_cataloque xls test pdf hilfe pdf witch flounder Illa wit_trip127_27b jpg Test protocol NA redfish protocol_na_redfish doc add protocol Figure 38 List of protocols Click edit in designated key row to edit the settings Or Click add key to add a new key After completion click Save button Click Cancel button to cancel your settings Edit protocol Protocol name Current file upload file Durchsuchen Cancel Cancel Figure 39 Edit protocol Page 46 WebGR users manual v1 0a 5 6 Edit expertise The expertise is a combination of area species e subject respectively type of structure Every user can have expertises Expertises are related to a species an area and a subject 3 stages are available Beginner Intermediate and Expert See my user data for selecting personal expertise Click edit expertises to see the available expertises see Figure 40 List of expertises Test area 51 all ICES IX Clupea harengus bone ICES Illa Glyptocephalus cynoglossus otolith North Sea Limanda limanda gonad North Sea Pleuronectes platessa gonad add expertise Figure 40 List of expertises Click edit in designated expertise row to edit the settings Or click add expertise to add a new expertise After completion click Save button Click Cancel button to cancel your setti
17. Web ser Search fish search field combination and Cor Fish length cm FROM Fish length cm TO Fish weight kg FROM Fish weight kg TO Researching institutes M AZTI F IEO l IFREMER T IPIMAR PT gender Please select simple Text H Stock H Sample year FROM H Sample year TO Figure 15 Search for fish 4 6 3 Search image In an image search the search filter contains fish and image attributes so there are more possibilities to specify your search In addition to a fish search you can filter attributes like resolution black white or color images and so on Page 17 WebGR users manual v1 0a Search image Search field combination and or Image resolution dpi FROM Image resolution dpi TO subject J Please select Fish length cm FROM Fish length cm TO Fish weight kg FROM Fish weight kg TO Researching institutes Tio TD IFREMER T IPIMAR E vt gender Please select simple Text H Stock s _____ Figure 16 Search for image 4 6 4 Search user It is possible to search for a special expertise here to get a list of the knowledge carriers Page 18 WebGR users manual v1 0a WebGR Web m Search user Search field combination and Cor Username e mail adress First name Last name Institution Please select Street gt City m Country Please select Se
18. WebGR users manual v1 0a WebGR User s manual The WebGR Consortium http webgr wiki azti de Page 1 WebGR users manual v1 0a Table of contents 1 Applications web address an Deu 3 2 Usergroups and TOMAS a ca ee aha ee BE es Beet T 3 2 1 B deis Tel 3 2 2 P arlieipantirole Lel nes ae 4 A ee TREE Ekel 5 3 1 Register ad OI art iaa 5 4 Reader Quick start Training exercise nn nenne 6 AY Training calibration exereise een er ralkerebalge 6 4 2 Make an annotation ac see einen 8 4 3 Compare and copy other readers annotations 44444444444ennnnee nenn 11 AA Leave Me trainihg enter eine 12 4 9 My userdata iaa 13 AO DIC UI elc EEE Er 14 4 6 1 General usage of search omm eee eee 14 4 6 11 lt a Te au ee 14 4 0 1 2 Ranges 2 22 see nie O pS 15 4 6 1 3 Multiple search select 15 4 8 2 Search fish ee ROLE REN o 16 400 3 SC arch IMAGES anne taa 16 AOA Search Us 17 4 6 5 The search Tesla ae era ae 18 2 7 Workshop T sit NA A chau anes ARALAR A A ap Fale 21 4 8 My Calibration exereises sei 22 4 9 Calibration exercise SIS OS ae a Brenn 22 4 10 AMOS ION Si A en ren 23 4 10 1 Make ANOETA SAA A AS a A TR ASA 23 4 10 2 Annotation levels of a calibration exerciae eee eee 25 AST Browse AMOO Sid 27 9 Data Managers A ae ne ad 28 3 1 SHOW AID US an A A Ab 28 5 2 Download attribute CSV MM ai 30 9 32 Image upload en energie et 33 5 4 Batch image u
19. ail is clickable too and opens the image in a new tab of the browser Page 21 WebGR users manual v1 0a KR Main menu RC1 List of users e Register new user e My user data Add to participants Reset e Forgot password e Help E 3 T superuser zadi de admin Firstname Lastname superuser zadi de Federal Yilichgasse Bonn e My calibration exerci edit Agency for e My wi Agriculture Start new trainin ns calibration exercise s T l C f i E 7 rauthe zadi de admin Norman Rauthe rauthe zadi de Federal Willichgasse Bonn e Search edit a Browse annotation by and Food image and fish Germany E pforr zadi de admin Ingmar Pforr T pforr zadi de Federal neue stra e S edit Agency for Laad Agriculture s Image upload Food e Batch image upload Lame n 7 moksness Qimr no ws manager Erlend Moksness moksness imr no Edit protocols M Edit expertises edit 4 e Start new workshop E iquincoces azti es admin I aki iquincoces azti es AZTI Txatxarramendi Sukarriete e Edit attributes edit Foundation irla e Download attribute csv Ge 7 maria hansson fiskeriverket se reader Maria Hansson maria hansson fiskeriverket se User name pforr zadi de edit User role admin T T Logout 7 sardador ipimar pt reader F tima Cardador cardador ipimar pt edit 7 ernesto ipimar pt admin Ernesto Jardim ernesto ipimar pt Laborat rio A edit Nacional de O amp
20. annotations Page 5 WebGR users manual v1 0a 3 Guest A Main menu RC1 e Register new user e Forgot password e Help elcome to WebGR ject that aims to develop Open Source software for supporting studies of fish growth and reproduction Usage of online services to organize calibration workshops alibration workshops are carried out for a long time between scientists reading otoliths to identify individual age so that all cientists tune their interpretation of the ageing protocols lt has recently being extended to also cover identification of maturity stages with gonads In general it can be applied to all situations where distinct scientists have to discuss the interpretation of a e My calibration exercises protocol to identify status of biological material e My workshops Tun lc in in nn 1 P Main menu RC1 User form e Register new user r Username e mail adress me institute org e Forgot password First name O e Help i Last name e My calibration exercises li Password wi e Start new training calibration exercise Repeat Password im n Institution Please select e Search Sean E Street AAA image and fish City 0007 e Show attributes Phone number Faxsimile number Country Imprint Funded by EC DGMARE These fields are required Figure 1 Start screen and registration form 3
21. arch Expertise Please select List details D Figure 17 Search for user Check details if you want to list the personal expertises of the users in addition Due to aggregation of these values ordering of this field is not possible 4 6 5 The search result lists In most cases result lists from successful searches can be ordered by clicking the heading of the attribute Page 19 WebGR users manual v1 0a We 1 7 Main menu RC1 Calibration exercise list e Register new user e My user data Forgot password e Help browse protocol_na_redfish doc annotations e My calibration exercises annotate s My workshops e Start new traini statistics calibration exercise details edit e Search delete not possible e Browse annotation b RAW DELETE Image ano fish browse Plaice fecundity WKMSSPDF2010 annotations macroscopic Show attributes T EREEREER j Annotation not allowed Image upload statistics e Batch image upload details e Edit protocols edit e Edit expertises delete Start new workshop RAW DELETE e Edit attributes gt Download attribute CSV User name pforr zadi de User role admin Logout SOME RIGHTS RESERVED Egsative Imprint Funded by Figure 18 Search result list for calibration exercises In some columns of the dataset the data is clickable when presented as a link e g written in blue or purple Before
22. ave to discuss the interpretation of a Mvcalibraionexereises Protocol to identify status of biological material G My workshops The consortium is constituted by Laboratorio Nacional de Recursos Biol gicos IPIMAR Portugal Consortium leader The e Start new training Agri Food amp Biosciences Institute UK AZTI Tecnalia Foundation Spain Federal Agency for Agriculture and Food Germany calibration exercise Johann Heinrich von Th nen Institute Germany Hellenic Centre for Marine Research Greece Instituto Espa ol de Oceanografia Spain Institut francais de recherche pour l exploitation de la mer France Institute for Marine Resources amp Ecosystem Studies e Search The Netherlands Institute of Marine Research Norway Swedish Board of Fisheries Sweden Italian Society for Marine Biology Browse annotation by Italy image and fish Note that all information uploaded will be under a Creative Commons Attribution Share Alike 3 0 Unported License Show attributes For more information please visit http A4webgr berlios de Enjoy The WebGR team SOME RIGHTS RESERVE ERRER e mail Imprint me institute org password login Funded by EC DGMARE Figure 2 Log in into WebGR 4 1 Training calibration exercise Choose the training calibration exercise you want to look at see Figure 3 Note If you want to continue an old exercise click on My calibration exercises You will see it in th
23. ck assessment At the end of the table you see the group value the value all readers gave the image collaboratively The results at the right side show the Average percent errror the coefficient of variation and standard deviation and variance These values are aggregated for fishes so in case you look at two images from the same fish they are the same The results at the bottom show the single readers absolut mean of distances to the mean of the image values At first all annotations of the calibration exercise are shown You are able to select only trainees intermediates or experts or only readers values that have stock assessment 4 10 Annotations 4 10 1 Make annotations After creating an new annotation you are able to announce it into a group so that all other users can see and discuss it see Figure 23 Click Finalize to announce the annotation Page 24 WebGR users manual v1 0a Fish Image Annotations Images Zoom 128 my annotations Cour Dec Sub Acceptance a ES or ERGO Your annotation as a group reference all annotations refresh Reade Count Dec Acceptance he Group level shows only group annotations test annotation Figure 23 Announce the annotation You can also copy an annotation from any other group member and work on it by clicking the copy button inside the all annotations list Now you can save it as your own annotation without dele
24. d images in the system 4 The CSV headers must be unique It s possible to have completely other headings in the CSV file straight export from other system Either you rename them to match the WebGR schema or you associate them manually inside the import 5 4 7 4 Datasets For the attribute details on click Show attributes gt show detail in WebGR Date format YYYY MM DD a MySQL standard Date time format YY MM DD HH MM SS a MySQL standard e Time format HH MM SS a MySQL standard e Latitude Longtitude format G decimal right 10 0987 wrong 10 5 922 wrong 10 5 55 3 wrong S 10 1 016 W 10 5 922 Page 43 WebGR users manual v1 0a e Decimal separator sign point like 9876 54 a MySQL standard e Thousands separator sign NOT USED right 1000000 wrong 1 000 000 wrong 1 000 000 1 The data fields cells for select fields e g subject or multiple select fields must match existing value lists for the given attribute This can require to transform coded data from source coding to destination coding If the value is not required it can be left empty Examples 1 1 female or f female gt female 2 GR or Griechenland gt Greece 2 The cells for numbers must only countain a number no unit percent signs degree signs quotation or double quotations signs monetary signs or other additional information e right 19 9 e right 19 90 e wron
25. e ignore undefined gender Fish sex fish Fish weight Fish weight fish H Fish sex ignore undefined Researching institutes i Fish researching institute fish H Stock i Stock fish IMAGE_ORIGINAL_FILENAME IMAGE_ORIGINAL_FILENAME undefined H Sample year Sample year fish Go on with the import by checking the data tiim e Figure 35 associate CSV file columns to system attributes manually 5 4 3 System checks before import The several checks with the CSV file and the image files will be reported to the user There are different boxes for different fields If an initial error occurs invalid CSV file there will be a message If an error occurs you will see which check has this erroreous data in the result code Erroreous data columns and rows will not be imported If an warning occurs the data will be processed but perhaps the user expected something different If the results code states success the specific check was all successful 5 4 4 Import If the test results showed no error you are able to click Import Only valid datasets will be imported Click Exit Page 39 WebGR users manual v1 0a Important Once imported fishes images will not be extended That means if you upload datasets again e g with more columns or information provided the data of existing datasets is neither overwritten nor extended Unintentionally imported fishes and images must be deleted before im
26. e checkbox form type The input type resp form element in select radiobuttons if edit forms value list Use single checkbox for YES NO multiselect multicheckbox selection if value list and is multiple Use radio button for single selection from long list Use multicheckbox for multiple selection from long list See Form elements has valuelist Decide wether attribute has free value on if select multiselect open or certain defined values radiobuttons closed multicheckbox off if text textarea checkbox sequence The sequence number in forms and 1 highest 999999 tables See is standard too very low O lowest number can be used multiple times is multiple Object has multiple values for this attribute show in list Decide wether search result table attribute group The object which the attribute belongs to E g the fish form the image form fish image system Page 55 WebGR users manual v1 0a After completion click Save button 7 3 2 2 Units UNIT is an special system attribute that is available for all attributes and that shows up after the attributes in forms One attribute can have only one unit 7 3 2 3 Value lists If the attribute has an value list box has valuelist is checked you can edit the possible values Click Add value list or Edit value list Edit the current values and click Update button Or enter new entry and click Add button
27. e list Page 7 WebGR users manual v1 0a A gt Create training calibration exercise Expertise Please select Please select 13 777 Clupea harengus otolith 121V Y VI VII VII Hake otolith Z baltic seatestgonade Figure 3 Select training calibration exercise You get a list of image sets grouped by protocol where you can create training calibration exercises Choose one training calibration exercise see Figure 4 Note If there are no references for a expertise then a training calibration exercise is not available per definition Page 8 WebGR users manual v1 0a WebGR Web Create training calibration exercise 6 lreland Hake otolith ist of imagesets grouped by key table Beta 1 KeyTable 21 2 0 Create training calibration exercise Hake ageing key 5 1 1 Create training calibration exercise Figure 4 List of image sets grouped by key table 4 2 Make an annotation Now you can start the exercise inside the annotation interface see Figure 5 Page 9 WebGR users manual v1 0a Annotation Compare Images oom Maximize A Fr Count Age Acceptance 4 1 681 82 y 358 18 08 06 2009 LENGTH SAMPLING_SOURCE on board SPECIES Glyptocephalus cynoglos 7 4 IM pa gt Coordinate input RESPONSABLE_SCIENTI Barbara Bland AREA Illa WEIGHT 3g SAMPLING_INSTITUTE Swedish Board of Fisheri LL r SEX undefined TYPE_OF_STRUCTURE otolith SOME RIG
28. e redirected to the workshop edit form After completion click Save button Page 48 WebGR users manual v1 0a 6 1 2 Workshop information To show the information about a workshop click List workshops info in the designated workshop row 6 1 2 1 Calibration exercise statistics Click on statistics in the designated calibration exercise row to view the statistical tables See calibration exercise statistics 6 1 2 2 Link repository Click on add link to add a new web link for the workshop for additional workshop information 6 1 2 3 File repository Click on add file to add a new file for the workshop for additional workshop information Enter a desciption select a file and click the Save button 6 2 Start new calibration exercise The following chapters describe how to set up a calibration exercise including the main settinigs the participants and the definition and building of a image set 6 2 1 Main settings Click List workshops edit in the designated workshop row start new calibration exercise Enter a name and description and click the Save button Now you can edit the details Page 49 WebGR users manual v1 0a Calibration exercise EJ01 ID 1 Imageset attributes CE is running stop calibration exercise FISH_COMMENT Remove attribute Calibration exercise name EJ01 Description _save My CE fish Protocol protocol_na_redfish doc Test
29. ead much other image file formats too It s freeware for non commercial use please download under http www irfanview net IrfanView is running under Linux too with Wine Page 40 WebGR users manual v1 0a 1 Start IrfanView 2 Click File gt Batch Conversion 3 Navigate into image directory you should see all the image files in the list container 4 Click Use this directory as output to store the jpg images in the same directory so you won t have to create another one 5 Choose Output format JPG JPEG Format 6 For highest quality click Options 7 Click the slider setting Save quality to outer right to 100 leave all other settings 8 Click OK 9 Finally click Start and the images will be converted 10 After the conversion is finished close IrfanView Page 41 WebGR users manual v1 0a 5 4 7 Creation of a character separated value file CSV suitable for WebGR 5 4 7 1 Software and CSV file specifications e Use spreadsheet software or editor of choice it must be able to export UTF 8 e g OpenOffice Calc Notepad2 e First row must contain headers e Further rows must contain the data e Save under specific file name not test1 csv Speichem in E WebGR_PHP Occ Fe Zuletzt verwendete D Desktop settings Eigene Dateien e Sr Arbeitsplatz NC ea EAN Dateiname test bung CSV cs Abbrechen Dateityp Y Automatische Dateinam
30. enserweiterung F Hit Kennwort speichern T Filtereinstellungen bearbeiten A Figure 36 Operating system Save as e choose CSV Textexport x Feldoptionen _ _ 222 Feldtrenner Texttrenner IV Zellinhalt wie angezeigt Feste Spaltenbreite Figure 37 OpenOffice CSV save settings Page 42 WebGR users manual v1 0a s File name must be import csv e CSV file character set must be UTF 8 coded as is the application scripts database s Field separator must be comma Text delimiter enclosures must be double quotation marks e Check cell content as presented e Click OK 5 4 7 2 Further CSV file specifications Note If you use OpenOffice Calc you don t need to know this because this is handled in the spreadsheet software After one dataset line break is used Line break within a cell content is only possible when the cell content is enclosed within text delimiters For line break allowed control characters are LF Unix systems etc or CR LF Microsoft Windows systems etc For NULL no character is written Example 4711 means 4711 NULL NULL 5 4 7 3 Data headings For the possible headings click Show attributes in WebGR 1 The image file names must match the entries in column IMAGE_ORIGINAL_FILENAME 2 The fish sample code must be in the column FISH_SAMPLE_CODE 3 The CSV headers must match data columns in the system for fishes an
31. forr zadi de User role admin Logout SOME RIGHTS RESERUED Egsative z common Imprint Funded by Figure 10 User data functions User form and personal data My expertise T 46 ICES 1x 401 1010 T 18 North Sea 404 1001 T 19 North Sea 410 1001 T 47 ICES llla 426 1002 T 15 all Hake otolith m 14 Test area 51 Test species otolith Username e mail adress pfor zadi de First name Ingmar Last name Institution Street City Phone number Faxsimile number Pfarr Federal Agency for Agriculture and Food Germany m Country l Germany Submit Change password My images My fishes Submit Delete my user account From here you can search the images that only you uploaded and the fish data sets that only you created You can change your password You can delete your user account The data that you provided will be stored anonymously Page 14 WebGR users manual v1 0a 4 6 Search function Additionaly a search function is applied for you Here you can search for calibration exercises fishes images or users Main menu RC1 Search e Register new user e My user data e Search calibration exercises Forgot password e Search fish e Help e Search image e Search user e My calibration exercises e List all workshops e My workshops e Start new trainin calibration exercise e Search Browse annotation by image and f
32. g 19 9 e wrong EUR 19 90 3 The cells for numbers must be in the right destination unit e g gallon hektoliter must be transformed to liter miles to kilometer cm to mm 4 The cells must be in the right coding standard if there is an coding standard assigned with the attribute e g Area could have coding standard from ICES NAFO 5 The datasets have to be valid against the image and fish attributes like in the context of a form E g a required value can not be empty Example 1 a data in spread sheet presentation extract H Sample year H Fish length FISH_SAMPLE_CODE Fish length simple Text IMAGE_ORIGINAL_FILENAME subject 2000 19 50 19test beta3 1 i50 jpg otolith 2000 17 52 17 test beta3 2 i52 jpg otolith 2000 15 53 15 test beta3 3 i53 jpg otolith 2000 14 54 14 test beta34 i54 jpg otolith Table 1 import data in spread sheet presentation extract 1 b same data in CSV representation H Sample year H Fish length FISH_SAMPLE_CODE Fish length simple Text IMAGE_ORIGINAL_FILENAME Image resolution subject 2000 19 50 19 test beta3 1 i50 jpg otolith Page 44 WebGR users manual v1 0a 2000 17 52 17 test beta3 2 i52 jpg otolith 2000 15 53 15 test beta3 3 i53 jpg otolith 2000 14 54 14 test beta3 4 i54 jpg otolith 2 corresponding uploaded files import csv i50 jpg i52 jpg i53 jpg i54 jpg All the conditio
33. he Bundesanstalt f r Landwirtschaft und Ern hrung Page 60
34. ibules coat 51 6 2 5 Calibration exercise final notes 52 EAS O ee A MN A triada 53 Tl PVA Tira Es AE la Sah E ERA RA 53 1 2 elel ANO OU a bes 53 Too Preparation seeren e E E aE 53 TaN EdICUSET ce cia 20 re en er 53 7 3 2 Edit attribute descripta 53 EPA a a eee ne O r ESSA 53 13 22 DIS A er ait See 55 E O A a ea erh 55 7 3 3 Further preparation au ae a a nen 55 g FAQ ee mim E 56 9 Form elements ea RE cia 58 TO Abbreyidlions asien 59 Page 3 WebGR users manual v1 0a 1 Applications web address You can find the Beta version of WebGR Web services for support of Growth and Reproduction Studies under the URL http preview webor zadi de The web address is dependent of your installation of WebGR so your contact partner will be your local system admininstator Start your browser Firefox version 3 Enter the adress After that the WebGR application website should be visible For further using make sure the latest Flash plugin is installed 2 User groups and rights The user rights are divided into two levels of availability The first level is the user level A user is true for the whole application The second level is the participant level A participant is only true for one calibration exercise 2 1 User role rights group 1 guest can visit public part start page contact or Terms of service create own new account user group 2 reader succeed rights from guest login into the non p
35. ish e Show attributes e Image upload Batch image upload e Edit protocols e Edit expertises e Start new worksho e Edit attributes e Download attribute CSV User name pforr zadi de User role admin Logout GEILEN Imprint Funded by EC DGMARE Figure 11 search functions In detail you have the possibility to contain your search with appointing the search attributes The attributes you can choose are different for the diverse searches You can choose between a search for and and or You can also contain your search by enter limitate subjects or select the Institutes you want to search in In the other searches are also functions to specialize your search application see Figure 15 Figure 16 and Figure 17 4 6 1 General usage of search forms 4 6 1 1 Text fields Placeholders and wildcards are not supported MySQL s LIKE is used with wildcards before it and behind it Page 15 WebGR users manual v1 0a Fisherman Figure 12 Simple text search field Example The expression part finds appartment 4 6 1 2 Ranges Type in a FROM and a TO value This is defined with greater than or equal and less than or equal to To get just one value type in the same FROM and TO value Note To function properly the entries in the database and in the search fields must have the same format Fish date of capture FROM Fish date of capture TO Figure 13 FROM and TO tex
36. ject otolith SEAN Click Save and you can see your first annotation in the list With clicking on the annotation you can reload it in your workspace see Figure 8 You can edit the dots add crosses or remove them by scrolling over the crosses and clicking After this you only have to click the Update button to update the annotation If you don t want to edit the old annotation just click Save and a new one will be created e Save creates a new annotation Update overwrites your own current annotation All this functions are available in the standard calibration exercises too 4 3 Compare and copy other readers annotations First click your annotation which you want to compare To compare select the tab Compare see Figure 9 Page 12 WebGR users manual v1 0a Annotation Compare Imageg b J Zoom 55 Marx refresh 17 y 174 55 J IS Read Coun Age Acceptance i copy Ma reg Selected annotation 12 5 5 on OO T m Dots of the two annotations All annotations list Brightness 10 Exit lt gt 2 A les Contrast _ A 49 Reset Color 227 Group a annotation comment a annotation WS Ref comment en la OAs er Figure 9 Compare annotations Click another annotation You can control click to select several annotations If you want to modify your own or another public annotation from the all annotations list click the
37. ngs see Figure 41 Add expertise Species Please select I H Type of structure Please select Cancel Cancel Figure 41 Add edit expertise Page 47 WebGR users manual v1 0a 6 Workshop manager 6 1 Workshop 6 1 1 Start new workshop A workshop is an event where a group of people discuss the criteria used to classify a biological structure commonly otoliths or gonads with the aim of getting a better agreement among them for one species A calibration exercise may be followed by a workshop and further calibration exercises will take place within a workshop Only the administrator is allowed to start anew or delete a workshop and set a new manager Click start new workshop Create new workshop Location Please select y Startdate VYYY MM DD IMERECECIEN Sukarrieta Enddate YY YY MM DD Test Bonn Institution Please select Z p i Manager forr zadi de change ws manager change ws manager Save Save Figure 42 Add workshop form Fill out the form The available items in the selectboxes e g Location shown in Figure 42 and Institution can be extended by the admin The default workshop manager is you to select another user e Click on change ws manager e Click Search user if necessary enter filter criteria Search button e Click the radio button next to the user in the designated user row e Click set as workshop manager You ar
38. ns will be tested before any data is imported to the system The results are reported to the user If a dataset with a new image and an existing fish checked with fish sample code is read the fish data is ignored only the image data will be imported for this row It s not allowed to overwrite existing fish datasets within an import An detailed import closing report will be available 5 4 8 Technical details of import First conditions are tested checks the CSV and prepares the datasets for import and gives detailled arrays back for single steps for further processing and report 1 checks the CSV file column against uploaded files 2 checks the header 3 checks the columns with value list entries and changes from strings to IDs 4 splits and checks the datasets against given fish and image format 5 checks the fish and image datasets against datasets already in the database Second files are read and imported Page 45 WebGR users manual v1 0a 5 5 Edit protocols Note In earlier versions protocols where named key or key table With this feature you can upload protocol files e g PDF You can select one protocol file in a calibration exercise Users can see and call this file in their calibration exercise list A protocol is used to define the processing and goal of a calibration exercise A protocol has a describing name Click Edit protocols to see the available keys List of protocols
39. pload Mp caida 36 9 41 NO o aa o une 36 5 4 2 Manual association of CSV file columns to system attributes 37 5 4 3 System checks before import en nn 38 e IMPORT ee ee ee ee 38 5 4 5 Conditions for an IMPOM air anna a angel 39 SAD HO Menue enge 39 94 52 Image M S 2 esse 39 5 4 6 Converting other image formats with IrfanView 39 5 4 7 Creation of a character separated value file CSV suitable for WebGR 41 5 4 7 1 Software and CSV file specifications nennen 41 5 4 7 2 Further CSV file specificationsS cooooocccccccncccnononnononcncnccnnnnnnnons 42 BA cf 3 Datalheadings ai 42 5 4 7 4 Datasels ae ae co 42 5 4 8 Technical details of Import aaa di 44 9 9 TCE ORONO CONS o Saco 45 3 8 EdIESXPOTUSE cin A ia ee 46 WebGR users manual v1 0a Workshop managet id AAN 47 Bl VWIOTRSNO Prat A A AN DA dd 47 5 1 1 Statt NEW Workshop reines 47 6 1 2 Workshop infromation ssa erinnern 48 6 1 2 1 Calibration exercise statisaicCS eeaeee ennenen ennen 48 6 1 2 2 Link repositoryo a cdo 48 621 23 File repository r ee Renee 48 6 2 Start new calibration exereise nsnknsna in 48 6 2 1 o re ee 48 0 2 2 Shown QUINDIO al 49 6 2 3 Participants rise 49 023 Add DARI CID Tn 50 6 2 3 2 Remove PAIPA Sivad a A IN AR AAA 50 6 2 3 3 Assign values to participant S ooooccccnnncncnnncccoccccccnccconnnnnnnn cnn 50 0 2 4 lmageset ltr
40. porting again In case of image data and image files you will get a warning if images for the specific fish identified over FISH SAMPLE CODE e are already existing e are existing with the filename provided For the start you can e generate a blank spread sheet with the current attributes all required and optional fish and image attributes use Download attribute CSV e look up the available attributes and value lists in the system 5 4 5 Conditions for an import An import set consists in a CSV character separated values file and corresponding image files 5 4 5 1 CSV file For detailed information about the CSV file look at 5 4 7 Creation of a character separated value file CSV suitable for WebGR 5 4 5 2 Image files Supported image formats e JPEG e GIF e PNG Currently TIFF is NOT supported Either NOT supported is Photoshop or other graphic utility program files Image size Images can be very big several megabyte and megapixel the images will be shrinked Image file names Theoretically image names can be repeated in another import but this is not recommended for identifying and export reasons 5 4 6 Converting other image formats with IrfanView We suggest you use IrfanView we use version 3 98 here on Windows to convert the images to copies in JPG format all at once automatically The original files e g TIFF files will not be overwritten IrfanView is able to rotate single images and r
41. r Textbox TO numbers dates times Free text PE aas playing 1A h Textarea Textarea Text field with line break Select one Select Multicheckbox Value list value value from a set Male i Radio Multicheckbox Value list value Female button easier than Select but more space required Select Multiselect Multicheckbox Value list multiple Option 2 value multiple values from a Option 3 rows normal set Option 4 attributes are Option 5 repeated one row multiple A ttribut r E opona Multicheckb Multicheckbox a a M Option 2 Ox easier V Option 3 than P option 5 but more E space SERD required Page 59 WebGR users manual v1 0a 10 Abbreviations Specific project WebGR abbreviations CE calibration exercise CS calcified structure TE WS workshop formerly used in WebGR WK workshop used in real life General project abbreviations berliOS Berlin Open Source as seen as domain name in URLs communication plattform for users developers and service providers of open source software BLE Bundesanstalt f r Landwirtschaft und Ern hrung CSV Comma Character separated values FK Foreign key GUID Globally unique ID Identity number key PDF Portable document format PK Primary key URL Unique resource locator ZADI as seen as domain name in URLs Zentralstelle f r Agrardokumentation und information former government institute integrated as Gruppe 42 group 42 into t
42. re 44 Edit participants form 6 2 3 1 Add participants Click Search user s to add if necessary enter filter criteria Search button Check the boxes next to the users in the designated user rows Click Add to participants button 6 2 3 2 Remove participants Check the boxes next to the participants in the designated participant rows Click Remove from participants button 6 2 3 3 Assign values to participant s With this special form you can apply settings to all checked participants at once Page 51 WebGR users manual v1 0a 1 Check the boxes next to the participants in the designated participant rows Check the attribute boxes next to the attributes you want to assign reassign Select values for the attributes Click the Apply to selected button Note Current values for the participants will be overwritten Click Back to go back the the calibration exercise details 6 2 4 Imageset attributes The imageset is the selection of images for an calibration exercise Only these exercise specific images will be available in the annotation module List of images r EZ NA Q1 SL1 OTO 5 jpg IVA Q1 SL1 OTO 5 1280 960 NA Q1 SL1 OTO B jpg NA Q1 SL1 OTO 6 1280 960 IVA Q1 SL1 OTO 8 jpg IVA Q1 SL1 OTO8 1280 960 IVA Q1 SL2 OTO 5 jpg IVA Q1 SL20TO 6 1280 960 ae IVA Q1 SL2 OTO 8 jpg IVA Q1 SL20TO 8 1280 960 IVA Q1 SL3 OTO 2 jpg IVA Q1 SL3 OTO 2 1280 960 NA Q1 SL3
43. s button this function is only interesting for long lasting CE sessions then you have the possibility to see instantly the new annotation from the other readers which have been made in the meantime N Do we have the possibility to test the higher permission levels E g are we able to upgrade a final reading to a workshop agreed annotation The coordinator is able to manage this please ask them N Is it possible to see my personal information e g permission levels etc without having to leave the calibration exercise On the bottom of the first tab fish image you see your participant role What other information do you want to see N How can we close the session and return to the menu now we use back but this is not the way we think is appropriate its ok but you can use the button My CEs Page 57 WebGR users manual v1 0a Permissions If someone is in a calibration exercise this person should not be allowed to see the reference annotation because otherwise you ll never have a proper calibration exercise N You can setup this in the CE administration interface Page 58 WebGR users manual v1 0a 9 Form elements Purpose Graphical example Edit form Search form Result list form Check yes or I have a car L Checkbox Checkbox single 1 on or no single O off not set Free text First name Textbox Textbox FROM Text field also fo
44. starts Choose characterset Unicode UTF 8 leave everything else and click OK Page 32 WebGR users manual v1 0a Textimport import cs x x l Zeichensatz Unicode UTF 8 Abbrechen Ab Zeile 1 Trennoptionen ____ _ _ Hilfe C Feste Breite Getrennt F Tabulator IV Komma Andere Semikolon Leerzeichen 7 Feldtrenner zusammenfassen Texttrenner n X Felder Spaltentyp Standard Standard Standard standard Standard Ste E FISH_SAMPLE_CODE LENGTH SPECIES FISH COMMENT GEAR CA Figure 30 OpenOffice text import The file opens Page 33 WebGR users manual v1 0a 44 import cs schreibgeschiitzt OpenOffice org Calc Datei Bearbeiten Ansicht Einf gen Format Extras Daten Fenster Hilfe A Ed BER Es Er SR 2 asa A zu Bus A mr ern A er Ban O A WISH SAMPLE CODE LENGTH SPECIES FISH_COMMENT GEAR CAPTURE DATE AREA ARCHIYINI Figure 31 OpenOffice CSV file Save the file under another name to edit it 5 3 Image upload Currently graphic formats GIF JPG PNG are supported In every case the original uploaded file will be stored on the file system of the server Select an image on your drive with Search button The file open dialog starts and you can select one file and go back to the form You can upload up to 4 images at once with this buttons All images will be assigned to the same fish that you specify over the fish sample code Page 34
45. t search fields 4 6 1 3 Multiple search selects Checkboxes and multi select boxes offer the ability to search for objects with attributes with value lists For usability reasons only checkboxes see Figure 14 are used Inside of an attribute there is always an OR combination used that means only one of the checked value list entries has to be found Fish scient name Mm Clupea harengus D Engraulis encrasicolus T Gadus morhua T Limanda limanda O Melanogrammus aeglefiunus O Merlangius merlangus T Merluccius merluccius O Micromesistius poutassou E Platichthys flesus T Pleuronectes platessa T Psetta maxima E Sardina pilchardus I Scomber scombrus E Scophthalmus rhombus I Solea solea E Sprattus sprattus T Trachurus trachurus Figure 14 Multicheckbox search field In the example fishes are found either of species Clupea harengus Engraulis encrasicolus or Gadus morhua This is also the case for multi value attributes Note In some search results you will find one and the same object multiple times This Page 16 WebGR users manual v1 0a results from multiselected or multichecked attributes e g a fish sample could have many examining institutes which the sample has passed in an otolith exchange 4 6 2 Search fish Here you can search a certain fish or a group of fishes by one ore more attributes E g physical attributes like length and weight can be used here vices WebGR
46. the expertises and protocols see Figure 25 Main menu RC1 UREN Calibration exercise list Register r ew user e My user data e Forgot password browse annotations Plaice fecundity macroscopic YyKMSSPDF2010 Test area 51 Test species otolith 2 e Help annotate e My calibration exercises statistics e My workshops details e Start new training alibrati xercise e Search e Browse annotation b image and fish e Show attributes e Image upload e Batch image upload e Edit protocols iti i en Additional functions e Download attribute CSV User name ipforr gmx de User role datamanager Logout SOME RIGHTS RESERUED ein common Imprint Funded by Figure 25 Additional functions for data managing 5 1 Show attributes Click on show attributes to get a list of all attributes that are available in the system Fish and image attributes are available in the edit forms the search forms and the result lists so they have a huge effect on the system Page 29 WebGR users manual v1 0a Attribute descriptor list mm total length of the fish in millimeter g weight of the fish sample in gramm RESOLUTION i dpi Image scanprint resolution in dots per inch Subject it Subject of visual analysis otolith otolith gonade gonade etc STOCK Individual informationiclassification about fish stock refers to the spatial distribution of a population ARCHIVING_CODE i Internal institute code to s
47. ting system screen Navigate to your source directory and choose your files to upload import csv and image files Note You can select multiple files with control click select single element and shift click select all elements until 5 Click Open 6 The files are in the list now select and click Remove file s if you selected too much files 7 Click Upload file s to upload the listed files 5 4 2 Manual association of CSV file columns to system attributes For the manual association of CSV file columns to system attributes you can choose the destination field in a table For supporting the association the select boxes are preset where there are equal column names provided in the CSV file Select the destination attribute system for each of the source attribute file Note For more information about the attributes click show attributes before your import If you need more destination attributes the Admin can add new ones to the system If you want to ignore the column e g a temporary column for calculations or a value not needed in the system leave the select box on ignore Page 38 WebGR users manual v1 0a allocating attributes csv file attributes system attributes 1 Fish length i Fish length fish v subject Subject image wu FISH_SAMPLE_CODE FISH_SAMPLE_CODE undefined v H Landing month Landing month fish A H DEPRECATED Fish cod
48. ting the original one Page 25 WebGR users manual v1 0a 4 10 2 Annotation levels of a calibration exercise The calibration exercise defines the protocol and expertise s If the calibration exercise is set to non comparable the group reference workshop reference WebGR reference modes are not available and the all annotations list is not shown The calibration exercise can be changed to comparable in the meantime The following table shows and explains the different annotation levels the goal of the level and the possible kinds of annotations Annotation level Goal All annotations list Kind of annotation Explanation Possible number of anno tations Page 26 WebGR users manual v1 0a Annotation Goal All annotations list system wide for this key amp expertise with same key amp expertise as this CE level Final Final annotations of this CE 0 n eve all readers Group Group reference of this CE 0 1 Personal ae pence Make final Workshop WS reference of CEs within this 0 1 otate annotation for workshop with same key amp image in CE expertise as CE WebGR WebGR reference of image with 0 1 same key 8 expertise as this CE Final Final annotations of this CE 0 n Group Group reference of this CE 0 1 Group Workshop WS reference of CEs within this 0 1 Group Make group workshop with
49. tore the physical structure SEX gender sex of fish female male undefined AREA referes to a geographic region area code like ICES and NAFO CAPTURE_DATE T Date of capture of fish format YYYY MM DD SOME RIGHTS RESERUED oggative commons u NS ID FISH_COMMENT just additional comment to this dataset IMAGE COMMENT i just additional comment to this dataset MAGNIFICATION it Magnification of subject for image creation show PREPARATION_METHOD image Preparation method of subject shown on detail m Figure 26 Attribute descriptor list Click on show details to get the details Page 30 WebGR users manual v1 0a Attribute descriptor superusertdzadi de description weight of the fish sample in gramm has valuelist sequence last sequence fish 2 last sequence image 1 CE u EEE O VW Vv Value is required and cant be empty is multiple C show in list IV attribute group fish Figure 27 Details of attribute Note If the value that you want to import for a specific attribute is not listed here the import for this datarows is not possible It s possible to edit the details and edit and add entries to the value list if you have sufficient rights See edit attributes 5 2 Download attribute CSV file It s possible to download a blank CSV file with only the available attributes as headings Click Download attribute CSV file Page 31 WebGR users manual v1
50. tribute descriptor 7 3 2 1 Attributes Attributes are used in many places in the application s if you add or edit an image or fish edit form e if you search an image or fish search form s inthe calibration exercise as saved list show attributes as saved filter form with saved filter values imageset attributes in the search result result table s in the import To add or edit meta data fields to image or fish click Attribute description Attributes can be used and seen in search and edit forms Click edit in designated attribute row to edit the settings Or Click add attribute descriptor to add a new attribute descriptor Page 54 WebGR users manual v1 0a Detail Description Restriction constraint Admin has to take care owner Only owner and admin can change delete the attribute name The used name in input forms and tables unit A unit for the attribute value see unit description The discription default value Enter a default value for a prefilled form field shows this attribute value is required Check if field has to be filled out in edit forms is standard Check if field has high priority in form is shown first See sequence too active Check to allow general usage if attribute is shown in search edit forms result tables data type The data type integer if select multiselect radiobuttons multicheckbox boolean if singl
51. ublic part make temporary annotations private calibration exercise search for images annotations or fish group 3 data manager succeed rights from reader upload edit and delete own image files and fish data edit own fish and image optional parameter administrate the keys maturity stage group 4 workshop manager succeed rights from data manager and coordinator edit own workshop settings declare WebGR reference annotation for his expertise create new calibration exercise Page 4 WebGR users manual v1 0a group 5 admin succeed rights from each workshop manager and data manager administrate the whole application administrate users user roles start new workshop and set a new manager 2 2 Participant role rights The participant role rights are always limited by the expertise of the user these roles deal only with participants group 6 trainee succeed rights from reader create and edit own annotations read all workshop results declare group accepted annotations group 7 expert succeed rights from trainee upload edit and delete own image files and fish data group 8 coordinator succeed rights from data manager and expert administrate participants add remove participants and admin their role membership declare calibration exercise annotations upload information files pdf files links edit own calibrations settings declare WebGR reference
52. w only stock assesment My calibration exercises e My workshops Start new training Expertise Trainee Trainee Expert Expert Expert Trainee Trainee Intermediate Trainee Trainee Trainee Trainee Trainee Trainee Trainee Trainee Trainee Calibration exercise level Stock no no no mo no no no no no no no no no no no no no e Search assessment Browse annotation b IVA QU SL1 E 5 S Is E 5 a E E O 2091 78 2391 3 2078 10 2900 OTO 5 jpg T NAIS 0 5 o Is S 5 S S S 11 2 1951 78 2391 3 2078 10 2900 e Show attributes OTO 5ipg e Image uploa WA Gt SLI 4 gt 5 x 5 5556 11 1111 05000 0 2500 z OTO Bjpg T e Edit protocols NA 5 S S 5 z S E E lt 0000 0000 00000 0 0000 IVA Qt SL2 5 s 6 E 6 E 5 00000 0 0000 0 0000 0 0000 G N OTO 8 jpg e Editaftibutes IVA QU SL2 6 6 z 6 E E 0 0000 0 0000 0 0000 0 0000 e Download attribute CSV OTO 8 jpg User name pforr zadi de 2 a S x S N E lt 0 0000 0 0000 0 0000 0 0000 Bl Meanot 3 0000 0 3571 3 0000 EST 0 5000 T lean ol l 1 F a distances to mean Mean ot 11 0000 5 5000 11 0000 5 5000 5 5000 distances to group Imprint download as CSV file Funded by EC DGMARE Figure 22 Statistics of calibration exercise annotations Under the readers number you see the expertise level and sto

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