Multi-state Spatial Database to Assess Threats to Mussels
Contents
1. Figure 22 Selected upstream NHDFlowlines from the Clubshell mussel locations The USWS Mussel Threats tool can then be run and report generated once all the dropboxes are filled in Remember if there are more than 500 NHDFlowline features selected a dialog box appears with an error message stating that the tool will not run and the box will also show how many features are selected Clicking OK will dismiss the box remove the selection and the user should try again with selecting either fewer Flowlines A 16 Figure 23 shows the list of the nine possible options available in the Netweork Utility Analyst When using placed flags and or barriers some trace options may not be available Help for the Network Utility Analyst can be found online at http resources arcgis com en help main 1 0 1 index html 002r00000028000000 Find Common Ancestors Find Connected Find Loops Find Disconnected Find Path Upstream Find Path Find Upstream Accumulation Trace Upstream Figure 23 List of Find and Trace options2. Layout Network Analyst NSS Regressions Parcel Editor Publisher Raster Painting Representation Route Editing Schematic Schematic Editor Schematic Network Analyst Snapping Spatial Adjustment Spatial Analyst Standard Streamstats Setup SWFWMD Connectivity Tools f Tablet TIN Editing d Tools Topology Tracking Analyst Versioning WindImage Toolbar For ArcMap Customize Figure 9 Turning on Toolbars in ArcMap A 7 Q USFWSMusselsThreats_10_1 mxd ArcMap loloj File Edit View Bookmarks Insert Selection Geoprocessing Customize Windows Help dead eb 1 10 000 000 SGSSO p Table Of Contents Maesa 3 amp Layers s Q is 5 Task Target i ty Edit Tools Help Mussels Clubshell Pleurobema clava e E Curtis Pearlymussel Epioblasma florentina curtisi Kx AK x a K K e E HigginsEye Pearlymussel Lampsilis higginsii 3 Buffer Size meters gt Select line within distance meters Launch PDF Reader Select Flowline 1 r 44 YU DIODIa a ODNGUda Ca Vy e Winged Mapleleaf Quadrula fragosa eo O All Mussels Threats Y NHD Dams D US EPA ICIS Facilities a US EPA ICIS Outfalls gt u u Z US EPA TRI 2010 GH US EPA 303 d Impaired Waters u a MI HVDRN Met linrtiane p Rivers amp Streams j ba AE EATEN 4 e ni 105634 299 3002882 837 Meters yueas i Gojeyeo
3. y ILLINOIS NATURAL vo HISTORY SURVEY PRAIRIE RESEARCH INSTITUTE Multi state Spatial Database to Assess Threats to Mussels Final Performance Report 2012 Tari Tweddale George Krumins and Kevin Cummings Prepared for U S Fish and Wildlife Service Division of Endangered Species Region 3 5600 American Blvd West Suite 900 Bloomington MN 55437 1458 Illinois Natural History Survey 1816 South Oak Street Champaign Illinois 61820 INHS Technical Report 2012 40 Date of issue 28 December 2012 Prairie Research Institute University of Illinois at Uroana Champaign William Shilts Executive Director Illinois Natural History Survey Brian D Anderson Director 1816 South Oak Street Champaign IL 61820 217 333 6830 Multi state Spatial Database to Assess Threats to Mussels Final Performance Report 2012 April 12 2011 October 31 2012 Tari Tweddale George Krumins and Kevin Cummings U S Fish and Wildlife Service Division of Endangered Species Region 3 5600 American Blvd West Suite 900 Bloomington MN 55437 1458 Illinois Natural History Survey 1816 South Oak Street Champaign Illinois 61820 INHS Technical Report 2012 40 Date of issue 28 December 2012 Background Freshwater mussels are one of the most imperiled fauna in North America approximately 70 of the 297 species within this group are considered endangered threatened or of special concern In the Upper Midwest Region 3 seventeen mussels
4. Figure 3 Python code for Mussel Threats Tool Components in the Python Add In Wizard Reports are created using ArcMap From the menu bar open View gt Reports the choose Create or Load When creating a new report there are two formats for the tables in the report writer stepped and outline The stepped report groups by page while the outline report shows alternately the field headings and the field records It does not matter where on the computer the files are kept to create the add ins however for this project all the files for the add in can be found in the MusselThreats AddInFiles AddIns folder Running the makeaddin py file followed by the Addins esriaddin creates the add in in the Windows user s folder at C Users lt username gt AppData Local ESRI Desktop10 1 AssemblyCache as a key of length of 36 characters for example SASED9A5 53AC E681 6567 A921D95AC237 The user who executes the Addins esriaddin has the add in automatically installed into the ArcMap extensions If the add in needs to be shared by a network share the instructions can be found at http resources arcgis com en help main 1 0 1 index html 0 14p000000 1m000000 15 16 Appendix A User Manual for USFWS Mussels Threats Tool Version 1 0 for ArcMap 10 1 USFWS Mussels Threats Tool Functionality The purpose of the USFWS Mussels Threats Tool version 1 0 is use GIS technology to investigate and report on possible threats to eigh
5. MUS FPA 303fd Imnaired Waters ad T j el parem g Figure 11 Mussel Threats Tool with the following options selected White Cat s Paw Pearly Mussel NHDFlowline US EPA 303 d Impaired Waters Buffer size 100 line distance 1500 and Yes to launch the PDF reader After running for a brief time the first dialog box will pop up allowing the user a choice of where to save the output shapefile Selecting Yes will save the shapefile in the directory defined by the environment variable MUSSELSTHREATS plus the string ThreatsOutput for example if MUSSELSTHREATS is set to C MusselsThreats then the default location for the shapefile will be C MusselsThreats ThreatsOutput If No is selected a dialog box will open and the user can browse to any directory which has write access For this example select Yes Figure 12 A 9 NOTE Do not use the slash instead of the backslash i e do not use C MusselsThreats as the tool will not work using the slash USFWSMusselsThreats_10_1 mxd ArcMap oB X File Edit View Bookmarks Insert Selection Geoprocessing Customize Windows Help Deue X 9 12 320 725 oI E be HYDRO_Net v Flowy Analysisy Find Common Ancestors Terrain Preprocessing Terrain Morphology Watershed Processing Attribute Tools Network Tools ApUtilities 5 3 ge K B Help Select Mussels White Cats Paw Pearl Select Flowline NHDFlowline Se
6. are listed as federally endangered or threatened five are candidates for listing and two are federal species of concern Numerous others are on state threatened and endangered lists These species are experiencing significant declines in both distribution and abundance and the viability of these small and isolated populations is doubtful without intervention Mussels are sessile organisms without the ability to quickly retreat from threats so they depend on the water quality and habitat conditions of their immediate environment to support them and their host fish populations Widespread habitat degradation e g pollution channelization siltation dams and impoundments is the primary cause of the declines observed over the last century Siltation from poor agricultural practices and chemical contaminants from point 1 e ammonia and metals and non point sources 1 e pesticides and fertilizers for example are major threats to many of the mussel species in the Upper Midwest Region Acute spills may directly kill mussels while chronic exposure to chemical contaminants can reduce population size by inhibiting growth and long term reproductive success Habitat destruction is confounded by the rapid expansion of exotic invasive species populations that compete with native mussels for food and space Eurasian zebra mussels Dreissena polymorpha for example have been spreading throughout the Mississippi River basin since the early 1990s and are quick
7. linked to the NHD using a linear referencing system on NHDFlowlines The use of events is a key characteristic of the NHD by allowing vast amounts of scientific information to be linked to the NHD while keeping the design simple and by making advanced analysis techniques possible The HEM tool was developed by the Department of the Interior Bureau of Land Management and can be downloaded from the USGS NHD website at http nhd usgs gov tools html Arc Hydro Tools for ArcGIS can also be used but is not required The latest version is Arc Hydro Tools for 10 1 BETA and can be downloaded for free from ESRI s ArcGIS Resources at http blogs esri com esri arcgis 2012 1 1 26 are you using arc hydro tools for 10 1 beta Arc Hydro is a set of data models and tools that operates within ArcGIS to support geospatial and temporal data analyses Arc Hydro is used to delineate and characterize watersheds in raster and vector formats define and analyze hydro geometric networks manage time series data and configure and export data to numerical models Initial Set up One Environment Variable needs to be set manually in the Windows operating system ArcMap only works in Windows in order for the Mussel tool to work This variable contains the path to the directory where the MusselsThreats database and associated files is located Environment Variables are set in the System Control Panel and can be accessed by right clicking on the Computer or My Computer icon
8. listed in Table 3 The field names are limited to 10 characters so some of the field names needed to be edited because they first share these first 10 characters in common Table 3 List of original and final edited names in the final TRI2010 data layer Original Name FACILITY_NAME FACILITY_STREET FACILITY_CITY FACILITY_COUNTY FACILITY_STATE FACILITY_ZIP_CODE ENTIRE_FACILITY_IND PARTIAL_FACILITY_IND FEDERAL _FACILITY_IND GOCO_FACILITY_IND PRIMARY_SIC_CODE PUBLIC_CONTACT_NAME PUBLIC_CONTACT_PHONE PRIMARY_NAICS_CODE NAICS_CODE_2 NAICS_CODE_3 NAICS_CODE_4 NAICS_CODE_5 NAICS_CODE_6 Edited Name FAC_NAME FAC_STREET FAC_CITY FAC_COUNTY FAC_STATE FAC_ZIPCOD EN_FAC_IND PARTFACIND FEDFAC_IND GOCO_IND PRI_SIC_CO PUB_NAME PUB_PHONE PRI_NAICS NAICS_2 NAICS_3 NAICS_4 NAICS_5 NAICS_6 The US EPA 303 d impaired waters data identifies waters that are too polluted or otherwise degraded to meet the state water quality standards This data was downloaded from http www epa gov waters data downloads html State and Watershed Geospatial Data The downloaded data is a file geodatabase and the only layer used for this project is the rad_303_1 feature class The only editing this data needed was to re projected the data from Geographic Coordinate System GCS to USA Albers Equal Area Conic USGS The US EPA National Pollutant Discharge Elimination System NPDES permit program controls water pollution by regulating point sources that disch
9. o s njea 4 34ea10 E m Figure 10 Utility Network Analyst Hydro Event Management Tools Arc Hydro Tools and the USFWS Mussel Threats Toolbars turned on in ArcMap Below are the basic steps to use the Mussels Threats tool l The user selects layers and other selections from the dropdown lists in the Mussels Threats toolbar These selections are processed by the Python script The NHDFlowline stream segments which intersect the selected mussel points layer are buffered and a polygon layer is created for this buffer and then intersected with a selected threats layer This buffer layer is added to the Output group in the ArcMap Table of Contents TOC A report in PDF file format is created from the selected point records and displayed as formatted tables with one record for each point The newly created layer is added to the TOC and therefore the map Duplicate names are not allowed if a duplicated name is chosen the new shapefile and report will replace the old shapefile and report The user has the ability to rename the output layer in the process There are a total of six selections needed to run the tool Start by selecting a mussel species already listed in the TOC for example the White Cat s Paw Pearly Mussel which contains 74 locations in Indiana and Ohio The user can also highlight a few mussel points of interest in a specific area then right click and select Data Export Data and save these record
10. selecting Properties then selecting Advanced System Settings to open the System Properties dialog box selecting the Advanced tab and clicking the Environment Variables button The dialog for Environment Variables opens and then the second New button should be clicked The four steps are labeled in Figure 1 A 1 Control Panel Home Step 2 Open Manag Delete Map network drive Disconnect network drive Create shortcut E Q jE Control Panel All Control Panel Items gt System View basic information about your computer Device Manager Windows edition 2 Remote settings Windows 7 Enterprise X System protection Copyright 2009 Microsoft Corporation All rights reserved Advanced system settings Service Pack 1 You must be logged on as an Administrator to make most of these changes Performance Visual effects processor scheduling memory usage and virtual memory User Profiles Desktop settings related to your logon Startup and Recovery System startup system failure and debugging information Environment Variables System variables lo e x JJ Search Contro Pane Value USERPROFILE AppData Local Temp USERPROFILE AppData Local Temp Variable ACROBATPATH Value 2m C Program Files x86 Adobe Acrobat AGSDESKTOPJAVA C ArcGIS Desktop 10 1 ARCGIS_LICENS ARCHOME 28004 esri webstore illinois
11. the Python exe file doesn t have to referenced by the entire path 1 e Python exe versus C Python27 Python exe Another helpful Python module which needs to be installed allows the use of message boxes with the command msgbox where the parentheses contain the message to be displayed in a dialog box with a button used to dismiss the box This Python module is named EasyGUI and is available at http easygui sourceforge net Follow the instructions on the website to install but make sure the install location is within the PYTHONPATH or edit the path to include the install location Python Add ins for ArcGIS Desktop 10 1 The tool uses the ESRI Python Add In Wizard In order to create and use an Add In project in ArcMap 10 1 the Python Add In Wizard needs to be downloaded and unzipped This is available at http www arcgis com home item html id 5f3aete77f6b416 lad3e4c62f30bif3b The help file for this can be found at http resources arcgis com en help main 10 1 index html What_is_a_Python_add_in 014p000000250 00000 The Python Add In Wizard is launched from the AddInFiles directory either by double clicking on the shortcut named addin_assistant_shortcut which assumes the MUSSELSTHREATS environment variable has been set or by opening the bin subfolder and double clicking on the addin_assistant exe file Click on the Select Folder button and navigate to the AddIns folder which in this example is located in C M
12. the number of specimens was not recorded Indicates the number of relict shells An x means that the number of specimens was not recorded Indicates the number of soft parts preserved in the collection An x means that the number of specimens was not recorded A common description of the location Typically a private collection later donated to a museum Collector s of the specimen The year or range of years the specimen was collected The year the specimen was collect or earliest year if only a range was listed The month if listed the specimen was collected The day if listed the specimen was collected The person who identified the specimen The person who donated the specimen The person who determined the source of the latitude and longitude coordinates A general remarks field that contains various types of data or comments Data from some of the heritage databases on the last observed occurrence of the species A code used in the INHS collection to track unique collection sites within a given county Field Name Description Lat_Long Latitude and longitude coordinates indicated in the same field Lat The latitude or north south position of the specimen Long The longitude or east west position of the specimen RiverMile Mississippi or Ohio River mile as designated by the US Army Corp of Engineers or the USGS Site Number A site number given by the collector QuadName USGS 7 5 minute topographic quadrangle name TRS The Pu
13. visible scale range for the NHDFlowline layer is set to 1 200 000 it may be necessary to reset the minimum scale to show all the selected features as in the example shown in Figure 16 To add an Add Barrier Flag Tool select the blue flag with the X at the base of the icon and click a point view belonging to the HYDRO_Net_Junctions layer If Trace Downstream is selected in the next dropdown list and the Solve button is clicked the downstream segment will be selected This segment can be quite lengthy If a barrier is placed downstream the selected segment s will stop at that barrier as seen in Figure 17 Specifically the flag starts with a selection of the Flowline segment it intersects and for the barrier the segment selections stops on the previous line segment Notice that the Edge Barrier Tool marker is somewhat hard to see since the marker is a thin red X The appearance of this marker cannot be changed In this figure the Display Arrows has been selected from the Flow dropdown list w r i _ al ae F C a r p r ro a Edge junction j C gt a b a i Me A re i p pri F P i os f A j ii N Qo Y ra i i i i ff a i ie i OL l Ma i S i s yan 7 i a a r l d i s i f 4 a i Thee S SY 3 b p a j E 4 E Sr P AAY i oo j Edge barrier k A Pa a BD ca iny a Figure 17 Flowline selection using Trace Downstream fro
14. S Region 3 Federal State T amp E Coordinators meeting in October 2012 focus for future threats to mussels should include the following layers e Eurasian zebra mussels Dreissena polymorpha locations Dredging sites Fish host sites Superfund sites Sewage treatments plants In stream gravel mining Ammonia and copper concentrations Final Data and Mussel Threats Tool The USFWS Mussel Threats tool and all final data are located in a folder called MusselThreats This folder can be copied to any location on a desktop computer or network computer as long as an environment variable is set to the location of this folder otherwise the tool will not work Instructions for initial setup and use of the USFWS Mussel Threat tool can be found in Appendix A The final data for the project is stored in a file geodatabase named USFWS_Region3_MusselsDatabase_Albers10 gdb and the Mussel Threat tool and data have been organized and symbolized in the ArcMap document named USFWSMiusselsThreats_10_1 mxd The geographic extent of nearly all of the GIS layers has been clipped to the USFWS Region 3 layer buffered by 10 miles The GIS layers are grouped in the ArcMap table of contents TOC in a way that mirrors their grouping as feature datasets in the geodatabase for these layers Mussels Threats and Rivers amp Streams The minimum scale was set to 1 200 000 for the Rivers amp Streams layers which includes the NHD Flowlines The Mussels group contains the eight
15. adata or creates its own metadata if there is none Version 2 0 works on ArcGIS 9 2 while version 2 1 works on ArcGIS 9 3 2 2 works on ArcGIS 10 This was the only tool that worked to re project the entire NHD geodatabase from Geographic Coordinate System GCS to USA Albers Equal Area Conic USGS but it only seems to work in ArcGIS 10 0 so this is the version of the software which was used to completed the final geodatabase for the project A toolbox which calls a python script created from a previous project was provided by Erik Olson at the USFWS This python script appends NHDFlowline classes from multiple geodatabases for use in a network Because NHD databases are often served in smaller sets than may be needed for a regional project the datasets often have some overlapping features when combined for a large project This tool combines them without duplication Python scripts for each of the feature classes in the NHD geodatabase were created and a toolbox with all toolbox tools used called NHD_tools tbx is included in the final deliverables Arc Hydro Tools Version 2 0 was downloaded from http blogs esri com esri arcgis 20 1 1 10 12 arc hydro tools version 2 0 are now available Arc Hydro is a set of data models and tools that operates within ArcGIS to support geospatial and temporal data analyses Arc Hydro is used to delineate and characterize watersheds in raster and vector formats define and analyze hydro geometric networks manage
16. arge pollutants into waters of the United States Data for permitted discharges as of April 2010 US EPA ICIS Facilities and US EPA ICIS Outtfalls was obtained from the US EPA Region 5 All states except Iowa have moved to the more recent Integrated Compliance Information System ICIS database for reporting so two separate files were sent for each layer as the fields don t match exactly Metadata was not included for these datasets but can be found at http water epa gov scitech datait models basins pcs cfm 10 The text field sizes in each of the data files needed to be edited to match exactly so they could be appended together in one file In particular the Iowa layer needed to have the NPDES text field sized up to 16 characters the FACILITY_N facility name to 57 from 32 the STATUS from 6 to 15 and the field RECEIVING_ receiving waters field from 32 to 50 characters The other layer which includes the remains seven states in USFWS Region 3 needed the TYPE field changed from 8 characters to 10 Once these changes were complete the two layers were appended together and re projected from Geographic Coordinate System GCS to USA Albers Equal Area Conic USGS Time ran out on the project before we could gather all valuable threats data layers for this project However the GIS tool developed for the project was designed to be able to easy add additional threats data layers as needed After discussions with mussel biologists at the USFW
17. blic Land Survey System PLSS Township Range and Section information SpecimenRemarks A remarks field for a specific specimen that contains various types of data or comments Once the data was obtained from each source it was then parsed to conform to list of fields identified in Table above Latitiude and longitude coordinates were generated for those records only listing a common location using the NGA GEOnet Names Server GNS database http earth info nga mil gns html index html and ACME Mapper http mapper acme com Museum records regarded as spurious were discarded and mussel condition live dead and relict was noted if possible In many cases it was not possible to tell whether or not the mussels in question were collected alive or represented old shells Once the data from all sources was parsed the final data with all mussel locations was exported out of FileMaker Pro as Excel 2010 Records which still contain no latitude and longitude information were removed since they can t be used for the project The excel file was then saved back to an Excel Workbook 1997 2003 format so that is can be read by ArcGIS The excel file was added to ArcMap and all locations were plotted using the File Add Data Add XY data tool Points were inspected for outliers or incorrect locations and corrected if necessary The data was then re projected from Geographic Coordinate System GCS to USA Albers Equal Area Conic USGS projection which i
18. e layers are created when the network is built from the NHDFlowline feature layers This can be done using ArcCatalog When the new network is built 1f there are errors these are written to an error table named HYDRO_BUILDERR If the network needs to be rebuilt the HY DRO_NET geometric network HYDRO_NET_Junctions point feature class and the Object table HY DRO_NET_BUILDERR all need to be deleted before the rebuild The WBD feature dataset contains eight feature classes Each feature class represents a hydrologic unit level in increments of two with the largest areas being WBD_HU2 and the smallest areas being WBD_HUI6 The hydrologic unit is a drainage area delineated to nest in a multi level hierarchical drainage system Its boundaries are defined by hydrographic and topographic criteria that delineate an area of land upstream from a specific point on a river stream or similar surface waters Information about the NHD also can be obtained in a series of associated tables This includes metadata stored in NHDFeaturetoMetadata and NHDMetadata sources given in NHDSourceCitation identification of model and data version given in NHDProcessingParameters flow relations given in NHDFlow reach code histories given in NHDReachCrossReference the domain of feature codes given in NHDF Code and others The largest area for which the NHD data can be downloaded is at the state level so the latest statewide high resolution NHD data was downloaded for each o
19. e location of where the user saved the shapefile will be identified here Shapefile saved In the default location C MusselThreats ThreatsOutput Figure 13 Verification indicating the saved location of output shapefile The phyton script will run and the final output shapefile will be added to the TOC and symbolized according to the current symbology of the selected threat layer and the PDF report of records in the A 10 selected threat layer will be opened Figure 14 The PDF report files are saved in the same location as the newly created shapefiles and are available to open at any time SEL US EPA 303d Impaired Waters Buffer 100m Line within 1500m White Cuts Paw Pearkynussel Epioblasma obliquata perobliqual pd Adobe Acrobat Pro Hoe _BPAee eoyrvRGs HOBIT gt a B US EPA 3080 bnpanred Waters Buffer 100m Line within 1500m Whate Cats Paw Pearhmussel Epioblasma obliquata perotiigua Parmaneh binbir SE FA AAEL B opi Pasiune Conia Pree deg Bell CSE L Y Wp apes H aoe A LLR a y p a bo TES TLE bee Tepa T p op WED HIK IZ Spbysieghad of Paria conia Pol ire gh et Permanent Identifier SA2ES002 3A L AMBA E280 SAGAESOL IIE Source Chinato N Page 1 ef 2d Figure 14 US EPA 303 d Impaired Water PDF report for White Cat s Paw Pearlymussel A dialog box indicating that the process was successfully completed will also appear Figure 15 Successfully completed Figure 15 Verificatio
20. ed in the final deliverables The USFWS Region Boundaries file was downloaded from http www fws gov gis data national index html USFWS Region 3 which is the study area for the project was selected and exported as a feature class and is included in the final geodatabase The USFWS Region 3 layer was buffered by 10 miles and saved as an additional feature class This buffered layer was used to clip the mussel locations and various threats data layers to ensure capturing enough of the extra data needed The 1 24 000 scale high resolution National Hydrography Dataset NHD specifically the NHDFlowline is the main base data layer that is used for the mussel threats tool The NHD is stored in a file geodatabase and is organized into several forms of geometry and into several supporting tables The geodatabase contains two Feature Datasets of geometry The Hydrography feature dataset contains the NHD whereas the Hydrographic Units feature dataset contains the Watershed Boundary Dataset WBD These data are designed to be used in general mapping and in the analysis of surface water systems The Hydrography feature dataset contains eight forms of geometry known as Feature Classes e NHDFlowline this is the fundamental flow network consisting predominantly of stream river and artificial path vector features It represents the spatial geometry carries the attributes models the water flow and contains linear referencing measures for l
21. edu 2800 C ArcGIS Pesktop 10 1 ws ep x cance Learn more online a a Wild Wine Performance Information and Tools M ii Figure 1 Setting the environment variable Once the New button is clicked the New System Variable dialog appears Set the Variable Name to MUSSELSTHREATS this is the name of the environment variable as referenced in the tool and must always be set to this text string Then set the Variable Value to the location of the home directory where the MusselsThreats data that was delivered for the project is located In this example the location has been set to C Mussels Threats Figure 2 Then click OK three times to close the last three dialog boxes Environment Yanables amp Se oe ee SS T Musee Threate variae Value C Windows system 32 emd ent 1 FP_NO_HOST_C NO St Figure 2 Creating a new environment variable A 2 Installing the USFWS Mussel Threats Python Add In Open the ArcMap document named USFWSMusselsThreats_10_1 mxd in the home directory the Same one as Set in the MUSSELSTHREATS environment variable Select Add In Manager from the Customize Menu Figure 3 to open the Add In Manager dialog box Figure 4 Customize Windows Toolbars Help Fide QQ t ocessing 9 z Extensions ICeSsINg fa Customize Mode 4 Add I
22. el Lampsilis higgi 9 Northern Riffleshell Epioblasma torulosa b wl g Purple Cats Paw Pearlymussel Epioblasrr u a g Scaleshell Leptodea leptodon m P g White Cats Paw Pearlymussel Epioblasm f e g Winged Mapleleaf Quadrula fragosa amp O All Mussels aad g Threats li M NHD Dams l E a g US EPA ICIS Facilities a g US EPA ICIS Outfalls o B A g US EPA TRI 2010 o g US EPA 303 d Impaired Waters g Rivers amp Streams amp O HYDRO_Net_Junctions E NHDFlowline i O NHDLine amp O HUC 8 Watersheds O NHDWaterbody amp O NHDArea O NHDPointEventFC E USFWS Region3 A mg be me amg Drawing e Oe Ar El Ama 0 BT uA Oe Bee we 701998 48 1936523 147 Meters Figure 19 Clubshell mussel locations selected along the North Folk of the Vermillion River in Vermilion County IL On the HEM toolbar select the convert points to flags barriers icon Figure 20 x Hydro Event Management Tools Targ et we AI tt Edit Tools Help h P Task Figure 20 Convert Points to Flags Barriers icon Select Flags and then click OK Figure 21 A 15 ad Convert Points to Flag Barri Create Flags or Barriers Flags Barriers Figure 21 Convert Points to Flags Barriers Dialog Box The mussel locations are converted to flags and are indicated as such with big green squares Now using the Utility Network Analyst tool
23. erable geodatabase By the end of the project only Natural Heritage data and agreements for Illinois Indiana Iowa Missouri Ohio and Wisconsin were obtained as this project doesn t currently fit under the current agreement expectation for Michigan and data for Minnesota was unable to be obtained in time for use on this project Data from 12 different museum collections make up the majority of the point locations used for the project but National Heritage data from 6 states as well as Higgin s Eye re location data from the US Army Corps of Engineers project along the Mississippi River were combined to create a regional database with consistent data structure Table 2 Table 2 Data sources used for mussel locations Data Source ANSP CHAS CM FMNH IA Heritage IL Heritage IN Heritage INHS INSM ISM MCZ MO Heritage Not Saved OH Heritage OSUM UMMZ USACE MCT USNM WI Heritage Description Academy of Natural Science of Philadelphia Chicago Academy of Science Carnegie Museum Field Museum of Natural History Chicago Data obtained from the Iowa Natural Heritage collections Data obtained from the Illinois Natural Heritage collections Data obtained from the Indiana Natural Heritage collections Illinois Natural History Survey Indiana State Museum Illinois State Museum Museum of Comparative Zoology Harvard University Data obtained from the Missouri Natural Heritage collections Unknown collection Data obtained fro
24. f the eight states in USFWS Region 3 from ftp nhdftp usgs gov DataSets Staged States FileGDB HighResolution In order to create custom functionality for the USFWS Mussel Threats tool a single seamless regional geodatabase containing all the NHD and WBD layers is needed The process of merging together all eight states to create single geodatabase re project this geodatabase from Geographic Coordinate System GCS to USA Albers Equal Area Conic USGS and then re build the geometric network was a much larger task than originally anticipated We ran into many technical difficulties and tried numerous tools using three different versions of ArcGIS software version 9 3 1 10 0 and 10 1 The method and tools which finally worked is discussed below The USFS Reprojection Tool Version 2 0 was downloaded from http nhd usgs gov tools html The USFS Reprojection Toolbar changes geographic projection and can transform datums using all available ESRI ArcObjects algorithms It was developed by the USDA Forest Service for the National Hydrography Dataset NHD NHDinGEO format but can function on any personal or file geodatabase This is an add on toolbar written for ESRI s ArcGIS 9 2 9 3 and 10 and is used in ArcCatalog The advantage is that it re projects whole personal and file geodatabases at once and updates the metadata at both the Geodatabase Dataset and Feature class levels in both the Data Quality and Spatial Reference sections of standard FGDC met
25. freshwater mussel species listed as federally endangered in USFWS Region 3 There are feature classes for each separate species snapped to the NHD Flowlines and a feature class which contains all eight species together snapped to the NHD Flowlines The user is encouraged to create separate feature classes or shapefiles which contains a subset of the mussel points in order to make the process quicker and more manageable Additional locations from other sources can easily be added in the future by adding the layer in ArcMap and then moving that layer to the Mussels group The Threats group contains the following five threats layers gathered for the project NHD Dams US EPA Toxic Release Inventory TRI 2010 US EPA ICIS Facilities US EPA ICIS Outtalls and US 11 EPA 303 d Impaired Waters Each layer is clipped to the 10 mile buffer USFWS Region 3 polygon Additional threats layers can also easily be added in the future by adding the layer in ArcMap and then moving that layer to the Threats group The Rivers amp Streams group contains the NHD layers which includes the NHDFlowlines and other water features consisting of point line polygon and network features Additional stream network layers can also easily be added in the future by adding the layer in ArcMap and then moving that layer to the Rivers and Streams group Throughout the course of the project a number of tools various GIS datasets and even various versions of ArcGIS software
26. hing a geoprocessing tool is doable using VB NET or C from a programming perspective the higher level language of Python is much easier to program with fewer lines of code needed and an application written in VB NET or C still would export variables and functionality to ModelBuilder Python and the Python geoprocessing tools which are compatible with the ModelBuilder 12 This research of various tools in various versions took a considerable amount of time and the final decision to go with ArcGIS 10 1 wasn t made until August 2012 which only gave us a couple months to develop and complete the tool It was well worth the time to thoroughly research the best options for the development of the tool as once the tool is complete this Python functionality will be more future proof because it can be added to and expanded by the next developers and programmers in a relatively easy manner Python Notes When Python is installed it should create the PY THONPATH environment variable but it doesn t always do so and this may need to be set up manually This path variable should include the path to your Python install folder G e Python27 and also the path to the ArcGIS Python install 1 e C ArcGIS Desktop10 1 arcpy It appears the trailing slash might be needed and is certainly allowed It also doesn t hurt to put the Python executable path within the computer Path variable so that when installing extra Python modules the command using
27. how how many features are selected Clicking OK will dismiss the box remove the selection and the user should try again with selecting either fewer Flowlines Start by selecting the Analysis dropdown select Options select the Results tab and in the Results format pane select Selection instead of Drawings This will ensure that features which are selected using the Utility Network Analyst can be used for the reporting process The next feature of the toolbar depicted by the blue flag with an X at its base see Figure 16 is one of four tools of the blue and red flag and barrier icons which can be used to help select NHDFlowline stream segments for reporting Four network selection tools are available 1 Add Junction Flag Tool this flag marks the start of a navigation path at a junction 2 Add Edge Flag Tool this flag marks the start of a navigation path along an edge 3 Add Junction Barrier Tool this flag marks the end of a navigation path at a junction 4 Add Edge Barrier Tool this flag marks the end of a navigation path along an edge Add Junction Flag Tool Add a junction flag to the network Figure 16 Choosing the Flag or Barrier to select network features The HYDRO_Net_Junctions point layer in the Rivers amp Steams group shows the locations of the junctions and can be used for the Junction Flag Tool and Junction Barrier Tool The Edge tools can be placed anywhere along the NHDFlowline Note that since the minimum
28. hreats e Libraries 5 amp NHD Dams a A i E amp M US EPA ICIS Facilities yeas l 5012423 o KA yK lt u ar Delete 4 saunjea ajeal ES a hal K k f Desktop J o amp USEPA ICIS Outfalls gt S amp USEPA TRI 2010 So E fg US EPA 303 d Impaired Waters Ra G o cB Et L Pa a M Rivers amp Streams Oxtsitr em s ym memes mM HVNRN Net binctiane ar I f f Sowth Gar otitra vr lt 1 t me ou i 146644 798 3043893 336 Meters Figure 5 Selecting the USFWS Mussel Tool Add In file Click on Install Add In button to properly install the USFWS Mussel Threats Tool Figure 6 A 4 l Customize Please confirm Add in file installation Active content such as Macros and Add In files can contain viruses or other secunty hazards Do not install this content unless you trust the source of this file USFWS Mussels Threats r er ersion 1 0 George Krumins Digital Signatures This Add In file is not digitially signed Signed By signed date Show Certificate Source is trusted i Figure 6 ESRI ArcGIS Add In Installation Utility Once the tool is installed a dialog box with a list of Added Objects will appear Click OK Figure 7 USFWS Mussels Threats Run USFWS Mussels Threats Select Mussels USFWS Mussels Threats Select Howline USFWS Mussels Threats Select Threat USFWS M
29. lect Threat US EPA 303 d Im Buffer Size meters 100 Select line within distance a 1500 Launch PDF Reader Yes Run a Table Of Contents ax l E aesa Layers US EPA 303 d Impaired Waters Buffer 100m Line within Lf o 44 E Mussels O Clubshell Pleurobema clava B 3 O Curtis Pearlymussel Epioblasma florentina curtisi O HigginsEye Pearlymussel Lampsilis higginsii As a shapefile in the default location C MusselThreats ThreatsOutput 3 O Northern Riffleshell Epioblasma torulosa rangiana Selecting No will allow saving in another location or with a custom name yeas l ojeg amp KA uk ku AK Would you like to save this layer t z saJn ea 4 ajeald E 3 O Purple Cats Paw Pearlymussel Epioblasma obliqua amp O Scaleshell Leptodea leptodon oe b E White Cats Paw Pearlymussel Epioblasma obliquat b 3 O Winged Mapleleaf Quadrula fragosa amp O All Mussels Threats y NHD Dams ote hi Hae 7y a x lt E Z US EPA ICIS Facilities B fy US EPA ICIS Outfalls f US FPA TRI 2010 m El i malen 4 Figure 12 Pop up allowing the user a choice of where to save the output shapefile The next dialog box will pop up and indicate the location where the shapefile is saved In this example the location is the default location which is C MusselThreats ThreatsOutput Figure 13 If No was selected th
30. ly invading remaining native mussel refugia Environmental degradation and invasive species invasions threaten numerous freshwater mussels with extinction throughout the Upper Midwest Comprehensively being able to spatially display threats that exist throughout the region will help direct freshwater mussel protection and restoration efforts greatly reducing the extinction risk for these species This project will focus on the following eight listed mussel species in USFWS Region 3 which includes Illinois Indiana Iowa Michigan Minnesota Missouri Ohio and Wisconsin e Clubshell Pleurobema clava Curtis Pearlymussel Epioblasma florentina curtisi Higgins Eye Pearlymussel Lampsilis higginsii Northern Riffleshell Epioblasma torulosa rangiana Purple Cat s Paw Pearlymussel Epioblasma obliquata obliquata Scaleshell Leptodea leptodon White Cat s Paw Pearlymussel Epioblasma obliquata perobliqua Winged Mapleleaf Quadrula fragosa The objectives of this project are 1 to create a GIS database of locations of these eight listed mussel species within USFWS Region 3 2 to make available a GIS database of water quality information and threats that may be relevant to listed mussels 3 to use GIS tools to identify where threats may be impacting mussels and 4 to provide field biologists access to all of the data and analysis tools developed in an easy to use format Data Layers Methods and Issues Mussel Locations An attemp
31. m Edge Flag to Edge Barrier To clear the flags and barriers select Clear Flags or Clear Barriers from the Analysis dropdown list Figure 18 Lf l A SD il F EF Flow a DF Reader Yes R Disable Layers Clear Flags Cle Clear Barriers Op Clears the barriers from the current network Figure 18 Use the Analysis dropdown list to clear flags and barriers A 14 The user can also select certain mussel locations and then use the Hydrography Event Management Tool to set those selected locations as flags For example zoom to the North Folk of the Vermillion River in Vermilion County IL then right click on the Clubshell mussel layer and select Selection Make this the only Selectable Layer Use the selection button to select the Clubshell points in this area Figure 19 Q USFWSMusselsThreats_v10 mxd ArcMap ArcInfo File Edit View Bookmarks Insert Selection Geoprocessing Customize Windows Help De GS BB XI d 1548 2 SS Od 07 E Editor po Lys T B Za J r iTe p 7 _ ht Task Target 2 HJ ty Edit Tools Help Network HYDRO_Net v Flow Analysis E Trace Task Find Path Upstream v Table Of Contents ax a ee z Q amp 2 z a w Q is Layers a Mussels t E Clubshell Pleurobema clava FA Q e oD ue E Curtis Pearlymussel Epioblasma florentir D aK KA e ux g HigginsEye Pearlymuss
32. m the Ohio Natural Heritage collections Ohio State University Museum of Zoology University of Michigan Museum of Zoology Higgins Eye re location project data along the Mississippi River United States National Museum Data obtained from the Wisconsin Natural Heritage collections The final USFWS Region 3 mussel database contains a total of 3 247 records with a breakdown of the following e Clubshell Pleurobema clava 1 580 records Curtis Pearlymussel Epioblasma florentina curtisi 80 records Higgins Eye Pearlymussel Lampsilis higginsii 595 records Northern Riffleshell Epioblasma torulosa rangiana 499 records Purple Cat s Paw Pearlymussel Epioblasma obliquata obliquata 43 records Scaleshell Leptodea leptodon 303 records 5 e White Cat s paw Pearlymussel Epioblasma obliquata perobliqua 74 records e Winged Mapleleaf Quadrula fragosa 73 records NOTE Data from all sources were kept however there may be duplicate point locations obtained from the various state Natural Heritage programs and the museum collection data as many of the museum records were sent to the various state Natural Heritage Programs once they were collected Base Data Layers and Tools The USA Base Map layer file USA Base Map lyr from ESRI Data and Maps 10 is used as a background data layer in the final ArcMap document named USFWSMusselsThreats_10_1l mxd This layer file as well as associated data layers is includ
33. n Manager Review and manage the ArcGls Desktop add ins currently installed on your system Add ins make it easy to develop distribute and use additional functionality To install an add in choose Customize gt Customize Mode click Add From File then drag and drop the commands from the add in into your menus or toolbars Shared Add Ins ArclS Online created by Esri Jreates a view into AreGlS Online Creates a view into Arc alS Online Types Commands Delete this Add In To install Add Ins and configure the user interface with Add In use the customize dialog Figure 4 Add In Manager dialog box Click the Customize button to open the Customize dialog box and then click on the Add From File button Navigate to the Addins esriaddin file which is located in the MusselThreats home directory under AddInFiles AddIns and select Open Figure 5 Q USFWSMusselsThreats_10_1 mxd ArcMap File Edit View Bookmarks Insert Selection Geoprocessing Customize Windows Help De eaea t lt AB xX D A 1 10 000 000 v apron pi Q Table Of Contents A k SBE o SBE Mussels Clubs e B Curtis imati Rename 9 a M Higgi g Nort hi Lookin Addins O rer m t a M Purple i Name Date modified Type ex ji Images 1 28 2013 12 24 PM__File folder Recent Places install 1 28 2013 12 07 PM__File folder A 5 M White Addins esriaddin 1 28 2013 342 PM__Esri Addn amp Winge e e O AllM S M T
34. n that process was successfully completed Since the Python script creates the dropdown lists by TOC group and matching names as partial character strings to correctly find the mussels layers for selection the mussel layers must be contained A 1I1 in the TOC within the Mussels group the threats if they are in the Threats group and the NHDFlowline layer if they are in the Rivers amp Streams group These rules exist to prevent incorrect selections For example if the layer for the Clubshell mussels is added to the TOC from the geodatabase the name of the layer would be by default Clubshell_SnappedToNHDFlowline If the user adds the layer to the correct group that is the Mussels group when selecting from the dropdown boxes this layer is only available in the correct Select Mussels list Using the Utility Network Analyst and the Hydrography Event Management Tool Another method is to use the Utility Network Analyst tool to select the interested NHDFlowlines instead of selecting a mussel point layer and then run the tool and report on these selected NHDFlowlines All the dropdown boxes in the USFWS Mussel Threats tool must still be selected even though the selection for the mussel s layer is not used in this case because the script will not run with blank choices If there are more than 500 NHDFlowline features selected a dialog box appears with an error message stating that the tool will not run and the box will also s
35. nto the regional NHD geodatabase Once the regional NHD geodatabase containing feature classes and tables from all layers was completed the USFS Reprojection Toolbar was used to re project the regional geodatabase from Geographic Coordinate System GCS to USA Albers Equal Area Conic USGS The geometric network was then created in ArcCatalog with no issues Set Flow Direction located under the Network Tools in the Arc Hydro toolbar was then used to set the flow direction of the NHDFlowlines for use with the USFWS Mussel Threats tool Threats Layers An initial list of potential threats to mussels was identified and includes the following e Dams and Impoundments Channelization Siltation from poor agricultural practices Leaking Underground Storage Tanks LUST Chemicals Non Point Source Pollutants o Pesticides o Fertilizers o Ammonia o Nitrogen o Phosphorus e Heavy Metals Point Source Pollutants o Copper o Cadmium e Water Quality Data o 303 d listed impaired waters o NAWQA o 2009 Beach NHD Indexed o 2002 impaired waters baseline data The United States Environmental Protection Agency USEPA and the United States Geologic Survey USGS have been identified as the main sources of data with some covering the entire USFWS Region 3 area while other layers like LUST pesticides and the chemicals have been identified for most but not all states Many of the statewide datasets need to be extracted and it seems like lots of editing is needed
36. ocating events on the network Additional NHDFlowline features are canal ditch pipeline connector underground conduit and coastline e NADLine contains linear features not core to the network e NHDPoint contains hydrography related point features e NHDWaterbody basic waterbodies such as lake pond features are represented here They portray the spatial geometry and the attributes of the feature These water polygons may contain NHDFlowline artificial paths to allow the representation of water flow Other NHDWaterbody features are swamp marsh reservoir playa estuary and ice mass e NHDArea contains many additional features of water polygons One of the more important is the stream river feature It represents the aerial extent of the water in a wide stream river with a basic set of attributes They typically contain NHDFlowline artificial paths that are used to model the stream river Artificial path carries the critical attributes of the stream river whereas NHDArea represents the geometric extent e NHDPointEventhC NHDLineEventFC and NHDAreaEventFC represent point line and area data events that behave as map features and linearly referenced events Streamgages which are 6 point features can be displayed and identified in the network through linear referencing with a network address Also contained in the Hydrography feature dataset are HYDRO_NET geometric network and related point feature class HYDRO_NET_Junctions Thes
37. r Q USFWSMusselsThreats_10_1 mxd ArcMap 987751 687 2148126 204 Meters yeas Oi 5018429 s sainjea 84e 19 EN ecs File Edit View Bookmarks Insert Selection Geoprocessing Customize Windows Help beds B 1 2 447 937 x 2 GG BC P Hypro_Net v Flow Analysis Find Common Ancestors ain Drenro eccing ain Wifaidalalailate na N ate heri H Ba Attrih ale Y WNerwilh ale van tilities y 2 PAI al Select Mussels White Cats Paw Pearl Select Flowline NHDFlowline Select Threat US EPA 303 d Im Buffer Size meters 100 Select line within distance meters 1500 Launch PDF Reader Yes a ow ZZ ee sh Layers a w 2 m Mussels _ Q J Clubshell Pleurobema clava e we P e aR a n O Curtis Pearlymussel Epioblasma florentina curtisi p oe bad P 4 O HigginsEye Pearlymussel Lampsilis higginsii hd O Northern Riffleshell Epioblasma torulosa rangiana he T O Purple Cats Paw Pearlymussel Epioblasma obliqua he b 3 C Scaleshell Leptodea leptodon fed f White Cats Paw Pearlymussel Epioblasma obliqua O Winged Mapleleaf Quadrula fragosa z e aad 3 O All Mussels figi Threats i Z NHD Dams s ol M US EPA ICIS Facilities SB 3 5 US EPA ICIS Outfalls 4 iF 3 z fg US EPA TRI 2010
38. rces were collected for the project The catalogue or reference number associated with the specimens for a particular museum This only refers to the University of Illinois Museum of Natural History UIMNH collection which was transferred to the INHS The catalogue or reference number associated with the University of Illinois Collection Mussel family name Mussel genus name Mussel species name Mussel subspecies name A concatenation of genus species and subspecies fields Name as it appeared in a collection or database typically a synonym The common name of the species Author of the scientific name The state where the species is located Field Name County 1 County2 Stream Drainage NoVouchered D SP CommonLocation Collection Collectors YearRange Year Month Day OriginalDetermination ReceivedFrom LatLongSource Remarks LastObserved CountyCode Description The county where the species is located The second county if located one or near the edge where the species 1s located Body of water where the species was located The larger unit of water to which the actual stream or lake flows into The number of specimens physically present in the collection this can be different from the number observed in the field Indicates the number of dead shells An x means that dead shells were found but the number of specimens was not recorded Indicates the number of live specimens An x means that
39. rom this folder Add ins can also be shared between users within an organization using a centralized network share Add ins at ArcGIS 10 can only be authored using NET or Java along with Extensible Markup Language XML and there are still no native Utility Network Analyst geoprocessing tools available for programming at this version so it was also thrown out In reviewing the Desktop Add ins at ArcGIS 10 1 we learned that Python had been added to the list of languages for authoring Desktop Add ins as well as the geoprocessing tools as native Python applications Python script functionality for the Utility Network Analyst This means the frontend which is the dialog box for selection of the NHDFlowline mussels and threats layers is being recreated natively in Python so that Models and Python scripts can use these specific geoprocessing tools Once that is done the added advantage of using the NHDPlus 2 1 layers including the raster GIS data layers will provide much functionality and expandability so this project can be a stepping stone to the future rather than being stuck in the past with version 9 3 or even 10 0 This is an important point because ArcGIS technology continues to evolve specifically using 10 1 will allow the custom geoprocessing tool to be published to the Web as a geoprocessing service using ArcGIS Server 10 1 This is not possible using ArcGIS 9 3 or 10 0 which incorporate VBA code Though it appears that creating and publis
40. s as a shapefile in any location When A 8 asked if you want to add the exported data to the map as a layer select yes This new layer is added to the top of the TOC and in order to be able to select this layer from the Select Mussels pulldown list the user will need to move the layer so that it appears in the Mussels Group layer Second select the NHDFlowline layer Third select a threats layer for example US EPA 303 d Impaired Waters Fourth select a buffer distance in meters for example 100 This is the distance the NHDFlowline streams that intersect the mussel points will be buffered Fifth select a line distance in meters for which additional streams than those already selected in the fourth step will be selected and buffered for example 1500 Finally select yes or no to launch the PDF reader after the tool is run A default program must be associated to open PDF report files automatically typically this is Adobe Acrobat Reader but nearly any application which opens PDF files will work The default option on the Mussels Threats toolbar is set to No but if Yes is selected the Mussels Threats tool will open the PDF report automatically This PDF report contains the formatted tabular records which correspond to the threats points selected geographically by the tool with one record shown per point After all the selections are made click the Run button and the script is launched using the selected values Figure 11
41. s the chosen projection for the project as areas are proportional and directions are true in limited areas This projection is good for regional and US wide datasets and is widely used by the US Geological Survey and US Census Bureau The mussel points were then snapped to the National Hydrography Dataset NHD flowline streams using ArcGIS processing tools as this layer is the primary base layer used in the GIS tool so it is important that the mussel locations fall directly on the streams A number of different tools and commands were evaluated to snap the points to line G e Hawth s tools Near etc but some only worked in earlier versions of ArcGIS or numerous steps were needed to get to the final output The RTWTools for ArcGIS toolbox was downloaded from https github com robintw RTW ToolsForArcGIS which includes a Python script incorporated into an ArcGIS Toolbox This was the choice tool used for the project and is included with the data deliverables This Python script uses the Near tool located under Analysis Tools Proximity in ArcToolbox but also incorporates the necessary code to create a new point layer using the NEAR_X and NEAR_Y fields generated by the Near command A feature class containing all original mussel locations a feature class containing all mussel locations snapped to the NHD flowline and eight 4 features classes each containing a single mussel species snapped to the NHD flowline are included in the final deliv
42. t federally endangered mussel species The tool runs in ESRI s ArcMap 10 1 with SP1 and uses a Python Add In using version 2 7 2 to geographically select possible environmental threats to mussels and then create tabular reports on these threats Though the tool is complete it is also designed to allow future upgrades and expansion with both data and functionality Additional GIS layers can be easily added to the ArcMap document mxd file especially new point location data and threat layers and the tool will select on these layers as well as the previously existing layers The default coordinate system is USA Contiguous Albers Equal Area Conic USGS The Albers projection is a conic equal area map projection that distorts scale and distance except along standard parallels Areas are proportional and directions are true in limited areas This projection is used by the United States US Geological Survey US Census Bureau etc and other large countries with a larger east west than north south extent In order to fully use the USFWS Mussel Tool ESRI s Utility Network Analyst Extension and the Hydrography Event Management HEM Tool is required The Utility Network Analyst is for analysis on geometric networks and is used in conjunction with the National Hydrography Dataset NHD which is the base data layer used in the tool The HEM Tool provides full functionality for adding and editing events in the NHD Events are informational data that are
43. t to get data agreements in place with each of the eight states National Heritage Programs so this data can be used for the project was done by the USFWS In the meantime museum collection data as well as data from other sources if any was gathered by Illinois Natural History Survey INHS staff Point locations for the entire range of each of the species was gathered even though the project area only covers USFWS Region 3 as it will be beneficial to the INHS and future projects if data is available for an entire species range Currently INHS uses FileMaker Pro software to store and manage various collections databases so the database will be created and stored in FileMaker Pro and then exported so that a GIS layer can be created for the project Once data from the a few museum collections and a few of the National Heritage Programs were obtained the data was evaluated and a list fields was determined so that a regional database with a consistent data structure could be built for use on the project The fields included in the final mussel locations layer with an explanation of each are listed in Table 1 Table 1 List of fields included in the final mussel locations layer Field Name Museum CatalogueNo OriginalMuseum UIMNHCatalogNo Family Genus Species Subspecies Genus Species Original Name CommonName SpecificAuthority State Description Institution in which the specimens if present reside Data from 19 different sou
44. te layer called NHD_Dams Toxics Release Inventory TRI data is published annual by the US EPA which contains pertinent information about locations of toxic chemical releases TRI data for reporting year 2010 was downloaded from http www epa gov tri tridata data basicplus index html The file is a zipped file US_2010_v10 zip and when unzipped contains seven text files These files are tab delimited with the first row being the header row There are about 208 fields most of which aren t needed All the fields were initially created as text fields and by default have a length of 255 characters which 1s way more than is needed for many of the fields The data was imported into an Excel file and saved as Excel Workbook 1997 2003 format so that is can be read by ArcGIS The excel file was added to ArcMap 10 1 and all locations were plotted using the File Add Data Add XY data tool The data was exported and saved as a shapefile and then re projected from Geographic Coordinate System GCS to USA Albers Equal Area Conic USGS Due to limitations of the GIS shapefile format shapefiles are used as the export format when the reports are generated from the USFWS Mussel Threats tool the total record length needed to be restricted to 4 000 bytes and because of this a number of fields needed to be deleted before the layer was created In order to create a good report 9 the TRI attribute fields were edited from the original data layer and are
45. the user can select one of the Trace Tasks for example Find Path Upstream and click Solve to select NHDFlowlines Figure 22 r Q USFWSMusselsThreats_v10 mxd ArcMap ArcInfo File Edit View Bookmarks Insert Selection Geoprocessing Customize Windows Help Deue Ae d 1 45 438 gt Z SSS BO fo 072 Editor 7 p is Y 7 Task Target i ty Edit Tools Help Network HYDRO_Net v Flowr Analysis F Trace Task Find Path Upstream lt Table Of Contents ax P 3 SS g amp Layers A a Mussels a G E Curtis Pearlymussel Epioblasma florentir b HigginsEye Pearlymussel Lampsilis higgi e Northern Riffleshell Epioblasma torulosa b Purple Cats Paw Pearlymussel Epioblasrr Scaleshell Leptodea leptodon Bojejed fe O42 KA yK Kx AK yeas i White Cats Paw Pearlymussel Epioblasm b Winged Mapleleaf Quadrula fragosa b O All Mussels Threats NHD Dams oe oth B E Gx 7 alls 4 E E US EPA ICIS Facilities x lt gt z US EPA ICIS Outfalls A l 2 E US EPA TRI 2010 e US EPA 303 d Impaired Waters a Rivers amp Streams O HYDRO_Net_Junctions E NHDFlowline O NHDLine O HUC 8 Watersheds O NHDWaterbody O NHDArea O NHDPointEventFC g USFWS Region3 m amp amp 4 m 7 meala n 4 Drawing amp O A Arial 0 Biu A De amp P gt 708250 006 1936571 235 Meters
46. time series data and configure and export data to numerical models The Arc Hydro toolbar contains many choices with many functions For the creation and manipulation of the datasets for this project only a few of the functions were used Since of most of the Arc Hydro functionality is beyond the scope of this document if the user wants to further explore the uses of Arc Hydro it is recommended to search online for a variety of documentation tutorials and exercises Re projecting each of the eight state NHD geodatabases from GCS to Albers and then running the append python scripts on the Albers geodatabase was tried first All seemed to go fine except when we tried to re create the geometric network on the Albers regional NHDFlowline layer ArcMap seemed to always hang up and it would not create the geometrics network Thus the reverse of running the python scripts to append each of the eight states together in GCS and then re projecting the regional geodatabase from GCS to Albers was tried This seemed to be the method which worked best however only a few states could be appended together at a time otherwise we would get errors when rebuilding the geometric network Thus the regional database needed to be completed in two steps using four states at a time rather than all in one step The Append tool followed by the Delete Identical located under Data Management Tools General in ArcToolbox was used to combine all the geodatabase tables i
47. to get it into a usable format for use on this project Since we were having lots of technical issues trying to get the NHD streams data completed which is the base data layer used in the mussel threats tool less time was available to gather and edit threats data layers for the project Since one of the objectives of the project is to develop a GIS tool to identify where threats maybe be impacting mussels we have decided to focus on using five different threats layer these are mainly USEPA datasets which cover the entire USFWS Region 3 area and design the tool so that the user can add additional threats data at any time The five threats layers that are included with the final mussel geodatabase include NHD Dams US EPA Toxic Release Inventory TRI sites US EPA 303 d impaired waters US EPA ICIS Facilities and US EPA ICIS Outfalls and are discussed in more detail below Data for Dams was downloaded from National Atlas http nationalatlas gov as well as from the USGS NHD data http nhd usgs gov data html The feature class called NHDPointEventFC contains information for Dams as well as Gaging and Water Quality Stations from the USGS The data from both these sources was very similar but since we are already using the NHD data as the base layer for the tool we decided to just go ahead and use the USGS NHDPointEventFC for the Dams layer The only editing this data needed was to extract out only the Dams from this layer and save it as a separa
48. ussels Threats Buffer Size meters USFWS Mussels Threats Select line within distance 1 USFWS Mussels Threats Launch PDF Reader USFWS Mussels Threats Figure 7 Objects added as part of the USFWS Mussel Threat Tool A 5 USFWS Mussel Threats should now show up under the list of available Toolbars Check the box next to the USFWS Mussels Threats to turn on the toolbar Then click Close Figure 8 Teobars Streamstats Setup SWFWMD Connectivity Tools Rename E Tablet Delete E Versioning WindImage Toolbar For ArcMap EES Figure 8 USFWS Mussel Threats Tool Using the USFWS Mussel Tool in ArcMap If the USWFWS toolbar is already installed but not turned on the user should right click on an empty spot in the toolbar area selecting the USFWS Mussels Threats tool See Figure 9 The Utility Network Analyst Hydrography Event Management Tool and Arc Hydro Tools should also be selected and then each toolbar can be docked to the top of the screen by moving them to the top Figure 10 A 6 au q ETTE Flowy Analysis a CcOGO Data Driven Pages Data Frame Tools Distributed Geodatabase Draw Edit Vertices Editor Effects EPA Aggregator Feature Cache Feature Construction Geocoding Geodatabase History GeolCPR Tools Geometric Network Editing Georeferencing Geostatistical Analyst GPS Graphics Image Classification Impact Analysis Tools Labeling LAS Dataset
49. usselsThreats AddInFiles AddIns Clicking on the Add In Contents tab shows the included extensions menus and toolbars Figure 1 13 jy HP drivers bgl M5OCache Figure 1 Python Add In Wizard Selecting the Select Mussels tool will list the name of the class in the Python code which in this case is named ComboBox MusselsClass Figure 2 TD Variable Name Addins addin MT leombobox Teale Message Hiit Text Help Content Figure 2 Mussel Threats Tool Components in the Python Add In Wizard 14 Each of the classes has their own class as a block of code in the Python script The script is saved in the AddIns Install folder The AddIns folder can be opened by clicking on the Open Folder button of the Python Add In Wizard Figure 3 E AreGlS Python Add In Wizard Python Add In Wizard E Project Setings Add in Combats Nie EXTENSIONS eN Active View Extension Combo Box MENUS TOOLBARS USFWS Mussels Threats Class Name CombofloxMuscelsClass Select Mussels Capion Seebeck Mussel Select Aowine ID Varish Name Adee adta MT oombas Select Threat 9 Search acing Organize Include in library Share with Bum ew fobder Ww Fanaa Date modified E Desktop d Images ip Downloads dL Install 1 Recent Places ta Adis esnaddm 1 28 2013 JA42 PM E config g Libraries makesddin py Documents README tet ai Music R 6 items
50. were reviewed Since the NHD 1s the base layer to be used in the mussel threat tool and the most current geodatabases downloaded were for ArcGIS 9 3 1 first attempts were made to develop the tool using ArcGIS 9 3 1 It was also initially thought that for maximum backward compatibility the best choice would be ArcGIS 9 3 as opposed to version 10 0 or 10 1 This version was quickly thrown out because we didn t want to spend a lot of time customizing a tool using a combination of Python and Visual Basic for Applications VBA code as VBA is already being retired by ESRI There are also no native Utility Network Analyst geoprocessing tools available for programming We then looked into using ArcGIS 10 as this is the version that were able to finally get the USFS Reprojection Tool Version 2 to work which allowed us to merge and reproject the eight individual state NHD data into a seamless regional NHD streams database ArcGIS 10 introduced a new and innovative way to customize and extend the ArcGIS Desktop applications which is by using a Desktop add in model The new add in model provides one with a declaratively based framework for creating a collection of customizations conveniently packaged within a single compressed file Add ins are easily shared between users as they do not require installation programs or Component Object Model COM registration they are added to a system by simply copying them to a well known folder and removed by deleting them f
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