JEM Wader Distribution Evaluation Modeling (WADEM) Change Log

• Update for Java 11
• Move Software Requirements to README.txt file
• Update to supporting libraries that have been migrated to Java 11
• Add javax.annotation to dependencies
• Update org.eclipse.jdt.core.prefs and org.eclipse.jdt.ui.prefs for Java 11 and warn on missing javadocs for private visibility

• Library updates (some may not apply):
• edu.ucar.unidata.netcdf;bundle-version="5.3.3",
• gov.usgs.jem.cerp.netcdf;bundle-version="3.0.0",
• gov.usgs.jem.cerp.netcdf.ug;bundle-version="3.0.0",
• gov.usgs.jem.spatial.model;bundle-version="2.0.0",
• gov.usgs.jem.spatial.expressions;bundle-version="2.0.0",
• gov.usgs.jem.hydro.processing;bundle-version="2.0.0",
• gov.usgs.jem.netcdf.depthcreator.ui;bundle-version="2.0.0",
• gov.usgs.jem.netcdf.ncmlcreator.ui;bundle-version="2.0.0",
• gov.usgs.jem.thredds.ui;bundle-version="2.0.0"
• Attempt to resolve the majority of compiler warnings through a combination of mechanisms:
• refactor deprecated to current usage where possible, suppress deprecation otherwise;
• add javadocs in some cases, but suppress where documentation was largely ignored or code is not otherwise actively maintained;
• suppress or address other compiler warnings (e.g. resource; unused)

• If --dd-output-folder is provided with --enable-dd-with-dc, then properly set the output folder for depth files

• Update feature.xml to remove "org.apache.lucene.analysis"
• Update tycho to 1.4.0
• org.joda.time;bundle-version="2.10.3",
• org.apache.commons.math;bundle-version="3.6.1",
• org.apache.httpcomponents;bundle-version="4.5.12",
• org.jfree.jfreechart;bundle-version="1.5.0",
• gov.usgs.jem.everview.dataviewer.colorramp;bundle-version="1.2.0",
• gov.usgs.jem.mail;bundle-version="1.4.0",
• gov.usgs.jem.internal;bundle-version="1.7.0",
• guava;bundle-version="29.0.0",
• org.apache.commons.csv;bundle-version="1.8.0",
• org.geotools.plugin;bundle-version="23.0.0",
• edu.ucar.unidata.netcdf;bundle-version="5.1.0",
• gov.usgs.jem.cerp.netcdf;bundle-version="2.0.0",
• gov.usgs.jem.spatial.model;bundle-version="1.4.0",
• gov.usgs.jem.spatial.expressions;bundle-version="1.4.0",
• gov.usgs.jem.thredds.ui;bundle-version="1.2.0",
• gov.usgs.jem.netcdf.depthcreator.ui;bundle-version="1.3.0",
• gov.usgs.jem.hydro.processing;bundle-version="1.4.0",
• gov.usgs.jem.netcdf.ncmlcreator.ui;bundle-version="1.3.0"

• Update for hydroperiod output file: fixed summary attribute

• Bug fix in Scenario Analyst where SFC month-of-year means and monthly means summaries could fail due to incorrect

file listing order in aggregation NcML file (Java's File.listFiles() method does not guarantee an order)

• Additional refactoring related to command line data download and depth creator: managers have been refactored and

moved to one of the supporting libraries (thredds downloader; depth creator; ncml creator)

• Refactoring also affects UI data download, depth creator, and ncml creator

• Refactoring related to command line data download and depth creator: now uses library classes and methods

• Command line options to set preferences, for example to enable animated gif output

• Updates for internal library changes
• Depth Aggregator (NcML Creator) now updated to be able to stitch files like Batch Processing does
• NcML Creator can now create NetCDF files alongside NcML output files
• Fix issue where bundled species files were sometimes not detected
• Fix for headless mode not properly trapping exceptions when parameterizing the model
• Fix for headless mode not setting regions file indices if custom regions file used

• Removed Sparrow Helper tool. It now spun off into a separate application.
• Headless: if user-provided year range is invalid, print specified year range and available year range
• Headless: print modeling year range being used
• Headless: ensure depth file has been provided before attempting to determine year range
• Headless: added option --w-depth-folder to enable pointing to folder containing depth NetCDF files, NcML will be

created automatically

• Fix occasional bug where Data Download depth files where not being skipped if up-to-date
• Add new headless option: --enable-dd-with-dc
• Enable the THREDDS Data Download tool with Depth Creator tool. This mode will examine the time stamps of existing

files and skip them if they're up to date, and additionally create a NcML file of the results.

• Headless: --dd-output-folder also sets ThreddsUIPreferences.DATA_FOLDER preference
• Headless: --enable-depth-creator adds data mirror folder contents if no files specified
• Headless: --enable-depth-creator sets output folder if not specified

• Cap nest success output at 1
• Bug fix for color ramp used on maps

• Update points extractor to match only one grid cell for each input point
• Update to points extractor output file names: remove empty space, keep original file name parts
• Update to points extractor to detect "east" and "north" as x, y column heading names
• Bug fix for batch processing mode calculation of number of jobs to use (out of memory error)
• Bug fix for depth creator not removing existing files on new browse
• Bug fix for data downloader not updating datasets on destination change
• Bug fix for data downloader sometimes showing duplicate progress dialogs
• Bug fix for points extractor: if validation fail, reset "is running" flag
• Bug fix for depth creator "Output Directory Required" error

• Data Download accessible headlessly (see --headless --help and --enable-data-download)
• Depth Creator accessible headlessly (see --headless --help and --enable-depth-creator)
• Main WADEM model accessible headlessly (see --headless --help and --enable-wadem)
• WADEM batch model accessible headlessly (see --headless --help and --enable-wadem-batch)
• Scenario Analyst accessible headlessly (see --headless --help and --enable-scenario-analyst)
• Fix for Sparrow Helper max consecutive dry days calculation, which reported most recent instead of max

• Improved the performance of TemporalAggregator for "Overall" calculations by using thread pool and batched reads
• Update for https THREDDS catalogs and https OPeNDAP datasets, move to use gov.usgs.jem.thredds.ui plug-in
• Plot 3-year trailing average for given month, by region, of TFC individuals. Also plot cubic fit to data.
• Use gov.usgs.jem.netcdf.depthcreator.ui plug-in for depth creator view
• Minor tweaks to progress reporting when running multi-year summary
• Fix for scenario analyst regional hydrograph comparison when leap years are included
• Fix for scenario analyst temporal aggregation not using correct time dimension in some cases for NcML
• Sparrow Helper is now accessible headlessly (see --headless --help and --enable-sparrow-helper)

• Switch to org.apache.commons.csv instead of au.com.opencsv
• Added nesting effort and success indicators
• Added maps and NetCDF of monthly TFC averages by region, and overall monthly averages
• Only calculate SFC scores for cells with depth within the 5-95% suitable depth range.
• Track and map active cells: number of days a cell is used when depth is suitable
• SFC maps where value is 0.0 are now colored gray
• Added "Report Bug" to error dialog to ease bug reporting
• Fixed a memory leak / misallocation when loading species parameters
• If Data Downloader tool cannot read remote catalog, report the error log to the user
• Fixed message for multi-year summary progress dialog
• Fix for "individual_tfc_monthly_delta" values: these were being calculated as delta from

start of month to end of month when it should have been the mean of daily deltas

• Fix for SFC regions: attempt to use partial matches between defined regions and regions in file
• Fix for detection of available depth data variables in a file
• Fix for depth map values that are out of range of the color ramp
• Multi-year summary shows an additional, sortable column for parameter file type
• Allow enable/disable of region files & specific modules (Advanced UI)
• Allow enable/disable of random temporal effects in TFC (Advanced UI: preferences)
• Parallelized (now uses multiple CPU cores): BinaryOperationNetCDF (e.g. for interaction variables)

Days Since Drydown, Recession Rate, Reversal, Hydroperiod, NetCDF image plotter, Spatial

Foraging Conditions, and Region Aggregator

• Point Extractor can accept floating-point coordinates and does not require an exact match
• Updated Point Extractor to run in batch mode
• Added a Batch Processing tab for running multiple instances of WADEM
• Data Downloader adds bounds metadata to variables
• Output NetCDF files include title, summary, and keywords metadata attributes
• Added output with the number of cells by region in 'misc' folder
• Added output for number of cells in depth window by species (daily averages/hydro vars/depth)
• Hydroperiod "Create" is selected by default when selecting a new depth file
• Bird Parameters Editor: If the user 'clears' a value in a field, set its value as 0 rather

than removing the term value

• Addition of days since dry or wet output
• Addition of days since dry or wet, 7-day recession, and days since dry or wet x 7-day

recession SFC fixed effects

• SFC landscape estimate y-axis is now labeled "Mean Birds per Survey"
• Support exponential back-transform
• Produce plots for 7-day recession
• Produce plots for days since dry or wet
• Do not output Gif for atemporal datasets.
• Reopen on the same monitor that WADEM was last used on
• Initial version of Sparrow Helper added
• Bug fix for dates before 1970
• Verify that a user-supplied hydroperiod file has same spatial dimensions as the depth file
• GE, WI, WS modeling ranges will now be Nov 1 - May 31
• When performing a run with multiple species, their date ranges / season must match
• SFC Patch Abudance series name (in CSV) changed to remove year
• Produce SFC Patch Abudance CSV in multi-year summary
• Added Scenario Analyst tool to allow scenario comparisons
• When loading species and regions files, if file does not exist, scan the bundled data folder

for a file of the same name and use it if one is found

• Minimum requirements updated to Java 8

• Public release

• Warn the user if the expected data download time is expected to be > 1min; give a rough

estimate of expected download time

• Hide Depth Creator and Depth Aggregator when the simple UI is enabled
• Check for number format exception when attempting to parse the history attribute of downloaded

files

• Fix for NetCDF library dependency breaking some output functionality

• Fix for local directory structure not being properly created before downloading remote datasets

• Updated WADEM manuscript citation: http://dx.plos.org/10.1371/journal.pone.0128182
• Updated help documentation to reflect changes since v0.1
• Added Data Downloader tool. This tools synchronizes with remote THREDDS servers to download

remote datasets locally.

• Use a consistent color ramp scale for days since dry maps
• If parameters have not been saved, display an asterisk ("*") in the main WADEM view title
• Automatically prompt to save parameters file when WADEM is run
• If append is not enabled, prompt the user to enable it when WADEM is run
• Added a preference for "simple" vs. "advanced" user interface, with "simple" enabled by default
• WADEM now automatically populates some bundled files (regions files, species) (advanced UI)
• Turned off animated GIF map creation by default. It can be re-enabled in preferences.
• Changed the folder structure of WADEM output files: now spread across "Maps", "NetCDFs",

"Daily Averages", and "Parameters" folders

• Bug fixes for systems that use larger text displays - controls now resize more dynamically so

that buttons aren't cut off with the default startup size

• Miscelleneous UI tweaks (e.g. table column dynamic resizing; consistent font sizes; etc.)

• Break out wood stork cell use index maps into fewer color bands - same as great egret and

white ibis

• Updated color ramp schemes for great egret and white ibis cell use index maps to use reds for

upper ranges

• Added a preference for GIF animation delay
• Scan for existing SFC output when determining value ranges to use for cell use index maps

• WADEM now scans /data directory for EverVIEW Color Ramp files. If found, map images will use

the appropriate color ramp. Color ramps are found by two schemes:

1. Color ramp file name matches the NetCDF variable name (e.g. depth)

2. Color ramp 'var' property matches NetCDF variable name and 'name' property is part

of the NetCDF file name (e.g. var="recession", name="recession14")

• Includes depth and 14-day recession rate color ramp files
• Added animated gif output for map images
• NcML Creator view is renamed Depth Aggregator to be more user-friendly
• Depth Creator and Depth Aggregator views are now open by default
• Browse for species files, regions files, and parameters files default to WADEM's "data" folder
• Reorganization and cleanup of output to reduce the number of files generated
• Added special color ramp schemes for great egret and white ibis cell use index maps to accentuate

color bands

• For multi-year summary tool, include aggregations of TFC individual abundance by region, TFC

individual abundance for landscape, TFC flocking ratio by region, TFC flocking ratio for

landscape, and breeding conditions foraging index by combining multiple years into the same

file

• When "Create" hydroperiod is used:
• Bug fix: use 10 year hydroperiod instead of 12
• Use trailing/rolling 10 years instead of an initial static 10 year hydroperiod
• Static map and legend plot output file names now include the input file name
• Hydroperiod Creator:
• Default to using full time range instead of most recent 10 years
• Bug fix for year range where start was missing first 2 years and end was missing last year

• Check input values against conventional fill values AND attribute fill value
• Preserve data type when reading input values and checking against fill value before converting

to floating point.

• Bug fix for map plots of atemporal variables when input x or y coordinates aren't in ascending order

• Updates to hydrologic variables to allow non-cm depth to be converted to cm

(Filter, RecessionRate, Reversal; unaffected: Hydroperiod, Days Since Dry)

• Force filtered depth file to use float data type instead of short to avoid arithmetic overflows

when computing depth x depth

• Updated WademCsv to use one additional date format string: MM/dd/yyyy
• Bug fix for map plots when input x or y coordinates aren't in ascending order

• Bug fix for TFC depth use x availability not being properly initialized when append mode is used

• Bug fix for Days Since Dry: using short datatype lead to arithmetic overflow when computing

dsd x dsd

• Bug fix for BinaryOperationNetCDF: result was not being checked against fill value before

updating attribute for "max" value

• Bug fix for determining available modeling years when a hydroperiod file is provided

• Append mode implemented: application can resume when new depth days are added without processing

from start of year

• Added spatial plots of NetCDF datasets
• Added Point Extractor tool for extracting specific points from a NetCDF file to CSV
• Added additional attribution in About; attribution in Getting Started and Help
• Better organization of output files into subfolders
• Updated "X" icon in tables

• Initial release includes modeling of temporal and spatial foraging conditions, and breeding conditions
• Additional tools include:
• Multi-year plots - for combining outputs from multiple modeling years into grouped plots
• Hydroperiod creator - for creating custom hydroperiod files using in modeling
• Depth creator - for created depth files from water surfaces and ground elevation
• NcML creator - for creating an "aggregated" depth file from multiple NetCDF files
• Bird parameters editor - for advanced users only