Merge branch 'master' into v8

scripts/ExampleScript_1.py → scripts/ExampleScript_ExecTracking.py

@@ -11,6 +11,9 @@
 from fiji.plugin.trackmate.detection import LogDetectorFactory
 from fiji.plugin.trackmate.tracking.jaqaman import SparseLAPTrackerFactory
 from fiji.plugin.trackmate.gui.displaysettings import DisplaySettingsIO
+from fiji.plugin.trackmate.gui.displaysettings.DisplaySettings import TrackMateObject
+from fiji.plugin.trackmate.features.track import TrackIndexAnalyzer
+
 import fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayer as HyperStackDisplayer
 import fiji.plugin.trackmate.features.FeatureFilter as FeatureFilter
 
@@ -105,6 +108,9 @@
 
 # Read the default display settings.
 ds = DisplaySettingsIO.readUserDefault()
+# Color by tracks.
+ds.setTrackColorBy( TrackMateObject.TRACKS, TrackIndexAnalyzer.TRACK_INDEX )
+ds.setSpotColorBy( TrackMateObject.TRACKS, TrackIndexAnalyzer.TRACK_INDEX )
 
 displayer =  HyperStackDisplayer( model, selectionModel, imp, ds )
 displayer.render()

scripts/ExampleScript_ExportToFiles.py

@@ -0,0 +1,158 @@
+from fiji.plugin.trackmate.visualization.hyperstack import HyperStackDisplayer
+from fiji.plugin.trackmate.io import TmXmlReader
+from fiji.plugin.trackmate.io import TmXmlWriter
+from fiji.plugin.trackmate.io import CSVExporter
+from fiji.plugin.trackmate.visualization.table import TrackTableView
+from fiji.plugin.trackmate.action import ExportTracksToXML
+from fiji.plugin.trackmate import Logger
+from java.io import File
+import sys
+
+# We have to do the following to avoid errors with UTF8 chars generated in 
+# TrackMate that will mess with our Fiji Jython.
+reload(sys)
+sys.setdefaultencoding('utf-8')
+
+
+# This script demonstrates several ways by which TrackMate data
+# can be exported to files. Mainly: 1/ to a TrackMate XML file,
+# 2/ & 3/ to CSV files, 4/ to a simplified XML file, for linear tracks.
+
+
+#----------------------------------
+# Loading an example tracking data.
+#----------------------------------
+
+# For this script to work, you need to edit the path to the XML below.
+# It can be any TrackMate file, that we will re-export in the second
+# part of the script.
+
+# Put here the path to the TrackMate file you want to load
+input_filename = '/Users/tinevez/Desktop/FakeTracks.xml'
+input_file = File( input_filename )
+
+# We have to feed a logger to the reader.
+logger = Logger.IJ_LOGGER
+
+reader = TmXmlReader( input_file )
+if not reader.isReadingOk():
+    sys.exit( reader.getErrorMessage() )
+
+# Load the model.
+model = reader.getModel()
+# Load the image and tracking settings.
+imp = reader.readImage()
+settings = reader.readSettings(imp)
+# Load the display settings.
+ds = reader.getDisplaySettings()
+# Load the log.
+log = reader.getLog()
+log = """Hey, I have read this TrackMate file in a Jython 
+script and modified it before resaving it.
+Here is the original log:
+"""  + log
+
+
+#-------------------------------
+# 1/ Resave to a TrackMate file.
+#-------------------------------
+
+# The following will generate a TrackMate XML file.
+# This is the file type you will be able to load with
+# the GUI, using the command 'Plugins > Tracking > Load a TrackMate file'
+# in Fiji.
+
+target_xml_filename = input_filename.replace( '.xml', '-resaved.xml' )
+target_xml_file = File( target_xml_filename )
+writer = TmXmlWriter( target_xml_file, logger )
+
+# Append content. Only the model is mandatory.
+writer.appendLog( log )
+writer.appendModel( model )
+writer.appendSettings( settings )
+writer.appendDisplaySettings( ds )
+
+# We want TrackMate to show the view config panel when 
+# reopening this file.
+writer.appendGUIState( 'ConfigureViews' )
+
+# Actually write the file.
+writer.writeToFile()
+
+
+
+#-------------------------------------------------------
+# 2/ Export spots data to a CSV file in a headless mode.
+#-------------------------------------------------------
+
+# This will export a CSV table containing the spots data. The table will
+# include all spot features, their ID, the track they belong to, name etc.
+# But it will not include the edge and track features. Also if you have
+# splitting and merging events in your data, the content of the CSV file
+# will not be enough to reconstruct the tracks. 
+
+# Nonetheless, the advantage of using this snippet, with the 'CSVExporter'
+# is that it can work in headless mode. It does not depend on Fiji GUI
+# being launched. So you can use it a 'headless' script, called from the 
+# command line. See this page for more information:
+# https://imagej.net/scripting/headless
+
+out_file_csv = input_filename.replace( '.xml', '.csv' )
+only_visible = True # Export only visible tracks
+# If you set this flag to False, it will include all the spots,
+# the ones not in tracks, and the ones not visible.
+CSVExporter.exportSpots( out_file_csv, model, only_visible )
+
+
+
+#----------------------------------------------------
+# 3/ Export spots, edges and track data to CSV files.
+#----------------------------------------------------
+
+# The following uses the tables that are displayed in the TrackMate
+# GUI. As a consequence the snippet cannot be used in 'headless' mode.
+# If you launch the script from the Fiji script editor, we won't
+# have a problem.
+
+# Spot table. Will contain only the spots that are in visible tracks.
+spot_table = TrackTableView.createSpotTable( model, ds )
+spot_table_csv_file = File( input_filename.replace( '.xml', '-spots.csv' ) )
+spot_table.exportToCsv( spot_table_csv_file )
+
+# Edge table.
+edge_table = TrackTableView.createEdgeTable( model, ds )
+edge_table_csv_file = File( input_filename.replace( '.xml', '-edges.csv' ) )
+edge_table.exportToCsv( edge_table_csv_file )
+
+# Track table.
+track_table = TrackTableView.createTrackTable( model, ds )
+track_table_csv_file = File( input_filename.replace( '.xml', '-tracks.csv' ) )
+track_table.exportToCsv( track_table_csv_file )
+
+
+
+#------------------------------------
+# 4/ Export to a simplified XML file.
+#------------------------------------
+
+# During the ISBI Single-Particle Tracking challenge the organizers used
+# a special file format, in a XML fie, to store tracks. Because of the 
+# scope of the challenge, this works well ONLY for linear tracks. That is:
+# tracks that have no merging or splitting events. 
+
+# The file looks like this:
+# <?xml version="1.0" encoding="UTF-8"?>
+# <Tracks nTracks="7" spaceUnits="pixel" frameInterval="1.0" timeUnits="sec" generationDateTime="Tue, 16 Apr 2024 18:36:11" from="TrackMate v7.12.2-SNAPSHOT-4a56a0a4e34f1590f1acc341368f2fcf336e1c80">
+#   <particle nSpots="49">
+#     <detection t="0" x="116.25803433315897" y="118.01058828304035" z="0.0" />
+#     <detection t="1" x="116.35642718798508" y="117.70622315532961" z="0.0" />
+#     <detection t="2" x="116.46312406173281" y="117.69830578342241" z="0.0" />
+#     <detection t="3" x="116.3916284518453" y="117.58156664808513" z="0.0" />
+# etc.
+
+# In this folder, the MATLAB script 'importTrackMateTracks.m' can open such a file
+# in MATLAB. But of course, it is not a TrackMate file that TrackMate can open.
+
+simple_xml_file = File( input_filename.replace( '.xml', '-simple-tracks.xml' ) )
+ExportTracksToXML.export( model, settings, simple_xml_file )
+

scripts/ExampleScript_3.py → scripts/ExampleScript_GetTrackingData.py

@@ -25,6 +25,12 @@
 imp.show()
 
 
+# This script demonstrates how to query the data model for specific
+# numerical values: how to get the position of a spot in a script, 
+# how to get the content of a track, etc. In this script, we just 
+# output some values to the IJ log window.
+
+
 #-------------------------
 # Instantiate model object
 #-------------------------

scripts/ExampleScript_2.py → scripts/ExampleScript_ReadTrackMateFile.py

@@ -57,8 +57,8 @@
 # A selection.
 sm = SelectionModel( model )
 
-# Read the default display settings.
-ds = DisplaySettingsIO.readUserDefault()
+# Read the display settings that was saved in the file.
+ds = reader.getDisplaySettings()
 
 # The viewer.
 displayer =  HyperStackDisplayer( model, sm, ds ) 

src/main/java/fiji/plugin/trackmate/LoadTrackMatePlugIn.java

@@ -8,12 +8,12 @@
  * it under the terms of the GNU General Public License as
  * published by the Free Software Foundation, either version 3 of the
  * License, or (at your option) any later version.
- * 
+ *
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- * 
+ *
  * You should have received a copy of the GNU General Public
  * License along with this program.  If not, see
  * <http://www.gnu.org/licenses/gpl-3.0.html>.
@@ -138,10 +138,16 @@ public void run( final String filePath )
 		 * Read settings.
 		 */
 
-		final Settings settings = reader.readSettings( imp );
+		Settings settings = reader.readSettings( imp );
 		if ( !reader.isReadingOk() )
 			logger.error( "Problem reading the settings:\n" + reader.getErrorMessage() );
 
+		if ( settings == null )
+		{
+			logger.error( "Problem reading the settings:\n" + "The file did not contain a settings element. Using default values." );
+			settings = new Settings( imp );
+		}
+
 		/*
 		 * Declare the analyzers that are in the settings to the model. This is
 		 * required when we are loading a file that does not have the analyzer

src/main/java/fiji/plugin/trackmate/io/TmXmlReader.java

@@ -8,12 +8,12 @@
  * it under the terms of the GNU General Public License as
  * published by the Free Software Foundation, either version 3 of the
  * License, or (at your option) any later version.
- * 
+ *
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- * 
+ *
  * You should have received a copy of the GNU General Public
  * License along with this program.  If not, see
  * <http://www.gnu.org/licenses/gpl-3.0.html>.
@@ -446,6 +446,8 @@ public Settings readSettings( final ImagePlus imp )
 	/**
 	 * Reads the settings element of the file, and sets the fields of the
 	 * specified {@link Settings} object according to the xml file content.
+	 * Returns <code>null</code> if the settings element cannot be found in the
+	 * file.
 	 *
 	 * @param imp
 	 *            the image to store in the new Settings object.