Example script that demonstrates how to export to other file formats.

scripts/ExampleScript_ExportToFiles.py

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+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 )
+