diff --git a/src/imcflibs/imagej/trackmate.py b/src/imcflibs/imagej/trackmate.py index b8a634fc..7f16b325 100644 --- a/src/imcflibs/imagej/trackmate.py +++ b/src/imcflibs/imagej/trackmate.py @@ -236,20 +236,22 @@ def spot_filtering( def set_spotfilter(settings, filter_key, filter_value): - """Sets a TrackMate spot filter with specified filter key and values. + """Set a TrackMate spot filter with specified filter key and values. Parameters ---------- settings : fiji.plugin.trackmate.Settings - Dictionary containing all the settings to use for TrackMate. - filter_name : str - The name of the filter to be applied. You must use the keys of the features, not their name. - Here is the table of the feature keys and names for the spot features: - https://imagej.net/plugins/trackmate/scripting/trackmate-detectors-trackers-keys + Settings object to use for TrackMate. + filter_key : str + The key-name of the filter to be applied (as opposed to the filter + "name" shown in ImageJ. Refer to the spot features table on the related + ImageJ wiki page: + https://imagej.net/plugins/trackmate/scripting/trackmate-detectors-trackers-keys#the-feature-penalty-map filter_value : list - A list containing two values for the filter. The first value is - applied as an above-threshold filter, and the second as a below-threshold filter. - + A list containing two values for the filter. The first value is applied + as an above-threshold filter, and the second as a below-threshold + filter. + Returns ------- Settings @@ -257,10 +259,12 @@ def set_spotfilter(settings, filter_key, filter_value): Example ------- - >>> # Set an above-threshold filter value for spot "QUALITY" without a below-threshold value - >>> tm_settings = set_trackmate_spotfilter(tm_settings, 'QUALITY', [120, None]) + + To set an above-threshold filter value for spot `QUALITY` without a + below-threshold value use: + + >>> settings = set_trackmate_spotfilter(tm_settings, 'QUALITY', [120, None]) """ - settings.addAllAnalyzers() if filter_value[0] != None: filter_low = FeatureFilter(filter_key, filter_value[0], True) @@ -272,7 +276,6 @@ def set_spotfilter(settings, filter_key, filter_value): return settings - def sparse_lap_tracker(settings): """Create a sparse LAP tracker with default settings.