Added ImageJ example

model_server/clients/imagej/example_simple_ilastik.py

+import os
+import sys
+
+from ij import IJ
+from ij.plugin.filter import ParticleAnalyzer
+from ij.plugin.frame import Recorder, RoiManager
+
+sys.path.append(
+	os.path.join(
+		os.path.expanduser('~'), 'model_server', 'source', 'model_server', 'clients'
+	)
+)
+
+from imagej.adapter import run_request_sequence
+import ilastik_map_objects_simple
+from ij import IJ
+
+params = {
+	'pixel_classifier_path': 'c:/Users/rhodes/projects/proj0011-plankton-seg/exp0019/px-03.ilp',
+	'object_classifier_path': 'c:/Users/rhodes/projects/proj0011-plankton-seg/exp0019/obj-07.ilp',
+	'debug': True,
+	'channel': 4,  # zero-index
+	'object_class': 3
+}
+
+IJ.run('Remove Overlay')
+imp_czi = IJ.getImage()
+
+imp_obmap = run_request_sequence(
+	imp_czi,
+	ilastik_map_objects_simple.main,
+	params,
+)
+
+# transfer objects of specified class to image's overlay
+imp_obmap.show()
+IJ.run(imp_obmap, "glasbey on dark", "")
+IJ.setThreshold(imp_obmap, params['object_class'], params['object_class'])
+rm = RoiManager.getRoiManager()
+Recorder.setBlackBackground()
+imp_obmap.createThresholdMask()
+rm.reset()
+IJ.run(imp_obmap, "Analyze Particles...", "display exclude clear include add") 
+rm.run('Show All')
+
+rm.moveRoisToOverlay(imp_czi)
+if not params['debug']:
+	imp_obmap.close()
+imp_czi.show()
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