Reorganzed ImageJ example to exist outside this codebase

model_server/clients/examples/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': 'z:/pepperkok/rhodes/projects/proj0011-plankton-seg/exp0019/px-03.ilp',
-	'object_classifier_path': 'z:/pepperkok/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()
\ No newline at end of file

model_server/clients/imagej/example_simple_ilastik.py

-from os.path import join, expanduser
-
-# top-level directory <user>/model_server that contains codebase
-root = join(expanduser('~'), 'model_server')
-
-# USER: change this to look for ilastik models in some place other than <user>/model_server/ilastik
-classifier_directory = join(root, 'ilastik')
-
-# USER: set filenames and channels to build ilastik pipeline
-params = {
-	'pixel_classifier': 'px-03.ilp',
-	'object_classifier': 'obj-07.ilp',
-	'debug': True,
-	'channel': 4,  # zero-index
-	'object_class': 3
-}
-
-# load ImageJ API then Jython dependencies that are maintained in model_server codebase
-import sys
-from ij import IJ
-from ij.plugin.frame import Recorder, RoiManager
-
-sys.path.append(join(root, 'source', 'model_server', 'clients'))
-from imagej.adapter import run_request_sequence
-import ilastik_map_objects_simple
-
-# call the server to run ilastik analysis
-params['pixel_classifier_path'] = join(classifier_directory, params['pixel_classifier'])
-params['object_classifier_path'] = join(classifier_directory, params['object_classifier'])
-
-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()
\ No newline at end of file