diff --git a/model_server/clients/examples/example_simple_ilastik.py b/model_server/clients/examples/example_simple_ilastik.py deleted file mode 100644 index 3b1ad9f292252f21e640c9a6414fd69b9731deb8..0000000000000000000000000000000000000000 --- a/model_server/clients/examples/example_simple_ilastik.py +++ /dev/null @@ -1,49 +0,0 @@ -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 diff --git a/model_server/clients/ilastik_map_objects_simple.py b/model_server/clients/ilastik_map_objects.py similarity index 100% rename from model_server/clients/ilastik_map_objects_simple.py rename to model_server/clients/ilastik_map_objects.py diff --git a/model_server/clients/imagej/example_simple_ilastik.py b/model_server/clients/imagej/example_simple_ilastik.py deleted file mode 100644 index 4dd5392daf435e5f790f794f3c72a7497700b172..0000000000000000000000000000000000000000 --- a/model_server/clients/imagej/example_simple_ilastik.py +++ /dev/null @@ -1,54 +0,0 @@ -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