Started editing in ImageJ script editor

clients/imagej/client.py

@@ -6,7 +6,7 @@ import sys
 print(sys.version)
 
 HOST = '127.0.0.1'
-PORT = 8001
+PORT = 8000
 uri = 'http://{}:{}/'.format(HOST, PORT)
 
 def hit_endpoint(method, endpoint, params=None, verbose=False):

clients/imagej/example.py

-# example top-level script in ImageJ
-
-
-#
-# add scripts dir to python path
-#
-from clients.imagej.zstack_to_ilastik import get_object_map
+import os
+import sys
 
 from ij import IJ
 
-
-
-CHANNEL_TO_ILASTIK = 1 # i.e. index of color channel from confocal stack
-CHANNEL_CHLOROPHYL = 4
-OBJECT_CLASS_FOR_PHOTOACTIVATION = 1
-CHLOROPHYL_THRESHOLD = 0.000 # minimum percent of ROI that should contain chlorophyl
-ILASTIK_PATH = "C:/Program Files/ilastik-1.4.0/ilastik.exe"
-PIXEL_CLASSIFIER_PATH = "D:/DATA/TREC_STOP_15_Kristineberg/Vincent/230805_automic_AI_PA/ilastik/pix.ilp"
-OBJECT_CLASSIFIER_PATH = "D:/DATA/TREC_STOP_15_Kristineberg/Vincent/230805_automic_AI_PA/ilastik/obj.ilp"
-DEBUG = True
-
-# HOST = '127.0.0.1'
-# PORT = 8001
-# uri = 'http://{}:{}/'.format(HOST, PORT)
-
-abspath = IJ.getImage().getProp('Location')
-# input_filename = os.path.split(abspath)[-1]
-
-channel = 0
-pixel_classifier = 'demo_px.ilp'
-object_classifier = 'demo_ob.ilp'
-outpath = 'C:\\Users\\rhodes\\projects\\proj0015-model-server\\resources\\testdata'
-
-
-get_object_map(...)
-
-# pipeline: remove any existing overlay
-IJ.run("Remove Overlay")
-
-imp_czi = IJ.getImage()
-czi_fn = imp_czi.getTitle()
-czi_desc = czi_fn.split('.')[0]
-imp_czi.setDisplayMode(IJ.GRAYSCALE)
-IJ.run("Make Subset...", "channels=" + CHANNEL_TO_ILASTIK)
-imp_to_ilastik = IJ.getImage()
+# add directory of current script to search path
+scripts_dir = os.path.dirname(sys.argv[0])
+sys.path.append(scripts_dir) 
+
+from ilastik_obmaps import ilastik_map_objects_simple
+
+CHANNEL_TO_ILASTIK = 1 # i.e. index of color channel from confocal stack
+OBJECT_CLASS_FOR_PHOTOACTIVATION = 1
+ROOT = 'c:/Users/rhodes/projects/proj0004-marine-photoactivation/data/exp0021/'
+PIXEL_CLASSIFIER_PATH = ROOT + 'ilastik/px-01.ilp'
+OBJECT_CLASSIFIER_PATH = ROOT + 'ilastik/obj-04.ilp'
+DEBUG = True
+
+#obmap = ilastik_map_objects_simple(
+#    IJ.getImage(),
+#    PIXEL_CLASSIFIER_PATH,
+#    OBJECT_CLASSIFIER_PATH,
+#    CHANNEL_TO_ILASTIK
+#)
+
+# pipeline: remove any existing overlay
+IJ.run("Remove Overlay")
+
+resp = hit_endpoint(
+    'GET',
+    '/ilastik/pixel_then_object_classification/infer',
+    {
+        'px_model_id': id_px_mod,
+        'ob_model_id': id_ob_mod,
+        'input_filename': basename(abspath),
+        'channel': channel,
+    }
+)
+
+
+imp_czi = IJ.getImage()
+#czi_fn = imp_czi.getTitle()
+#czi_desc = czi_fn.split('.')[0]
+#imp_czi.setDisplayMode(IJ.GRAYSCALE)
+IJ.run("Make Subset...", "channels=" + str(CHANNEL_TO_ILASTIK))
+imp_to_ilastik = IJ.getImage()
+
+#obmap = ilastik_map_objects_simple(
+#    imp_to_ilastik,
+#    PIXEL_CLASSIFIER_PATH,
+#    OBJECT_CLASSIFIER_PATH,
+#    CHANNEL_TO_ILASTIK
+#)

clients/imagej/zstack_to_ilastik.py → clients/imagej/ilastik_obmaps.py

-from pathlib import Path
-
-from clients.imagej.client import hit_endpoint
+from client import hit_endpoint
+from os.path import basename, dirname
 
 from ij import IJ
 from ij import ImagePlus
 
-def get_object_map(imp, px_ilp, ob_ilp, pxmap_threshold, pxmap_foreground_channel, segmentation_channel, patches_channel, zmask_filters):
-    """
-
-    :param pixel_classifier: (str)
-    :param object_classifier: (str)
-    :return: ImagePlus
-    """
-    # get info from input ImagePlus
-    abspath = Path(imp.getProp('Location'))
-    image_directory = abspath.parent
-    input_filename = abspath.name
-
+def setup(where, px_ilp):
     # configure input and output paths
     resp = hit_endpoint(
         'PUT',
         '/paths/watch_input',
         {
-            'path': image_directory,
+            'path': where,
         }
     )
     assert resp.status_code == 200, 'Error setting up image directory'
@@ -30,7 +18,7 @@ def get_object_map(imp, px_ilp, ob_ilp, pxmap_threshold, pxmap_foreground_channe
         'PUT',
         '/paths/watch_output',
         {
-            'path': image_directory,
+            'path': where,
         }
     )
     assert resp.status_code == 200, 'Error setting up image directory'
@@ -45,12 +33,25 @@ def get_object_map(imp, px_ilp, ob_ilp, pxmap_threshold, pxmap_foreground_channe
         },
     )
     assert resp.status_code == 200, 'Error loading pixel classifier: ' + {px_ilp}
-    id_px_mod = resp['model_id']
+    return resp['model_id']
+
+
+def ilastik_map_objects_simple(imp, px_ilp, ob_ilp, channel):
+    """
 
+    :param pixel_classifier: (str)
+    :param object_classifier: (str)
+    :return: ImagePlus
+    """
+    # get info from input ImagePlus
+    abspath = imp.getProp('Location')
 
-    # load pixel classifier first time only
+    # assert imp is not z-stack
+    id_px_mod = setup(dirname(abspath), px_ilp)
+
+    # load object classifier
     resp = hit_endpoint(
-        'PUT', '/ilastik/object_classification/load/',
+        'PUT', '/ilastik/pxmap_to_obj/load/',
         {
             'project_file': ob_ilp,
             'duplicate': False,
@@ -59,17 +60,54 @@ def get_object_map(imp, px_ilp, ob_ilp, pxmap_threshold, pxmap_foreground_channe
     assert resp.status_code == 200, 'Error loading object classifier: ' + {ob_ilp}
     id_ob_mod = resp['model_id']
 
-    return id_px_mod, id_ob_mod
+    # run inference
+    resp = hit_endpoint(
+        'PUT',
+        '/ilastik/pixel_then_object_classification/infer',
+        {
+            'px_model_id': id_px_mod,
+            'ob_model_id': id_ob_mod,
+            'input_filename': basename(abspath),
+            'channel': channel,
+        }
+    )
+    assert resp.status_code == 200, 'Error calling workfow'
+    obmap = resp.json()['object_map_filepath']
+
+    return obmap # obviously need imp
+
+def ilastik_map_objects_with_zmask(imp, px_ilp, ob_ilp, pxmap_threshold, pxmap_foreground_channel, segmentation_channel, patches_channel, zmask_filters):
+    """
+
+    :param pixel_classifier: (str)
+    :param object_classifier: (str)
+    :return: ImagePlus
+    """
+    # get info from input ImagePlus
+    abspath = imp.getProp('Location')
+
+    # assert imp is not z-stack
+    id_px_mod = setup(dirname(abspath), px_ilp)
 
+    # load object classifier
+    resp = hit_endpoint(
+        'PUT', '/ilastik/seg_to_obj/load/',
+        {
+            'project_file': ob_ilp,
+            'duplicate': False,
+        },
+    )
+    assert resp.status_code == 200, 'Error loading object classifier: ' + {ob_ilp}
+    id_ob_mod = resp['model_id']
 
     # run inference
     resp = hit_endpoint(
         'PUT',
         '/chaeo/classify_zstack/infer',
         {
-            'px_model_id': id_px_mod
+            'px_model_id': id_px_mod,
             'ob_model_id': id_ob_mod,
-            'input_filename': input_filename,
+            'input_filename': basename(abspath),
             'pxmap_threshold': pxmap_threshold,
             'pxmap_foreground_channel': pxmap_foreground_channel,
             'segmentation_channel': segmentation_channel,
@@ -78,5 +116,6 @@ def get_object_map(imp, px_ilp, ob_ilp, pxmap_threshold, pxmap_foreground_channe
         }
     )
     assert resp.status_code == 200, 'Error calling workfow'
+    obmap = resp.json()['output_path']
 
-    return IJ.ImagePlus()
\ No newline at end of file
+    return obmap # obviously need imp