Still drafting ImageJ-side client

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
 
 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
@@ -13,12 +19,12 @@ PIXEL_CLASSIFIER_PATH = "D:/DATA/TREC_STOP_15_Kristineberg/Vincent/230805_automi
 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)
+# HOST = '127.0.0.1'
+# PORT = 8001
+# uri = 'http://{}:{}/'.format(HOST, PORT)
 
 abspath = IJ.getImage().getProp('Location')
-input_filename = os.path.split(abspath)[-1]
+# input_filename = os.path.split(abspath)[-1]
 
 channel = 0
 pixel_classifier = 'demo_px.ilp'

clients/imagej/zstack_to_ilastik.py

+from pathlib import Path
+
 from clients.imagej.client import hit_endpoint
 
 from ij import IJ
+from ij import ImagePlus
 
-def setup(pixel_classifier, object_classifier, input_path):
+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:
+    :return: ImagePlus
     """
-    result = []
-    # configure input path - no endpoint yet
+    # get info from input ImagePlus
+    abspath = Path(imp.getProp('Location'))
+    image_directory = abspath.parent
+    input_filename = abspath.name
 
-    # configure output path - no endpoint yet
+    # configure input and output paths
+    resp = hit_endpoint(
+        'PUT',
+        '/paths/watch_input',
+        {
+            'path': image_directory,
+        }
+    )
+    assert resp.status_code == 200, 'Error setting up image directory'
+    resp = hit_endpoint(
+        'PUT',
+        '/paths/watch_output',
+        {
+            'path': image_directory,
+        }
+    )
+    assert resp.status_code == 200, 'Error setting up image directory'
 
-    # load pixel classifier first time only
+    # load pixel classifier
     resp = hit_endpoint(
         'PUT',
-        '/models/ilastik/pixel_classification/load/',
+        '/ilastik/pixel_classification/load/',
         {
-            'project_file': pixel_classifier,
+            'project_file': px_ilp,
             'duplicate': False,
         },
     )
-    result['pxmid'] = resp['model_id']
+    assert resp.status_code == 200, 'Error loading pixel classifier: ' + {px_ilp}
+    id_px_mod = resp['model_id']
+
 
     # load pixel classifier first time only
     resp = hit_endpoint(
-        'PUT', '/models/ilastik/object_classification/load/',
+        'PUT', '/ilastik/object_classification/load/',
         {
-            'project_file': object_classifier,
+            'project_file': ob_ilp,
             'duplicate': False,
         },
     )
-    result['obmid'] = resp['model_id']
-    resp = hit_endpoint('GET', '/models', verbose=True)
-    return result
+    assert resp.status_code == 200, 'Error loading object classifier: ' + {ob_ilp}
+    id_ob_mod = resp['model_id']
 
-def get_object_map(pixel_classifier, object_classifier, input_path, input_filename, channel):
-    """
+    return id_px_mod, id_ob_mod
 
-    :param pixel_classifier: (str)
-    :param object_classifier: (str)
-    :return:
-    """
-    # eventually split this off
-    ids = setup(pixel_classifier, object_classifier, input_path)
 
+    # run inference
     resp = hit_endpoint(
         'PUT',
         '/chaeo/classify_zstack/infer',
         {
-            'px_model_id': ids['pxmid']
-            'ob_model_id': ids['obmid'],
+            'px_model_id': id_px_mod
+            'ob_model_id': id_ob_mod,
             'input_filename': input_filename,
-            'channel': channel
+            'pxmap_threshold': pxmap_threshold,
+            'pxmap_foreground_channel': pxmap_foreground_channel,
+            'segmentation_channel': segmentation_channel,
+            'patches_channel': patches_channel,
+            'zmask_filters': zmask_filters,
         }
     )
-    imp =
+    assert resp.status_code == 200, 'Error calling workfow'
 
     return IJ.ImagePlus()
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