ilastik prereqs run now

extensions/chaeo/conf/testing.py

@@ -13,3 +13,10 @@ multichannel_zstack = {
 pixel_classifier = {
     'path': root / 'ilastik' / 'AF405-bodies_boundaries.ilp'
 }
+
+pipeline_params = {
+    'threshold': 0.6,
+}
+
+output_path = root / 'testing_output' / 'chaeo'
+output_path.mkdir(parents=True, exist_ok=True)
\ No newline at end of file

extensions/chaeo/test_zstack.py

 import unittest
 
-from extensions.chaeo.conf.testing import multichannel_zstack, pixel_classifier
+from conf.testing import output_path
+
+from extensions.chaeo.conf.testing import multichannel_zstack, pixel_classifier, pipeline_params
 from extensions.chaeo.zstack import build_stack_mask
-from model_server.accessors import generate_file_accessor, InMemoryDataAccessor
+from model_server.accessors import generate_file_accessor, InMemoryDataAccessor, write_accessor_data_to_file
 from extensions.ilastik.models import IlastikObjectClassifierModel, IlastikPixelClassifierModel
 
 class TestZStackDerivedDataProducts(unittest.TestCase):
@@ -12,11 +14,14 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
         self.zstack = generate_file_accessor(multichannel_zstack['path'])
 
         pxmodel = IlastikPixelClassifierModel(
-            project_file=pixel_classifier['path']
+            {'project_file': pixel_classifier['path']},
         )
-        self.pxmap = None
-        self.obmap = None
-        self.stack = None
+        mip = InMemoryDataAccessor(self.zstack.get_one_channel_data(channel=0).data.max(axis=-1, keepdims=True))
+        self.pxmap, result = pxmodel.infer(mip)
+
+        write_accessor_data_to_file(output_path / 'pxmap.tif', self.pxmap)
+        self.obmap = InMemoryDataAccessor((self.pxmap.data > pipeline_params['threshold']).astype('uint8'))
+        write_accessor_data_to_file(output_path / 'obmap.tif', self.obmap)
 
     def test_zmask_makes_correct_boxes(self):
         zmask, meta = build_stack_mask(