Re-merged option to automatically MIP z-stacks sent to ilastik workflow

model_server/base/accessors.py

@@ -38,9 +38,12 @@ class GenericImageDataAccessor(ABC):
     def is_mask(self):
         return is_mask(self._data)
 
-    def get_one_channel_data (self, channel: int):
+    def get_one_channel_data (self, channel: int, mip: bool = False):
         c = int(channel)
-        return InMemoryDataAccessor(self.data[:, :, c:(c+1), :])
+        if mip:
+            return InMemoryDataAccessor(self.data[:, :, c:(c+1), :].max(axis=-1))
+        else:
+            return InMemoryDataAccessor(self.data[:, :, c:(c+1), :])
 
     @property
     def pixel_scale_in_micrometers(self):
@@ -101,7 +104,7 @@ class TifSingleSeriesFileAccessor(GenericImageFileAccessor):
             tf = tifffile.TiffFile(fpath)
             self.tf = tf
         except Exception:
-            FileAccessorError(f'Unable to access data in {fpath}')
+            raise FileAccessorError(f'Unable to access data in {fpath}')
 
         if len(tf.series) != 1:
             raise DataShapeError(f'Expect only one series in {fpath}')

model_server/extensions/ilastik/router.py

@@ -48,7 +48,7 @@ def load_seg_to_obj_model(project_file: str, duplicate: bool = True) -> dict:
     return load_ilastik_model(ilm.IlastikObjectClassifierFromSegmentationModel, project_file, duplicate=duplicate)
 
 @router.put('/pixel_then_object_classification/infer')
-def infer_px_then_ob_maps(px_model_id: str, ob_model_id: str, input_filename: str, channel: int = None) -> dict:
+def infer_px_then_ob_maps(px_model_id: str, ob_model_id: str, input_filename: str, channel: int = None, mip: bool = False) -> dict:
     inpath = session.paths['inbound_images'] / input_filename
     validate_workflow_inputs([px_model_id, ob_model_id], [inpath])
     try:
@@ -57,7 +57,8 @@ def infer_px_then_ob_maps(px_model_id: str, ob_model_id: str, input_filename: st
             session.models[px_model_id]['object'],
             session.models[ob_model_id]['object'],
             session.paths['outbound_images'],
-            channel=channel
+            channel=channel,
+            mip=mip,
         )
     except AssertionError:
         raise HTTPException(f'Incompatible models {px_model_id} and/or {ob_model_id}')

tests/test_accessors.py

@@ -44,6 +44,16 @@ class TestCziImageFileAccess(unittest.TestCase):
         sc = cf.get_one_channel_data(c)
         self.assertEqual(sc.shape, (h, w, 1, nz))
 
+    def test_get_single_channel_mip_from_zstack(self):
+        w = 256
+        h = 512
+        nc = 4
+        nz = 11
+        c = 3
+        cf = InMemoryDataAccessor(np.random.rand(h, w, nc, nz))
+        sc = cf.get_one_channel_data(c, mip=True)
+        self.assertEqual(sc.shape, (h, w, 1, 1))
+
     def test_write_single_channel_tif(self):
         ch = 4
         cf = CziImageFileAccessor(czifile['path'])