Removed min_sobel, which was there for debugging

model_server/base/roiset.py

@@ -945,7 +945,7 @@ class RoiSet(object):
             ph, pw, pc, pz = patch3d.shape
 
             # make a 3d patch
-            if make_3d or not expanded:
+            if make_3d:
                 patch = patch3d
 
             # make a 2d patch, find optimal z-position determined by focus_metric function on each channel separately
@@ -1166,7 +1166,7 @@ class RoiSet(object):
         def _poly_from_mask(roi):
             mask = roi.binary_mask
             if len(mask.shape) != 2:
-                raise PatchMaskShapeError(f'Patch mask needs to be two dimensions to fit a polygon')
+                raise PatchShapeError(f'Patch mask needs to be two dimensions to fit a polygon')
 
             # label and fill holes
             labeled = label(mask)
@@ -1402,7 +1402,7 @@ class MissingSegmentationError(Error):
     pass
 
 
-class PatchMaskShapeError(Error):
+class PatchShapeError(Error):
     pass
 
 

tests/base/test_roiset.py

@@ -125,6 +125,7 @@ class TestRoiSetMonoProducts(BaseTestRoiSetMonoProducts, unittest.TestCase):
             draw_bounding_box=True,
             expanded=True,
             pad_to=256,
+            make_3d=False,
         )
         df = roiset.get_df()
         for f in se_res:
@@ -133,6 +134,7 @@ class TestRoiSetMonoProducts(BaseTestRoiSetMonoProducts, unittest.TestCase):
             roi_q = df.loc[df.label == la, :]
             self.assertEqual(len(roi_q), 1)
             self.assertEqual((256, 256), acc.hw)
+            self.assertEqual(1, acc.nz)
 
     def test_make_tight_2d_patches(self):
         roiset = self._make_roi_set()
@@ -140,7 +142,7 @@ class TestRoiSetMonoProducts(BaseTestRoiSetMonoProducts, unittest.TestCase):
         se_res = roiset.export_patches(
             where,
             draw_bounding_box=True,
-            expanded=False
+            expanded=False,
         )
         df = roiset.get_df()
         for f in se_res:  # all exported files are same shape as bounding boxes in RoiSet's datatable
@@ -150,6 +152,7 @@ class TestRoiSetMonoProducts(BaseTestRoiSetMonoProducts, unittest.TestCase):
             self.assertEqual(len(roi_q), 1)
             roi = roi_q.iloc[0]
             self.assertEqual((roi.h, roi.w), acc.hw)
+            self.assertEqual(1, acc.nz)
 
     def test_make_expanded_3d_patches(self):
         roiset = self._make_roi_set()