By default, return non-expanded patches and masks; allow contour and mask...

By default, return non-expanded patches and masks; allow contour and mask overlays in non-expanded patches

model_server/base/roiset.py

@@ -200,7 +200,7 @@ class RoiSet(object):
 
         df['slice'] = df.apply(
             lambda r:
-            np.s_[int(r.y0): int(r.y1), int(r.x0): int(r.x1), :, int(r.zi): int(r.zi + 1) + 1],
+            np.s_[int(r.y0): int(r.y1), int(r.x0): int(r.x1), :, int(r.zi): int(r.zi + 1)],
             axis=1
         )
         df['expanded_slice'] = df.apply(
@@ -279,14 +279,12 @@ class RoiSet(object):
             projected = self.acc_raw.data.max(axis=-1)
         return projected
 
-    # TODO: rename get_patches_acc
-    def get_raw_patches(self, channel=None, pad_to=256, make_3d=False):  # padded, un-annotated 2d patches
+    def get_patches_acc(self, channel=None, **kwargs):  # padded, un-annotated 2d patches
         if channel:
-            patches_df = self.get_patches(white_channel=channel, pad_to=pad_to)
+            patches_df = self.get_patches(white_channel=channel, **kwargs)
         else:
-            patches_df = self.get_patches(pad_to=pad_to)
-        patches = list(patches_df['patch'])
-        return PatchStack(patches)
+            patches_df = self.get_patches(**kwargs)
+        return PatchStack(list(patches_df.patch))
 
     def export_annotated_zstack(self, where, prefix='zstack', **kwargs) -> Path:
         annotated = InMemoryDataAccessor(draw_boxes_on_3d_image(self, **kwargs))
@@ -335,8 +333,8 @@ class RoiSet(object):
 
         # do this on a patch basis, i.e. only one object per frame
         obmap_patches = object_classification_model.label_patch_stack(
-            self.get_raw_patches(channel=channel, pad_to=256),
-            self.get_patch_masks_acc(expanded=True, pad_to=256)
+            self.get_patches_acc(channel=channel, expaned=False, pad_to=None),
+            self.get_patch_masks_acc(expanded=False, pad_to=None)
         )
 
         om = np.zeros(self.acc_obj_ids.shape, self.acc_obj_ids.dtype)
@@ -419,13 +417,13 @@ class RoiSet(object):
     def get_patches(
             self,
             rescale_clip: float = 0.0,
-            pad_to: int = 256,
+            pad_to: int = None,
             make_3d: bool = False,
             focus_metric: str = None,
             rgb_overlay_channels: list = None,
             rgb_overlay_weights: list = [1.0, 1.0, 1.0],
             white_channel: int = None,
-            expanded=True,
+            expanded=False,
             **kwargs
     ) -> pd.DataFrame:
 
@@ -503,6 +501,12 @@ class RoiSet(object):
 
             assert len(patch.shape) == 4
 
+            mask = np.zeros(patch3d.shape[0:2], dtype=bool)
+            if expanded:
+                mask[roi.relative_slice[0:2]] = roi.binary_mask
+            else:
+                mask = roi.binary_mask
+
             if rescale_clip is not None:
                 patch = rescale(patch, rescale_clip)
 
@@ -520,15 +524,15 @@ class RoiSet(object):
 
             if kwargs.get('draw_mask'):
                 mci = kwargs.get('mask_channel', 0)
-                mask = np.zeros(patch.shape[0:2], dtype=bool)
-                mask[roi.relative_slice[0:2]] = roi.binary_mask
+                # mask = np.zeros(patch.shape[0:2], dtype=bool)
+                # mask[roi.relative_slice[0:2]] = roi.binary_mask
                 for zi in range(0, patch.shape[3]):
                     patch[:, :, mci, zi] = np.invert(mask) * patch[:, :, mci, zi]
 
             if kwargs.get('draw_contour'):
                 mci = kwargs.get('contour_channel', 0)
-                mask = np.zeros(patch.shape[0:2], dtype=bool)
-                mask[roi.relative_slice[0:2]] = roi.binary_mask
+                # mask = np.zeros(patch.shape[0:2], dtype=bool)
+                # mask[roi.relative_slice[0:2]] = roi.binary_mask
 
                 for zi in range(0, patch.shape[3]):
                     patch[:, :, mci, zi] = draw_contours_on_patch(

model_server/extensions/ilastik/tests/test_ilastik.py

@@ -329,8 +329,8 @@ class TestIlastikObjectClassification(unittest.TestCase):
 
 
     def test_classify_patches(self):
-        raw_patches = self.roiset.get_raw_patches()
-        patch_masks = self.roiset.get_patch_masks()
+        raw_patches = self.roiset.get_patches_acc()
+        patch_masks = self.roiset.get_patch_masks_acc()
         res_patches = self.object_classifier.label_instance_class(raw_patches, patch_masks)
         self.assertEqual(res_patches.count, self.roiset.count)
         res_patches.export_pyxcz(output_path / 'res_patches.tif')

tests/test_roiset.py

@@ -105,7 +105,8 @@ class TestRoiSetMonoProducts(BaseTestRoiSetMonoProducts, unittest.TestCase):
         files = roiset.export_patches(
             output_path / 'expanded_2d_patches',
             draw_bounding_box=True,
-            expanded=True
+            expanded=True,
+            pad_to=256,
         )
         df = roiset.get_df()
         for f in files:
@@ -113,9 +114,6 @@ class TestRoiSetMonoProducts(BaseTestRoiSetMonoProducts, unittest.TestCase):
             la = int(re.search(r'la([\d]+)', str(f)).group(1))
             roi_q = df.loc[df.label == la, :]
             self.assertEqual(len(roi_q), 1)
-            roi = roi_q.iloc[0]
-            h = int(roi.ebb_y1 - roi.ebb_y0)
-            w = int(roi.ebb_x1 - roi.ebb_x0)
             self.assertEqual((256, 256), acc.hw)
 
     def test_make_tight_2d_patches(self):
@@ -201,10 +199,11 @@ class TestRoiSetMonoProducts(BaseTestRoiSetMonoProducts, unittest.TestCase):
 
     def test_raw_patches_are_correct_shape(self):
         roiset = self._make_roi_set()
-        patches = roiset.get_raw_patches()
+        patches = roiset.get_patches_acc()
         np, h, w, nc, nz = patches.shape
         self.assertEqual(np, roiset.count)
         self.assertEqual(nc, roiset.acc_raw.chroma)
+        self.assertEqual(nz, 1)
 
     def test_patch_masks_are_correct_shape(self):
         roiset = self._make_roi_set()