Added height, width fields for convenience

model_server/base/roiset.py

@@ -178,6 +178,8 @@ class RoiSet(object):
 
         # compute expanded bounding boxes
         h, w, c, nz = acc_raw.shape
+        df['h'] = df['y1'] - df['y0']
+        df['w'] = df['x1'] - df['x0']
         ebxy, ebz = expand_box_by
         df['ebb_y0'] = (df.y0 - ebxy).apply(lambda x: max(x, 0))
         df['ebb_y1'] = (df.y1 + ebxy).apply(lambda x: min(x, h))
@@ -563,7 +565,7 @@ class RoiSet(object):
 
         # export dataframe and patch masks
         record['dataframe'] = self.export_dataframe(where / 'dataframe' / (prefix + '.csv'))
-        self.export_patch_masks(where / 'patch_masks', prefix=prefix, pad_to=None)
+        self.export_patch_masks(where / 'tight_patch_masks', prefix=prefix, pad_to=None, expanded=False)
 
         for k in params.dict().keys():
             subdir = where / k

tests/test_roiset.py

@@ -45,7 +45,7 @@ class TestRoiSetMonoProducts(BaseTestRoiSetMonoProducts, unittest.TestCase):
         for roi in roiset.get_df().itertuples():
             self.assertEqual(roi.binary_mask.dtype, 'bool')
             sh = roi.binary_mask.shape
-            self.assertEqual(sh, (roi.y1 - roi.y0, roi.x1 - roi.x0))
+            self.assertEqual(sh, (roi.h, roi.w))
             self.assertGreaterEqual(sh[0] * sh[1], roi.area)
 
     def test_roi_zmask(self, **kwargs):
@@ -87,7 +87,7 @@ class TestRoiSetMonoProducts(BaseTestRoiSetMonoProducts, unittest.TestCase):
         for roi in roiset:
             ma = roi.binary_mask
             self.assertEqual(ma.dtype, 'bool')
-            self.assertEqual(ma.shape, (roi.y1 - roi.y0, roi.x1 - roi.x0))
+            self.assertEqual(ma.shape, (roi.h, roi.w))
 
     def test_rel_slices_are_valid(self):
         roiset = self._make_roi_set()
@@ -130,9 +130,7 @@ class TestRoiSetMonoProducts(BaseTestRoiSetMonoProducts, unittest.TestCase):
             roi_q = df.loc[df.label == la, :]
             self.assertEqual(len(roi_q), 1)
             roi = roi_q.iloc[0]
-            h = int(roi.y1 - roi.y0)
-            w = int(roi.x1 - roi.x0)
-            self.assertEqual((h, w), acc.hw)
+            self.assertEqual((roi.h, roi.w), acc.hw)
 
     def test_make_expanded_3d_patches(self):
         roiset = self._make_roi_set()
@@ -218,8 +216,8 @@ class TestRoiSetMonoProducts(BaseTestRoiSetMonoProducts, unittest.TestCase):
             h, w, nc, nz = roi.patch_mask.shape
             self.assertEqual(nc, 1)
             self.assertEqual(nz, 1)
-            self.assertEqual(h, roi.y1 - roi.y0)
-            self.assertEqual(w, roi.x1 - roi.x0)
+            self.assertEqual(h, roi.h)
+            self.assertEqual(w, roi.w)
 
 
 class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCase):
@@ -379,25 +377,22 @@ class TestRoiSetFromZmask(unittest.TestCase):
             output_path / 'roiset_from_3d',
             roiset_test_data['pipeline_params']['segmentation_channel'],
             'ref',
-            params=RoiSetExportParams(patch_masks={'pad_to': 256}, dataframe=True)
+            params=RoiSetExportParams()
         )
         where_df = output_path / 'roiset_from_3d' / 'dataframe' / 'ref.csv'
         self.assertTrue(where_df.exists())
-
         df_test = pd.read_csv(where_df)
 
         # check that patches are correct size
-        where_patch_masks = output_path / 'roiset_from_3d' / 'patch_masks'
+        where_patch_masks = output_path / 'roiset_from_3d' / 'tight_patch_masks'
         for pmf in where_patch_masks.iterdir():
             self.assertTrue(pmf.suffix.upper() == '.PNG')
             la = int(re.search(r'la([\d]+)', str(pmf)).group(1))
             roi_q = df_test.loc[df_test.label == la, :]
             self.assertEqual(len(roi_q), 1)
             roi = roi_q.iloc[0]
-            h = int(roi.y1 - roi.y0)
-            w = int(roi.x1 - roi.x0)
             m_acc = generate_file_accessor(pmf)
-            self.assertEqual((h, w), m_acc.hw)
+            self.assertEqual((roi.h, roi.w), m_acc.hw)
 
 
         # df_test = pd.read_csv(where_df)