Merge branch 'dev_connectivity_patch_obmaps' into 'staging'

Connectivity of labeling

See merge request !44

model_server/base/accessors.py

@@ -73,6 +73,9 @@ class GenericImageDataAccessor(ABC):
     def dtype(self):
         return self.data.dtype
 
+    def write(self, fp: Path, mkdir=True):
+        write_accessor_data_to_file(fp, self, mkdir=mkdir)
+
     def get_axis(self, ch):
         return self.axes.index(ch.upper())
 
@@ -122,6 +125,10 @@ class GenericImageFileAccessor(GenericImageDataAccessor): # image data is loaded
             raise FileAccessorError(f'Could not find file at {fpath}')
         self.fpath = fpath
 
+    @staticmethod
+    def read(fp: Path):
+        return generate_file_accessor(fp)
+
 class TifSingleSeriesFileAccessor(GenericImageFileAccessor):
     def __init__(self, fpath: Path):
         super().__init__(fpath)

model_server/base/roiset.py

@@ -73,14 +73,18 @@ def _get_label_ids(acc_seg_mask: GenericImageDataAccessor, allow_3d=False, conne
     """
     if allow_3d and connect_3d:
         nda_la = label(
-            acc_seg_mask.data[:, :, 0, :]
+            acc_seg_mask.data[:, :, 0, :],
+            connectivity=3,
         ).astype('uint16')
         return InMemoryDataAccessor(np.expand_dims(nda_la, 2))
     elif allow_3d and not connect_3d:
         nla = 0
         la_3d = np.zeros((*acc_seg_mask.hw, 1, acc_seg_mask.nz), dtype='uint16')
         for zi in range(0, acc_seg_mask.nz):
-            la_2d = label(acc_seg_mask.data[:, :, 0, zi]).astype('uint16')
+            la_2d = label(
+                acc_seg_mask.data[:, :, 0, zi],
+                connectivity=2,
+            ).astype('uint16')
             la_2d[la_2d > 0] = la_2d[la_2d > 0] + nla
             nla = la_2d.max()
             la_3d[:, :, 0, zi] = la_2d
@@ -88,7 +92,8 @@ def _get_label_ids(acc_seg_mask: GenericImageDataAccessor, allow_3d=False, conne
     else:
         return InMemoryDataAccessor(
             label(
-                acc_seg_mask.data[:, :, 0, :].max(axis=-1)
+                acc_seg_mask.data[:, :, 0, :].max(axis=-1),
+                connectivity=1,
             ).astype('uint16')
         )
 

tests/test_roiset.py

@@ -455,7 +455,6 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
             self.assertTrue(pa.exists())
             pacc = generate_file_accessor(pa)
             self.assertEqual(pacc.hw, (256, 256))
-        print('res')
 
     def test_run_export_mono_2d_patch(self):
         p = RoiSetExportParams(**{