Merge pull request #203 from mzouink/main

Raise informative error if padding mode is not a valid option

gunpowder/contrib/nodes/add_vector_map.py

@@ -215,9 +215,9 @@ def __get_vector_map(self, batch, request, vector_map_array_key):
                     if num_src_vectors_per_trg_loc > 0:
                         dist_to_locs = {}
                         for phys_loc in relevant_partner_loc:
-                            dist_to_locs[
-                                np.linalg.norm(node.location - phys_loc)
-                            ] = phys_loc
+                            dist_to_locs[np.linalg.norm(node.location - phys_loc)] = (
+                                phys_loc
+                            )
                         for nr, dist in enumerate(
                             reversed(np.sort(list(dist_to_locs.keys())))
                         ):

gunpowder/nodes/defect_augment.py

@@ -159,9 +159,11 @@ def prepare(self, request):
             logger.debug("before growth: %s" % spec.roi)
             growth = Coordinate(
                 tuple(
-                    0
-                    if d == self.axis
-                    else raw_voxel_size[d] * self.deformation_strength
+                    (
+                        0
+                        if d == self.axis
+                        else raw_voxel_size[d] * self.deformation_strength
+                    )
                     for d in range(spec.roi.dims)
                 )
             )
@@ -267,9 +269,11 @@ def process(self, batch, request):
             old_roi = request[self.intensities].roi
             logger.debug("resetting roi to %s" % old_roi)
             crop = tuple(
-                slice(None)
-                if d == self.axis
-                else slice(self.deformation_strength, -self.deformation_strength)
+                (
+                    slice(None)
+                    if d == self.axis
+                    else slice(self.deformation_strength, -self.deformation_strength)
+                )
                 for d in range(raw.spec.roi.dims)
             )
             raw.data = raw.data[crop]

gunpowder/nodes/pad.py

@@ -44,6 +44,11 @@ def __init__(self, key, size, mode="constant", value=None):
         self.key = key
         self.size = size
         self.mode = mode
+        if self.mode not in ["constant", "reflect"]:
+            raise ValueError(
+                "Invalid padding mode %s provided. Must be 'constant' or 'reflect'."
+                % self.mode
+            )
         self.value = value
 
     def setup(self):
@@ -129,8 +134,13 @@ def __expand(self, a, from_roi, to_roi, value):
         lower_pad = from_roi.begin - to_roi.begin
         upper_pad = to_roi.end - from_roi.end
         pad_width = [(0, 0)] * num_channels + list(zip(lower_pad, upper_pad))
-        if self.mode == "constant":
-            padded = np.pad(a, pad_width, "constant", constant_values=value)
-        elif self.mode == "reflect":
+        if self.mode == "reflect":
             padded = np.pad(a, pad_width, "reflect")
+        elif self.mode == "constant":
+            padded = np.pad(a, pad_width, "constant", constant_values=value)
+        else:
+            raise ValueError(
+                "Invalid padding mode %s provided. Must be 'constant' or 'reflect'."
+                % self.mode
+            )
         return padded

gunpowder/nodes/simple_augment.py

@@ -203,9 +203,11 @@ def process(self, batch, request):
                 location_in_total_offset = np.asarray(node.location) - total_roi_offset
                 node.location = np.asarray(
                     [
-                        total_roi_end[dim] - location_in_total_offset[dim]
-                        if m
-                        else node.location[dim]
+                        (
+                            total_roi_end[dim] - location_in_total_offset[dim]
+                            if m
+                            else node.location[dim]
+                        )
                         for dim, m in enumerate(self.mirror)
                     ],
                     dtype=graph.spec.dtype,
@@ -255,9 +257,11 @@ def __mirror_roi(self, roi, total_roi, mirror):
         end_of_roi_in_total = roi_in_total_offset + roi_shape
         roi_in_total_offset_mirrored = total_roi_shape - end_of_roi_in_total
         roi_offset = Coordinate(
-            total_roi_offset[d] + roi_in_total_offset_mirrored[d]
-            if mirror[d]
-            else roi_offset[d]
+            (
+                total_roi_offset[d] + roi_in_total_offset_mirrored[d]
+                if mirror[d]
+                else roi_offset[d]
+            )
             for d in range(self.dims)
         )
 

gunpowder/nodes/specified_location.py

@@ -106,9 +106,9 @@ def process(self, batch, request):
         for array_key, spec in request.array_specs.items():
             batch.arrays[array_key].spec.roi = spec.roi
             if self.extra_data is not None:
-                batch.arrays[array_key].attrs[
-                    "specified_location_extra_data"
-                ] = self.extra_data[self.loc_i]
+                batch.arrays[array_key].attrs["specified_location_extra_data"] = (
+                    self.extra_data[self.loc_i]
+                )
 
         for graph_key, spec in request.graph_specs.items():
             batch.points[graph_key].spec.roi = spec.roi

tests/cases/simple_augment.py

@@ -233,9 +233,9 @@ def test_mismatched_voxel_multiples():
 
     test_array = ArrayKey("TEST_ARRAY")
     data = np.zeros([3, 3])
-    data[
-        2, 1
-    ] = 1  # voxel has Roi((4, 2) (2, 2)). Contained in Roi((0, 0), (6, 4)). at 2, 1
+    data[2, 1] = (
+        1  # voxel has Roi((4, 2) (2, 2)). Contained in Roi((0, 0), (6, 4)). at 2, 1
+    )
     source = ArraySource(
         test_array,
         Array(