Make image reader stateless to fix cubing (#460)

* test cubing with start_z and padding

* make image_reader stateless to fix cubing

* fix lint

* update changelog

* make methods static

* unify the static method calls

wkcuber/Changelog.md

@@ -13,6 +13,7 @@ For upgrade instructions, please check the respective *Breaking Changes* section
 ### Added
 ### Changed
 ### Fixed
+- Fixed two bugs in `cubing` (regarding `start_z` and `pad`). As a result, the ImageConverters do no longer cache metadata. [#460](https://github.com/scalableminds/webknossos-libs/pull/460)
 
 ## [v0.8.18](https://github.com/scalableminds/webknossos-cuber/releases/tag/v0.8.18) - 2021-10-18
 [Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.8.16...v0.8.18)

wkcuber/tests/scripts/tiff_cubing_with_padding.sh

@@ -0,0 +1,13 @@
+set -xe
+mkdir -p testoutput/tiff_pad
+python -m wkcuber.cubing \
+  --jobs 2 \
+  --batch_size 8 \
+  --layer_name color \
+  --scale 1,1,1 \
+  --start_z 4 \
+  --pad \
+  testdata/tiff_with_different_dimensions testoutput/tiff_pad
+[ -d testoutput/tiff_pad/color ]
+[ -d testoutput/tiff_pad/color/1 ]
+[ -e testoutput/tiff_pad/datasource-properties.json ]

wkcuber/wkcuber/cubing.py

@@ -28,7 +28,7 @@
     setup_logging,
     add_scale_flag,
 )
-from .image_readers import image_reader, refresh_global_image_reader
+from .image_readers import image_reader
 
 BLOCK_LEN = 32
 
@@ -181,7 +181,6 @@ def cubing_job(
         InterpolationModes,
         List[str],
         int,
-        Tuple[int, int],
         bool,
         Optional[int],
         Optional[int],
@@ -193,7 +192,6 @@ def cubing_job(
         interpolation_mode,
         source_file_batches,
         batch_size,
-        image_size,
         pad,
         channel_index,
         sample_index,
@@ -229,15 +227,15 @@ def cubing_job(
 
                 if not pad:
                     assert (
-                        image.shape[0:2] == image_size
+                        image.shape[0:2] == target_view.size[0:2]
                     ), "Section z={} has the wrong dimensions: {} (expected {}). Consider using --pad.".format(
-                        z, image.shape, image_size
+                        z, image.shape, target_view.size[0:2]
                     )
                 slices.append(image)
 
             if pad:
-                x_max = max(_slice.shape[0] for _slice in slices)
-                y_max = max(_slice.shape[1] for _slice in slices)
+                x_max = target_view.size[0]
+                y_max = target_view.size[1]
 
                 slices = [
                     np.pad(
@@ -313,11 +311,16 @@ def cubing(
     executor_args: Namespace,
 ) -> Layer:
     source_files = find_source_filenames(source_path)
-    # we need to refresh the image readers because they are no longer stateless for performance reasons
-    refresh_global_image_reader()
 
-    # All images are assumed to have equal dimensions
-    num_x, num_y = image_reader.read_dimensions(source_files[0])
+    all_num_x, all_num_y = zip(
+        *[
+            image_reader.read_dimensions(source_files[i])
+            for i in range(len(source_files))
+        ]
+    )
+    num_x = max(all_num_x)
+    num_y = max(all_num_y)
+    # All images are assumed to have equal channels and samples
     num_channels = image_reader.read_channel_count(source_files[0])
     num_samples = image_reader.read_sample_count(source_files[0])
     num_output_channels = num_channels * num_samples
@@ -415,13 +418,12 @@ def cubing(
                 (
                     target_mag_view.get_view(
                         (0, 0, z + start_z),
-                        (num_x, num_y, start_z + max_z - z),
+                        (num_x, num_y, max_z - z),
                     ),
                     target_mag,
                     interpolation_mode,
                     source_files_array,
                     batch_size,
-                    (num_x, num_y),
                     pad,
                     channel_index,
                     sample_index,