Make scale parameter required (#116)

* make scale parameter required and remove scale parameter from downsampling tool

* remove scale parameter from tests as well

* ensure an initial datasource-properties.json is written directly after cubing and refreshed again after downsampling

* do meta data generation test directly after cubing so that downsampling can access the datasource properties

.circleci/config.yml

@@ -65,6 +65,10 @@ jobs:
           name: Test simple tiff cubing (no compression)
           command: tests/scripts/simple_tiff_cubing_no_compression.sh
 
+      - run:
+          name: Test metadata generation
+          command: tests/scripts/meta_generation.sh
+
       - run:
           name: Test KNOSSOS conversion
           command: tests/scripts/knossos_conversion.sh
@@ -89,10 +93,6 @@ jobs:
           name: Test in-place compression
           command: tests/scripts/in_place_compression.sh
 
-      - run:
-          name: Test metadata generation
-          command: tests/scripts/meta_generation.sh
-
       - run:
           name: Remove reference magnification data
           command: rm -r testdata/tiff_mag_2_reference/

tests/scripts/anisotropic_downsampling.sh

@@ -37,7 +37,6 @@ docker run \
   --max 16 \
   --buffer_cube_size 128 \
   --layer_name color \
-  --scale 11.24,11.24,25 \
   /testoutput/tiff
 [ -d testoutput/tiff/color/8-8-2 ]
 [ -d testoutput/tiff/color/16-16-4 ]

tests/scripts/simple_anisotropic_tiff_cubing.sh

@@ -10,7 +10,6 @@ docker run \
   --batch_size 8 \
   --layer_name color \
   --max 8 \
-  --scale 11.24,25,11.24 \
   --name awesome_data \
   /testdata/tiff /testoutput/tiff3
 [ -d testoutput/tiff3/color ]

wkcuber/__main__.py

@@ -5,7 +5,7 @@
     DEFAULT_EDGE_LEN,
 )
 from .compress import compress_mag_inplace
-from .metadata import write_webknossos_metadata
+from .metadata import write_webknossos_metadata, refresh_metadata
 from .utils import add_isotropic_flag, setup_logging, add_scale_flag
 from .mag import Mag
 
@@ -50,6 +50,14 @@ def create_parser():
         args,
     )
 
+    write_webknossos_metadata(
+        args.target_path,
+        args.name,
+        scale,
+        compute_max_id=False,
+        exact_bounding_box=bounding_box,
+    )
+
     if not args.no_compress:
         compress_mag_inplace(args.target_path, args.layer_name, Mag(1), args)
 
@@ -78,10 +86,4 @@ def create_parser():
             args,
         )
 
-    write_webknossos_metadata(
-        args.target_path,
-        args.name,
-        scale,
-        compute_max_id=False,
-        exact_bounding_box=bounding_box,
-    )
+    refresh_metadata(args.target_path)

wkcuber/downsampling.py

@@ -21,7 +21,6 @@
     get_executor_for_args,
     wait_and_ensure_success,
     add_isotropic_flag,
-    add_scale_flag,
     setup_logging,
 )
 
@@ -109,7 +108,6 @@ def create_parser():
         action="store_true",
     )
 
-    add_scale_flag(parser)
     add_verbose_flag(parser)
     add_isotropic_flag(parser)
     add_distribution_flags(parser)
@@ -604,9 +602,7 @@ def detect_larger_and_smaller_dimension(scale):
 
     from_mag = Mag(args.from_mag)
     max_mag = Mag(args.max)
-    scale = (
-        [float(x) for x in args.scale.split(",")] if hasattr(args, "scale") else None
-    )
+
     if args.anisotropic_target_mag:
         anisotropic_target_mag = Mag(args.anisotropic_target_mag)
 
@@ -621,16 +617,15 @@ def detect_larger_and_smaller_dimension(scale):
             args,
         )
     elif not args.isotropic:
-        if scale is None:
-            try:
-                scale = read_datasource_properties(args.path)["scale"]
-            except Exception as exc:
-                logging.error(
-                    "Could not determine scale which is necessary "
-                    "to find target magnifications for anisotropic downsampling. "
-                    "Does the provided dataset have a datasource-properties.json file?"
-                )
-                raise exc
+        try:
+            scale = read_datasource_properties(args.path)["scale"]
+        except Exception as exc:
+            logging.error(
+                "Could not determine scale which is necessary "
+                "to find target magnifications for anisotropic downsampling. "
+                "Does the provided dataset have a datasource-properties.json file?"
+            )
+            raise exc
 
         downsample_mags_anisotropic(
             args.path,

wkcuber/utils.py

@@ -66,7 +66,7 @@ def add_scale_flag(parser):
         "--scale",
         "-s",
         help="Scale of the dataset (e.g. 11.2,11.2,25). This is the size of one voxel in nm.",
-        default="1,1,1",
+        required=True,
     )