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,
  )