cellmap-analyze 0.4.0__tar.gz → 0.4.2__tar.gz

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Files changed (68) hide show
  1. {cellmap_analyze-0.4.0/src/cellmap_analyze.egg-info → cellmap_analyze-0.4.2}/PKG-INFO +1 -1
  2. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/pyproject.toml +1 -1
  3. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/analyze/measure.py +8 -1
  4. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/cythonizing/bresenham3D.c +321 -168
  5. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/cythonizing/centers.cpp +1129 -416
  6. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/cythonizing/process_arrays.c +334 -181
  7. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/cythonizing/touching.c +1129 -416
  8. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/process/connected_components.py +29 -5
  9. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/process/skeletonize.py +317 -65
  10. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/util/dask_util.py +18 -4
  11. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/util/image_data_interface.py +6 -1
  12. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/util/precomputed_io.py +5 -0
  13. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/util/skeleton_util.py +29 -4
  14. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/util/voxel_size_utils.py +21 -3
  15. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/util/zarr_io.py +117 -0
  16. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2/src/cellmap_analyze.egg-info}/PKG-INFO +1 -1
  17. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze.egg-info/SOURCES.txt +2 -0
  18. cellmap_analyze-0.4.2/tests/test_dask_local_directory.py +51 -0
  19. cellmap_analyze-0.4.2/tests/test_scale_resolution.py +109 -0
  20. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/LICENSE +0 -0
  21. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/MANIFEST.in +0 -0
  22. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/README.md +0 -0
  23. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/setup.cfg +0 -0
  24. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/setup.py +0 -0
  25. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/__init__.py +0 -0
  26. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/analyze/__init__.py +0 -0
  27. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/analyze/assign_to_organelles.py +0 -0
  28. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/analyze/fit_lines_to_segmentations.py +0 -0
  29. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/cythonizing/__init__.py +0 -0
  30. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/cythonizing/bresenham3D.pyx +0 -0
  31. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/cythonizing/centers.pyx +0 -0
  32. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/cythonizing/impl/centers.hpp +0 -0
  33. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/cythonizing/process_arrays.pyx +0 -0
  34. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/cythonizing/touching.pyx +0 -0
  35. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/process/__init__.py +0 -0
  36. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/process/clean_connected_components.py +0 -0
  37. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/process/contact_sites.py +0 -0
  38. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/process/fill_holes.py +0 -0
  39. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/process/filter_ids.py +0 -0
  40. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/process/label_with_mask.py +0 -0
  41. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/process/morphological_operations.py +0 -0
  42. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/process/mutex_watershed.py +0 -0
  43. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/util/__init__.py +0 -0
  44. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/util/block_util.py +0 -0
  45. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/util/cellmap_array.py +0 -0
  46. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/util/information_holders.py +0 -0
  47. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/util/io_util.py +0 -0
  48. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/util/mask_util.py +0 -0
  49. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/util/measure_util.py +0 -0
  50. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/util/mixins.py +0 -0
  51. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/util/neuroglancer_util.py +0 -0
  52. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/util/sharded_skeleton.py +0 -0
  53. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/util/zarr_util.py +0 -0
  54. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze.egg-info/dependency_links.txt +0 -0
  55. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze.egg-info/entry_points.txt +0 -0
  56. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze.egg-info/requires.txt +0 -0
  57. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze.egg-info/top_level.txt +0 -0
  58. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cli/__init__.py +0 -0
  59. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cli/cli.py +0 -0
  60. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/tests/test_kvstore_anonymous.py +0 -0
  61. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/tests/test_non_integer_voxel_size_integration.py +0 -0
  62. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/tests/test_precomputed_read.py +0 -0
  63. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/tests/test_s3_read.py +0 -0
  64. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/tests/test_unique_tmp_dirs.py +0 -0
  65. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/tests/test_utils.py +0 -0
  66. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/tests/test_voxel_size_utils.py +0 -0
  67. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/tests/test_wave_scheduling.py +0 -0
  68. {cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/tests/test_zarr_v3.py +0 -0
{cellmap_analyze-0.4.0/src/cellmap_analyze.egg-info → cellmap_analyze-0.4.2}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: cellmap-analyze
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- Version: 0.4.0
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+ Version: 0.4.2
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  Summary: Code to perform analysis on segmentations like those produced by CellMap
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  Author-email: David Ackerman <ackermand@janelia.hhmi.org>
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  Maintainer-email: David Ackerman <ackermand@janelia.hhmi.org>
{cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
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  [project]
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  name = "cellmap-analyze"
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- version = "0.4.0"
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+ version = "0.4.2"
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  description = "Code to perform analysis on segmentations like those produced by CellMap"
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  readme = "README.md"
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  license-files = ["LICENSE"]
{cellmap_analyze-0.4.0 → cellmap_analyze-0.4.2}/src/cellmap_analyze/analyze/measure.py RENAMED
@@ -98,7 +98,14 @@ class Measure(ComputeConfigMixin):
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  if "raw_path" in kwargs and kwargs["raw_path"]:
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  self.raw_path = kwargs["raw_path"]
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- self.raw_idi = ImageDataInterface(self.raw_path, chunk_shape=chunk_shape)
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+ # If raw_path is a multiscale group (no scale level given), pick
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+ # the level whose voxel size best matches the input segmentation
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+ # so intensities line up with minimal resampling.
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+ self.raw_idi = ImageDataInterface(
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+ self.raw_path,
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+ chunk_shape=chunk_shape,
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+ target_voxel_size=self.input_idi.original_voxel_size,
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+ )
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  # Align scale factors between raw and input
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  raw_sf = compute_common_scale_factor(
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  self.input_idi.voxel_size_scale_factor,