cellmap-analyze 0.2.2__tar.gz → 0.2.3__tar.gz

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Files changed (60) hide show
  1. {cellmap_analyze-0.2.2/src/cellmap_analyze.egg-info → cellmap_analyze-0.2.3}/PKG-INFO +2 -2
  2. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/README.md +1 -1
  3. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/pyproject.toml +1 -1
  4. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/analyze/assign_to_organelles.py +3 -2
  5. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/cythonizing/bresenham3D.c +1581 -2272
  6. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/cythonizing/centers.cpp +1806 -2497
  7. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/cythonizing/process_arrays.c +1593 -2284
  8. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/cythonizing/touching.c +1785 -2476
  9. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/process/mutex_watershed.py +4 -0
  10. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/process/skeletonize.py +185 -76
  11. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/util/dask_util.py +74 -1
  12. cellmap_analyze-0.2.3/src/cellmap_analyze/util/sharded_skeleton.py +214 -0
  13. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/util/skeleton_util.py +25 -31
  14. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3/src/cellmap_analyze.egg-info}/PKG-INFO +2 -2
  15. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze.egg-info/SOURCES.txt +1 -0
  16. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/LICENSE +0 -0
  17. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/MANIFEST.in +0 -0
  18. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/setup.cfg +0 -0
  19. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/setup.py +0 -0
  20. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/__init__.py +0 -0
  21. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/analyze/__init__.py +0 -0
  22. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/analyze/fit_lines_to_segmentations.py +0 -0
  23. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/analyze/measure.py +0 -0
  24. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/cythonizing/__init__.py +0 -0
  25. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/cythonizing/bresenham3D.pyx +0 -0
  26. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/cythonizing/centers.pyx +0 -0
  27. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/cythonizing/impl/centers.hpp +0 -0
  28. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/cythonizing/process_arrays.pyx +0 -0
  29. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/cythonizing/touching.pyx +0 -0
  30. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/process/__init__.py +0 -0
  31. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/process/clean_connected_components.py +0 -0
  32. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/process/connected_components.py +0 -0
  33. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/process/contact_sites.py +0 -0
  34. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/process/fill_holes.py +0 -0
  35. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/process/filter_ids.py +0 -0
  36. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/process/label_with_mask.py +0 -0
  37. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/process/morphological_operations.py +0 -0
  38. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/util/__init__.py +0 -0
  39. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/util/block_util.py +0 -0
  40. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/util/cellmap_array.py +0 -0
  41. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/util/image_data_interface.py +0 -0
  42. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/util/information_holders.py +0 -0
  43. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/util/io_util.py +0 -0
  44. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/util/mask_util.py +0 -0
  45. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/util/measure_util.py +0 -0
  46. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/util/mixins.py +0 -0
  47. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/util/neuroglancer_util.py +0 -0
  48. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/util/voxel_size_utils.py +0 -0
  49. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/util/zarr_io.py +0 -0
  50. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/util/zarr_util.py +0 -0
  51. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze.egg-info/dependency_links.txt +0 -0
  52. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze.egg-info/entry_points.txt +0 -0
  53. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze.egg-info/requires.txt +0 -0
  54. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze.egg-info/top_level.txt +0 -0
  55. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cli/__init__.py +0 -0
  56. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/src/cli/cli.py +0 -0
  57. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/tests/test_non_integer_voxel_size_integration.py +0 -0
  58. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/tests/test_utils.py +0 -0
  59. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/tests/test_voxel_size_utils.py +0 -0
  60. {cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/tests/test_zarr_v3.py +0 -0
{cellmap_analyze-0.2.2/src/cellmap_analyze.egg-info → cellmap_analyze-0.2.3}/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: 0.2.2
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+ Version: 0.2.3
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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>
@@ -148,7 +148,7 @@ jobqueue:
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  cores: 12 # threads per process (1 thread each)
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  memory: 120GB # 15 GB per slot
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  walltime: 08:00
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- mem: 12000000000
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+ mem: 120000000000
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  use-stdin: true
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  log-directory: job-logs
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  name: cellmap-analyze
{cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/README.md RENAMED
@@ -114,7 +114,7 @@ jobqueue:
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  cores: 12 # threads per process (1 thread each)
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  memory: 120GB # 15 GB per slot
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  walltime: 08:00
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- mem: 12000000000
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+ mem: 120000000000
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  use-stdin: true
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  log-directory: job-logs
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  name: cellmap-analyze
{cellmap_analyze-0.2.2 → cellmap_analyze-0.2.3}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
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  [project]
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  name = "cellmap-analyze"
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- version = "0.2.2"
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+ version = "0.2.3"
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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-0.2.2 → cellmap_analyze-0.2.3}/src/cellmap_analyze/analyze/assign_to_organelles.py RENAMED
@@ -16,6 +16,7 @@ import logging
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  import pandas as pd
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  import numpy as np
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  import os
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+ import shutil
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  from scipy import spatial
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  import fastremap
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  import fastmorph
@@ -333,7 +334,7 @@ class AssignToOrganelles(ComputeConfigMixin):
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  df.at[row_idx, id_col] = org_id
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  df[id_col] = df[id_col].astype(int)
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- os.remove(coms_path)
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+ shutil.rmtree(os.path.dirname(coms_path), ignore_errors=True)
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  def assign_to_n_nearest_organelles(self, df, n, organelle_name):
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  coms = df[["COM Z (nm)", "COM Y (nm)", "COM X (nm)"]].to_numpy()
@@ -379,7 +380,7 @@ class AssignToOrganelles(ComputeConfigMixin):
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  merge_info=(AssignToOrganelles._merge_dicts, output_dir),
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  )
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- os.remove(coms_path)
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+ shutil.rmtree(os.path.dirname(coms_path), ignore_errors=True)
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  # Apply results to DataFrame
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  id_col = f"{organelle_name} ID"