Rhapso 0.3.2__tar.gz → 0.3.4__tar.gz

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  1. {rhapso-0.3.2 → rhapso-0.3.4}/PKG-INFO +1 -17
  2. {rhapso-0.3.2 → rhapso-0.3.4}/README.md +0 -16
  3. rhapso-0.3.4/Rhapso/evaluation/ip_metrics_and_viz.py +1243 -0
  4. rhapso-0.3.4/Rhapso/evaluation/matching_metrics_and_viz.py +1515 -0
  5. rhapso-0.3.4/Rhapso/evaluation/max_projection.py +523 -0
  6. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/evaluation/ph_corr_qc.py +239 -545
  7. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/matching/ransac_matching.py +11 -9
  8. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/pipelines/ray/aws/alignment_pipeline.py +7 -4
  9. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/pipelines/ray/interest_point_matching.py +11 -10
  10. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/pipelines/ray/local/alignment_pipeline.py +8 -5
  11. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/solver/compute_tiles.py +10 -2
  12. rhapso-0.3.4/Rhapso/solver/global_optimization.py +532 -0
  13. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/solver/pre_align_tiles.py +1 -1
  14. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/util/bdv_checkerboard_tile_colors.py +1 -1
  15. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/util/filter_tiles_from_xml.py +6 -6
  16. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso.egg-info/PKG-INFO +1 -17
  17. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso.egg-info/SOURCES.txt +3 -3
  18. {rhapso-0.3.2 → rhapso-0.3.4}/setup.py +1 -1
  19. rhapso-0.3.2/Rhapso/evaluation/detection_visualization.py +0 -74
  20. rhapso-0.3.2/Rhapso/evaluation/matching_visualization.py +0 -166
  21. rhapso-0.3.2/Rhapso/solver/global_optimization.py +0 -410
  22. rhapso-0.3.2/Rhapso/util/hcr_upload_hpc.py +0 -364
  23. {rhapso-0.3.2 → rhapso-0.3.4}/LICENSE +0 -0
  24. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/__init__.py +0 -0
  25. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/affine_fusion/__init__.py +0 -0
  26. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/affine_fusion/compute_bbox.py +0 -0
  27. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/affine_fusion/compute_grid.py +0 -0
  28. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/affine_fusion/fuse_cell.py +0 -0
  29. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/affine_fusion/generate_fusion_instructions.py +0 -0
  30. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/affine_fusion/initialize_output_zarr.py +0 -0
  31. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/affine_fusion/overlapping_blocks.py +0 -0
  32. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/affine_fusion/overlapping_views.py +0 -0
  33. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/data_prep/__init__.py +0 -0
  34. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/data_prep/n5_reader.py +0 -0
  35. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/data_prep/s3_big_stitcher_reader.py +0 -0
  36. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/data_prep/xml_to_dataframe.py +0 -0
  37. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/detection/__init__.py +0 -0
  38. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/detection/advanced_refinement.py +0 -0
  39. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/detection/difference_of_gaussian.py +0 -0
  40. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/detection/image_reader.py +0 -0
  41. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/detection/metadata_builder.py +0 -0
  42. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/detection/overlap_detection.py +0 -0
  43. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/detection/points_validation.py +0 -0
  44. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/detection/save_interest_points.py +0 -0
  45. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/detection/view_transform_models.py +0 -0
  46. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/evaluation/__init__.py +0 -0
  47. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/matching/__init__.py +0 -0
  48. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/matching/load_and_transform_points.py +0 -0
  49. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/matching/save_matches.py +0 -0
  50. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/matching/xml_parser.py +0 -0
  51. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/multiscale/__init__.py +0 -0
  52. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/multiscale/array_and_chunk_prep.py +0 -0
  53. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/multiscale/block_planner.py +0 -0
  54. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/multiscale/ome_metadata.py +0 -0
  55. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/multiscale/pyramid_executor.py +0 -0
  56. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/pipelines/__init__.py +0 -0
  57. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/pipelines/ray/__init__.py +0 -0
  58. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/pipelines/ray/affine_fusion.py +0 -0
  59. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/pipelines/ray/aws/__init__.py +0 -0
  60. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/pipelines/ray/aws/config/__init__.py +0 -0
  61. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/pipelines/ray/aws/config/dev/__init__.py +0 -0
  62. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/pipelines/ray/aws/fusion_pipeline.py +0 -0
  63. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/pipelines/ray/interest_point_detection.py +0 -0
  64. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/pipelines/ray/local/__init__.py +0 -0
  65. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/pipelines/ray/local/fusion_pipeline.py +0 -0
  66. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/pipelines/ray/multiscale.py +0 -0
  67. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/pipelines/ray/param/__init__.py +0 -0
  68. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/pipelines/ray/param/alignment/__init__.py +0 -0
  69. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/pipelines/ray/param/fusion/__init__.py +0 -0
  70. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/pipelines/ray/param/template/__init__.py +0 -0
  71. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/pipelines/ray/solver.py +0 -0
  72. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/pipelines/ray/split_dataset.py +0 -0
  73. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/pipelines/ray/util/__init__.py +0 -0
  74. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/pipelines/ray/util/fusion_progress.py +0 -0
  75. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/solver/__init__.py +0 -0
  76. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/solver/concatenate_models.py +0 -0
  77. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/solver/connected_graphs.py +0 -0
  78. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/solver/data_prep.py +0 -0
  79. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/solver/model_and_tile_setup.py +0 -0
  80. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/solver/save_results.py +0 -0
  81. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/solver/view_transforms.py +0 -0
  82. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/solver/xml_to_dataframe_solver.py +0 -0
  83. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/split_dataset/__init__.py +0 -0
  84. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/split_dataset/compute_grid_rules.py +0 -0
  85. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/split_dataset/save_points.py +0 -0
  86. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/split_dataset/save_xml.py +0 -0
  87. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/split_dataset/split_images.py +0 -0
  88. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/split_dataset/xml_to_dataframe_split.py +0 -0
  89. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/util/__init__.py +0 -0
  90. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/util/bdv_split_checkerboard.py +0 -0
  91. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/util/check_intensity_levels.py +0 -0
  92. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/util/check_multiscale.py +0 -0
  93. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/util/filter_tiles_from_split_xml.py +0 -0
  94. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/util/generate_processing_metadata.py +0 -0
  95. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/util/increase_overlap.py +0 -0
  96. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/util/ng_link_gen_z1.py +0 -0
  97. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/util/ng_tile_viewer_proteomics.py +0 -0
  98. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/util/single_channel_xml.py +0 -0
  99. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/util/sort+rename_xml_views.py +0 -0
  100. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso/util/tile_analyzer.py +0 -0
  101. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso.egg-info/dependency_links.txt +0 -0
  102. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso.egg-info/requires.txt +0 -0
  103. {rhapso-0.3.2 → rhapso-0.3.4}/Rhapso.egg-info/top_level.txt +0 -0
  104. {rhapso-0.3.2 → rhapso-0.3.4}/pyproject.toml +0 -0
  105. {rhapso-0.3.2 → rhapso-0.3.4}/setup.cfg +0 -0
  106. {rhapso-0.3.2 → rhapso-0.3.4}/tests/__init__.py +0 -0
  107. {rhapso-0.3.2 → rhapso-0.3.4}/tests/test_detection.py +0 -0
  108. {rhapso-0.3.2 → rhapso-0.3.4}/tests/test_matching.py +0 -0
  109. {rhapso-0.3.2 → rhapso-0.3.4}/tests/test_solving.py +0 -0
{rhapso-0.3.2 → rhapso-0.3.4}/PKG-INFO RENAMED
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  Metadata-Version: 2.4
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  Name: Rhapso
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- Version: 0.3.2
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+ Version: 0.3.4
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  Summary: A python package for aligning and stitching light sheet fluorescence microscopy images
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  Author: ND
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  Author-email: sean.fite@alleninstitute.org
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  <br>
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- ## Performance
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- **Interest Point Detection Performance Example (130TB Zarr dataset)**
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- | Environment | Resources | Avg runtime |
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- |:----------------------|:---------------------|:-----------:|
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- | Local single machine | 10 CPU, 10 GB RAM | ~120 min |
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- | AWS Ray cluster | 560 CPU, 4.4 TB RAM | ~10 min |
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- *Actual times vary by pipeline components, dataset size, tiling, and parameter choices.*
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- ---
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  ## Ray
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  **Ray** is a Python framework for parallel and distributed computing. It lets you run regular Python functions in parallel on a single machine **or** scale them out to a cluster (e.g., AWS) with minimal code changes. In Rhapso, we use Ray to process large scale datasets.
{rhapso-0.3.2 → rhapso-0.3.4}/README.md RENAMED
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- ## Performance
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- **Interest Point Detection Performance Example (130TB Zarr dataset)**
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- | Environment | Resources | Avg runtime |
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- | Local single machine | 10 CPU, 10 GB RAM | ~120 min |
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- | AWS Ray cluster | 560 CPU, 4.4 TB RAM | ~10 min |
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- *Actual times vary by pipeline components, dataset size, tiling, and parameter choices.*
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- ---
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- <br>
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  ## Ray
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  **Ray** is a Python framework for parallel and distributed computing. It lets you run regular Python functions in parallel on a single machine **or** scale them out to a cluster (e.g., AWS) with minimal code changes. In Rhapso, we use Ray to process large scale datasets.