waveorder 2.2.1b0__py3-none-any.whl → 3.0.0__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (58) hide show
  1. waveorder/_version.py +16 -3
  2. waveorder/acq/__init__.py +0 -0
  3. waveorder/acq/acq_functions.py +166 -0
  4. waveorder/assets/HSV_legend.png +0 -0
  5. waveorder/assets/JCh_legend.png +0 -0
  6. waveorder/assets/waveorder_plugin_logo.png +0 -0
  7. waveorder/calib/Calibration.py +1512 -0
  8. waveorder/calib/Optimization.py +470 -0
  9. waveorder/calib/__init__.py +0 -0
  10. waveorder/calib/calibration_workers.py +464 -0
  11. waveorder/cli/apply_inverse_models.py +328 -0
  12. waveorder/cli/apply_inverse_transfer_function.py +379 -0
  13. waveorder/cli/compute_transfer_function.py +432 -0
  14. waveorder/cli/gui_widget.py +58 -0
  15. waveorder/cli/main.py +39 -0
  16. waveorder/cli/monitor.py +163 -0
  17. waveorder/cli/option_eat_all.py +47 -0
  18. waveorder/cli/parsing.py +122 -0
  19. waveorder/cli/printing.py +16 -0
  20. waveorder/cli/reconstruct.py +67 -0
  21. waveorder/cli/settings.py +187 -0
  22. waveorder/cli/utils.py +175 -0
  23. waveorder/filter.py +1 -2
  24. waveorder/focus.py +136 -25
  25. waveorder/io/__init__.py +0 -0
  26. waveorder/io/_reader.py +61 -0
  27. waveorder/io/core_functions.py +272 -0
  28. waveorder/io/metadata_reader.py +195 -0
  29. waveorder/io/utils.py +175 -0
  30. waveorder/io/visualization.py +160 -0
  31. waveorder/models/inplane_oriented_thick_pol3d_vector.py +3 -3
  32. waveorder/models/isotropic_fluorescent_thick_3d.py +92 -0
  33. waveorder/models/isotropic_fluorescent_thin_3d.py +331 -0
  34. waveorder/models/isotropic_thin_3d.py +73 -72
  35. waveorder/models/phase_thick_3d.py +103 -4
  36. waveorder/napari.yaml +36 -0
  37. waveorder/plugin/__init__.py +9 -0
  38. waveorder/plugin/gui.py +1094 -0
  39. waveorder/plugin/gui.ui +1440 -0
  40. waveorder/plugin/job_manager.py +42 -0
  41. waveorder/plugin/main_widget.py +1605 -0
  42. waveorder/plugin/tab_recon.py +3294 -0
  43. waveorder/scripts/__init__.py +0 -0
  44. waveorder/scripts/launch_napari.py +13 -0
  45. waveorder/scripts/repeat-cal-acq-rec.py +147 -0
  46. waveorder/scripts/repeat-calibration.py +31 -0
  47. waveorder/scripts/samples.py +85 -0
  48. waveorder/scripts/simulate_zarr_acq.py +204 -0
  49. waveorder/util.py +1 -1
  50. waveorder/visuals/napari_visuals.py +1 -1
  51. waveorder-3.0.0.dist-info/METADATA +350 -0
  52. waveorder-3.0.0.dist-info/RECORD +69 -0
  53. {waveorder-2.2.1b0.dist-info → waveorder-3.0.0.dist-info}/WHEEL +1 -1
  54. waveorder-3.0.0.dist-info/entry_points.txt +5 -0
  55. {waveorder-2.2.1b0.dist-info → waveorder-3.0.0.dist-info/licenses}/LICENSE +13 -1
  56. waveorder-2.2.1b0.dist-info/METADATA +0 -187
  57. waveorder-2.2.1b0.dist-info/RECORD +0 -27
  58. {waveorder-2.2.1b0.dist-info → waveorder-3.0.0.dist-info}/top_level.txt +0 -0
waveorder/napari.yaml ADDED
@@ -0,0 +1,36 @@
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+ name: waveorder
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+ display_name: waveorder
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+ contributions:
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+ commands:
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+ - id: waveorder.MainWidget
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+ title: Create Main Widget
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+ python_name: waveorder.plugin.main_widget:MainWidget
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+ - id: waveorder.get_reader
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+ title: Read ome-zarr and ome-tif files
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+ python_name: waveorder.io._reader:napari_get_reader
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+ - id: waveorder.polarization_target_data
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+ title: Polarization Target Data
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+ python_name: waveorder.scripts.samples:read_polarization_target_data
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+ - id: waveorder.polarization_target_reconstruction
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+ title: Polarization Target Data
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+ python_name: waveorder.scripts.samples:read_polarization_target_reconstruction
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+ - id: waveorder.zebrafish_embryo_reconstruction
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+ title: Zebrafish Embryo Reconstruction
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+ python_name: waveorder.scripts.samples:read_zebrafish_embryo_reconstruction
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+ readers:
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+ - command: waveorder.get_reader
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+ accepts_directories: true
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+ filename_patterns: ['*.zarr', '*.tif']
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+ widgets:
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+ - command: waveorder.MainWidget
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+ display_name: Main Menu
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+ sample_data:
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+ - command: waveorder.polarization_target_data
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+ key: polarization-target-data
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+ display_name: Polarization Target Data (10 MB)
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+ - command: waveorder.polarization_target_reconstruction
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+ key: polarization-target-reconstruction
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+ display_name: Polarization Target Reconstruction (10 MB)
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+ - command: waveorder.zebrafish_embryo_reconstruction
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+ key: zebrafish-embryo-reconstruction
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+ display_name: Zebrafish Embryo Reconstruction (92 MB)
waveorder/plugin/__init__.py ADDED
@@ -0,0 +1,9 @@
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+ # qtpy defaults to PyQt5/PySide2 which can be present in upgraded environments
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+ try:
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+ import qtpy
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+
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+ qtpy.API_NAME # check qtpy API name - one is required for GUI
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+
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+ except RuntimeError as error:
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+ if type(error).__name__ == "QtBindingsNotFoundError":
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+ print("WARNING: QtBindings (PyQT or PySide) was not found for GUI")