imaging-server-kit 0.1.1__tar.gz → 0.1.2__tar.gz

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Files changed (108) hide show
  1. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/PKG-INFO +1 -1
  2. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/docs/sections/04_multialgo.ipynb +7 -1
  3. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/docs/sections/05_streams.ipynb +3 -3
  4. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/_version.py +3 -3
  5. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/demo/examples.py +1 -1
  6. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/template/cookiecutter.json +1 -1
  7. imaging_server_kit-0.1.1/src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }}/main.py → imaging_server_kit-0.1.2/src/imaging_server_kit/template/serverkit-{{cookiecutter.name}}/main.py +7 -7
  8. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit.egg-info/PKG-INFO +1 -1
  9. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit.egg-info/SOURCES.txt +8 -8
  10. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/.dockerignore +0 -0
  11. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/.gitattributes +0 -0
  12. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/.github/workflows/deploy.yml +0 -0
  13. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/.github/workflows/publish.yml +0 -0
  14. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/.gitignore +0 -0
  15. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/CITATION.cff +0 -0
  16. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/Dockerfile +0 -0
  17. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/Dockerfile-GPU +0 -0
  18. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/LICENSE +0 -0
  19. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/MANIFEST.in +0 -0
  20. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/README.md +0 -0
  21. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/build.sh +0 -0
  22. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/docs/_config.yml +0 -0
  23. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/docs/_static/oripy_threshold.mp4 +0 -0
  24. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/docs/_static/progressive_threshold.mp4 +0 -0
  25. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/docs/_static/server_napari.mp4 +0 -0
  26. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/docs/_static/stardist_blobs.mp4 +0 -0
  27. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/docs/_static/tiles.mp4 +0 -0
  28. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/docs/_static/tiling2.mp4 +0 -0
  29. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/docs/_static/yolo-stream.mp4 +0 -0
  30. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/docs/_toc.yml +0 -0
  31. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/docs/assets/demo_napari_screenshot.png +0 -0
  32. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/docs/assets/gaussian_result.png +0 -0
  33. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/docs/assets/meta_sc.png +0 -0
  34. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/docs/assets/samples_sc.png +0 -0
  35. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/docs/assets/screenshot_napari_threshold.png +0 -0
  36. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/docs/assets/screenshot_server.png +0 -0
  37. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/docs/assets/server_running.png +0 -0
  38. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/docs/assets/threshold_qupath.png +0 -0
  39. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/docs/index.md +0 -0
  40. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/docs/logo.ico +0 -0
  41. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/docs/sections/00_getting_started.md +0 -0
  42. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/docs/sections/01_algorithm.ipynb +0 -0
  43. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/docs/sections/02_samples.ipynb +0 -0
  44. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/docs/sections/03_metadata.ipynb +0 -0
  45. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/docs/sections/06_tiled.ipynb +0 -0
  46. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/docs/sections/07_server.md +0 -0
  47. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/docs/sections/08_python.ipynb +0 -0
  48. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/docs/sections/09_docker.md +0 -0
  49. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/docs/sections/10_types.md +0 -0
  50. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/docs/sections/11_examples.md +0 -0
  51. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/examples/readme.md +0 -0
  52. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/pyproject.toml +0 -0
  53. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/setup.cfg +0 -0
  54. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/__init__.py +0 -0
  55. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/cli.py +0 -0
  56. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/core/__init__.py +0 -0
  57. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/core/_etc.py +0 -0
  58. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/core/algorithm.py +0 -0
  59. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/core/app.py +0 -0
  60. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/core/client.py +0 -0
  61. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/core/encoding.py +0 -0
  62. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/core/errors.py +0 -0
  63. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/core/multialgo.py +0 -0
  64. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/core/results.py +0 -0
  65. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/core/runner.py +0 -0
  66. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/core/serialization.py +0 -0
  67. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/core/static/css/index.css +0 -0
  68. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/core/static/css/info.css +0 -0
  69. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/core/templates/index.html +0 -0
  70. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/core/templates/info.html +0 -0
  71. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/core/tiling.py +0 -0
  72. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/demo/__init__.py +0 -0
  73. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/demo/sample_images/blobs.tif +0 -0
  74. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/demo/sample_images/tracks.tif +0 -0
  75. {imaging_server_kit-0.1.1/src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }} → imaging_server_kit-0.1.2/src/imaging_server_kit/template/serverkit-{{cookiecutter.name}}}/.dockerignore +0 -0
  76. {imaging_server_kit-0.1.1/src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }} → imaging_server_kit-0.1.2/src/imaging_server_kit/template/serverkit-{{cookiecutter.name}}}/.gitignore +0 -0
  77. {imaging_server_kit-0.1.1/src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }} → imaging_server_kit-0.1.2/src/imaging_server_kit/template/serverkit-{{cookiecutter.name}}}/Dockerfile +0 -0
  78. {imaging_server_kit-0.1.1/src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }} → imaging_server_kit-0.1.2/src/imaging_server_kit/template/serverkit-{{cookiecutter.name}}}/README.md +0 -0
  79. {imaging_server_kit-0.1.1/src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }} → imaging_server_kit-0.1.2/src/imaging_server_kit/template/serverkit-{{cookiecutter.name}}}/docker-compose.yml +0 -0
  80. {imaging_server_kit-0.1.1/src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }} → imaging_server_kit-0.1.2/src/imaging_server_kit/template/serverkit-{{cookiecutter.name}}}/requirements.txt +0 -0
  81. {imaging_server_kit-0.1.1/src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }} → imaging_server_kit-0.1.2/src/imaging_server_kit/template/serverkit-{{cookiecutter.name}}}/samples/blobs.tif +0 -0
  82. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/types/__init__.py +0 -0
  83. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/types/_bool.py +0 -0
  84. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/types/_boxes.py +0 -0
  85. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/types/_choice.py +0 -0
  86. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/types/_float.py +0 -0
  87. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/types/_image.py +0 -0
  88. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/types/_integer.py +0 -0
  89. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/types/_mask.py +0 -0
  90. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/types/_notification.py +0 -0
  91. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/types/_null.py +0 -0
  92. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/types/_paths.py +0 -0
  93. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/types/_points.py +0 -0
  94. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/types/_string.py +0 -0
  95. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/types/_tracks.py +0 -0
  96. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/types/_vectors.py +0 -0
  97. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/types/common.py +0 -0
  98. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/types/data_layer.py +0 -0
  99. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit.egg-info/dependency_links.txt +0 -0
  100. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit.egg-info/entry_points.txt +0 -0
  101. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit.egg-info/requires.txt +0 -0
  102. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit.egg-info/top_level.txt +0 -0
  103. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/tests/sample_images/blobs.tif +0 -0
  104. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/tests/test_basic.py +0 -0
  105. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/tests/test_multialgo.py +0 -0
  106. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/tests/test_results.py +0 -0
  107. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/tests/test_streaming.py +0 -0
  108. {imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/tests/test_tiling.py +0 -0
{imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
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  Name: imaging-server-kit
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- Version: 0.1.1
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+ Version: 0.1.2
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  Summary: Convert image processing functions to GUIs, FastAPI servers, and more.
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  Author-email: Mallory Wittwer <mallory.wittwer@epfl.ch>
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  License: Copyright (c) 2024, EPFL
{imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/docs/sections/04_multialgo.ipynb RENAMED
@@ -80,8 +80,14 @@
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  "\n",
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  "## Next steps\n",
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  "\n",
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- "In the next section, we will explore the concept of streamed inference in Imaging Server Kit."
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+ "In the next section, we will explore the concept of *live updates* in Imaging Server Kit."
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  ]
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+ },
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+ {
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+ "cell_type": "markdown",
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+ "id": "57909c69",
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+ "metadata": {},
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+ "source": []
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  }
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  ],
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  "metadata": {
{imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/docs/sections/05_streams.ipynb RENAMED
@@ -5,9 +5,9 @@
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  "id": "9ec31672",
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  "metadata": {},
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  "source": [
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- "# Streamed inference\n",
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+ "# Live updates\n",
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  "\n",
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- "Streamed inference allows an algorithm to send **intermediate outputs** to the client application before it has finished running. This makes it possible for user interfaces, such as the Napari Viewer, to update in real time.\n",
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+ "Algorithms can send **intermediate outputs** to the client application before they have finished running. This makes it possible for user interfaces, such as the Napari Viewer, to update in real time.\n",
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  "\n",
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  "For example, you might \"stream\":\n",
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  "\n",
@@ -56,7 +56,7 @@
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  "id": "c5f4b3d1",
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  "metadata": {},
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  "source": [
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- "Running this algorithm in Napari results in a \"streamed output\" showcasing a segmentation mask progressively updating as the threshold value increases.\n",
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+ "When running this algorithm in Napari, the displayed segmentation mask progressively gets updated as the threshold value increases.\n",
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  "\n",
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  "<video width=512 controls loop autoplay>\n",
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  " <source src=\"../_static/progressive_threshold.mp4\" type=\"video/mp4\">\n",
{imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/_version.py RENAMED
@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
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  commit_id: COMMIT_ID
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  __commit_id__: COMMIT_ID
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- __version__ = version = '0.1.1'
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- __version_tuple__ = version_tuple = (0, 1, 1)
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+ __version__ = version = '0.1.2'
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+ __version_tuple__ = version_tuple = (0, 1, 2)
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- __commit_id__ = commit_id = 'g81870ea47'
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+ __commit_id__ = commit_id = 'g7132691fd'
{imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/demo/examples.py RENAMED
@@ -50,7 +50,7 @@ def threshold_algo(image, threshold, dark_background):
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  mask = image > thresh_rel
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  else:
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  mask = image <= thresh_rel
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- return sk.Mask(mask, name="Binary mask (manual)")
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+ return sk.Mask(mask, name="Binarized image")
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  ## Automatic threshold
{imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit/template/cookiecutter.json RENAMED
@@ -1,5 +1,5 @@
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  {
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- "name": "Threshold",
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+ "name": "threshold",
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  "project_url": "https://github.com/scikit-image/scikit-image",
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  "python_version": "3.9"
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  }
imaging_server_kit-0.1.1/src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }}/main.py → imaging_server_kit-0.1.2/src/imaging_server_kit/template/serverkit-{{cookiecutter.name}}/main.py RENAMED
@@ -15,20 +15,20 @@ import imaging_server_kit as sk
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  project_url="{{ cookiecutter.project_url }}",
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  tags=["Segmentation"],
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  parameters={
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- "image": sk.Image(dimensionality=[2, 3]),
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+ "image": sk.Image(),
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  "threshold": sk.Float(
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  name="Threshold",
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- default=0.5,
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- min=0.0,
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- max=1.0,
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- step=0.1,
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- auto_call=True,
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+ default=128,
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+ min=0,
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+ max=255,
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+ step=1,
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+ auto_call=False,
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  ),
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  },
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  samples=[
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  {
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  "image": Path(__file__).parent / "samples" / "blobs.tif",
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- "threshold": 0.7,
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+ "threshold": 140,
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  }
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  ],
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  )
{imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: imaging-server-kit
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- Version: 0.1.1
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+ Version: 0.1.2
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  Summary: Convert image processing functions to GUIs, FastAPI servers, and more.
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  Author-email: Mallory Wittwer <mallory.wittwer@epfl.ch>
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  License: Copyright (c) 2024, EPFL
{imaging_server_kit-0.1.1 → imaging_server_kit-0.1.2}/src/imaging_server_kit.egg-info/SOURCES.txt RENAMED
@@ -73,14 +73,14 @@ src/imaging_server_kit/demo/examples.py
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  src/imaging_server_kit/demo/sample_images/blobs.tif
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  src/imaging_server_kit/demo/sample_images/tracks.tif
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  src/imaging_server_kit/template/cookiecutter.json
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- src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }}/.dockerignore
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- src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }}/.gitignore
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- src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }}/Dockerfile
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- src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }}/README.md
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- src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }}/docker-compose.yml
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- src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }}/main.py
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- src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }}/requirements.txt
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- src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }}/samples/blobs.tif
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+ src/imaging_server_kit/template/serverkit-{{cookiecutter.name}}/.dockerignore
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+ src/imaging_server_kit/template/serverkit-{{cookiecutter.name}}/.gitignore
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+ src/imaging_server_kit/template/serverkit-{{cookiecutter.name}}/Dockerfile
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+ src/imaging_server_kit/template/serverkit-{{cookiecutter.name}}/README.md
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+ src/imaging_server_kit/template/serverkit-{{cookiecutter.name}}/docker-compose.yml
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+ src/imaging_server_kit/template/serverkit-{{cookiecutter.name}}/main.py
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+ src/imaging_server_kit/template/serverkit-{{cookiecutter.name}}/requirements.txt
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+ src/imaging_server_kit/template/serverkit-{{cookiecutter.name}}/samples/blobs.tif
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  src/imaging_server_kit/types/__init__.py
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  src/imaging_server_kit/types/_bool.py
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  src/imaging_server_kit/types/_boxes.py