imaging-server-kit 0.0.9__tar.gz → 0.0.10__tar.gz

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Files changed (127) hide show
  1. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/PKG-INFO +1 -1
  2. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/_version.py +2 -2
  3. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/core/decorator.py +28 -1
  4. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit.egg-info/PKG-INFO +1 -1
  5. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/.dockerignore +0 -0
  6. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/.gitattributes +0 -0
  7. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/.github/workflows/deploy.yml +0 -0
  8. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/.github/workflows/publish.yml +0 -0
  9. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/.gitignore +0 -0
  10. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/Dockerfile +0 -0
  11. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/Dockerfile-GPU +0 -0
  12. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/LICENSE +0 -0
  13. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/MANIFEST.in +0 -0
  14. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/README.md +0 -0
  15. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/build.sh +0 -0
  16. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/docs/_config.yml +0 -0
  17. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/docs/_toc.yml +0 -0
  18. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/docs/assets/screenshot_napari_threshold.png +0 -0
  19. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/docs/assets/screenshot_running_server.png +0 -0
  20. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/docs/index.md +0 -0
  21. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/docs/logo.ico +0 -0
  22. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/docs/sections/algorithm_server.md +0 -0
  23. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/docs/sections/api_endpoints.md +0 -0
  24. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/docs/sections/authentication.md +0 -0
  25. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/docs/sections/client_apps.md +0 -0
  26. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/docs/sections/docker.md +0 -0
  27. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/docs/sections/examples.md +0 -0
  28. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/docs/sections/getting_started.md +0 -0
  29. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/docs/sections/multi_algo_server.md +0 -0
  30. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/basic/auto_threshold.py +0 -0
  31. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/basic/multi_algo.py +0 -0
  32. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/basic/sample_images/blobs.tif +0 -0
  33. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/basic/threshold.py +0 -0
  34. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/docker-compose.yml +0 -0
  35. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-cellpose/Dockerfile +0 -0
  36. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-cellpose/README.md +0 -0
  37. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-cellpose/docker-compose.yml +0 -0
  38. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-cellpose/main.py +0 -0
  39. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-cellpose/requirements.txt +0 -0
  40. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-cellpose/sample_images/nuclei_2d.tif +0 -0
  41. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-orientationpy/Dockerfile +0 -0
  42. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-orientationpy/README.md +0 -0
  43. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-orientationpy/docker-compose.yml +0 -0
  44. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-orientationpy/main.py +0 -0
  45. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-orientationpy/requirements.txt +0 -0
  46. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-orientationpy/sample_images/image1_from_OrientationJ.tif +0 -0
  47. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-rembg/Dockerfile +0 -0
  48. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-rembg/README.md +0 -0
  49. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-rembg/docker-compose.yml +0 -0
  50. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-rembg/main.py +0 -0
  51. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-rembg/requirements.txt +0 -0
  52. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-rembg/sample_images/astronaut.tif +0 -0
  53. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-skimage-log/Dockerfile +0 -0
  54. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-skimage-log/README.md +0 -0
  55. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-skimage-log/docker-compose.yml +0 -0
  56. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-skimage-log/main.py +0 -0
  57. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-skimage-log/requirements.txt +0 -0
  58. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-skimage-log/sample_images/blobs.tif +0 -0
  59. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-skimage-log/sample_images/tracks.tif +0 -0
  60. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-stardist/Dockerfile +0 -0
  61. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-stardist/README.md +0 -0
  62. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-stardist/docker-compose.yml +0 -0
  63. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-stardist/main.py +0 -0
  64. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-stardist/requirements.txt +0 -0
  65. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-stardist/sample_images/nuclei_2d.tif +0 -0
  66. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-trackpy/Dockerfile +0 -0
  67. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-trackpy/README.md +0 -0
  68. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-trackpy/docker-compose.yml +0 -0
  69. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-trackpy/main.py +0 -0
  70. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-trackpy/requirements.txt +0 -0
  71. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/examples/servers/serverkit-trackpy/sample_images/tracks.tif +0 -0
  72. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/main.py +0 -0
  73. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/pyproject.toml +0 -0
  74. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/setup.cfg +0 -0
  75. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/__init__.py +0 -0
  76. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/auth/__init__.py +0 -0
  77. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/auth/authenticated_server.py +0 -0
  78. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/auth/static/css/login.css +0 -0
  79. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/auth/static/css/register.css +0 -0
  80. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/auth/static/js/login_script.js +0 -0
  81. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/auth/static/js/register_script.js +0 -0
  82. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/auth/templates/login.html +0 -0
  83. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/auth/templates/register.html +0 -0
  84. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/auth/utils/__init__.py +0 -0
  85. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/auth/utils/db.py +0 -0
  86. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/auth/utils/schemas.py +0 -0
  87. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/auth/utils/users.py +0 -0
  88. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/cli.py +0 -0
  89. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/client/__init__.py +0 -0
  90. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/client/client.py +0 -0
  91. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/core/__init__.py +0 -0
  92. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/core/encoding.py +0 -0
  93. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/core/errors.py +0 -0
  94. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/core/geometry.py +0 -0
  95. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/core/serialization.py +0 -0
  96. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/core/server.py +0 -0
  97. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/core/static/css/index.css +0 -0
  98. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/core/static/css/info.css +0 -0
  99. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/core/templates/index.html +0 -0
  100. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/core/templates/info.html +0 -0
  101. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/core/ui_library.py +0 -0
  102. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/demo/__init__.py +0 -0
  103. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/demo/sample_images/blobs.tif +0 -0
  104. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/demo/threshold.py +0 -0
  105. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/hub/__init__.py +0 -0
  106. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/hub/algorithm_hub.py +0 -0
  107. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/hub/multialgo_server.py +0 -0
  108. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/template/cookiecutter.json +0 -0
  109. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }}/.dockerignore +0 -0
  110. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }}/.gitignore +0 -0
  111. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }}/Dockerfile +0 -0
  112. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }}/README.md +0 -0
  113. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }}/docker-compose.yml +0 -0
  114. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }}/main.py +0 -0
  115. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }}/requirements.txt +0 -0
  116. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }}/sample_images/blobs.tif +0 -0
  117. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit.egg-info/SOURCES.txt +0 -0
  118. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit.egg-info/dependency_links.txt +0 -0
  119. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit.egg-info/entry_points.txt +0 -0
  120. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit.egg-info/requires.txt +0 -0
  121. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/src/imaging_server_kit.egg-info/top_level.txt +0 -0
  122. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/start_algorithm_hub.py +0 -0
  123. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/tests/test_error_paths.py +0 -0
  124. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/tests/test_import.py +0 -0
  125. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/tests/test_multialgo_server.py +0 -0
  126. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/tests/test_parameter_schema.py +0 -0
  127. {imaging_server_kit-0.0.9 → imaging_server_kit-0.0.10}/tests/test_simple_server.py +0 -0
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: imaging-server-kit
3
- Version: 0.0.9
3
+ Version: 0.0.10
4
4
  Summary: Deploy image processing algorithms in FastAPI servers.
5
5
  Author-email: Mallory Wittwer <mallory.wittwer@epfl.ch>
6
6
  License: Copyright (c) 2024, EPFL
@@ -17,5 +17,5 @@ __version__: str
17
17
  __version_tuple__: VERSION_TUPLE
18
18
  version_tuple: VERSION_TUPLE
19
19
 
20
- __version__ = version = '0.0.9'
21
- __version_tuple__ = version_tuple = (0, 0, 9)
20
+ __version__ = version = '0.0.10'
21
+ __version_tuple__ = version_tuple = (0, 0, 10)
@@ -20,7 +20,17 @@ def decode_image_array(cls, v, dimensionality) -> "np.ndarray":
20
20
 
21
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  return image_array
22
22
 
23
- # TODO - we could also validate the points or vectors dimensionality
23
+ def decode_points_array(cls, v, dimensionality) -> "np.ndarray":
24
+ points_array = decode_contents(v)
25
+
26
+ if points_array.shape[1] not in dimensionality:
27
+ raise ValueError("Array has the wrong dimensionality.")
28
+
29
+ return points_array
30
+
31
+ def decode_generic(cls, v, dimensionality) -> "np.ndarray":
32
+ # TODO: there should also be functions to validate dimensionality for tracks and vectors.
33
+ return decode_contents(v)
24
34
 
25
35
  def parse_params(parameters: dict) -> BaseModel:
26
36
  fields = {}
@@ -48,6 +58,7 @@ def parse_params(parameters: dict) -> BaseModel:
48
58
  "widget_type"
49
59
  ] = param_details.widget_type
50
60
 
61
+
51
62
  if param_details.widget_type in ["image", "mask"]:
52
63
  validated_func = partial(
53
64
  decode_image_array, dimensionality=param_details.dimensionality
@@ -56,6 +67,22 @@ def parse_params(parameters: dict) -> BaseModel:
56
67
  validators[validator_name] = field_validator(param_name, mode="after")(
57
68
  validated_func
58
69
  )
70
+ elif param_details.widget_type == "points":
71
+ validated_func = partial(
72
+ decode_points_array, dimensionality=param_details.dimensionality
73
+ )
74
+ validator_name = f"validate_{param_name}_image"
75
+ validators[validator_name] = field_validator(param_name, mode="after")(
76
+ validated_func
77
+ )
78
+ elif param_details.widget_type in ["vectors", "tracks", "shapes"]:
79
+ validated_func = partial(
80
+ decode_generic, dimensionality=param_details.dimensionality
81
+ )
82
+ validator_name = f"validate_{param_name}_image"
83
+ validators[validator_name] = field_validator(param_name, mode="after")(
84
+ validated_func
85
+ )
59
86
 
60
87
  fields[param_name] = (param_details.type, Field(**field_constraints))
61
88
 
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: imaging-server-kit
3
- Version: 0.0.9
3
+ Version: 0.0.10
4
4
  Summary: Deploy image processing algorithms in FastAPI servers.
5
5
  Author-email: Mallory Wittwer <mallory.wittwer@epfl.ch>
6
6
  License: Copyright (c) 2024, EPFL