@aics/vole-app 2.11.0

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 (135) hide show
  1. package/LICENSE +33 -0
  2. package/LICENSE.txt +26 -0
  3. package/README.md +45 -0
  4. package/es/aics-image-viewer/assets/fonts/open-sans/open-sans-500.eot +0 -0
  5. package/es/aics-image-viewer/assets/fonts/open-sans/open-sans-500.js +2337 -0
  6. package/es/aics-image-viewer/assets/fonts/open-sans/open-sans-500.svg +604 -0
  7. package/es/aics-image-viewer/assets/fonts/open-sans/open-sans-500.ttf +0 -0
  8. package/es/aics-image-viewer/assets/fonts/open-sans/open-sans-500.woff +0 -0
  9. package/es/aics-image-viewer/assets/fonts/open-sans/open-sans-500.woff2 +0 -0
  10. package/es/aics-image-viewer/assets/fonts/open-sans/open-sans-700.eot +0 -0
  11. package/es/aics-image-viewer/assets/fonts/open-sans/open-sans-700.js +2336 -0
  12. package/es/aics-image-viewer/assets/fonts/open-sans/open-sans-700.svg +604 -0
  13. package/es/aics-image-viewer/assets/fonts/open-sans/open-sans-700.ttf +0 -0
  14. package/es/aics-image-viewer/assets/fonts/open-sans/open-sans-700.woff +0 -0
  15. package/es/aics-image-viewer/assets/fonts/open-sans/open-sans-700.woff2 +0 -0
  16. package/es/aics-image-viewer/assets/fonts/open-sans/open-sans-regular.eot +0 -0
  17. package/es/aics-image-viewer/assets/fonts/open-sans/open-sans-regular.js +2337 -0
  18. package/es/aics-image-viewer/assets/fonts/open-sans/open-sans-regular.svg +604 -0
  19. package/es/aics-image-viewer/assets/fonts/open-sans/open-sans-regular.ttf +0 -0
  20. package/es/aics-image-viewer/assets/fonts/open-sans/open-sans-regular.woff +0 -0
  21. package/es/aics-image-viewer/assets/fonts/open-sans/open-sans-regular.woff2 +0 -0
  22. package/es/aics-image-viewer/assets/icons/axes.js +20 -0
  23. package/es/aics-image-viewer/assets/icons/boundingBox.js +18 -0
  24. package/es/aics-image-viewer/assets/icons/camera.js +15 -0
  25. package/es/aics-image-viewer/assets/icons/channels.js +15 -0
  26. package/es/aics-image-viewer/assets/icons/closePanel.js +18 -0
  27. package/es/aics-image-viewer/assets/icons/download.js +17 -0
  28. package/es/aics-image-viewer/assets/icons/dropdownArrow.js +15 -0
  29. package/es/aics-image-viewer/assets/icons/index.js +24 -0
  30. package/es/aics-image-viewer/assets/icons/metadata.js +15 -0
  31. package/es/aics-image-viewer/assets/icons/preferences.js +15 -0
  32. package/es/aics-image-viewer/assets/icons/resetView.js +16 -0
  33. package/es/aics-image-viewer/assets/icons/svg.d.js +0 -0
  34. package/es/aics-image-viewer/assets/icons/turnTable.js +18 -0
  35. package/es/aics-image-viewer/assets/styles/animatedEllipsis.css +21 -0
  36. package/es/aics-image-viewer/assets/styles/globals.css +35 -0
  37. package/es/aics-image-viewer/assets/styles/noui-slider-override.css +1 -0
  38. package/es/aics-image-viewer/assets/styles/variables.css +1 -0
  39. package/es/aics-image-viewer/components/App/ChannelUpdater.js +96 -0
  40. package/es/aics-image-viewer/components/App/index.js +849 -0
  41. package/es/aics-image-viewer/components/App/styles.css +60 -0
  42. package/es/aics-image-viewer/components/App/types.js +1 -0
  43. package/es/aics-image-viewer/components/AxisClipSliders/index.js +285 -0
  44. package/es/aics-image-viewer/components/AxisClipSliders/styles.css +257 -0
  45. package/es/aics-image-viewer/components/BottomPanel/index.js +70 -0
  46. package/es/aics-image-viewer/components/BottomPanel/styles.css +85 -0
  47. package/es/aics-image-viewer/components/CellViewerCanvasWrapper/index.js +113 -0
  48. package/es/aics-image-viewer/components/CellViewerCanvasWrapper/styles.css +12 -0
  49. package/es/aics-image-viewer/components/ChannelsWidget.js +100 -0
  50. package/es/aics-image-viewer/components/ChannelsWidgetRow/index.js +158 -0
  51. package/es/aics-image-viewer/components/ChannelsWidgetRow/styles.css +38 -0
  52. package/es/aics-image-viewer/components/ColorPicker.js +120 -0
  53. package/es/aics-image-viewer/components/ControlPanel/index.js +180 -0
  54. package/es/aics-image-viewer/components/ControlPanel/styles.css +169 -0
  55. package/es/aics-image-viewer/components/CustomizeWidget.js +46 -0
  56. package/es/aics-image-viewer/components/ErrorAlert/index.js +144 -0
  57. package/es/aics-image-viewer/components/ErrorAlert/styles.css +22 -0
  58. package/es/aics-image-viewer/components/GlobalVolumeControls.js +38 -0
  59. package/es/aics-image-viewer/components/MetadataViewer/index.js +99 -0
  60. package/es/aics-image-viewer/components/MetadataViewer/styles.css +81 -0
  61. package/es/aics-image-viewer/components/StyleProvider/index.js +210 -0
  62. package/es/aics-image-viewer/components/TfEditor/index.js +584 -0
  63. package/es/aics-image-viewer/components/TfEditor/styles.css +88 -0
  64. package/es/aics-image-viewer/components/Toolbar/DownloadButton.js +55 -0
  65. package/es/aics-image-viewer/components/Toolbar/ViewModeRadioButtons.js +22 -0
  66. package/es/aics-image-viewer/components/Toolbar/index.js +274 -0
  67. package/es/aics-image-viewer/components/Toolbar/styles.css +241 -0
  68. package/es/aics-image-viewer/components/ViewerStateProvider/ResetStateProvider.js +160 -0
  69. package/es/aics-image-viewer/components/ViewerStateProvider/index.js +261 -0
  70. package/es/aics-image-viewer/components/ViewerStateProvider/types.js +1 -0
  71. package/es/aics-image-viewer/components/shared/NumericInput/index.js +147 -0
  72. package/es/aics-image-viewer/components/shared/NumericInput/styles.css +64 -0
  73. package/es/aics-image-viewer/components/shared/SharedCheckBox.js +17 -0
  74. package/es/aics-image-viewer/components/shared/SliderRow/index.js +31 -0
  75. package/es/aics-image-viewer/components/shared/SliderRow/styles.css +19 -0
  76. package/es/aics-image-viewer/components/shared/SmarterSlider.js +40 -0
  77. package/es/aics-image-viewer/components/shared/ViewerIcon.js +22 -0
  78. package/es/aics-image-viewer/shared/colorPalette.js +19 -0
  79. package/es/aics-image-viewer/shared/constants.js +164 -0
  80. package/es/aics-image-viewer/shared/enums.js +18 -0
  81. package/es/aics-image-viewer/shared/types.js +6 -0
  82. package/es/aics-image-viewer/shared/utils/colorRepresentations.js +16 -0
  83. package/es/aics-image-viewer/shared/utils/controlPointsToLut.js +182 -0
  84. package/es/aics-image-viewer/shared/utils/hooks.js +51 -0
  85. package/es/aics-image-viewer/shared/utils/httpClient.js +57 -0
  86. package/es/aics-image-viewer/shared/utils/playControls.js +97 -0
  87. package/es/aics-image-viewer/shared/utils/sceneStore.js +140 -0
  88. package/es/aics-image-viewer/shared/utils/sliderValuesToImageValues.js +36 -0
  89. package/es/aics-image-viewer/shared/utils/test/viewerChannelSettings.test.js +132 -0
  90. package/es/aics-image-viewer/shared/utils/utilsService.js +54 -0
  91. package/es/aics-image-viewer/shared/utils/viewerChannelSettings.js +152 -0
  92. package/es/aics-image-viewer/shared/utils/viewerState.js +69 -0
  93. package/es/aics-image-viewer/shared/utils/webgl-debug.js +1103 -0
  94. package/es/index.js +4 -0
  95. package/package.json +130 -0
  96. package/type-declarations/aics-image-viewer/assets/icons/index.d.ts +14 -0
  97. package/type-declarations/aics-image-viewer/components/App/ChannelUpdater.d.ts +16 -0
  98. package/type-declarations/aics-image-viewer/components/App/index.d.ts +6 -0
  99. package/type-declarations/aics-image-viewer/components/App/types.d.ts +45 -0
  100. package/type-declarations/aics-image-viewer/components/AxisClipSliders/index.d.ts +24 -0
  101. package/type-declarations/aics-image-viewer/components/BottomPanel/index.d.ts +11 -0
  102. package/type-declarations/aics-image-viewer/components/CellViewerCanvasWrapper/index.d.ts +33 -0
  103. package/type-declarations/aics-image-viewer/components/ChannelsWidget.d.ts +19 -0
  104. package/type-declarations/aics-image-viewer/components/ChannelsWidgetRow/index.d.ts +17 -0
  105. package/type-declarations/aics-image-viewer/components/ColorPicker.d.ts +13 -0
  106. package/type-declarations/aics-image-viewer/components/ControlPanel/index.d.ts +20 -0
  107. package/type-declarations/aics-image-viewer/components/CustomizeWidget.d.ts +15 -0
  108. package/type-declarations/aics-image-viewer/components/ErrorAlert/index.d.ts +12 -0
  109. package/type-declarations/aics-image-viewer/components/GlobalVolumeControls.d.ts +21 -0
  110. package/type-declarations/aics-image-viewer/components/MetadataViewer/index.d.ts +7 -0
  111. package/type-declarations/aics-image-viewer/components/StyleProvider/index.d.ts +5 -0
  112. package/type-declarations/aics-image-viewer/components/TfEditor/index.d.ts +19 -0
  113. package/type-declarations/aics-image-viewer/components/Toolbar/DownloadButton.d.ts +8 -0
  114. package/type-declarations/aics-image-viewer/components/Toolbar/ViewModeRadioButtons.d.ts +8 -0
  115. package/type-declarations/aics-image-viewer/components/Toolbar/index.d.ts +31 -0
  116. package/type-declarations/aics-image-viewer/components/ViewerStateProvider/ResetStateProvider.d.ts +34 -0
  117. package/type-declarations/aics-image-viewer/components/ViewerStateProvider/index.d.ts +33 -0
  118. package/type-declarations/aics-image-viewer/components/ViewerStateProvider/types.d.ts +105 -0
  119. package/type-declarations/aics-image-viewer/components/shared/NumericInput/index.d.ts +19 -0
  120. package/type-declarations/aics-image-viewer/components/shared/SharedCheckBox.d.ts +9 -0
  121. package/type-declarations/aics-image-viewer/components/shared/SliderRow/index.d.ts +17 -0
  122. package/type-declarations/aics-image-viewer/components/shared/SmarterSlider.d.ts +5 -0
  123. package/type-declarations/aics-image-viewer/components/shared/ViewerIcon.d.ts +9 -0
  124. package/type-declarations/aics-image-viewer/shared/constants.d.ts +40 -0
  125. package/type-declarations/aics-image-viewer/shared/enums.d.ts +15 -0
  126. package/type-declarations/aics-image-viewer/shared/types.d.ts +15 -0
  127. package/type-declarations/aics-image-viewer/shared/utils/colorRepresentations.d.ts +10 -0
  128. package/type-declarations/aics-image-viewer/shared/utils/controlPointsToLut.d.ts +53 -0
  129. package/type-declarations/aics-image-viewer/shared/utils/hooks.d.ts +14 -0
  130. package/type-declarations/aics-image-viewer/shared/utils/playControls.d.ts +27 -0
  131. package/type-declarations/aics-image-viewer/shared/utils/sceneStore.d.ts +17 -0
  132. package/type-declarations/aics-image-viewer/shared/utils/sliderValuesToImageValues.d.ts +10 -0
  133. package/type-declarations/aics-image-viewer/shared/utils/viewerChannelSettings.d.ts +46 -0
  134. package/type-declarations/aics-image-viewer/shared/utils/viewerState.d.ts +10 -0
  135. package/type-declarations/index.d.ts +7 -0
package/LICENSE ADDED
@@ -0,0 +1,33 @@
1
+ Allen Institute Software License – This software license is the 2-clause BSD
2
+ license plus clause a third clause that prohibits redistribution and use for
3
+ commercial purposes without further permission.
4
+
5
+ Copyright © 2020. Allen Institute. All rights reserved.
6
+
7
+ Redistribution and use in source and binary forms, with or without
8
+ modification, are permitted provided that the following conditions are met:
9
+
10
+ 1. Redistributions of source code must retain the above copyright notice, this
11
+ list of conditions and the following disclaimer.
12
+
13
+ 2. Redistributions in binary form must reproduce the above copyright notice,
14
+ this list of conditions and the following disclaimer in the documentation
15
+ and/or other materials provided with the distribution.
16
+
17
+ 3. Redistributions and use for commercial purposes are not permitted without
18
+ the Allen Institute’s written permission. For purposes of this license,
19
+ commercial purposes are the incorporation of the Allen Institute's software
20
+ into anything for which you will charge fees or other compensation or use of
21
+ the software to perform a commercial service for a third party. Contact
22
+ terms@alleninstitute.org for commercial licensing opportunities.
23
+
24
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
25
+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
26
+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
27
+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
28
+ FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
29
+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
30
+ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
31
+ CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
32
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
33
+ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
package/LICENSE.txt ADDED
@@ -0,0 +1,26 @@
1
+ Allen Institute Software License – This software license is the 2-clause BSD license
2
+ plus clause a third clause that prohibits redistribution for commercial purposes without further permission.
3
+
4
+ Copyright © 2017. Allen Institute. All rights reserved.
5
+
6
+ Redistribution and use in source and binary forms, with or without modification, are permitted provided that the
7
+ following conditions are met:
8
+
9
+ 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the
10
+ following disclaimer.
11
+
12
+ 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the
13
+ following disclaimer in the documentation and/or other materials provided with the distribution.
14
+
15
+ 3. Redistributions for commercial purposes are not permitted without the Allen Institute’s written permission.
16
+ For purposes of this license, commercial purposes is the incorporation of the Allen Institute's software into
17
+ anything for which you will charge fees or other compensation. Contact terms@alleninstitute.org for commercial
18
+ licensing opportunities.
19
+
20
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
21
+ INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
22
+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
23
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
24
+ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
25
+ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
26
+ USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
package/README.md ADDED
@@ -0,0 +1,45 @@
1
+ # Vol-E App
2
+
3
+ Volume Explorer (Vol-E) is a browser based volume viewer built with React and WebGL (Three.js). This package wraps the [vole-core](https://github.com/allen-cell-animated/vole-core) library.
4
+
5
+ For the latest stable release, please visit [https://vole.allencell.org](https://vole.allencell.org)
6
+
7
+ Volume data is provided to the core 3d viewer via one of the following file formats:
8
+
9
+ - a url to a OME-ZARR image
10
+ - a url to a OME-TIFF file
11
+ - a json file containing dimensions and other metadata, and texture atlases (png files containing volume slices tiled across the 2d image). These texture atlases must be prepared in advance before loading into this viewer.
12
+
13
+ The volume shader itself is a heavily modified version of one that has distant origins in [Bisque](http://bioimage.ucsb.edu/bisque).
14
+
15
+ ## to use
16
+
17
+ - `https://vole.allencell.org/?url=path/to/ZARR`
18
+ - for more url parameters, see [`URL_SPEC.md`](documentation\URL_SPEC.md)
19
+
20
+ or as React component:
21
+
22
+ - `npm install @aics/vole-app`
23
+ - import the app as `import { ImageViewerApp } from "@aics/vole-app"`
24
+ - send in props as is shown in [`public/index.jsx`](public/index.tsx)
25
+
26
+ ```jsx
27
+ <ImageViewerApp
28
+ baseUrl="http://dev-aics-dtp-001.corp.alleninstitute.org/cellviewer-1-4-0/Cell-Viewer_Thumbnails/"
29
+ cellPath="AICS-17/AICS-17_4187_23618_atlas.json"
30
+ // ... (also see src/aics-image-viewer/components/App/types.ts for full props specification) ...
31
+ />
32
+ ```
33
+
34
+ ### Running with Docker
35
+
36
+ Clone the repository and run the following commands in the root of the project:
37
+
38
+ ```cmd
39
+ docker build -t vole-app-image .
40
+ docker run --rm -p 9020:80 --name vole-app vole-app-image
41
+ ```
42
+
43
+ This will create a new docker image called `vole-app` and run it on port 9020. You can access the viewer by navigating to [http://localhost:9020](http://localhost:9020) in your browser.
44
+
45
+ To rebuild changes, run the above commands again. (The `--rm` flag will automatically delete the existing container when it is stopped.)