@jax-data-science/sci-image-visualizer 0.8.2 → 0.9.0

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 (525) hide show
  1. package/README.md +201 -460
  2. package/esm2022/index.mjs +28 -15
  3. package/esm2022/lib/channel-histogram/channel-histogram.component.mjs +163 -91
  4. package/esm2022/lib/contracts/capabilities.contract.mjs +4 -3
  5. package/esm2022/lib/contracts/cell-segmenter.contract.mjs +1 -1
  6. package/esm2022/lib/contracts/channel-histogram-api.contract.mjs +5 -1
  7. package/esm2022/lib/contracts/color.mjs +60 -0
  8. package/esm2022/lib/contracts/colormap-lut.mjs +213 -57
  9. package/esm2022/lib/contracts/coordinate-transform.contract.mjs +1 -1
  10. package/esm2022/lib/contracts/display-types.mjs +11 -1
  11. package/esm2022/lib/contracts/instance-segmenter.contract.mjs +1 -1
  12. package/esm2022/lib/contracts/intensity.mjs +48 -5
  13. package/esm2022/lib/contracts/plot-type-contribution.contract.mjs +1 -1
  14. package/esm2022/lib/contracts/plot-type.mjs +134 -17
  15. package/esm2022/lib/contracts/ports/image-state.port.mjs +4 -1
  16. package/esm2022/lib/contracts/ports/preferences.port.mjs +5 -1
  17. package/esm2022/lib/contracts/ports/region-io.port.mjs +2 -1
  18. package/esm2022/lib/contracts/ports/spatial-data.port.mjs +5 -1
  19. package/esm2022/lib/contracts/ports/tile-access.port.mjs +2 -1
  20. package/esm2022/lib/contracts/region-editor-api.contract.mjs +1 -1
  21. package/esm2022/lib/contracts/region-overlay.contract.mjs +1 -1
  22. package/esm2022/lib/contracts/sam.contract.mjs +1 -1
  23. package/esm2022/lib/contracts/semantic-segmenter.contract.mjs +1 -1
  24. package/esm2022/lib/contracts/spatial-dataset.contract.mjs +3 -1
  25. package/esm2022/lib/contracts/toolbar-tool.contract.mjs +6 -4
  26. package/esm2022/lib/contracts/visualizer.contract.mjs +1 -1
  27. package/esm2022/lib/contracts/viz-config.mjs +2 -1
  28. package/esm2022/lib/geometry/contour.mjs +63 -0
  29. package/esm2022/lib/geometry/raster.mjs +98 -0
  30. package/esm2022/lib/geometry/ring.mjs +201 -0
  31. package/esm2022/lib/hex-color-picker/hex-color-picker.component.mjs +202 -102
  32. package/esm2022/lib/implementations/base-store-visualizer.mjs +201 -48
  33. package/esm2022/lib/implementations/napari-js/napari-axes-gizmo.mjs +65 -0
  34. package/esm2022/lib/implementations/napari-js/napari-display-state.mjs +136 -0
  35. package/esm2022/lib/implementations/napari-js/napari-helpers.mjs +199 -0
  36. package/esm2022/lib/implementations/napari-js/napari-image-2d-scene.mjs +602 -0
  37. package/esm2022/lib/implementations/napari-js/napari-loading-badge.mjs +3 -4
  38. package/esm2022/lib/implementations/napari-js/napari-loading-state.mjs +66 -0
  39. package/esm2022/lib/implementations/napari-js/napari-region-overlay.mjs +157 -591
  40. package/esm2022/lib/implementations/napari-js/napari-scene.mjs +2 -0
  41. package/esm2022/lib/implementations/napari-js/napari-spatial-2d-scene.mjs +614 -0
  42. package/esm2022/lib/implementations/napari-js/napari-spatial-3d-scene.mjs +769 -0
  43. package/esm2022/lib/implementations/napari-js/napari-spatial-encoding.mjs +199 -0
  44. package/esm2022/lib/implementations/napari-js/napari-spatial-hover.mjs +263 -0
  45. package/esm2022/lib/implementations/napari-js/napari-spatial-scene.mjs +159 -0
  46. package/esm2022/lib/implementations/napari-js/napari-spatial-tiles.mjs +106 -1408
  47. package/esm2022/lib/implementations/napari-js/napari-spatial-tooltip.mjs +2 -2
  48. package/esm2022/lib/implementations/napari-js/napari-surface-scene.mjs +271 -0
  49. package/esm2022/lib/implementations/napari-js/napari-tile-client.mjs +562 -0
  50. package/esm2022/lib/implementations/napari-js/napari-tool-bridge.mjs +344 -0
  51. package/esm2022/lib/implementations/napari-js/napari-visualizer.service.mjs +361 -4184
  52. package/esm2022/lib/implementations/napari-js/napari-volume-scene.mjs +439 -0
  53. package/esm2022/lib/implementations/napari-js/napari-volume-z-handle.mjs +6 -6
  54. package/esm2022/lib/implementations/napari-js/region-overlay/overlay-projection.mjs +96 -0
  55. package/esm2022/lib/implementations/napari-js/region-overlay/region-edit.mjs +35 -0
  56. package/esm2022/lib/implementations/napari-js/region-overlay/region-svg-renderer.mjs +182 -0
  57. package/esm2022/lib/implementations/napari-js/spatial-tiles/categorical-lookup.mjs +30 -0
  58. package/esm2022/lib/implementations/napari-js/spatial-tiles/cell-layers.mjs +274 -0
  59. package/esm2022/lib/implementations/napari-js/spatial-tiles/density-layer.mjs +144 -0
  60. package/esm2022/lib/implementations/napari-js/spatial-tiles/layer-groups.mjs +165 -0
  61. package/esm2022/lib/implementations/napari-js/spatial-tiles/plan-context.mjs +78 -0
  62. package/esm2022/lib/implementations/napari-js/spatial-tiles/transcript-hover.mjs +182 -0
  63. package/esm2022/lib/implementations/napari-js/spatial-tiles/transcript-jobs.mjs +369 -0
  64. package/esm2022/lib/implementations/napari-js/spatial-tiles/transcript-layers.mjs +306 -0
  65. package/esm2022/lib/implementations/osd/display-pipeline.mjs +102 -40
  66. package/esm2022/lib/implementations/osd/histogram-sampler.mjs +56 -31
  67. package/esm2022/lib/implementations/osd/openseadragon-viewer-options.mjs +128 -0
  68. package/esm2022/lib/implementations/osd/openseadragon-visualizer.service.mjs +333 -1685
  69. package/esm2022/lib/implementations/osd/osd-coordinate-transform.mjs +1 -1
  70. package/esm2022/lib/implementations/osd/osd-coords.mjs +5 -6
  71. package/esm2022/lib/implementations/osd/osd-export.mjs +122 -0
  72. package/esm2022/lib/implementations/osd/osd-lib.mjs +15 -1
  73. package/esm2022/lib/implementations/osd/osd-navigator-chrome.mjs +205 -0
  74. package/esm2022/lib/implementations/osd/osd-pixel-readback.mjs +68 -0
  75. package/esm2022/lib/implementations/osd/osd-region-overlay-draw.mjs +153 -0
  76. package/esm2022/lib/implementations/osd/osd-region-overlay.mjs +185 -718
  77. package/esm2022/lib/implementations/osd/osd-scale-bar.mjs +52 -60
  78. package/esm2022/lib/implementations/osd/osd-tile-source.mjs +105 -0
  79. package/esm2022/lib/implementations/osd/osd-viewer-like.mjs +2 -0
  80. package/esm2022/lib/implementations/osd/osd-viewer-mount.mjs +44 -0
  81. package/esm2022/lib/implementations/osd/osd-viewport.mjs +184 -0
  82. package/esm2022/lib/implementations/osd/osd-zoom.mjs +7 -1
  83. package/esm2022/lib/implementations/osd/simple-source.mjs +395 -0
  84. package/esm2022/lib/implementations/osd/slice-cache.mjs +53 -48
  85. package/esm2022/lib/implementations/osd/tile-client.mjs +32 -11
  86. package/esm2022/lib/implementations/osd/tile-recolor.mjs +330 -0
  87. package/esm2022/lib/implementations/plotly/omics-trace-builders.mjs +161 -73
  88. package/esm2022/lib/implementations/plotly/plotly-coordinate-transform.mjs +1 -1
  89. package/esm2022/lib/implementations/plotly/plotly-image-loader.mjs +112 -0
  90. package/esm2022/lib/implementations/plotly/plotly-image-recolor.mjs +178 -0
  91. package/esm2022/lib/implementations/plotly/plotly-intensity-inset.mjs +33 -0
  92. package/esm2022/lib/implementations/plotly/plotly-isosurface-controls.mjs +83 -0
  93. package/esm2022/lib/implementations/plotly/plotly-layouts.mjs +121 -0
  94. package/esm2022/lib/implementations/plotly/plotly-readback.mjs +117 -0
  95. package/esm2022/lib/implementations/plotly/plotly-region-overlay.mjs +19 -10
  96. package/esm2022/lib/implementations/plotly/plotly-shape-projection.mjs +223 -0
  97. package/esm2022/lib/implementations/plotly/plotly-trace-builders.mjs +79 -19
  98. package/esm2022/lib/implementations/plotly/plotly-zoom-controller.mjs +223 -0
  99. package/esm2022/lib/implementations/plotly/plotly.service.mjs +439 -1655
  100. package/esm2022/lib/implementations/region-centroids.mjs +47 -0
  101. package/esm2022/lib/implementations/simple-slice-access.service.mjs +22 -12
  102. package/esm2022/lib/implementations/spatial-data-http/spatial-data-http.service.mjs +172 -92
  103. package/esm2022/lib/implementations/spatial-data-http/spatial-wire.mjs +103 -22
  104. package/esm2022/lib/implementations/tile-server/index.mjs +6 -0
  105. package/esm2022/lib/implementations/tile-server/native-histogram.mjs +30 -0
  106. package/esm2022/lib/implementations/tile-server/poll-descriptor.mjs +65 -0
  107. package/esm2022/lib/implementations/tile-server/tile-protocol.mjs +42 -0
  108. package/esm2022/lib/implementations/tile-server/transport.mjs +135 -0
  109. package/esm2022/lib/intensity/intensity-profile.mjs +107 -0
  110. package/esm2022/lib/intensity/intensity-profile.service.mjs +223 -0
  111. package/esm2022/lib/intensity-inset/intensity-inset.component.mjs +133 -0
  112. package/esm2022/lib/models/bezier.mjs +1 -11
  113. package/esm2022/lib/models/class-preset.mjs +41 -3
  114. package/esm2022/lib/models/geometry.mjs +27 -164
  115. package/esm2022/lib/models/polygon-edit.mjs +254 -0
  116. package/esm2022/lib/models/polygon-factory.mjs +118 -0
  117. package/esm2022/lib/models/region-clone.mjs +68 -0
  118. package/esm2022/lib/models/region-geojson.mjs +373 -0
  119. package/esm2022/lib/models/region.mjs +34 -33
  120. package/esm2022/lib/models/shape.mjs +18 -16
  121. package/esm2022/lib/plot-mode/contribution-host.mjs +297 -0
  122. package/esm2022/lib/plot-mode/plot-mode-controller.mjs +9 -6
  123. package/esm2022/lib/plot-mode/plot-type-menu.mjs +85 -0
  124. package/esm2022/lib/plot-mode/tool-params-model.mjs +87 -0
  125. package/esm2022/lib/plot.utilities.mjs +296 -473
  126. package/esm2022/lib/processing/image-crop.mjs +1 -1
  127. package/esm2022/lib/processing/processing-image.mjs +28 -15
  128. package/esm2022/lib/provide-visualization.mjs +40 -14
  129. package/esm2022/lib/region-editor/classes-panel/classes-panel.component.mjs +99 -0
  130. package/esm2022/lib/region-editor/file-stem.mjs +13 -0
  131. package/esm2022/lib/region-editor/manage-classes-dialog/manage-classes-dialog.component.mjs +118 -0
  132. package/esm2022/lib/region-editor/mask-export.service.mjs +98 -0
  133. package/esm2022/lib/region-editor/mask-raster.mjs +11 -5
  134. package/esm2022/lib/region-editor/region-color-dialog/region-color-dialog.component.mjs +56 -0
  135. package/esm2022/lib/region-editor/region-editor-help/region-editor-help.component.mjs +28 -0
  136. package/esm2022/lib/region-editor/region-editor.component.mjs +402 -651
  137. package/esm2022/lib/region-editor/region-metrics.mjs +68 -0
  138. package/esm2022/lib/region-editor/region-persistence.service.mjs +134 -0
  139. package/esm2022/lib/region-editor/region-table/region-table.component.mjs +153 -0
  140. package/esm2022/lib/region-editor/save-mask-dialog/save-mask-dialog.component.mjs +91 -0
  141. package/esm2022/lib/region-editor/save-regions-dialog/save-regions-dialog.component.mjs +92 -0
  142. package/esm2022/lib/region-ops.service.mjs +28 -70
  143. package/esm2022/lib/region-overlay/region-geometry.mjs +360 -0
  144. package/esm2022/lib/region-overlay/region-hit-test.mjs +103 -0
  145. package/esm2022/lib/region-overlay/svg-region-renderer.mjs +228 -0
  146. package/esm2022/lib/render-orchestrator.mjs +14 -11
  147. package/esm2022/lib/render-session.mjs +207 -0
  148. package/esm2022/lib/routing-visualizer.service.mjs +459 -411
  149. package/esm2022/lib/spatial/density-raster.mjs +14 -0
  150. package/esm2022/lib/spatial/embedding-compute-coordinator.mjs +239 -0
  151. package/esm2022/lib/spatial/embedding-compute.mjs +43 -10
  152. package/esm2022/lib/spatial/gene-search.mjs +1 -1
  153. package/esm2022/lib/spatial/glyphs.mjs +97 -0
  154. package/esm2022/lib/spatial/lod.mjs +187 -0
  155. package/esm2022/lib/spatial/spatial-controls.facade.mjs +200 -0
  156. package/esm2022/lib/spatial/spatial-density.mjs +25 -16
  157. package/esm2022/lib/spatial/spatial-encoding.mjs +26 -82
  158. package/esm2022/lib/spatial/spatial-expression.mjs +43 -42
  159. package/esm2022/lib/spatial/spatial-framing.mjs +1 -1
  160. package/esm2022/lib/spatial/spatial-heatmap.mjs +6 -3
  161. package/esm2022/lib/spatial/spatial-hover.mjs +5 -33
  162. package/esm2022/lib/spatial/spatial-panel-model.mjs +282 -0
  163. package/esm2022/lib/spatial/spatial-sections.mjs +1 -1
  164. package/esm2022/lib/spatial/spatial-selection.mjs +33 -46
  165. package/esm2022/lib/spatial/spatial-tile-merge.mjs +219 -0
  166. package/esm2022/lib/spatial/spatial-tiles.mjs +12 -648
  167. package/esm2022/lib/spatial/spatial-volume-image.mjs +2 -4
  168. package/esm2022/lib/spatial/stats.mjs +71 -0
  169. package/esm2022/lib/spatial/transcript-grouping.mjs +307 -0
  170. package/esm2022/lib/spatial-controls/spatial-cells-panel/spatial-cells-panel.component.mjs +150 -0
  171. package/esm2022/lib/spatial-controls/spatial-charts/chart-data-model.mjs +309 -0
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  183. package/esm2022/lib/spatial-controls/spatial-key/spatial-key.model.mjs +67 -0
  184. package/esm2022/lib/spatial-controls/spatial-marker-genes-form/spatial-marker-genes-form.component.mjs +147 -0
  185. package/esm2022/lib/spatial-controls/spatial-observations-panel/spatial-observations-panel.component.mjs +300 -0
  186. package/esm2022/lib/spatial-controls/spatial-transcripts-panel/spatial-transcripts-panel.component.mjs +370 -0
  187. package/esm2022/lib/store/class-color.util.mjs +46 -3
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  201. package/esm2022/lib/toolbar/segmentation/cell-segment-tool.service.mjs +74 -78
  202. package/esm2022/lib/toolbar/segmentation/cellpose-segmenter.service.mjs +50 -8
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