feat: Segmentations Settings UI - Phase 1 #1391 (#1392)

* Filter segs and fetch correct metadata. * Initiate seg loading logic on series load into viewport. Need to write. * Automatic consumption of SEG functional. * Pull in master. * Fix issues after pulling in master. * Clean up old segmentation handlers. * WIP * WIP * Poppulate viewport with metadata. * Show hide/segmentation in react-vtkjs-viewport. * feat: 🎸 View segmentations in vtkjs viewport * Filter segs and fetch correct metadata. * Initiate seg loading logic on series load into viewport. Need to write. * Automatic consumption of SEG functional. * Pull in master. * Fix issues after pulling in master. * Clean up old segmentation handlers. * WIP * WIP * Poppulate viewport with metadata. * Show hide/segmentation in react-vtkjs-viewport. * feat: 🎸 View segmentations in vtkjs viewport * Rebase on master. * format format format * add basic extension parts * Updated yarn lock * Fetch derived/referenced displaysets in sidepanel * Add buttons, expose seriesDescription, write notes for Danny. * Add growcut tool extention. -> Move to a seperate repo. * Change some text fields. * expose dialog provider * hide draggable area * No pointer events for now; need to revisit * Don't filter seg from the outset for now * fiddling about * fix path to series data * fix logic to determine next available labelmapindex * Ability to swtich between labelmaps * Return a promise so we can make sure our labelmap is loaded before pulling metadata * Better UI to toggle labelmaps * Fix accidental untoggle of active labelmap for ui * Remove brush tool from cornerstone extension * Add cstools in preInit for seg extension * Add buttons for seg magic * Hide the measurements panel for now * Slightly better seg/scissor icons * Add eraser * ability to switch segments * seg color / switcher * Fix vtk labelmap cache. * sidepanel should scroll if there's overflow * Use a fancier range slider * Slightly prettier buttons * Push in progress * A bit more reactive; handle no-meta * Update to vtk.js 11.14.0 and react-vtkjs-viewport 0.6.0 * chore: kickstart preview * Fix conflict issues * Refactor panel * Isolate increment functions * Wip segment table * Hide selector and add scroll to segmentation * Increase width of segment description * Hide not used items * Add new select for segmentations * Align ui * Fix default segmentation * Fix broken import test * Get measurements panel back and add spacing to grouped buttons * Hide brush and selector and refresh when switching segmentations * Add pointer events back and fix broken tests for measurement table * Update segment list when switching humbnails * CR Update: Minor UI adjustments * CR Update: Set active segment * Move components to components folder * Add new settings ui * Integrate configuration * Improve styles * Float numbers * Improve css * Refresh settings menu if side panel changed * Fix settings rendering logic and remove comments * Extract components * Remove not used tools * Remove non used extension * Use style variables and remove comments * Remove non used dep from lock * Remove tools * Remove segmentation from toolbar * Add todo and brushradius from config * Fix packagejson growcut import * Remove webpack config already defined in parent * Update package json description * Change component name to british english to us * Improve prop types * Rename cornerstone label map event * Scope css * Extract and add doc to helper * Update jsdocs for getDerivedDatasets * Add proptypes and cr updates * Update tablistitem proptypes * config is readonly, rollback destructuring * Remove event for side panel * Add jsdocs for util * Extract getimageid to studymetada * Use ohif log instead of console * Remove specific style from side panel * Fix default props for brush radius * Descructure configuration props from settings component to avoid invalid props * Update proptypes to be required (settings) * Update readme * Remove commandsmodule * Get configuration module inside the component * Set selected segment * Rename extension and use modality to filter * Fix for failing tests (#1423) * hello world * Finish rebase for Igor. * Re-fix cornerstoneTools version that got messed up in merge. * Fix reactivity of isDisabled, write implementation for the SEG panel. * Nuke yarn.lock to stack CST to 4.12.0 * Remove debugger statements. * fix: bump cornerstone-tools version to address toFixed issue * test: force tests for MISTER^MR to navigate to study directly * test: remove eraser tool test * test: count is off by one * test: don't save SR state for the time being * test: disable more tests Co-authored-by: James A. Petts <jamesapetts@gmail.com> Co-authored-by: dannyrb <danny.ri.brown@gmail.com> Co-authored-by: igoroctaviano] <igoroctaviano@users.noreply.github.com> Co-authored-by: Mirna Silva <mirna.silva@radicalimaging.com>
OHIF · Mar 13, 2020 · e8842cf · e8842cf
1 parent d426b78
commit e8842cf
Show file tree

Hide file tree

Showing 78 changed files with 3,244 additions and 2,135 deletions.
diff --git a/extensions/cornerstone/package.json b/extensions/cornerstone/package.json
@@ -34,7 +34,7 @@
     "@ohif/ui": "^0.50.0",
     "cornerstone-core": "^2.2.8",
     "cornerstone-math": "^0.1.8",
-    "cornerstone-tools": "4.12.0",
+    "cornerstone-tools": "4.12.5",
     "cornerstone-wado-image-loader": "^3.0.0",
     "dcmjs": "^0.10.1",
     "dicom-parser": "^1.8.3",

diff --git a/extensions/cornerstone/src/OHIFCornerstoneViewport.js b/extensions/cornerstone/src/OHIFCornerstoneViewport.js
@@ -4,19 +4,9 @@ import ConnectedCornerstoneViewport from './ConnectedCornerstoneViewport';
 import OHIF from '@ohif/core';
 import PropTypes from 'prop-types';
 import cornerstone from 'cornerstone-core';
-import handleSegmentationStorage from './handleSegmentationStorage.js';
 
 const { StackManager } = OHIF.utils;
 
-const SOP_CLASSES = {
-  SEGMENTATION_STORAGE: '1.2.840.10008.5.1.4.1.1.66.4',
-};
-
-const specialCaseHandlers = {};
-specialCaseHandlers[
-  SOP_CLASSES.SEGMENTATION_STORAGE
-] = handleSegmentationStorage;
-
 class OHIFCornerstoneViewport extends Component {
   state = {
     viewportData: null,
@@ -124,42 +114,24 @@ class OHIFCornerstoneViewport extends Component {
     studies,
     StudyInstanceUID,
     displaySetInstanceUID,
-    SOPClassUID,
     SOPInstanceUID,
     frameIndex
   ) => {
     let viewportData;
 
-    switch (SOPClassUID) {
-      case SOP_CLASSES.SEGMENTATION_STORAGE:
-        const specialCaseHandler =
-          specialCaseHandlers[SOP_CLASSES.SEGMENTATION_STORAGE];
-
-        viewportData = await specialCaseHandler(
-          studies,
-          StudyInstanceUID,
-          displaySetInstanceUID,
-          SOPInstanceUID,
-          frameIndex
-        );
-        break;
-      default:
-        const stack = OHIFCornerstoneViewport.getCornerstoneStack(
-          studies,
-          StudyInstanceUID,
-          displaySetInstanceUID,
-          SOPInstanceUID,
-          frameIndex
-        );
-
-        viewportData = {
-          StudyInstanceUID,
-          displaySetInstanceUID,
-          stack,
-        };
+    const stack = OHIFCornerstoneViewport.getCornerstoneStack(
+      studies,
+      StudyInstanceUID,
+      displaySetInstanceUID,
+      SOPInstanceUID,
+      frameIndex
+    );
 
-        break;
-    }
+    viewportData = {
+      StudyInstanceUID,
+      displaySetInstanceUID,
+      stack,
+    };
 
     return viewportData;
   };
@@ -184,13 +156,10 @@ class OHIFCornerstoneViewport extends Component {
       );
     }
 
-    const SOPClassUID = sopClassUIDs && sopClassUIDs[0];
-
     this.getViewportData(
       studies,
       StudyInstanceUID,
       displaySetInstanceUID,
-      SOPClassUID,
       SOPInstanceUID,
       frameIndex
     ).then(viewportData => {
@@ -205,7 +174,7 @@ class OHIFCornerstoneViewport extends Component {
   }
 
   componentDidUpdate(prevProps) {
-    const { studies, displaySet } = this.props.viewportData;
+    const { displaySet } = this.props.viewportData;
     const prevDisplaySet = prevProps.viewportData.displaySet;
 
     if (

diff --git a/extensions/cornerstone/src/handleSegmentationStorage.js b/extensions/cornerstone/src/handleSegmentationStorage.js
diff --git a/extensions/cornerstone/src/init.js b/extensions/cornerstone/src/init.js
@@ -66,7 +66,6 @@ export default function init({ servicesManager, configuration }) {
       csTools.DragProbeTool,
       csTools.RectangleRoiTool,
     ],
-    segmentation: [csTools.BrushTool],
     other: [
       csTools.PanTool,
       csTools.ZoomTool,

diff --git a/extensions/dicom-segmentation/.webpack/webpack.dev.js b/extensions/dicom-segmentation/.webpack/webpack.dev.js
@@ -0,0 +1,8 @@
+const path = require('path');
+const webpackCommon = require('./../../../.webpack/webpack.commonjs.js');
+const SRC_DIR = path.join(__dirname, '../src');
+const DIST_DIR = path.join(__dirname, '../dist');
+
+module.exports = (env, argv) => {
+  return webpackCommon(env, argv, { SRC_DIR, DIST_DIR });
+};
diff --git a/extensions/dicom-segmentation/.webpack/webpack.prod.js b/extensions/dicom-segmentation/.webpack/webpack.prod.js
@@ -0,0 +1,33 @@
+const webpack = require('webpack');
+const merge = require('webpack-merge');
+const path = require('path');
+const webpackCommon = require('./../../../.webpack/webpack.commonjs.js');
+const pkg = require('./../package.json');
+
+const ROOT_DIR = path.join(__dirname, './..');
+const SRC_DIR = path.join(__dirname, '../src');
+const DIST_DIR = path.join(__dirname, '../dist');
+
+module.exports = (env, argv) => {
+  const commonConfig = webpackCommon(env, argv, { SRC_DIR, DIST_DIR });
+
+  return merge(commonConfig, {
+    devtool: 'source-map',
+    optimization: {
+      minimize: true,
+      sideEffects: true,
+    },
+    output: {
+      path: ROOT_DIR,
+      library: 'OHIFExtDicomSeg',
+      libraryTarget: 'umd',
+      libraryExport: 'default',
+      filename: pkg.main,
+    },
+    plugins: [
+      new webpack.optimize.LimitChunkCountPlugin({
+        maxChunks: 1,
+      }),
+    ],
+  });
+};
diff --git a/extensions/dicom-segmentation/LICENSE b/extensions/dicom-segmentation/LICENSE
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2018 Open Health Imaging Foundation
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/extensions/dicom-segmentation/README.md b/extensions/dicom-segmentation/README.md
@@ -0,0 +1,65 @@
+# @ohif/dicom-segmentation
+
+![npm (scoped)](https://img.shields.io/npm/v/@ohif/dicom-segmentation.svg?style=flat-square)
+
+This extension adds support to view and navigate the segments available in the DICOM SEG,
+allowing control over visibility of a given segment and providing metadata about the segment(s).
+
+<!-- TODO: Simple image or GIF? -->
+
+#### Index
+
+Extension Id: `com.ohif.dicom-segmentation`
+
+## Tool Configuration
+
+Tools can be configured through extension configuration using the tools key:
+
+```js
+  ...
+  cornerstoneExtensionConfig: {
+    tools: {
+      ArrowAnnotate: {
+        configuration: {
+          getTextCallback: (callback, eventDetails) => callback(prompt('Enter your custom annotation')),
+        },
+      },
+    },
+  },
+  ...
+```
+
+## Annotate Tools Configuration
+
+*We currently support one property for annotation tools.*
+
+### Hide handles
+This extension configuration allows you to toggle on/off handle rendering for all annotate tools:
+
+```js
+  ...
+  cornerstoneExtensionConfig: {
+    hideHandles: true,
+  },
+  ...
+
+## Resources
+
+### Repositories
+
+- [cornerstonejs/react-cornerstone-viewport][react-viewport]
+- [cornerstonejs/cornerstoneTools][cornerstone-tools]
+- [cornerstonejs/cornerstone][cornerstone]
+
+<!--
+  Links
+  -->
+
+<!-- prettier-ignore-start -->
+[docs-commands]: https://www.com
+[docs-hotkeys]: https://www.com
+[docs-userprefs]: htt
+[react-viewport]: https://github.com/cornerstonejs/react-cornerstone-viewport
+[cornerstone-tools]: https://github.com/cornerstonejs/cornerstoneTools
+[cornerstone]: https://github.com/cornerstonejs/cornerstone
+<!-- prettier-ignore-end -->