fix(SR): Added support for spline and live wire SR items. (#5870)

* fix(SR): Added support for spline and live wire SR items.

* Apply suggestion from @greptile-apps[bot]

Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com>

* Add a script to checkout a worktree for test builds

* fix: Allow download for testing sr validator

* Remove script that wasn't intended to be included

* Bump CS3D version.

* PR comments - simplify code and use single codepath for download

* Allow both download and save buttons for SEG and RTSTRUCT

---------

Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com>
Co-authored-by: Bill Wallace <wayfarer3130@gmail.com>

extensions/cornerstone-dicom-seg/src/commandsModule.ts

@@ -2,9 +2,8 @@ import dcmjs from 'dcmjs';
 import { classes, Types, utils } from '@ohif/core';
 import { cache, metaData } from '@cornerstonejs/core';
 import { segmentation as cornerstoneToolsSegmentation } from '@cornerstonejs/tools';
-import { adaptersRT, helpers, adaptersSEG } from '@cornerstonejs/adapters';
+import { adaptersRT, adaptersSEG } from '@cornerstonejs/adapters';
 import { createReportDialogPrompt, useUIStateStore } from '@ohif/extension-default';
-import { DicomMetadataStore } from '@ohif/core';
 
 import PROMPT_RESPONSES from '../../default/src/utils/_shared/PROMPT_RESPONSES';
 
@@ -29,11 +28,11 @@ const {
   },
 } = adaptersRT;
 
-const { downloadDICOMData } = helpers;
 
 const commandsModule = ({
   servicesManager,
   extensionManager,
+  commandsManager,
 }: Types.Extensions.ExtensionParams): Types.Extensions.CommandsModule => {
   const { segmentationService, displaySetService, viewportGridService } =
     servicesManager.services as AppTypes.Services;
@@ -194,8 +193,11 @@ const commandsModule = ({
       const generatedSegmentation = actions.generateSegmentation({
         segmentationId,
       });
-
-      downloadDICOMData(generatedSegmentation.dataset, `${segmentationInOHIF.label}`);
+      const storeFn = commandsManager.runCommand('createStoreFunction', {
+        dataSource: 'download',
+        defaultFileName: `${segmentationInOHIF.label}.dcm`,
+      });
+      storeFn(generatedSegmentation.dataset);
     },
     /**
      * Stores a segmentation based on the provided segmentationId into a specified data source.
@@ -217,11 +219,10 @@ const commandsModule = ({
       }
 
       const { label, predecessorImageId } = segmentation;
-      const defaultDataSource = dataSource ?? extensionManager.getActiveDataSource()[0];
 
       const {
         value: reportName,
-        dataSourceName: selectedDataSource,
+        dataSourceName,
         series,
         priorSeriesNumber,
         action,
@@ -231,50 +232,58 @@ const commandsModule = ({
         predecessorImageId,
         title: 'Store Segmentation',
         modality,
+        enableDownload: true,
       });
 
-      if (action === PROMPT_RESPONSES.CREATE_REPORT) {
-        try {
-          const selectedDataSourceConfig = selectedDataSource
-            ? extensionManager.getDataSources(selectedDataSource)[0]
-            : defaultDataSource;
+      if (action !== PROMPT_RESPONSES.CREATE_REPORT) {
+        return;
+      }
 
-          const args = {
-            segmentationId,
-            options: {
-              SeriesDescription: series ? undefined : reportName || label || 'Contour Series',
-              SeriesNumber: series ? undefined : 1 + priorSeriesNumber,
-              predecessorImageId: series,
-            },
-          };
-          const generatedDataAsync =
-            (modality === 'SEG' && actions.generateSegmentation(args)) ||
-            (modality === 'RTSTRUCT' && actions.generateContour(args));
-          const generatedData = await generatedDataAsync;
+      const defaultFileName =
+        modality === 'RTSTRUCT'
+          ? `rtss-${segmentationId}.dcm`
+          : `${label || 'segmentation'}.dcm`;
 
-          if (!generatedData || !generatedData.dataset) {
-            throw new Error('Error during segmentation generation');
-          }
+      const storeFn = commandsManager.runCommand('createStoreFunction', {
+        dataSource: dataSourceName,
+        defaultFileName,
+      });
 
-          const { dataset: naturalizedReport } = generatedData;
+      if (!storeFn) {
+        throw new Error(`No valid store for dataSource: ${dataSourceName}`);
+      }
 
-          // DCMJS assigns a dummy study id during creation, and this can cause problems, so clearing it out
-          if (naturalizedReport.StudyID === 'No Study ID') {
-            naturalizedReport.StudyID = '';
-          }
+      try {
+        const args = {
+          segmentationId,
+          options: {
+            SeriesDescription: series ? undefined : reportName || label || 'Contour Series',
+            SeriesNumber: series ? undefined : 1 + priorSeriesNumber,
+            predecessorImageId: series,
+          },
+        };
+        const generatedDataAsync =
+          (modality === 'SEG' && actions.generateSegmentation(args)) ||
+          (modality === 'RTSTRUCT' && actions.generateContour(args));
+        const generatedData = await generatedDataAsync;
 
-          await selectedDataSourceConfig.store.dicom(naturalizedReport);
-
-          // add the information for where we stored it to the instance as well
-          naturalizedReport.wadoRoot = selectedDataSourceConfig.getConfig().wadoRoot;
-
-          DicomMetadataStore.addInstances([naturalizedReport], true);
-
-          return naturalizedReport;
-        } catch (error) {
-          console.debug('Error storing segmentation:', error);
-          throw error;
+        if (!generatedData?.dataset) {
+          throw new Error('Error during segmentation generation');
         }
+
+        const { dataset: naturalizedReport } = generatedData;
+
+        // DCMJS assigns a dummy study id during creation, and this can cause problems, so clearing it out
+        if (naturalizedReport.StudyID === 'No Study ID') {
+          naturalizedReport.StudyID = '';
+        }
+
+        await storeFn(naturalizedReport, {});
+
+        return naturalizedReport;
+      } catch (error) {
+        console.debug('Error storing segmentation:', error);
+        throw error;
       }
     },
 
@@ -307,14 +316,11 @@ const commandsModule = ({
     downloadRTSS: async args => {
       const { dataset } = await actions.generateContour(args);
       const { InstanceNumber: instanceNumber = 1, SeriesInstanceUID: seriesUID } = dataset;
-
-      try {
-        //Create a URL for the binary.
-        const filename = `rtss-${seriesUID}-${instanceNumber}.dcm`;
-        downloadDICOMData(dataset, filename);
-      } catch (e) {
-        console.warn(e);
-      }
+      const storeFn = commandsManager.runCommand('createStoreFunction', {
+        dataSource: 'download',
+        defaultFileName: `rtss-${seriesUID}-${instanceNumber}.dcm`,
+      });
+      await storeFn(dataset);
     },
 
     toggleActiveSegmentationUtility: ({ itemId: buttonId }) => {