feat(KOS): Key object selection (KOS) structured report (SR)

Bump DCMTK to include changes for fixing dcmsr. This will include the fix for accepting the hyperlink prefix for key object references as an argument (std::string). $ git shortlog 66fce68..f9da0c6 Shreeraj Jadhav (1): ENH: Replace HTML_HYPERLINK_PREFIX_FOR_CGI with std::string argument Modify operation structured-report-to-html to accept the hyperlink prefix as a string argument. This will be passed to the DSRDocument::renderHTML() function. Generate/update TS bindings for structured-report-to-html.
InsightSoftwareConsortium · Oct 5, 2022 · 564255c · 564255c
1 parent 4220397
commit 564255c
Show file tree

Hide file tree

Showing 9 changed files with 72 additions and 27 deletions.
diff --git a/dist/dicom/src/StructuredReportToHtmlOptions.ts b/dist/dicom/src/StructuredReportToHtmlOptions.ts
@@ -57,6 +57,9 @@ interface StructuredReportToHtmlOptions {
 by Specific Character Set (0008,0005) to UTF-8 */
   convertToUtf8?: boolean
 
+  /** URL: string. Append specificed URL prefix to hyperlinks of referenced composite objects in the document. */
+  urlPrefix?: string
+
   /** use only HTML version 3.2 compatible features */
   html32?: boolean
 

diff --git a/dist/dicom/src/readDicomEncapsulatedPdf.ts b/dist/dicom/src/readDicomEncapsulatedPdf.ts
@@ -1,6 +1,7 @@
 import {
   BinaryStream,
   InterfaceTypes,
+  PipelineInput,
   runPipeline
 } from 'itk-wasm'
 
@@ -23,7 +24,7 @@ async function readDicomEncapsulatedPdf(
   const desiredOutputs = [
     { type: InterfaceTypes.BinaryStream },
   ]
-  const inputs = [
+  const inputs: [ PipelineInput ] = [
     { type: InterfaceTypes.BinaryFile, data: { data: dicomFile, path: "file0" }  },
   ]
 

diff --git a/dist/dicom/src/readDicomEncapsulatedPdfNode.ts b/dist/dicom/src/readDicomEncapsulatedPdfNode.ts
@@ -1,6 +1,7 @@
 import {
   BinaryStream,
   InterfaceTypes,
+  PipelineInput,
   runPipelineNode
 } from 'itk-wasm'
 
@@ -24,7 +25,7 @@ async function readDicomEncapsulatedPdfNode(  dicomFile: Uint8Array,
   const desiredOutputs = [
     { type: InterfaceTypes.BinaryStream },
   ]
-  const inputs = [
+  const inputs: [ PipelineInput ] = [
     { type: InterfaceTypes.BinaryFile, data: { data: dicomFile, path: "file0" }  },
   ]
 

diff --git a/dist/dicom/src/structuredReportToHtml.ts b/dist/dicom/src/structuredReportToHtml.ts
@@ -1,6 +1,7 @@
 import {
   TextStream,
   InterfaceTypes,
+  PipelineInput,
   runPipeline
 } from 'itk-wasm'
 
@@ -23,7 +24,7 @@ async function structuredReportToHtml(
   const desiredOutputs = [
     { type: InterfaceTypes.TextStream },
   ]
-  const inputs = [
+  const inputs: [ PipelineInput ] = [
     { type: InterfaceTypes.BinaryFile, data: { data: dicomFile, path: "file0" }  },
   ]
 
@@ -80,14 +81,17 @@ async function structuredReportToHtml(
     args.push('--charset-require')
   }
   if (options.charsetAssume) {
-    args.push('--charset-assume', '1')
+    args.push('--charset-assume', options.charsetAssume.toString())
   }
   if (options.charsetCheckAll) {
     args.push('--charset-check-all')
   }
   if (options.convertToUtf8) {
     args.push('--convert-to-utf8')
   }
+  if (options.urlPrefix) {
+    args.push('--url-prefix', options.urlPrefix.toString())
+  }
   if (options.html32) {
     args.push('--html-3.2')
   }
@@ -101,10 +105,14 @@ async function structuredReportToHtml(
     args.push('--add-document-type')
   }
   if (options.cssReference) {
-    args.push('--css-reference', '2')
+    const inputCountString = inputs.length.toString()
+    inputs.push({ type: InterfaceTypes.TextStream, data: { data: options.cssReference } })
+    args.push('--css-reference', inputCountString)
   }
   if (options.cssFile) {
-    args.push('--css-file', '3')
+    const inputFile = 'file' + inputs.length.toString()
+    inputs.push({ type: InterfaceTypes.TextFile, data: { data: options.cssFile, path: inputFile } })
+    args.push('--css-file', inputFile)
   }
   if (options.expandInline) {
     args.push('--expand-inline')

diff --git a/dist/dicom/src/structuredReportToHtmlNode.ts b/dist/dicom/src/structuredReportToHtmlNode.ts
@@ -1,6 +1,7 @@
 import {
   TextStream,
   InterfaceTypes,
+  PipelineInput,
   runPipelineNode
 } from 'itk-wasm'
 
@@ -24,7 +25,7 @@ async function structuredReportToHtmlNode(  dicomFile: Uint8Array,
   const desiredOutputs = [
     { type: InterfaceTypes.TextStream },
   ]
-  const inputs = [
+  const inputs: [ PipelineInput ] = [
     { type: InterfaceTypes.BinaryFile, data: { data: dicomFile, path: "file0" }  },
   ]
 
@@ -81,14 +82,17 @@ async function structuredReportToHtmlNode(  dicomFile: Uint8Array,
     args.push('--charset-require')
   }
   if (options.charsetAssume) {
-    args.push('--charset-assume', '1')
+    args.push('--charset-assume', options.charsetAssume.toString())
   }
   if (options.charsetCheckAll) {
     args.push('--charset-check-all')
   }
   if (options.convertToUtf8) {
     args.push('--convert-to-utf8')
   }
+  if (options.urlPrefix) {
+    args.push('--url-prefix', options.urlPrefix.toString())
+  }
   if (options.html32) {
     args.push('--html-3.2')
   }
@@ -102,10 +106,14 @@ async function structuredReportToHtmlNode(  dicomFile: Uint8Array,
     args.push('--add-document-type')
   }
   if (options.cssReference) {
-    args.push('--css-reference', '2')
+    const inputCountString = inputs.length.toString()
+    inputs.push({ type: InterfaceTypes.TextStream, data: { data: options.cssReference } })
+    args.push('--css-reference', inputCountString)
   }
   if (options.cssFile) {
-    args.push('--css-file', '3')
+    const inputFile = 'file' + inputs.length.toString()
+    inputs.push({ type: InterfaceTypes.TextFile, data: { data: options.cssFile, path: inputFile } })
+    args.push('--css-file', inputFile)
   }
   if (options.expandInline) {
     args.push('--expand-inline')

diff --git a/dist/dicom/src/structuredReportToText.ts b/dist/dicom/src/structuredReportToText.ts
@@ -1,6 +1,7 @@
 import {
   TextStream,
   InterfaceTypes,
+  PipelineInput,
   runPipeline
 } from 'itk-wasm'
 
@@ -23,7 +24,7 @@ async function structuredReportToText(
   const desiredOutputs = [
     { type: InterfaceTypes.TextStream },
   ]
-  const inputs = [
+  const inputs: [ PipelineInput ] = [
     { type: InterfaceTypes.BinaryFile, data: { data: dicomFile, path: "file0" }  },
   ]
 

diff --git a/dist/dicom/src/structuredReportToTextNode.ts b/dist/dicom/src/structuredReportToTextNode.ts
@@ -1,6 +1,7 @@
 import {
   TextStream,
   InterfaceTypes,
+  PipelineInput,
   runPipelineNode
 } from 'itk-wasm'
 
@@ -24,7 +25,7 @@ async function structuredReportToTextNode(  dicomFile: Uint8Array,
   const desiredOutputs = [
     { type: InterfaceTypes.TextStream },
   ]
-  const inputs = [
+  const inputs: [ PipelineInput ] = [
     { type: InterfaceTypes.BinaryFile, data: { data: dicomFile, path: "file0" }  },
   ]
 

diff --git a/src/docker/itk-wasm-base/Dockerfile b/src/docker/itk-wasm-base/Dockerfile
@@ -21,7 +21,7 @@ RUN git clone https://github.com/KitwareMedical/ITK.git && \
 RUN sed -i -e '/^set(DCMTK_GIT_REPOSITORY/c\set(DCMTK_GIT_REPOSITORY "https://github.com/InsightSoftwareConsortium/DCMTK.git")' \
     /ITK/Modules/ThirdParty/DCMTK/DCMTKGitTag.cmake
 
-RUN sed -i -e '/^set(DCMTK_GIT_TAG/c\set(DCMTK_GIT_TAG "66fce6822afb16bcfd926ac8a5f4ed8d7cd10981")' \
+RUN sed -i -e '/^set(DCMTK_GIT_TAG/c\set(DCMTK_GIT_TAG "f9da0c6a79bac564cd5c102bb470c4524279d351")' \
     /ITK/Modules/ThirdParty/DCMTK/DCMTKGitTag.cmake
 
 ARG CMAKE_BUILD_TYPE=Release

diff --git a/src/io/internal/pipelines/dicom/structured-report-to-html.cxx b/src/io/internal/pipelines/dicom/structured-report-to-html.cxx
@@ -37,6 +37,7 @@
  *
  */
 #include "itkPipeline.h"
+#include "itkInputTextStream.h"
 #include "itkOutputTextStream.h"
 
 #include "dcmtk/config/osconfig.h"    /* make sure OS specific configuration is included first */
@@ -79,7 +80,8 @@ static OFCondition renderFile(STD_NAMESPACE ostream &out,
                               const size_t readFlags,
                               const size_t renderFlags,
                               const OFBool checkAllStrings,
-                              const OFBool convertToUTF8)
+                              const OFBool convertToUTF8,
+                              const std::string& urlPrefixForReferencedObjects)
 {
     OFCondition result = EC_Normal;
 
@@ -169,8 +171,20 @@ static OFCondition renderFile(STD_NAMESPACE ostream &out,
                     }
                 }
                 if (result.good())
-                    result = dsrdoc->renderHTML(out, renderFlags, cssName);
-            } else {
+                {
+                    if (urlPrefixForReferencedObjects.empty())
+                    {
+                        // this allows to set the default argument value: HTML_HYPERLINK_PREFIX_FOR_CGI
+                        result = dsrdoc->renderHTML(out, renderFlags, cssName);
+                    }
+                    else
+                    {
+                        result = dsrdoc->renderHTML(out, renderFlags, cssName, urlPrefixForReferencedObjects);
+                    }
+                }
+            }
+            else
+            {
                 OFLOG_FATAL(dsr2htmlLogger, OFFIS_CONSOLE_APPLICATION << ": error (" << result.text()
                     << ") parsing file: " << ifname);
             }
@@ -251,6 +265,9 @@ int main(int argc, char * argv[])
   pipeline.add_flag("--convert-to-utf8", convertToUTF8, "convert all element values that are affected\nby Specific Character Set (0008,0005) to UTF-8");
 #endif
   // Group("output options:")
+  std::string urlPrefixValue;
+  pipeline.add_option("--url-prefix", urlPrefixValue, "URL: string. Append specificed URL prefix to hyperlinks of referenced composite objects in the document.");
+
   //   SubGroup("HTML/XHTML compatibility:")
   bool html32{false}, html40{false}, xhtml11{false}, addDocumentType{false};
   auto html32CliOption = pipeline.add_flag("--html-3.2", html32, "use only HTML version 3.2 compatible features");
@@ -259,12 +276,12 @@ int main(int argc, char * argv[])
   pipeline.add_flag("--add-document-type", addDocumentType, "add reference to SGML document type definition");
 
   //   SubGroup("cascading style sheet (CSS), not with HTML 3.2:")
-  std::string cssReferenceValue;
-  auto cssReferenceValueCliOption = pipeline.add_option("--css-reference", cssReferenceValue, "URL: string. Add reference to specified CSS to document")->type_name("INPUT_TEXT_STREAM");
-  cssReferenceValueCliOption->excludes(html32CliOption);
-  std::string cssFileValue;
-  auto cssFileValueCliOption = pipeline.add_option("--css-file", cssFileValue, "[f]ilename: string. Embed content of specified CSS into document")->type_name("INPUT_TEXT_STREAM");
-  cssFileValueCliOption->excludes(html32CliOption);
+  itk::wasm::InputTextStream cssReference;
+  auto cssReferenceCliOption = pipeline.add_option("--css-reference", cssReference, "URL: string. Add reference to specified CSS to document")->type_name("INPUT_TEXT_STREAM");
+  cssReferenceCliOption->excludes(html32CliOption);
+  std::string cssFile;
+  auto cssFileCliOption = pipeline.add_option("--css-file", cssFile, "[f]ilename: string. Embed content of specified CSS into document")->check(CLI::ExistingFile)->type_name("INPUT_TEXT_FILE");
+  cssFileCliOption->excludes(html32CliOption);
 
   //   SubGroup("general rendering:");
   bool expandInline{false};
@@ -311,6 +328,11 @@ int main(int argc, char * argv[])
   E_TransferSyntax opt_ixfer = EXS_Unknown;
   OFBool opt_checkAllStrings = OFFalse;
   OFBool opt_convertToUTF8 = OFFalse;
+
+  std::string cssReferenceContent;
+  if(cssReference.GetPointer() != nullptr) {
+    cssReferenceContent = std::string{ std::istreambuf_iterator<char>(cssReference.Get()), std::istreambuf_iterator<char>() };
+  }
 
   /* input options */
   if(readFileOnly) {
@@ -403,21 +425,21 @@ int main(int argc, char * argv[])
   }
 
   /* cascading style sheet */
-  if (!cssReferenceValue.empty())
+  if (!cssReferenceContent.empty())
   {
     if((opt_renderFlags & DSRTypes::HF_HTML32Compatibility) > 0) {
       std::cerr << "--css-reference and --html-3.2 are conflicting options." << std::endl;
     }
     opt_renderFlags &= ~DSRTypes::HF_copyStyleSheetContent;
-    opt_cssName = cssReferenceValue.c_str();
+    opt_cssName = cssReferenceContent.c_str();
   }
-  if (!cssFileValue.empty())
+  if (!cssFile.empty())
   {
     if ((opt_renderFlags & DSRTypes::HF_HTML32Compatibility) > 0) {
       std::cerr << "--css-file and --html-3.2 are conflicting options." << std::endl;
     }
     opt_renderFlags |= DSRTypes::HF_copyStyleSheetContent;
-    opt_cssName = cssFileValue.c_str();
+    opt_cssName = cssFile.c_str();
   }
 
   /* general rendering */
@@ -518,7 +540,7 @@ int main(int argc, char * argv[])
   const char *ifname = dicomFileName.c_str();
 
   if (renderFile(outputText.Get(), ifname, opt_cssName, opt_defaultCharset, opt_readMode, opt_ixfer, opt_readFlags,
-    opt_renderFlags, opt_checkAllStrings, opt_convertToUTF8).bad())
+    opt_renderFlags, opt_checkAllStrings, opt_convertToUTF8, urlPrefixValue).bad())
   {
     result = 3;
   }