ENH: add an option to pass DICOM directory to the PM converter

see QIICR#186 deficiencies described in QIICR#182 apply
fedorov · Feb 1, 2017 · 38f83cf · 38f83cf
1 parent d02c98f
commit 38f83cf
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Showing 5 changed files with 56 additions and 17 deletions.
diff --git a/apps/paramaps/Testing/CMakeLists.txt b/apps/paramaps/Testing/CMakeLists.txt
@@ -26,7 +26,7 @@ dcmqi_add_test(
   COMMAND $<TARGET_FILE:${MODULE_NAME}>
     --inputMetadata ${CMAKE_SOURCE_DIR}/doc/examples/pm-example.json
     --inputImage ${BASELINE}/pm-example.nrrd
-    --inputDICOM ${BASELINE}/pm-example-slice.dcm
+    --inputDICOMList ${BASELINE}/pm-example-slice.dcm
     --outputDICOM ${TEMP_DIR}/paramap.dcm
   )
 
@@ -36,7 +36,7 @@ dcmqi_add_test(
   COMMAND $<TARGET_FILE:${MODULE_NAME}>
     --inputMetadata ${CMAKE_SOURCE_DIR}/doc/examples/pm-example-float.json
     --inputImage ${BASELINE}/pm-example-float.nrrd
-    --inputDICOM ${BASELINE}/pm-example-slice.dcm
+    --inputDICOMList ${BASELINE}/pm-example-slice.dcm
     --outputDICOM ${TEMP_DIR}/paramap-float.dcm
   )
 

diff --git a/apps/paramaps/itkimage2paramap.cxx b/apps/paramaps/itkimage2paramap.cxx
@@ -5,6 +5,13 @@
 #undef HAVE_SSTREAM // Avoid redefinition warning
 #include "dcmqi/ParaMapConverter.h"
 
+#ifdef _WIN32
+#include "dirent_win.h"
+#else
+#include <dirent.h>
+#endif
+
+
 int main(int argc, char *argv[])
 {
   PARSE_ARGS;
@@ -19,18 +26,37 @@ int main(int argc, char *argv[])
   reader->Update();
   ImageType::Pointer parametricMapImage = reader->GetOutput();
 
-  DcmDataset* dcmDataset = NULL;
-  if (!dicomImageFileName.empty()) {
-    DcmFileFormat *sliceFF = new DcmFileFormat();
-    CHECK_COND(sliceFF->loadFile(dicomImageFileName.c_str()));
-    dcmDataset = sliceFF->getDataset();
+  vector<DcmDataset*> dcmDatasets;
+
+  DcmFileFormat* sliceFF = new DcmFileFormat();
+  for(size_t dcmFileNumber=0; dcmFileNumber<dicomImageFileList.size(); dcmFileNumber++){
+    if(sliceFF->loadFile(dicomImageFileList[dcmFileNumber].c_str()).good()){
+      dcmDatasets.push_back(sliceFF->getAndRemoveDataset());
+    }
+  }
+
+  // solution from
+  //  http://stackoverflow.com/questions/612097/how-can-i-get-the-list-of-files-in-a-directory-using-c-or-c
+  if(dicomDirectory.size()){
+    DIR *dir;
+    struct dirent *ent;
+    if ((dir = opendir (dicomDirectory.c_str())) != NULL) {
+      while ((ent = readdir (dir)) != NULL) {
+        if(sliceFF->loadFile((dicomDirectory+"/"+ent->d_name).c_str()).good()){
+          dcmDatasets.push_back(sliceFF->getAndRemoveDataset());
+        }
+      }
+      closedir (dir);
+    } else {
+      cerr << "Cannot open input DICOM directory!" << endl;
+    }
   }
 
   ifstream metainfoStream(metaDataFileName.c_str(), ios_base::binary);
   std::string metadata( (std::istreambuf_iterator<char>(metainfoStream) ),
                         (std::istreambuf_iterator<char>()));
 
-  DcmDataset* result = dcmqi::ParaMapConverter::itkimage2paramap(parametricMapImage, dcmDataset, metadata);
+  DcmDataset* result = dcmqi::ParaMapConverter::itkimage2paramap(parametricMapImage, dcmDatasets, metadata);
 
   if (result == NULL) {
     return EXIT_FAILURE;

diff --git a/apps/paramaps/itkimage2paramap.xml b/apps/paramaps/itkimage2paramap.xml
@@ -35,13 +35,22 @@
       <description>File name of the DICOM Parametric map object with the result of the conversion.</description>
     </file>
 
-    <file>
-      <name>dicomImageFileName</name>
+    <string-vector>
+      <name>dicomImageFileList</name>
       <label>DICOM images file name</label>
       <channel>input</channel>
-      <longflag>inputDICOM</longflag>
+      <longflag>inputDICOMList</longflag>
       <default></default>
       <description>File name of the DICOM image file that should be used to populate the composite context (attributes related to the patient and imaging study).</description>
+    </string-vector>
+
+    <file>
+      <name>dicomDirectory</name>
+      <label>Source DICOM directory</label>
+      <channel>input</channel>
+      <longflag>inputDICOMDirectory</longflag>
+      <default></default>
+      <description>Directory with the source DICOM images that were used to generate the parametric map.</description>
     </file>
 
   </parameters>

diff --git a/include/dcmqi/ParaMapConverter.h b/include/dcmqi/ParaMapConverter.h
@@ -35,7 +35,7 @@ namespace dcmqi {
   class ParaMapConverter : public ConverterBase {
 
   public:
-    static DcmDataset* itkimage2paramap(const ImageType::Pointer &parametricMapImage, DcmDataset* dcmDataset,
+    static DcmDataset* itkimage2paramap(const ImageType::Pointer &parametricMapImage, vector<DcmDataset*> dcmDatasets,
                                         const string &metaData);
 
     static pair <ImageType::Pointer, string> paramap2itkimage(DcmDataset *pmapDataset);

diff --git a/libsrc/ParaMapConverter.cpp b/libsrc/ParaMapConverter.cpp
@@ -10,7 +10,7 @@ using namespace std;
 
 namespace dcmqi {
 
-  DcmDataset* ParaMapConverter::itkimage2paramap(const ImageType::Pointer &parametricMapImage, DcmDataset* dcmDataset,
+  DcmDataset* ParaMapConverter::itkimage2paramap(const ImageType::Pointer &parametricMapImage, vector<DcmDataset*> dcmDatasets,
                                          const string &metaData) {
 
     MinMaxCalculatorType::Pointer calculator = MinMaxCalculatorType::New();
@@ -50,8 +50,12 @@ namespace dcmqi {
 
     DPMParametricMapIOD* pMapDoc = OFget<DPMParametricMapIOD>(&obj);
 
-    if (dcmDataset != NULL)
-      CHECK_COND(pMapDoc->import(*dcmDataset, OFTrue, OFTrue, OFFalse, OFTrue));
+    DcmDataset* srcDataset = NULL;
+    if(dcmDatasets.size()){
+      srcDataset = dcmDatasets[0];
+    }
+    if (srcDataset)
+      CHECK_COND(pMapDoc->import(*srcDataset, OFTrue, OFTrue, OFFalse, OFTrue));
 
     /* Initialize dimension module */
     char dimUID[128];
@@ -232,9 +236,9 @@ namespace dcmqi {
 
   {
     string bodyPartAssigned = metaInfo.getBodyPartExamined();
-    if(dcmDataset != NULL && bodyPartAssigned.empty()) {
+    if(srcDataset != NULL && bodyPartAssigned.empty()) {
       OFString bodyPartStr;
-      if(dcmDataset->findAndGetOFString(DCM_BodyPartExamined, bodyPartStr).good()) {
+      if(srcDataset->findAndGetOFString(DCM_BodyPartExamined, bodyPartStr).good()) {
         if (!bodyPartStr.empty())
           bodyPartAssigned = bodyPartStr.c_str();
       }