Merge pull request #381 from fedorov/improve-error-handling

ENH: improve error handling
QIICR · May 2, 2019 · c3b40ac · c3b40ac
2 parents e074b95 + 2c9740f
commit c3b40ac
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Showing 7 changed files with 81 additions and 59 deletions.
diff --git a/apps/paramaps/itkimage2paramap.cxx b/apps/paramaps/itkimage2paramap.cxx
@@ -36,23 +36,29 @@ int main(int argc, char *argv[])
   vector<DcmDataset*> dcmDatasets = helper::loadDatasets(dicomImageFileList);
 
   if(dcmDatasets.empty()){
-    cerr << "Error: no DICOM could be loaded from the specified list/directory" << endl;
+    cerr << "ERROR: no DICOM could be loaded from the specified list/directory" << endl;
     return EXIT_FAILURE;
   }
 
   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, dcmDatasets, metadata);
+  try {
+    DcmDataset* result = dcmqi::ParaMapConverter::itkimage2paramap(parametricMapImage, dcmDatasets, metadata);
 
-  if (result == NULL) {
-    return EXIT_FAILURE;
-  } else {
-    DcmFileFormat segdocFF(result);
-    CHECK_COND(segdocFF.saveFile(outputParaMapFileName.c_str(), EXS_LittleEndianExplicit));
+    if (result == NULL) {
+      std::cerr << "ERROR: Conversion failed." << std::endl;
+      return EXIT_FAILURE;
+    } else {
+      DcmFileFormat segdocFF(result);
+      CHECK_COND(segdocFF.saveFile(outputParaMapFileName.c_str(), EXS_LittleEndianExplicit));
 
-    COUT << "Saved parametric map as " << outputParaMapFileName << endl;
-    return EXIT_SUCCESS;
+      COUT << "Saved parametric map as " << outputParaMapFileName << endl;
+      return EXIT_SUCCESS;
+    }
+  } catch (int e) {
+    std::cerr << "Fatal error encountered." << std::endl;
+    return EXIT_FAILURE;
   }
 }
diff --git a/apps/paramaps/paramap2itkimage.cxx b/apps/paramaps/paramap2itkimage.cxx
@@ -25,27 +25,32 @@ int main(int argc, char *argv[])
   CHECK_COND(sliceFF.loadFile(inputFileName.c_str()));
   DcmDataset* dataset = sliceFF.getDataset();
 
-  pair <FloatImageType::Pointer, string> result =  dcmqi::ParaMapConverter::paramap2itkimage(dataset);
-
-  string fileExtension = helper::getFileExtensionFromType(outputType);
-
-  typedef itk::ImageFileWriter<FloatImageType> WriterType;
-  string outputPrefix = prefix.empty() ? "" : prefix + "-";
-  WriterType::Pointer writer = WriterType::New();
-  stringstream imageFileNameSStream;
-  imageFileNameSStream << outputDirName << "/" << outputPrefix << "pmap" << fileExtension;
-  writer->SetFileName(imageFileNameSStream.str().c_str());
-  writer->SetInput(result.first);
-  writer->SetUseCompression(1);
-  writer->Update();
-
-  stringstream jsonOutput;
-  jsonOutput << outputDirName << "/" << outputPrefix << "meta.json";
-
-  ofstream outputFile;
-  outputFile.open(jsonOutput.str().c_str());
-  outputFile << result.second;
-  outputFile.close();
-
-  return EXIT_SUCCESS;
+  try {
+    pair <FloatImageType::Pointer, string> result =  dcmqi::ParaMapConverter::paramap2itkimage(dataset);
+
+    string fileExtension = helper::getFileExtensionFromType(outputType);
+
+    typedef itk::ImageFileWriter<FloatImageType> WriterType;
+    string outputPrefix = prefix.empty() ? "" : prefix + "-";
+    WriterType::Pointer writer = WriterType::New();
+    stringstream imageFileNameSStream;
+    imageFileNameSStream << outputDirName << "/" << outputPrefix << "pmap" << fileExtension;
+    writer->SetFileName(imageFileNameSStream.str().c_str());
+    writer->SetInput(result.first);
+    writer->SetUseCompression(1);
+    writer->Update();
+
+    stringstream jsonOutput;
+    jsonOutput << outputDirName << "/" << outputPrefix << "meta.json";
+
+    ofstream outputFile;
+    outputFile.open(jsonOutput.str().c_str());
+    outputFile << result.second;
+    outputFile.close();
+
+    return EXIT_SUCCESS;
+  } catch (int e) {
+    std::cerr << "Fatal error encountered." << std::endl;
+    return EXIT_FAILURE;
+  }
 }
diff --git a/apps/seg/itkimage2segimage.cxx b/apps/seg/itkimage2segimage.cxx
@@ -91,26 +91,31 @@ int main(int argc, char *argv[])
     segmentations = segmentationsReordered;
   }
 
-  DcmDataset* result = dcmqi::ImageSEGConverter::itkimage2dcmSegmentation(dcmDatasets, segmentations, metadata, skipEmptySlices);
+  try {
+    DcmDataset* result = dcmqi::ImageSEGConverter::itkimage2dcmSegmentation(dcmDatasets, segmentations, metadata, skipEmptySlices);
 
-  if (result == NULL){
-    return EXIT_FAILURE;
-  } else {
-    DcmFileFormat segdocFF(result);
-    bool compress = false;
-    if(compress){
-      CHECK_COND(segdocFF.saveFile(outputSEGFileName.c_str(), EXS_DeflatedLittleEndianExplicit));
+    if (result == NULL){
+      std::cerr << "ERROR: Conversion failed." << std::endl;
+      return EXIT_FAILURE;
     } else {
-      CHECK_COND(segdocFF.saveFile(outputSEGFileName.c_str(), EXS_LittleEndianExplicit));
-    }
+      DcmFileFormat segdocFF(result);
+      bool compress = false;
+      if(compress){
+        CHECK_COND(segdocFF.saveFile(outputSEGFileName.c_str(), EXS_DeflatedLittleEndianExplicit));
+      } else {
+        CHECK_COND(segdocFF.saveFile(outputSEGFileName.c_str(), EXS_LittleEndianExplicit));
+      }
 
-    COUT << "Saved segmentation as " << outputSEGFileName << endl;
-  }
+      COUT << "Saved segmentation as " << outputSEGFileName << endl;
+    }
 
-  for(size_t i=0;i<dcmDatasets.size();i++) {
-    delete dcmDatasets[i];
+    for(size_t i=0;i<dcmDatasets.size();i++) {
+      delete dcmDatasets[i];
+    }
+    if (result != NULL)
+      delete result;
+    return EXIT_SUCCESS;
+  } catch (int e) {
+    std::cerr << "Fatal error encountered." << std::endl;
   }
-  if (result != NULL)
-    delete result;
-  return EXIT_SUCCESS;
 }
diff --git a/apps/seg/segimage2itkimage.cxx b/apps/seg/segimage2itkimage.cxx
@@ -55,5 +55,6 @@ int main(int argc, char *argv[])
     return EXIT_SUCCESS;
   } catch (int e) {
     std::cerr << "Fatal error encountered." << std::endl;
+    return EXIT_FAILURE;
   }
 }
diff --git a/libsrc/JSONParametricMapMetaInformationHandler.cpp b/libsrc/JSONParametricMapMetaInformationHandler.cpp
@@ -112,6 +112,7 @@ namespace dcmqi {
     try {
       istringstream metainfoStream(this->jsonInput);
       metainfoStream >> this->metaInfoRoot;
+      //std::cout << this->metaInfoRoot.asString() << std::endl;
       this->seriesDescription = this->metaInfoRoot.get("SeriesDescription", "Segmentation").asString();
       this->seriesNumber = this->metaInfoRoot.get("SeriesNumber", "300").asString();
       this->instanceNumber = this->metaInfoRoot.get("InstanceNumber", "1").asString();
@@ -158,7 +159,9 @@ namespace dcmqi {
       }
 
     } catch (exception& e) {
-      cout << e.what() << endl;
+      cerr << "ERROR: JSON parameter file could not be parsed!" << std::endl;
+      cerr << "You can validate the JSON file here: http://qiicr.org/dcmqi/#/validators" << std::endl;
+      cerr << "Exception details (probably not very useful): " << e.what() << endl;
       throw JSONReadErrorException();
     }
   }

diff --git a/libsrc/JSONSegmentationMetaInformationHandler.cpp b/libsrc/JSONSegmentationMetaInformationHandler.cpp
@@ -52,8 +52,10 @@ namespace dcmqi {
       this->bodyPartExamined = this->metaInfoRoot.get("BodyPartExamined", "").asString();
 
       this->readSegmentAttributes();
-    } catch (exception &e) {
-      cout << e.what() << '\n';
+    } catch (exception& e) {
+      cerr << "ERROR: JSON parameter file could not be parsed!" << std::endl;
+      cerr << "You can validate the JSON file here: http://qiicr.org/dcmqi/#/validators" << std::endl;
+      cerr << "Exception details (probably not very useful): " << e.what() << endl;
       throw JSONReadErrorException();
     }
   }

diff --git a/libsrc/ParaMapConverter.cpp b/libsrc/ParaMapConverter.cpp
@@ -220,7 +220,7 @@ namespace dcmqi {
         bval->getEntireConceptNameCodeSequence().push_back(qCodeName);
         bval->getEntireMeasurementUnitsCodeSequence().push_back(bvalUnits);
         if(bval->setNumericValue(metaInfo.metaInfoRoot["SourceImageDiffusionBValues"][static_cast<int>(bvalId)].asCString()).bad())
-          cout << "Failed to insert the value!" << endl;;
+          cout << "ERROR: Failed to insert the value!" << endl;;
         realWorldValueMappingItem->getEntireQuantityDefinitionSequence().push_back(bval);
         cout << bval->toString() << endl;
       }
@@ -301,8 +301,8 @@ namespace dcmqi {
                                                    metaInfo.getDerivationDescription().c_str(),
                                                    derimgItem));
         } else {
-          cerr << "DerivationCode must be specified in the input metadata!" << endl;
-          return NULL;
+          cerr << "ERROR: DerivationCode must be specified in the input metadata!" << endl;
+          throw -1;
         }
 
         //cout << "Total of " << siVector.size() << " source image items will be added" << endl;
@@ -453,7 +453,7 @@ namespace dcmqi {
     FGInterface &fgInterface = pMapDoc->getFunctionalGroups();
     FloatImageType::DirectionType direction;
     if(getImageDirections(fgInterface, direction)){
-      cerr << "Failed to get image directions" << endl;
+      cerr << "ERROR: Failed to get image directions" << endl;
       throw -1;
     }
 
@@ -466,14 +466,14 @@ namespace dcmqi {
 
     FloatImageType::PointType imageOrigin;
     if(computeVolumeExtent(fgInterface, sliceDirection, imageOrigin, computedSliceSpacing, computedVolumeExtent)){
-      cerr << "Failed to compute origin and/or slice spacing!" << endl;
+      cerr << "ERROR: Failed to compute origin and/or slice spacing!" << endl;
       throw -1;
     }
 
     FloatImageType::SpacingType imageSpacing;
     imageSpacing.Fill(0);
     if(getDeclaredImageSpacing(fgInterface, imageSpacing)){
-      cerr << "Failed to get image spacing from DICOM!" << endl;
+      cerr << "ERROR: Failed to get image spacing from DICOM!" << endl;
       throw -1;
     }
 
@@ -616,7 +616,7 @@ namespace dcmqi {
 
     OFvariant<OFCondition,DPMParametricMapIOD*> result = DPMParametricMapIOD::loadDataset(*pmapDataset);
     if (OFCondition* pCondition = OFget<OFCondition>(&result)) {
-      cerr << "Failed to load parametric map! " << pCondition->text() << endl;
+      cerr << "ERROR: Failed to load parametric map! " << pCondition->text() << endl;
       throw -1;
     }
     DPMParametricMapIOD* pMapDoc = *OFget<DPMParametricMapIOD*>(&result);