--- /dev/null
+
+ /*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: exDicomRTStructSetFile.cxx,v $
+ Language: C++
+ Date: $Date: 2007/06/18 12:02:54 $
+ Version: $Revision: 1.1 $
+
+ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
+ l'Image). All rights reserved. See Doc/License.txt or
+ http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+
+ /* =================================================
+ * freely inspired from : clitkDicomRTIOCommon.cxx
+ * written by : Laurent ZAGNI
+ * on : 18 August 2006
+ *
+ =================================================*/
+
+
+#include "gdcmFile.h"
+// ----------
+//#include "gdcmValEntry.h"
+#include "gdcmDataEntry.h"
+// ----------
+#include "gdcmSeqEntry.h"
+#include "gdcmSQItem.h"
+#include "gdcmDocEntrySet.h"
+#include "gdcmSerieHelper.h"
+#include "gdcmDirList.h"
+#include "gdcmUtil.h"
+
+// ----------
+#define GetEntryValue(g,e) GetEntryString(g,e)
+#define GetValEntry(g,e) GetDataEntry(g,e)
+#define GetValue() GetString()
+#define ValEntry DataEntry
+#define InsertValEntry(a,b,c) InsertEntryString(a,b,c) // warning mind the VR!
+// ----------
+
+#define itkGenericExceptionMacro(a) std::cout<<"===========================Exception "a<<std::endl;return false;
+
+#include "gdcmArgMgr.h"
+
+bool TestDicomRTStructSetFile(gdcm::File* file);
+bool TestDicomCTSerie(const gdcm::FileList serie);
+
+ //====================================================================
+
+ //====================================================================
+ //In a dicom seq try to find an item with a gived tag/(int)value pair, else creates it
+ gdcm::SQItem* GetAnItemWithTagValue(gdcm::SeqEntry* seqEntry, const uint16_t group,
+ const uint16_t elem, const int value, const bool writeItem) {
+ int foundValue;
+ std::stringstream valueStream;
+ valueStream<<value;
+ std::string strValue = valueStream.str();
+ gdcm::SQItem* curItem = seqEntry->GetFirstSQItem();
+ gdcm::ValEntry* valEntry;
+ while (curItem != NULL) {
+ valEntry = curItem->GetValEntry(group,elem);
+ std::istringstream(valEntry->GetValue())>>foundValue;
+ if (foundValue == value) {
+ return curItem;
+ }
+ curItem = seqEntry->GetNextSQItem();
+ }
+ if (writeItem == true) {
+ unsigned int newItemNumber = seqEntry->GetNumberOfSQItems ();
+// ----------
+ //gdcm::SQItem* newItem = new gdcm::SQItem(seqEntry->GetDepthLevel()+1);
+ gdcm::SQItem* newItem = gdcm::SQItem::New(seqEntry->GetDepthLevel()+1);
+// ----------
+ seqEntry->AddSQItem(newItem,(int)newItemNumber);
+ newItem->InsertValEntry(strValue, group, elem); /// \TODO : si VR absent, le chercher dans le dict!
+ return newItem;
+ } else {
+ return NULL;
+ }
+ }
+
+
+ /* =================================================
+ * freely inspired from : clitkDicomRTIOCommon.cxx
+ * written by : Laurent ZAGNI
+ * on : 18 August 2006
+ *
+ =================================================*/
+ // Test if a file list is a valid CT serie
+
+ bool TestDicomCTSerie(const gdcm::FileList serie) {
+
+ if (serie.size() < 2) {
+ itkGenericExceptionMacro(<<"Serie must contain at least 2 files !");
+ }
+
+ float firstSliceImagePosition[3];
+ float currentSliceImagePosition[3];
+
+ gdcm::FileList::const_iterator first = serie.begin();
+ gdcm::FileList::const_iterator it = first ++;
+
+ bool res = (*first)->GetImageOrientationPatient(firstSliceImagePosition);
+ if (!res) {
+ itkGenericExceptionMacro(<<"No ImagePositionPatient found;");
+ }
+
+ while (it != serie.end()) {
+ if (!gdcm::Util::DicomStringEqual((*it)->GetEntryValue(0x0008,0x0016),"1.2.840.10008.5.1.4.1.1.2")) {
+ itkGenericExceptionMacro();
+ //CT Dicom slices must have a SOP Class UID [0008|0016] = [1.2.840.10008.5.1.4.1.1.2] ==> [CT Image Storage]
+ }
+
+ if (!gdcm::Util::DicomStringEqual((*it)->GetEntryValue(0x0008,0x0060),"CT")) {
+ itkGenericExceptionMacro();
+ //CT Dicom slices must have a Modality [0008|0060] = [CT]
+ }
+
+ if (!gdcm::Util::DicomStringEqual((*it)->GetEntryValue(0x0020,0x0037),"1.0000\\0.0000\\0.0000\\0.0000\\1.0000\\0.0000")) {
+ itkGenericExceptionMacro("CT Dicom slices must an Image Orientation [0020|0037]"
+ <<" = [1.0000\0.0000\0.0000\0.0000\1.0000\0.0000]");
+ }
+
+ res =(*it)->GetImageOrientationPatient(currentSliceImagePosition);
+ if (!res) {
+ itkGenericExceptionMacro(<<"No ImagePositionPatient found;");
+ }
+ if ((firstSliceImagePosition[0] != currentSliceImagePosition[0])||(firstSliceImagePosition[1] != currentSliceImagePosition[1])){
+ itkGenericExceptionMacro("All CT Dicom slices must have same image position on x and y [0020|0032]");
+ }
+
+ if ((*it)->GetEntryValue(0x0028,0x0030) != (*first)->GetEntryValue(0x0028,0x0030).c_str()) {
+ itkGenericExceptionMacro("All CT Dicom slices must have same Pixel Spacing [0028|0030]");
+ }
+
+ if ((*it)->GetEntryValue(0x0028,0x0010) != (*first)->GetEntryValue(0x0028,0x0010).c_str()) {
+ itkGenericExceptionMacro("All CT Dicom slices must have same Rows number [0028|0010]");
+ }
+
+ if ((*it)->GetEntryValue(0x0028,0x0011) != (*first)->GetEntryValue(0x0028,0x0011).c_str()) {
+ itkGenericExceptionMacro("All CT Dicom slices must have same Columns number [0028|0011]");
+ }
+
+ if ((*it)->GetEntryValue(0x0018,0x0050) != (*first)->GetEntryValue(0x0018,0x0050).c_str()) {
+ itkGenericExceptionMacro("All CT Dicom slices must have same slice thickness [0018|0050]");
+ }
+ it++;
+ }
+ //it = serie.begin();
+ // while (it != serie.end()) {
+ // fileName = (*it)->GetFileName();
+ // std::cout << fileName << std::endl;
+ // it++;
+ // }
+ }
+
+
+
+
+// -----------------------------------------------------------------------------------------------------------------
+ /* =================================================
+ * freely inspired from : clitkDicomRTIOCommon.cxx
+ * written by : Laurent ZAGNI
+ * on : 18 August 2006
+ *
+ =================================================*/
+
+ // Test if a file is a valid Dicom-RT Structure-Set file (readable by us)
+ bool TestDicomRTStructSetFile(gdcm::File* file) {
+// ----------
+ //gdcm::ValEntry* valEntry;
+ gdcm::DataEntry* valEntry;
+// ----------
+
+ std::string exception0 = "Not a [RT Structure Set Storage]";
+ std::string exception1 = "2 or more different 'Roi Referenced Frame UID'!";
+ std::string exception2 = "No 'Series Instance UID'!";
+ std::string exception3 = "Modality not= RTSTRUCT";
+
+ //Verify if the file is a RT-Structure-Set dicom file
+ if (!gdcm::Util::DicomStringEqual(file->GetEntryValue(0x0008,0x0016),"1.2.840.10008.5.1.4.1.1.481.3")) { //SOP clas UID
+ itkGenericExceptionMacro(<<exception0);
+ // (the file must have a SOP Class UID [0008|0016] = 1.2.840.10008.5.1.4.1.1.481.3 ==> [RT Structure Set Storage] !
+ }
+
+ if (!gdcm::Util::DicomStringEqual(file->GetEntryValue(0x0008,0x0060),"RTSTRUCT")) { //SOP clas UID
+ itkGenericExceptionMacro(<<exception3);
+ // (the file must have a Modality tag = RTSTRUCT !
+ }
+
+ //Verify only one Referenced Frame UID and one or more Series UID
+
+ gdcm::SeqEntry* seqEntry;
+ gdcm::SQItem* currentItem;
+ std::string currentFrameRefUID;
+
+ seqEntry = file->GetSeqEntry(0x3006,0x0020); //Structure Set ROI sequence
+ if (seqEntry->GetNumberOfSQItems() > 1) {
+ currentItem = seqEntry->GetFirstSQItem();
+ valEntry = currentItem->GetValEntry(0x3006,0x0024); //Roi Frame of Reference UID
+ currentFrameRefUID = valEntry->GetValue();
+ currentItem = seqEntry->GetNextSQItem();
+ while (currentItem != NULL) {
+ valEntry = currentItem->GetValEntry(0x3006,0x0024); //Roi Frame of Reference UID
+ if (valEntry->GetValue() != currentFrameRefUID) {
+ // std::cout<<"..ref UID"<<currentFrameRefUID<<std::endl;
+ // std::cout<<"..new UID"<<valEntry->GetValue().c_str()<<std::endl;
+ // std::cout<<"..exception"<<std::endl;
+ itkGenericExceptionMacro(<<exception1);
+ }
+ currentItem = seqEntry->GetNextSQItem();
+ }
+ }
+
+ seqEntry = file->GetSeqEntry(0x3006,0x0010); //Referenced Frame of Reference Sequence
+ currentItem = seqEntry->GetFirstSQItem();
+ while (currentItem != NULL) {
+ valEntry = currentItem->GetValEntry(0x0020,0x0052); //Frame of Reference UID
+ if (valEntry->GetValue() == currentFrameRefUID) { //search for the ROI Frame of Reference UID
+ break;
+ }else {
+ currentItem = seqEntry->GetNextSQItem();
+ }
+ }
+ if (currentItem == NULL) {
+ itkGenericExceptionMacro(<<exception1);
+ }
+
+ gdcm::SeqEntry* seqEntry2 = currentItem->GetSeqEntry(0x3006,0x0012); //Referenced Study sequence
+ if (seqEntry2->GetNumberOfSQItems() < 1) {
+ itkGenericExceptionMacro(<<exception2);
+ }
+
+ valEntry = file->GetValEntry(0x0020,0x0010); //study ID
+ if ((valEntry == 0) || (valEntry->GetValue() == "")) { //(type 1 : mandatory attribute)
+ itkGenericExceptionMacro("RT-Structure-Set file must contain Study ID [0020|0010] !");
+ }
+
+ valEntry = file->GetValEntry(0x3006,0x002); //structure set label
+ if ((valEntry == 0) || (valEntry->GetValue() == "")) { //(type 1 : mandatory attribute)
+ itkGenericExceptionMacro("RT-Structure-Set file must contain Structure Set Label [0006|0002] !");
+ }
+
+ seqEntry = file->GetSeqEntry(0x3006,0x0020); //Structure Set ROI sequence
+ if (seqEntry != 0) {
+ currentItem = seqEntry->GetFirstSQItem();
+ while (currentItem != NULL) {
+ valEntry = currentItem->GetValEntry(0x3006,0x0022); //Roi number
+ if ((valEntry == 0) || (valEntry->GetValue() == "")) { //(type 1 : mandatory attribute)
+ itkGenericExceptionMacro("All ROI in Structure Set Roi Sequence must contain Roi Number [3006|0022] !");
+ }
+ currentItem = seqEntry->GetNextSQItem();
+ }
+ }
+
+ seqEntry = file->GetSeqEntry(0x3006,0x0080); //ROI Observation sequence
+ if (seqEntry == 0) { //(type 1 : mandatory attribute)
+ itkGenericExceptionMacro("RT-Structure-Set file must contain ROI Observations Sequence [3006|0080] !");
+ }
+
+ seqEntry = file->GetSeqEntry(0x3006,0x0039); //ROI Contour sequence
+ if (seqEntry == 0) { //(type 1 : mandatory attribute)
+ itkGenericExceptionMacro("RT-Structure-Set file must contain ROI Contour Sequence [3006|0039] !");
+ }
+ std::cout<<"..."<<file->GetFileName()<<" is a valid DICOM RT-Structure-Set file"<<std::endl;
+ }
+
+// -------------------------------------------------------------------------------------------------------
+
+int main(int argc, char *argv[])
+{
+ START_USAGE(usage)
+ "\n exExtractCSA :\n ",
+ "Extracts and displays the CSA tag(s) of gdcm-parsable Dicom file ",
+ " ",
+ "usage: exExtractCSA {filein=inputFileName|dirin=inputDirectoryName} ",
+ " tmp=temporaryWorkFileName ",
+ " [extract=listOfElementsToExtract] ",
+ " [ { [noshadowseq] | [noshadow][noseq] } ] [debug] ",
+ " inputFileName : Name of the (single) file user wants to anonymize ",
+ " listOfElementsExtract : group-elem,g2-e2,... (in hexa, no space) ",
+ " of Elements to extract ",
+ " default : 0029-1210,0029-1220 ",
+ " noshadowseq: user doesn't want to load Private Sequences ",
+ " noshadow : user doesn't want to load Private groups (odd number) ",
+ " noseq : user doesn't want to load Sequences ",
+ " verbose : developper wants to run the program in 'verbose mode' ",
+ " debug : developper wants to run the program in 'debug mode' ",
+ FINISH_USAGE
+
+ // ----- Initialize Arguments Manager ------
+
+ GDCM_NAME_SPACE::ArgMgr *am = new GDCM_NAME_SPACE::ArgMgr(argc, argv);
+
+ if (am->ArgMgrDefined("usage") || argc == 1)
+ {
+ am->ArgMgrUsage(usage); // Display 'usage'
+ delete am;
+ return 0;
+ }
+
+ if (am->ArgMgrDefined("debug"))
+ GDCM_NAME_SPACE::Debug::DebugOn();
+
+ bool verbose = am->ArgMgrDefined("verbose");
+
+ const char *fileName = am->ArgMgrGetString("filein");
+
+ /* if unused Param we give up */
+ if ( am->ArgMgrPrintUnusedLabels() )
+ {
+ am->ArgMgrUsage(usage);
+ delete am;
+ return 0;
+ }
+ delete am; // ------ we don't need Arguments Manager any longer ------
+
+// ============================================================
+// Read the input image.
+// ============================================================
+
+ gdcm::File *f = gdcm::File::New( );
+
+ //f->SetLoadMode(gdcm::LD_NOSEQ | gdcm::LD_NOSHADOW);
+ f->SetFileName( fileName );
+ f->SetMaxSizeLoadEntry(0xffff);
+ bool res = f->Load();
+
+ if( gdcm::Debug::GetDebugFlag())
+ {
+ std::cout << "---------------------------------------------" << std::endl;
+ f->Print();
+ std::cout << "---------------------------------------------" << std::endl;
+ }
+ if (!res) {
+ std::cerr << "Sorry, " << fileName << " not a gdcm-readable "
+ << "DICOM / ACR File"
+ << std::endl;
+ f->Delete();
+ return 1;
+ }
+ std::cout << " ... is readable " << std::endl;
+
+
+ TestDicomRTStructSetFile(f);
+ std::cout << " ... is readable " << std::endl;
+
+
+
+ f->Delete();
+return 0;
+}
+
git://git.creatis.insa-lyon.fr / gdcm.git / commitdiff