--- /dev/null
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: exExtractCSA.cxx,v $
+ Language: C++
+ Date: $Date: 2007/06/07 16:13:14 $
+ 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.
+
+=========================================================================*/
+
+/*
+ * http://www.enac.northwestern.edu/~tew/archives/2003/02/25/incomplete-dicom-headers/
+ * http://www.nmr.mgh.harvard.edu/~rudolph/software/vox2ras/download/vox2ras_rsolve.m
+ * http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg03409.html
+ * http://www.mmrrcc.upenn.edu/CAMRIS/cfn/dicomhdr.html
+ */
+
+// See this one :
+// http://www.mmrrcc.upenn.edu/CAMRIS/cfn/dicomhdr.html
+
+#include <iostream>
+#include <fstream>
+#include <stdint.h>
+#include <assert.h>
+#include <vector>
+#include <map>
+
+#include "gdcmFile.h"
+#include "gdcmFileHelper.h"
+#include "gdcmCommon.h"
+#include "gdcmDebug.h"
+#include "gdcmDocEntry.h"
+#include "gdcmDataEntry.h"
+#include "gdcmSeqEntry.h"
+#include "gdcmSQItem.h"
+#include "gdcmArgMgr.h"
+
+// Looks like there is mapping in between syngodt and vr...
+// O <=> UN
+// 3 <=> DS
+// 4 <=> FD
+// 5 <=> FL
+// 6 <=> IS
+// 9 <=> UL
+// 10 <=> US
+// 16 <=> CS
+// 19 <=> LO
+// 20 <=> LT
+// 22 <=> SH
+// 25 <=> UI
+
+// --------------------------------------------------------
+
+typedef struct {
+ uint32_t Item_xx[4];
+ int Len;
+ std::string Value;
+} CSA_item;
+
+typedef std::vector<CSA_item *> ItemVector;
+
+typedef struct {
+ std::string Name;
+ int VM;
+ std::string VR;
+ int Syngodt;
+ int Nitems;
+ ItemVector Items_set;
+} CSA_entry;
+
+typedef std::map<std::string, CSA_entry *> CSA_content;
+
+// --------------------------------------------------------
+
+
+struct equ
+{
+ uint32_t syngodt;
+ char vr[2+1];
+};
+
+static equ mapping[] = {
+ { 0 , "UN" },
+ { 3 , "DS" },
+ { 4 , "FD" },
+ { 5 , "FL" },
+ { 6 , "IS" },
+ { 9 , "UL" },
+ { 10 , "US" },
+ { 16 , "CS" },
+ { 19 , "LO" },
+ { 20 , "LT" },
+ { 22 , "SH" },
+ { 23 , "ST" },
+ { 25 , "UI" },
+};
+
+bool check_mapping(uint32_t syngodt, const char *vr)
+{
+ static const unsigned int max = sizeof(mapping) / sizeof(equ);
+ unsigned int s = 0;
+ const equ *p = mapping;
+ assert( syngodt <= mapping[max-1].syngodt );
+ while(p->syngodt < syngodt )
+ {
+ //std::cout << "mapping:" << p->vr << std::endl;
+ ++p;
+ }
+ assert( p->syngodt == syngodt ); // or else need to update mapping
+ const char* lvr = p->vr;
+ int check = strcmp(vr, lvr) == 0;
+ assert( check );
+ return true;
+}
+
+
+ ///\to fix the Desctructor!
+void DeleteCSA_content (CSA_content &myMap) {
+ for ( CSA_content::const_iterator it = myMap.begin();
+ it != myMap.end();
+ ++it)
+ {
+ ItemVector item_v = (*it).second->Items_set;
+ for ( ItemVector::const_iterator it2 = item_v.begin();
+ it2 != item_v.end();
+ ++it2)
+ {
+ // delete (*it2);
+ }
+ //delete (*it).second;
+ }
+}
+
+void PrintCSA_content(CSA_content &myMap) {
+ int item_no;
+ for ( CSA_content::const_iterator it = myMap.begin();
+ it != myMap.end();
+ ++it)
+ {
+ std::cout << "[" << (*it).second->Name << "] : VR=[" << (*it).second->VR
+ << "] vm = " << (*it).second->VM << std::endl;
+ item_no = 0;
+ ItemVector item_v = (*it).second->Items_set;
+ for ( ItemVector::const_iterator it2 = item_v.begin();
+ it2 != item_v.end();
+ ++it2)
+ {
+ std::cout << " --- item no : " << item_no << std::endl;
+ std::cout << " Item_xxx : " << (*it2)->Item_xx[0] << " "
+ << (*it2)->Item_xx[1]
+ << " " << (*it2)->Item_xx[2] << " " << (*it2)->Item_xx[3]
+ << std::endl;
+
+ std::cout << " Len = " << (*it2)->Len ;
+ std::cout << " Value = [" << (*it2)->Value << "]" << std::endl;
+
+ item_no++;
+ }
+ }
+}
+
+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");
+
+ int loadMode = GDCM_NAME_SPACE::LD_ALL;
+ if ( am->ArgMgrDefined("noshadowseq") )
+ loadMode |= GDCM_NAME_SPACE::LD_NOSHADOWSEQ;
+ else
+ {
+ if ( am->ArgMgrDefined("noshadow") )
+ loadMode |= GDCM_NAME_SPACE::LD_NOSHADOW;
+ if ( am->ArgMgrDefined("noseq") )
+ loadMode |= GDCM_NAME_SPACE::LD_NOSEQ;
+ }
+
+ const char *tempWorkFile = am->ArgMgrGetString("tmp");
+
+ int extractNb;
+ uint16_t *elemsToExtract;
+ if (am->ArgMgrDefined("extract"))
+ am->ArgMgrGetXInt16Enum("extract", &extractNb);
+ else
+ {
+ elemsToExtract = new uint16_t[4];
+ elemsToExtract[0] = 0x0029;
+ elemsToExtract[1] = 0x1210;
+ elemsToExtract[2] = 0x0029;
+ elemsToExtract[3] = 0x1220;
+ extractNb=2;
+ }
+
+ /* 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;
+
+
+// --------------------------------------------------------
+CSA_content myMap;
+CSA_entry *myEntry;
+CSA_item *myItem;
+// --------------------------------------------------------
+
+// For each tag user wants to extract :
+
+for (int tag_no=0; tag_no<extractNb; tag_no++) {
+
+ uint16_t group = elemsToExtract[2*tag_no];
+ uint16_t elem = elemsToExtract[2*tag_no+1];
+
+ std::string dicom_tag_value = f->GetEntryString(group, elem);
+ if (dicom_tag_value == gdcm::GDCM_UNFOUND)
+ {
+ gdcm::DictEntry *dictEntry = f->GetPubDict()->GetEntry( group, elem);
+ std::cerr << "Image doesn't contain any tag: " << dictEntry->GetName()
+ << std::endl;
+ f->Delete();
+ return 1;
+ }
+
+ gdcm::DocEntry *dicom_tag_doc = f->GetDocEntry(group, elem);
+ gdcm::DataEntry *dicom_tag = dynamic_cast<gdcm::DataEntry *>(dicom_tag_doc);
+ if( !dicom_tag )
+ {
+ std::cerr << "Sorry DataEntry only please" << std::endl;
+ f->Delete();
+ return 1;
+ }
+
+ // Write out the data as a file:
+ std::ofstream o(tempWorkFile);
+ if( !o )
+ {
+ std::cerr << "Problem opening file: [" << tempWorkFile << "]"
+ << std::endl;
+ f->Delete();
+ return 1;
+ }
+ o.write((char*)dicom_tag->GetBinArea(), dicom_tag->GetLength());
+ o.close();
+
+
+std::ifstream is( tempWorkFile );
+char dummy[4+1];
+dummy[4] = 0;
+is.read(dummy, 4);
+if (verbose)
+ std::cout << dummy << std::endl;
+if( strcmp( dummy, "SV10" ) )
+{
+ std::cerr << "Either not a SV10 header or filled with 0..." << std::endl;
+ return 1;
+}
+// wotsit ?
+is.read(dummy, 4);
+if( strcmp( dummy, "\4\3\2\1" ) )
+{
+ std::cerr << "Either not a SV10 header or filled with 0..." << std::endl;
+ return 1;
+}
+if (verbose)
+ std::cout << (int)dummy[0] << (int)dummy[1] << (int)dummy[2]
+ << (int)dummy[3]<< std::endl;
+uint32_t n;
+is.read((char*)&n, sizeof(n));
+if (verbose)
+ std::cout << "number of entries " <<n << std::endl;
+uint32_t unused;
+is.read((char*)&unused, sizeof(unused));
+if (verbose)
+ std::cout << "unused " << unused<< std::endl;
+assert( unused == 77 ); // 'M' character...
+
+for(uint32_t i = 0; i < n; ++i)
+{
+if (verbose)
+ std::cout << "============================================== " << i <<
+ std::endl;
+ char name[64+1];
+ name[64] = 0; // security
+ //std::cout << "Pos 0x" << std::hex << is.tellg() << std::dec << std::endl;
+ is.read(name, 64);
+if (verbose)
+ std::cout << "Name=[" << name << "]" << std::endl;
+ uint32_t vm;
+ is.read((char*)&vm, sizeof(vm));
+if (verbose)
+ std::cout << "vm=" << vm << std::endl;
+ char vr[4];
+ is.read(vr, 4);
+ assert( vr[2] == vr[3] && vr[2] == 0 );
+if (verbose)
+ std::cout << "vr=[" << vr << "]" <<std::endl;
+ uint32_t syngodt;
+ is.read((char*)&syngodt, sizeof(syngodt));
+ check_mapping(syngodt, vr);
+
+if (verbose)
+ std::cout << "syngodt=" << syngodt << std::endl;
+ uint32_t nitems;
+ is.read((char*)&nitems, sizeof(nitems));
+if (verbose)
+ std::cout << "nitems=" << nitems<< std::endl;
+ uint32_t xx;
+ is.read((char*)&xx, sizeof(xx));
+ //std::cout << "xx=" << xx<< std::endl;
+ assert( xx == 77 || xx == 205 );
+
+ myEntry = new CSA_entry;
+ myEntry->Name = name;
+ myEntry->VM = vm;
+ myEntry->VR = vr;
+ myEntry->Syngodt = syngodt;
+ myEntry->Nitems = nitems;
+
+ for( uint32_t j = 0; j < nitems; ++j)
+ {
+if (verbose)
+ std::cout << "-------------------------------------------- " << j
+ << std::endl;
+ uint32_t item_xx[4];
+ is.read((char*)&item_xx, 4*sizeof(uint32_t));
+if (verbose)
+ std::cout << "item_xx=" << item_xx[0] << " " << item_xx[1] << " "
+ << item_xx[2] << " " << item_xx[3] << std::endl;
+ //std::cout << "0x" << std::hex << is.tellg() << std::dec << std::endl;
+ assert( item_xx[2] == 77 || item_xx[2] == 205 );
+ uint32_t len = item_xx[1]; // 2nd element
+if (verbose)
+ std::cout << "len=" << len << std::endl;
+ assert( item_xx[0] == item_xx[1] && item_xx[1] == item_xx[3] );
+ char *val = new char[len+1];
+ val[len] = 0; // security
+ is.read(val,len);
+ // WARNING vr does not means anything AFAIK,
+ // simply print the value as if it was IS/DS or LO (ASCII)
+if (verbose)
+ std::cout << "val=[" << val << "]" << std::endl;
+
+ char dummy[4];
+ uint32_t dummy_len = (4 - len % 4) % 4;
+ is.read(dummy, dummy_len );
+
+
+ for(uint32_t d= 0; d < dummy_len; ++d)
+ {
+ // I think dummy should always be 0
+ if( dummy[d] )
+ {
+if (verbose)
+ std::cout << "dummy=" << (int)dummy[d] << std::endl;
+ }
+ }
+
+ myItem = new CSA_item;
+ for (int i2=0; i2<4; i2++)
+ myItem->Item_xx[i2] = item_xx[i2];
+ myItem->Len = len;
+ myItem->Value = val;
+
+ myEntry->Items_set.push_back(myItem);
+ delete[] val;
+
+ }
+ myMap[name] = myEntry;
+ }
+
+std::cout << "================================================================"
+ << std::endl
+ << "=== Extract :" << std::hex << group << " " << elem << "========"
+ << std::endl
+ << "================================================================"
+ << std::endl;
+
+ PrintCSA_content (myMap);
+ DeleteCSA_content (myMap);
+}
+
+f->Delete();
+return 0;
+}
projects / gdcm.git / commitdiff