--- /dev/null
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: exConvert3DplusT.cxx,v $
+ Language: C++
+ Date: $Date: 2006/07/19 09:03:24 $
+ 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.
+
+=========================================================================*/
+//
+// This program is used to convert huge amounts of functionnal (3D + T) MR images
+// into 'image tiles' (one title per volume) processable by clinical softwares
+//
+#include "gdcmFile.h"
+#include "gdcmFileHelper.h"
+#include "gdcmCommon.h"
+#include "gdcmDebug.h"
+#include "gdcmDirList.h"
+#include "gdcmUtil.h"
+
+#include "gdcmArgMgr.h"
+
+#include <iostream>
+#include <sstream>
+#include <string.h> // for memset
+
+int main(int argc, char *argv[])
+{
+ START_USAGE(usage)
+ "\n exConvert3plusT :\n ",
+ " Converts the Dicom files inside a single-level Directory ",
+ " into a '3D + T' image set ",
+ " usage: exConvert3plusT ",
+ " dirin=inputDirectoryName ",
+ " dirout=outputDirectoryName ",
+ " [studyUID = ] [patName = ] ",
+ " [ { [noshadowseq] | [noshadow][noseq] } ] [debug] [verbose]",
+ " ",
+ " dirin : single-level Directory containing the images ",
+ " (no recursive parsing) ",
+ " dirout : will be created if doesn't exist ",
+ " ",
+ " [imdimx = ] [imdimy = ] [imgline = ] [imgcol = ] ",
+ " [pixelsize = ] [imagesinvolume = ] ",
+ " ",
+ " studyUID : *aware* user wants to add the serie ",
+ " to an already existing study ",
+ " imdimx,imdimy : 'elementary image' size (default : 64) ",
+ " used to reject erroneous images ",
+ " imgline, imgcol : sizes of the 'image tile' defaulted as 6x6 ",
+ " pixelsize : in bytes; defaulted as 2 (uint16_t) ",
+ " used to reject erroneous images ",
+ " imagesinvolume : we have no way to guess it! ",
+ " defaulted as imgline*imgcol ",
+ " 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 : user wants to run the program in 'verbose mode' ",
+ " debug : developper wants to run the program in 'debug mode' ",
+ FINISH_USAGE
+
+
+ // ----- Initialize Arguments Manager ------
+
+ gdcm::ArgMgr *am = new gdcm::ArgMgr(argc, argv);
+
+ if (am->ArgMgrDefined("usage") || argc == 1)
+ {
+ am->ArgMgrUsage(usage); // Display 'usage'
+ delete am;
+ return 0;
+ }
+
+ if (am->ArgMgrDefined("debug"))
+ gdcm::Debug::DebugOn();
+ int verbose = am->ArgMgrDefined("verbose");
+ int oververbose = am->ArgMgrDefined("oververbose");
+
+ std::string patName = am->ArgMgrGetString("patname", "g^PatientName");
+ //float zSpacing = am->ArgMgrGetFloat("zSpacing", 1.0);
+
+ const char *dirIn = am->ArgMgrGetString("dirin");
+ const char *dirOut = am->ArgMgrGetString("dirout");
+
+ bool userDefinedStudy = am->ArgMgrDefined("studyUID");
+ const char *studyUID = am->ArgMgrGetString("studyUID");
+
+// not described *on purpose* in the Usage !
+ bool userDefinedSerie = am->ArgMgrDefined("serieUID");
+ const char *serieUID = am->ArgMgrGetString("serieUID");
+
+
+ int imageDimX = am->ArgMgrGetInt("imdimx",64);
+ int imageDimY = am->ArgMgrGetInt("imdimy",64);
+ int imagePixelSize = am->ArgMgrGetInt("pixelsize", 2);
+ int imagetteLineNumber = am->ArgMgrGetInt("imgline",6);
+ int imagetteRowNumber = am->ArgMgrGetInt("imgcol",6);
+ int nbOfImagesInVolume = am->ArgMgrGetInt("imagesinvolume",
+ imagetteLineNumber*imagetteRowNumber);
+
+ int loadMode = gdcm::LD_ALL;
+ if ( am->ArgMgrDefined("noshadowseq") )
+ loadMode |= gdcm::LD_NOSHADOWSEQ;
+ else
+ {
+ if ( am->ArgMgrDefined("noshadow") )
+ loadMode |= gdcm::LD_NOSHADOW;
+ if ( am->ArgMgrDefined("noseq") )
+ loadMode |= gdcm::LD_NOSEQ;
+ }
+
+ /* 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 ------
+
+ // ====== Deal with a (single level, single Patient) Directory ======
+
+
+ //std::cout << "dirIn [" << dirIn << "]" << std::endl;
+ if ( ! gdcm::DirList::IsDirectory(dirIn) )
+ {
+ std::cout << "KO : [" << dirIn << "] is not a Directory." << std::endl;
+ return 0;
+
+ }
+ else
+ {
+ if (verbose)
+ std::cout << "OK : [" << dirIn << "] is a Directory." << std::endl;
+ }
+
+ std::string systemCommand;
+ std::string strDirNameout(dirOut); // to please gcc 4
+ if (verbose)
+ std::cout << "Check for output directory :[" << dirOut << "]."
+ <<std::endl;
+ if ( ! gdcm::DirList::IsDirectory(dirOut) ) // dirout not found
+ {
+ systemCommand = "mkdir " +strDirNameout; // create it!
+ if (verbose)
+ std::cout << systemCommand << std::endl;
+ system (systemCommand.c_str());
+ if ( ! gdcm::DirList::IsDirectory(dirOut) ) // be sure it worked
+ {
+ std::cout << "KO : not a dir : [" << dirOut
+ << "] (creation failure ?)" << std::endl;
+ return 0;
+
+ }
+ else
+ {
+ if (verbose)
+ std::cout << "Directory [" << dirOut << "] created." << std::endl;
+ }
+ }
+ else
+ {
+ if (verbose)
+ std::cout << "Output Directory [" << dirOut
+ << "] already exists; Used as is." << std::endl;
+ }
+
+ gdcm::DirList dirList(dirIn,false); // gets (at single level) the file list
+ gdcm::DirListType fileList = dirList.GetFilenames();
+
+ // 'Study Instance UID'
+ // The user is allowed to create his own Study,
+ // keeping the same 'Study Instance UID' for various images
+ // The user may add images to a 'Manufacturer Study',
+ // adding new Series to an already existing Study
+ std::string strStudyUID;
+ if ( !userDefinedStudy)
+ strStudyUID = gdcm::Util::CreateUniqueUID();
+ else
+ strStudyUID = studyUID;
+
+
+ // 'Serie Instance UID'
+ // The user is allowed to create his own Series,
+ // keeping the same 'Serie Instance UID' for various images
+ // The user shouldn't add any image to a 'Manufacturer Serie'
+ // but there is no way no to prevent him for doing that
+
+ std::string strSerieUID;
+ if ( !userDefinedSerie)
+ strSerieUID = gdcm::Util::CreateUniqueUID();
+ else
+ strSerieUID = serieUID;
+
+ std::ostringstream str;
+
+ size_t totalNumberOfPixels = imageDimX*imageDimY * imagetteLineNumber*imagetteRowNumber;
+ int16_t *imageTable = new int16_t[totalNumberOfPixels];
+
+ //std::cout << " imageTable length " << totalNumberOfPixels;
+ memset(imageTable, 0, totalNumberOfPixels * imagePixelSize);
+
+ int16_t **tabImageData = new int16_t *[nbOfImagesInVolume];
+
+ gdcm::File *f;
+ gdcm::FileHelper *fh;
+ std::string fullFilename, lastFilename;
+ float zPositionComponent = 0.0;
+
+ int imageNumber = 0;
+
+ for( gdcm::DirListType::iterator it = fileList.begin();
+ it != fileList.end();
+ ++it )
+ {
+ fullFilename = *it;
+ f = gdcm::File::New( );
+ f->SetLoadMode(loadMode);
+ f->SetFileName( it->c_str() );
+
+ if (verbose)
+ std::cout << "file [" << it->c_str() << "]" << std::endl;
+ if ( !f->Load() )
+ {
+ if (verbose)
+ std::cout << "fail to load [" << it->c_str() << "]" << std::endl;
+ f->Delete();
+ continue;
+ }
+
+ // Load the pixels in RAM.
+
+ fh = gdcm::FileHelper::New(f);
+ // Don't convert (Gray Pixels + LUT) into (RGB pixels) ?!?
+
+ tabImageData[imageNumber] = (int16_t *)fh->GetImageDataRaw();
+ if (!tabImageData[imageNumber])
+ {
+ std::cout << "fail to read [" << it->c_str() << std::endl;
+ continue;
+ }
+ int16_t mini=32000;
+ int16_t maxi=-32000;
+
+ if (imageNumber == nbOfImagesInVolume)
+ {
+ for(imageNumber=0; imageNumber < nbOfImagesInVolume; imageNumber++)
+ {
+ int debMove = (imageNumber%imagetteRowNumber) * imageDimX
+ + (imageNumber/imagetteRowNumber) *imageDimX*imageDimY*imagetteRowNumber;
+
+ if (verbose)
+ std::cout << "imageNumber " << imageNumber << " debMove " << debMove << std::endl;
+
+ for(int i=0; i<imageDimY; i++)
+ {
+ int debLigne = debMove + i*imagetteRowNumber*imageDimX;
+ //if (oververbose)
+ // std::cout << "numLigne " << i << " debLigne " << debLigne
+ // << ": " << debMove << " + " << i << " * " << imagetteRowNumber*imageDimX << std::endl;
+ for (int j=0; j<imageDimX; j++)
+ {
+ //std::cout << "j " << j << std::endl;
+
+ imageTable[debLigne + j] = *(tabImageData[imageNumber] + i*imageDimY + j);
+ if (imageTable[debLigne + j] < 0) imageTable[debLigne + j]=0;
+ if (imageTable[debLigne + j] > 100) imageTable[debLigne + j]=100;
+ //std::cout << debLigne + j << " : " << imageTable[debLigne + j] << std::endl;
+
+ if (*(tabImageData[imageNumber] + i*imageDimY + j) < mini)
+ mini=*(tabImageData[imageNumber] + i*imageDimY + j);
+ else if (*(tabImageData[imageNumber] + i*imageDimY + j) > maxi)
+ maxi=*(tabImageData[imageNumber] + i*imageDimY + j);
+ }
+ }
+ }
+ // if (oververbose)
+ // std::cout << " mini = " << mini << " maxi = " << maxi << std::endl;
+ // just to check (actually, it's useless)
+ /*
+ int16_t mini=32000;
+ int16_t maxi=-32000;
+ for (int k=0; k < totalNumberOfPixels; k++)
+ {
+ if (imageTable[k] < mini) mini=imageTable[k];
+ else if (imageTable[k] > maxi) maxi=imageTable[k];
+ }
+
+ // if (oververbose)
+ // std::cout << " mini = " << mini << " maxi = " << maxi << std::endl;
+ /// \todo : FIXME what do I do ? Smallest/Largest Image Pixel Value is vr=US, Pixels are signed ?!?
+
+ str.str("");
+ str << mini;
+ fh->InsertEntryString(str.str(),0x0028,0x0106, "US"); // Smallest Image Pixel Value
+
+ str.str("");
+ str << maxi;
+ fh->InsertEntryString(str.str(),0x0028,0x0107, "US"); // Largest Image Pixel Value
+*/
+ imageNumber = 0;
+
+ // write the imagette
+
+ // Set the image size
+ str.str("");
+ str << imageDimX*imagetteRowNumber;
+ fh->InsertEntryString(str.str(),0x0028,0x0011, "US"); // Columns
+
+ str.str("");
+ str << imageDimY*imagetteLineNumber;
+ fh->InsertEntryString(str.str(),0x0028,0x0010, "US"); // Rows
+
+ fh->InsertEntryString(strStudyUID,0x0020,0x000d,"UI");
+ fh->InsertEntryString(strSerieUID,0x0020,0x000e,"UI");
+ fh->InsertEntryString(patName,0x0010,0x0010, "PN"); // Patient's Name
+
+ fh->SetImageData((uint8_t *)imageTable, totalNumberOfPixels * imagePixelSize);
+
+// ==================================================================================================
+
+// This is a dirty heuristics, but no other way :-(
+
+// if Image Orientation (Patient) is not present
+// I create one, (as Axial)
+// if Image Position (Patient) is not present
+// I create one, incrementing zPositionComponent up by user supplied zSpacing
+// if Slice Location is not present
+// I create one, as zPositionComponent
+//
+// Aware use is free to supply his own one !
+
+/*
+ if (! f->CheckIfEntryExist(0x0020,0x0037) ) // 0020 0037 DS 6 Image Orientation (Patient)
+ {
+ fh->InsertEntryString("1.0\\0.0\\0.0\\0.0\\1.0\\0.0",0x0020,0x0037, "DS"); //[1\0\0\0\1\0] : Axial
+
+ char charImagePosition[256];
+
+ sprintf(charImagePosition,"%f\\0.0\\0.0",zPositionComponent);
+ zPositionComponent += zSpacing;
+
+ if (! f->CheckIfEntryExist(0x0020,0x0032) ) //0020 0032 DS 3 Image Position (Patient)
+ fh->InsertEntryString(charImagePosition,0x0020,0x0032, "DS");
+
+ if (! f->CheckIfEntryExist(0x0020,0x1041) ) // 0020 0x1041 DS 1 Slice Location
+ {
+ sprintf(charImagePosition,"%f",zPositionComponent);
+ fh->InsertEntryString(charImagePosition,0x0020,0x1041, "DS");
+ }
+ }
+
+*/
+
+// ==================================================================================================
+
+ fh->SetWriteTypeToDcmExplVR();
+ fh->SetContentType(gdcm::UNMODIFIED_PIXELS_IMAGE);
+
+
+ lastFilename = gdcm::Util::GetName( fullFilename );
+ std::string fullWriteFilename = strDirNameout + gdcm::GDCM_FILESEPARATOR
+ + lastFilename;
+ if (verbose)
+ std::cout << "Write : [" << fullWriteFilename << "]" << std::endl;
+ if (!fh->Write(fullWriteFilename))
+ {
+ std::cout << "Fail to write :[" << fullWriteFilename << "]"
+ << std::endl;
+ }
+ //break;
+ } // end : 'write the imagette'
+ else
+ {
+ imageNumber++;
+ }
+ fh->Delete();
+ f->Delete();
+ }
+}
git://git.creatis.insa-lyon.fr / gdcm.git / commitdiff