Program: gdcm
Module: $RCSfile: exConvert3DplusT.cxx,v $
Language: C++
- Date: $Date: 2007/06/21 15:06:13 $
- Version: $Revision: 1.5 $
+ Date: $Date: 2008/02/13 19:02:39 $
+ Version: $Revision: 1.6 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
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 <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 ",
" [pixelsize = ] [imagesinvolume = ] ",
" ",
" studyUID : *aware* user wants to add the serie ",
- " to an already existing study ",
+ " 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 ",
" 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_NAME_SPACE::ArgMgr *am = new GDCM_NAME_SPACE::ArgMgr(argc, argv);
-
if (am->ArgMgrDefined("usage") || argc == 1)
{
am->ArgMgrUsage(usage); // Display 'usage'
GDCM_NAME_SPACE::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 *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");
-
+// 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 loadMode = GDCM_NAME_SPACE::LD_ALL;
if ( am->ArgMgrDefined("noshadowseq") )
loadMode |= GDCM_NAME_SPACE::LD_NOSHADOWSEQ;
- else
+ else
{
if ( am->ArgMgrDefined("noshadow") )
loadMode |= GDCM_NAME_SPACE::LD_NOSHADOW;
if ( am->ArgMgrDefined("noseq") )
loadMode |= GDCM_NAME_SPACE::LD_NOSEQ;
}
-
+
/* if unused Param we give up */
if ( am->ArgMgrPrintUnusedLabels() )
{
}
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_NAME_SPACE::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
+ std::string strDirNameout(dirOut); // to please gcc 4
if (verbose)
std::cout << "Check for output directory :[" << dirOut << "]."
<<std::endl;
{
std::cout << "KO : not a dir : [" << dirOut
<< "] (creation failure ?)" << std::endl;
- return 0;
-
+ return 0;
}
else
{
else
{
if (verbose)
- std::cout << "Output Directory [" << dirOut
+ std::cout << "Output Directory [" << dirOut
<< "] already exists; Used as is." << std::endl;
}
GDCM_NAME_SPACE::DirList dirList(dirIn,false); // gets (at single level) the file list
GDCM_NAME_SPACE::DirListType fileList = dirList.GetFilenames();
-
// hope sorting on the filename is enough!
// anyway, *no* filed is available to perform anything more clever.
-
std::sort(fileList.begin(), fileList.end() );
// 'Study Instance UID'
strStudyUID = studyUID;
// 'Serie Instance UID'
- // The user is allowed to create his own Series,
+ // 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)
+ std::string strSerieUID;
+ if ( !userDefinedSerie)
strSerieUID = GDCM_NAME_SPACE::Util::CreateUniqueUID();
- else
+ else
strSerieUID = serieUID;
std::ostringstream str;
-
- size_t totalNumberOfPixels = imageDimX*imageDimY * imagetteLineNumber*imagetteRowNumber;
- int16_t *imageTable = new int16_t[totalNumberOfPixels];
-
+ size_t totalNumberOfPixels = imageDimX*imageDimY * imagetteLineNumber*imagetteRowNumber;
+ int16_t *imageTable = new int16_t[totalNumberOfPixels];
+
memset(imageTable, 0, totalNumberOfPixels * imagePixelSize);
-
- int16_t **tabImageData = new int16_t *[nbOfImagesInVolume];
+
+ int16_t **tabImageData = new int16_t *[nbOfImagesInVolume];
GDCM_NAME_SPACE::File **f = new GDCM_NAME_SPACE::File *[nbOfImagesInVolume];
GDCM_NAME_SPACE::FileHelper **fh = new GDCM_NAME_SPACE::FileHelper *[nbOfImagesInVolume];
-
+
std::string fullFilename, lastFilename;
float zPositionComponent = 0.0;
-
int imageNumber = 0;
-
for( GDCM_NAME_SPACE::DirListType::iterator it = fileList.begin();
it != fileList.end();
++it )
if (verbose)
std::cout << "file [" << it->c_str() << "], as imageNumber : " << imageNumber << std::endl;
-
+
if ( !f[imageNumber]->Load() )
{
if (verbose)
- std::cout << "fail to load [" << it->c_str() << "]" << std::endl;
+ std::cout << "fail to load [" << it->c_str() << "]" << std::endl;
f[imageNumber]->Delete();
continue;
}
- // Load the pixels in RAM.
-
- fh[imageNumber] = GDCM_NAME_SPACE::FileHelper::New(f[imageNumber]);
+ // Load the pixels in RAM.
+
+ fh[imageNumber] = GDCM_NAME_SPACE::FileHelper::New(f[imageNumber]);
// Don't convert (Gray Pixels + LUT) into (RGB pixels) ?!?
tabImageData[imageNumber] = (int16_t *)fh[imageNumber]->GetImageDataRaw();
-
if (!tabImageData[imageNumber])
{
std::cout << "fail to read [" << it->c_str() << std::endl;
}
int16_t mini=32000;
int16_t maxi=-32000;
-
if (imageNumber == nbOfImagesInVolume-1)
- {
+ {
for(imageNumber=0; imageNumber < nbOfImagesInVolume; imageNumber++)
{
int debMove = (imageNumber%imagetteRowNumber) * imageDimX
if (verbose)
std::cout << "imageNumber " << imageNumber << " debMove " << debMove << std::endl;
-
for(int i=0; i<imageDimY; i++)
{
int debLigne = debMove + i*imagetteRowNumber*imageDimX;
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;
//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)
+ // 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];
+ else if (imageTable[k] > maxi) maxi=imageTable[k];
}
// if (oververbose)
str.str("");
str << imageDimY*imagetteLineNumber;
- fh[imageNumber]->InsertEntryString(str.str(),0x0028,0x0010, "US"); // Rows
+ fh[imageNumber]->InsertEntryString(str.str(),0x0028,0x0010, "US"); // Rows
- fh[imageNumber]->InsertEntryString(strStudyUID,0x0020,0x000d,"UI");
+ fh[imageNumber]->InsertEntryString(strStudyUID,0x0020,0x000d,"UI");
fh[imageNumber]->InsertEntryString(strSerieUID,0x0020,0x000e,"UI");
fh[imageNumber]->InsertEntryString(patName,0x0010,0x0010, "PN"); // Patient's Name
// This is a dirty heuristics, but no other way :-(
// if Image Orientation (Patient) is not present
-// I create one, (as Axial)
+// 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
+// if Slice Location is not present
// I create one, as zPositionComponent
//
-// Aware use is free to supply his own one !
+// Aware user is free to supply his own one !
/*
if (! f[imageNumber]->CheckIfEntryExist(0x0020,0x0037) ) // 0020 0037 DS 6 Image Orientation (Patient)
fh[imageNumber]->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[imageNumber]->CheckIfEntryExist(0x0020,0x0032) ) //0020 0032 DS 3 Image Position (Patient)
- fh[imageNumber]->InsertEntryString(charImagePosition,0x0020,0x0032, "DS");
-
+ fh[imageNumber]->InsertEntryString(charImagePosition,0x0020,0x0032, "DS");
if (! f[imageNumber]->CheckIfEntryExist(0x0020,0x1041) ) // 0020 0x1041 DS 1 Slice Location
{
sprintf(charImagePosition,"%f",zPositionComponent);
fh[imageNumber]->InsertEntryString(charImagePosition,0x0020,0x1041, "DS");
- }
- }
+ }
+ }
*/
// ==================================================================================================
- fh[imageNumber]->SetWriteTypeToDcmExplVR();
+ fh[imageNumber]->SetWriteTypeToDcmExplVR();
fh[imageNumber]->SetContentType(GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE);
-
lastFilename = GDCM_NAME_SPACE::Util::GetName( fullFilename );
std::string fullWriteFilename = strDirNameout + GDCM_NAME_SPACE::GDCM_FILESEPARATOR
+ lastFilename;
if (verbose)
std::cout << "Write : [" << fullWriteFilename << "]" << std::endl;
-
if (!fh[imageNumber]->Write(fullWriteFilename))
{
std::cout << "Fail to write :[" << fullWriteFilename << "]"
}
} // end : 'write the imagette'
-
else // start a new 'volume'
{
imageNumber++;
}
}
-}
+}
+
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