Program: gdcm
Module: $RCSfile: ReWrite.cxx,v $
Language: C++
- Date: $Date: 2007/09/04 13:06:12 $
- Version: $Revision: 1.32 $
+ Date: $Date: 2007/09/14 08:23:34 $
+ Version: $Revision: 1.33 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
case 'R' :
case 'r' :
- // Writting a Raw File,
+ // Writting a Raw File,
std::cout << "WriteRaw" << std::endl;
fh->WriteRawData(outputFileName);
break;
case 'J' :
case 'j' :
- // writting a DICOM Jpeg Lossless
+ // writting a DICOM Jpeg Lossless
// from a full gdcm readable File
std::cout << "WriteDCM Jpeg Lossless" << std::endl;
fh->SetWriteTypeToJPEG();
break;
case '2' :
- // writting a DICOM Jpeg 2000
+ // writting a DICOM Jpeg 2000
// from a full gdcm readable File
std::cout << "WriteDCM Jpeg 2000" << std::endl;
fh->SetWriteTypeToJPEG2000();
- break;
-
+ break;
+
// Just for fun :
// Write a 'Video inverse' version of the file.
- // *Not* described, on purpose, in the USAGE
+ // *Not* described, on purpose, in the USAGE
case 'V' :
case 'v' :
if ( fh->GetFile()->GetBitsAllocated() == 8)
{
std::cout << "videoinv for 8 bits" << std::endl;
- for (int i=0; i<dataSize; i++)
+ for (int i=0; i<dataSize; i++)
{
((uint8_t*)imageData)[i] = 255 - ((uint8_t*)imageData)[i];
}
}
else
{
- std::cout << "videoinv for 16 bits" << std::endl;
- for (int i=0; i<dataSize/2; i++)
+ std::cout << "videoinv for 16 bits" << std::endl;
+ for (int i=0; i<dataSize/2; i++)
{
((uint16_t*)imageData)[i] = 65535 - ((uint16_t*)imageData)[i];
}
break;
}
-
//
// user wants to keep only a part of the image (ROI, and/or some frames)
// ---------------------------------------------------------------------
// (==> this is no longer really 'ReWrite' !)
int subImDimX = nX;
- int subImDimY = nY;
+ int subImDimY = nY;
if (roi)
- {
+ {
if (roiBoundVal[0]<0 || roiBoundVal[0]>=nX)
{
std::cout << "xBegin out of bounds; 'roi' ignored" << std::endl;
if (roiBoundVal[0] > roiBoundVal[1])
{
std::cout << "xBegin greater than xEnd; 'roi' ignored" << std::endl;
- fail = true;
+ fail = true;
}
if (roiBoundVal[2]<0 || roiBoundVal[2]>=nY)
- {
+ {
std::cout << "yBegin out of bounds; 'roi' ignored" << std::endl;
- fail = true;
+ fail = true;
}
if (roiBoundVal[3]<0 || roiBoundVal[3]>=nY)
- {
+ {
std::cout << "yEnd out of bounds; 'roi' ignored" << std::endl;
- fail = true;
+ fail = true;
}
if (roiBoundVal[2] > roiBoundVal[3])
- {
+ {
std::cout << "yBegin greater than yEnd; 'roi' ignored" << std::endl;
- fail = true;
- }
- }
+ fail = true;
+ }
+ }
else
- {
+ {
roiBoundVal = new int[4];
roiBoundVal[0] = 0;
roiBoundVal[1] = nX-1;
roiBoundVal[3] = nY-1;
}
- subImDimX = roiBoundVal[1]-roiBoundVal[0]+1;
- subImDimY = roiBoundVal[3]-roiBoundVal[2]+1;
-
+ subImDimX = roiBoundVal[1]-roiBoundVal[0]+1;
+ subImDimY = roiBoundVal[3]-roiBoundVal[2]+1;
+
if (roi || beg != -1 || end != -1)
- {
+ {
if (beg == -1)
beg = 0;
if (end == -1)
end = nZ-1;
-
+
std::ostringstream str;
-
+
// Set the data that will be *actually* written.
int pixelSize = fh->GetFile()->GetPixelSize();
size_t lgrSubLine = subImDimX* pixelSize * numberOfScalarComponents;
size_t lgrSubFrame = subImDimY*lgrSubLine;
- ;
+
int lgrSubImage = (end-beg+1) * lgrSubFrame;
-
+
uint8_t * subImage = new uint8_t[lgrSubImage];
-
+
uint8_t * srcCopy = (uint8_t *) imageData;
uint8_t * destCopy = subImage;
int lineSize = nX*pixelSize*numberOfScalarComponents;
- int frameSize = nY*lineSize;
+ int frameSize = nY*lineSize;
int lineOffset = roiBoundVal[0]*pixelSize * numberOfScalarComponents;
memcpy( (void *)(destCopy + frameCount*lgrSubFrame + lineCount*lgrSubLine),
(void *)(srcCopy + frameNb*frameSize + lineNb*lineSize + lineOffset ),
lgrSubLine);
- }
+ }
}
// Set the image size
//----------------------------------- Write, now! ---------------------------------
if (mode[0] != 'R' && mode[0] != 'r')
- fh->Write(outputFileName);
+ res = fh->Write(outputFileName);
+
+ if(!res)
+ std::cout <<"Fail to write [" << outputFileName << "]" <<std::endl;
f->Delete();
fh->Delete();
Program: gdcm
Module: $RCSfile: exExtractOverlaysACR.cxx,v $
Language: C++
- Date: $Date: 2007/09/12 10:43:47 $
- Version: $Revision: 1.1 $
+ Date: $Date: 2007/09/14 08:23:34 $
+ Version: $Revision: 1.2 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include "gdcmCommon.h"
#include "gdcmDebug.h"
#include "gdcmDocEntry.h"
+#include "gdcmArgMgr.h"
+
#include <iostream>
-#include <stdio.h> // for fseek... FIXME
#include <stdlib.h> // for atoi
-#include "gdcmArgMgr.h"
-
- // WARNING :
- // unfinished : DO NOT to be used as is !
+ /* SIEMENS_GBS_III-16-ACR_NEMA_1.acr
- /*
// Example (sorry, we've got no more than this one ...)
-V 0028|0010[US] [Rows] [256] x(100)
-V 0028|0011[US] [Columns] [256] x(100)
-V 0028|0030[DS] [Pixel Spacing] [01.56\1.56]
-V 0028|0100[US] [Bits Allocated] [16] x(10)
-V 0028|0101[US] [Bits Stored] [12] x(c)
-V 0028|0102[US] [High Bit] [11] x(b)
-V 0028|0103[US] [Pixel Representation] [0] x(0)
+0028|0010[US] [Rows] [256] x(100)
+0028|0011[US] [Columns] [256] x(100)
+0028|0030[DS] [Pixel Spacing] [01.56\1.56]
+0028|0100[US] [Bits Allocated] [16] x(10)
+0028|0101[US] [Bits Stored] [12] x(c)
+0028|0102[US] [High Bit] [11] x(b)
+0028|0103[US] [Pixel Representation] [0] x(0)
-V 6000|0000[UL] [Group Length] [96] x(60)
-V 6000|0010[US] [Rows] [256] x(100)
-V 6000|0011[US] [Columns] [256] x(100)
-V 6000|0040[CS] [Overlay Type] [R ]
-V 6000|0050[SS] [Overlay Origin] [23601\8241] x(5c31)
-V 6000|0100[US] [Overlay Bits Allocated] [16] x(10)
-V 6000|0102[US] [Overlay Bit Position] [12] x(c)
+6000|0000[UL] [Group Length] [96] x(60)
+6000|0010[US] [Rows] [256] x(100)
+6000|0011[US] [Columns] [256] x(100)
+6000|0040[CS] [Overlay Type] [R ]
+6000|0050[SS] [Overlay Origin] [23601\8241] x(5c31)
+6000|0100[US] [Overlay Bits Allocated] [16] x(10)
+6000|0102[US] [Overlay Bit Position] [12] x(c)
...
...
-V 6006|0000[UL] [Group Length] [96] x(60)
-V 6006|0010[US] [Rows] [256] x(100)
-V 6006|0011[US] [Columns] [256] x(100)
-V 6006|0040[CS] [Overlay Type] [R ]
-V 6006|0050[SS] [Overlay Origin] [23601\8241] x(5c31)
-V 6006|0100[US] [Overlay Bits Allocated] [16] x(10)
-V 6006|0102[US] [Overlay Bit Position] [15] x(f)
+6006|0000[UL] [Group Length] [96] x(60)
+6006|0010[US] [Rows] [256] x(100)
+6006|0011[US] [Columns] [256] x(100)
+6006|0040[CS] [Overlay Type] [R ]
+6006|0050[SS] [Overlay Origin] [23601\8241] x(5c31)
+6006|0100[US] [Overlay Bits Allocated] [16] x(10)
+6006|0102[US] [Overlay Bit Position] [15] x(f)
*/
int main(int argc, char *argv[])
-{
+{
START_USAGE(usage)
" \n exExtractOverlaysACR :\n ",
" Extract ACR-NEMA style overlays from an image ",
- " usage: exExtractOverlaysACR filein=inputDirectoryName [debug] ",
+ " usage: exExtractOverlaysACR filein=inputFileName [debug] ",
" debug : developper wants to run the program in 'debug mode' ",
FINISH_USAGE
delete am;
return 0;
}
-
- // "SIEMENS_GBS_III-16-ACR_NEMA_1.acr"
-
- const char *fileName = am->ArgMgrWantString("filein", usage);
+
+ const char *fileName = am->ArgMgrWantString("filein", usage);
if (am->ArgMgrDefined("debug"))
GDCM_NAME_SPACE::Debug::DebugOn();
delete am; // we don't need Argument Manager any longer
+ // ========================== Now, we can do the job! ================
- // ========================== Now, we can do the job! ================
-
GDCM_NAME_SPACE::File *f;
-
// ============================================================
// Read the input image.
// ============================================================
- //std::cout << argv[1] << std::endl;
-
f = GDCM_NAME_SPACE::File::New( );
f->SetLoadMode(GDCM_NAME_SPACE::LD_NOSEQ | GDCM_NAME_SPACE::LD_NOSHADOW);
f->SetFileName( fileName );
bool res = f->Load();
- if( GDCM_NAME_SPACE::Debug::GetDebugFlag() )
- {
- std::cout << "---------------------------------------------" << std::endl;
- f->Print();
- std::cout << "---------------------------------------------" << std::endl;
- }
+
if (!res) {
std::cout << "Sorry, " << fileName <<" not a gdcm-readable "
<< "DICOM / ACR File"
f->Delete();
return 0;
}
- std::cout << " ... is readable " << std::endl;
+ std::cout << fileName << " ... is readable " << std::endl;
// ============================================================
// Check whether image contains Overlays ACR-NEMA style.
f->Delete();
return 0;
}
- std::cout << " File is read! " << std::endl;
+ std::cout << fileName << " is read! " << std::endl;
// ============================================================
// Load the pixels in memory.
// ============================================================
- int nx = f->GetXSize();
- int ny = f->GetYSize();
-
GDCM_NAME_SPACE::FileHelper *fh1 = GDCM_NAME_SPACE::FileHelper::New(f);
fh1->SetKeepOverlays(true);
uint16_t *pixels = (uint16_t *)fh1->GetImageDataRaw();
int lgt = fh1->GetImageDataRawSize();
-
+
if( GDCM_NAME_SPACE::Debug::GetDebugFlag() )
- std::cout << "Pixels read as expected : length = " << lgt << std::endl;
-
+ std::cout << "Pixels read as expected : length = " << lgt << std::endl;
+
// ============================================================
// Prepare the stuff
// ============================================================
-
- uint8_t *tabPixels = new uint8_t[nx*ny]; // uint8 is enought to hold 1 bit !
-
- uint16_t currentOvlGroup = 0x6000;
+
+ unsigned int nx = f->GetXSize();
+ unsigned int ny = f->GetYSize();
+ unsigned int nxy=nx*ny;
+ uint16_t currentOvlGroup;
+ int i;
+
+ std::ostringstream str;
+
+ uint8_t *outputData = new uint8_t[nxy]; // uint8 is enought to hold 1 bit !
+
std::string strOvlBitPosition;
int ovlBitPosition;
uint16_t mask;
- int i = 0;
uint16_t overlayLocation;
- std::ostringstream str;
-
std::string strOverlayLocation;
-
+
GDCM_NAME_SPACE::File *fileToBuild = 0;
GDCM_NAME_SPACE::FileHelper *fh = 0;
// ============================================================
-// Get each overlay Bit into an image
+// Get each overlay Bit into the image
// ============================================================
- for(i=0, currentOvlGroup=0x6000; i<32; i+=2 ,currentOvlGroup+=2)
+ for(i=0, currentOvlGroup=0x6000; i<32; i+=2 ,currentOvlGroup+=2)
{
if ( (strOvlBitPosition = f->GetEntryString(currentOvlGroup, 0x0102))
== GDCM_NAME_SPACE::GDCM_UNFOUND )
continue;
-
- if( GDCM_NAME_SPACE::Debug::GetDebugFlag() )
- std::cout << "Current Overlay Group " << std::hex << currentOvlGroup
+
+ if( GDCM_NAME_SPACE::Debug::GetWarningFlag() )
+ std::cout << "Current Overlay Group " << std::hex << currentOvlGroup
<< " OvlBitPosition " << strOvlBitPosition << std::endl;
-
+
strOverlayLocation = f->GetEntryString(currentOvlGroup, 0x0200);
if ( strOverlayLocation != GDCM_NAME_SPACE::GDCM_UNFOUND )
{
continue;
}
}
+
+ // ============================================================
+ // DICOM Overlay Image data generation
+ // ============================================================
+
ovlBitPosition = atoi(strOvlBitPosition.c_str());
mask = 1 << ovlBitPosition;
-
- if( GDCM_NAME_SPACE::Debug::GetDebugFlag() )
- std::cout << "Mask :[" <<std::hex << mask << "]" << std::endl;
- for (int j=0; j<nx*ny ; j++)
+
+ if( GDCM_NAME_SPACE::Debug::GetDebugFlag() )
+ std::cout << "Mask :[" <<std::hex << mask << "]" << std::endl;
+ for (int j=0; j<nxy; j++)
{
if( GDCM_NAME_SPACE::Debug::GetDebugFlag() )
if (pixels[j] >= 0x1000)// if it contains at least one overlay bit
printf("%d : %04x\n",j, pixels[j]);
if ( (pixels[j] & mask) == 0 )
- tabPixels[j] = 0;
+ outputData[j] = 0;
else
- tabPixels[j] = 128;
+ outputData[j] = 128;
}
- if( GDCM_NAME_SPACE::Debug::GetDebugFlag() )
- std::cout << "About to built empty file" << std::endl;
+ // ============================================================
+ // Write a new file
+ // ============================================================
fileToBuild = GDCM_NAME_SPACE::File::New();
-
- if( GDCM_NAME_SPACE::Debug::GetDebugFlag() )
- std::cout << "Finish to built empty file" << std::endl;
-
str.str("");
str << nx;
- fileToBuild->InsertEntryString(str.str(),0x0028,0x0011); // Columns
+ fileToBuild->InsertEntryString(str.str(),0x0028,0x0011, "US"); // Columns
str.str("");
str << ny;
- fileToBuild->InsertEntryString(str.str(),0x0028,0x0010); // Rows
+ fileToBuild->InsertEntryString(str.str(),0x0028,0x0010, "US"); // Rows
- fileToBuild->InsertEntryString("8",0x0028,0x0100); // Bits Allocated
- fileToBuild->InsertEntryString("8",0x0028,0x0101); // Bits Stored
- fileToBuild->InsertEntryString("7",0x0028,0x0102); // High Bit
- fileToBuild->InsertEntryString("0",0x0028,0x0103); // Pixel Representation
- fileToBuild->InsertEntryString("1",0x0028,0x0002); // Samples per Pixel
+ fileToBuild->InsertEntryString("8",0x0028,0x0100, "US"); // Bits Allocated
+ fileToBuild->InsertEntryString("8",0x0028,0x0101, "US"); // Bits Stored
+ fileToBuild->InsertEntryString("7",0x0028,0x0102, "US"); // High Bit
+ fileToBuild->InsertEntryString("0",0x0028,0x0103, "US"); // Pixel Representation
+ fileToBuild->InsertEntryString("1",0x0028,0x0002, "US"); // Samples per Pixel
+ fileToBuild->InsertEntryString("MONOCHROME2 ",0x0028,0x0004, "LO");
- fileToBuild->InsertEntryString("MONOCHROME2 ",0x0028,0x0004);
+ // feel free to add any field (Dicom Data Entry) you like, here.
+ // ...
// Other mandatory fields will be set automatically,
// just before Write(), by FileHelper::CheckMandatoryElements()
- if( GDCM_NAME_SPACE::Debug::GetDebugFlag() )
- std::cout << "-------------About to built FileHelper" << std::endl;
-
fh = GDCM_NAME_SPACE::FileHelper::New(fileToBuild);
- if( GDCM_NAME_SPACE::Debug::GetDebugFlag() )
- std::cout << "-------------Finish to built FileHelper" << std::endl;
-
- fh->SetImageData(tabPixels,nx*ny);
+ fh->SetImageData(outputData,nx*ny);
fh->SetWriteTypeToDcmExplVR();
std::ostringstream tmp;
{
std::cout << "Failed\n"
<< "File [" << str.str() << "] is unwrittable" << std::endl;
- /*
- fh->Delete();
- if (fileToBuild)
- fileToBuild->Delete();
- delete pixels;
- delete tabPixels;
- return 0;
- */
}
else
{
std::cout << "File written successfully [" << str.str() << "]" << std::endl;
}
- }
-
+
+ } // end on loop on 60xx
+
if (f)
fh->Delete();
if (fileToBuild)
fileToBuild->Delete();
f->Delete();
delete pixels;
- delete tabPixels;
+ delete outputData;
return 0;
}
Program: gdcm
Module: $RCSfile: exExtractOverlaysDCM.cxx,v $
Language: C++
- Date: $Date: 2007/09/12 10:43:47 $
- Version: $Revision: 1.1 $
+ Date: $Date: 2007/09/14 08:23:34 $
+ Version: $Revision: 1.2 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
PURPOSE. See the above copyright notices for more information.
=========================================================================*/
-
-
#include "gdcmFile.h"
#include "gdcmFileHelper.h"
#include "gdcmCommon.h"
#include "gdcmDebug.h"
#include "gdcmDataEntry.h"
#include "gdcmDirList.h"
-
#include "gdcmArgMgr.h"
+
#include <iostream>
// Each BIT of Overlay Data (0x6000,0x3000) corresponds
return;
}
-
int main(int argc, char *argv[])
{
START_USAGE(usage)
" \n ExtractOverlays :\n ",
- " Extract overlay images from all DICOM image within a directory ",
- " Warning : probably segfaults if no overlay ",
- " usage: ExtractOverlays dirin=inputDirectoryName [debug] ",
+ " Extract DICOM style overlays from an image ",
+ " usage: exExtractOverlaysDCM filein=inputFileName [debug] ",
" debug : developper wants to run the program in 'debug mode' ",
FINISH_USAGE
delete am;
return 0;
}
-
- const char *dirIn = am->ArgMgrWantString("dirin", usage);
+
+ const char *fileName = am->ArgMgrWantString("filein", usage);
if (am->ArgMgrDefined("debug"))
GDCM_NAME_SPACE::Debug::DebugOn();
delete am; // we don't need Argument Manager any longer
-
// ========================== Now, we can do the job! ================
-
- // ======================== more checking on the params ==============
-
- if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(dirIn) )
- {
- std::cout << "KO : [" << dirIn << "] is not a Directory." << std::endl;
- return 0;
-
- }
-
- char outputFileName[1024]; // Hope it's enough for a file name!
-
GDCM_NAME_SPACE::File *f;
-
- GDCM_NAME_SPACE::DirList dirList(dirIn,true); // gets (recursively) the file list
- GDCM_NAME_SPACE::DirListType fileList = dirList.GetFilenames();
- for( GDCM_NAME_SPACE::DirListType::iterator it = fileList.begin();
- it != fileList.end();
- ++it )
- {
- // Just to see *all* the file names:
- // std::cout << "file [" << it->c_str() << "]" << std::endl;
-
- // Read the input file.
-
- if( GDCM_NAME_SPACE::Debug::GetWarningFlag() )
- std::cerr << "Deal with [" << it->c_str()
- << "] File" <<std::endl;
- f = GDCM_NAME_SPACE::File::New( );
- f->SetLoadMode( GDCM_NAME_SPACE::LD_ALL );
- f->SetFileName( it->c_str() );
+// ============================================================
+// Read the input image.
+// ============================================================
+
+ f = GDCM_NAME_SPACE::File::New( );
f->AddForceLoadElement(0x6000,0x3000); // Overlay Data
f->AddForceLoadElement(0x6002,0x3000);
f->AddForceLoadElement(0x601a,0x3000);
f->AddForceLoadElement(0x601c,0x3000);
f->AddForceLoadElement(0x601e,0x3000); // Hope it's enought : Dicom says 60xx ...
-
- int res = f->Load();
- if ( !res )
- {
- std::cerr << "Sorry, " << it->c_str() <<" not a gdcm-readable "
- << "DICOM / ACR File" <<std::endl;
- f->Delete();
- continue;
+ f->SetLoadMode(GDCM_NAME_SPACE::LD_NOSEQ | GDCM_NAME_SPACE::LD_NOSHADOW);
+ f->SetFileName( fileName );
+ bool res = f->Load();
+
+ if (!res) {
+ std::cout << "Sorry, " << fileName <<" not a gdcm-readable "
+ << "DICOM / ACR File"
+ <<std::endl;
+ f->Delete();
+ return 0;
}
+ std::cout << fileName << " ... is readable " << std::endl;
- if( GDCM_NAME_SPACE::Debug::GetWarningFlag() )
- std::cout << " ... is readable " << std::endl;
+// ============================================================
+// Check whether image contains Overlays DICOM style.
+// ============================================================
- // ============================================================
- // Load Overlay info in memory
- // ============================================================
+ unsigned int nx = f->GetXSize();
+ unsigned int ny = f->GetYSize();
+ unsigned int nxy=nx*ny;
+ uint16_t currentOvlGroup;
+ int i;
-/// \todo : deal with *each* overlay Data Element (not only the first one!)
+ std::ostringstream str;
- uint16_t ovlyGroup = 0x6000;
-
- for (int k=0; k<32; k+=2)
- {
-
- GDCM_NAME_SPACE::DataEntry *e10 = f->GetDataEntry(ovlyGroup+k, 0x0010); // nb Row Ovly
- if (e10 == 0)
- {
- if( GDCM_NAME_SPACE::Debug::GetWarningFlag() )
- std::cout << " Image doesn't contain Overlay on " <<std::hex
- << ovlyGroup+k << std::endl;
- continue;
- }
-
- // ============================================================
- // Image data preparation
- // ============================================================
+ uint8_t *outputData = new uint8_t[nxy]; // uint8 is enought to hold 1 bit !
- unsigned int dimX= f->GetXSize();
- unsigned int dimY= f->GetYSize();
- unsigned int dimXY=dimX*dimY;
+ GDCM_NAME_SPACE::File *fileToBuild = 0;
+ GDCM_NAME_SPACE::FileHelper *fh = 0;
- unsigned char *outputData = new unsigned char[dimXY];
-
-
- GDCM_NAME_SPACE::DataEntry *e = f->GetDataEntry(ovlyGroup+k, 0x3000);
- if (e == 0)
+// ============================================================
+// Get each overlay
+// ============================================================
+ for(i=0, currentOvlGroup=0x6000; i<32; i+=2 ,currentOvlGroup+=2)
{
- if( GDCM_NAME_SPACE::Debug::GetWarningFlag() )
- std::cout << " Image doesn't contain DICOM Overlay Data " <<std::hex
- << ovlyGroup+k << std::endl;
-
- // ============================================================
- // DICOM Overlay Image data generation
- // ============================================================
-
- GDCM_NAME_SPACE::FileHelper *fh = GDCM_NAME_SPACE::FileHelper::New(f);
- uint8_t *pixelData= fh->GetImageDataRaw();
-
- if (pixelData == 0)
+ GDCM_NAME_SPACE::DataEntry *e10 = f->GetDataEntry(currentOvlGroup, 0x0010); // nb Row Ovly
+ if (e10 == 0)
{
- std::cerr << "Sorry, Pixel Data of [" << it->c_str() <<"] are not "
- << " gdcm-readable." << std::endl;
- continue;
- }
-
- }
- else
- {
- uint8_t *overlay = (uint8_t *)(e->GetBinArea());
- if ( overlay == 0 )
+ if( GDCM_NAME_SPACE::Debug::GetWarningFlag() )
+ std::cout << " Image doesn't contain Overlay on " <<std::hex
+ << currentOvlGroup+i << std::endl;
+ continue;
+ }
+
+ uint8_t *outputData = new uint8_t[nxy];
+
+ GDCM_NAME_SPACE::DataEntry *e = f->GetDataEntry(currentOvlGroup, 0x3000);
+ if (e == 0)
{
- std::cerr << "Sorry, Overlays of [" << it->c_str() <<"] are not "
- << " gdcm-readable." << std::endl;
- continue;
+ if( GDCM_NAME_SPACE::Debug::GetWarningFlag() )
+ std::cout << " Image doesn't contain DICOM Overlay Data " <<std::hex
+ << currentOvlGroup+i << std::endl;
}
- if( GDCM_NAME_SPACE::Debug::GetWarningFlag() )
- std::cout << " Overlay on group [" << std::hex << ovlyGroup+k << "] is read! " << std::endl;
-
+ else
+ {
+ uint8_t *overlay = (uint8_t *)(e->GetBinArea());
+ if ( overlay == 0 )
+ {
+ std::cerr << "Sorry, Overlays of [" << fileName << "] are not "
+ << " gdcm-readable." << std::endl;
+ continue;
+ }
+ if( GDCM_NAME_SPACE::Debug::GetWarningFlag() )
+ std::cout << " Overlay on group [" << std::hex << currentOvlGroup<< "] is read! " << std::endl;
+
// ============================================================
// DICOM Overlay Image data generation
- // ============================================================
-
+ // ============================================================
- unsigned char *result=outputData;
- for (unsigned int i=0;i<(dimXY/8);i++)
- {
- explodeByte(overlay[i], result);
- result+=8;
+ unsigned char *result=outputData;
+ for (unsigned int i=0;i<(nxy/8);i++)
+ {
+ explodeByte(overlay[i], result);
+ result+=8;
+ }
}
- }
// ============================================================
// Write a new file
// ============================================================
-
- GDCM_NAME_SPACE::File *f2;
- f2 = GDCM_NAME_SPACE::File::New( );
- GDCM_NAME_SPACE::FileHelper *fh2 = GDCM_NAME_SPACE::FileHelper::New(f2);
-
- char temp[256];
-
- sprintf(temp,"%d ",dimX);
- f2->InsertEntryString(temp,0x0028,0x0011, "US"); // Columns
- sprintf(temp,"%d ",dimY);
- f2->InsertEntryString(temp,0x0028,0x0010, "US"); // Rows
- f2->InsertEntryString("8",0x0028,0x0100, "US"); // Bits Allocated
- f2->InsertEntryString("8",0x0028,0x0101, "US"); // Bits Stored
- f2->InsertEntryString("7",0x0028,0x0102, "US"); // High Bit
- f2->InsertEntryString("0",0x0028,0x0103, "US"); // Pixel Representation
- f2->InsertEntryString("1",0x0028,0x0002, "US"); // Samples per Pixel
- f2->InsertEntryString("MONOCHROME2 ",0x0028,0x0004, "LO");
-
- // feel free to add any field (Dicom Data Entry) you like, here.
- // ...
-
- sprintf(outputFileName, "../%s.ovly.%04x.dcm",it->c_str(), ovlyGroup+k);
-
- fh2->SetImageData(outputData,dimXY);
- fh2->WriteDcmExplVR(outputFileName);
-
- std::cout <<"File written successfully [" << outputFileName << "]" <<std::endl;
-
- delete outputData;
- f2->Delete();
- fh2->Delete();
-
- } // end on loop on 60xx
-
+
+ fileToBuild = GDCM_NAME_SPACE::File::New();
+ str.str("");
+ str << nx;
+ fileToBuild->InsertEntryString(str.str(),0x0028,0x0011, "US"); // Columns
+ str.str("");
+ str << ny;
+ fileToBuild->InsertEntryString(str.str(),0x0028,0x0010, "US"); // Rows
+
+ fileToBuild->InsertEntryString("8",0x0028,0x0100, "US"); // Bits Allocated
+ fileToBuild->InsertEntryString("8",0x0028,0x0101, "US"); // Bits Stored
+ fileToBuild->InsertEntryString("7",0x0028,0x0102, "US"); // High Bit
+ fileToBuild->InsertEntryString("0",0x0028,0x0103, "US"); // Pixel Representation
+ fileToBuild->InsertEntryString("1",0x0028,0x0002, "US"); // Samples per Pixel
+ fileToBuild->InsertEntryString("MONOCHROME2 ",0x0028,0x0004, "LO");
+
+ // feel free to add any field (Dicom Data Entry) you like, here.
+ // ...
+ // Other mandatory fields will be set automatically,
+ // just before Write(), by FileHelper::CheckMandatoryElements()
+
+ fh = GDCM_NAME_SPACE::FileHelper::New(fileToBuild);
+
+ fh->SetImageData(outputData,nx*ny);
+ fh->SetWriteTypeToDcmExplVR();
+
+std::ostringstream tmp;
+tmp <<std::hex;
+tmp <<currentOvlGroup;
+
+ str.str("");
+// -> Why doesn't it work ?!?
+ //str << fileName << std::hex << currentOvlGroup << ".dcm" << std::ends;
+
+str << fileName << ".ovly." << tmp.str() << ".dcm" << std::ends;
+
+ // Write the current 'overlay' file
+
+ if( !fh->Write(str.str()) )
+ {
+ std::cout << "Failed\n"
+ << "File [" << str.str() << "] is unwrittable" << std::endl;
+ }
+ else
+ {
+ std::cout << "File written successfully [" << str.str() << "]" << std::endl;
+ }
+
+ } // end on loop on 60xx
+
+ if (f)
+ fh->Delete();
+ if (fileToBuild)
+ fileToBuild->Delete();
f->Delete();
-
-} // end of loop on files ( DirListType::iterator )
-
return 0;
}
git://git.creatis.insa-lyon.fr / gdcm.git / commitdiff