Program: gdcm
Module: $RCSfile: ReWrite.cxx,v $
Language: C++
- Date: $Date: 2006/04/19 10:23:56 $
- Version: $Revision: 1.20 $
+ Date: $Date: 2007/03/06 10:19:00 $
+ Version: $Revision: 1.21 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include "gdcmArgMgr.h"
+#include <string.h> // for memcpy
#include <iostream>
int main(int argc, char *argv[])
" ",
" usage: ReWrite filein=inputFileName fileout=outputFileName ",
" [mode=write mode] [noshadow] [noseq][debug] ",
+ " --> The following line to 'rubout' a burnt-in Patient name ",
" [rubout=xBegin,xEnd,yBegin,yEnd [ruboutvalue=n (<255)] ] ",
+ " --> The 2 following lines, to extract a sub image withon some frames ",
+ " [ROI=xBegin,xEnd,yBegin,yEnd] ",
+ " [firstframe=beg] [lastframe=end] ",
" ",
" mode = a (ACR), x (Explicit VR Dicom), r (RAW : only pixels) ",
" 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 ",
" rgb : user wants to tranform LUT (if any) to RGB pixels ",
- " debug : user wants to run the program in 'debug mode' ",
+ " debug : developper wants to run the program in 'debug mode' ",
FINISH_USAGE
// ----- Initialize Arguments Manager ------
rubout = true;
}
+ int *roiBoundVal;
+ bool roi = false;
+ if (am->ArgMgrDefined("roi"))
+ {
+ int nbRoiBound;
+ roiBoundVal = am->ArgMgrGetListOfInt("roi", &nbRoiBound);
+
+ if (nbRoiBound !=4)
+ {
+ std::cout << "Illegal number of 'ROI' boundary values (expected : 4, found:"
+ << nbRoiBound << "); 'ROI' ignored" << std::endl;
+ fail = true;
+ }
+ else
+ roi = true;
+ }
+
+ int beg = am->ArgMgrGetInt("firstFrame",-1);
+ int end = am->ArgMgrGetInt("lastFrame",-1);
// if unused Params we give up
if ( am->ArgMgrPrintUnusedLabels() )
f->Delete();
return 0;
}
-
+
if (!f->IsReadable())
{
std::cerr << "Sorry, not a Readable DICOM / ACR File" <<std::endl;
f->Delete();
return 0;
}
+
gdcm::FileHelper *fh = gdcm::FileHelper::New(f);
void *imageData;
int dataSize;
-
- if (rgb)
- {
- dataSize = fh->GetImageDataSize();
- imageData = fh->GetImageData(); // somewhat important... can't remember
- fh->SetWriteModeToRGB();
- }
- else
- {
- dataSize = fh->GetImageDataRawSize();
- imageData = fh->GetImageDataRaw();// somewhat important... can't remember
- fh->SetWriteModeToRaw();
- }
-
- if ( imageData == 0 ) // to avoid warning
- {
- std::cout << "Was unable to read pixels " << std::endl;
- }
- std::cout <<std::endl <<" dataSize " << dataSize << std::endl;
- int nX,nY,nZ,sPP,planarConfig;
+
+ int nX,nY,nZ,sPP,planarConfig;
std::string pixelType, transferSyntaxName;
nX=f->GetXSize();
nY=f->GetYSize();
nZ=f->GetZSize();
+
std::cout << " DIMX=" << nX << " DIMY=" << nY << " DIMZ=" << nZ << std::endl;
pixelType = f->GetPixelType();
transferSyntaxName = f->GetTransferSyntaxName();
std::cout << " TransferSyntaxName= [" << transferSyntaxName << "]"
<< std::endl;
+
+
+ if (rgb)
+ {
+ dataSize = fh->GetImageDataSize();
+ imageData = fh->GetImageData(); // somewhat important : Loads the Pixels in memory !
+ fh->SetWriteModeToRGB();
+ }
+ else
+ {
+ dataSize = fh->GetImageDataRawSize();
+ imageData = fh->GetImageDataRaw();// somewhat important : Loads the Pixels in memory !
+ fh->SetWriteModeToRaw();
+ }
+
+ if ( imageData == 0 ) // to avoid warning
+ {
+ std::cout << "Was unable to read pixels " << std::endl;
+ }
+ printf(" dataSize %d imageData %p\n",dataSize, imageData);
// Since we just ReWrite the image, we know no modification
// was performed on the pixels.
fh->SetContentType(gdcm::UNMODIFIED_PIXELS_IMAGE);
+ /// \todo : think about rubbing out a part of a *multiframe* image!
if (rubout)
{
if (boundVal[0]<0 || boundVal[0]>nX)
}
}
+//
+// 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;
+
+ if (roi)
+ {
+ if (roiBoundVal[0]<0 || roiBoundVal[0]>=nX)
+ {
+ std::cout << "xBegin out of bounds; 'roi' ignored" << std::endl;
+ fail = true;
+ }
+ if (roiBoundVal[1]<0 || roiBoundVal[1]>=nX)
+ {
+ std::cout << "xEnd out of bounds; 'roi' ignored" << std::endl;
+ fail = true;
+ }
+ if (roiBoundVal[0] > roiBoundVal[1])
+ {
+ std::cout << "xBegin greater than xEnd; 'roi' ignored" << std::endl;
+ fail = true;
+ }
+
+ if (roiBoundVal[2]<0 || roiBoundVal[2]>=nY)
+ {
+ std::cout << "yBegin out of bounds; 'roi' ignored" << std::endl;
+ fail = true;
+ }
+ if (roiBoundVal[3]<0 || roiBoundVal[3]>=nY)
+ {
+ std::cout << "yEnd out of bounds; 'roi' ignored" << std::endl;
+ fail = true;
+ }
+ if (roiBoundVal[2] > roiBoundVal[3])
+ {
+ std::cout << "yBegin greater than yEnd; 'roi' ignored" << std::endl;
+ fail = true;
+ }
+ }
+ else
+ {
+ roiBoundVal = new int(4);
+ roiBoundVal[0] = 0;
+ roiBoundVal[1] = nX-1;
+ roiBoundVal[2] = 0;
+ roiBoundVal[3] = nY-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;
+
+ 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 lineOffset = roiBoundVal[0]*pixelSize * numberOfScalarComponents;
+
+ for (unsigned int frameNb=beg, frameCount=0; frameNb<=end; frameNb++, frameCount++)
+ {
+ for (unsigned int lineNb=roiBoundVal[2], lineCount=0; lineNb<=roiBoundVal[3]; lineNb++, lineCount++)
+ {
+ /// \todo increment data pointer, don't multiply so much!
+ memcpy( (void *)(destCopy + frameCount*lgrSubFrame + lineCount*lgrSubLine),
+ (void *)(srcCopy + frameNb*frameSize + lineNb*lineSize + lineOffset ),
+ lgrSubLine);
+ }
+ }
+
+ // Set the image size
+ str.str("");
+ str << subImDimX ;
+ fh->InsertEntryString(str.str(),0x0028,0x0011,"US"); // Columns
+
+ str.str("");
+ str << subImDimY;
+ fh->InsertEntryString(str.str(),0x0028,0x0010,"US"); // Rows
+ str.str("");
+ str << end-beg+1;
+ fh->InsertEntryString(str.str(),0x0028,0x0008, "IS"); // Number of Frames
+
+ fh->SetImageData(subImage,lgrSubImage);
+
+ }
+
+
+//----------------------------------- Write, now! ---------------------------------
+
switch (mode[0])
{
case 'A' :
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