From: jpr Date: Tue, 6 Mar 2007 10:19:00 +0000 (+0000) Subject: Allow user to extract a subimage, within a limited number of frames. X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=commitdiff_plain;h=6431ad8820a924bfddca7707abdf8a537fef61af;p=gdcm.git Allow user to extract a subimage, within a limited number of frames. (OK, this is not *really* a 'ReWrite' problem, but so many users asked for it) new optional keywords : ROI=xBegin,xEnd,yBegin,yEnd firstframe=beg lastframe=end --- diff --git a/Example/ReWrite.cxx b/Example/ReWrite.cxx index dab56fb6..ac672f06 100644 --- a/Example/ReWrite.cxx +++ b/Example/ReWrite.cxx @@ -3,8 +3,8 @@ 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 @@ -21,6 +21,7 @@ #include "gdcmArgMgr.h" +#include // for memcpy #include int main(int argc, char *argv[]) @@ -32,14 +33,18 @@ 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 ------ @@ -105,6 +110,25 @@ int main(int argc, char *argv[]) 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() ) @@ -127,41 +151,25 @@ int main(int argc, char *argv[]) f->Delete(); return 0; } - + if (!f->IsReadable()) { std::cerr << "Sorry, not a Readable DICOM / ACR File" <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 <GetXSize(); nY=f->GetYSize(); nZ=f->GetZSize(); + std::cout << " DIMX=" << nX << " DIMY=" << nY << " DIMZ=" << nZ << std::endl; pixelType = f->GetPixelType(); @@ -181,6 +189,26 @@ int main(int argc, char *argv[]) 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. @@ -188,6 +216,7 @@ int main(int argc, char *argv[]) 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) @@ -235,6 +264,116 @@ int main(int argc, char *argv[]) } } +// +// 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' :