Program: gdcm
Module: $RCSfile: ReWrite.cxx,v $
Language: C++
- Date: $Date: 2007/03/29 10:50:14 $
- Version: $Revision: 1.24 $
+ Date: $Date: 2008/05/16 10:40:23 $
+ Version: $Revision: 1.35 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
" Re write a full gdcm-readable Dicom image ",
" (usefull when the file header is not very straight). ",
" ",
- " usage: ReWrite filein=inputFileName fileout=outputFileName ",
- " [mode=write mode] [noshadow] [noseq][debug] ",
+ " usage: ReWrite filein=inputFileName fileout=outputFileName ",
+ " [keepoverlays] [mode=write mode] [monochrome1] ",
+ " [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 ",
+ " --> The 2 following lines, to extract a sub image within some frames ",
" [ROI=xBegin,xEnd,yBegin,yEnd] ",
" [firstframe=beg] [lastframe=end] ",
" ",
" mode = a (ACR), x (Explicit VR Dicom), r (RAW : only pixels) ",
+ " j (jpeg lossless), 2 (jpeg2000) ",
+ " NOTE : JPEG encapsulated in a Dicom File, not JPEG File !",
+ " keepoverlays : user wants to keep ACR-NEMA-like overlays ",
+ " monochrome1 = user wants MONOCHROME1 photom. interp. (0=white) ",
" 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 ",
- " warning : developper wants to run the program in 'warning mode'",
+ " rgb : user wants to transform LUT (if any) to RGB pixels ",
+ " warning : developper wants to run the program in 'warning mode'",
" debug : developper wants to run the program in 'debug mode' ",
FINISH_USAGE
- // ----- Initialize Arguments Manager ------
- gdcm::ArgMgr *am = new gdcm::ArgMgr(argc, argv);
+ // ----- Initialize Arguments Manager ------
+
+ GDCM_NAME_SPACE::ArgMgr *am = new GDCM_NAME_SPACE::ArgMgr(argc, argv);
if (argc == 1 || am->ArgMgrDefined("usage"))
{
am->ArgMgrUsage(usage); // Display 'usage'
delete am;
- return 0;
+ return 1;
}
char *fileName = am->ArgMgrWantString("filein",usage);
if ( fileName == NULL )
{
std::cout << "'filein= ...' is mandatory" << std::endl;
delete am;
- return 0;
+ return 1;
}
char *outputFileName = am->ArgMgrWantString("fileout",usage);
{
std::cout << "'fileout= ...' is mandatory" << std::endl;
delete am;
- return 0;
+ return 1;
}
const char *mode = am->ArgMgrGetString("mode","X");
- int loadMode = gdcm::LD_ALL;
+ int loadMode = GDCM_NAME_SPACE::LD_ALL;
if ( am->ArgMgrDefined("noshadowseq") )
- loadMode |= gdcm::LD_NOSHADOWSEQ;
+ loadMode |= GDCM_NAME_SPACE::LD_NOSHADOWSEQ;
else
{
if ( am->ArgMgrDefined("noshadow") )
- loadMode |= gdcm::LD_NOSHADOW;
+ loadMode |= GDCM_NAME_SPACE::LD_NOSHADOW;
if ( am->ArgMgrDefined("noseq") )
- loadMode |= gdcm::LD_NOSEQ;
+ loadMode |= GDCM_NAME_SPACE::LD_NOSEQ;
}
- bool rgb = ( 0 != am->ArgMgrDefined("RGB") );
-
+ bool rgb = ( 0 != am->ArgMgrDefined("RGB") );
+ bool keepoverlays = ( 0 != am->ArgMgrDefined("keepoverlays") );
+ bool monochrome1 = ( 0 != am->ArgMgrDefined("monochrome1") );
+
if (am->ArgMgrDefined("debug"))
- gdcm::Debug::DebugOn();
+ GDCM_NAME_SPACE::Debug::DebugOn();
if (am->ArgMgrDefined("warning"))
- gdcm::Debug::WarningOn();
+ GDCM_NAME_SPACE::Debug::WarningOn();
bool fail = false;
int *boundVal;
delete am; // we don't need Argument Manager any longer
// ----------- End Arguments Manager ---------
-
- gdcm::File *f = gdcm::File::New();
+ GDCM_NAME_SPACE::File *f = GDCM_NAME_SPACE::File::New();
+
+ f->SetMaxSizeLoadEntry(0x7fffffff);
f->SetLoadMode( loadMode );
f->SetFileName( fileName );
+
bool res = f->Load();
- if ( !res )
+ if ( !res )
{
f->Delete();
- return 0;
+ return 1;
}
if (!f->IsReadable())
{
std::cerr << "Sorry, not a Readable DICOM / ACR File" <<std::endl;
f->Delete();
- return 0;
+ return 1;
}
-
- gdcm::FileHelper *fh = gdcm::FileHelper::New(f);
- void *imageData;
+ GDCM_NAME_SPACE::FileHelper *fh = GDCM_NAME_SPACE::FileHelper::New(f);
+ uint8_t *imageData;
int dataSize;
- int nX,nY,nZ,sPP,planarConfig;
+ int nX,nY,nZ,sPP,planarConfig;
std::string pixelType, transferSyntaxName;
nX=f->GetXSize();
nY=f->GetYSize();
std::cout << " TransferSyntaxName= [" << transferSyntaxName << "]"
<< std::endl;
+ fh->SetKeepOverlays( keepoverlays );
+
+ if(monochrome1)
+ fh->SetPhotometricInterpretationToMonochrome1();
if (rgb)
{
// Since we just ReWrite the image, we know no modification
// was performed on the pixels.
// We don't want this image appears as a 'Secondary Captured image'
- fh->SetContentType(gdcm::UNMODIFIED_PIXELS_IMAGE);
+ fh->SetContentType(GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE);
/// \todo : think about rubbing out a part of a *multiframe* image!
}
}
+
+//------------------------------ Set the Writing mode ---------------------------------
+
+ switch (mode[0])
+ {
+ case 'A' :
+ case 'a' :
+ // Writting an ACR file
+ // from a full gdcm readable File
+ std::cout << "WriteACR" << std::endl;
+ fh->SetWriteTypeToAcr();
+ break;
+
+ case 'D' : // Not documented in the 'usage', because the method
+ case 'd' : // is known to be bugged.
+ // Writting a DICOM Implicit VR file
+ // from a full gdcm readable File
+ std::cout << "WriteDCM Implicit VR" << std::endl;
+ fh->SetWriteTypeToDcmImplVR();
+ break;
+
+ case 'X' :
+ case 'x' :
+ // writting a DICOM Explicit VR
+ // from a full gdcm readable File
+ std::cout << "WriteDCM Explicit VR" << std::endl;
+ // fh->WriteDcmExplVR(outputFileName);
+ // Try this one :
+ fh->SetWriteTypeToDcmExplVR();
+
+ break;
+
+ case 'R' :
+ case 'r' :
+ // Writting a Raw File,
+ std::cout << "WriteRaw" << std::endl;
+ fh->WriteRawData(outputFileName);
+ break;
+
+ case 'J' :
+ case 'j' :
+ // 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
+ // from a full gdcm readable File
+ std::cout << "WriteDCM Jpeg 2000" << std::endl;
+ fh->SetWriteTypeToJPEG2000();
+ break;
+
+ // Just for fun :
+ // Write a 'Video inverse' version of the file.
+ // *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++)
+ {
+ ((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++)
+ {
+ ((uint16_t*)imageData)[i] = 65535 - ((uint16_t*)imageData)[i];
+ }
+ }
+ std::cout << "WriteDCM Explicit VR + VideoInv" << std::endl;
+ fh->SetWriteTypeToDcmExplVR();
+ 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;
{
for (int lineNb=roiBoundVal[2], lineCount=0; lineNb<=roiBoundVal[3]; lineNb++, lineCount++)
{
- /// \todo increment data pointer, don't multiply so much!
+ /// \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 << end-beg+1;
fh->InsertEntryString(str.str(),0x0028,0x0008, "IS"); // Number of Frames
- fh->SetImageData(subImage,lgrSubImage);
-
- }
-
+ //fh->SetImageData(subImage,lgrSubImage);
+ fh->SetUserData(subImage,lgrSubImage); // ensures the compression (if any)
+ }
+ else
+ {
+ fh->SetUserData(imageData,dataSize); // ensures the compression (if any)
+ }
-//----------------------------------- Write, now! ---------------------------------
- switch (mode[0])
- {
- case 'A' :
- case 'a' :
- // Writting an ACR file
- // from a full gdcm readable File
- std::cout << "WriteACR" << std::endl;
- fh->WriteAcr(outputFileName);
- break;
- case 'D' : // Not documented in the 'usage', because the method
- case 'd' : // is known to be bugged.
- // Writting a DICOM Implicit VR file
- // from a full gdcm readable File
- std::cout << "WriteDCM Implicit VR" << std::endl;
- fh->WriteDcmImplVR(outputFileName);
- break;
-
- case 'X' :
- case 'x' :
- // writting a DICOM Explicit VR
- // from a full gdcm readable File
- std::cout << "WriteDCM Explicit VR" << std::endl;
- // fh->WriteDcmExplVR(outputFileName);
- // Try this one :
- fh->SetWriteTypeToDcmExplVR();
- fh->Write(outputFileName);
- break;
+//----------------------------------- Write, now! ---------------------------------
- case 'R' :
- case 'r' :
- // Writting a Raw File,
- std::cout << "WriteRaw" << std::endl;
- fh->WriteRawData(outputFileName);
- break;
-
- // Just for fun :
- // Write a 'Video inverse' version of the file.
- // *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++)
- {
- ((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++)
- {
- ((uint16_t*)imageData)[i] = 65535 - ((uint16_t*)imageData)[i];
- }
- }
- std::cout << "WriteDCM Explicit VR + VideoInv" << std::endl;
- fh->WriteDcmExplVR(outputFileName);
- break;
- }
+ if (mode[0] != 'R' && mode[0] != 'r')
+ res = fh->Write(outputFileName);
+
+ if(!res)
+ std::cout <<"Fail to write [" << outputFileName << "]" <<std::endl;
f->Delete();
fh->Delete();
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff