1 /*=========================================================================
4 Module: $RCSfile: ReWrite.cxx,v $
6 Date: $Date: 2008/05/16 10:40:23 $
7 Version: $Revision: 1.35 $
9 Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
10 l'Image). All rights reserved. See Doc/License.txt or
11 http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
13 This software is distributed WITHOUT ANY WARRANTY; without even
14 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 PURPOSE. See the above copyright notices for more information.
17 =========================================================================*/
19 #include "gdcmFileHelper.h"
20 #include "gdcmDebug.h"
22 #include "gdcmArgMgr.h"
24 #include <string.h> // for memcpy
27 int main(int argc, char *argv[])
31 " Re write a full gdcm-readable Dicom image ",
32 " (usefull when the file header is not very straight). ",
34 " usage: ReWrite filein=inputFileName fileout=outputFileName ",
35 " [keepoverlays] [mode=write mode] [monochrome1] ",
36 " [noshadow] [noseq][debug] ",
37 " --> The following line to 'rubout' a burnt-in Patient name ",
38 " [rubout=xBegin,xEnd,yBegin,yEnd [ruboutvalue=n (<255)] ] ",
39 " --> The 2 following lines, to extract a sub image within some frames ",
40 " [ROI=xBegin,xEnd,yBegin,yEnd] ",
41 " [firstframe=beg] [lastframe=end] ",
43 " mode = a (ACR), x (Explicit VR Dicom), r (RAW : only pixels) ",
44 " j (jpeg lossless), 2 (jpeg2000) ",
45 " NOTE : JPEG encapsulated in a Dicom File, not JPEG File !",
46 " keepoverlays : user wants to keep ACR-NEMA-like overlays ",
47 " monochrome1 = user wants MONOCHROME1 photom. interp. (0=white) ",
48 " noshadowseq: user doesn't want to load Private Sequences ",
49 " noshadow : user doesn't want to load Private groups (odd number)",
50 " noseq : user doesn't want to load Sequences ",
51 " rgb : user wants to transform LUT (if any) to RGB pixels ",
52 " warning : developper wants to run the program in 'warning mode'",
53 " debug : developper wants to run the program in 'debug mode' ",
56 // ----- Initialize Arguments Manager ------
58 GDCM_NAME_SPACE::ArgMgr *am = new GDCM_NAME_SPACE::ArgMgr(argc, argv);
60 if (argc == 1 || am->ArgMgrDefined("usage"))
62 am->ArgMgrUsage(usage); // Display 'usage'
66 char *fileName = am->ArgMgrWantString("filein",usage);
67 if ( fileName == NULL )
69 std::cout << "'filein= ...' is mandatory" << std::endl;
74 char *outputFileName = am->ArgMgrWantString("fileout",usage);
75 if ( outputFileName == NULL )
77 std::cout << "'fileout= ...' is mandatory" << std::endl;
82 const char *mode = am->ArgMgrGetString("mode","X");
84 int loadMode = GDCM_NAME_SPACE::LD_ALL;
85 if ( am->ArgMgrDefined("noshadowseq") )
86 loadMode |= GDCM_NAME_SPACE::LD_NOSHADOWSEQ;
89 if ( am->ArgMgrDefined("noshadow") )
90 loadMode |= GDCM_NAME_SPACE::LD_NOSHADOW;
91 if ( am->ArgMgrDefined("noseq") )
92 loadMode |= GDCM_NAME_SPACE::LD_NOSEQ;
95 bool rgb = ( 0 != am->ArgMgrDefined("RGB") );
96 bool keepoverlays = ( 0 != am->ArgMgrDefined("keepoverlays") );
97 bool monochrome1 = ( 0 != am->ArgMgrDefined("monochrome1") );
99 if (am->ArgMgrDefined("debug"))
100 GDCM_NAME_SPACE::Debug::DebugOn();
102 if (am->ArgMgrDefined("warning"))
103 GDCM_NAME_SPACE::Debug::WarningOn();
109 if (am->ArgMgrDefined("rubout"))
112 boundVal = am->ArgMgrGetListOfInt("rubout", &nbBound);
116 std::cout << "Illegal number of 'rubout' boundary values (expected : 4, found:"
117 << nbBound << "); 'rubout' ignored" << std::endl;
121 ruboutVal = am->ArgMgrGetInt("ruboutvalue", 0);
127 if (am->ArgMgrDefined("roi"))
130 roiBoundVal = am->ArgMgrGetListOfInt("roi", &nbRoiBound);
134 std::cout << "Illegal number of 'ROI' boundary values (expected : 4, found:"
135 << nbRoiBound << "); 'ROI' ignored" << std::endl;
142 int beg = am->ArgMgrGetInt("firstFrame",-1);
143 int end = am->ArgMgrGetInt("lastFrame",-1);
145 // if unused Params we give up
146 if ( am->ArgMgrPrintUnusedLabels() )
148 am->ArgMgrUsage(usage);
153 delete am; // we don't need Argument Manager any longer
155 // ----------- End Arguments Manager ---------
156 GDCM_NAME_SPACE::File *f = GDCM_NAME_SPACE::File::New();
158 f->SetMaxSizeLoadEntry(0x7fffffff);
159 f->SetLoadMode( loadMode );
160 f->SetFileName( fileName );
162 bool res = f->Load();
169 if (!f->IsReadable())
171 std::cerr << "Sorry, not a Readable DICOM / ACR File" <<std::endl;
176 GDCM_NAME_SPACE::FileHelper *fh = GDCM_NAME_SPACE::FileHelper::New(f);
180 int nX,nY,nZ,sPP,planarConfig;
181 std::string pixelType, transferSyntaxName;
186 std::cout << " DIMX=" << nX << " DIMY=" << nY << " DIMZ=" << nZ << std::endl;
188 pixelType = f->GetPixelType();
189 sPP = f->GetSamplesPerPixel();
190 planarConfig = f->GetPlanarConfiguration();
192 std::cout << " pixelType=" << pixelType
193 << " SampleserPixel=" << sPP
194 << " PlanarConfiguration=" << planarConfig
195 << " PhotometricInterpretation="
196 << f->GetEntryString(0x0028,0x0004)
199 int numberOfScalarComponents=f->GetNumberOfScalarComponents();
200 std::cout << "NumberOfScalarComponents " << numberOfScalarComponents
202 transferSyntaxName = f->GetTransferSyntaxName();
203 std::cout << " TransferSyntaxName= [" << transferSyntaxName << "]"
206 fh->SetKeepOverlays( keepoverlays );
209 fh->SetPhotometricInterpretationToMonochrome1();
213 dataSize = fh->GetImageDataSize();
214 imageData = fh->GetImageData(); // somewhat important : Loads the Pixels in memory !
215 fh->SetWriteModeToRGB();
219 dataSize = fh->GetImageDataRawSize();
220 imageData = fh->GetImageDataRaw();// somewhat important : Loads the Pixels in memory !
221 fh->SetWriteModeToRaw();
224 if ( imageData == 0 ) // to avoid warning
226 std::cout << "Was unable to read pixels " << std::endl;
228 printf(" dataSize %d imageData %p\n",dataSize, imageData);
230 // Since we just ReWrite the image, we know no modification
231 // was performed on the pixels.
232 // We don't want this image appears as a 'Secondary Captured image'
233 fh->SetContentType(GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE);
236 /// \todo : think about rubbing out a part of a *multiframe* image!
239 if (boundVal[0]<0 || boundVal[0]>nX)
241 std::cout << "xBegin out of bounds; 'rubout' ignored" << std::endl;
244 if (boundVal[1]<0 || boundVal[1]>nX)
246 std::cout << "xEnd out of bounds; 'rubout' ignored" << std::endl;
249 if (boundVal[0] > boundVal[1])
251 std::cout << "xBegin greater than xEnd; 'rubout' ignored" << std::endl;
254 if (boundVal[2]<0 || boundVal[2]>nY)
256 std::cout << "yBegin out of bounds; 'rubout' ignored" << std::endl;
259 if (boundVal[3]<0 || boundVal[3]>nY)
261 std::cout << "yEnd out of bounds; 'rubout' ignored" << std::endl;
264 if (boundVal[2] > boundVal[3])
266 std::cout << "yBegin greater than yEnd; 'rubout' ignored" << std::endl;
271 int pixelLength = f->GetBitsAllocated()/8;
272 int lineLength = nX * sPP * pixelLength;
273 size_t lengthToRubout = (boundVal[1]-boundVal[0])*sPP*pixelLength;
274 int offsetToBeginOfRubout = boundVal[0]*sPP*pixelLength+lineLength*boundVal[2];
276 for(int rbl=boundVal[2]; rbl<boundVal[3];rbl++)
278 memset((char *)imageData+offsetToBeginOfRubout, ruboutVal, lengthToRubout);
279 offsetToBeginOfRubout += lineLength;
285 //------------------------------ Set the Writing mode ---------------------------------
291 // Writting an ACR file
292 // from a full gdcm readable File
293 std::cout << "WriteACR" << std::endl;
294 fh->SetWriteTypeToAcr();
297 case 'D' : // Not documented in the 'usage', because the method
298 case 'd' : // is known to be bugged.
299 // Writting a DICOM Implicit VR file
300 // from a full gdcm readable File
301 std::cout << "WriteDCM Implicit VR" << std::endl;
302 fh->SetWriteTypeToDcmImplVR();
307 // writting a DICOM Explicit VR
308 // from a full gdcm readable File
309 std::cout << "WriteDCM Explicit VR" << std::endl;
310 // fh->WriteDcmExplVR(outputFileName);
312 fh->SetWriteTypeToDcmExplVR();
318 // Writting a Raw File,
319 std::cout << "WriteRaw" << std::endl;
320 fh->WriteRawData(outputFileName);
325 // writting a DICOM Jpeg Lossless
326 // from a full gdcm readable File
327 std::cout << "WriteDCM Jpeg Lossless" << std::endl;
328 fh->SetWriteTypeToJPEG();
332 // writting a DICOM Jpeg 2000
333 // from a full gdcm readable File
334 std::cout << "WriteDCM Jpeg 2000" << std::endl;
335 fh->SetWriteTypeToJPEG2000();
339 // Write a 'Video inverse' version of the file.
340 // *Not* described, on purpose, in the USAGE
343 if ( fh->GetFile()->GetBitsAllocated() == 8)
345 std::cout << "videoinv for 8 bits" << std::endl;
346 for (int i=0; i<dataSize; i++)
348 ((uint8_t*)imageData)[i] = 255 - ((uint8_t*)imageData)[i];
353 std::cout << "videoinv for 16 bits" << std::endl;
354 for (int i=0; i<dataSize/2; i++)
356 ((uint16_t*)imageData)[i] = 65535 - ((uint16_t*)imageData)[i];
359 std::cout << "WriteDCM Explicit VR + VideoInv" << std::endl;
360 fh->SetWriteTypeToDcmExplVR();
365 // user wants to keep only a part of the image (ROI, and/or some frames)
366 // ---------------------------------------------------------------------
367 // (==> this is no longer really 'ReWrite' !)
374 if (roiBoundVal[0]<0 || roiBoundVal[0]>=nX)
376 std::cout << "xBegin out of bounds; 'roi' ignored" << std::endl;
379 if (roiBoundVal[1]<0 || roiBoundVal[1]>=nX)
381 std::cout << "xEnd out of bounds; 'roi' ignored" << std::endl;
384 if (roiBoundVal[0] > roiBoundVal[1])
386 std::cout << "xBegin greater than xEnd; 'roi' ignored" << std::endl;
390 if (roiBoundVal[2]<0 || roiBoundVal[2]>=nY)
392 std::cout << "yBegin out of bounds; 'roi' ignored" << std::endl;
395 if (roiBoundVal[3]<0 || roiBoundVal[3]>=nY)
397 std::cout << "yEnd out of bounds; 'roi' ignored" << std::endl;
400 if (roiBoundVal[2] > roiBoundVal[3])
402 std::cout << "yBegin greater than yEnd; 'roi' ignored" << std::endl;
408 roiBoundVal = new int[4];
410 roiBoundVal[1] = nX-1;
412 roiBoundVal[3] = nY-1;
415 subImDimX = roiBoundVal[1]-roiBoundVal[0]+1;
416 subImDimY = roiBoundVal[3]-roiBoundVal[2]+1;
418 if (roi || beg != -1 || end != -1)
425 std::ostringstream str;
427 // Set the data that will be *actually* written.
429 int pixelSize = fh->GetFile()->GetPixelSize();
430 size_t lgrSubLine = subImDimX* pixelSize * numberOfScalarComponents;
431 size_t lgrSubFrame = subImDimY*lgrSubLine;
433 int lgrSubImage = (end-beg+1) * lgrSubFrame;
435 uint8_t * subImage = new uint8_t[lgrSubImage];
437 uint8_t * srcCopy = (uint8_t *) imageData;
438 uint8_t * destCopy = subImage;
439 int lineSize = nX*pixelSize*numberOfScalarComponents;
440 int frameSize = nY*lineSize;
442 int lineOffset = roiBoundVal[0]*pixelSize * numberOfScalarComponents;
444 for (int frameNb=beg, frameCount=0; frameNb<=end; frameNb++, frameCount++)
446 for (int lineNb=roiBoundVal[2], lineCount=0; lineNb<=roiBoundVal[3]; lineNb++, lineCount++)
448 /// \todo : increment data pointer, don't multiply so much!
449 memcpy( (void *)(destCopy + frameCount*lgrSubFrame + lineCount*lgrSubLine),
450 (void *)(srcCopy + frameNb*frameSize + lineNb*lineSize + lineOffset ),
455 // Set the image size
458 fh->InsertEntryString(str.str(),0x0028,0x0011,"US"); // Columns
462 fh->InsertEntryString(str.str(),0x0028,0x0010,"US"); // Rows
465 fh->InsertEntryString(str.str(),0x0028,0x0008, "IS"); // Number of Frames
467 //fh->SetImageData(subImage,lgrSubImage);
468 fh->SetUserData(subImage,lgrSubImage); // ensures the compression (if any)
472 fh->SetUserData(imageData,dataSize); // ensures the compression (if any)
477 //----------------------------------- Write, now! ---------------------------------
479 if (mode[0] != 'R' && mode[0] != 'r')
480 res = fh->Write(outputFileName);
483 std::cout <<"Fail to write [" << outputFileName << "]" <<std::endl;