1 /*=========================================================================
4 Module: $RCSfile: ReWrite.cxx,v $
6 Date: $Date: 2008/02/13 18:55:28 $
7 Version: $Revision: 1.34 $
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 " keepoverlays : user wants to keep ACR-NEMA-like overlays ",
46 " monochrome1 = user wants MONOCHROME1 photom. interp. (0=white) ",
47 " noshadowseq: user doesn't want to load Private Sequences ",
48 " noshadow : user doesn't want to load Private groups (odd number)",
49 " noseq : user doesn't want to load Sequences ",
50 " rgb : user wants to transform LUT (if any) to RGB pixels ",
51 " warning : developper wants to run the program in 'warning mode'",
52 " debug : developper wants to run the program in 'debug mode' ",
55 // ----- Initialize Arguments Manager ------
57 GDCM_NAME_SPACE::ArgMgr *am = new GDCM_NAME_SPACE::ArgMgr(argc, argv);
59 if (argc == 1 || am->ArgMgrDefined("usage"))
61 am->ArgMgrUsage(usage); // Display 'usage'
65 char *fileName = am->ArgMgrWantString("filein",usage);
66 if ( fileName == NULL )
68 std::cout << "'filein= ...' is mandatory" << std::endl;
73 char *outputFileName = am->ArgMgrWantString("fileout",usage);
74 if ( outputFileName == NULL )
76 std::cout << "'fileout= ...' is mandatory" << std::endl;
81 const char *mode = am->ArgMgrGetString("mode","X");
83 int loadMode = GDCM_NAME_SPACE::LD_ALL;
84 if ( am->ArgMgrDefined("noshadowseq") )
85 loadMode |= GDCM_NAME_SPACE::LD_NOSHADOWSEQ;
88 if ( am->ArgMgrDefined("noshadow") )
89 loadMode |= GDCM_NAME_SPACE::LD_NOSHADOW;
90 if ( am->ArgMgrDefined("noseq") )
91 loadMode |= GDCM_NAME_SPACE::LD_NOSEQ;
94 bool rgb = ( 0 != am->ArgMgrDefined("RGB") );
95 bool keepoverlays = ( 0 != am->ArgMgrDefined("keepoverlays") );
96 bool monochrome1 = ( 0 != am->ArgMgrDefined("monochrome1") );
98 if (am->ArgMgrDefined("debug"))
99 GDCM_NAME_SPACE::Debug::DebugOn();
101 if (am->ArgMgrDefined("warning"))
102 GDCM_NAME_SPACE::Debug::WarningOn();
108 if (am->ArgMgrDefined("rubout"))
111 boundVal = am->ArgMgrGetListOfInt("rubout", &nbBound);
115 std::cout << "Illegal number of 'rubout' boundary values (expected : 4, found:"
116 << nbBound << "); 'rubout' ignored" << std::endl;
120 ruboutVal = am->ArgMgrGetInt("ruboutvalue", 0);
126 if (am->ArgMgrDefined("roi"))
129 roiBoundVal = am->ArgMgrGetListOfInt("roi", &nbRoiBound);
133 std::cout << "Illegal number of 'ROI' boundary values (expected : 4, found:"
134 << nbRoiBound << "); 'ROI' ignored" << std::endl;
141 int beg = am->ArgMgrGetInt("firstFrame",-1);
142 int end = am->ArgMgrGetInt("lastFrame",-1);
144 // if unused Params we give up
145 if ( am->ArgMgrPrintUnusedLabels() )
147 am->ArgMgrUsage(usage);
152 delete am; // we don't need Argument Manager any longer
154 // ----------- End Arguments Manager ---------
155 GDCM_NAME_SPACE::File *f = GDCM_NAME_SPACE::File::New();
157 f->SetMaxSizeLoadEntry(0x7fffffff);
158 f->SetLoadMode( loadMode );
159 f->SetFileName( fileName );
161 bool res = f->Load();
168 if (!f->IsReadable())
170 std::cerr << "Sorry, not a Readable DICOM / ACR File" <<std::endl;
175 GDCM_NAME_SPACE::FileHelper *fh = GDCM_NAME_SPACE::FileHelper::New(f);
179 int nX,nY,nZ,sPP,planarConfig;
180 std::string pixelType, transferSyntaxName;
185 std::cout << " DIMX=" << nX << " DIMY=" << nY << " DIMZ=" << nZ << std::endl;
187 pixelType = f->GetPixelType();
188 sPP = f->GetSamplesPerPixel();
189 planarConfig = f->GetPlanarConfiguration();
191 std::cout << " pixelType=" << pixelType
192 << " SampleserPixel=" << sPP
193 << " PlanarConfiguration=" << planarConfig
194 << " PhotometricInterpretation="
195 << f->GetEntryString(0x0028,0x0004)
198 int numberOfScalarComponents=f->GetNumberOfScalarComponents();
199 std::cout << "NumberOfScalarComponents " << numberOfScalarComponents
201 transferSyntaxName = f->GetTransferSyntaxName();
202 std::cout << " TransferSyntaxName= [" << transferSyntaxName << "]"
205 fh->SetKeepOverlays( keepoverlays );
208 fh->SetPhotometricInterpretationToMonochrome1();
212 dataSize = fh->GetImageDataSize();
213 imageData = fh->GetImageData(); // somewhat important : Loads the Pixels in memory !
214 fh->SetWriteModeToRGB();
218 dataSize = fh->GetImageDataRawSize();
219 imageData = fh->GetImageDataRaw();// somewhat important : Loads the Pixels in memory !
220 fh->SetWriteModeToRaw();
223 if ( imageData == 0 ) // to avoid warning
225 std::cout << "Was unable to read pixels " << std::endl;
227 printf(" dataSize %d imageData %p\n",dataSize, imageData);
229 // Since we just ReWrite the image, we know no modification
230 // was performed on the pixels.
231 // We don't want this image appears as a 'Secondary Captured image'
232 fh->SetContentType(GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE);
235 /// \todo : think about rubbing out a part of a *multiframe* image!
238 if (boundVal[0]<0 || boundVal[0]>nX)
240 std::cout << "xBegin out of bounds; 'rubout' ignored" << std::endl;
243 if (boundVal[1]<0 || boundVal[1]>nX)
245 std::cout << "xEnd out of bounds; 'rubout' ignored" << std::endl;
248 if (boundVal[0] > boundVal[1])
250 std::cout << "xBegin greater than xEnd; 'rubout' ignored" << std::endl;
253 if (boundVal[2]<0 || boundVal[2]>nY)
255 std::cout << "yBegin out of bounds; 'rubout' ignored" << std::endl;
258 if (boundVal[3]<0 || boundVal[3]>nY)
260 std::cout << "yEnd out of bounds; 'rubout' ignored" << std::endl;
263 if (boundVal[2] > boundVal[3])
265 std::cout << "yBegin greater than yEnd; 'rubout' ignored" << std::endl;
270 int pixelLength = f->GetBitsAllocated()/8;
271 int lineLength = nX * sPP * pixelLength;
272 size_t lengthToRubout = (boundVal[1]-boundVal[0])*sPP*pixelLength;
273 int offsetToBeginOfRubout = boundVal[0]*sPP*pixelLength+lineLength*boundVal[2];
275 for(int rbl=boundVal[2]; rbl<boundVal[3];rbl++)
277 memset((char *)imageData+offsetToBeginOfRubout, ruboutVal, lengthToRubout);
278 offsetToBeginOfRubout += lineLength;
284 //------------------------------ Set the Writing mode ---------------------------------
290 // Writting an ACR file
291 // from a full gdcm readable File
292 std::cout << "WriteACR" << std::endl;
293 fh->SetWriteTypeToAcr();
296 case 'D' : // Not documented in the 'usage', because the method
297 case 'd' : // is known to be bugged.
298 // Writting a DICOM Implicit VR file
299 // from a full gdcm readable File
300 std::cout << "WriteDCM Implicit VR" << std::endl;
301 fh->SetWriteTypeToDcmImplVR();
306 // writting a DICOM Explicit VR
307 // from a full gdcm readable File
308 std::cout << "WriteDCM Explicit VR" << std::endl;
309 // fh->WriteDcmExplVR(outputFileName);
311 fh->SetWriteTypeToDcmExplVR();
317 // Writting a Raw File,
318 std::cout << "WriteRaw" << std::endl;
319 fh->WriteRawData(outputFileName);
324 // writting a DICOM Jpeg Lossless
325 // from a full gdcm readable File
326 std::cout << "WriteDCM Jpeg Lossless" << std::endl;
327 fh->SetWriteTypeToJPEG();
331 // writting a DICOM Jpeg 2000
332 // from a full gdcm readable File
333 std::cout << "WriteDCM Jpeg 2000" << std::endl;
334 fh->SetWriteTypeToJPEG2000();
338 // Write a 'Video inverse' version of the file.
339 // *Not* described, on purpose, in the USAGE
342 if ( fh->GetFile()->GetBitsAllocated() == 8)
344 std::cout << "videoinv for 8 bits" << std::endl;
345 for (int i=0; i<dataSize; i++)
347 ((uint8_t*)imageData)[i] = 255 - ((uint8_t*)imageData)[i];
352 std::cout << "videoinv for 16 bits" << std::endl;
353 for (int i=0; i<dataSize/2; i++)
355 ((uint16_t*)imageData)[i] = 65535 - ((uint16_t*)imageData)[i];
358 std::cout << "WriteDCM Explicit VR + VideoInv" << std::endl;
359 fh->SetWriteTypeToDcmExplVR();
364 // user wants to keep only a part of the image (ROI, and/or some frames)
365 // ---------------------------------------------------------------------
366 // (==> this is no longer really 'ReWrite' !)
373 if (roiBoundVal[0]<0 || roiBoundVal[0]>=nX)
375 std::cout << "xBegin out of bounds; 'roi' ignored" << std::endl;
378 if (roiBoundVal[1]<0 || roiBoundVal[1]>=nX)
380 std::cout << "xEnd out of bounds; 'roi' ignored" << std::endl;
383 if (roiBoundVal[0] > roiBoundVal[1])
385 std::cout << "xBegin greater than xEnd; 'roi' ignored" << std::endl;
389 if (roiBoundVal[2]<0 || roiBoundVal[2]>=nY)
391 std::cout << "yBegin out of bounds; 'roi' ignored" << std::endl;
394 if (roiBoundVal[3]<0 || roiBoundVal[3]>=nY)
396 std::cout << "yEnd out of bounds; 'roi' ignored" << std::endl;
399 if (roiBoundVal[2] > roiBoundVal[3])
401 std::cout << "yBegin greater than yEnd; 'roi' ignored" << std::endl;
407 roiBoundVal = new int[4];
409 roiBoundVal[1] = nX-1;
411 roiBoundVal[3] = nY-1;
414 subImDimX = roiBoundVal[1]-roiBoundVal[0]+1;
415 subImDimY = roiBoundVal[3]-roiBoundVal[2]+1;
417 if (roi || beg != -1 || end != -1)
424 std::ostringstream str;
426 // Set the data that will be *actually* written.
428 int pixelSize = fh->GetFile()->GetPixelSize();
429 size_t lgrSubLine = subImDimX* pixelSize * numberOfScalarComponents;
430 size_t lgrSubFrame = subImDimY*lgrSubLine;
432 int lgrSubImage = (end-beg+1) * lgrSubFrame;
434 uint8_t * subImage = new uint8_t[lgrSubImage];
436 uint8_t * srcCopy = (uint8_t *) imageData;
437 uint8_t * destCopy = subImage;
438 int lineSize = nX*pixelSize*numberOfScalarComponents;
439 int frameSize = nY*lineSize;
441 int lineOffset = roiBoundVal[0]*pixelSize * numberOfScalarComponents;
443 for (int frameNb=beg, frameCount=0; frameNb<=end; frameNb++, frameCount++)
445 for (int lineNb=roiBoundVal[2], lineCount=0; lineNb<=roiBoundVal[3]; lineNb++, lineCount++)
447 /// \todo : increment data pointer, don't multiply so much!
448 memcpy( (void *)(destCopy + frameCount*lgrSubFrame + lineCount*lgrSubLine),
449 (void *)(srcCopy + frameNb*frameSize + lineNb*lineSize + lineOffset ),
454 // Set the image size
457 fh->InsertEntryString(str.str(),0x0028,0x0011,"US"); // Columns
461 fh->InsertEntryString(str.str(),0x0028,0x0010,"US"); // Rows
464 fh->InsertEntryString(str.str(),0x0028,0x0008, "IS"); // Number of Frames
466 //fh->SetImageData(subImage,lgrSubImage);
467 fh->SetUserData(subImage,lgrSubImage); // ensures the compression (if any)
471 fh->SetUserData(imageData,dataSize); // ensures the compression (if any)
476 //----------------------------------- Write, now! ---------------------------------
478 if (mode[0] != 'R' && mode[0] != 'r')
479 res = fh->Write(outputFileName);
482 std::cout <<"Fail to write [" << outputFileName << "]" <<std::endl;