1 /*=========================================================================
4 Module: $RCSfile: exReadPapyrus.cxx,v $
6 Date: $Date: 2005/11/28 10:55:00 $
7 Version: $Revision: 1.6 $
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 "gdcmDocument.h"
21 #include "gdcmDataEntry.h"
22 #include "gdcmSeqEntry.h"
23 #include "gdcmSQItem.h"
24 #include "gdcmDebug.h"
27 #include "gdcmArgMgr.h"
33 #include <unistd.h> //for access, unlink
35 #include <io.h> //for _access
38 // return true if the file exists
39 bool FileExists(const char *filename)
42 # define access _access
47 if ( access(filename, R_OK) != 0 )
57 bool RemoveFile(const char *source)
60 #define _unlink unlink
62 return unlink(source) != 0 ? false : true;
65 // ----------------------------------------------------------------------
66 // Here we load a supposed to be Papyrus File (gdcm::File compliant)
67 // and then try to get the pixels, using low-level SeqEntry accessors.
68 // Since it's not a general purpose Papyrus related program
69 // (just a light example) we suppose *everything* is clean
70 // and we don't perform any integrity check
71 // ----------------------------------------------------------------------
73 int main(int argc, char *argv[])
77 " \n exReadPapyrus :\n",
78 " Reads a Papyrus V3 File, Writes a Multiframe Dicoim V3 File ",
79 " (just to show gdcm can do it ...) ",
81 " usage: exReadPapyrus filein=inputPapyrusFileName fileout=outputDicomFileName",
83 " debug : user wants to run the program in 'debug mode' ",
87 // ----- Initialize Arguments Manager ------
89 gdcm::ArgMgr *am = new gdcm::ArgMgr(argc, argv);
91 if (am->ArgMgrDefined("usage"))
93 am->ArgMgrUsage(usage); // Display 'usage'
97 char *fileName = am->ArgMgrWantString("filein",usage);
98 if ( fileName == NULL )
104 char *outputFileName = am->ArgMgrWantString("fileout",usage);
105 if ( outputFileName == NULL )
111 if (am->ArgMgrDefined("debug"))
112 gdcm::Debug::DebugOn();
114 // if unused Params we give up
115 if ( am->ArgMgrPrintUnusedLabels() )
117 am->ArgMgrUsage(usage);
122 delete am; // we don't need Argument Manager any longer
124 // ----------- End Arguments Manager ---------
126 if( FileExists( outputFileName ) )
128 if( !RemoveFile( outputFileName ) )
130 std::cerr << "Ouch, the file exist, but I cannot remove it" << std::endl;
135 int loadMode = 0x0; // load everything
136 gdcm::File *f = gdcm::File::New();
137 f->SetLoadMode( loadMode );
138 f->SetFileName( fileName );
139 bool res = f->Load();
147 // Look for private Papyrus Sequence
148 gdcm::SeqEntry *seqPapyrus= f->GetSeqEntry(0x0041, 0x1050);
151 std::cout << "NOT a Papyrus File : " << fileName <<std::endl;
156 // gdcm::FileHelper *original = new gdcm::FileHelper( fileName );
157 // gdcm::File *h = original->GetFile();
159 //gdcm::FileHelper *f1 = new gdcm::FileHelper(f);
160 gdcm::SQItem *sqi = seqPapyrus->GetFirstSQItem();
163 std::cout << "NO SQItem found within private Papyrus Sequence"
169 std::string TransferSyntax;
170 std::string StudyDate;
171 std::string StudyTime;
172 std::string Modality;
173 std::string PatientName;
174 std::string MediaStSOPinstUID;
176 // Get informations on the file :
177 // Modality, Transfer Syntax, Study Date, Study Time
178 // Patient Name, Media Storage SOP Instance UID, etc
180 MediaStSOPinstUID = f->GetEntryString(0x0002,0x0002);
181 TransferSyntax = f->GetEntryString(0x0002,0x0010);
182 StudyDate = sqi->GetEntryString(0x0008,0x0020);
183 StudyTime = sqi->GetEntryString(0x0008,0x0030);
184 Modality = sqi->GetEntryString(0x0008,0x0060);
185 PatientName = sqi->GetEntryString(0x0010,0x0010);
187 std::cout << "TransferSyntax " << TransferSyntax << std::endl;
191 std::string SamplesPerPixel;
192 std::string BitsAllocated;
193 std::string BitsStored;
195 std::string PixelRepresentation;
198 // we brutally suppose all the images within a Papyrus file
199 // have the same caracteristics.
200 // if you're aware they have not, just move the GetEntryString
203 // Get caracteristics of the first image
204 SamplesPerPixel = sqi->GetEntryString(0x0028,0x0002);
205 Rows = sqi->GetEntryString(0x0028,0x0010);
206 Columns = sqi->GetEntryString(0x0028,0x0011);
207 BitsAllocated = sqi->GetEntryString(0x0028,0x0100);
208 BitsStored = sqi->GetEntryString(0x0028,0x0101);
209 HighBit = sqi->GetEntryString(0x0028,0x0102);
210 PixelRepresentation = sqi->GetEntryString(0x0028,0x0103);
212 // just convert those needed to compute PixelArea length
213 int iRows = (uint32_t) atoi( Rows.c_str() );
214 int iColumns = (uint32_t) atoi( Columns.c_str() );
215 int iSamplesPerPixel = (uint32_t) atoi( SamplesPerPixel.c_str() );
216 int iBitsAllocated = (uint32_t) atoi( BitsAllocated.c_str() );
218 int lgrImage = iRows*iColumns * iSamplesPerPixel * (iBitsAllocated/8);
220 // compute number of images
221 int nbImages = seqPapyrus->GetNumberOfSQItems();
222 std::cout <<"Number of frames :" << nbImages << std::endl;
224 // allocate enough room to get the pixels of all images.
225 uint8_t *PixelArea = new uint8_t[lgrImage*nbImages];
226 uint8_t *currentPosition = PixelArea;
227 gdcm::DataEntry *pixels;
229 // declare and open the file
231 Fp = new std::ifstream(fileName, std::ios::in | std::ios::binary);
234 std::cout << "Cannot open file: " << fileName << std::endl;
239 // to be sure to be at the beginning
240 Fp->seekg(0, std::ios::end);
243 std::string previousRows = Rows;
244 sqi = seqPapyrus->GetFirstSQItem();
247 std::cout << "One more image read. Keep waiting" << std::endl;
248 Rows = sqi->GetEntryString(0x0028,0x0010);
249 // minimum integrity check
250 if (Rows != previousRows)
252 std::cout << "Consistency check failed " << std::endl;
255 // get the images pixels
256 pixels = sqi->GetDataEntry(0x7fe0,0x0010);
257 offset = pixels->GetOffset();
258 // perform a fseek, on offset length on the 'right' length
259 Fp->seekg(offset, std::ios::beg);
260 // perform a fread into the right place
261 Fp->read((char *)currentPosition, (size_t)lgrImage);
262 currentPosition +=lgrImage;
264 std::string previousRowNb = Rows;
266 sqi = seqPapyrus->GetNextSQItem();
269 // build up a new File, with file info + images info + global pixel area.
271 std::string NumberOfFrames = gdcm::Util::Format("%d", nbImages);
273 gdcm::File *n = gdcm::File::New();
275 n->InsertEntryString(MediaStSOPinstUID, 0x0002,0x0002);
276 // Whe keep default gdcm Transfer Syntax (Explicit VR Little Endian)
277 // since using Papyrus one (Implicit VR Little Endian) is a mess
278 //n->InsertEntryString(TransferSyntax, 0x0002,0x0010);
279 n->InsertEntryString(StudyDate, 0x0008,0x0020);
280 n->InsertEntryString(StudyTime, 0x0008,0x0030);
281 n->InsertEntryString(Modality, 0x0008,0x0060);
282 n->InsertEntryString(PatientName, 0x0010,0x0010);
284 n->InsertEntryString(SamplesPerPixel, 0x0028,0x0002);
285 n->InsertEntryString(NumberOfFrames, 0x0028,0x0008);
286 n->InsertEntryString(Rows, 0x0028,0x0010);
287 n->InsertEntryString(Columns, 0x0028,0x0011);
288 n->InsertEntryString(BitsAllocated, 0x0028,0x0100);
289 n->InsertEntryString(BitsStored, 0x0028,0x0101);
290 n->InsertEntryString(HighBit, 0x0028,0x0102);
291 n->InsertEntryString(PixelRepresentation,0x0028,0x0103);
294 gdcm::FileHelper *file = gdcm::FileHelper::New(n);
296 file->SetImageData(PixelArea,lgrImage*nbImages);
297 file->SetWriteTypeToDcmExplVR();
299 //file->SetPrintLevel(2);
303 file->Write(outputFileName);
306 std::cout <<"Fail to open (write) file:[" << outputFileName << "]" << std::endl;;