--- /dev/null
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: DenseMultiFramesToDicom.cxx,v $
+ Language: C++
+ Date: $Date: 2006/07/20 17:15:28 $
+ Version: $Revision: 1.1 $
+
+ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
+ l'Image). All rights reserved. See Doc/License.txt or
+ http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+
+#include <fstream>
+#include <iostream>
+//#include <values.h>
+
+#include "gdcmFile.h"
+#include "gdcmFileHelper.h"
+#include "gdcmDebug.h"
+#include "gdcmDirList.h"
+#include "gdcmUtil.h"
+
+#include "gdcmArgMgr.h"
+
+/**
+ * \brief
+ * - explores recursively the (single Patient, single Study) directory
+ * - examines the ".txt" Dense multiframe files
+ * - Converts the files into 16 bits Dicom Files
+ * WARNING : directory must contain ONLY .txt files
+ */
+
+
+void Load(std::ifstream &from, std::string imageName, std::string patName,
+ std::string strStudyUID, int serieNumber);
+
+//std::ifstream& eatwhite(std::ifstream& is);
+
+/*
+window center (level) and width, are defined in the DICOM
+standard very precisely as follows (see PS 3.3 C.11.2.1.2):
+>
+>"These Attributes are applied according to the following pseudo-code,
+>where :
+x is the input value,
+y is an output value with a range from ymin to ymax,
+c is Window Center (0028,1050)
+w is Window Width (0028,1051):
+>
+> if (x <= c - 0.5 - (w-1)/2), then y = ymin
+> else if (x > c - 0.5 + (w-1)/2), then y = ymax,
+> else y = ((x - (c - 0.5)) / (w-1) + 0.5) * (ymax - ymin)+ ymin
+
+*/
+/*
+From: David Clunie - view profile
+Date: Thurs, Jun 1 2006 3:03 pm
+Email: David Clunie <dclu...@dclunie.com>
+Groups: comp.protocols.dicom
+
+The value of x is the output of the preceding step, the so-called
+"modality LUT", which may either be:
+
+- identity (no rescale values or Modality LUT, or the SOP Class is
+ PET and rescale values are ignored), in which case x is the stored
+ pixel value in (7FE0,0010)
+
+- Rescale Slope and Intercept (as typically used in CT), in which
+ case x is the value obtained from applying the rescale values to
+ the stored pixel value
+
+- an actual LUT, in which case x is the value stored in the LUT
+ corresponding to the LUT index value that is the stored pixel
+ value
+
+The ymin and ymax are intended to represent the output range; for
+example, if the hypothetical Presentation LUT step that follows
+the VOI LUT (window) stage is an identity operation, then the
+ymin and ymax represent P-Values, which might be the range of
+digital driving levels for your display (calibrated to the GSDF),
+in the 8-bit wide output case ranging from 0 to 255, for example.
+
+The terms brightness and contrast are not used in radiology imaging
+-the window center and width are used instead.
+*/
+
+int main(int argc, char *argv[])
+{
+ START_USAGE(usage)
+ " \n DenseMultiframeToDicom :\n ",
+ " - explores recursively the given (single Patient, single Study) directory",
+ " - examines the '.txt' files ",
+ " - Converts the files into 16 bits Dicom files, ",
+ " WARNING : directory must contain ONLY .txt files ",
+ " usage: ",
+ " DenseMultiframeToDicom dirin=rootDirectoryName ",
+ " [studyUID = ] [patName = ] ",
+ " [listonly] [verbose] [debug] ",
+ " ",
+ "studyUID : *aware* user wants to add the serie ",
+ " to an already existing study ",
+ " verbose : user wants to run the program in 'verbose mode' ",
+ " debug : *developer* wants to run the program in 'debug mode' ",
+ FINISH_USAGE
+
+ // ----- Initialize Arguments Manager ------
+
+ gdcm::ArgMgr *am = new gdcm::ArgMgr(argc, argv);
+
+ if (argc == 1 || am->ArgMgrDefined("usage"))
+ {
+ am->ArgMgrUsage(usage); // Display 'usage'
+ delete am;
+ return 0;
+ }
+
+ const char *dirNamein;
+ dirNamein = am->ArgMgrGetString("dirin",".");
+
+ if (am->ArgMgrDefined("debug"))
+ gdcm::Debug::DebugOn();
+
+ int verbose = am->ArgMgrDefined("verbose");
+ int listonly = am->ArgMgrDefined("listonly");
+ std::string patName = am->ArgMgrGetString("patname", "g^PatientName");
+
+ bool userDefinedStudy = am->ArgMgrDefined("studyUID");
+ const char *studyUID = am->ArgMgrGetString("studyUID");
+
+// not described *on purpose* in the Usage !
+ bool userDefinedSerie = am->ArgMgrDefined("serieUID");
+ const char *serieUID = am->ArgMgrGetString("serieUID");
+
+
+ // if unused Param we give up
+ if ( am->ArgMgrPrintUnusedLabels() )
+ {
+ am->ArgMgrUsage(usage);
+ delete am;
+ return 0;
+ }
+ delete am; // we don't need Argument Manager any longer
+
+ // ----- Begin Processing -----
+
+ if ( ! gdcm::DirList::IsDirectory(dirNamein) )
+ {
+ std::cout << "KO : [" << dirNamein << "] is not a Directory."
+ << std::endl;
+ return 0;
+ }
+ else
+ {
+ std::cout << "OK : [" << dirNamein << "] is a Directory." << std::endl;
+ }
+
+ std::string strDirNamein(dirNamein);
+ gdcm::DirList dirList(strDirNamein, true); // (recursively) the list of files
+
+ if (listonly)
+ {
+ std::cout << "------------List of found files ------------" << std::endl;
+ dirList.Print();
+ std::cout << std::endl;
+ return 0;
+ }
+
+ std::string filenameout;
+
+ std::string strStudyUID;
+ strStudyUID = gdcm::Util::CreateUniqueUID();
+ int serieNumber =0;
+ gdcm::DirListType fileNames;
+ fileNames = dirList.GetFilenames();
+ for (gdcm::DirListType::iterator it = fileNames.begin();
+ it != fileNames.end();
+ ++it)
+ {
+
+
+ std::ifstream from( (*it).c_str() );
+ if ( !from )
+ {
+ std::cout << "Can't open file" << *it << std::endl;
+ //return 0;
+ }
+ else
+ {
+ std::cout << "Success in open file" << *it << std::endl;
+ Load(from, *it, patName, strStudyUID, serieNumber);
+ serieNumber++;
+ //return 0;
+ }
+ }
+}
+
+
+void Load(std::ifstream &from, std::string imageName, std::string patName,
+ std::string strStudyUID, int serieNumber)
+{
+ if (!from)
+ return;
+
+/* was OK for single frames
+eg :
+---------------------------
+ Array dimensions = 58 x 56
+The following is the 2D array of peak circumferential strain map, all zero value
+pixels are outside the mask
+ 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
+-----------------------------
+ std::string str1;
+ int nx, ny;
+ // Get nx, ny
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> nx;
+ from >> str1;
+ from >> ny;
+
+ std::cout << "nx " << nx << " ny " << ny << std::endl;
+
+ // Skip 2 lines.
+ std::getline(from, str1);
+ std::cout << "[" << str1 << "]" << std::endl;
+ std::getline(from, str1);
+ std::cout << "[" << str1 << "]" << std::endl;
+ std::getline(from, str1);
+ std::cout << "[" << str1 << "]" << std::endl;
+ */
+
+ /* now, we deal with multiframes
+ eg :
+ ------------------------------------------
+X dim, Y dim, N of frames = 52x59x14
+Temporal resolution = 31.9200 ms
+First frame starts at 47.9600 ms
+The following are the 3D arrays of peak circumferential strain map and the magnitude images,
+All pixels with zero strain values are outside the masks.
+ 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
+--------------------------------------------
+*/
+ std::string str1;
+ int nx, ny, nf;
+ from >> str1; // X dim,
+ from >> str1;
+ from >> str1; // Y dim,
+ from >> str1;
+ from >> str1; // N of frames =
+ from >> str1;
+ from >> str1;
+ from >> str1;
+ from >> str1; // 52x59x14
+
+ std::cout << "[" << str1 << "]" << std::endl;
+
+ sscanf( str1.c_str(),"%dx%dx%d", &nx,&ny,&nf);
+ std::cout << nx << " " << ny << " " << nf << std::endl;
+
+ // Skip 4 lines.
+ for (int k=0; k<4; k++)
+ {
+ std::getline(from, str1);
+ std::cout << str1 << std::endl;
+ }
+
+ //float *f = new float(nx*ny);
+ float *f = (float *) malloc(nx*ny*nf*sizeof(float));
+ // float mini = FLT_MAX, maxi = FLT_MIN;
+ float val;
+
+
+ std::string strSerieUID;
+ strSerieUID = gdcm::Util::CreateUniqueUID();
+
+ for (int l=0; l<nf; l++) // Loop on the frames
+ {
+ for( int j=0; j<ny; j++)
+ {
+ int l =0;
+ for (int i=0; i<nx; i++)
+ {
+ //eatwhite(from);
+ char c;
+ for (;;)
+ {
+ if (!from.get(c))
+ break;
+ if (!isspace(c))
+ {
+ from.putback(c);
+ break;
+ }
+ }
+ from >> str1;
+ val = (float)atof(str1.c_str());
+ // std::cout << " " << val;
+ *(f+ /*l*nx*ny + */j*nx+i) = val;
+
+ if(from.eof())
+ {
+ std::cout << "Missing values at [" << j <<"," << i << "]"
+ << std::endl;
+ break;
+ }
+ l++;
+ }
+
+ std::cout << std::endl;
+ //std::cout << std::endl << " line nb : " << j
+ // << " line length : " << l << std::endl;
+
+ }
+
+
+ // std::cout << "mini : "<< mini << " maxi : " << maxi << std::endl;
+/*
+// values are expressed as % as a fraction, actually!)
+// It's useless to rescale them as uint16_t : just *100
+ uint16_t *img = new uint16_t[ny*nx];
+ uint16_t *ptr = img;
+ float *tmp = f;
+ float div = maxi-mini;
+ std::cout << "div : " << div << " mini : " << mini << std::endl;
+ for( int k=0; k<ny*nx; k++)
+ {
+ *ptr = (uint16_t)((*tmp * 65535.0) / div);
+ tmp ++;
+ ptr++;
+ }
+*/
+ uint16_t *img = new uint16_t[ny*nx];
+ uint16_t *ptr = img;
+ float *tmp = f /* + l*ny*nx */ ; // start on image nb l.
+ for( int k=0; k<ny*nx; k++)
+ {
+ if(*tmp < 0) // artefacted pixel
+ *ptr = 0;
+ else /// \todo FIXME : what about max threshold ?
+ *ptr = (int16_t)(*tmp *100);
+
+ //std::cout << std::dec << "[" << *tmp <<" : " << *ptr << "] ";
+ tmp ++;
+ ptr++;
+ }
+
+ // gdcm::Debug::DebugOn();
+
+ std::ostringstream str;
+ gdcm::File *file;
+ file = gdcm::File::New();
+
+ // Set the image size
+ str.str("");
+ str << nx;
+ file->InsertEntryString(str.str(),0x0028,0x0011,"US"); // Columns
+ str.str("");
+ str << ny;
+ file->InsertEntryString(str.str(),0x0028,0x0010,"US"); // Rows
+
+ // Set the pixel type
+ // 16; //8, 16, 32
+ file->InsertEntryString("16",0x0028,0x0100,"US"); // Bits Allocated
+ str.str("");
+ str << 16; // may be 12 or 16 if componentSize =16
+ file->InsertEntryString("16",0x0028,0x0101,"US"); // Bits Stored
+
+ file->InsertEntryString("15",0x0028,0x0102,"US"); // High Bit
+
+ // Set the pixel representation // 0/1 1 : signed
+ file->InsertEntryString("0",0x0028,0x0103, "US"); // Pixel Representation
+
+ // Set the samples per pixel // 1:Grey level, 3:RGB
+ file->InsertEntryString("1",0x0028,0x0002, "US"); // Samples per Pixel
+
+/*
+ // Set Rescale Intercept
+ str.str("");
+ str << div;
+ file->InsertEntryString(str.str(),0x0028,0x1052,"DS");
+
+ // Set Rescale Slope
+ str.str("");
+ str << mini;
+ file->InsertEntryString(str.str(),0x0028,0x1053,"DS");
+*/
+
+// 0020 0037 DS 6 Image Orientation (Patient)
+ file->InsertEntryString("1.0\\0.0\\0.0\\0.0\\1.0\\0.0",0x0020,0x0037, "DS"); //[1\0\0\0\1\0] : Axial
+
+// 0020 0032 DS 3 Image Position (Patient)
+ char charImagePosition[256];
+ sprintf(charImagePosition,"0.0\\0.0\\%f",float(l%nf));
+
+// 0020 0x1041 DS 1 Slice Location
+ sprintf(charImagePosition,"%f",float(l%nf));
+ file->InsertEntryString(charImagePosition,0x0020,0x1041, "DS");
+
+//0008 103e LO 1 Series Description
+ file->InsertEntryString(imageName,0x0008,0x103e, "LO");
+
+ file->InsertEntryString(strStudyUID,0x0020,0x000d,"UI");
+ file->InsertEntryString(strSerieUID,0x0020,0x000e,"UI");
+ file->InsertEntryString(patName,0x0010,0x0010, "PN"); // Patient's Name
+
+//0020 0011 "IS" Series Number
+ sprintf(charImagePosition,"%04d",serieNumber);
+ file->InsertEntryString(charImagePosition,0x0020,0x0011, "IS");
+
+ // file->Print();
+
+ gdcm::FileHelper *fh;
+ fh = gdcm::FileHelper::New(file);
+ // cast is just to avoid warnings (*no* conversion)
+ fh->SetImageData((uint8_t *)img,nx*ny*sizeof(uint16_t));
+ fh->SetWriteModeToRaw();
+ fh->SetWriteTypeToDcmExplVR();
+
+ fh->SetWriteTypeToDcmExplVR();
+
+
+ char numero[10];
+ sprintf(numero, "%02d", l);
+ std::string fileName = imageName + "." + numero + ".dcm";
+ std::cout << "fileName " << fileName << std::endl;
+
+ if( !fh->Write(fileName))
+ std::cout << "Failed for [" << fileName << "]\n"
+ << " File is unwrittable" << std::endl;
+
+ delete img;
+ } // end loop on frames
+
+ from.close();
+}
projects / gdcm.git / commitdiff