CASToR  2.0
Tomographic Reconstruction (PET/SPECT/CT)
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gDataConversionUtilities.hh
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1 /*
2 This file is part of CASToR.
3 
4  CASToR is free software: you can redistribute it and/or modify it under the
5  terms of the GNU General Public License as published by the Free Software
6  Foundation, either version 3 of the License, or (at your option) any later
7  version.
8 
9  CASToR is distributed in the hope that it will be useful, but WITHOUT ANY
10  WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
11  FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
12  details.
13 
14  You should have received a copy of the GNU General Public License along with
15  CASToR (in file GNU_GPL.TXT). If not, see <http://www.gnu.org/licenses/>.
16 
17 Copyright 2017-2018 all CASToR contributors listed below:
18 
19  --> current contributors: Thibaut MERLIN, Simon STUTE, Didier BENOIT, Claude COMTAT, Marina FILIPOVIC, Mael MILLARDET
20  --> past contributors: Valentin VIELZEUF
21 
22 This is CASToR version 2.0.
23 */
24 
31 #ifndef UTILS_HH
32 #define UTILS_HH 1
33 
34 #include "gVariables.hh"
35 #include "gOptions.hh"
36 #include "iDataFilePET.hh"
37 #include "sOutputManager.hh"
38 #include "sScannerManager.hh"
39 #include "oInterfileIO.hh"
40 
41 #ifdef CASTOR_ROOT
42  #ifdef _WIN32
43  #include "Windows4Root.h"
44  #endif
45  #include "TROOT.h"
46  #include "TApplication.h"
47  #include "TGClient.h"
48  #include "TCanvas.h"
49  #include "TSystem.h"
50  #include "TTree.h"
51  #include "TBranch.h"
52  #include "TFile.h"
53 #endif
54 
63 #define GATE_SYS_UNKNOWN -1
64 
65 #define GATE_SYS_CYLINDRICAL 0
66 
67 #define GATE_SYS_ECAT 1
68 
69 #define GATE_SYS_SPECT 2
70 
73 #define GATE_NB_MAX_LAYERS 4 // Max number of layer in GATE = 4
74 
75 
85 vector<string> CheckGATECommand(const string& a_key, const string& a_line);
86 
93 vector<string> Split(string a_line);
94 
95 
102 void ConvertValuesTomm(vector<string>& values);
103 
104 
111 template <class T>
112 string toString(T a_val)
113 {
114  stringstream ss;
115  ss << a_val;
116  return ss.str();
117 }
118 
119 
128 template <typename T>
129 int WriteVector(ofstream& file, const string& a_key, vector <T> a_vals);
130 
139 int WriteVector(ofstream& file, const string& a_key, vector <string> a_vals);
140 
149 int WriteVector(ofstream& file, const string& a_key, vector <vector<string> > a_vals);
150 
151 
152 
159 int GetGATESystemType(const string& a_pathMac);
160 
161 
162 
163 
171 int GetGATEMacFiles(const string& a_pathMac, vector<string> &ap_pathToMacFiles);
172 
173 
174 
175 
194 int GetGATEAliasesCylindrical(vector<string> path_mac_files,
195  string& rsector_name,
196  string& module_name,
197  string& submodule_name,
198  string& crystal_name,
199  vector<string>& layers_name ,
200  int vb );
201 
202 
203 
204 
218 int GetGATEAliasesEcat(vector<string> path_mac_files,
219  string& block_name,
220  string& crystal_name,
221  int vb );
222 
223 
224 
225 
241 int GetGATEAliasesSPECT(vector<string> path_mac_files,
242  string& base_name,
243  string& crystal_name,
244  string& pixel_name,
245  int vb );
246 
247 
248 
249 
266 uint32_t ConvertIDecat(int32_t nBlocksPerRing,
267  int32_t nBlocksLine,
268  int32_t nCrystalsTransaxial,
269  int32_t nCrystalsAxial,
270  int32_t crystalID,
271  int32_t blockID);
272 
273 
274 
275 
276 
289 uint32_t ConvertIDSPECTRoot1( int32_t a_headID,
290  float_t a_rotAngle,
291  float_t a_angStep,
292  uint32_t a_nProjectionsByHead);
293 
294 
295 
326 uint32_t ConvertIDSPECTRoot2( uint32_t a_nbSimulatedPixels,
327  uint32_t a_nPixTrs,
328  uint32_t a_nPixAxl,
329  int32_t a_headID,
330  int32_t a_crystalID,
331  int32_t a_pixelID,
332  float_t a_rotAngle,
333  float_t a_headAngPitch,
334  float_t a_crystalSizeAxl,
335  float_t a_crystalSizeTrs,
336  float_t a_gPosX,
337  float_t a_gPosY,
338  float_t a_gPosZ);
339 
340 
341 
342 
383 uint32_t ConvertIDcylindrical(uint32_t nRsectorsAngPos,
384  uint32_t nRsectorsAxial,
385  int a_rsectorIdOrder,
386  uint32_t nModulesTransaxial,
387  uint32_t nModulesAxial,
388  uint32_t nSubmodulesTransaxial,
389  uint32_t nSubmodulesAxial,
390  uint32_t nCrystalsTransaxial,
391  uint32_t nCrystalsAxial,
392  uint8_t nLayers,
393  uint32_t* nCrystalPerLayer,
394  vector<uint32_t> nLayersRptTransaxial,
395  vector<uint32_t> nLayersRptAxial,
396  int32_t layerID,
397  int32_t crystalID,
398  int32_t submoduleID,
399  int32_t moduleID,
400  int32_t rsectorID);
401 
415 int ComputeKindGATEEvent(uint32_t eventID1, uint32_t eventID2,
416  int comptonPhantom1, int comptonPhantom2,
417  int rayleighPhantom1, int rayleighPhantom2);
418 
419 
420 
442 int ReadMacECAT(string a_pathMac,
443  uint32_t &nCrystalsTot,
444  uint32_t &nCrystalsAxial,
445  uint32_t &nCrystalsTransaxial,
446  uint32_t &nBlocksLine,
447  uint32_t &nBlocksPerRing,
448  uint32_t &start_time_ms,
449  uint32_t &duration_ms,
450  int vb);
451 
452 
489 int ReadMacSPECT( string a_pathMac,
490  float_t &distToDetector,
491  uint32_t &nHeads,
492  uint32_t &nPixAxl,
493  uint32_t &nPixTrs,
494  float_t &crystalSizeAxl,
495  float_t &crystalSizeTrs,
496  uint32_t &nProjectionsTot,
497  uint32_t &nProjectionsByHead,
498  float_t &head1stAngle,
499  float_t &headAngPitch,
500  float_t &headAngStepDeg,
501  int &headRotDirection,
502  uint32_t &start_time_ms,
503  uint32_t &duration_ms,
504  int vb);
505 
506 
507 
508 
509 
545 int ReadIntfSPECT(string a_pathIntf,
546  float_t &ap_distToDetector,
547  uint32_t &ap_nHeads,
548  uint32_t &ap_nPixAxl,
549  uint32_t &ap_nPixTrs,
550  float_t &ap_crystalSizeAxl,
551  float_t &ap_crystalSizeTrs,
552  uint32_t &ap_nProjectionsTot,
553  uint32_t &ap_nProjectionsByHead,
554  float_t &ap_head1stAngle,
555  float_t &ap_headAngPitch,
556  float_t &headAngStepDeg,
557  int &ap_headRotDirection,
558  uint32_t &ap_start_time_ms,
559  uint32_t &ap_duration_ms,
560  int vb);
561 
562 
563 
564 
603 int ReadMacCylindrical( string a_pathMac,
604  uint8_t &nLayers,
605  uint32_t *nb_crystal_per_layer,
606  uint32_t &nCrystalsTot,
607  uint32_t &nCrystalsAxial,
608  uint32_t &nCrystalsTransaxial,
609  vector<uint32_t> &nLayersRptAxial,
610  vector<uint32_t> &nLayersRptTransaxial,
611  uint32_t &nSubmodulesAxial,
612  uint32_t &nSubmodulesTransaxial,
613  uint32_t &nModulesAxial,
614  uint32_t &nModulesTransaxial,
615  uint32_t &nRsectorsAxial,
616  uint32_t &nRsectorsAngPos,
617  int &rsector_id_order,
618  uint32_t &start_time_ms,
619  uint32_t &duration_ms,
620  int vb);
621 
622 
623 
631 int CreateGeomWithECAT(string a_pathMac, string a_pathGeom);
632 
633 
634 
635 
643 int CreateGeomWithCylindrical(string a_pathMac, string a_pathGeom);
644 
645 
646 
647 
655 int CreateGeomWithSPECT(string a_pathMac, string a_pathGeom);
656 
657 #endif
uint32_t ConvertIDSPECTRoot1(int32_t a_headID, float_t a_rotAngle, float_t a_angStep, uint32_t a_nProjectionsByHead)
Compute a CASToR projection index of a GATE SPECThead system.
void ConvertValuesTomm(vector< string > &values)
Check if the vector of strings passed in parameter contains the 'cm' unit In this case...
This header file is mainly used to declare some macro definitions and all includes needed from the st...
vector< string > CheckGATECommand(const string &a_key, const string &a_line)
Check if the line contains the provided GATE command. In this case, parse the line and returns the va...
int ReadMacSPECT(string a_pathMac, float_t &distToDetector, uint32_t &nHeads, uint32_t &nPixAxl, uint32_t &nPixTrs, float_t &crystalSizeAxl, float_t &crystalSizeTrs, uint32_t &nProjectionsTot, uint32_t &nProjectionsByHead, float_t &head1stAngle, float_t &headAngPitch, float_t &headAngStepDeg, int &headRotDirection, uint32_t &start_time_ms, uint32_t &duration_ms, int vb)
Recover informations about the scanner element of an ECAT system, and acquisition duration...
int GetGATEAliasesSPECT(vector< string > path_mac_files, string &base_name, string &crystal_name, string &pixel_name, int vb)
Loop over a list of path to GATE macro files passed in parameter to recover aliases of the different ...
int GetGATEAliasesEcat(vector< string > path_mac_files, string &block_name, string &crystal_name, int vb)
Loop over a list of path to GATE macro files passed in parameter to recover aliases of the different ...
Declaration of class iDataFilePET.
uint32_t ConvertIDcylindrical(uint32_t nRsectorsAngPos, uint32_t nRsectorsAxial, int a_rsectorIdOrder, uint32_t nModulesTransaxial, uint32_t nModulesAxial, uint32_t nSubmodulesTransaxial, uint32_t nSubmodulesAxial, uint32_t nCrystalsTransaxial, uint32_t nCrystalsAxial, uint8_t nLayers, uint32_t *nCrystalPerLayer, vector< uint32_t > nLayersRptTransaxial, vector< uint32_t > nLayersRptAxial, int32_t layerID, int32_t crystalID, int32_t submoduleID, int32_t moduleID, int32_t rsectorID)
Compute a CASToR crystal index of a GATE cylindricalPET system from its indexes (rsector/module/submo...
int GetGATEAliasesCylindrical(vector< string > path_mac_files, string &rsector_name, string &module_name, string &submodule_name, string &crystal_name, vector< string > &layers_name, int vb)
Loop over a list of path to GATE macro files passed in parameter to recover aliases of the different ...
int ReadMacCylindrical(string a_pathMac, uint8_t &nLayers, uint32_t *nb_crystal_per_layer, uint32_t &nCrystalsTot, uint32_t &nCrystalsAxial, uint32_t &nCrystalsTransaxial, vector< uint32_t > &nLayersRptAxial, vector< uint32_t > &nLayersRptTransaxial, uint32_t &nSubmodulesAxial, uint32_t &nSubmodulesTransaxial, uint32_t &nModulesAxial, uint32_t &nModulesTransaxial, uint32_t &nRsectorsAxial, uint32_t &nRsectorsAngPos, int &rsector_id_order, uint32_t &start_time_ms, uint32_t &duration_ms, int vb)
Recover informations about the scanner element of a cylindricalPET system and acquisition duration...
int ComputeKindGATEEvent(uint32_t eventID1, uint32_t eventID2, int comptonPhantom1, int comptonPhantom2, int rayleighPhantom1, int rayleighPhantom2)
Determine kind of a given coincidence event, from its attributes.
int ReadMacECAT(string a_pathMac, uint32_t &nCrystalsTot, uint32_t &nCrystalsAxial, uint32_t &nCrystalsTransaxial, uint32_t &nBlocksLine, uint32_t &nBlocksPerRing, uint32_t &start_time_ms, uint32_t &duration_ms, int vb)
Recover informations about the scanner element of an ECAT system and acquisition duration, from a GATE macro file.
Declaration of class sScannerManager.
int CreateGeomWithECAT(string a_pathMac, string a_pathGeom)
Read a GATE macro file containing the description of an ecat system, and convert it to a geom file...
int WriteVector(ofstream &file, const string &a_key, vector< T > a_vals)
Write the key and its values in the file provided in parameter.
string toString(T a_val)
Convert a value of any type into string.
Declaration of class sOutputManager.
int GetGATEMacFiles(const string &a_pathMac, vector< string > &ap_pathToMacFiles)
Extract the paths to each macro file contained in the main macro file.
This file is used for all kind of different functions designed for options parsing and ASCII file rea...
vector< string > Split(string a_line)
Split the line provided in parameter into a vector of strings (separator is blankspace) ...
This group of functions manages Interfile image file format.
uint32_t ConvertIDecat(int32_t nBlocksPerRing, int32_t nBlocksLine, int32_t nCrystalsTransaxial, int32_t nCrystalsAxial, int32_t crystalID, int32_t blockID)
Compute a CASToR crystal index of a GATE ecat system from its indexes (block/crystal) and the system ...
int ReadIntfSPECT(string a_pathIntf, float_t &ap_distToDetector, uint32_t &ap_nHeads, uint32_t &ap_nPixAxl, uint32_t &ap_nPixTrs, float_t &ap_crystalSizeAxl, float_t &ap_crystalSizeTrs, uint32_t &ap_nProjectionsTot, uint32_t &ap_nProjectionsByHead, float_t &ap_head1stAngle, float_t &ap_headAngPitch, float_t &headAngStepDeg, int &ap_headRotDirection, uint32_t &ap_start_time_ms, uint32_t &ap_duration_ms, int vb)
Recover informations about the scanner element of an ECAT system, and acquisition duration...
int GetGATESystemType(const string &a_pathMac)
Read a GATE macro file and identify the system type from the 'gate/systems/' command lines...
int CreateGeomWithCylindrical(string a_pathMac, string a_pathGeom)
Read a GATE macro file containing the description of a cylindricalPET system, and convert it to a geo...
int CreateGeomWithSPECT(string a_pathMac, string a_pathGeom)
Read a GATE macro file containing the description of a SPECThead system, and convert it to a geom fil...
uint32_t ConvertIDSPECTRoot2(uint32_t a_nbSimulatedPixels, uint32_t a_nPixTrs, uint32_t a_nPixAxl, int32_t a_headID, int32_t a_crystalID, int32_t a_pixelID, float_t a_rotAngle, float_t a_headAngPitch, float_t a_crystalSizeAxl, float_t a_crystalSizeTrs, float_t a_gPosX, float_t a_gPosY, float_t a_gPosZ)
Compute a CASToR crystal index of a GATE SPECThead system.