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25 // 25 //
26 // This example is provided by the Geant4-DNA 26 // This example is provided by the Geant4-DNA collaboration
27 // Any report or published results obtained us 27 // Any report or published results obtained using the Geant4-DNA software
28 // shall cite the following Geant4-DNA collabo 28 // shall cite the following Geant4-DNA collaboration publication:
29 // Med. Phys. 37 (2010) 4692-4708 29 // Med. Phys. 37 (2010) 4692-4708
30 // and papers 30 // and papers
31 // M. Batmunkh et al. J Radiat Res Appl Sci 8 31 // M. Batmunkh et al. J Radiat Res Appl Sci 8 (2015) 498-507
32 // O. Belov et al. Physica Medica 32 (2016) 15 << 32 // O. Belov et al. Physica Medica 32 (2016) 1510-1520
33 // The Geant4-DNA web site is available at htt 33 // The Geant4-DNA web site is available at http://geant4-dna.org
34 // << 34 //
35 // ------------------------------------------- 35 // -------------------------------------------------------------------
36 // November 2016 36 // November 2016
37 // ------------------------------------------- 37 // -------------------------------------------------------------------
38 // 38 //
39 // << 39 //
40 /// \file NeuronLoadDataFile.cc 40 /// \file NeuronLoadDataFile.cc
41 /// \brief Implementation of the NeuronLoadDat 41 /// \brief Implementation of the NeuronLoadDataFile class
42 42
43 #include "NeuronLoadDataFile.hh" 43 #include "NeuronLoadDataFile.hh"
44 << 44 #include "G4VPhysicalVolume.hh"
45 #include "CommandLineParser.hh" <<
46 <<
47 #include "G4Colour.hh" <<
48 #include "G4LogicalVolume.hh" 45 #include "G4LogicalVolume.hh"
49 #include "G4PhysicalConstants.hh" <<
50 #include "G4RotationMatrix.hh" <<
51 #include "G4SystemOfUnits.hh" 46 #include "G4SystemOfUnits.hh"
52 #include "G4UImanager.hh" <<
53 #include "G4UnitsTable.hh" 47 #include "G4UnitsTable.hh"
54 #include "G4VPhysicalVolume.hh" << 48 #include "G4PhysicalConstants.hh"
>> 49 #include "G4Colour.hh"
55 #include "G4VisAttributes.hh" 50 #include "G4VisAttributes.hh"
>> 51 #include "G4RotationMatrix.hh"
56 #include "G4ios.hh" 52 #include "G4ios.hh"
57 #include "globals.hh" << 53 #include <algorithm>
58 <<
59 #include <algorithm> <<
60 #include <fstream> 54 #include <fstream>
61 #include <iostream> 55 #include <iostream>
62 #include <limits> 56 #include <limits>
63 #include <sstream> 57 #include <sstream>
>> 58 #include "globals.hh"
>> 59 #include "CommandLineParser.hh"
>> 60 #include "G4UImanager.hh"
64 61
65 using namespace std; 62 using namespace std;
66 using namespace G4DNAPARSER; 63 using namespace G4DNAPARSER;
67 64
68 //....oooOO0OOooo........oooOO0OOooo........oo 65 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
69 << 66
70 NeuronLoadDataFile::NeuronLoadDataFile() 67 NeuronLoadDataFile::NeuronLoadDataFile()
71 { 68 {
72 Command* commandLine(nullptr); 69 Command* commandLine(nullptr);
73 << 70
74 // 1. Load single neuron morphology and obta 71 // 1. Load single neuron morphology and obtain parameters.
75 // Default SWC file name of neuron 72 // Default SWC file name of neuron
76 fNeuronFileNameSWC = "GranuleCell-Nr2.CNG.sw << 73 fNeuronFileNameSWC = "GranuleCell-Nr2.CNG.swc";
77 74
78 // 2. Load neural network and obtain paramet 75 // 2. Load neural network and obtain parameters.
79 // Default prepared data filename of neural 76 // Default prepared data filename of neural network with single/multi-layer.
80 // Small network of 10 pyramidal neurons wit 77 // Small network of 10 pyramidal neurons with single layer
81 fNeuronFileNameDATA = "NeuralNETWORK.dat"; << 78 fNeuronFileNameDATA = "NeuralNETWORK.dat";
82 79
83 // Load/change SWC or DAT as "CommandLinePar 80 // Load/change SWC or DAT as "CommandLineParser" class
84 if ((commandLine = CommandLineParser::GetPar << 81 if((commandLine=CommandLineParser::GetParser()->GetCommandIfActive("-swc"))) {
85 fNeuronFileNameSWC = G4String(commandLine- 82 fNeuronFileNameSWC = G4String(commandLine->GetOption());
86 } 83 }
87 if ((commandLine = CommandLineParser::GetPar 84 if ((commandLine = CommandLineParser::GetParser()->GetCommandIfActive("-network"))) {
88 auto ss = G4String(commandLine->GetOption( 85 auto ss = G4String(commandLine->GetOption());
89 if ("" != ss) { << 86 if ("" != ss) { fNeuronFileNameDATA = ss; }
90 fNeuronFileNameDATA = ss; << 87 NeuralNetworkDATAfile(fNeuronFileNameDATA);
91 } <<
92 NeuralNetworkDATAfile(fNeuronFileNameDATA) <<
93 } 88 }
94 else { 89 else {
95 SingleNeuronSWCfile(fNeuronFileNameSWC); 90 SingleNeuronSWCfile(fNeuronFileNameSWC);
96 } 91 }
97 } 92 }
98 93
99 //....oooOO0OOooo........oooOO0OOooo........oo 94 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
100 95
101 void NeuronLoadDataFile::SingleNeuronSWCfile(c 96 void NeuronLoadDataFile::SingleNeuronSWCfile(const G4String& filename)
102 { 97 {
103 // ----------- 98 // -----------
104 // 12 November 2012 - code created 99 // 12 November 2012 - code created
105 // ----------------------------------------- 100 // -------------------------------------------------------------------
106 // November 2012: First model of neuron[*] a << 101 // November 2012: First model of neuron[*] adapted into Geant4 microdosimetry
107 // from Claiborne`s database[ 102 // from Claiborne`s database[**] by M. Batmunkh.
108 // February 2013: Loading SWC file from Neur << 103 // February 2013: Loading SWC file from NeuronMorpho.Org[***]
109 // suggested by L. Bayarchime 104 // suggested by L. Bayarchimeg.
110 // [*] http://lt-jds.jinr.ru/record/62124/fi 105 // [*] http://lt-jds.jinr.ru/record/62124/files/lrb_e_2012.pdf
111 // [**] http://www.utsa.edu/claibornelab/ 106 // [**] http://www.utsa.edu/claibornelab/
112 // [***] http://neuromorpho.org 107 // [***] http://neuromorpho.org
113 // ----------------------------------------- 108 // -------------------------------------------------------------------
114 109
115 G4String sLine = ""; 110 G4String sLine = "";
116 std::ifstream infile; 111 std::ifstream infile;
117 infile.open(filename.c_str()); 112 infile.open(filename.c_str());
118 if (!infile.is_open()) { 113 if (!infile.is_open()) {
119 G4ExceptionDescription ed; 114 G4ExceptionDescription ed;
120 ed << "Datafile " << filename << " is not 115 ed << "Datafile " << filename << " is not opened!";
121 G4Exception("NeuronLoadDataFile::SingleNeu << 116 G4Exception("NeuronLoadDataFile::SingleNeuronSWCfile()","dna014",
122 "Check file path"); << 117 FatalException, ed, "Check file path");
123 return; 118 return;
124 } << 119 }
125 G4int nrows, nlines; << 120 G4int nrows,nlines;
126 nrows = 0; << 121 nrows=0; nlines=0;
127 nlines = 0; << 122 for(;;) {
128 for (;;) { <<
129 getline(infile, sLine); 123 getline(infile, sLine);
130 if (infile.eof()) { << 124 if (infile.eof()) { break; }
131 break; <<
132 } <<
133 ++nrows; 125 ++nrows;
134 } 126 }
135 infile.close(); 127 infile.close();
136 << 128
137 G4cout << "NeuronLoadDataFile::SingleNeuronS << 129 G4cout << "NeuronLoadDataFile::SingleNeuronSWCfile: number of strings="<< nrows
138 << filename << G4endl; << 130 << " in file " << filename << G4endl;
139 << 131
140 infile.open(filename.c_str()); 132 infile.open(filename.c_str());
141 << 133
142 G4double TotVolSoma, TotVolDend, TotVolAxon, 134 G4double TotVolSoma, TotVolDend, TotVolAxon, TotVolSpine;
143 TotVolSoma = TotVolDend = TotVolAxon = TotVo << 135 TotVolSoma=TotVolDend=TotVolAxon=TotVolSpine=0.;
144 G4double TotSurfSoma, TotSurfDend, TotSurfAx 136 G4double TotSurfSoma, TotSurfDend, TotSurfAxon, TotSurfSpine;
145 TotSurfSoma = TotSurfDend = TotSurfAxon = To << 137 TotSurfSoma=TotSurfDend=TotSurfAxon=TotSurfSpine=0.;
146 G4int nNcomp; // current index of neuronal << 138 G4int nNcomp; // current index of neuronal compartment
147 G4int typeNcomp; // type of neuron structur << 139 G4int typeNcomp; // type of neuron structures: soma, axon, dendrite, etc.
148 G4double x, y, z; // cartesian coordinates << 140 G4double x,y,z; // cartesian coordinates of each compartment in micrometer
149 G4double radius; // radius of each compartm << 141 G4double radius; // radius of each compartment in micrometer
150 G4int pNcomp; // linked compartment, indica << 142 G4int pNcomp; // linked compartment, indicates branch points of dendrites
151 G4double minX, minY, minZ; << 143 G4double minX,minY,minZ;
152 G4double maxX, maxY, maxZ; << 144 G4double maxX,maxY,maxZ;
153 G4double maxRad = -1e+09; 145 G4double maxRad = -1e+09;
154 minX = minY = minZ = 1e+09; << 146 minX=minY=minZ=1e+09;
155 maxX = maxY = maxZ = -1e+09; << 147 maxX=maxY=maxZ=-1e+09;
156 G4double density = 1.0 * (g / cm3); // wate << 148 G4double density = 1.0 * (g/cm3) ; // water medium
157 G4double Piconst = (4.0 / 3.0) * pi; << 149 G4double Piconst = (4.0/3.0)*pi ;
158 150
159 fMassSomacomp.resize(nrows, 0); 151 fMassSomacomp.resize(nrows, 0);
160 fPosSomacomp.resize(nrows); 152 fPosSomacomp.resize(nrows);
161 fRadSomacomp.resize(nrows, 0); << 153 fRadSomacomp.resize(nrows, 0);
162 std::vector<G4ThreeVector> PosDendcomp(nrows 154 std::vector<G4ThreeVector> PosDendcomp(nrows);
163 fRadDendcomp.resize(nrows, 0); 155 fRadDendcomp.resize(nrows, 0);
164 fHeightDendcomp.resize(nrows, 0); 156 fHeightDendcomp.resize(nrows, 0);
165 fMassDendcomp.resize(nrows, 0); 157 fMassDendcomp.resize(nrows, 0);
166 fDistADendSoma.resize(nrows, 0); 158 fDistADendSoma.resize(nrows, 0);
167 fDistBDendSoma.resize(nrows, 0); 159 fDistBDendSoma.resize(nrows, 0);
168 fPosDendcomp.resize(nrows); 160 fPosDendcomp.resize(nrows);
169 fRotDendcomp.resize(nrows); 161 fRotDendcomp.resize(nrows);
170 std::vector<G4ThreeVector> PosAxoncomp(nrows 162 std::vector<G4ThreeVector> PosAxoncomp(nrows);
171 fRadAxoncomp.resize(nrows, 0); 163 fRadAxoncomp.resize(nrows, 0);
172 fHeightAxoncomp.resize(nrows, 0); 164 fHeightAxoncomp.resize(nrows, 0);
173 fMassAxoncomp.resize(nrows, 0); 165 fMassAxoncomp.resize(nrows, 0);
174 fDistAxonsoma.resize(nrows, 0); 166 fDistAxonsoma.resize(nrows, 0);
175 fPosAxoncomp.resize(nrows); 167 fPosAxoncomp.resize(nrows);
176 fRotAxoncomp.resize(nrows); 168 fRotAxoncomp.resize(nrows);
177 fMassSpinecomp.resize(nrows, 0); 169 fMassSpinecomp.resize(nrows, 0);
178 fPosSpinecomp.resize(nrows); 170 fPosSpinecomp.resize(nrows);
179 fRadSpinecomp.resize(nrows, 0); << 171 fRadSpinecomp.resize(nrows, 0);
180 fRadNeuroncomp.resize(nrows, 0); 172 fRadNeuroncomp.resize(nrows, 0);
181 fHeightNeuroncomp.resize(nrows, 0); 173 fHeightNeuroncomp.resize(nrows, 0);
182 fDistNeuronsoma.resize(nrows, 0); 174 fDistNeuronsoma.resize(nrows, 0);
183 fPosNeuroncomp.resize(nrows); 175 fPosNeuroncomp.resize(nrows);
184 fRotNeuroncomp.resize(nrows); 176 fRotNeuroncomp.resize(nrows);
185 fPosNeuroncomp.resize(nrows); 177 fPosNeuroncomp.resize(nrows);
186 fRadNeuroncomp.resize(nrows, 0); << 178 fRadNeuroncomp.resize(nrows, 0);
187 fTypeN.resize(nrows, 0); 179 fTypeN.resize(nrows, 0);
188 G4ThreeVector base; 180 G4ThreeVector base;
189 << 181
190 // to read datafile containing numbers, alph 182 // to read datafile containing numbers, alphabets and symbols..,
191 for (;;) { 183 for (;;) {
192 getline(infile, sLine); 184 getline(infile, sLine);
193 if (infile.eof()) { << 185 if (infile.eof()) { break; }
194 break; << 186 if ("#" == sLine.substr(0, 1)) { continue; };
195 } <<
196 if ("#" == sLine.substr(0, 1)) { <<
197 continue; <<
198 }; <<
199 187
200 std::istringstream form(sLine); 188 std::istringstream form(sLine);
201 form >> nNcomp >> typeNcomp >> x >> y >> z 189 form >> nNcomp >> typeNcomp >> x >> y >> z >> radius >> pNcomp;
202 /* 190 /*
203 G4cout << "NeuronLoadDataFile::SingleNeuronS << 191 G4cout << "NeuronLoadDataFile::SingleNeuronSWCfile: typeNcomp="
204 << typeNcomp << " nNcomp=" << nNcomp << 192 << typeNcomp << " nNcomp=" << nNcomp << " pNcomp=" << pNcomp << " N1="
205 << fnbSomacomp << " N2=" << fnbAxonco << 193 << fnbSomacomp << " N2=" << fnbAxoncomp << " N3=" << fnbDendritecomp << G4endl;
206 */ 194 */
207 // ======================================= 195 // =======================================================================
208 // to find the largest and the smallest va 196 // to find the largest and the smallest values of compartment positions
209 // for parameters of bounding slice, spher 197 // for parameters of bounding slice, sphere medium and shift of neuron.
210 if (minX > x) minX = x; 198 if (minX > x) minX = x;
211 if (minY > y) minY = y; 199 if (minY > y) minY = y;
212 if (minZ > z) minZ = z; 200 if (minZ > z) minZ = z;
213 if (maxX < x) maxX = x; 201 if (maxX < x) maxX = x;
214 if (maxY < y) maxY = y; 202 if (maxY < y) maxY = y;
215 if (maxZ < z) maxZ = z; << 203 if (maxZ < z) maxZ = z;
216 // max diameter of compartments << 204 // max diameter of compartments
217 if (maxRad < radius) maxRad = radius; << 205 if (maxRad < radius) maxRad = radius;
218 << 206
219 // ======================================= 207 // =======================================================================
220 // Soma compartments represented as Sphere 208 // Soma compartments represented as Sphere or Ellipsoid solid
221 if (typeNcomp == 1) { << 209 if (typeNcomp == 1) {
222 // Sphere volume and surface area 210 // Sphere volume and surface area
223 G4double VolSomacomp = Piconst * pow(rad << 211 G4double VolSomacomp = Piconst*pow(radius*um, 3);
224 TotVolSoma = TotVolSoma + VolSomacomp; 212 TotVolSoma = TotVolSoma + VolSomacomp;
225 G4double SurSomacomp = 3. * Piconst * po << 213 G4double SurSomacomp = 3.*Piconst*pow(radius*um, 2);
226 TotSurfSoma = TotSurfSoma + SurSomacomp; 214 TotSurfSoma = TotSurfSoma + SurSomacomp;
227 fMassSomacomp[fnbSomacomp] = density * V << 215 fMassSomacomp[fnbSomacomp] = density*VolSomacomp;
228 fMassSomaTot = fMassSomaTot + fMassSomac << 216 fMassSomaTot = fMassSomaTot + fMassSomacomp[fnbSomacomp];
229 G4ThreeVector vSoma(x, y, z); << 217 G4ThreeVector vSoma(x, y, z);
230 fPosSomacomp[fnbSomacomp] = vSoma; << 218 fPosSomacomp[fnbSomacomp] = vSoma;
231 fRadSomacomp[fnbSomacomp] = radius; 219 fRadSomacomp[fnbSomacomp] = radius;
232 if (0 == fnbSomacomp) { 220 if (0 == fnbSomacomp) {
233 base = G4ThreeVector(fRadSomacomp[0], << 221 base = G4ThreeVector(fRadSomacomp[0], fRadSomacomp[0], fRadSomacomp[0]);
234 } 222 }
235 ++fnbSomacomp; 223 ++fnbSomacomp;
236 } 224 }
237 225
238 // ======================================= 226 // =======================================================================
239 // Apical and basal dendritic compartments 227 // Apical and basal dendritic compartments represented as cylinderical solid
240 if (typeNcomp == 3 || typeNcomp == 4) { 228 if (typeNcomp == 3 || typeNcomp == 4) {
241 G4ThreeVector vDend(x, y, z); 229 G4ThreeVector vDend(x, y, z);
242 // Position and Radius of compartments 230 // Position and Radius of compartments
243 PosDendcomp[fnbDendritecomp] = vDend; 231 PosDendcomp[fnbDendritecomp] = vDend;
244 fRadDendcomp[fnbDendritecomp] = radius; 232 fRadDendcomp[fnbDendritecomp] = radius;
245 // To join two tracing points along the << 233 // To join two tracing points along the dendritic branches.
246 // To calculate length, center and rotat 234 // To calculate length, center and rotation angles of each cylinder
247 fPosDendcomp[fnbDendritecomp] = vDend; << 235 fPosDendcomp[fnbDendritecomp] = vDend; //translmDend;
248 // delta of position A and position B of << 236 // delta of position A and position B of cylinder
249 G4ThreeVector dend; 237 G4ThreeVector dend;
250 // primary dendritic branch should be co << 238 //primary dendritic branch should be connect with Soma
251 if (0 == fnbDendritecomp) { 239 if (0 == fnbDendritecomp) {
252 dend = PosDendcomp[fnbDendritecomp] - << 240 dend = PosDendcomp[fnbDendritecomp] - fPosSomacomp[0] - base;
253 } 241 }
254 else { 242 else {
255 dend = PosDendcomp[fnbDendritecomp] - << 243 dend = PosDendcomp[fnbDendritecomp] - PosDendcomp[fnbDendritecomp - 1];
256 } 244 }
257 // Height of compartment 245 // Height of compartment
258 G4double lengthDendcomp = dend.mag(); 246 G4double lengthDendcomp = dend.mag();
259 fHeightDendcomp[fnbDendritecomp] = lengt 247 fHeightDendcomp[fnbDendritecomp] = lengthDendcomp;
260 248
261 // Distance from Soma 249 // Distance from Soma
262 G4ThreeVector dendDis = fPosSomacomp[0] 250 G4ThreeVector dendDis = fPosSomacomp[0] - fPosDendcomp[fnbDendritecomp];
263 if (typeNcomp == 3) fDistADendSoma[fnbDe 251 if (typeNcomp == 3) fDistADendSoma[fnbDendritecomp] = dendDis.mag();
264 if (typeNcomp == 4) fDistBDendSoma[fnbDe 252 if (typeNcomp == 4) fDistBDendSoma[fnbDendritecomp] = dendDis.mag();
265 << 253
266 // Cylinder volume and surface area 254 // Cylinder volume and surface area
267 G4double VolDendcomp = pi * pow(radius * << 255 G4double VolDendcomp = pi*pow(radius*um,2)*(lengthDendcomp*um);
268 TotVolDend = TotVolDend + VolDendcomp; 256 TotVolDend = TotVolDend + VolDendcomp;
269 G4double SurDendcomp = 2. * pi * radius << 257 G4double SurDendcomp = 2.*pi*radius*um*(radius+lengthDendcomp)*um;
270 TotSurfDend = TotSurfDend + SurDendcomp; 258 TotSurfDend = TotSurfDend + SurDendcomp;
271 fMassDendcomp[fnbDendritecomp] = density << 259 fMassDendcomp[fnbDendritecomp] = density*VolDendcomp;
272 fMassDendTot = fMassDendTot + fMassDendc << 260 fMassDendTot = fMassDendTot + fMassDendcomp[fnbDendritecomp];
273 << 261
274 dend = dend.unit(); 262 dend = dend.unit();
275 << 263
276 // Euler angles of each compartment 264 // Euler angles of each compartment
277 G4double theta_eulerDend = dend.theta(); 265 G4double theta_eulerDend = dend.theta();
278 G4double phi_eulerDend = dend.phi(); 266 G4double phi_eulerDend = dend.phi();
279 G4double psi_eulerDend = 0; 267 G4double psi_eulerDend = 0;
280 268
281 // Rotation Matrix, Euler constructor bu << 269 //Rotation Matrix, Euler constructor build inverse matrix.
282 G4RotationMatrix rotmDendInv = << 270 G4RotationMatrix rotmDendInv = G4RotationMatrix(phi_eulerDend+pi/2,
283 G4RotationMatrix(phi_eulerDend + pi / << 271 theta_eulerDend,
>> 272 psi_eulerDend);
284 fRotDendcomp[fnbDendritecomp] = rotmDend 273 fRotDendcomp[fnbDendritecomp] = rotmDendInv.inverse();
285 ++fnbDendritecomp; 274 ++fnbDendritecomp;
286 } 275 }
287 << 276
288 // ======================================= 277 // =======================================================================
289 // Axon compartments represented as cylind 278 // Axon compartments represented as cylinderical solid
290 if (typeNcomp == 2 || typeNcomp == 7) { 279 if (typeNcomp == 2 || typeNcomp == 7) {
291 G4ThreeVector vAxon(x, y, z); << 280 G4ThreeVector vAxon(x, y, z);
292 // Position and Radius of compartments 281 // Position and Radius of compartments
293 PosAxoncomp[fnbAxoncomp] = vAxon; 282 PosAxoncomp[fnbAxoncomp] = vAxon;
294 fRadAxoncomp[fnbAxoncomp] = radius; 283 fRadAxoncomp[fnbAxoncomp] = radius;
295 // To join two tracing points in loaded << 284 // To join two tracing points in loaded SWC data file.
296 // To calculate length, center and rotat << 285 // To calculate length, center and rotation angles of each cylinder
297 286
298 // delta of position A and position B of << 287 // delta of position A and position B of cylinder
299 G4ThreeVector Axon; 288 G4ThreeVector Axon;
300 // primary axon point should be connect << 289 //primary axon point should be connect with Soma
301 if (0 == fnbAxoncomp) { 290 if (0 == fnbAxoncomp) {
302 Axon = PosAxoncomp[fnbAxoncomp] - fPos << 291 Axon = PosAxoncomp[fnbAxoncomp] - fPosSomacomp[0] - base;
303 } 292 }
304 else { 293 else {
305 Axon = PosAxoncomp[fnbAxoncomp] - PosA << 294 Axon = PosAxoncomp[fnbAxoncomp] - PosAxoncomp[fnbAxoncomp - 1];
306 } 295 }
307 G4double lengthAxoncomp = Axon.mag(); 296 G4double lengthAxoncomp = Axon.mag();
308 // Height of compartment 297 // Height of compartment
309 fHeightAxoncomp[fnbAxoncomp] = lengthAxo 298 fHeightAxoncomp[fnbAxoncomp] = lengthAxoncomp;
310 << 299
311 // Distance from Soma 300 // Distance from Soma
312 G4ThreeVector AxonDis = fPosSomacomp[0] 301 G4ThreeVector AxonDis = fPosSomacomp[0] - fPosAxoncomp[fnbAxoncomp];
313 fDistAxonsoma[fnbAxoncomp] = AxonDis.mag 302 fDistAxonsoma[fnbAxoncomp] = AxonDis.mag();
314 << 303
315 // Cylinder volume and surface area 304 // Cylinder volume and surface area
316 G4double VolAxoncomp = pi * pow(radius * << 305 G4double VolAxoncomp = pi*pow(radius*um, 2)*(lengthAxoncomp*um);
317 TotVolAxon = TotVolAxon + VolAxoncomp; 306 TotVolAxon = TotVolAxon + VolAxoncomp;
318 G4double SurAxoncomp = 2. * pi * radius << 307 G4double SurAxoncomp = 2.*pi*radius*um*(radius+lengthAxoncomp)*um;
319 TotSurfAxon = TotSurfAxon + SurAxoncomp; 308 TotSurfAxon = TotSurfAxon + SurAxoncomp;
320 fMassAxoncomp[fnbAxoncomp] = density * V << 309 fMassAxoncomp[fnbAxoncomp] = density*VolAxoncomp;
321 fMassAxonTot += fMassAxoncomp[fnbAxoncom 310 fMassAxonTot += fMassAxoncomp[fnbAxoncomp];
322 Axon = Axon.unit(); 311 Axon = Axon.unit();
323 << 312
324 // Euler angles of each compartment 313 // Euler angles of each compartment
325 G4double theta_eulerAxon = Axon.theta(); 314 G4double theta_eulerAxon = Axon.theta();
326 G4double phi_eulerAxon = Axon.phi(); 315 G4double phi_eulerAxon = Axon.phi();
327 G4double psi_eulerAxon = 0; 316 G4double psi_eulerAxon = 0;
328 317
329 // Rotation Matrix, Euler constructor bu << 318 //Rotation Matrix, Euler constructor build inverse matrix.
330 G4RotationMatrix rotmAxonInv = << 319 G4RotationMatrix rotmAxonInv = G4RotationMatrix(phi_eulerAxon+pi/2,
331 G4RotationMatrix(phi_eulerAxon + pi / << 320 theta_eulerAxon,
>> 321 psi_eulerAxon);
332 G4RotationMatrix rotmAxon = rotmAxonInv. 322 G4RotationMatrix rotmAxon = rotmAxonInv.inverse();
333 fRotAxoncomp[fnbAxoncomp] = rotmAxon; 323 fRotAxoncomp[fnbAxoncomp] = rotmAxon;
334 ++fnbAxoncomp; 324 ++fnbAxoncomp;
335 } 325 }
336 // ======================================= 326 // =======================================================================
337 // checking additional types 327 // checking additional types
338 if (typeNcomp != 1 && typeNcomp != 2 && ty 328 if (typeNcomp != 1 && typeNcomp != 2 && typeNcomp != 3 && typeNcomp != 4) {
339 G4cout << " Additional types:--> " << t << 329 G4cout << " Additional types:--> "<< typeNcomp <<G4endl;
340 } 330 }
341 << 331
342 // If tracing points including spines, use 332 // If tracing points including spines, user can be define spine morphology
343 // including stubby, mushroom, thin, long << 333 // including stubby, mushroom, thin, long thin, filopodia and
344 // branched with heads and necks! 334 // branched with heads and necks!
345 << 335
346 if (typeNcomp == 5) { 336 if (typeNcomp == 5) {
347 // Sphere volume and surface area 337 // Sphere volume and surface area
348 G4double VolSpinecomp = Piconst * pow(ra << 338 G4double VolSpinecomp = Piconst*pow(radius*um,3.) ;
349 TotVolSpine = TotVolSpine + VolSpinecomp 339 TotVolSpine = TotVolSpine + VolSpinecomp;
350 G4double SurSpinecomp = 3. * Piconst * p << 340 G4double SurSpinecomp = 3.*Piconst*pow(radius*um,2.) ;
351 TotSurfSpine = TotSurfSpine + SurSpineco 341 TotSurfSpine = TotSurfSpine + SurSpinecomp;
352 fMassSpinecomp[fnbSpinecomp] = density * << 342 fMassSpinecomp[fnbSpinecomp] = density*VolSpinecomp;
353 fMassSpineTot = fMassSpineTot + fMassSpi 343 fMassSpineTot = fMassSpineTot + fMassSpinecomp[fnbSpinecomp];
354 // OR << 344 // OR
355 // Ellipsoid volume and Approximate for << 345 // Ellipsoid volume and Approximate formula of surface area
356 // ... 346 // ...
357 G4ThreeVector vSpine(x, y, z); << 347 G4ThreeVector vSpine (x, y, z);
358 fPosSpinecomp[fnbSpinecomp] = vSpine; << 348 fPosSpinecomp[fnbSpinecomp] = vSpine;
359 fRadSpinecomp[fnbSpinecomp] = radius; << 349 fRadSpinecomp[fnbSpinecomp] = radius;
360 ++fnbSpinecomp; 350 ++fnbSpinecomp;
361 } 351 }
362 ++nlines; 352 ++nlines;
363 } 353 }
364 infile.close(); 354 infile.close();
365 // ========================================= 355 // =======================================================================
366 356
367 fnbNeuroncomp = nlines; 357 fnbNeuroncomp = nlines;
368 G4cout << " Total number of compartments int << 358 G4cout << " Total number of compartments into Neuron : "
>> 359 << fnbNeuroncomp << G4endl;
369 G4cout << G4endl; 360 G4cout << G4endl;
370 << 361
371 // to calculate SHIFT value for neuron trans 362 // to calculate SHIFT value for neuron translation
372 fshiftX = (minX + maxX) / 2.; << 363 fshiftX = (minX + maxX)/2. ;
373 fshiftY = (minY + maxY) / 2.; << 364 fshiftY = (minY + maxY)/2. ;
374 fshiftZ = (minZ + maxZ) / 2.; << 365 fshiftZ = (minZ + maxZ)/2. ;
375 << 366
376 // width, height, depth of bounding slice vo 367 // width, height, depth of bounding slice volume
377 fwidthB = std::fabs(minX - maxX) + maxRad; << 368 fwidthB = std::fabs(minX - maxX) + maxRad;
378 fheightB = std::fabs(minY - maxY) + maxRad; 369 fheightB = std::fabs(minY - maxY) + maxRad;
379 fdepthB = std::fabs(minZ - maxZ) + maxRad; << 370 fdepthB = std::fabs(minZ - maxZ) + maxRad;
380 371
381 // diagonal length of bounding slice, that g 372 // diagonal length of bounding slice, that give diameter of sphere
382 // for particle direction and fluence! << 373 // for particle direction and fluence!
383 fdiagnlLength = std::sqrt(fwidthB * fwidthB << 374 fdiagnlLength = std::sqrt(fwidthB*fwidthB + fheightB*fheightB
384 << 375 + fdepthB*fdepthB);
385 fTotVolNeuron = TotVolSoma + TotVolDend + To << 376
386 fTotSurfNeuron = TotSurfSoma + TotSurfDend + << 377 fTotVolNeuron = TotVolSoma+TotVolDend+TotVolAxon;
387 fTotMassNeuron = fMassSomaTot + fMassDendTot << 378 fTotSurfNeuron = TotSurfSoma+TotSurfDend+TotSurfAxon;
388 << 379 fTotMassNeuron = fMassSomaTot+fMassDendTot+fMassAxonTot;
389 fTotVolSlice = fwidthB * um * fheightB * um << 380
390 fTotSurfSlice = << 381 fTotVolSlice = fwidthB*um*fheightB*um*fdepthB*um;
391 2 * (fwidthB * um * fheightB * um + fheigh << 382 fTotSurfSlice = 2*(fwidthB*um*fheightB*um+fheightB*um*fdepthB*um+
392 fTotMassSlice = 1.0 * (g / cm3) * fTotVolSli << 383 fwidthB*um*fdepthB*um);
393 << 384 fTotMassSlice = 1.0 * (g/cm3) *fTotVolSlice;
394 fTotVolMedium = Piconst * pow(fdiagnlLength << 385
395 fTotSurfMedium = 3. * Piconst * pow(fdiagnlL << 386 fTotVolMedium = Piconst*pow(fdiagnlLength*um/2.,3.) ;
396 fTotMassMedium = 1.0 * (g / cm3) * fTotVolMe << 387 fTotSurfMedium = 3.*Piconst*pow(fdiagnlLength*um/2.,2);
>> 388 fTotMassMedium = 1.0 * (g/cm3) *fTotVolMedium;
397 } 389 }
398 390
399 //....oooOO0OOooo........oooOO0OOooo........oo 391 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
400 392
401 // Load prepared data file of neural network w 393 // Load prepared data file of neural network with single and multiple layers
402 void NeuronLoadDataFile::NeuralNetworkDATAfile 394 void NeuronLoadDataFile::NeuralNetworkDATAfile(const G4String& filename)
403 { << 395 {
404 G4String sLine = ""; 396 G4String sLine = "";
405 std::ifstream infile; 397 std::ifstream infile;
406 infile.open(filename.c_str()); 398 infile.open(filename.c_str());
407 if (!infile.is_open()) { 399 if (!infile.is_open()) {
408 G4ExceptionDescription ed; 400 G4ExceptionDescription ed;
409 ed << "Datafile " << filename << " is not 401 ed << "Datafile " << filename << " is not opened!";
410 G4Exception("NeuronLoadDataFile::NeuralNet << 402 G4Exception("NeuronLoadDataFile::NeuralNetworkDATAfile()","dna014",
411 "Check file path"); << 403 FatalException, ed, "Check file path");
412 return; 404 return;
413 } 405 }
414 G4cout << "NeuronLoadDataFile::NeuralNetwork << 406 G4cout << "NeuronLoadDataFile::NeuralNetworkDATAfile: opened "
>> 407 << filename << G4endl;
415 408
416 G4int nlines, nbSoma, nbDendrite; 409 G4int nlines, nbSoma, nbDendrite;
417 nlines = 0; 410 nlines = 0;
418 fnbSomacomp = 0; // total number of compart << 411 fnbSomacomp = 0 ; // total number of compartment into Soma
419 fnbDendritecomp = 0; // total number of com << 412 fnbDendritecomp = 0 ; // total number of compartment into Dendrites
420 fnbAxoncomp = 0; // total number of compart << 413 fnbAxoncomp = 0 ; // total number of compartment into Axon
421 fnbSpinecomp = 0; // total number of compar << 414 fnbSpinecomp = 0 ; // total number of compartment into Spines
422 G4double TotVolSoma, TotVolDend, TotVolAxon; 415 G4double TotVolSoma, TotVolDend, TotVolAxon;
423 TotVolSoma = TotVolDend = TotVolAxon = 0.; << 416 TotVolSoma=TotVolDend=TotVolAxon=0.;
424 G4double TotSurfSoma, TotSurfDend, TotSurfAx 417 G4double TotSurfSoma, TotSurfDend, TotSurfAxon;
425 TotSurfSoma = TotSurfDend = TotSurfAxon = 0. << 418 TotSurfSoma=TotSurfDend=TotSurfAxon=0.;
426 G4int typeNcomp; // types of structure: som << 419 G4int typeNcomp; // types of structure: soma, axon, apical dendrite, etc.
427 G4double x1, y1, z1, x2, y2, z2; // cartesi << 420 G4double x1,y1,z1,x2,y2,z2; // cartesian coordinates of each compartment
428 G4double radius; // radius of each compartm << 421 G4double radius; // radius of each compartment in micrometer
429 G4double height; // height of each compartm << 422 G4double height; // height of each compartment in micrometer
430 G4double maxRad = -1e+09; 423 G4double maxRad = -1e+09;
431 G4double density = 1.0 * (g / cm3); // wate << 424 G4double density = 1.0 * (g/cm3) ; // water medium
432 G4double Piconst = (4.0 / 3.0) * pi; << 425 G4double Piconst = (4.0/3.0)*pi ;
433 << 426
434 for (;;) { 427 for (;;) {
435 getline(infile, sLine); 428 getline(infile, sLine);
436 if (infile.eof()) { << 429 if (infile.eof()) { break; }
437 break; <<
438 } <<
439 std::istringstream form(sLine); 430 std::istringstream form(sLine);
440 if (nlines == 0) { 431 if (nlines == 0) {
441 // to read total number of compartments 432 // to read total number of compartments
442 form >> fnbNeuroncomp >> nbSoma >> nbDen << 433 form >> fnbNeuroncomp >> nbSoma >> nbDendrite ;
443 fMassSomacomp.resize(nbSoma, 0); 434 fMassSomacomp.resize(nbSoma, 0);
444 fPosSomacomp.resize(nbSoma); 435 fPosSomacomp.resize(nbSoma);
445 fRadSomacomp.resize(nbSoma, 0); << 436 fRadSomacomp.resize(nbSoma, 0);
446 fRadDendcomp.resize(nbDendrite, 0); << 437 fRadDendcomp.resize(nbDendrite, 0);
447 fHeightDendcomp.resize(nbDendrite, 0); 438 fHeightDendcomp.resize(nbDendrite, 0);
448 fMassDendcomp.resize(nbDendrite, 0); 439 fMassDendcomp.resize(nbDendrite, 0);
449 fDistADendSoma.resize(nbDendrite, 0); 440 fDistADendSoma.resize(nbDendrite, 0);
450 fDistBDendSoma.resize(nbDendrite, 0); 441 fDistBDendSoma.resize(nbDendrite, 0);
451 fPosDendcomp.resize(nbDendrite); 442 fPosDendcomp.resize(nbDendrite);
452 fRotDendcomp.resize(nbDendrite); 443 fRotDendcomp.resize(nbDendrite);
453 } 444 }
454 // ======================================= 445 // =======================================================================
455 // Soma compartments represented as Sphere 446 // Soma compartments represented as Sphere or Ellipsoid solid
456 if (nlines > 0 && nlines <= nbSoma) { 447 if (nlines > 0 && nlines <= nbSoma) {
457 form >> typeNcomp >> x1 >> y1 >> z1 >> r << 448 form >> typeNcomp >> x1 >> y1 >> z1 >> radius ;
458 if (typeNcomp != 1) break; << 449 if (typeNcomp !=1) break;
459 // max diameter of compartments << 450 // max diameter of compartments
460 if (maxRad < radius) maxRad = radius; << 451 if (maxRad < radius) maxRad = radius;
461 // Sphere volume and surface area 452 // Sphere volume and surface area
462 G4double VolSomacomp = Piconst * pow(rad << 453 G4double VolSomacomp = Piconst*pow(radius*um,3.) ;
463 TotVolSoma = TotVolSoma + VolSomacomp; 454 TotVolSoma = TotVolSoma + VolSomacomp;
464 G4double SurSomacomp = 3. * Piconst * po << 455 G4double SurSomacomp = 3.*Piconst*pow(radius*um,2.) ;
465 TotSurfSoma = TotSurfSoma + SurSomacomp; 456 TotSurfSoma = TotSurfSoma + SurSomacomp;
466 fMassSomacomp[fnbSomacomp] = density * V << 457 fMassSomacomp[fnbSomacomp] = density*VolSomacomp;
467 fMassSomaTot = fMassSomaTot + fMassSomac 458 fMassSomaTot = fMassSomaTot + fMassSomacomp[fnbSomacomp];
468 << 459
469 G4ThreeVector vSoma(x1, y1, z1); << 460 G4ThreeVector vSoma (x1 ,y1 ,z1);
470 fPosSomacomp[fnbSomacomp] = vSoma; << 461 fPosSomacomp[fnbSomacomp] = vSoma;
471 fRadSomacomp[fnbSomacomp] = radius; << 462 fRadSomacomp[fnbSomacomp]= radius;
472 ++fnbSomacomp; << 463 ++fnbSomacomp;
473 } 464 }
474 // ======================================= 465 // =======================================================================
475 // Apical and basal dendritic compartments << 466 // Apical and basal dendritic compartments represented as cylinderical solid
476 if (nlines > nbSoma && nlines <= fnbNeuron 467 if (nlines > nbSoma && nlines <= fnbNeuroncomp) {
477 form >> typeNcomp >> x1 >> y1 >> z1 >> x 468 form >> typeNcomp >> x1 >> y1 >> z1 >> x2 >> y2 >> z2 >> radius >> height;
478 if (typeNcomp != 3) break; // || typeNc << 469 if (typeNcomp != 3 ) break; // || typeNcomp != 4
479 << 470
480 // To calculate length, center and rotat << 471 // To calculate length, center and rotation angles of each cylinder
481 // Center-position of each cylinder 472 // Center-position of each cylinder
482 G4double Dendxx = x1 + x2; << 473 G4double Dendxx= x1 + x2;
483 G4double Dendyy = y1 + y2; << 474 G4double Dendyy= y1 + y2;
484 G4double Dendzz = z1 + z2; << 475 G4double Dendzz= z1 + z2;
485 G4ThreeVector translmDend = G4ThreeVecto << 476 G4ThreeVector translmDend = G4ThreeVector(Dendxx/2. ,
486 fPosDendcomp[fnbDendritecomp] = translmD << 477 Dendyy/2. , Dendzz/2.) ;
487 fRadDendcomp[fnbDendritecomp] = radius; << 478 fPosDendcomp [fnbDendritecomp] = translmDend;
>> 479 fRadDendcomp [fnbDendritecomp]= radius;
488 G4double lengthDendcomp = height; 480 G4double lengthDendcomp = height;
489 // Height of compartment 481 // Height of compartment
490 fHeightDendcomp[fnbDendritecomp] = lengt << 482 fHeightDendcomp [fnbDendritecomp]= lengthDendcomp;
491 // Distance from Soma 483 // Distance from Soma
492 << 484
493 // Cylinder volume and surface area 485 // Cylinder volume and surface area
494 G4double VolDendcomp = pi * pow(radius * << 486 G4double VolDendcomp = pi*pow(radius*um,2)*(lengthDendcomp*um);
495 TotVolDend = TotVolDend + VolDendcomp; 487 TotVolDend = TotVolDend + VolDendcomp;
496 G4double SurDendcomp = 2. * pi * radius << 488 G4double SurDendcomp = 2.*pi*radius*um*(radius+lengthDendcomp)*um;
497 TotSurfDend = TotSurfDend + SurDendcomp; 489 TotSurfDend = TotSurfDend + SurDendcomp;
498 fMassDendcomp[fnbDendritecomp] = density << 490 fMassDendcomp[fnbDendritecomp] = density*VolDendcomp;
499 fMassDendTot = fMassDendTot + fMassDendc << 491 fMassDendTot = fMassDendTot + fMassDendcomp[fnbDendritecomp];
500 << 492
501 G4double Dendx = x1 - x2; << 493 G4double Dendx= x1 - x2;
502 G4double Dendy = y1 - y2; << 494 G4double Dendy= y1 - y2;
503 G4double Dendz = z1 - z2; << 495 G4double Dendz= z1 - z2;
504 Dendx = Dendx / lengthDendcomp; << 496 Dendx=Dendx/lengthDendcomp;
505 Dendy = Dendy / lengthDendcomp; << 497 Dendy=Dendy/lengthDendcomp;
506 Dendz = Dendz / lengthDendcomp; << 498 Dendz=Dendz/lengthDendcomp;
507 << 499
508 // Euler angles of each compartment 500 // Euler angles of each compartment
509 G4ThreeVector directionDend = G4ThreeVec << 501 G4ThreeVector directionDend = G4ThreeVector(Dendx,Dendy,Dendz);
510 G4double theta_eulerDend = directionDend 502 G4double theta_eulerDend = directionDend.theta();
511 G4double phi_eulerDend = directionDend.p 503 G4double phi_eulerDend = directionDend.phi();
512 G4double psi_eulerDend = 0; 504 G4double psi_eulerDend = 0;
513 505
514 // Rotation Matrix, Euler constructor bu << 506 //Rotation Matrix, Euler constructor build inverse matrix.
515 G4RotationMatrix rotmDendInv = << 507 G4RotationMatrix rotmDendInv = G4RotationMatrix(phi_eulerDend+pi/2,
516 G4RotationMatrix(phi_eulerDend + pi / << 508 theta_eulerDend,
>> 509 psi_eulerDend);
517 G4RotationMatrix rotmDend = rotmDendInv. 510 G4RotationMatrix rotmDend = rotmDendInv.inverse();
518 << 511
519 fRotDendcomp[fnbDendritecomp] = rotmDend 512 fRotDendcomp[fnbDendritecomp] = rotmDend;
520 ++fnbDendritecomp; 513 ++fnbDendritecomp;
521 } 514 }
522 ++nlines; 515 ++nlines;
523 } 516 }
524 << 517
525 // ========================================= 518 // =======================================================================
526 519
527 G4cout << " Total number of compartments int << 520 G4cout << " Total number of compartments into Neuron : " <<
528 << 521 fnbNeuroncomp << G4endl;
>> 522
529 // to calculate SHIFT value for neuron trans 523 // to calculate SHIFT value for neuron translation
530 fshiftX = 0.; //(minX + maxX)/2. ; << 524 fshiftX = 0.; //(minX + maxX)/2. ;
531 fshiftY = 0.; //(minY + maxY)/2. ; << 525 fshiftY = 0.; //(minY + maxY)/2. ;
532 fshiftZ = 0.; //(minZ + maxZ)/2. ; << 526 fshiftZ = 0.; //(minZ + maxZ)/2. ;
533 << 527
534 // width, height, depth of bounding slice vo 528 // width, height, depth of bounding slice volume
535 fwidthB = 640.; << 529 fwidthB = 640.;
536 fheightB = 280.; 530 fheightB = 280.;
537 fdepthB = 25.; << 531 fdepthB = 25.;
538 // diagonal length of bounding slice, that g 532 // diagonal length of bounding slice, that give diameter of sphere
539 // for particle direction and fluence! << 533 // for particle direction and fluence!
540 fdiagnlLength = std::sqrt(fwidthB * fwidthB << 534 fdiagnlLength = std::sqrt(fwidthB*fwidthB + fheightB*fheightB
541 << 535 + fdepthB*fdepthB);
542 fTotVolNeuron = TotVolSoma + TotVolDend + To << 536
543 fTotSurfNeuron = TotSurfSoma + TotSurfDend + << 537 fTotVolNeuron = TotVolSoma+TotVolDend+TotVolAxon;
544 fTotMassNeuron = fMassSomaTot + fMassDendTot << 538 fTotSurfNeuron = TotSurfSoma+TotSurfDend+TotSurfAxon;
545 << 539 fTotMassNeuron = fMassSomaTot+fMassDendTot+fMassAxonTot;
546 fTotVolSlice = fwidthB * um * fheightB * um << 540
547 fTotSurfSlice = << 541 fTotVolSlice = fwidthB*um*fheightB*um*fdepthB*um;
548 2 * (fwidthB * um * fheightB * um + fheigh << 542 fTotSurfSlice = 2*(fwidthB*um*fheightB*um+fheightB*um*fdepthB*um+
549 fTotMassSlice = 1.0 * (g / cm3) * fTotVolSli << 543 fwidthB*um*fdepthB*um);
550 << 544 fTotMassSlice = 1.0 * (g/cm3) *fTotVolSlice;
551 fTotVolMedium = Piconst * pow(fdiagnlLength << 545
552 fTotSurfMedium = 3. * Piconst * pow(fdiagnlL << 546 fTotVolMedium = Piconst*pow(fdiagnlLength*um/2.,3.) ;
553 fTotMassMedium = 1.0 * (g / cm3) * fTotVolMe << 547 fTotSurfMedium = 3.*Piconst*pow(fdiagnlLength*um/2.,2);
>> 548 fTotMassMedium = 1.0 * (g/cm3) *fTotVolMedium;
554 549
555 infile.close(); 550 infile.close();
556 } 551 }
557 552
558 //....oooOO0OOooo........oooOO0OOooo........oo 553 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
559 554
560 void NeuronLoadDataFile::ComputeTransformation << 555 void NeuronLoadDataFile::ComputeTransformation
>> 556 (const G4int copyNo, G4VPhysicalVolume* physVol) const
561 { 557 {
562 // to calculate Euler angles from Rotation M 558 // to calculate Euler angles from Rotation Matrix after Inverse!
563 // 559 //
564 G4RotationMatrix rotmNeuron = G4RotationMatr 560 G4RotationMatrix rotmNeuron = G4RotationMatrix(fRotNeuroncomp[copyNo]);
565 G4double cosX = std::sqrt(rotmNeuron.xx() * << 561 G4double cosX = std::sqrt (rotmNeuron.xx()*rotmNeuron.xx() +
>> 562 rotmNeuron.yx()*rotmNeuron.yx()) ;
566 G4double euX, euY, euZ; 563 G4double euX, euY, euZ;
567 if (cosX > 16 * FLT_EPSILON) { << 564 if (cosX > 16*FLT_EPSILON) {
568 euX = std::atan2(rotmNeuron.zy(), rotmNeur << 565 euX = std::atan2 (rotmNeuron.zy(),rotmNeuron.zz());
569 euY = std::atan2(-rotmNeuron.zx(), cosX); << 566 euY = std::atan2 (-rotmNeuron.zx(),cosX);
570 euZ = std::atan2(rotmNeuron.yx(), rotmNeur << 567 euZ = std::atan2 (rotmNeuron.yx(),rotmNeuron.xx());
571 } << 568 }
572 else { 569 else {
573 euX = std::atan2(-rotmNeuron.yz(), rotmNeu << 570 euX = std::atan2 (-rotmNeuron.yz(),rotmNeuron.yy());
574 euY = std::atan2(-rotmNeuron.zx(), cosX); << 571 euY = std::atan2 (-rotmNeuron.zx(),cosX);
575 euZ = 0.; << 572 euZ = 0. ;
576 } 573 }
577 G4RotationMatrix* rot = new G4RotationMatrix 574 G4RotationMatrix* rot = new G4RotationMatrix();
578 rot->rotateX(euX); 575 rot->rotateX(euX);
579 rot->rotateY(euY); 576 rot->rotateY(euY);
580 rot->rotateZ(euZ); << 577 rot->rotateZ(euZ);
581 578
582 physVol->SetRotation(rot); << 579 physVol->SetRotation(rot);
583 580
584 // shift of cylinder compartments << 581 // shift of cylinder compartments
585 G4ThreeVector originNeuron((fPosNeuroncomp[c << 582 G4ThreeVector originNeuron((fPosNeuroncomp[copyNo].x()-fshiftX) * um,
586 (fPosNeuroncomp[c << 583 (fPosNeuroncomp[copyNo].y()-fshiftY) * um,
587 (fPosNeuroncomp[c << 584 (fPosNeuroncomp[copyNo].z()-fshiftZ) * um);
588 physVol->SetTranslation(originNeuron); 585 physVol->SetTranslation(originNeuron);
589 } 586 }
590 587
591 //....oooOO0OOooo........oooOO0OOooo........oo 588 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
592 589
593 void NeuronLoadDataFile::ComputeDimensions(G4T << 590 void NeuronLoadDataFile::ComputeDimensions
594 con << 591 (G4Tubs& fcylinderComp, const G4int copyNo, const G4VPhysicalVolume*) const
595 { << 592 {
596 fcylinderComp.SetInnerRadius(0 * um); << 593 fcylinderComp.SetInnerRadius(0*um);
597 fcylinderComp.SetOuterRadius(fRadNeuroncomp[ << 594 fcylinderComp.SetOuterRadius(fRadNeuroncomp[copyNo]*um);
598 fcylinderComp.SetZHalfLength(fHeightNeuronco << 595 fcylinderComp.SetZHalfLength(fHeightNeuroncomp[copyNo]*um /2.);
599 fcylinderComp.SetStartPhiAngle(0. * deg); << 596 fcylinderComp.SetStartPhiAngle(0.*deg);
600 fcylinderComp.SetDeltaPhiAngle(360. * deg); << 597 fcylinderComp.SetDeltaPhiAngle(360.*deg);
601 } 598 }
602 599
603 //....oooOO0OOooo........oooOO0OOooo........oo 600 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
604 601