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Commit d86c3eae authored by Pilar Cossio's avatar Pilar Cossio
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Tidying up tutorial

parent 9768552f
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Showing with 4664 additions and 38 deletions
Tutorial_BioEM/List_Quat_ProRun 0 → 100644
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Tutorial_BioEM/MODEL_COMPARISION/Param_Input_ModelComparision
View file @ d86c3eae
......@@ -6,9 +6,11 @@ PIXEL_SIZE 1.32
USE_QUATERNIONS
##### Constrast transfer integration: #######
CTF_B_ENV 100.0 300.5 8
CTF_DEFOCUS 1.0 6.0 5
CTF_AMPLITUDE 0.01 0.5 3
CTF_B_ENV 10.0 500. 5
CTF_DEFOCUS 0.5 4.5 8
CTF_AMPLITUDE 0.01 0.401 4
SIGMA_PRIOR_B_CTF 50.
##### Center displacement: #######
DISPLACE_CENTER 10 2
DISPLACE_CENTER 40 1
Tutorial_BioEM/Param_Input_Cross-Cor
View file @ d86c3eae
......@@ -7,9 +7,9 @@ GRIDPOINTS_ALPHA 10
GRIDPOINTS_BETA 5
##### Constrast transfer integration: #######
CTF_B_FACTOR 100.0 300.5 8
CTF_DEFOCUS 1.0 6.0 5
CTF_AMPLITUDE 0.1 0.1 1
CTF_B_ENV 10.0 300.5 3
CTF_DEFOCUS 0.5 4.5 5
CTF_AMPLITUDE 0.01 0.2 2
##### Center displacement: #######
DISPLACE_CENTER 10 2
......
Tutorial_BioEM/Param_Input_Priors
View file @ d86c3eae
......@@ -7,9 +7,9 @@ GRIDPOINTS_ALPHA 2
GRIDPOINTS_BETA 2
##### Constrast transfer integration: #######
CTF_B_FACTOR 100.0 300.5 2
CTF_DEFOCUS 1.0 6.0 5
CTF_AMPLITUDE 0.1 0.1 1
CTF_B_ENV 10.0 300.5 3
CTF_DEFOCUS 0.5 4.5 5
CTF_AMPLITUDE 0.01 0.2 3
##### Center displacement: #######
DISPLACE_CENTER 10 2
......
Tutorial_BioEM/Param_Input_WritePAng
View file @ d86c3eae
......@@ -7,7 +7,7 @@ GRIDPOINTS_ALPHA 10
GRIDPOINTS_BETA 5
##### Constrast transfer integration: #######
CTF_B_FACTOR 100.0 300.5 8
CTF_B_ENV 100.0 300.5 8
CTF_DEFOCUS 1.0 6.0 5
CTF_AMPLITUDE 0.1 0.1 1
......
Tutorial_BioEM/Param_Print_MAP
View file @ d86c3eae
......@@ -8,8 +8,8 @@ BEST_DX -10
BEST_DY 5
######## Normalization and Offset ################
BEST_NORM 1
BEST_OFFSET 0
BEST_NORM 0.03
BEST_OFFSET -0.001
######## Euler Angles ################
BEST_ALPHA -0.464793
......@@ -23,12 +23,14 @@ BEST_PSF_PHASE 0.004
BEST_PSF_AMP 1
##### Using CTF #######
BEST_CTF_B_FACTOR 200.5
BEST_CTF_B_ENV 200.5
BEST_CTF_DEFOCUS 3.5
BEST_CTF_AMP 0.3
######## ADDING NOISE ###########
WITHNOISE 5.476
### In this case the standard deviation of the noise is 6.476
WITHNOISE 6.476
########## Printing the 3d Model rotation ###########
PRINT_ROTATED_MODELS
#PRINT_ROTATED_MODELS
Tutorial_BioEM/Param_ProRun
View file @ d86c3eae
......@@ -7,8 +7,8 @@ USE_QUATERNIONS
##### Constrast transfer integration: #######
CTF_B_ENV 10.0 500. 5.
CTF_DEFOCUS 1.0 6.0 10.
CTF_AMPLITUDE 0.1 0.9 5.
CTF_DEFOCUS 0.5 4.5 8.
CTF_AMPLITUDE 0.01 0.401 4.
## Gaussian width of Prior of b-parameter
SIGMA_PRIOR_B_CTF 50.
......
bioem.cpp
View file @ d86c3eae
......@@ -296,10 +296,7 @@ int bioem::configure(int ac, char* av[])
#ifdef WITH_MPI
// Contros for MPI
if(mpi_size > param.nTotGridAngles){
cout << "EXIT: Wrong MPI setup More MPI processes than orientations\n"; exit(1);
}
// ********************* MPI inizialization/ Transfer of parameters******************
if (mpi_size > 1)
......@@ -443,6 +440,10 @@ int bioem::run()
if (mpi_rank == 0) printf("\tInitializing Probabilities\n");
// Contros for MPI
if(mpi_size > param.nTotGridAngles){
cout << "EXIT: Wrong MPI setup More MPI processes than orientations\n"; exit(1);
}
// Inizialzing Probabilites to zero and constant to -Infinity
for (int iRefMap = 0; iRefMap < RefMap.ntotRefMap; iRefMap ++)
......@@ -759,13 +760,15 @@ int bioem::run()
}else {
if(param.usepsf){
// if( localcc[rx * param.param_device.NumberPixels + ry] <
outputProbFile << "Notation= RefMap: MapNumber ; Maximizing Param: MaxLogProb - q1 - q2 - q3 - PSF amp - PSF phase - PSF envelope - center x - center y - normalization - offsett \n";
outputProbFile << "Notation= RefMap: MapNumber ; Maximizing Param: MaxLogProb - q1 - q2 - q3 - q4 -PSF amp - PSF phase - PSF envelope - center x - center y - normalization - offsett \n";
}else{
outputProbFile << "Notation= RefMap: MapNumber ; Maximizing Param: MaxLogProb - q1 - q2 - q3 - CTF amp - CTF defocus - CTF B-Env - center x - center y - normalization - offsett \n";
outputProbFile << "Notation= RefMap: MapNumber ; Maximizing Param: MaxLogProb - q1 - q2 - q3 - q4 - CTF amp - CTF defocus - CTF B-Env - center x - center y - normalization - offsett \n";
}}
if(param.writeCTF) outputProbFile << " RefMap: MapNumber ; CTFMaxParm: defocus - b-Env (B ref. Penzeck 2010)\n";
if(param.yespriorAngles) outputProbFile << "**** Remark: Using Prior Proability in Angles ****\n";
outputProbFile <<"************************* HEADER:: NOTATION *******************************************\n\n";
// Loop over reference maps
// ************* Over all maps ***************
......@@ -794,18 +797,20 @@ int bioem::run()
// *** Param that maximize probability****
// outputProbFile << (pProbMap.Constoadd + 0.5 * log(M_PI) + (1 - param.param_device.Ntotpi * 0.5) * (log(2 * M_PI) + 1) + log(param.param_device.volu)) << " ";
outputProbFile << param.angles[pProbMap.max.max_prob_orient].pos[0] << " [ ] ";
outputProbFile << param.angles[pProbMap.max.max_prob_orient].pos[1] << " [ ] ";
outputProbFile << param.angles[pProbMap.max.max_prob_orient].pos[2] << " [ ] ";
outputProbFile << param.CtfParam[pProbMap.max.max_prob_conv].pos[0] << " [ ] ";
outputProbFile << param.angles[pProbMap.max.max_prob_orient].pos[0] << " [] ";
outputProbFile << param.angles[pProbMap.max.max_prob_orient].pos[1] << " [] ";
outputProbFile << param.angles[pProbMap.max.max_prob_orient].pos[2] << " [] ";
if(param.doquater)outputProbFile << param.angles[pProbMap.max.max_prob_orient].quat4 << " [] ";
outputProbFile << param.CtfParam[pProbMap.max.max_prob_conv].pos[0] << " [] ";
if(!param.usepsf){outputProbFile << param.CtfParam[pProbMap.max.max_prob_conv].pos[1]/ 2.f /M_PI / param.elecwavel * 0.0001 << " [micro-m] ";
}else{outputProbFile << param.CtfParam[pProbMap.max.max_prob_conv].pos[1] << " [1/A²] ";}
if(!param.usepsf){outputProbFile << param.CtfParam[pProbMap.max.max_prob_conv].pos[2] << " [A²] ";}
else{outputProbFile << param.CtfParam[pProbMap.max.max_prob_conv].pos[2] << " [1/A²] ";}
outputProbFile << pProbMap.max.max_prob_cent_x << " [pix] ";
outputProbFile << pProbMap.max.max_prob_cent_y << " [pix] " ;
outputProbFile << pProbMap.max.max_prob_norm << " [ ] " ;
outputProbFile << pProbMap.max.max_prob_mu << " [ ] ";
outputProbFile << pProbMap.max.max_prob_norm << " [] " ;
outputProbFile << pProbMap.max.max_prob_mu << " [] ";
outputProbFile << "\n";
// Writing out CTF parameters if requiered
......@@ -862,6 +867,7 @@ int bioem::run()
int rx=0;
int ry=0;
myfloat_t localcc[ (param.param_device.NumberPixels+1) * (param.param_device.NumberPixels+1) ];
int used[(param.param_device.NumberPixels+1) * (param.param_device.NumberPixels+1)];
halfPix = param.param_device.NumberPixels / 2 ;
// Ordering the centers of the Cross Correlation
......@@ -871,6 +877,7 @@ int bioem::run()
for (int ry = 0; ry < param.param_device.NumberPixels ; ry++)
{
localcc[ rx * param.param_device.NumberPixels + ry ] = 0.0;
used[ rx * param.param_device.NumberPixels + ry ]= 0;
}
}
......@@ -904,36 +911,42 @@ int bioem::run()
}else{
localcc[ rx * param.param_device.NumberPixels + ry ] = log(pProbCC.forCC)+pProbCC.ConstCC;
}
used[ rx * param.param_device.NumberPixels + ry] = 1;
cc++;
}
// ccProbfile << "\n";
}
if(!param.ignoreCCoff){
for (int rx = param.param_device.CCdisplace; rx < param.param_device.NumberPixels ; rx = rx + param.param_device.CCdisplace)
/* for (int rx = param.param_device.CCdisplace; rx < param.param_device.NumberPixels ; rx = rx + param.param_device.CCdisplace)
{
for (int ry = param.param_device.CCdisplace; ry < param.param_device.NumberPixels ; ry = ry + param.param_device.CCdisplace)
{
if(localcc[ rx * param.param_device.NumberPixels + ry ] > -FLT_MAX){
{*/
for (int rx = param.param_device.CCdisplace; rx < param.param_device.NumberPixels ; rx++)
{
for (int ry = param.param_device.CCdisplace; ry < param.param_device.NumberPixels ; ry++)
{
if(used[ rx * param.param_device.NumberPixels + ry ] == 1){
ccProbfile << "RefMap: "<< iRefMap << " " << rx << " " << ry << " " << localcc[ rx * param.param_device.NumberPixels + ry ] << "\n" ;
}else{
ccProbfile << "RefMap: "<< iRefMap << " " << rx << " " << ry << " " << -FLT_MAX << "\n" ;
if(localcc[ rx * param.param_device.NumberPixels + ry ] <= -FLT_MAX)ccProbfile << "RefMap: "<< iRefMap << " " << rx << " " << ry << " " << -FLT_MAX << "\n" ;
}
// cout << " cc " << rx << " " << ry << " " << localcc[ rx * param.param_device.NumberPixels + ry ] <<"\n" ;
}
ccProbfile << "\n";
// ccProbfile << "\n";
}
}else{
for (int rx = param.param_device.CCdisplace; rx < param.param_device.NumberPixels ; rx++)
{
for (int ry = param.param_device.CCdisplace; ry < param.param_device.NumberPixels ; ry++)
{
if(localcc[ rx * param.param_device.NumberPixels + ry ] > -FLT_MAX){
if(used[ rx * param.param_device.NumberPixels + ry ] == 1){
ccProbfile << "RefMap: "<< iRefMap << " " << rx << " " << ry << " " << localcc[ rx * param.param_device.NumberPixels + ry ] << "\n" ;
}else{
ccProbfile << "RefMap: "<< iRefMap << " " << rx << " " << ry << " " << -FLT_MAX << "\n" ;
if(localcc[ rx * param.param_device.NumberPixels + ry ] <= -FLT_MAX)ccProbfile << "RefMap: "<< iRefMap << " " << rx << " " << ry << " " << -FLT_MAX << "\n" ;
}
}
ccProbfile << "\n";
// ccProbfile << "\n";
}
}
......
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