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ptycho/+ptychotomo/private/get_golden_ratio_groups.m
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%GET_GOLDEN_RATIO_GROUPS use the provided angle to select Ngroups groups containing
%the most orthogonal set of projections
%
% group_ind = get_golden_ratio_groups(theta_all, Ngroups)
%
% Inputs:
% **theta_all - list of angles in degrees
% **Ngroups - number of sets to split the angles
% *returns*
% ++group_ind - cells containing indices for each set
% Academic License Agreement
%
% Source Code
%
% Introduction
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the PtychoShelves
% computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
%
% Terms and Conditions of the LICENSE
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
% hereinafter set out and until termination of this license as set forth below.
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
% in the commercial use, application or exploitation of works similar to the PROGRAM.
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
% another computing language:
% "Data processing was carried out using the PtychoShelves package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
% Scherrer Institut, Switzerland."
%
% Additionally, any publication using the package, or any translation of the code into another computing language should cite
% K. Wakonig, H.-C. Stadler, M. Odstrčil, E.H.R. Tsai, A. Diaz, M. Holler, I. Usov, J. Raabe, A. Menzel, M. Guizar-Sicairos, PtychoShelves, a versatile
% high-level framework for high-performance analysis of ptychographic data, J. Appl. Cryst. 53(2) (2020). (doi: 10.1107/S1600576720001776)
% and for difference map:
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
% (doi: 10.1126/science.1158573),
% for maximum likelihood:
% P. Thibault and M. Guizar-Sicairos, Maximum-likelihood refinement for coherent diffractive imaging, New J. Phys. 14, 063004 (2012).
% (doi: 10.1088/1367-2630/14/6/063004),
% for LSQ-ML:
% M. Odstrčil, A. Menzel, and M. Guizar-Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Opt. Express 26(3), 3108 (2018).
% (doi: 10.1364/OE.26.003108),
% for mixed coherent modes:
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
% and/or for multislice:
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
% (doi: 10.1364/OE.24.029089),
% and/or for OPRP:
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, Ptychographic coherent diffractive imaging with orthogonal probe relaxation.
% Opt. Express 24.8 (8360-8369) 2016. (doi: 10.1364/OE.24.008360).
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
% the courts of Zürich, Switzerland.
function group_ind = get_golden_ratio_groups(theta_all, Ngroups)
Nangles = length(theta_all);
if all(theta_all == theta_all(1))
group_ind = {};
for ll = 1:Ngroups
ind = 1+(ll-1)*ceil(Nangles/Ngroups):min(Nangles, (ll)*ceil(Nangles/Ngroups));
group_ind{end+1} = (ind);
end
return
end
theta_aux = theta_all;
Nangles = length(theta_all);
start_index = 200;
for ll = 1:Nangles
% golden ratio angle selector
gold_angle = mod((ll + start_index) * (1+sqrt(5))/2* 360, 360);
theta = theta_aux(math.argmin(abs(theta_aux-gold_angle)));
theta_aux = setdiff(theta_aux, theta);
index(ll) = find(theta_all== theta);
end
group_ind = {};
for ll = 1:Ngroups
ind = 1+(ll-1)*ceil(Nangles/Ngroups):min(Nangles, (ll)*ceil(Nangles/Ngroups));
group_ind{end+1} = index(ind);
end
end
ptycho/+ptychotomo/private/set_to_block_gpu.cu
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/*
SET_TO_BLOCK_GPU Set complex views to a large complex object without memory copy of the large volume
set_to_block_gpu(volData, volData_block, uint16(ind));
Inputs:
**volData - 3D array, single precision
**volData_block - 3D array, that will be written into the volData
**ind - 1D array, uint16, indices into which lines of volData will be volData_block written
Outputs:
none, results are written to volData directly
Recompile:
mexcuda -output +engines/+GPU/+shared/private/set_views_gpu_mex +engines/+GPU/+shared/private/set_views_gpu_mex.cu
*/
#include "mex.h"
#include "gpu/mxGPUArray.h"
#include <math.h>
#include <stdio.h>
typedef const unsigned int cuint;
typedef const uint16_T cuint16;
// unfortunatelly ~10800 is the maximum of const memory
const unsigned int MAX_IND_READ = 10800;
static const unsigned MAX_IND_READ_DEV = MAX_IND_READ;
__constant__ uint16_T gC_ind[MAX_IND_READ_DEV];
int checkLastError(char * msg)
{
cudaError_t cudaStatus = cudaGetLastError();
if (cudaStatus != cudaSuccess) {
char err[512];
sprintf(err, "setprojection failed \n %s: %s. \n", msg, cudaGetErrorString(cudaStatus));
mexPrintf(err);
return 1;
}
return 0;
}
/*
* Device code
*/
__global__ void addToArray_c( float2 const * sarray, float2 * larray, cuint Nx,cuint Ny, cuint Npos) {
// Location in a 3D matrix
int idx= blockIdx.x * blockDim.x + threadIdx.x;
int idy= blockIdx.y * blockDim.y + threadIdx.y;
if ( idx < Nx & idy < Ny ) {
int idz, id_large, id_small;
for(idz = 0; idz < Npos; idz++)
{
id_large = idx + Nx*idy + Nx*Ny*(gC_ind[idz]-1); // go only through some of the indices
id_small = idx + Nx*idy + Nx*Ny*idz;
larray[id_large].x = sarray[ id_small ].x;
larray[id_large].y = sarray[ id_small ].y;
}
}
}
void mexFunction(int nlhs, mxArray *plhs[],
int nrhs, const mxArray *prhs[])
{
int i ;
char const * const errId = "parallel:gpu:mexGPUExample:InvalidInput";
char const * const errMsg = "Invalid input to MEX file.";
// Check for proper number of arguments.
if (nrhs != 3)
mexErrMsgTxt("Three input arguments required");
// Input must be of type single.
for (i=0; i < 2; i++) {
if ( !mxIsGPUArray(prhs[i]) ){
printf("Input %d is not cell array\n",i+1);
mexErrMsgIdAndTxt("MexError:ptycho","Inputs must be of correct type.");
}
}
// Input must be of type int16.
for (i=2; i<3; i++){
if (mxIsUint16(prhs[i]) != 1){
printf("Input %d is not integer\n",i+1);
mexErrMsgIdAndTxt("MexError:ptycho","Inputs must be of correct type uint16.");
}
}
// It cannot be one-dimensional
if(mxGetNumberOfDimensions(prhs[0]) > 3) {
printf("The 1st input argument must have at least three dimensions.");
mexErrMsgIdAndTxt("MexError:ptycho","wrong number of dimensions");
}
// It cannot be more than 3-dimensional
if(mxGetNumberOfDimensions(prhs[0]) > 3) {
printf("The 1st input argument must have at most three dimensions.");
mexErrMsgIdAndTxt("MexError:ptycho","wrong number of dimensions");
}
// Check that arrays are complex
const mxGPUArray * m_sarray = mxGPUCreateFromMxArray(prhs[1]);
if ((mxGPUGetClassID(m_sarray) != mxSINGLE_CLASS)) {
mexPrintf("m_sarray\n");
mexErrMsgIdAndTxt(errId, errMsg);
}
// write results directly to the output array
mxGPUArray * m_larray = const_cast<mxGPUArray*>(mxGPUCreateFromMxArray(prhs[0])); // mxGPUCopyFromMxArray(prhs[1]);
if ((mxGPUGetClassID(m_larray) != mxSINGLE_CLASS)) {
mexPrintf("m_larray\n");
mexErrMsgIdAndTxt(errId, errMsg);
}
if (mxGPUGetComplexity(m_larray) != mxCOMPLEX) {
mexPrintf("m_larray complexity has to be the COMPLEX \n");
mexErrMsgIdAndTxt(errId, errMsg);
}
if (mxGPUGetComplexity(m_larray) != mxGPUGetComplexity(m_sarray)) {
mexPrintf("m_larray and m_sarray complexity has to be the same \n");
mexErrMsgIdAndTxt(errId, errMsg);
}
const mxGPUArray * m_ind = mxGPUCreateFromMxArray(prhs[2]);
if ((mxGPUGetClassID(m_ind) != mxUINT16_CLASS)) {
mexPrintf("m_ind\n");
mexErrMsgIdAndTxt(errId, errMsg);
}
const uint16_T * p_ind = (uint16_T *)mxGPUGetDataReadOnly(m_ind);
// Get dimension of probe and object
const unsigned int Ndims = (unsigned int)mxGPUGetNumberOfDimensions(m_sarray);
const mwSize * Np_l = mxGPUGetDimensions(m_larray);
const mwSize * Np_s = mxGPUGetDimensions(m_sarray);
const unsigned int Npos = mxGPUGetNumberOfElements(m_ind);
if (Ndims == 3 && Npos > Np_s[2]) {
printf("wrong size of update / positions %i", Ndims);
mexErrMsgIdAndTxt("MexError:ptycho","wrong size of update / positions");
}
cudaMemcpyToSymbol(gC_ind, p_ind, Npos*sizeof(uint16_T), 0, cudaMemcpyHostToDevice);
checkLastError("after cudaMemcpyToSymbol pos");
// Choose a reasonably sized number of threads in each dimension for the block.
int const threadsPerBlockEachDim = 32;
// Compute the thread block and grid sizes based on the board dimensions.
int const blocksPerGrid_M = (Np_s[0] + threadsPerBlockEachDim - 1) / threadsPerBlockEachDim;
int const blocksPerGrid_N = (Np_s[1] + threadsPerBlockEachDim - 1) / threadsPerBlockEachDim;
int const blocksPerGrid_O = 1;
dim3 const dimBlock(blocksPerGrid_M, blocksPerGrid_N, blocksPerGrid_O);
dim3 const dimThread(threadsPerBlockEachDim, threadsPerBlockEachDim, 1);
checkLastError("after dimThread");
checkLastError("after cudaMemcpyToSymbol");
// ================== call the right kernel ===================
const float2 * p_sarray = (float2 *)mxGPUGetDataReadOnly(m_sarray);
float2 * p_larray = (float2 *)mxGPUGetData(m_larray);
addToArray_c<<<dimBlock, dimThread>>>(p_sarray,p_larray, Np_l[0],Np_l[1], Npos);
checkLastError("after kernel");
mxGPUDestroyGPUArray(m_larray);
mxGPUDestroyGPUArray(m_ind);
cudaThreadSynchronize();
// plhs[0] = mxGPUCreateMxArrayOnGPU(m_larray);
mxGPUDestroyGPUArray(m_sarray);
return;
}