swim/fold_slice
1
0
Fork 0
mirror of https://github.com/c-sooyoung/fold_slice.git synced 2026-09-17 20:39:08 +09:00
Code Issues Packages Projects Releases Wiki Activity

initial commit

Browse Source
This commit is contained in:
swim
2026-08-07 15:56:42 +09:00
commit 91ad25aca9
1012 changed files with 159314 additions and 0 deletions
Download Patch File Download Diff File Expand all files Collapse all files
ptycho/+engines/+ML_MS/calc_ms_err.c
+169
View File
@@ -0,0 +1,169 @@
/* Compile from matlab with:
mex -largeArrayDims 'CFLAGS="\$CFLAGS -std=c99 -fopenmp"' LDFLAGS="\$LDFLAGS -fopenmp" -lmkl_core -lmkl_intel_ilp64 -lmkl_sequential -lmkl_avx2 calc_ms_err.c
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 cSAXS
ptychography MATLAB package 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 cSAXS ptychography MATLAB 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 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 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).
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.
*/
#include "mex.h"
#include <mkl.h>
#include <omp.h>
void mexFunction(int n_out, mxArray *p_out[], int n_in, const mxArray *p_in[])
{
// read input values
MKL_Complex16 *xopt = (MKL_Complex16 *) mxGetData(p_in[0]);
size_t num_objs = (size_t) mxGetScalar(p_in[1]); // can be either 1 or 2
size_t num_slices = (size_t) mxGetScalar(p_in[2]);
size_t obj_rows = (size_t) mxGetScalar(p_in[3]);
size_t obj_cols = (size_t) mxGetScalar(p_in[4]);
size_t scan_num = mxGetM(p_in[5]);
size_t *scan_pos_row = (size_t *) mxGetData(p_in[5]);
size_t *scan_pos_col = (size_t *) mxGetData(p_in[6]);
size_t scan_rows = (size_t) mxGetScalar(p_in[7]);
size_t scan_cols = (size_t) mxGetScalar(p_in[8]);
MKL_Complex16 *prop = (MKL_Complex16 *) mxGetData(p_in[9]);
double fnorm_inv = mxGetScalar(p_in[10]);
double dz = mxGetScalar(p_in[11]);
char *fmask = (char *) mxGetData(p_in[12]);
double *fmag = mxGetPr(p_in[13]);
// Decompose xopt into object slices and a probe
size_t i, j;
MKL_Complex16 *obj[num_objs][num_slices];
for (i = 0; i < num_objs; i++) {
for (j = 0; j < num_slices; j++) {
obj[i][j] = xopt + (i*num_slices+j)*obj_rows*obj_cols;
}
}
MKL_Complex16 *probe = xopt+(num_objs*num_slices)*obj_rows*obj_cols;
// arrange FFT descriptor
DFTI_DESCRIPTOR_HANDLE desc_handle;
MKL_LONG l[2];
l[0] = scan_rows; l[1] = scan_cols;
DftiCreateDescriptor(&desc_handle, DFTI_DOUBLE, DFTI_COMPLEX, 2, l);
DftiSetValue(desc_handle, DFTI_COMPLEX_STORAGE, DFTI_COMPLEX_COMPLEX);
DftiSetValue(desc_handle, DFTI_BACKWARD_SCALE, 1./(scan_rows*scan_cols));
DftiCommitDescriptor(desc_handle);
// calculate error
double err = 0.0;
size_t ind_obj, ind_scan;
#pragma omp parallel private(j, ind_obj, ind_scan) reduction(+:err)
{
MKL_Complex16 *obj_s0, *obj_s1;
MKL_Complex16 *temp = (MKL_Complex16 *) mkl_malloc(scan_rows*scan_cols*sizeof(MKL_Complex16), 64);
double *buff = (double *) mkl_malloc(scan_rows*scan_cols*sizeof(double), 64);
// loop over beam positions
#pragma omp for
for (i = 0; i < scan_num; i++) {
ind_obj = scan_pos_col[i]*obj_rows + scan_pos_row[i];
ind_scan = i*scan_rows*scan_cols;
if (num_objs == 1) {
obj_s0 = obj[0][0];
obj_s1 = obj[0][1];
} else {
obj_s0 = (i < scan_num/2) ? obj[0][0] : obj[1][0];
obj_s1 = (i < scan_num/2) ? obj[0][1] : obj[1][1];
}
for (j = 0; j < scan_cols; j++) {
vzMul(scan_rows, &obj_s0[ind_obj+j*obj_rows], &probe[j*scan_rows], &temp[j*scan_rows]);
}
if (dz != 0) {
DftiComputeForward(desc_handle, temp);
vzMul(scan_rows*scan_cols, temp, prop, temp);
DftiComputeBackward(desc_handle, temp);
}
for (j = 0; j < scan_cols; j++) {
vzMul(scan_rows, &temp[j*scan_rows], &obj_s1[ind_obj+j*obj_rows], &temp[j*scan_rows]);
}
DftiComputeForward(desc_handle, temp);
vzAbs(scan_rows*scan_cols, temp, buff);
for (j = 0; j < scan_rows*scan_cols; j++) {
buff[j] = buff[j]*fnorm_inv-fmag[ind_scan+j];
err += fmask[ind_scan+j]*buff[j]*buff[j];
}
}
mkl_free(temp);
mkl_free(buff);
}
DftiFreeDescriptor(&desc_handle);
mkl_free_buffers();
// create output stack of slices
p_out[0] = mxCreateNumericMatrix(1, 1, mxDOUBLE_CLASS, mxREAL);
double *out = mxGetPr(p_out[0]);
*out = err;
}
ptycho/+engines/+ML_MS/calc_ms_grad.c
+299
View File
@@ -0,0 +1,299 @@
/* Compile from matlab with:
mex -largeArrayDims 'CFLAGS="\$CFLAGS -std=c99 -fopenmp"' LDFLAGS="\$LDFLAGS -fopenmp" -lmkl_core -lmkl_intel_ilp64 -lmkl_sequential -lmkl_avx2 calc_ms_grad.c
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 cSAXS
ptychography MATLAB package 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 cSAXS ptychography MATLAB 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 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 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).
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.
*/
#include "mex.h"
#include <mkl.h>
#include <omp.h>
void mexFunction(int n_out, mxArray *p_out[], int n_in, const mxArray *p_in[])
{
// read input values
MKL_Complex16 *xopt = (MKL_Complex16 *) mxGetData(p_in[0]);
size_t num_objs = (size_t) mxGetScalar(p_in[1]); // can be either 1 or 2
size_t num_slices = (size_t) mxGetScalar(p_in[2]);
size_t obj_rows = (size_t) mxGetScalar(p_in[3]);
size_t obj_cols = (size_t) mxGetScalar(p_in[4]);
size_t scan_num = mxGetM(p_in[5]);
size_t *scan_pos_row = (size_t *) mxGetData(p_in[5]);
size_t *scan_pos_col = (size_t *) mxGetData(p_in[6]);
size_t scan_rows = (size_t) mxGetScalar(p_in[7]);
size_t scan_cols = (size_t) mxGetScalar(p_in[8]);
size_t scan_size = scan_rows*scan_cols;
MKL_Complex16 *prop = (MKL_Complex16 *) mxGetData(p_in[9]);
MKL_Complex16 *prop_der = (MKL_Complex16 *) mxGetData(p_in[10]);
double fnorm_inv = mxGetScalar(p_in[11]);
double dz = mxGetScalar(p_in[12]);
char *fmask = (char *) mxGetData(p_in[13]);
double *fmag = mxGetPr(p_in[14]);
double opt_dz = mxGetScalar(p_in[15]);
// Decompose xopt into object slices and a probe
size_t i, j;
MKL_Complex16 *obj[num_objs][num_slices];
for (i = 0; i < num_objs; i++) {
for (j = 0; j < num_slices; j++) {
obj[i][j] = xopt + (i*num_slices+j)*obj_rows*obj_cols;
}
}
MKL_Complex16 *probe = xopt+(num_objs*num_slices)*obj_rows*obj_cols;
// allocate output gradients
size_t cell_size[] = {num_objs, 1, num_slices}; // single mode obj
p_out[1] = mxCreateCellArray(3, cell_size);
mxArray *temp_ptr;
double *grad_obj_r[num_objs][num_slices];
double *grad_obj_i[num_objs][num_slices];
for (i = 0; i < num_objs; i++) {
for (j = 0; j < num_slices; j++) {
temp_ptr = mxCreateNumericMatrix(obj_rows, obj_cols, mxDOUBLE_CLASS, mxCOMPLEX);
mxSetCell(p_out[1], i*num_slices+j, temp_ptr);
grad_obj_r[i][j] = mxGetPr(temp_ptr);
grad_obj_i[i][j] = mxGetPi(temp_ptr);
}
}
p_out[2] = mxCreateNumericMatrix(scan_rows, scan_cols, mxDOUBLE_CLASS, mxCOMPLEX);
double *grad_probe_r = mxGetPr(p_out[2]);
double *grad_probe_i = mxGetPi(p_out[2]);
p_out[3] = mxCreateNumericMatrix(1, 1, mxDOUBLE_CLASS, mxREAL);
double *grad_z = mxGetPr(p_out[3]);
// arrange FFT descriptor
DFTI_DESCRIPTOR_HANDLE desc_handle;
MKL_LONG l[2];
l[0] = scan_rows; l[1] = scan_cols;
DftiCreateDescriptor(&desc_handle, DFTI_DOUBLE, DFTI_COMPLEX, 2, l);
DftiSetValue(desc_handle, DFTI_COMPLEX_STORAGE, DFTI_COMPLEX_COMPLEX);
DftiSetValue(desc_handle, DFTI_BACKWARD_SCALE, 1./scan_size);
DftiCommitDescriptor(desc_handle);
// calculate error and gradients
double err = 0.0, gradz_temp = 0.0;
size_t ind_obj, ind_scan, k;
#pragma omp parallel private(j, k, ind_obj, ind_scan) reduction(+:err,gradz_temp)
{
MKL_Complex16 *obj_s0, *obj_s1;
double *grad_obj_s0_r, *grad_obj_s0_i, *grad_obj_s1_r, *grad_obj_s1_i;
MKL_Complex16 *incident = (MKL_Complex16 *) mkl_malloc(scan_size*sizeof(MKL_Complex16), 64);
MKL_Complex16 *psiq = (MKL_Complex16 *) mkl_malloc(scan_size*sizeof(MKL_Complex16), 64);
MKL_Complex16 *psiq_der = (MKL_Complex16 *) mkl_malloc(scan_size*sizeof(MKL_Complex16), 64);
MKL_Complex16 *chi = (MKL_Complex16 *) mkl_malloc(scan_size*sizeof(MKL_Complex16), 64);
MKL_Complex16 *grado_temp = (MKL_Complex16 *) mkl_malloc(scan_size*sizeof(MKL_Complex16), 64);
double *buff = (double *) mkl_malloc(scan_size*sizeof(double), 64);
double *coeff = (double *) mkl_malloc(scan_size*sizeof(double), 64);
// loop over beam positions
#pragma omp for
for (i = 0; i < scan_num; i++) {
ind_obj = scan_pos_col[i]*obj_rows + scan_pos_row[i];
ind_scan = i*scan_size;
if (num_objs == 1) {
obj_s0 = obj[0][0];
obj_s1 = obj[0][1];
} else {
obj_s0 = (i < scan_num/2) ? obj[0][0] : obj[1][0];
obj_s1 = (i < scan_num/2) ? obj[0][1] : obj[1][1];
}
for (j = 0; j < scan_cols; j++) {
vzMul(scan_rows, &probe[j*scan_rows], &obj_s0[ind_obj+j*obj_rows], &psiq[j*scan_rows]);
}
if (dz != 0) {
DftiComputeForward(desc_handle, psiq);
vzMul(scan_size, psiq, prop, incident);
DftiComputeBackward(desc_handle, incident);
} else {
cblas_zcopy(scan_size, psiq, 1, incident, 1);
}
for (j = 0; j < scan_cols; j++) {
vzMul(scan_rows, &incident[j*scan_rows], &obj_s1[ind_obj+j*obj_rows], &psiq[j*scan_rows]);
}
DftiComputeForward(desc_handle, psiq);
vzAbs(scan_size, psiq, buff);
for (j = 0; j < scan_size; j++) {
coeff[j] = fmask[ind_scan+j]*(1.0-fmag[ind_scan+j]/(buff[j]*fnorm_inv));
chi[j].real = coeff[j]*psiq[j].real;
chi[j].imag = coeff[j]*psiq[j].imag;
buff[j] = buff[j]*fnorm_inv-fmag[ind_scan+j];
err += fmask[ind_scan+j]*buff[j]*buff[j];
}
DftiComputeBackward(desc_handle, chi);
if (num_objs == 1) {
grad_obj_s0_r = grad_obj_r[0][0];
grad_obj_s0_i = grad_obj_i[0][0];
grad_obj_s1_r = grad_obj_r[0][1];
grad_obj_s1_i = grad_obj_i[0][1];
} else {
grad_obj_s0_r = (i < scan_num/2) ? grad_obj_r[0][0] : grad_obj_r[1][0];
grad_obj_s0_i = (i < scan_num/2) ? grad_obj_i[0][0] : grad_obj_i[1][0];
grad_obj_s1_r = (i < scan_num/2) ? grad_obj_r[0][1] : grad_obj_r[1][1];
grad_obj_s1_i = (i < scan_num/2) ? grad_obj_i[0][1] : grad_obj_i[1][1];
}
vzMulByConj(scan_size, chi, incident, grado_temp);
for (j = 0; j < scan_cols; j++) {
for (k = 0; k < scan_rows; k++) {
#pragma omp atomic
grad_obj_s1_r[ind_obj+j*obj_rows+k] += 2*grado_temp[j*scan_rows+k].real;
#pragma omp atomic
grad_obj_s1_i[ind_obj+j*obj_rows+k] += 2*grado_temp[j*scan_rows+k].imag;
}
vzMulByConj(scan_rows, &chi[j*scan_rows], &obj_s1[ind_obj+j*obj_rows], &chi[j*scan_rows]);
}
if (dz != 0) {
DftiComputeForward(desc_handle, chi);
vzMulByConj(scan_size, chi, prop, chi);
DftiComputeBackward(desc_handle, chi);
}
vzMulByConj(scan_size, chi, probe, grado_temp);
for (j = 0; j < scan_cols; j++) {
for (k = 0; k < scan_rows; k++) {
#pragma omp atomic
grad_obj_s0_r[ind_obj+j*obj_rows+k] += 2*grado_temp[j*scan_rows+k].real;
#pragma omp atomic
grad_obj_s0_i[ind_obj+j*obj_rows+k] += 2*grado_temp[j*scan_rows+k].imag;
}
vzMulByConj(scan_rows, &chi[j*scan_rows], &obj_s0[ind_obj+j*obj_rows], &chi[j*scan_rows]);
for (k = 0; k < scan_rows; k++) {
#pragma omp atomic
grad_probe_r[j*scan_rows+k] += 2*chi[j*scan_rows+k].real;
#pragma omp atomic
grad_probe_i[j*scan_rows+k] += 2*chi[j*scan_rows+k].imag;
}
}
if (opt_dz != 0) {
for (j = 0; j < scan_cols; j++) {
vzMul(scan_rows, &probe[j*scan_rows], &obj_s0[ind_obj+j*obj_rows], &psiq_der[j*scan_rows]);
}
DftiComputeForward(desc_handle, psiq_der);
if (dz != 0) {
vzMul(scan_size, psiq_der, prop, psiq_der);
}
vzMul(scan_size, psiq_der, prop_der, psiq_der);
DftiComputeBackward(desc_handle, psiq_der);
for (j = 0; j < scan_cols; j++) {
vzMul(scan_rows, &psiq_der[j*scan_rows], &obj_s1[ind_obj+j*obj_rows], &psiq_der[j*scan_rows]);
}
DftiComputeForward(desc_handle, psiq_der);
vzMulByConj(scan_size, psiq_der, psiq, psiq_der);
for (j = 0; j < scan_size; j++) {
gradz_temp += coeff[j]*psiq_der[j].real;
}
}
}
mkl_free(incident);
mkl_free(psiq);
mkl_free(psiq_der);
mkl_free(chi);
mkl_free(grado_temp);
mkl_free(buff);
mkl_free(coeff);
}
DftiFreeDescriptor(&desc_handle);
mkl_free_buffers();
// create output and assign it to err value
p_out[0] = mxCreateNumericMatrix(1, 1, mxDOUBLE_CLASS, mxREAL);
double *out = mxGetPr(p_out[0]);
*out = err;
*grad_z = 2*gradz_temp*fnorm_inv*fnorm_inv;
}
ptycho/+engines/+ML_MS/fun_ramp_unwrap.m
+129
View File
@@ -0,0 +1,129 @@
% This function (1) removes ramp and (2) unwrap
% 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 cSAXS
% ptychography MATLAB package 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 cSAXS ptychography MATLAB 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 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 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).
% 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 object_phase_unwrap = fun_ramp_unwrap(object, asize)
import utils.auto_mask_find
import utils.goldsteinunwrap2
import utils.remove_linear_phase_smart
deltax = asize(1)/2; % From edge of region to edge of image in x
rx = [1+deltax : size(object,2)-deltax];
ry = [asize(1)/2-50 : size(object,1)-asize(1)/2+50]; % Range in y
%% Remove ramp
%%%%%%%%%% Tweak automask parameters %%%%%%%%%%
smoothing = 25; % Size of smoothing window
gradientrange = 4; % Range of the phase gradient taken. In units of histogram bins
close_size = 15; % Size of closing window, removes dark bubbles from the mask ( = 1 for no effect)
open_size = 110; % Size of opening window, removes bright bubbles from mask ( = 1 for no effect)
sidex = deltax*4;
maskzero_columnrange = [1+sidex : size(object,2)-sidex]; % Columns to be forced so the mask is zero. e.g. = [200:500], could be useful for middle of cylinders
show_bivariate = 0; % Show the gradient bivariate histogram, input figure here
flag_plot = 1;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
pixel = [deltax+5,ry(end)-5];
mask1 = auto_mask_find(object,'margin',asize/2,'smoothing',smoothing,...
'gradientrange',gradientrange,'close_size',close_size,'open_size',open_size,'show_bivariate',show_bivariate,'zero_columns',maskzero_columnrange);
close;
[object ph_err] = remove_linear_phase_smart(object,'mask',mask1);
object_phase = angle(object);
object_size = size(object);
if flag_plot
figure(2017); clf
subplot(2,2,1);
imagesc(angle(object).*mask1);
axis xy equal tight
colormap bone
title('auto mask');
subplot(2,2,2);
absob = angle(object);
% imagesc(([1 object_size(2)]-floor(object_size(2)/2)+1)*dx_spec(2)*1e6,([1 object_size(1)]-floor(object_size(1)/2)+1)*dx_spec(1)*1e6,absob);
imagesc(absob);
axis xy equal tight
colormap bone
subplot(2,2,[3 4]);
line_mid = floor(size(object,1)/2);
plot(angle(object(line_mid,:))); grid on;
title(sprintf('Line %d profile',line_mid))
xlabel('\mum')
ylabel('\mum')
set(gca,'fontsize',10,'fontweight','bold');
end
%% Unwrap
sel = object_phase(ry,rx);
%sel_unwrap=unwrap(sel,[],2); % Matlab's routine, fast but problematic
%with noise
sel_unwrap=goldsteinunwrap2(sel,0); % Goldstein's method, very robust (gets slow if there are residues)
img_unwrap=object_phase;
img_unwrap(ry,rx) = sel_unwrap;
img_unwrap(ry,rx) = img_unwrap(ry,rx) - 2*pi*round(img_unwrap(pixel(2),pixel(1))/(2*pi));
object_phase_unwrap = img_unwrap;
fprintf('-- Done removing ramp and unwrapping.\n');
ptycho/+engines/+ML_MS/gradient_ptycho_MS.m
+350
View File
@@ -0,0 +1,350 @@
% This function is intended to be only a distributor for either only 'func', or 'func' and
% 'grad' calculation.
% 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 cSAXS
% ptychography MATLAB package 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 cSAXS ptychography MATLAB 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 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 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).
% 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 [func, grad, p] = gradient_ptycho_MS(xopt,p,fmag,fmag2,fmask,...
numobjs,object_size,numprobs,numscans,scanindexrange,initialerror,...
fnorm,probe_mask,errtitlestring,plot_mask,plot_ind,creg,smooth_gradient)
import utils.fract_hanning
import utils.fract_hanning_pad
import utils.verbose
% if p.object_modes ~= 1 || p.probe_modes ~= 1 || numprobs ~= 1 || numobjs ~= 2 || ...
% p.share_object || p.N_layer ~= 2 || ...
% p.ms_opt_flags_local(1) ~= 1 || p.ms_opt_flags_local(2) ~= 1 || ~strcmpi(p.opt_errmetric, 'l1')
% error(['Only double layer single-modes object/single-probe calculations are currently supported. ', ...
% 'E.g. N_layer = 2, numobjs = 2, numprobs = 1, p.object_modes = 1, p.probe_modes = 1, ', ...
% 'p.share_object = false, p.share_probe = true, p.ms_opt_flags_local(1) = true, ', ...
% 'p.ms_opt_flags_local(2) = true, p.opt_errmetric = l1'])
% end
if nargout == 1
% calculate only the error metric 'func'
func = feval(@ptycho_MS_err,xopt,p,fmag,fmag2,fmask,...
numobjs,object_size,numprobs,numscans,scanindexrange,initialerror,...
fnorm,probe_mask,errtitlestring,plot_mask,plot_ind,creg,smooth_gradient);
grad = [];
else
% calculate the error metric 'func' *and* gradients 'grad'
[func, grad] = feval(@ptycho_MS_grad,xopt,p,fmag,fmag2,fmask,...
numobjs,object_size,numprobs,numscans,scanindexrange,initialerror,...
fnorm,probe_mask,errtitlestring,plot_mask,plot_ind,creg,smooth_gradient);
end
end
function func = ptycho_MS_err(xopt,p,fmag,fmag2,fmask,...
numobjs,object_size,numprobs,numscans,scanindexrange,initialerror,...
fnorm,probe_mask,errtitlestring,plot_mask,plot_ind,creg,smooth_gradient)
import utils.fract_hanning
import utils.fract_hanning_pad
import utils.verbose
N_layer = p.N_layer;
if p.ms_opt_flags_local(3)
delta_z = xopt(end-N_layer+2:end);
else
delta_z = p.delta_z;
end
% Precalculate 'prop' and 'derivative_prop' values
k = 2*pi/p.lambda;
prop_der = 1i * k * sqrt(1-(p.lambda*p.Fx).^2-(p.lambda*p.Fy).^2);
prop = cell(1, N_layer-1);
for n = 1:N_layer-1
prop{n} = exp(delta_z(n)*prop_der);
end
prop = reshape([real(prop{1}(:)).'; imag(prop{1}(:)).'], [], 1);
asize = p.asize;
positions = p.positions;
fmask = logical(fmask); % the mex functions does not check data type!
func = engines.ML_MS.calc_ms_err(xopt, numobjs, N_layer, object_size(1,1), object_size(1,2), ...
uint64(positions(1:end, 1)), uint64(positions(1:end, 2)), asize(1), asize(2), ...
prop, 1/fnorm, delta_z, fmask, fmag);
func = func + initialerror;
%verbose(2, ['(Before regul.) Error = ' num2str(func, 20)])
%%% Object regularization %%%
% Normalized regularization to avoid the reduction of object amplitudes
% with the setting of intensity invariant
if (creg > 0) && p.ms_opt_flags_local(1)
last_ind = 0;
for obnum = 1:numobjs
o_size = object_size(obnum, :);
o_numel = prod(o_size);
for obmode = 1:p.object_modes
for n = 1:N_layer %% unused??
ob = reshape(xopt(last_ind+1:2:last_ind+2*o_numel), o_size) + ...
1i*reshape(xopt(last_ind+2:2:last_ind+2*o_numel), o_size);
last_ind = last_ind+2*o_numel;
R = sum(sum(abs(diff(ob, 1, 1)).^2)) + sum(sum(abs(diff(ob, 1, 2)).^2)) - ...
sum(abs(diff(ob(:,end), 1, 1)).^2) - sum(abs(diff(ob(end,:), 1, 2)).^2);
norm_r = sum(sum(abs(ob).^2));
func = func + creg*R/norm_r;
end
end
end
end
verbose(2, ['delta_z = ' num2str(delta_z*1e6,7) ' um, Error = ' num2str(func)]);
end
function [func, grad] = ptycho_MS_grad(xopt,p,fmag,fmag2,fmask,...
numobjs,object_size,numprobs,numscans,scanindexrange,initialerror,...
fnorm,probe_mask,errtitlestring,plot_mask,plot_ind,creg,smooth_gradient)
import utils.verbose
import utils.fract_hanning
import utils.fract_hanning_pad
optimize_object_layer = p.ms_opt_flags_local(1);
optimize_probes = p.ms_opt_flags_local(2);
optimize_delta_z = p.ms_opt_flags_local(3);
N_layer = p.N_layer;
if optimize_delta_z
delta_z = xopt(end-N_layer+2:end);
else
delta_z = p.delta_z;
end
verbose(2, 'Computing gradient');
% Precalculate 'prop' and 'derivative_prop' values
k = 2*pi/p.lambda;
prop_der = 1i * k * sqrt(1-(p.lambda*p.Fx).^2-(p.lambda*p.Fy).^2);
prop = cell(1, N_layer-1);
for n = 1:N_layer-1
prop{n} = exp(delta_z(n)*prop_der);
end
prop = reshape([real(prop{1}(:)).'; imag(prop{1}(:)).'], [], 1);
prop_der = reshape([real(prop_der(:)).'; imag(prop_der(:)).'], [], 1);
asize = p.asize;
positions = p.positions;
fmask = logical(fmask); % the mex functions does not check data type!
assert(isa(xopt, 'double'), 'Inputs has to be double')
[func, grado, gradp, gradz] = engines.ML_MS.calc_ms_grad(xopt, numobjs, N_layer, object_size(1,1), object_size(1,2), ...
uint64(positions(:, 1)), uint64(positions(:, 2)), asize(1), asize(2), ...
prop, prop_der, 1/fnorm, delta_z, fmask, fmag, double(optimize_delta_z));
verbose(2, ['(Before regul.) Error = ' num2str(func)])
%%% Sieves preconditioning %%%
if (any(smooth_gradient(:)) ~= 0) && optimize_object_layer
for obnum = 1:numobjs
for obmode = 1:p.object_modes
for n = 1:N_layer
grado{obnum,obmode,n} = conv2(grado{obnum,obmode,n}, smooth_gradient, 'same');
end
end
end
end
%%% Object regularization %%%
% Normalized regularization to avoid the reduction of object amplitudes
% with the setting of intensity invariant
if (creg > 0) && optimize_object_layer
last_ind = 0;
for obnum = 1:numobjs
o_size = object_size(obnum, :);
o_numel = prod(o_size);
for obmode = 1:p.object_modes
for n = 1:N_layer
ob = reshape(xopt(last_ind+1:2:last_ind+2*o_numel), o_size) + ...
1i*reshape(xopt(last_ind+2:2:last_ind+2*o_numel), o_size);
last_ind = last_ind+2*o_numel;
diff1 = diff(ob, 1, 1);
diff2 = diff(ob, 1, 2);
R = sum(sum(abs(diff1).^2)) + sum(sum(abs(diff2).^2)) - ...
sum(abs(diff(ob(:,end), 1, 1)).^2) - sum(abs(diff(ob(end,:), 1, 2)).^2);
norm_r = sum(sum(abs(ob).^2));
func = func + creg*R/norm_r;
diff1 = padarray(diff(diff1, 1, 1), [1, 0]);
diff2 = padarray(diff(diff2, 1, 2), [0, 1]);
diff1(:,1) = 0; diff1(:,end) = 0;
diff2(1,:) = 0; diff2(end,:) = 0;
ob(1,:) = 0; ob(end,:) = 0; ob(:,1) = 0; ob(:,end) = 0;
grado{obnum,obmode,n} = grado{obnum,obmode,n} + 2*creg*(R/norm_r*ob-diff1-diff2);
% -- Update only some roi by setting part of the gradient to 0
if ~isempty(p.ms_grado_roi)
apod = 100;
% mask_apod = fftshift(fract_hanning_pad(ob_dims(1), ob_dims(1)-asize+apod, ob_dims(1)-asize));
temp_grado = grado{obnum,obmode,n}(:,p.ms_grado_roi(1):p.ms_grado_roi(2));
mask_apod = fftshift(fract_hanning_pad(size(temp_grado,2), size(temp_grado,2)-apod*2+apod, size(temp_grado,2)-apod*2));
temp_grado_apod = temp_grado .* mask_apod(round(size(temp_grado,2)/2),:);
grado{obnum,obmode,n} = zeros(size(grado{obnum,obmode,n}));
grado{obnum,obmode,n}(:,p.ms_grado_roi(1):p.ms_grado_roi(2)) = temp_grado_apod;
end
end
end
end
end
if ~optimize_delta_z
core.errorplot(func);
end
iteration = length(core.errorplot([]));
verbose(2, 'Scan %s ; ML_iteration # %d of %d',errtitlestring, iteration, p.ms_opt_iter);
if optimize_delta_z
verbose(2, ['Starting linesearch, delta_z currently ' num2str(delta_z*1e6,5) ' um, Error = ' num2str(func)]);
else
verbose(2, ['Starting linesearch, delta_z fixed at ' num2str(delta_z*1e6,5) ' um, Error = ' num2str(func)]);
end
% if ~isempty(p.ms_grado_roi)
% if 0 %iteration==1 || mod(iteration,10)==0
% save(sprintf('%smatlab/ptycho/temp_grado_it%d.mat', p.base_path, iteration),'temp_grado');
% save(sprintf('%smatlab/ptycho/temp_grado_apod_it%d.mat', p.base_path, iteration),'temp_grado_apod');
% end
% end
%%% Probe support constratint %%%
if p.use_probe_support && optimize_probes
for prnum = 1:numprobs
for prmode = 1:p.probe_modes
gradp(:,:,prnum,prmode) = probe_mask.*gradp(:,:,prnum,prmode);
end
end
end
%%% Scaling preconditioning %%%
avobint = 0;
if p.scale_gradient && optimize_probes
for ii = 1:numscans
for n = 1:N_layer
if p.share_probe
grado_sum = 0;
for obmode = 1:p.object_modes
grado_sum = grado_sum + sum( abs(grado{obnum,obmode,n}(:)).^2 );
end
avobint = avobint + grado_sum;
if ii == numscans
avobint = avobint/numscans;
gradp = sqrt( avobint/sum( abs(gradp(:)).^2 ) )*gradp;
end
else
grado_sum = 0;
for obmode = 1:p.object_modes
grado_sum = grado_sum + sum( abs(grado{obnum,obmode,n}(:)).^2 );
end
gradp(:,:,ii,:) = sqrt(grado_sum / sum(sum(sum( abs(gradp(:,:,ii,:)).^2 )))) * gradp(:,:,ii,:);
end
end
end
end
%%% Arranging gradients vector %%%
if ~any(p.ms_opt_flags)
error('At least one element of flags must be 1');
end
grad = []; % Optimization vector
%figure(1000); clf
if optimize_object_layer
for obnum = 1:numobjs
for obmode = 1:p.object_modes
for n = 1:N_layer
fprintf('sum abs grado{%d,obmode,n%d} = %s \n', obnum, n, num2str(sum(abs(grado{obnum,obmode,n}(:)))) );
grad = [grad; reshape([real(grado{obnum,obmode,n}(:)).'; imag(grado{obnum,obmode,n}(:)).'], [], 1)];
%subplot(N_layer,1,n);
%hold on; plot(abs(grado{obnum,obmode,n}(:)));
%grid on; title(sprintf('Slice %d',n));
%axis tight
%drawnow
end
end
end
end
if optimize_probes
fprintf('sum abs gradp = %s \n', num2str(sum(abs(gradp(:)))));
grad = [grad; reshape([real(gradp(:)).'; imag(gradp(:)).'], [], 1)];
end
if optimize_delta_z
fprintf('sum abs gradz = %s \n', num2str(sum(abs(gradz(:)))));
grad = [grad; gradz(:)];
end
end