swim/fold_slice
1
0
Fork 0
mirror of https://github.com/c-sooyoung/fold_slice.git synced 2026-09-17 19:39:08 +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/+scans/+meta/artificial.m
+100
View File
@@ -0,0 +1,100 @@
%SPEC load meta data from a spec file
% 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 p = artificial(p)
import io.*
import utils.update_param
import utils.verbose
import utils.get_option
%%%%%%%%%%%%%%%%%%%
%%% new params %%%%
%%%%%%%%%%%%%%%%%%%
verbose(3,'- Preparing artificial scan')
%% LOAD DEFAULTS FOR THE SIMULAITON FROM p.artificial_data_file
assert(exist(p.artificial_data_file, 'file')>0, sprintf('Missing file %s\n', p.artificial_data_file))
run(fullfile(p.ptycho_matlab_path, p.artificial_data_file));
% enforce matlab preparator, python is not supported
p.prepare.data_preparator = 'matlab'; % use matlab data preparator
if ~strcmpi(p.detector.name, 'virtual')
p.detector.name = 'virtual'; % 'spec', 'omny' or empty (scan params are defined below)
verbose(2, 'Switching to "virtual" detector to generate artificial data')
end
% avoid legacy
if ~isfield(p.prepare, 'legacy')
p.prepare.legacy = false;
end
if ~isempty(p.scan_number)
assert(length(p.scan_number) == length(p.simulation.dataset ), 'Number of scans does not correspond to number of objects in artificial data template')
else
p.scan_number = 1:length(p.simulation.dataset );
end
p.scan_number = p.scan_number;
% rewrite some parameters by values in artificial_data_template
p.energy = p.simulation.energy;
p.numscans = length(p.simulation.dataset );
end
ptycho/+scans/+meta/spec.m
+121
View File
@@ -0,0 +1,121 @@
%SPEC load meta data from a spec file
% 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 p = spec(p)
import beamline.is_scan_finished
import beamline.is_scan_started
import io.*
import utils.verbose
% Wait for end of scan
for ii=1:numel(p.scan_number)
if isfield(p.spec,'waitforscanfinish')&&p.spec.waitforscanfinish
while ~is_scan_finished(p.specfile,p.scan_number(ii))
disp(p.specfile)
verbose(1, 'Waiting for scan %d to finish', p.scan_number(ii));
pause(0.5);
end
end
if isfield(p.spec,'check_nextscan_started')&&p.spec.check_nextscan_started
while ~is_scan_started(p.specfile,p.scan_number(ii)+1)
verbose(1, 'Waiting for next scan %d to start', p.scan_number(ii)+1);
pause(0.5);
end
end
end
% Spec data for all scans
spec_aux = spec_read(p.specfile,'ScanNr',p.scan_number);
if iscell(spec_aux)
for ii=1:numel(p.scan_number)
p.meta{ii}.spec = spec_aux{ii};
end
else
p.meta{1}.spec = spec_aux;
end
% Determine if its a ptycho scan defined in p.spec.isptycho
if (isfield(p.spec,'isptycho')&&(numel(p.spec.isptycho)>0))
isptycho = 0;
for jj = 1:numel(p.spec.isptycho)
if ~isempty(findstr(p.meta.spec{jj}.S,p.spec.isptycho{jj}))
isptycho = 1;
end
end
if ~isptycho
verbose(1,['Skipping non-ptycho scan, set with p.spec.isptycho']);
out = [];
return
end
end
% energy
if isempty(p.energy)
p.energy = p.meta{1}.spec.mokev;
end
% fourier ptycho - estimated magnification
if isfield(p, 'fourier_ptycho') && p.fourier_ptycho
scan_string = strsplit(p.meta{1}.spec.S, ' ');
if strcmpi(scan_string{3}, 'fermat2_spiral')
p.prealign.mag_est = str2double(scan_string{8})*1e3;
end
end
end
ptycho/+scans/+positions/hdf5_pos.m
+53
View File
@@ -0,0 +1,53 @@
%hdf5_pos loads ptycho scan positions from hdf5 files
%Written by YJ
function [ p ] = hdf5_pos( p )
for ii = 1:p.numscans
switch p.scan.type
case 'default'
pos_file = strcat(p.base_path,sprintf(p.scan.format, p.scan_number(ii)),'/data_roi',p.scan.roi_label,'_para.hdf5');
if exist(pos_file,'file')
ppX = h5read(pos_file,'/ppX');
ppY = h5read(pos_file,'/ppY');
ppX = ppX(:);
ppY = ppY(:);
positions_real = zeros(length(ppX),2);
positions_real(:,1) = -ppY;
positions_real(:,2) = -ppX;
else
disp(strcat(p.base_path,sprintf(p.scan.format, p.scan_number(ii)),'/data_roi',p.scan.roi_label,'_para.hdf5'))
error('Could not find function or data file %s', pos_file);
end
case 'custom'
if ~isempty(p.scan.custom_positions_source) %guess the position file name from base path
pos_file = p.scan.custom_positions_source;
else
error('Position file is not given');
end
try
r_output = load(pos_file,'outputs');
r_p = load(pos_file,'p');
ppX = r_output.outputs.probe_positions(:,1)*r_p.p.dx_spec(1);
ppY = r_output.outputs.probe_positions(:,2)*r_p.p.dx_spec(2);
ppX = ppX(:);
ppY = ppY(:);
positions_real = zeros(length(ppX),2);
positions_real(:,1) = -ppY;
positions_real(:,2) = -ppX;
catch
error('Failed to load positions from %s', pos_file);
end
otherwise
error('Unknown scan type %s.', p.scan.type);
end
utils.verbose(2, strcat('Loaded scan positions from:', pos_file))
p.numpts(ii) = size(positions_real,1);
p.positions_real = [p.positions_real ; positions_real]; %append position
end
end
ptycho/+scans/+positions/hdf5_pos_aps.m
+62
View File
@@ -0,0 +1,62 @@
%hdf5_pos_aps loads APS' data positions from hdf5 files (generated from python
%script)
%Written by YJ
function [ p ] = hdf5_pos_aps( p )
for ii = 1:p.numscans
positions_real = zeros(0,2);
switch p.scan.type
case 'custom'
if isempty(p.scan.custom_positions_source) %guess the position file name from base path
pos_file = strcat(p.base_path,sprintf(p.scan.format, p.scan_number(ii)),'/data_roi',p.scan.roi_label,'_para.hdf5');
else
pos_file = p.scan.custom_positions_source;
end
if exist(pos_file,'file')
ppX = h5read(pos_file,'/ppX');
ppY = h5read(pos_file,'/ppY');
ppX = ppX(:);
ppY = ppY(:);
positions_real = zeros(length(ppX),2);
positions_real(:,1) = -ppY;
positions_real(:,2) = -ppX;
else
disp(strcat(p.base_path,sprintf(p.scan.format, p.scan_number(ii)),'/data_roi',p.scan.roi_label,'_para.hdf5'))
error('Could not find function or data file %s', pos_file);
end
case 'pre_recon'
if ~isempty(p.scan.custom_positions_source) %guess the position file name from base path
pos_file = p.scan.custom_positions_source;
else
error('Position file is not given');
end
try
r_output = load(pos_file,'outputs');
r_p = load(pos_file,'p');
ppX = r_output.outputs.probe_positions(:,1)*r_p.p.dx_spec(1);
ppY = r_output.outputs.probe_positions(:,2)*r_p.p.dx_spec(2);
ppX = ppX(:);
ppY = ppY(:);
positions_real = zeros(length(ppX),2);
positions_real(:,1) = -ppY;
positions_real(:,2) = -ppX;
catch
error('Failed to load positions from %s', pos_file);
end
otherwise
error('Unknown scan type %s.', p.scan.type);
end
utils.verbose(2, strcat('Loaded scan positions from:', pos_file))
%scatter(ppX,ppY,'.');
p.numpts(ii) = size(positions_real,1);
p.positions_real = [p.positions_real ; positions_real]; %append position
end
end
ptycho/+scans/+positions/matlab_pos.m
+146
View File
@@ -0,0 +1,146 @@
%MATLAB_POS calculate scan parameters based on the values set in the
%template
function [ p ] = matlab_pos( p )
for ii = 1:p.numscans
positions_real = zeros(0,2);
switch p.scan.type
case 'raster'
scan_order_x = 1:p.scan.nx;
scan_order_y = 1:p.scan.ny;
% Added by ZC: flip positions similar to eng.custom_data_flip in GPU engines
if isfield(p.scan, 'custom_flip') && any(p.scan.custom_flip)
warning('Applying custom scan flip: %i %i %i ', p.scan.custom_flip(1), p.scan.custom_flip(2), p.scan.custom_flip(3))
if p.scan.custom_flip(1)
scan_order_x = fliplr(scan_order_x);
end
if p.scan.custom_flip(2)
scan_order_y = fliplr(scan_order_y);
end
end
for iy=1:length(scan_order_y) %modified by YJ. seems odd to begin with 0...
for ix=1:length(scan_order_x)
xy = [scan_order_y(iy) * p.scan.step_size_y, scan_order_x(ix) * p.scan.step_size_x] + ...
randn(1,2).*p.scan.step_randn_offset.*[ p.scan.step_size_y, p.scan.step_size_x];
positions_real(end+1,:) = xy; %#ok<AGROW>
end
end
if isfield(p.scan, 'custom_flip') && p.scan.custom_flip(3) % switch x/y by ZC
positions_real=fliplr(positions_real);
end
case 'round'
dr = (p.scan.radius_out - p.scan.radius_in)/ p.scan.nr;
for ir=1:p.scan.nr+1
rr = p.scan.radius_in + ir*dr;
dth = 2*pi / (p.scan.nth*ir);
for ith=0:p.scan.nth*ir-1
th = ith*dth;
xy = rr * [sin(th), cos(th)];
positions_real(end+1,:) = xy; %#ok<AGROW>
end
end
case 'round_roi'
rmax = sqrt((p.scan.lx/2)^2 + (p.scan.ly/2)^2);
nr = 1 + floor(rmax/p.scan.dr);
for ir=1:nr+1
rr = ir*p.scan.dr;
dth = 2*pi / (p.scan.nth*ir);
for ith=0:p.scan.nth*ir-1
th = ith*dth;
xy = rr * [sin(th), cos(th)];
if( abs(xy(1)) >= p.scan.ly/2 || (abs(xy(2)) > p.scan.lx/2) )
continue
end
positions_real(end+1,:) = xy; %#ok<AGROW>
end
end
case 'fermat'
% this should be changed to have the same variable
% conventions as in its spec implementation
phi=2*pi*((1+sqrt(5))/2.) + p.scan.b*pi;
start = 1;
if ~isempty(p.scan.lx)
for ir=start:p.scan.n_max
r=p.scan.step*0.57*sqrt(ir);
if abs(r*sin(ir*phi))> p.scan.ly/2
continue
end
if abs(r*cos(ir*phi))> p.scan.lx/2
continue
end
xy = [r*sin(ir*phi)+p.scan.cenxy(1) r*cos(ir*phi)+p.scan.cenxy(2)];
positions_real(end+1,:) = xy;
end
else
for ir=start:p.scan.n_max
r=p.scan.step*0.57*sqrt(ir);
xy = [r*sin(ir*phi)+p.scan.cenxy(1) r*cos(ir*phi)+p.scan.cenxy(2)];
positions_real(end+1,:) = xy;
end
end
case 'custom' %for PSI's data
fn_splt = strsplit(p.scan.custom_positions_source,'.');
if length(fn_splt)>1
% file already has an extension
ext = fn_splt(end);
if strcmp(ext, 'm')
[~, positions_real, ~] = p.scan.custom_positions_source(p);
elseif strcmp(ext, 'mat')
posi = load(p.scan.custom_positions_source, 'pos');
positions_real = posi.pos;
clear posi;
else
error('File extenstion %s is not supported.', ext)
end
else
% file does not have an extension
if exist([p.scan.custom_positions_source '.m'], 'file')
[~, positions_real, ~] = p.scan.custom_positions_source(p);
elseif exist([p.scan.custom_positions_source '.mat'], 'file')
posi = load(p.scan.custom_positions_source, 'pos');
positions_real = posi.pos;
clear posi;
else
error('Could not find function or data file %s', p.scan.custom_positions_source);
end
end
case 'custom_GPU' %added by YJ for customized GPU engines' output
if ~isempty(p.scan.custom_positions_source) %guess the position file name from base path
pos_file = p.scan.custom_positions_source;
else
error('Position file is not given');
end
try
r_output = load(pos_file,'outputs');
r_p = load(pos_file,'p');
ppX = r_output.outputs.probe_positions(:,1)*r_p.p.dx_spec(1);
ppY = r_output.outputs.probe_positions(:,2)*r_p.p.dx_spec(2);
ppX = ppX(:);
ppY = ppY(:);
positions_real = zeros(length(ppX),2);
positions_real(:,1) = -ppY;
positions_real(:,2) = -ppX;
catch
error('Failed to load positions from %s', pos_file);
end
otherwise
error('Unknown scan type %s.', p.scan.type);
end
p.numpts(ii) = size(positions_real,1);
p.positions_real = [p.positions_real ; positions_real];
end
end
ptycho/+scans/+positions/nexus_soleil.m
+93
View File
@@ -0,0 +1,93 @@
%NEXUS_SOLEIL load motor positions from a nexus file
% 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 p = nexus_soleil(p)
import io.*
% nexus motor - can be defined in template
if ~isfield(p.spec.motor, 'fine_motors') || isempty(p.spec.motor.fine_motors)
p.spec.motor.fine_motors{1} = 'tz4';
p.spec.motor.fine_motors{2} = 'tx4';
end
% PtychoShelves expect motor values in m.
if ~isfield(p.spec.motor, 'fine_motors_scale') || isempty(p.spec.motor.fine_motors_scale)
% scale is 1e-3, assuming that the motor values are in mm
p.spec.motor.fine_motors_scale = [1e-3 1e-3];
end
if numel(p.spec.motor.fine_motors) ~= numel(p.spec.motor.fine_motors_scale)
error('Number of motors and scaling parameters does not match!')
end
for ii = 1:length(p.scan_number)
read_path = p.raw_data_path_full{ii};
[~, files] = find_files(fullfile(read_path, sprintf([p.detector.data_prefix '%05d_*.nxs'], p.scan_number(ii))));
h = h5info(files(1).name);
gName = h.Groups.Name;
h5_path = [gName '/scan_data/'];
pos_temp{1} = io.HDF.hdf5_load(files(1).name, [h5_path p.spec.motor.fine_motors{1}]);
pos_temp{2} = io.HDF.hdf5_load(files(1).name, [h5_path p.spec.motor.fine_motors{2}]);
positions_real = [pos_temp{1}*p.spec.motor.fine_motors_scale(1) pos_temp{2}*p.spec.motor.fine_motors_scale(2)];
p.numpts(ii) = size(positions_real,1);
p.positions_real = [p.positions_real ; positions_real];
end
end
ptycho/+scans/+positions/orchestra.m
+82
View File
@@ -0,0 +1,82 @@
%OMNY Load positions from Orchestra scan file
function [ p ] = orchestra( p )
import beamline.*
import utils.*
if isempty(p.positions_file)
error('OMNY positions file is not specified. Please check p.positions_file in your template.')
end
if ~isfield(p,'angular_correction_setup') || isempty(p.angular_correction_setup)
error('p.angular_correction_setup is not specified. Please check p.angular_correction_setup in your template.')
end
if isfield(p,'omny_interferometer')
error(' p.omny_interferometer is not supported, use p.angular_correction_setup')
end
if ~isfield(p.detector,'burst_frames')||isempty(p.detector.burst_frames)
p.detector.burst_frames = 1;
end
switch lower(p.angular_correction_setup)
case 'omny'
p. orchestra.laser_height=-10.0e-3; % Height of horizontal laser beam on the sphere compared to pin tip (only for p.fromspec='opos_angle', 13.5e-3 for OMNI (not fully tested, better with opos than opos_angle), -10.0e-3 for OMNY)
p. orchestra.mirrdis=-9.0e-3; % Distance mirror-pin tip (only for p.fromspec='opos_angle', 22.0e-3 for OMNI (not fully tested, better with opos than opos_angle), -9.0e-3 for OMNY)
p. orchestra.beam_separation=7.5e-3; % Distance mirror-pin tip (only for p.fromspec='opos_angle', 13.0e-3 for OMNI (not fully tested, better with opos than opos_angle), 7.5e-3 for OMNY)
apply_correction = true;
case 'flomni'
p. orchestra.laser_height=-13.5e-3; % Height of horizontal laser beam on the sphere compared to pin tip (only for p.fromspec='opos_angle', 13.5e-3 for OMNI (not fully tested, better with opos than opos_angle), -10.0e-3 for OMNY)
p. orchestra.mirrdis=-17.4e-3; % Distance mirror-pin tip (only for p.fromspec='opos_angle', 22.0e-3 for OMNI (not fully tested, better with opos than opos_angle), -9.0e-3 for OMNY)
p. orchestra.beam_separation=-16e-3; % Distance mirror-pin tip (only for p.fromspec='opos_angle', 13.0e-3 for OMNI (not fully tested, better with opos than opos_angle), 7.5e-3 for OMNY)
apply_correction = true;
case {'lamni', 'none'}
apply_correction = false;
otherwise
error('Wrong p.angular_correction_setup, choose from ''omny'', ''flomni'',''lamni'',''none'' ')
end
for ii = 1:length(p.scan_number)
p.scan.is_cont = true; % So that burst data is prepared normally rather than integrated
if ~exist(sprintf(p.positions_file,p.scan_number(ii)), 'file' )
error('Missing OMNY specs file %s', sprintf(p.positions_file,p.scan_number(ii)))
end
out_orch = read_omny_pos(sprintf(p.positions_file,p.scan_number(ii)));
if ~isfield(out_orch,'Average_y_st_fzp') || ~isfield(out_orch,'Average_x_st_fzp')
out_orch.Average_y_st_fzp = out_orch.Average_y;
out_orch.Average_x_st_fzp = out_orch.Average_x;
end
if ~isfield(out_orch, 'Average_rotz_st')
apply_correction =false;
end
if ~apply_correction
if isfield(out_orch, 'Average_y_st_fzp')
positions_real = [out_orch.Average_y_st_fzp*1e-6 out_orch.Average_x_st_fzp*1e-6];
else % outdated position format
positions_real = [out_orch.Average_y*1e-6 out_orch.Average_x*1e-6];
end
else
deltax = p.orchestra.laser_height*out_orch.Average_rotz_st*1e-6/p.orchestra.beam_separation; % p.orchestra.beam_separation: separation between two laser beams for angular measurement
% p.orchestra.laser_height: height of horizontal laser beam on the sphere compared to pin tip
deltay = p.orchestra.mirrdis*out_orch.Average_rotz_st*1e-6/p.orchestra.beam_separation; % p.orchestra.beam_separation: separation between two laser beams for angular measurement
% p.orchestra.mirrdis dist mirror-pin tip
posx = out_orch.Average_x_st_fzp*1e-6 - deltax;
posy = out_orch.Average_y_st_fzp*1e-6 - deltay;
positions_real = [posy posx];
end
p.numpts(ii) = size(positions_real,1)*p.detector.burst_frames;
positions_tmp = zeros(p.numpts(ii), 2);
positions_tmp(:,1) = reshape(repmat(positions_real(:,1)',[p.detector.burst_frames 1]),[],1);
positions_tmp(:,2) = reshape(repmat(positions_real(:,2)',[p.detector.burst_frames 1]),[],1);
p.positions_real = [p.positions_real ; positions_tmp];
%size(p.positions_real)
end
end
ptycho/+scans/+positions/spec.m
+143
View File
@@ -0,0 +1,143 @@
%SPEC load motor positions from spec
% 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 p = spec(p)
import io.*
import utils.verbose
% make sure that spec data is available
if ~isfield(p.meta, 'spec')
spec_aux = spec_read(p.specfile,'ScanNr',p.scan_number);
if iscell(spec_aux)
for ii=1:numel(p.scan_number)
p.meta{ii}.spec = spec_aux{ii};
end
else
p.meta{1}.spec = spec_aux;
end
end
% check for continuous scans
for ii=1:numel(p.meta)
outspec2 = p.meta{ii}.spec;
if ~isempty(findstr(outspec2.S,'cont_line'))
verbose(2, 'Continuous scan detected')
p.scan.is_cont = true;
end
end
% spec motor - can be defined in template
if isempty(p.spec.motor.fine_motors)
verbose(2, 'Using default fine motor names: px, py')
p.spec.motor.fine_motors{1} = 'py';
p.spec.motor.fine_motors{2} = 'px';
end
% spec motor scaling - can be defined in template
if isempty(p.spec.motor.fine_motors_scale)
p.spec.motor.fine_motors_scale = [1e-6 1e-6];
end
if numel(p.spec.motor.fine_motors) ~= numel(p.spec.motor.fine_motors_scale)
error('Number of spec motors and scaling paramters does not match!')
end
for ii = 1:length(p.scan_number)
if p.scan.is_cont % If its a continuous scan and spec coordinates were requested (checked above)
% For cont_dmesh it needs defined coarse translations on template, piezo for slow axis and anything that
% does not move for fast axis, e.g. p.coarsex = 'samx'; p.coarsey
% = 'py'
% outspec2 = spec_read(p.specfile,'ScanNr',p.scan_number(ii));
% Parse command
remain = p.meta{ii}.spec.S;
for k = 1:4;
[fastmotor, remain] = strtok(remain);
end
[initrange, remain] = strtok(remain);
[finalrange, remain] = strtok(remain);
[numint, remain] = strtok(remain);
verbose(2,['Cont_line in ' fastmotor ' from ' initrange ' to ' finalrange ' in ' numint ' intervals']);
initrangedoub = str2double(initrange);
finalrangedoub = str2double(finalrange);
continterv = str2double(numint);
contstep = (finalrangedoub-initrangedoub)/(continterv+2); % (+2) is a correction for effective smaller interval for continuous scans
% Correction of range for average position in continuous scans
initrangedoub = initrangedoub + contstep/2;
finalrangedoub = finalrangedoub - contstep/2;
contpos = 1e-3*linspace(initrangedoub,finalrangedoub,contstep+1).';
% Note, in the above attempted to compensate for effective
% smaller range in average position of probes in cont scans,
% needs to be further tested
if strcmp(fastmotor,'px')
positions_real(:,2) = contpos;
positions_real(:,1) = 0;
elseif strcmp(fastmotor,'py')
positions_real(:,1) = contpos;
positions_real(:,2) = 0;
end
else
% Use defined spec motors and scaling
positions_real = [p.meta{ii}.spec.(p.spec.motor.fine_motors{1})*p.spec.motor.fine_motors_scale(1) p.meta{ii}.spec.(p.spec.motor.fine_motors{2})*p.spec.motor.fine_motors_scale(2)];
end
p.numpts(ii) = size(positions_real,1);
p.positions_real = [p.positions_real ; positions_real];
end
end
ptycho/+scans/+queue/+check_queue/filelist.m
+131
View File
@@ -0,0 +1,131 @@
%FILELIST Check for file queue
% checks for mat/dat files
% ** p p structure
%
% returns:
% ++ p p structure
% ++ status_ok status flag
%
% see also: scans.get_queue
% 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 [ p, status_ok ] = filelist(p)
import utils.verbose
p.queue.path = utils.abspath(p.queue.path);
% Prepare folders for queue if not done yet
if ~exist(fullfile(p.queue.path,'in_progress'))
mkdir(fullfile(p.queue.path,'in_progress'));
end
if ~exist(fullfile(p.queue.path,'failed'))
mkdir(fullfile(p.queue.path,'failed'));
end
fext = 'dat';
status_ok = true;
verbose(1,['p.queue.path is active, touching folder and looking for files in the queue in ' p.queue.path]);
[status, result] = system(['touch ' p.queue.path '.'], '-echo');
files_recons = dir([p.queue.path 'scan*.dat']);
if isempty(files_recons)
files_recons = dir(fullfile(p.queue.path,'*.mat'));
fext = 'mat';
end
% Now move this file to another folder
% Found one file to reconstruct
if ~isempty(files_recons)
if p.queue.recon_latest_first
p.queue.file_this_recons = files_recons(end).name;
else
p.queue.file_this_recons = files_recons(1).name;
end
verbose(1,['Found file in queue ' fullfile(p.queue.path,p.queue.file_this_recons)]);
% now move it quickly before someone else will take it
try
io.movefile_fast(fullfile(p.queue.path,p.queue.file_this_recons),fullfile(p.queue.path,'in_progress'))
verbose(1,['Moving file to ' fullfile(p.queue.path,'in_progress')]);
catch
verbose(1,['Failed moving file to ' fullfile(p.queue.path,'in_progress')]);
pause(1);
status_ok = false;
end
% and finally parse the file
verbose(2,['Parsing file ' fullfile(p.queue.path,p.queue.file_this_recons)]);
p = parse_queue_file(fullfile(p.queue.path,'in_progress',p.queue.file_this_recons),p, fext);
verbose(2,['Succesfully parsed file ' fullfile(p.queue.path,p.queue.file_this_recons)]);
else
verbose(1,'Did not find enough files in queue, pausing %gs seconds and then exiting', p.queue.file_queue_timeout)
pause(p.queue.file_queue_timeout)
status_ok = false;
end
end
ptycho/+scans/+queue/+check_queue/private/parse_queue_file.m
+140
View File
@@ -0,0 +1,140 @@
% p = ptycho_parse_omny_dat(filename,p)
% It parses dat files from queue to modify a ptychography
% p.structure. This allows for instance to change the scan number or
% another field. It also allows to define fields that do not exist.
% Inputs
% filename Filename with path of the dat file
% p Optional input, if it is given the output will be equal to p
% in all fields that are not modified
% Output
% p_out Structure with new, or modified fields.
% 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 p_out = parse_queue_file(filename,p, fext)
import utils.update_param
if nargin < 1
error('At least one argument, filename, should be given')
return
end
if exist('p')
if ~isstruct(p)
error('Second argument, p, must be a structure')
return
else
p_out = p;
end
else
p_out = struct;
end
if ~exist(filename,'file')
warning(sprintf('I did not find the file: %s. Output structure will be then the same as input structure', filename))
return
end
switch fext
case 'dat'
fid = fopen(filename,'r');
tline = fgetl(fid);
while ischar(tline)
str_parts = strsplit(tline, ' ');
if numel(str_parts)>1
fname = strtrim(str_parts{1});
if strcmpi(fname(1:2), 'p.')
% found p entry
val = [];
for ii=2:numel(str_parts)
if ~isempty(strtrim(str_parts{ii}))
if ~isnan(str2double(str_parts{ii}))
% found number
val = [val, str2double(str_parts{ii})];
else
% found char
val = [val, strtrim(str_parts{ii})];
end
end
end
p_out.(fname(3:end)) = val;
elseif strcmpi(str_parts{1}, 'samplename')
p_out.samplename = strjoin(strtrim(str_parts(2:end)), '_');
% keep only printable chars (prevent users to fill put unicode characters)
p_out.samplename = p_out.samplename(isstrprop(p_out.samplename, 'print'));
% remove spaces from the file name
p_out.samplename = replace(p_out.samplename, ' ', '_');
end
end
tline = fgetl(fid);
end
fclose(fid);
case 'mat'
% load mat file and make sure that the paths are updated correctly
f = load(filename);
p = update_param(p, f.p);
p_out = core.ptycho_prepare_paths(p, true);
otherwise
error('Unknown file extension %s.', fext);
end
end
ptycho/+scans/+queue/+check_queue/remote_queue.m
+91
View File
@@ -0,0 +1,91 @@
%REMOTE_QUEUE
% 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 [p, status_ok] = remote_queue(p)
import utils.verbose
import utils.update_param
status_ok = true;
verbose(1,['Remote queue is active, touching folder and looking for files in the queue in ' p.queue.remote_path]);
[~, ~] = system(['touch ' p.queue.remote_path '.'], '-echo');
files_recons = dir([p.queue.remote_path '*.mat']);
% Found one file to reconstruct
if ~isempty(files_recons)
if p.queue.recon_latest_first
p.queue.file_this_recons = files_recons(end).name;
else
p.queue.file_this_recons = files_recons(1).name;
end
verbose(1,['Found file in queue ' fullfile(p.queue.remote_path,p.queue.file_this_recons)]);
f = load(fullfile(p.queue.remote_path,p.queue.file_this_recons));
p = update_param(f.p, p);
% Now move this file to another folder
try
movefile(fullfile(p.queue.remote_path,p.queue.file_this_recons),fullfile(p.queue.remote_path,'in_progress'))
verbose(1,['Moving file to ' fullfile(p.queue.remote_path,'in_progress')]);
catch
verbose(1,['Failed moving file to ' fullfile(p.queue.remote_path,'in_progress')]);
pause(1);
status_ok = false;
end
else
verbose(1,'Did not find enough files in queue, pausing 10 seconds and then exiting')
pause(10)
status_ok = false;
end
end
ptycho/+scans/+queue/+update_queue/filelist.m
+86
View File
@@ -0,0 +1,86 @@
%UPDATE_FILELIST_QUEUE
% 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 filelist( p )
import utils.verbose
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% Update file queue %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if isfield(p.queue,'path')&&(~isempty(p.queue.path))
file_move_from = fullfile(p.queue.path,'in_progress',p.queue.file_this_recons);
file_move_to = fullfile(p.queue.path,'done',p.queue.file_this_recons);
% Now move this file to another folder
if ~exist(fullfile(p.queue.path,'done'))
mkdir(fullfile(p.queue.path,'done'));
end
io.movefile_fast(file_move_from,file_move_to)
verbose(1,sprintf('Ok its done, moving file to %s',file_move_to));
[~, ~, fext] = fileparts(p.queue.file_this_recons);
if exist(fullfile(p.queue.path,'failed', strrep(p.queue.file_this_recons, fext, '.log')), 'file')
delete(fullfile(p.queue.path,'failed', strrep(p.queue.file_this_recons, fext, '.log')))
end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
end
ptycho/+scans/+queue/+update_queue/remote_queue.m
+84
View File
@@ -0,0 +1,84 @@
%REMOTE_QUEUE
% 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 remote_queue( p )
import utils.verbose
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% Update remote file queue %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
file_move_from = fullfile(p.queue.remote_path,'in_progress',p.queue.file_this_recons);
file_move_to = fullfile(p.queue.remote_path,'done',p.queue.file_this_recons);
% Now move this file to another folder
if ~exist(fullfile(p.queue.remote_path,'done'))
mkdir(fullfile(p.queue.remote_path,'done'));
end
movefile(file_move_from,file_move_to)
verbose(1,sprintf('Ok its done, moving file to %s',file_move_to));
if exist(fullfile(p.queue.remote_path,'failed', strrep(p.queue.file_this_recons, 'mat', 'log')), 'file')
delete(fullfile(p.queue.remote_path,'failed', strrep(p.queue.file_this_recons, 'mat', 'log')))
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
end
ptycho/+scans/get_filenames_aps.m
+180
View File
@@ -0,0 +1,180 @@
%GET_FILENAMES_APS compile filenames of APS' hdf5 data files
% written by YJ based on PSI's code
function [p] = get_filenames_aps(p)
import utils.*
% get detector paramters
det = p.detectors(p.scanID).params;
read_path = p.raw_data_path_full{p.scanID};
detStorage = p.detectors(p.scanID).detStorage;
detStorage.files = [];
for ii = 1:p.numscans
detStorage.files{ii} = strcat(p.base_path,sprintf(p.scan.format, p.scan_number(ii)),'/data_roi',p.scan.roi_label,'_dp.hdf5');
end
%{
if isfield(det, 'filename_pattern')
if iscell(det.filename_pattern)
%% if filename patterns exist, use them to restrict the file search
det.filename_pattern_full = [p.detector.data_prefix];
fill = [];
for ii=1:size(det.filename_pattern,2)
fill = [fill det.filename_pattern{ii}.str det.filename_pattern{ii}.del];
det.filename_pattern_full = [det.filename_pattern_full det.filename_pattern{ii}.str det.filename_pattern{ii}.del];
del{ii} = det.filename_pattern{ii}.del;
switch det.filename_pattern{ii}.content
case 'burst'
burst = ii;
case 'scan'
scan = ii;
case 'pos'
pos = ii;
end
end
det.filename_pattern_full = [det.filename_pattern_full det.file_extension];
if exist('burst', 'var')
det.filename_pattern_burst = [p.detector.data_prefix];
parts = strsplit(fill, del);
parts{burst} = '*';
det.filename_pattern_burst = [det.filename_pattern_burst strjoin(parts, del) det.file_extension];
end
if exist('pos', 'var')
det.filename_pattern_pos = [p.detector.data_prefix];
parts = strsplit(fill, del);
parts{pos} = '*';
det.filename_pattern_pos = [det.filename_pattern_pos strjoin(parts, del) det.file_extension];
end
if exist('scan', 'var')
det.filename_pattern_scan = [p.detector.data_prefix];
parts = strsplit(fill, del);
if exist('burst', 'var')
parts{burst} = '*';
end
if exist('pos', 'var')
parts{pos} = '*';
end
det.filename_pattern_scan = [det.filename_pattern_scan strjoin(parts, del) det.file_extension];
end
input_vars = {};
if isfield(det, 'filename_pattern_pos')
k = 1;
for jj=1:length(det.filename_pattern)
switch det.filename_pattern{jj}.content
case 'pos'
continue
case 'burst'
input_vars{k} = det.filename_pattern{jj}.start;
case 'scan'
input_vars{k} = p.scan_number(p.scanID);
end
k = k+1;
end
filename_pattern_pos = fullfile(read_path, det.filename_pattern_pos);
filename_pos = sprintf(filename_pattern_pos, input_vars{:});
[~, pos_files] = find_files(filename_pos);
numpos = size(pos_files,2);
% apply natural sorting order i.e. sort 1,2,3,10,200 and not 1 10 100 2 20 200
% important if the file makes are not defined as S%05i but rather S%i
[~,idx] = natsort({pos_files.name});
pos_files = pos_files(idx);
end
if isfield(det, 'filename_pattern_burst')
k = 1;
for jj=1:length(det.filename_pattern)
switch det.filename_pattern{jj}.content
case 'pos'
input_vars{k} = det.filename_pattern{jj}.start;
case 'burst'
continue
case 'scan'
input_vars{k} = p.scan_number(p.scanID);
end
k = k+1;
end
filename_pattern_burst = fullfile(read_path, det.filename_pattern_burst);
filename_burst = sprintf(filename_pattern_burst, input_vars{:});
[~, burst_files] = find_files(filename_burst);
numburst = size(burst_files,2);
else
numburst = 1;
end
if numburst > 1
% if burst frames exist, we need to make sure that the file order is correct
file_args = '[';
for ii=1:length(det.filename_pattern)
switch ii
case burst
file_args = [file_args ' det.filename_pattern{ii}.start + burstID-1'];
case pos
file_args = [file_args ' det.filename_pattern{ii}.start + posID-1'];
case scan
file_args = [file_args ' p.scan_number(p.scanID)'];
end
end
file_args = [file_args ']'];
for posID=1:numpos
for burstID=1:numburst
files(burstID+(posID-1)*numburst).name = sprintf(det.filename_pattern_full, eval(file_args));
end
end
datadir = read_path;
else
% if there are no burst frames, use the pos files
datadir = read_path;
files = pos_files;
end
if numel(files)==0
error('Could not find any files using the filename pattern %s. \n ', fullfile(read_path, strrep(det.filename_pattern_full, '%', '%%')))
end
else
% use wildcards
files = find_files(fullfile(read_path, [det.filename_pattern det.file_extension]));
if numel(files)==0
error('Could not find any files using the filename pattern %s. \n ', fullfile(read_path, strrep(det.filename_pattern_full, '%', '%%')))
end
end
else
% if no filename pattern was specified, just load everything containing the specified file extension
[datadir, files] = find_files([read_path '*.' det.file_extension]);
if numel(files)==0
error('Could not find any files using the filename pattern %s.\n ', fullfile(read_path, ['*.' det.file_extension]))
end
end
detStorage.files = [];
for ii=1:length(files)
detStorage.files{ii} = fullfile(datadir, files(ii).name);
end
for ii=1:length(det.image_read_extraargs)
if strcmpi(det.image_read_extraargs{ii}, 'H5Location')
detStorage.h5_group{1} = det.image_read_extraargs{ii+1};
break;
end
end
%}
end
ptycho/+scans/get_filenames_aps_lynx.m
+185
View File
@@ -0,0 +1,185 @@
%GET_FILENAMES_APS compile filenames of APS' hdf5 data files
% written by YJ based on PSI's code
function [p] = get_filenames_aps_lynx(p)
import utils.*
% get detector paramters
det = p.detectors(p.scanID).params;
read_path = p.raw_data_path_full{p.scanID};
detStorage = p.detectors(p.scanID).detStorage;
detStorage.files = [];
for ii = 1:p.numscans
scan_no = p.scan_number(ii);
scan_dir = sprintf('eiger_4/S%05d-%05d/S%05d/',floor(scan_no/1000)*1000, ...
floor(scan_no/1000)*1000 + 999, ...
scan_no);
data_name = sprintf('run_%05d_000000000000.h5',scan_no);
detStorage.files{ii} = strcat(p.base_path,scan_dir,data_name);
end
%{
if isfield(det, 'filename_pattern')
if iscell(det.filename_pattern)
%% if filename patterns exist, use them to restrict the file search
det.filename_pattern_full = [p.detector.data_prefix];
fill = [];
for ii=1:size(det.filename_pattern,2)
fill = [fill det.filename_pattern{ii}.str det.filename_pattern{ii}.del];
det.filename_pattern_full = [det.filename_pattern_full det.filename_pattern{ii}.str det.filename_pattern{ii}.del];
del{ii} = det.filename_pattern{ii}.del;
switch det.filename_pattern{ii}.content
case 'burst'
burst = ii;
case 'scan'
scan = ii;
case 'pos'
pos = ii;
end
end
det.filename_pattern_full = [det.filename_pattern_full det.file_extension];
if exist('burst', 'var')
det.filename_pattern_burst = [p.detector.data_prefix];
parts = strsplit(fill, del);
parts{burst} = '*';
det.filename_pattern_burst = [det.filename_pattern_burst strjoin(parts, del) det.file_extension];
end
if exist('pos', 'var')
det.filename_pattern_pos = [p.detector.data_prefix];
parts = strsplit(fill, del);
parts{pos} = '*';
det.filename_pattern_pos = [det.filename_pattern_pos strjoin(parts, del) det.file_extension];
end
if exist('scan', 'var')
det.filename_pattern_scan = [p.detector.data_prefix];
parts = strsplit(fill, del);
if exist('burst', 'var')
parts{burst} = '*';
end
if exist('pos', 'var')
parts{pos} = '*';
end
det.filename_pattern_scan = [det.filename_pattern_scan strjoin(parts, del) det.file_extension];
end
input_vars = {};
if isfield(det, 'filename_pattern_pos')
k = 1;
for jj=1:length(det.filename_pattern)
switch det.filename_pattern{jj}.content
case 'pos'
continue
case 'burst'
input_vars{k} = det.filename_pattern{jj}.start;
case 'scan'
input_vars{k} = p.scan_number(p.scanID);
end
k = k+1;
end
filename_pattern_pos = fullfile(read_path, det.filename_pattern_pos);
filename_pos = sprintf(filename_pattern_pos, input_vars{:});
[~, pos_files] = find_files(filename_pos);
numpos = size(pos_files,2);
% apply natural sorting order i.e. sort 1,2,3,10,200 and not 1 10 100 2 20 200
% important if the file makes are not defined as S%05i but rather S%i
[~,idx] = natsort({pos_files.name});
pos_files = pos_files(idx);
end
if isfield(det, 'filename_pattern_burst')
k = 1;
for jj=1:length(det.filename_pattern)
switch det.filename_pattern{jj}.content
case 'pos'
input_vars{k} = det.filename_pattern{jj}.start;
case 'burst'
continue
case 'scan'
input_vars{k} = p.scan_number(p.scanID);
end
k = k+1;
end
filename_pattern_burst = fullfile(read_path, det.filename_pattern_burst);
filename_burst = sprintf(filename_pattern_burst, input_vars{:});
[~, burst_files] = find_files(filename_burst);
numburst = size(burst_files,2);
else
numburst = 1;
end
if numburst > 1
% if burst frames exist, we need to make sure that the file order is correct
file_args = '[';
for ii=1:length(det.filename_pattern)
switch ii
case burst
file_args = [file_args ' det.filename_pattern{ii}.start + burstID-1'];
case pos
file_args = [file_args ' det.filename_pattern{ii}.start + posID-1'];
case scan
file_args = [file_args ' p.scan_number(p.scanID)'];
end
end
file_args = [file_args ']'];
for posID=1:numpos
for burstID=1:numburst
files(burstID+(posID-1)*numburst).name = sprintf(det.filename_pattern_full, eval(file_args));
end
end
datadir = read_path;
else
% if there are no burst frames, use the pos files
datadir = read_path;
files = pos_files;
end
if numel(files)==0
error('Could not find any files using the filename pattern %s. \n ', fullfile(read_path, strrep(det.filename_pattern_full, '%', '%%')))
end
else
% use wildcards
files = find_files(fullfile(read_path, [det.filename_pattern det.file_extension]));
if numel(files)==0
error('Could not find any files using the filename pattern %s. \n ', fullfile(read_path, strrep(det.filename_pattern_full, '%', '%%')))
end
end
else
% if no filename pattern was specified, just load everything containing the specified file extension
[datadir, files] = find_files([read_path '*.' det.file_extension]);
if numel(files)==0
error('Could not find any files using the filename pattern %s.\n ', fullfile(read_path, ['*.' det.file_extension]))
end
end
detStorage.files = [];
for ii=1:length(files)
detStorage.files{ii} = fullfile(datadir, files(ii).name);
end
for ii=1:length(det.image_read_extraargs)
if strcmpi(det.image_read_extraargs{ii}, 'H5Location')
detStorage.h5_group{1} = det.image_read_extraargs{ii+1};
break;
end
end
%}
end
ptycho/+scans/get_filenames_cSAXS.m
+227
View File
@@ -0,0 +1,227 @@
%GET_FILENAMES_CSAXS compile filenames of raw data files
% receives
% 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 [p] = get_filenames_cSAXS(p)
import utils.*
% get detector paramters
det = p.detectors(p.scanID).params;
read_path = p.raw_data_path_full{p.scanID};
detStorage = p.detectors(p.scanID).detStorage;
if isfield(det, 'filename_pattern')
if iscell(det.filename_pattern)
%% if filename patterns exist, use them to restrict the file search
det.filename_pattern_full = [p.detector.data_prefix];
fill = [];
for ii=1:size(det.filename_pattern,2)
fill = [fill det.filename_pattern{ii}.str det.filename_pattern{ii}.del];
det.filename_pattern_full = [det.filename_pattern_full det.filename_pattern{ii}.str det.filename_pattern{ii}.del];
del{ii} = det.filename_pattern{ii}.del;
switch det.filename_pattern{ii}.content
case 'burst'
burst = ii;
case 'scan'
scan = ii;
case 'pos'
pos = ii;
end
end
det.filename_pattern_full = [det.filename_pattern_full det.file_extension];
if exist('burst', 'var')
det.filename_pattern_burst = [p.detector.data_prefix];
parts = strsplit(fill, del);
parts{burst} = '*';
det.filename_pattern_burst = [det.filename_pattern_burst strjoin(parts, del) det.file_extension];
end
if exist('pos', 'var')
det.filename_pattern_pos = [p.detector.data_prefix];
parts = strsplit(fill, del);
parts{pos} = '*';
det.filename_pattern_pos = [det.filename_pattern_pos strjoin(parts, del) det.file_extension];
end
if exist('scan', 'var')
det.filename_pattern_scan = [p.detector.data_prefix];
parts = strsplit(fill, del);
if exist('burst', 'var')
parts{burst} = '*';
end
if exist('pos', 'var')
parts{pos} = '*';
end
det.filename_pattern_scan = [det.filename_pattern_scan strjoin(parts, del) det.file_extension];
end
input_vars = {};
if isfield(det, 'filename_pattern_pos')
k = 1;
for jj=1:length(det.filename_pattern)
switch det.filename_pattern{jj}.content
case 'pos'
continue
case 'burst'
input_vars{k} = det.filename_pattern{jj}.start;
case 'scan'
input_vars{k} = p.scan_number(p.scanID);
end
k = k+1;
end
filename_pattern_pos = fullfile(read_path, det.filename_pattern_pos);
filename_pos = sprintf(filename_pattern_pos, input_vars{:});
[~, pos_files] = find_files(filename_pos);
numpos = size(pos_files,2);
% apply natural sorting order i.e. sort 1,2,3,10,200 and not 1 10 100 2 20 200
% important if the file makes are not defined as S%05i but rather S%i
[~,idx] = natsort({pos_files.name});
pos_files = pos_files(idx);
end
if isfield(det, 'filename_pattern_burst')
k = 1;
for jj=1:length(det.filename_pattern)
switch det.filename_pattern{jj}.content
case 'pos'
input_vars{k} = det.filename_pattern{jj}.start;
case 'burst'
continue
case 'scan'
input_vars{k} = p.scan_number(p.scanID);
end
k = k+1;
end
filename_pattern_burst = fullfile(read_path, det.filename_pattern_burst);
filename_burst = sprintf(filename_pattern_burst, input_vars{:});
[~, burst_files] = find_files(filename_burst);
numburst = size(burst_files,2);
else
numburst = 1;
end
if numburst > 1
% if burst frames exist, we need to make sure that the file order is correct
file_args = '[';
for ii=1:length(det.filename_pattern)
switch ii
case burst
file_args = [file_args ' det.filename_pattern{ii}.start + burstID-1'];
case pos
file_args = [file_args ' det.filename_pattern{ii}.start + posID-1'];
case scan
file_args = [file_args ' p.scan_number(p.scanID)'];
end
end
file_args = [file_args ']'];
for posID=1:numpos
for burstID=1:numburst
files(burstID+(posID-1)*numburst).name = sprintf(det.filename_pattern_full, eval(file_args));
end
end
datadir = read_path;
else
% if there are no burst frames, use the pos files
datadir = read_path;
files = pos_files;
end
if numel(files)==0
error('Could not find any files using the filename pattern %s. \n ', fullfile(read_path, strrep(det.filename_pattern_full, '%', '%%')))
end
else
% use wildcards
files = find_files(fullfile(read_path, [det.filename_pattern det.file_extension]));
if numel(files)==0
error('Could not find any files using the filename pattern %s. \n ', fullfile(read_path, strrep(det.filename_pattern_full, '%', '%%')))
end
end
else
% if no filename pattern was specified, just load everything containing the specified file extension
[datadir, files] = find_files([read_path '*.' det.file_extension]);
if numel(files)==0
error('Could not find any files using the filename pattern %s.\n ', fullfile(read_path, ['*.' det.file_extension]))
end
end
detStorage.files = [];
for ii=1:length(files)
detStorage.files{ii} = fullfile(datadir, files(ii).name);
end
for ii=1:length(det.image_read_extraargs)
if strcmpi(det.image_read_extraargs{ii}, 'H5Location')
detStorage.h5_group{1} = det.image_read_extraargs{ii+1};
break;
end
end
end
ptycho/+scans/get_filenames_cu.m
+183
View File
@@ -0,0 +1,183 @@
%GET_FILENAMES_APS compile filenames of APS' hdf5 data files
% written by YJ based on PSI's code
function [p] = get_filenames_cu(p)
import utils.*
% get detector paramters
det = p.detectors(p.scanID).params;
read_path = p.raw_data_path_full{p.scanID};
detStorage = p.detectors(p.scanID).detStorage;
%detStorage.files = strcat(p.base_path,'fly''data_roi',p.scan.roi_label,'_dp.hdf5');
detStorage.files = [];
for ii = 1:p.numscans
%detStorage.files{ii} = strcat(p.base_path,sprintf(p.scan.format, p.scan_number(ii)),'/data_dp.hdf5');
detStorage.files{ii} = strcat(p.base_path,sprintf(p.scan.format, p.scan_number(ii)),'/data_roi',p.scan.roi_label,'_dp.hdf5');
end
%{
if isfield(det, 'filename_pattern')
if iscell(det.filename_pattern)
%% if filename patterns exist, use them to restrict the file search
det.filename_pattern_full = [p.detector.data_prefix];
fill = [];
for ii=1:size(det.filename_pattern,2)
fill = [fill det.filename_pattern{ii}.str det.filename_pattern{ii}.del];
det.filename_pattern_full = [det.filename_pattern_full det.filename_pattern{ii}.str det.filename_pattern{ii}.del];
del{ii} = det.filename_pattern{ii}.del;
switch det.filename_pattern{ii}.content
case 'burst'
burst = ii;
case 'scan'
scan = ii;
case 'pos'
pos = ii;
end
end
det.filename_pattern_full = [det.filename_pattern_full det.file_extension];
if exist('burst', 'var')
det.filename_pattern_burst = [p.detector.data_prefix];
parts = strsplit(fill, del);
parts{burst} = '*';
det.filename_pattern_burst = [det.filename_pattern_burst strjoin(parts, del) det.file_extension];
end
if exist('pos', 'var')
det.filename_pattern_pos = [p.detector.data_prefix];
parts = strsplit(fill, del);
parts{pos} = '*';
det.filename_pattern_pos = [det.filename_pattern_pos strjoin(parts, del) det.file_extension];
end
if exist('scan', 'var')
det.filename_pattern_scan = [p.detector.data_prefix];
parts = strsplit(fill, del);
if exist('burst', 'var')
parts{burst} = '*';
end
if exist('pos', 'var')
parts{pos} = '*';
end
det.filename_pattern_scan = [det.filename_pattern_scan strjoin(parts, del) det.file_extension];
end
input_vars = {};
if isfield(det, 'filename_pattern_pos')
k = 1;
for jj=1:length(det.filename_pattern)
switch det.filename_pattern{jj}.content
case 'pos'
continue
case 'burst'
input_vars{k} = det.filename_pattern{jj}.start;
case 'scan'
input_vars{k} = p.scan_number(p.scanID);
end
k = k+1;
end
filename_pattern_pos = fullfile(read_path, det.filename_pattern_pos);
filename_pos = sprintf(filename_pattern_pos, input_vars{:});
[~, pos_files] = find_files(filename_pos);
numpos = size(pos_files,2);
% apply natural sorting order i.e. sort 1,2,3,10,200 and not 1 10 100 2 20 200
% important if the file makes are not defined as S%05i but rather S%i
[~,idx] = natsort({pos_files.name});
pos_files = pos_files(idx);
end
if isfield(det, 'filename_pattern_burst')
k = 1;
for jj=1:length(det.filename_pattern)
switch det.filename_pattern{jj}.content
case 'pos'
input_vars{k} = det.filename_pattern{jj}.start;
case 'burst'
continue
case 'scan'
input_vars{k} = p.scan_number(p.scanID);
end
k = k+1;
end
filename_pattern_burst = fullfile(read_path, det.filename_pattern_burst);
filename_burst = sprintf(filename_pattern_burst, input_vars{:});
[~, burst_files] = find_files(filename_burst);
numburst = size(burst_files,2);
else
numburst = 1;
end
if numburst > 1
% if burst frames exist, we need to make sure that the file order is correct
file_args = '[';
for ii=1:length(det.filename_pattern)
switch ii
case burst
file_args = [file_args ' det.filename_pattern{ii}.start + burstID-1'];
case pos
file_args = [file_args ' det.filename_pattern{ii}.start + posID-1'];
case scan
file_args = [file_args ' p.scan_number(p.scanID)'];
end
end
file_args = [file_args ']'];
for posID=1:numpos
for burstID=1:numburst
files(burstID+(posID-1)*numburst).name = sprintf(det.filename_pattern_full, eval(file_args));
end
end
datadir = read_path;
else
% if there are no burst frames, use the pos files
datadir = read_path;
files = pos_files;
end
if numel(files)==0
error('Could not find any files using the filename pattern %s. \n ', fullfile(read_path, strrep(det.filename_pattern_full, '%', '%%')))
end
else
% use wildcards
files = find_files(fullfile(read_path, [det.filename_pattern det.file_extension]));
if numel(files)==0
error('Could not find any files using the filename pattern %s. \n ', fullfile(read_path, strrep(det.filename_pattern_full, '%', '%%')))
end
end
else
% if no filename pattern was specified, just load everything containing the specified file extension
[datadir, files] = find_files([read_path '*.' det.file_extension]);
if numel(files)==0
error('Could not find any files using the filename pattern %s.\n ', fullfile(read_path, ['*.' det.file_extension]))
end
end
detStorage.files = [];
for ii=1:length(files)
detStorage.files{ii} = fullfile(datadir, files(ii).name);
end
for ii=1:length(det.image_read_extraargs)
if strcmpi(det.image_read_extraargs{ii}, 'H5Location')
detStorage.h5_group{1} = det.image_read_extraargs{ii+1};
break;
end
end
%}
end
ptycho/+scans/get_queue.m
+99
View File
@@ -0,0 +1,99 @@
%GET_QUEUE call queue functions in package directories
% 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 [ p, status ] = get_queue(p, update)
status = 1;
func_path = fullfile(p.ptycho_matlab_path, '+scans/+queue/');
if ~isfield(p.queue, 'name')
utils.verbose(3, ' p.queue.name is not set, using default p.queue.name = ''''')
p.queue.name = '';
end
if ~update
if isfield(p.queue, 'name') && ~isempty(p.queue.name)
% initial check if at least one function exists
f_chk = exist(sprintf([func_path '+check_queue/%s.m'], p.queue.name), 'file');
f_update_chk = exist(sprintf([func_path '+update_queue/%s.m'], p.queue.name), 'file');
if ~f_chk && ~f_update_chk
error('Queue ''%s'' was specified but no corresponding queue type was found. Please check your template for typos and +scans/+queue for completeness.', p.queue.name);
end
if f_chk
queue_func = str2func(['scans.queue.check_queue.' p.queue.name]);
[p, status] = queue_func(p);
if ~status
return
end
end
end
else
if isfield(p.queue, 'name') && ~isempty(p.queue.name)
if exist(sprintf([func_path '+update_queue/%s.m', p.queue.name]), 'file')
queue_func = str2func(['scans.queue.update_queue.' p.queue.name]);
queue_func(p);
if ~status
return
end
end
end
end
end
ptycho/+scans/read_metadata.m
+68
View File
@@ -0,0 +1,68 @@
%READ_METADATA load meta data and overwrite previous settings
% 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 p = read_metadata(p)
% read metadata
if ~isempty(p.src_metadata) && ~strcmpi(p.src_metadata, 'none')
metadata_func = str2func(sprintf('scans.meta.%s', p.src_metadata));
p = metadata_func(p);
end
end
ptycho/+scans/read_positions.m
+33
View File
@@ -0,0 +1,33 @@
%READ_POSITIONS load positions
function p = read_positions(p)
import utils.verbose
% check for continuous scan
p.scan.is_cont = false;
% Variables for all scans
p.positions_real = [];
p.positions_orig = [];
% read position data
if ~isfield(p,'src_positions') || isempty(p.src_positions)
error(' p.src_positions is not set')
end
% load the positions from a provided function if possible
position_func = str2func(sprintf('scans.positions.%s', p.src_positions));
p = position_func(p);
scanfirstindex = [1 cumsum(p.numpts)+1]; % First index for scan number
for ii = 1:p.numscans
p.scanindexrange(ii,:) = [scanfirstindex(ii) scanfirstindex(ii+1)-1];
p.scanidxs{ii} = p.scanindexrange(ii,1):p.scanindexrange(ii,end);
end
p.positions_orig = p.positions_real;
%size(p.positions_orig)
%scatter(p.positions_orig(:,1),p.positions_orig(:,2),'x')
end