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ptycho/+scans/+positions/hdf5_pos.m
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%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
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%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
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%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
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%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
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%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
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%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