mirror of
https://github.com/c-sooyoung/fold_slice.git
synced 2026-09-17 21:49:08 +09:00
initial commit
This commit is contained in:
@@ -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
|
||||
Reference in New Issue
Block a user