mirror of
https://github.com/c-sooyoung/fold_slice.git
synced 2026-09-17 18:29:08 +09:00
334 lines
11 KiB
Matlab
334 lines
11 KiB
Matlab
% function [varargout] = spec_plot(specDatFile, varargin)
|
||
% call 'spec_plot()' for further help
|
||
%
|
||
% please reports bugs, problems, suggestions for improvements to:
|
||
% CXS group
|
||
|
||
%*-----------------------------------------------------------------------*
|
||
%| |
|
||
%| Except where otherwise noted, this work is licensed under a |
|
||
%| Creative Commons Attribution-NonCommercial-ShareAlike 4.0 |
|
||
%| International (CC BY-NC-SA 4.0) license. |
|
||
%| |
|
||
%| Copyright (c) 2017 by Paul Scherrer Institute (http://www.psi.ch) |
|
||
%| |
|
||
%| Author: CXS group, PSI |
|
||
%*-----------------------------------------------------------------------*
|
||
% You may use this code with the following provisions:
|
||
%
|
||
% If the code is fully or partially redistributed, or rewritten in another
|
||
% computing language this notice should be included in the redistribution.
|
||
%
|
||
% If this code, or subfunctions or parts of it, is used for research in a
|
||
% publication or if it is fully or partially rewritten for another
|
||
% computing language the authors and institution should be acknowledged
|
||
% in written form in the publication: “Data processing was carried out
|
||
% using the “cSAXS matlab package” developed by the CXS group,
|
||
% Paul Scherrer Institut, Switzerland.”
|
||
% Variations on the latter text can be incorporated upon discussion with
|
||
% the CXS group if needed to more specifically reflect the use of the package
|
||
% for the published work.
|
||
%
|
||
% A publication that focuses on describing features, or parameters, that
|
||
% are already existing in the code should be first discussed with the
|
||
% authors.
|
||
%
|
||
% This code and subroutines are part of a continuous development, they
|
||
% are provided “as they are” without guarantees or liability on part
|
||
% of PSI or the authors. It is the user responsibility to ensure its
|
||
% proper use and the correctness of the results.
|
||
|
||
function [varargout] = spec_plot(specDatFile, varargin)
|
||
import io.spec_help
|
||
import io.spec_read
|
||
|
||
% check minimum number of input arguments
|
||
if (nargin<1)
|
||
spec_help(mfilename);
|
||
error('At least the spec data filename has to be specified as input parameter.')
|
||
end
|
||
|
||
% accept cell array with name/value pairs as well
|
||
no_of_in_arg = nargin;
|
||
if (nargin == 2)
|
||
if (isempty(varargin))
|
||
% ignore empty cell array
|
||
no_of_in_arg = no_of_in_arg -1;
|
||
else
|
||
if (iscell(varargin{1}))
|
||
% use a filled one given as first and only variable parameter
|
||
varargin = varargin{1};
|
||
no_of_in_arg = 1 + length(varargin);
|
||
end
|
||
end
|
||
end
|
||
% check number of input arguments
|
||
if (rem(no_of_in_arg,2) ~= 1)
|
||
error('The optional parameters have to be specified as ''name'',''value'' pairs');
|
||
end
|
||
|
||
% here the default parameters
|
||
unhandled_par_error = 1;
|
||
wait_for = 0;
|
||
axno = -1;
|
||
|
||
% parse the variable input arguments
|
||
vararg = cell(0,0);
|
||
for jj = 1:2:length(varargin)
|
||
name = varargin{jj};
|
||
value = varargin{jj+1};
|
||
switch name
|
||
case 'Counter'
|
||
counter = value;
|
||
case 'FigNo'
|
||
figno = value;
|
||
case 'Sleep'
|
||
wait_for = value;
|
||
case 'ContMesh'
|
||
saxis = value;
|
||
case 'PFunction'
|
||
pfunction = value;
|
||
counter = 'Pilatus';
|
||
vararg{end+1} = 'OutPut'; %#ok<AGROW>
|
||
vararg{end+1} = '+pilatus'; %#ok<AGROW>
|
||
case 'UnhandledParError'
|
||
unhandled_par_error = value;
|
||
otherwise
|
||
vararg{end+1} = name; %#ok<AGROW>
|
||
vararg{end+1} = value; %#ok<AGROW>
|
||
end
|
||
end
|
||
|
||
vararg{end+1} = 'Cell';
|
||
vararg{end+1} = 1;
|
||
vararg{end+1} = 'UnhandledParError';
|
||
vararg{end+1} = 0;
|
||
[S,vararg_new] = spec_read(specDatFile,vararg);
|
||
|
||
vararg = cell(0);
|
||
pilatusDir = cell(0);
|
||
for jj = 1:2:length(vararg_new)
|
||
name = vararg_new{jj};
|
||
value = vararg_new{jj+1};
|
||
switch name
|
||
case 'PilatusDir'
|
||
pilatusDir{end+1} = value;
|
||
otherwise
|
||
vararg{end+1} = name; %#ok<AGROW>
|
||
vararg{end+1} = value; %#ok<AGROW>
|
||
end
|
||
end
|
||
|
||
varargout{1} = cell(size(S));
|
||
for jj=1:numel(S)
|
||
S_j = S{jj};
|
||
titlestr = S_j.S;
|
||
if (isfield(S_j,counter))
|
||
scanstr = regexp(S_j.S,' *','split');
|
||
data = S_j.(counter);
|
||
if (iscell(data))
|
||
data = PilatusCounter(data,S_j.PilatusDir,pfunction);
|
||
numall = zeros(size(data));
|
||
for ii=1:numel(data)
|
||
numall(ii) = numel(data{ii});
|
||
end
|
||
if (all(numall==1))
|
||
for ii=1:numel(data)
|
||
numall(ii) = data{ii}{:};
|
||
end
|
||
data = numall;
|
||
end
|
||
end
|
||
if (numel(data)<=1 && ~iscell(data))
|
||
continue;
|
||
end
|
||
if (~exist('figno','var'))
|
||
figno = figure;
|
||
elseif (~ishandle(figno))
|
||
figure(figno)
|
||
else
|
||
switch get(figno,'type')
|
||
case 'figure'
|
||
figure(figno)
|
||
case 'axes'
|
||
axno = figno;
|
||
figno = get(figno,'parent');
|
||
otherwise
|
||
while (strcmp(get(figno,'type'),'axes'))
|
||
figno = get(figno,'parent');
|
||
end
|
||
axno = figno;
|
||
figno = get(figno,'parent');
|
||
end
|
||
if (ishandle(axno))
|
||
axes(axno);
|
||
cla;
|
||
end
|
||
end
|
||
if (~isempty(regexp(scanstr{3},'[ad][0-3]?scan','match')))
|
||
faxis = scanstr{4};
|
||
fpos = S_j.(faxis);
|
||
|
||
h = plot(fpos,data);
|
||
xlabel(faxis); ylabel(counter);
|
||
elseif (~isempty(regexp(scanstr{3},'loopscan','match')))
|
||
faxis = 'Time';
|
||
fpos = S_j.(faxis);
|
||
|
||
h = plot(fpos,data);
|
||
xlabel(faxis); ylabel(counter);
|
||
elseif (~isempty(regexp(scanstr{3},'cont_line','match')))
|
||
faxis = scanstr{4};
|
||
if (~exist('saxis','var'))
|
||
fpos = linspace(str2double(scanstr{5}),str2double(scanstr{6}), ...
|
||
str2double(scanstr{7})+1);
|
||
sdata = cell2mat(data{1});
|
||
h = plot(fpos,sdata);
|
||
xlabel(faxis); ylabel(pfunction,'Interpreter','None');
|
||
else
|
||
scannr = str2double(scanstr{2});
|
||
if (~exist('fpos','var'))
|
||
fpos = linspace(str2double(scanstr{5}),str2double(scanstr{6}), ...
|
||
str2double(scanstr{7})+1);
|
||
spos = S_j.(saxis);
|
||
sdata = cell2mat(data{1});
|
||
minnr = scannr;
|
||
maxnr = scannr;
|
||
else
|
||
fpos = [fpos, ...
|
||
linspace(str2double(scanstr{5}),str2double(scanstr{6}), ...
|
||
str2double(scanstr{7})+1)];
|
||
spos = [spos, S_j.(saxis)];
|
||
fpos = unique(fpos);
|
||
spos = unique(spos);
|
||
sdata = [sdata;cell2mat(data{1})];
|
||
minnr = min(minnr,scannr);
|
||
maxnr = max(minnr,scannr);
|
||
titlestr = sprintf('#S %05d-%05d cont_mesh %s %f %f %d %s %f %f %d %s %s', ...
|
||
minnr,maxnr, ...
|
||
faxis, min(fpos), max(fpos), numel(fpos)-1, ...
|
||
saxis, min(spos), max(spos), numel(spos)-1, ...
|
||
scanstr{8},scanstr{9});
|
||
end
|
||
|
||
h = imagesc(fpos,spos,sdata);
|
||
if (numel(spos)>1)
|
||
axis equal tight;
|
||
hold on
|
||
contour(fpos,spos,sdata,'k');
|
||
hold off
|
||
end
|
||
xlabel(faxis); ylabel(saxis);
|
||
colorbar;
|
||
end
|
||
elseif (~isempty(regexp(scanstr{3},'mesh','match')))
|
||
faxis = scanstr{4};
|
||
saxis = scanstr{8};
|
||
fpos = unique(S_j.(faxis));
|
||
spos = unique(S_j.(saxis));
|
||
|
||
if (numel(data) == numel(fpos)*numel(spos))
|
||
data = transpose(reshape(data,numel(fpos),numel(spos)));
|
||
elseif (mod(numel(data)/(numel(fpos)*numel(spos)),1) == 0)
|
||
data = reshape(data,[],numel(fpos),numel(spos));
|
||
data = transpose(squeeze(sum(data,1)));
|
||
end
|
||
if ((mod(numel(data)/(numel(fpos)*numel(spos)),1) == 0) && ...
|
||
numel(data) > 1)
|
||
h = imagesc(fpos,spos,data);
|
||
else
|
||
[fpos,spos,data,h] = plot_grid(S_j.(faxis),S_j.(saxis),data);
|
||
end
|
||
if (size(data,1)>1)
|
||
axis equal tight;
|
||
hold on
|
||
contour(fpos,spos,data,'k');
|
||
hold off
|
||
end
|
||
xlabel(faxis); ylabel(saxis);
|
||
colorbar;
|
||
elseif (~isempty(regexp(scanstr{3},'round_scan','match')))
|
||
faxis = scanstr{4};
|
||
saxis = scanstr{5};
|
||
[fpos,spos,data,h] = plot_grid(S_j.(faxis),S_j.(saxis),data);
|
||
axis equal tight;
|
||
hold on
|
||
contour(fpos,spos,data,'k');
|
||
hold off
|
||
xlabel(faxis); ylabel(saxis);
|
||
colorbar;
|
||
elseif (~isempty(regexp(scanstr{3},'round_roi_scan','match')))
|
||
faxis = scanstr{4};
|
||
saxis = scanstr{7};
|
||
[fpos,spos,data,h] = plot_grid(S_j.(faxis),S_j.(saxis),data);
|
||
axis equal tight;
|
||
hold on
|
||
contour(fpos,spos,data,'k');
|
||
hold off
|
||
xlabel(faxis); ylabel(saxis);
|
||
colorbar;
|
||
else
|
||
fprintf('unknown scan ''%s'' encountered\n', ...
|
||
scanstr{3})
|
||
end
|
||
title(titlestr,'Interpreter','None')
|
||
drawnow;
|
||
if (wait_for && jj<numel(S))
|
||
pause(wait_for);
|
||
end
|
||
else
|
||
error('Counter ''%s'' not found in scan ''%s''', ...
|
||
counter,S_j.S);
|
||
end
|
||
if (exist('h','var'))
|
||
varargout{1}{jj} = h;
|
||
end
|
||
end
|
||
|
||
if ((unhandled_par_error) && (~isempty(vararg)))
|
||
vararg %#ok<NOPRT>
|
||
error('Not all named parameters have been handled.');
|
||
end
|
||
varargout{2} = vararg;
|
||
return
|
||
end
|
||
%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||
function [x,y,Z,h] = plot_grid(xaxis,yaxis,data)
|
||
pos = [xaxis,yaxis];
|
||
diff = pos(2:end,:) - pos(1:end-1,:);
|
||
[y,x] = hist(sqrt(sum(diff.^2,2)),200);
|
||
[~,n] = max(y(2:end));
|
||
s = x(n)/2;
|
||
[X,Y] = meshgrid(linspace(min(xaxis)-s,max(xaxis)+s,200), ...
|
||
linspace(min(yaxis)-s,max(yaxis)+s,200));
|
||
Z = zeros(size(X));
|
||
N = Z;
|
||
for ii=1:numel(data)
|
||
Z = Z+data(ii)*exp(-((X-xaxis(ii)).^2 + (Y-yaxis(ii)).^2)/(2*s^2)); %/(2*pi*s^2);
|
||
N = N+ exp(-((X-xaxis(ii)).^2 + (Y-yaxis(ii)).^2)/(2*s^2)); %/(2*pi*s^2);
|
||
end
|
||
Z = Z./N;
|
||
x = X(1,:);
|
||
y = Y(:,1);
|
||
h = imagesc(x,y,Z);
|
||
end
|
||
%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||
function [data] = PilatusCounter(fnames,fpath,evalfunction)
|
||
if (iscell(fnames{1}))
|
||
data = cell(size(fnames));
|
||
else
|
||
data = -ones(size(fnames));
|
||
end
|
||
for ii=1:numel(fnames)
|
||
if (iscell(fnames{ii}))
|
||
data{ii} = cell(size(fnames{ii}));
|
||
for jj=1:numel(fnames{ii})
|
||
data{ii}{jj} = eval(sprintf(evalfunction, ...
|
||
strcat(fpath,fnames{ii}{jj})));
|
||
end
|
||
else
|
||
data(ii) = eval(sprintf(strcat(evalfunction,';'), ...
|
||
strcat(fpath,fnames{ii}{jj})));
|
||
end
|
||
end
|
||
end |