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% Call function without arguments for instructions on how to use it
% Filename: $RCSfile: image_show.m,v $
%
% $Revision: 1.18 $ $Date: 2011/05/29 13:52:28 $
% $Author: $
% $Tag: $
%
% Description:
% read and display a 2D data frame
%
% Note:
% Call without arguments for a brief help text.
%
% Dependencies:
% - image_read
%
%
% history:
%
% April 16th 2009:
% bug-fix in histogram scaling, the intensity base level was not properly
% taken into account,
% auto-scaling is activated by a separate parameter to allow for arbitrary
% scales
%
% February 23rd 2009:
% add histogram scaling
%
% September 4th 2009:
% add DisplayFtime and DisplayExptime parameters,
% use new rowcol_from field of th eframe structure rather than handling the
% region of interest specification here,
% remove leading home directory and beamline specific path from displayed
% filename
%
% February 23rd 2009:
% add ImageHandle parameter for updating existing plots,
% earlier the XScange and YScange parameters have been added
%
% August 28th 2008:
% plot 1D data using plot
%
% May 9th 2008:
% use image_read and named parameters, other changes since the last
% history entry, rename from pilatus_show to image_show
%
% November 2006: 1st version
%*-----------------------------------------------------------------------*
%|                                                                       |
%|  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 [frame,image_handle] = image_show(filename,varargin)
import io.*
import plotting.image_show
import utils.default_parameter_value
% 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
% set default values
fig_no = default_parameter_value(mfilename,'FigNo');
fig_clear = default_parameter_value(mfilename,'FigClear');
auto_scale = default_parameter_value(mfilename,'AutoScale');
axis_min = default_parameter_value(mfilename,'AxisMin');
axis_max = default_parameter_value(mfilename,'AxisMax');
hist_scale = default_parameter_value(mfilename,'HistScale');
log_scale = default_parameter_value(mfilename,'LogScale');
x_scale =default_parameter_value(mfilename,'XScale');
y_scale =default_parameter_value(mfilename,'YScale');
x_offs =default_parameter_value(mfilename,'XOffs');
display_colorbar = default_parameter_value(mfilename,'ColorBar');
display_axes = default_parameter_value(mfilename,'Axes');
display_time = default_parameter_value(mfilename,'DisplayTime');
display_ftime = default_parameter_value(mfilename,'DisplayFtime');
display_exptime = default_parameter_value(mfilename,'DisplayExptime');
color_map = default_parameter_value(mfilename,'ColorMap');
bgr_data = default_parameter_value(mfilename,'BgrData');
image_handle = default_parameter_value(mfilename,'ImageHandle');
frame_number = default_parameter_value(mfilename,'FrameNumber');
frame = [];
% check minimum number of input arguments and
% check number of input arguments
if ((nargin < 1) || (rem(no_of_in_arg,2) ~= 1))
image_read_help('ext',mfilename,'Examples',0,'ExtensionReturned',1);
fprintf('''BgrData'',<data array> subtract this background from the data read\n');
fprintf('''FrameNumber'',<integer> in case of multiple frames per file select one or 0 for the average of all frames, default is %d\n',frame_number);
fprintf('''FigNo'',<figure number> display figure in this window, default is %d\n',fig_no);
fprintf('''FigClear'',<0-no, 1-yes> clear figure before plotting, default is %d (only used if no image handle is specified)\n',fig_clear);
fprintf('''ImageHandle'',<handle number> update the specified image which may be faster and can be used to keep constant zoom level\n');
fprintf('''AutoScale'',<[0-no/1-yes 0-no/1-yes]> intensity auto scaling of lower/upper limit, default is [%d %d]\n',auto_scale(1),auto_scale(2));
fprintf('''AxisMin'',<value> intensity scaling if not in auto-scale mode, default is %.3e\n',axis_min);
fprintf('''AxisMax'',<value> intensity scaling if not in auto-scale mode, default is %.3e\n',axis_max);
fprintf('''AxisMinMax'',<[ min max]> specify both min and max value\n');
fprintf('''HistScale'',<[low high]> in case of auto scaling scale the data to see the portion of the intensity values from low to high, default is [ %.2f %.2f]\n',hist_scale(1),hist_scale(2));
fprintf('''LogScale'',<0-no,1-yes> default is %d\n',log_scale);
fprintf('''XScale'',<scaling factor> default is %.3e\n',x_scale);
fprintf('''YScale'',<scaling factor> default is %.3e\n',y_scale);
fprintf('''XOffs'',<scaling factor> default is %.3e\n',x_offs);
fprintf('''ColorBar'',<0-no,1-yes> display colorbar, default is %d\n',display_colorbar);
fprintf('''ColorMap'',<''map-name''> choose colormap, default is ''%s''\n',color_map);
fprintf('''Axes'',<0-no,1-yes> display axes, default is %d\n',display_axes);
fprintf('''TitleString'',<''text''> fixed part of the title\n');
fprintf('''DisplayTime'',<0-no,1-yes> default is yes\n');
fprintf('\n');
fprintf('\n');
fprintf('Examples:\n');
fprintf('[frame,image_handle]=%s(''~/Data10/pilatus/image_1_ct.cbf'');\n',mfilename);
fprintf('[frame,image_handle]=%s(''~/Data10/pilatus/image_1_ct.cbf'');\n',mfilename);
fprintf('[frame,image_handle]=%s(''~/Data10/pilatus/image_1_ct.cbf'',''RowFrom'',100,''RowTo'',800,''ColumnFrom'',200,''ColumnTo'',1200,''AxisMin'',1,''AxisMax'',1e6);\n',mfilename);
fprintf('[frame,image_handle]=%s(''~/Data10/pilatus/image_1_ct.cbf'',''AxisMax'',1e4);\n',mfilename);
fprintf('\n');
fprintf('The returned structure has the fields data, header and extension.\n');
if (nargin < 1)
error('At least the filename has to be specified as input parameter.');
else
error('The optional parameters have to be specified as ''name'',''value'' pairs');
end
end
% parse the variable input arguments not handled by or on purpose not
% passed to the image_read routine
vararg = cell(0,0);
for ind = 1:2:length(varargin)
name = varargin{ind};
value = varargin{ind+1};
switch name
case 'FigNo'
fig_no = value;
case 'FigClear'
fig_clear = value;
case 'ImageHandle'
image_handle = value;
case 'AxisMin'
axis_min = value;
case 'AxisMax'
axis_max = value;
case 'AxisMinMax'
axis_min = value(1);
axis_max = value(2);
case 'AutoScale'
auto_scale = value;
case 'HistScale'
hist_scale = value;
case 'LogScale'
log_scale = value;
case 'XScale'
x_scale = value;
case 'YScale'
y_scale = value;
case 'XOffs'
x_offs = value;
case 'ColorBar'
display_colorbar = value;
case 'ColorMap'
color_map = value;
case 'Axes'
display_axes = value;
case 'DisplayTime'
display_time = value;
case 'DisplayFtime'
display_ftime = value;
case 'DisplayExptime'
display_exptime = value;
case 'BgrData'
bgr_data = value;
case 'FrameNumber'
frame_number = value;
case 'Frame'
frame = value;
otherwise
vararg{end+1} = name; %#ok<AGROW>
vararg{end+1} = value; %#ok<AGROW>
end
end
% get the home directory path
[stat,homedir] = system('echo ~');
if (stat ~= 0)
homedir = '';
else
if (~isempty(homedir))
homedir = homedir(1:end-1);
end
end
% remove a beamline specific part
[stat,username] = system('echo $USER');
if (stat == 0)
if (~isempty(username))
username = username(1:end-1);
end
std_path = [ '/sls/X12SA/Data10/' username ];
if ((length(filename) > length(std_path)) && ...
(strcmp(filename(1:length(std_path)),std_path)))
filename = [ '~/Data10' filename(length(std_path)+1:end) ];
end
end
% read the frame
if (isempty(frame))
[frame] = image_read(filename,vararg);
end
if (isempty(frame.data))
fprintf('%s: frame empty (file %s)\n',mfilename,filename);
return;
end
if (axis_max <= axis_min)
error('AxisMax must be greater than AxisMin');
end
% subtract background
if (~isempty(bgr_data))
if (size(bgr_data) ~= size(frame.data))
error('Background data dimension does not match data dimension.');
end
frame.data = frame.data - bgr_data;
end
% define axes range
x = x_scale * ...
frame.rowcol_from{1}(2):(frame.rowcol_from{1}(2)+size(frame.data,2)-1) + ...
x_offs;
y = y_scale * ...
frame.rowcol_from{1}(1):(frame.rowcol_from{1}(1)+size(frame.data,1)-1);
% select the plot window
if ((isempty(image_handle)) || (image_handle <= 0))
if (gcf ~= fig_no)
figure(fig_no);
end
if (fig_clear)
hold off;
clf;
end
end
% for dat files (like MCS data) display the last data set as a 1D plot
if ((strcmp(frame.extension{1},'dat')) && (ndims(frame.data) > 1))
x = x_scale * (1:size(frame.data,1)) + x_offs;
y = y_scale;
end_ind = floor(frame.no_of_el_read{1} / length(x)) * length(x);
begin_ind = end_ind - length(x) +1;
if (begin_ind < 1)
begin_ind = 1;
end
frame_plot = frame.data(begin_ind:end_ind);
else
if (ndims(frame.data) > 2)
if (frame_number == 0)
frame_plot = squeeze(mean(frame.data,3));
else
frame_plot = squeeze(frame.data(:,:,frame_number));
end
else
frame_plot = frame.data;
end
end
% display the frame
if (log_scale)
frame_plot(frame_plot < 1e-15) = 1e-15;
end
ax_min = axis_min;
ax_max = axis_max;
if ((length(x) == 1) || (length(y) ==1))
if (length(y) == 1)
if (log_scale)
semilogy(x,frame_plot);
else
plot(x,frame_plot);
end
xlabel('x [ pixel ]','FontSize',12);
x_range = [ x(1) x(end) ];
else
if (log_scale)
semilogy(y,frame_plot);
else
plot(y,frame_plot);
end
xlabel('y [ pixel ]','FontSize',12);
x_range = [ y(1) y(end) ];
end
% axis scaling etc.
ylabel('intensity','FontSize',12);
as = axis;
as(1:2) = x_range;
% auto scale lower/upper limit if specified
if (auto_scale(1))
ax_min = min(min(frame_plot));
end
if (auto_scale(2))
ax_max = max(max(frame_plot));
end
as(3) = ax_min;
as(4) = ax_max;
if (as(4) <= as(3))
as(4) = as(3) +1;
end
axis(as);
else
if (log_scale)
ax_min = log10( axis_min );
ax_max = log10( axis_max );
frame_plot = log10( double(frame_plot) );
end
if ((isempty(image_handle)) || (image_handle <= 0))
% initialize a new plot
image_handle = imagesc(x,y,frame_plot);
axis xy;
axis equal;
axis tight;
if (~display_axes)
axis off;
end
jet_mod = jet;
for (i = 1:8)
jet_mod(i,3) = i/8;
end
if (isempty(color_map))
colormap(jet_mod);
else
colormap(color_map);
end
if (display_colorbar)
colorbar;
end
xlabel('x [ pixel ]','FontSize',12);
ylabel('y [ pixel ]','FontSize',12);
zlabel('intensity');
else
% update an existing plot
set(image_handle,'CData', frame_plot );
end
% auto scale, if specified
if (nnz(auto_scale))
% use one million intensity bins over the intensity range
int_min = min(min(frame_plot));
int_max = max(max(frame_plot));
int_step = (int_max-int_min) / 2^20;
% calculate the bin indices from the intensities
hist_ind = round((frame_plot(:)-int_min) / int_step) +1;
% increase each bin an index is pointing to by one
hist_bins = zeros(1,max(hist_ind)-min(hist_ind)+1);
for (ind_hist = 1:numel(hist_ind))
hist_bins(hist_ind(ind_hist)) = hist_bins(hist_ind(ind_hist)) +1;
end
% calculate the cumulative sum
hist_bins = cumsum(hist_bins);
% find the indices to the bins with more pixels than the threshold
n_low = find(hist_bins > hist_scale(1) * numel(frame_plot),1,'first');
if (n_low >= length(hist_bins))
n_low = length(hist_bins) -1;
end
n_high = find(hist_bins > hist_scale(2) * numel(frame_plot),1,'first');
if (n_high <= n_low)
n_high = n_low +1;
end
if (n_high > length(hist_bins))
n_high = length(hist_bins);
end
% use the corresponding intensities to scale the image
if (auto_scale(1))
ax_min = (n_low-1) * int_step + int_min;
end
if (auto_scale(2))
ax_max = (n_high-1) * int_step + int_min;
end
% for (hist_iter = 1:4)
% hist_bins = int_min:((int_max-int_min)/1e3):int_max;
% [no_of_int_values] = hist(frame.data(:),hist_bins);
% % calculate the cumulative sum and find the position above the
% % lower and upper number of pixels threshold
% cumsum_no_of_int_values = cumsum(no_of_int_values);
% n_low = find(cumsum_no_of_int_values > hist_scale(1) * numel(frame_plot),1,'first') -1;
% if (n_low >= length(hist_bins))
% n_low = length(hist_bins) -1;
% end
% if (n_low < 1)
% n_low = 1;
% end
% n_high = find(cumsum_no_of_int_values > hist_scale(2) * numel(frame_plot),1,'first');
% if (n_high <= n_low)
% n_high = n_low +1;
% end
% if (n_high > length(hist_bins))
% n_high = length(hist_bins);
% end
%
% % sufficiently fine resolution is reached
% if ((n_high > 5) && (n_high < length(hist_bins)))
% % fprintf('%d: %d %d',hist_iter,n_low,n_high);
% break;
% end
%
% % change to a finer histogram spacing
% int_min = hist_bins(n_low);
% int_max = hist_bins(n_high);
% end
% % use the corresponding intensities to scale the image
% if (ax_min <= 0)
% ax_min = hist_bins(n_low);
% end
% if (ax_max <= 0)
% ax_max = hist_bins(n_high);
% end
% frame_med = medfilt2(frame_plot,[ 3 3 ]);
% if (ax_min <= 0)
% ax_min = 0.1 * mean(mean(frame_med));
% end
% if (ax_max <= 0)
% ax_max = max(max(frame_med));
% end
end
caxis( [ ax_min ax_max ] );
end
% compile title string:
% replace home directory by tilde
if ((length(filename) > length(homedir)) && ...
(strcmp(filename(1:length(homedir)),homedir)))
title_str = [ '~' filename(length(homedir)+1:end) ];
else
title_str = filename;
end
% escape underscore characters from LaTeX-like use
title_str = strrep(title_str,'_','\_');
if (log_scale)
title_str = [ title_str ' (log.)' ];
end
% add current time
if (display_time)
clock_now = clock();
title_str = [ title_str ' ' ...
num2str(clock_now(4)) ':' num2str(clock_now(5),'%02.0f') ...
':' num2str(clock_now(6),'%02.0f') ];
end
% get and display date string from file
if (display_ftime)
title_str = [ title_str '\newlinefile date: ' ...
common_header_value(frame.header{1},frame.extension{1},'Date') ];
end
% get and display exposure time
if (display_exptime)
title_str = [ title_str ', exposure time = ' ...
num2str(common_header_value(frame.header{1},frame.extension{1},...
'ExposureTime'),'%.3f') ' sec' ];
end
% add the frame number to the title string
if (frame_number == 0)
title_str = [ title_str ', frame average' ];
else
title_str = [ title_str sprintf(', frame %d',frame_number) ];
end
% display the compiled title string
title(title_str,'FontSize',14);
return;