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SiBoRG/helpers/set_pixel_size.m
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set_pixel_size.m
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function params = set_pixel_size(params, pixel_size)
% SET_PIXEL_SIZE computes the actual size of the pixel in the image using the CCD
% camera pixel size, the magnification and the binning. In addition, it computes the
% other values in the parameter structure which values depend on "pixel_size"
% (see get_struct.m).
%
% OPTS = SET_PIXEL_SIZE(OPTS) computes pixel_size using the fields 'ccd_pixel_size',
% 'magnification' and 'binning' of the parameter structure OPTS (get_struct('options')).
% Using this value, it then computes the actual value of the dynamic fields of OPTS.
%
% OPTS = SET_PIXEL_SIZE(OPTS, PIXEL_SIZE) uses the provided value for pixel_size
% to set the value of the dynamic fields.
%
% OPTS = SET_PIXEL_SIZE uses the default value for OPTS too.
%
% NOTES ON USING DYNAMIC FIELD VALUES
% In case the value of the parameter you want to set depends on the size of the pixel
% (in um), you can substitute its value by the expression that computes it. In this
% expression, you can then use the variable 'pixel_size' which will contain the
% appropriate value. Simply put the whole expression in a string terminated by the
% usual ';' character. This function will then evaluate this expression using the
% value of 'pixel_size' and store the result into the same field.
%
% Multiple lines can be stored in a single field separated by ';'. This technique
% allows to define your own temporary variables. In this case you will need to
% explicit the assignment as in any normal expression using '='.
%
% Gonczy & Naef labs, EPFL
% Simon Blanchoud
% 10.12.2010
% Check if we need to get a new option structure
if (nargin == 0)
params = get_struct('options');
params = set_pixel_size(params);
return;
% Otherwise, we have only the option structure provided
elseif (nargin == 1 || isempty(pixel_size))
% We need at least these two fields to exist
if (isfield(params, 'ccd_pixel_size') && isfield(params, 'magnification'))
% Maybe there is even binning
if (isfield(params, 'binning'))
pixel_size = params.binning * params.ccd_pixel_size / params.magnification;
else
pixel_size = params.ccd_pixel_size / params.magnification;
end
% Store the pixel size
params.pixel_size = pixel_size;
else
pixel_size = [];
end
end
% If we have no data for the pixel_size, stop here
if (isempty(params))
return;
end
% Otherwise, we loop recursively on the parameter structure to try to set the
% dynamic fields
fields = fieldnames(params);
for n=1:length(params)
for i=1:length(fields)
% If it's a string, maybe we can set something here
if (ischar(params(n).(fields{i})) && ~isempty(pixel_size))
% Get the comamnds and split them per line
commands = params(n).(fields{i});
indx = [0 strfind(commands, ';')];
ncomma = length(indx) - 1;
% Loop over each command and execute it
for j=1:ncomma
% For the last one, we need to assign it back the structure field
if (j == ncomma)
eval(['params(n).(fields{i}) = ' commands(indx(j)+1:indx(j+1))]);
else
eval(commands(indx(j)+1:indx(j+1)));
end
end
% If it's a structure field, call set_pixel_size recursively
elseif (isstruct(params(n).(fields{i})))
params(n).(fields{i}) = set_pixel_size(params(n).(fields{i}), pixel_size);
end
end
end
return;
end
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