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% image_read_help(extension,m_file_name,varargin)
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% parameter help for image_read
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% Filename: $RCSfile: image_read_help.m,v $
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%
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% $Revision: 1.3 $ $Date: 2013/01/25 10:23:47 $
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% $Author: $
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% $Tag: $
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%
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% Description:
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% parameter help for image_read
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%
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% Note:
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% none
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%
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% Dependencies:
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% none
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%
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%
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% history:
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%
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% July 17th 2008:
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% add ForceFileType parameter and support for MAR CCD TIFF
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%
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% May 9th 2008: 1st version
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%*-----------------------------------------------------------------------*
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%| |
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%| Except where otherwise noted, this work is licensed under a |
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%| Creative Commons Attribution-NonCommercial-ShareAlike 4.0 |
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%| International (CC BY-NC-SA 4.0) license. |
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%| |
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%| Copyright (c) 2017 by Paul Scherrer Institute (http://www.psi.ch) |
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%| |
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%| Author: CXS group, PSI |
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%*-----------------------------------------------------------------------*
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% You may use this code with the following provisions:
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%
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% If the code is fully or partially redistributed, or rewritten in another
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% computing language this notice should be included in the redistribution.
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%
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% If this code, or subfunctions or parts of it, is used for research in a
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% publication or if it is fully or partially rewritten for another
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% computing language the authors and institution should be acknowledged
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% in written form in the publication: “Data processing was carried out
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% using the “cSAXS matlab package” developed by the CXS group,
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% Paul Scherrer Institut, Switzerland.”
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% Variations on the latter text can be incorporated upon discussion with
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% the CXS group if needed to more specifically reflect the use of the package
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% for the published work.
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%
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% A publication that focuses on describing features, or parameters, that
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% are already existing in the code should be first discussed with the
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% authors.
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%
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% This code and subroutines are part of a continuous development, they
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% are provided “as they are” without guarantees or liability on part
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% of PSI or the authors. It is the user responsibility to ensure its
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% proper use and the correctness of the results.
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function [] = image_read_help(extension,m_file_name,varargin)
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import io.*
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% check minimum number of input arguments
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if (nargin < 2)
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error('At least the extension and m-file name have to be specified as input parameter.');
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end
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% accept cell array with name/value pairs as well
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no_of_in_arg = nargin;
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if (nargin == 3)
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if (isempty(varargin))
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% ignore empty cell array
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no_of_in_arg = no_of_in_arg -1;
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else
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if (iscell(varargin{1}))
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% use a filled one given as first and only variable parameter
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varargin = varargin{1};
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no_of_in_arg = 2 + length(varargin);
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end
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end
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end
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% check number of input arguments
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if (rem(no_of_in_arg,2) ~= 0)
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error('The optional parameters have to be specified as ''name'',''value'' pairs');
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end
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% parse the variable input arguments
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examples = 1;
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vararg = cell(0,0);
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for ind = 1:2:length(varargin)
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name = varargin{ind};
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value = varargin{ind+1};
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switch name
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case 'Examples'
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examples = value;
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otherwise
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% pass unknown parameters to image_read_sub_help
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vararg{end+1} = name;
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vararg{end+1} = value;
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end
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end
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% do not display examples from image_read_sub_help
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vararg{end+1} = 'Examples';
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vararg{end+1} = 0;
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image_read_sub_help(m_file_name,extension,vararg)
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fprintf('''DataType'',<Matlab class> default is ''double'', other possibilities are ''single'', ''uint16'', ''int16'', ''uint32'', etc.\n');
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fprintf(' The conversion is done using ''cast'', i.e, out-of-range values are mapped to the minimum or maximum value\n');
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fprintf('''ForceFileType'',<''extension''> force the file types to be recognized by the here specified extension,\n');
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fprintf(' useful in case of no or other types of extensions, used by default as OrientExtension as well.\n');
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fprintf(' The extension ''mar'' and ''mccd'' can be used to read MAR CCD TIFF data.\n');
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fprintf('''RowFrom'',<0-max> region of interest definition, 0 or 1 for full frame\n');
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fprintf('''RowTo'',<0-max> region of interest definition, 0 for full frame\n');
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fprintf('''ColumnFrom'',<0-max> region of interest definition, 0 or 1 for full frame\n');
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fprintf('''ColumnTo'',<0-max> region of interest definition, 0 for full frame\n');
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image_orient_help(m_file_name,'ParametersOnly',1);
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fprintf('''IsFmask'',<0-no,1-yes> interprete the filename(s) as search mask that may include wildcards, default true\n');
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fprintf('''DisplayFilename'',<0-no,1-yes> display filename of a file before loading it, default yes\n');
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fprintf('''UnhandledParError'',<0-no,1-yes> exit in case not all named parameters are used/known, default is yes\n');
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fprintf('\n');
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fprintf('HDF5, H5 or NeXus specifics These files contain data and metadata hierarchically organized in groups and datasets,\n');
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fprintf(' each group or dataset can also have attributes. Such files are thus here treated in a special way.\n');
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fprintf(' If you provide only filename then the file contents, including links but excluding attributes,\n');
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fprintf(' will be recursively read and returned as a Matlab structure. See also hdf5_load.m\n');
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fprintf('''H5Location'',<location> If <location> is a group then it will be read recursively and returned as a Matlab structure.\n');
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fprintf(' If <location> is a dataset, the dataset will be read and returned within the field ''data'',\n');
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fprintf(' this is done in an effort to be compatible with the output of image_read for other file extensions. \n');
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fprintf(' Only in this case the data region options will be used, e.g ''RowFrom'', ''RowTo'', etc. \n');
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fprintf('''FrameRange'',<[first_fr last_fr]> Read only a subset of the frames available in the HDF5 file dataset specifed with ''H5Location''\n');
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fprintf(' This will only have an effect if ''H5Location'' is a dataset and not a group \n');
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fprintf('''ReadAttr'',<0-no,1-yes> Read the attributes of a dataset or group (default 0). The Name and Value of the attributes are \n');
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fprintf(' returned in a structure. Note with this option only the attributes (and not the dataset) are read\n');
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if (examples)
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fprintf('\n');
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fprintf('\n');
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fprintf('Examples:\n');
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fprintf('[frame]=%s(''~/Data10/pilatus/image_1_ct.cbf'');\n',...
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m_file_name);
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fprintf('[frame]=%s({''~/Data10/pilatus/image_1_ct1.cbf'',''~/Data10/pilatus/image_1_ct2.cbf''});\n',...
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m_file_name);
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fprintf('[frame]=%s(''~/Data10/pilatus/S00010/*.cbf'',''IsFmask'',1);\n',...
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m_file_name);
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fprintf('[frame]=%s(''~/Data10/pilatus/image_1_ct.cbf'',''RowFrom'',500,''RowTo'',600);\n',...
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m_file_name);
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fprintf('\n');
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fprintf('The returned structure has the fields data, header, filename and extension.\n');
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fprintf('\n');
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fprintf('\n');
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fprintf('Examples for HDF5:\n');
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fprintf('[data] = image_read(''scan_00300.hdf5'') Read all data in the file.\n')
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fprintf('[data] = image_read(''scan_00300.hdf5'',''H5Location'',''/entry/instrument'') Reads NeXus instrument group.\n')
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fprintf('[data] = image_read(''scan_00300.hdf5'',''H5Location'',''/entry/collection/data/spec'') Reads spec data which includes counters and motors that change during a scan.\n')
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fprintf('[data] = image_read(''scan_00300.hdf5'',''H5Location'',''/entry/collection/data/spec'',''ReadAttr'',1) Reads spec data that did not change during the scan, e.g. static motors.\n')
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fprintf('[data] = image_read(''scan_00300.hdf5'',''H5Location'',''/entry/instrument/Pilatus_2M/data'') Reads all Pilatus frames from the scan.\n')
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fprintf('[data] = image_read(''scan_00300.hdf5'',''H5Location'',''/entry/instrument/Pilatus_2M/data'',''FrameRange'',[5 10], ''RowFrom'',500,''RowTo'',Inf,''ColumnFrom'',200,''ColumnTo'',800 )\n')
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fprintf(' Reads the specified frame range and region of interest of the pilatus frames.\n')
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end
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