[357] | 1 | %'check_files': check the path, modification date and svn version for all the
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| 2 | % function in the toolbox UVMAT. Called at the opening of uvmat. Adds the
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| 3 | % uvmat path to the Matlab path if needed.
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| 4 | %----------------------------------------------------------------------
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[497] | 5 | % function [checkmsg,date_str,ver]=check_files
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[357] | 6 | %
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| 7 | % OUTPUT:
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[497] | 8 | % checkmsg: error message listing functions whose paths are not in the directory of uvmat.m
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[357] | 9 | % date_str: date of the most recent modification of a file in the toolbox
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| 10 | % ver : svn version in case this is a svn repository
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| 11 |
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| 12 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
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| 13 | % Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org.
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| 14 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
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| 15 | % This file is part of the toolbox UVMAT.
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| 16 | %
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| 17 | % UVMAT is free software; you can redistribute it and/or modify
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| 18 | % it under the terms of the GNU General Public License as published by
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| 19 | % the Free Software Foundation; either version 2 of the License, or
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| 20 | % (at your option) any later version.
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| 21 | %
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| 22 | % UVMAT is distributed in the hope that it will be useful,
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| 23 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
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| 24 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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| 25 | % GNU General Public License (file UVMAT/COPYING.txt) for more details.
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| 26 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
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| 27 |
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[497] | 28 | function [checkmsg,date_str,svn_info]=check_files
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| 29 | checkmsg={};%default
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[357] | 30 | svn_info.rep_rev=[];
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| 31 | svn_info.cur_rev=[];
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| 32 | svn_info.status=[];
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| 33 | list_fct={...
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[515] | 34 | 'calc_field_interp';...% defines fields (velocity, vort, div...) from civx data and calculate them
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| 35 | 'calc_field_tps';...% defines fields (velocity, vort, div...) and calculate them
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[357] | 36 | 'cell2tab';... %transform a Matlab cell in a character array suitable for display in a table
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| 37 | 'check_field_structure';...% check the validity of the field struture representation consistant with the netcdf format
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| 38 | 'check_files';...
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| 39 | 'civ';... %function associated with the interface 'civ.fig' for PIV and spline interpolation
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| 40 | 'civ.fig';...
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| 41 | 'civ_3D';... function associated with the interface 'civ_3D.fig' for PIV in volume (TODO: combine with civ.m)
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| 42 | 'civ_3D.fig';...
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| 43 | 'civ_matlab';...% civ programs, Matlab version (called by civ.m, option Civprogram/Matlab in the upper menu bar)
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| 44 | 'close_fig';...% function activated when a figure is closed
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| 45 | 'copyfields';...% copy fields between two matlab structures
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| 46 | 'create_grid';...% called by the GUI geometry_calib to create a physical grid
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| 47 | 'create_grid.fig';...% GUI corresponding to create_grid.m
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[506] | 48 | 'datatree_browser';...% function for scanning directories in a project
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| 49 | 'datatree_browser.fig';...% GUI corresponding to dataview
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[357] | 50 | 'delete_object';...%delete a projection object, defined by its index in the Uvmat list or by its graphic handle
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[475] | 51 | 'displ_uvmat';...
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[357] | 52 | 'editxml';...%display and edit xml files using a xls schema
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| 53 | 'editxml.fig';...%interface for editxml
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| 54 | 'fileparts_uvmat';...% extracts the root name,field indexes and nomenclature type from an input filename
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[497] | 55 | 'fill_GUI';...% fill a GUI with a set of parameters from a Matlab structure
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[476] | 56 | 'filter_tps';...% find the thin plate spline coefficients for interpolation-smoothing
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[512] | 57 | 'find_field_cells';...% group the variables of a 'field object' into 'field cells' and specify their structure
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[357] | 58 | 'find_file_series';...%check the content of an input file and find the corresponding file series
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[498] | 59 | 'find_imadoc';...% find the ImaDoc xml file associated with a given input file
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[357] | 60 | 'fullfile_uvmat';...%creates a file name from a root name and indices.
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| 61 | 'geometry_calib';...%performs geometric calibration from a set of reference points
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| 62 | 'geometry_calib.fig';...%interface for geometry_calib
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| 63 | 'get_field';...% choose and plot a field from a Netcdf file
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| 64 | 'get_field.fig';...%interface for get_field
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[380] | 65 | 'get_file_series';...% determine the list of file names and file indices for functions called by 'series'.
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| 66 | 'get_file_type';...% determine info about a file (image, multimage, civdata,...) .
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[357] | 67 | 'hist_update';...% update of a current global histogram by inclusion of a new field
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| 68 | 'imadoc2struct';...%convert the image documentation file ImaDoc into a Matlab structure
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| 69 | 'keyboard_callback';... % function activated when a key is pressed on the keyboard
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| 70 | 'ListDir';... scan the structure of the directory tree (for dataview.m)
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| 71 | 'mouse_down';% function activated when the mouse button is pressed on a figure (callback for 'WindowButtonDownFcn')
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| 72 | 'mouse_motion';...% permanently called by mouse motion over a figure (callback for 'WindowButtonMotionFcn')
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| 73 | 'mouse_up';... % function to be activated when the mouse button is released (callback for 'WindowButtonUpFcn')
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| 74 | 'msgbox_uvmat';... associated with GUI msgbox_uvmat.fig to display message boxes, for error, warning or input calls
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| 75 | 'msgbox_uvmat.fig';...
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| 76 | 'nc2struct';...% transform a netcdf file in a corresponding matlab structure
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| 77 | 'num2stra';...% transform number to the corresponding character string depending on the nomenclature
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| 78 | 'open_uvmat';...% open with uvmat the field selected in the list of 'civ/status' or 'series/check_data_files'
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| 79 | 'peaklock';...%
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| 80 | 'phys_XYZ';...% transform coordiantes from pixels to phys
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| 81 | 'px_XYZ';...% transform coordiantes from phys to pixels
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| 82 | 'plot_field';...%displays a vector field and/or scalar or images
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| 83 | 'plot_object';...%draws a projection object (points, line, plane...)
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| 84 | 'proj_field';...%project a field on a projection object (plane, line,...)
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| 85 | 'read_civxdata';...reads civx data from netcdf files
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| 86 | 'read_civdata';... reads new civ data from netcdf files
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[498] | 87 | 'read_field';...% read the fields from files in different formats (netcdf files, images, video)
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[357] | 88 | 'read_get_field';... read the list of selected variables from the GUI get_field (TODO: use read_GUI)
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[497] | 89 | 'read_GUI';... %read a GUI and provide the data as a Matlab structure
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[498] | 90 | 'read_image';...%read images or video objects
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[477] | 91 | 'read_multimadoc';... %read a set of Imadoc files and compare their timing of different file series
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[357] | 92 | 'read_xls';...%read excel files containing the list of the experiments
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| 93 | 'reinit';...% suppress the personal parameter file 'uvmat_perso.mat'
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| 94 | 'rotate_points';...%'rotate_points': associated with GUI rotate_points.fig to introduce (2D) rotation parameters
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| 95 | 'rotate_points.fig';...
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| 96 | 'RUN_STLIN';...% combine 2 displacement fields for stereo PIV
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| 97 | 'series';...% master function for analysis field series, with interface 'series.fig'
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| 98 | 'series.fig';...% interface for 'series'
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| 99 | 'set_col_vec';...% sets the color code for vectors depending on a scalar and input parameters (used for plot_field)
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| 100 | 'set_grid';...% creates a grid for PIV
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| 101 | 'set_grid.fig';...% interface for set_grid
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| 102 | 'set_object.m';...% edit a projection object
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| 103 | 'set_object.fig';...% interface for set_object
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| 104 | 'stra2num';...% transform letters (a, b, A, B,) or numerical strings ('1','2'..) to the corresponding numbers
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| 105 | 'sub_field';...% combine the two input fields,
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| 106 | 'struct2nc';...% %write fields in netcdf files
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| 107 | 'struct2xml';... transform a matlab structure to a xml tree.
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| 108 | 'tps_coeff';...% calculate the thin plate spline (tps) coefficients
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| 109 | 'tps_eval';... %calculate the thin plate spline (tps) interpolation at a set of points
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| 110 | 'tps_eval_dxy';...% calculate the derivatives of thin plate spline (tps) interpolation at a set of points (limited to the 2D case)
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| 111 | 'translate_points';...% associated with GUI translate_points.fig to display translation parameters
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| 112 | 'translate_points.fig';...
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| 113 | 'update_imadoc';... %update the ImaDoc xml file
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| 114 | 'update_waitbar';... update the waitbar display, used for ACTION functions in the GUI 'series'
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| 115 | 'uvmat';...% master function for file scanning and visualisation of 2D fields
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| 116 | 'uvmat.fig';... %interface for uvmat
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| 117 | 'view_field.m';...% function for visualisation of projected fields'
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| 118 | 'view_field.fig';...%GUI for view_field
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| 119 | 'write_plot_param';...%update plotting parameters after plot, TODO: change into a general function: fill_GUI
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| 120 | 'xml2struct';...% read an xml file as a Matlab structure, converts numeric character strings into numbers
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| 121 | };
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| 122 | dir_fct=which('uvmat');% path to uvmat
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[497] | 123 | pathuvmat=fileparts(dir_fct);
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[357] | 124 |
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| 125 | %% add the uvmat path to matlab if needed
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| 126 | if isempty(regexp(path,[pathuvmat '(:|\>)'],'once'))
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| 127 | addpath(pathuvmat);
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| 128 | end
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| 129 |
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| 130 |
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| 131 | %% loop on the list of functions in the uvmat package
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| 132 | icount=0;
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| 133 | datnum=zeros(1,length(list_fct));
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| 134 | for i=1:length(list_fct)
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| 135 | dir_fct=which(list_fct{i});% path to fct
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| 136 | if isempty(dir_fct)
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| 137 | icount=icount+1;
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[497] | 138 | checkmsg{icount}=[list_fct{i} ' not found'];% test for function not found
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[357] | 139 | else
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[497] | 140 | pth=fileparts(dir_fct);
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| 141 | if ~isequal(pathuvmat,pth) && ~isequal(fullfile(pathuvmat,'private'),pth)
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[357] | 142 | icount=icount+1;
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[497] | 143 | checkmsg{icount}=[dir_fct ' overrides the package UVMAT'];% bad path for the function
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[357] | 144 | end
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| 145 | datfile=dir(dir_fct);
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| 146 | if isfield(datfile,'datenum')
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| 147 | datnum(i)= datfile.datenum;
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| 148 | end
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| 149 | end
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| 150 | end
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| 151 | date_str=datestr(max(datnum));
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[497] | 152 |
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| 153 | %% check svn status
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[479] | 154 | [status,result]=system('svn --help');
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| 155 | if status==0
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| 156 | svn_info.rep_rev=0;svn_info.cur_rev=0;
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| 157 | [tild,result]=system(['svn info ' dir_fct]);
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| 158 | t=regexp(result,'R.vision\s*:\s*(?<rev>\d+)','names');
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| 159 | if ~isempty(t)
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[475] | 160 | svn_info.cur_rev=str2double(t.rev);
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[357] | 161 | end
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[497] | 162 | [tild,result]=system(['svn info -r ''HEAD'' ' pathuvmat]);
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[479] | 163 | t=regexp(result,'R.vision\s*:\s*(?<rev>\d+)','names');
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| 164 | if ~isempty(t)
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[497] | 165 | svn_info.rep_rev=str2double(t.rev);
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[479] | 166 | end
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[497] | 167 | [tild,result]=system(['svn status ' pathuvmat]);
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[479] | 168 | svn_info.status=result;
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[497] | 169 | checkmsg =[checkmsg {['SVN revision : ' num2str(svn_info.cur_rev)]}];
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[479] | 170 | if svn_info.rep_rev>svn_info.cur_rev
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[497] | 171 | checkmsg =[checkmsg ...
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[479] | 172 | {['Repository now at revision ' num2str(svn_info.rep_rev) '. Please type svn update in uvmat folder']}];
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| 173 | end
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| 174 | modifications=regexp(svn_info.status,'M\s[^(\n|\>)]+','match');
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| 175 | if ~isempty(modifications)
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[497] | 176 | for ilist=1:numel(modifications)
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| 177 | [tild,FileName,FileExt]=fileparts(modifications{ilist});
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| 178 | checkmsg=[checkmsg {[FileName FileExt ' modified']}];
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| 179 | end
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[479] | 180 | end
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| 181 | else
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[497] | 182 | checkmsg=[checkmsg {'SVN not available'}];
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[479] | 183 | end
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[497] | 184 | checkmsg=checkmsg';
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[357] | 185 |
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[505] | 186 | %% check dates of compilation
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| 187 | currentdir=pwd;
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| 188 | cd(pathuvmat)
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| 189 | list_compile=dir('*.sh');
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| 190 | for ilist=1:numel(list_compile)
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| 191 | mfile=regexprep(list_compile(ilist).name,'.sh$','.m');
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| 192 | datfile=dir(mfile);
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| 193 | if isfield(datfile,'datenum') && datfile.datenum>list_compile(ilist).datenum
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| 194 | checkmsg=[checkmsg;{[list_compile(ilist).name ' needs to be updated by compile_functions']}];
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| 195 | end
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| 196 | end
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| 197 |
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