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Nicola Viganò authored
Signed-off-by:Nicola Viganò <ben.vighy@gmail.com>
Nicola Viganò authoredSigned-off-by:
initialise_gt.m 11.84 KiB
function initialise_gt(ignore_id19, skip_functions_check)
% INITIALISE.M for Matlab installations on Windows, Macs, and Linux
%
% ADD DESIRED PATH ENTRIES TO THIS LIST FOLLOWING THE EXISTING FORMAT!!
%
% PT, big bug with image display due to openGL. crashed completely
% ganymedes. disabled the 03/12/07
% '/graintracking',... % Grain tracking project (WL,MHG,AK) * symlink *
% 24/05/2010 PT correction to ensure that personnal startup is read at the
% end of the initialisation if present for non DCT people
%
% 2011-2013, Modified and improved by Nicola Vigano', vigano@esrf.fr
% 2012, Modified and improved by Yoann Guilhem, guilhem@esrf.fr
% 2005, Create by Greg & Wolfgang
pathstruct={... % Tools from ID19's legacy code
{'/' },...
{'/art' },... % Algebraic reconstruction attempts
{'/util' },...
{'/stitching' },... % Image stitching code
{'/stitching/heprom' },...
{'/sliceomatic' },... % Viewing tool for volumes
{'/IBF' },... % IBF tools (Olivier Hignette & Greg Johnson)
{'/moretomo' },... % tomography tools in development
{'/tracking' },... % particle tracking (Weitzlab, www.harvard.edu)
{'/ringcorrection' },... % ring correction code
{'/imagej' },... % imagej support
{'/lsge-matlab' },... % fitting routines from the NPL in the UK
{'/lamino' }... % laminography specific (LH)
{'/tomotools', '-begin'}... % Tools for tomography
};
% {'/parallel' },... % embarrasingly parallel matlab (ML and GJ)
current_dir = pwd;
disp('Graintracking settings in progress...');
% No multi platform support, at the moment.
disp(['Machine is: ', computer]);
if (exist('ignore_id19', 'var') && ~ignore_id19)
deprecated_id19_paths = fullfile('/data','id19','archive','matlab');
% Linux machines
if (~exist(deprecated_id19_paths, 'dir'))
error(['ERROR: No folder called: "' deprecated_id19_paths '"']);
end
% Adding paths
for n = 1:length(pathstruct)
switch size(pathstruct{n}, 2)
case 1
addpath(fullfile(deprecated_id19_paths, pathstruct{n}{1}));
case 2
addpath(fullfile(deprecated_id19_paths, pathstruct{n}{1}), pathstruct{n}{2});
otherwise
disp(['Wrong parameters number for entry "', n, '"(', pathstruct{n}{1} ,') of structure "pathstruct"']);
addpath(fullfile(deprecated_id19_paths, pathstruct{n}{1}));
end
end
end
% suppress extra linefeeds in command window
format compact;
%%%%%%%%%%%%%%%%%%%%%%
% other special settings
% changing default settings at root level
set(0,'DefaultFigurePaperType','A4');
set(0,'DefaultFigurePaperUnits','centimeters');
% beamline (for alignment)
global FT_BL;
FT_BL = 'id19';
% volume selection in fasttomo; values are 'total', 'manual', 'graphics'
global FT_VOLSELECT;
FT_VOLSELECT = 'graphics';
% initialise path for graintracking project
disp('Adding graintracking specific folders to the path');
global GT_MATLAB_HOME;
if (isempty(GT_MATLAB_HOME))
GT_MATLAB_HOME = pwd;
end
disp(['Using the DCT code in directory ' GT_MATLAB_HOME]);
addpath(GT_MATLAB_HOME);
addpath(fullfile(GT_MATLAB_HOME, '1_preprocessing'));
addpath(fullfile(GT_MATLAB_HOME, '1_preprocessing', 'gtSetup_Utils'));
addpath(fullfile(GT_MATLAB_HOME, '2_difspot'));
addpath(fullfile(GT_MATLAB_HOME, '3_pairmatching'));
addpath(fullfile(GT_MATLAB_HOME, '3_pairmatchingGUI'));
addpath(fullfile(GT_MATLAB_HOME, '4_grains'));
addpath(fullfile(GT_MATLAB_HOME, '5_reconstruction'));
addpath(fullfile(GT_MATLAB_HOME, '6_rendering'));
addpath(fullfile(GT_MATLAB_HOME, '7_fed'));
addpath(fullfile(GT_MATLAB_HOME, '7_fed', 'AndyFunctions'));
addpath(fullfile(GT_MATLAB_HOME, '7_fed', 'geometry'));
addpath(fullfile(GT_MATLAB_HOME, '7_fed', 'Ccode_SpreadInt'));
addpath(fullfile(GT_MATLAB_HOME, '7_fed2'));
addpath(fullfile(GT_MATLAB_HOME, '8_optimization'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Analysis'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Boundaries'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Crack'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Cryst'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Cryst', 'file_cif'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Conf'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_DataStructures'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Deformation'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Deformation', 'plotting'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Deformation', 'test_generation'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_DB'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Distortion'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Drawing'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Drawing', 'cm_and_cb_utilities'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Drawing', 'freezeColors'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_EDF'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_ErrorHandling'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Fit'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_ForwardSim'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Geo'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_GUI'));
if (usejava('jvm') && verLessThan('matlab', '8.4.0'))
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_GUI', 'GUILayout-v1p17'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_GUI', 'GUILayout-v1p17', 'Patch'));
else
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_GUI', 'GUILayout-v2.2.1', 'layout'));
end
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_GUI', 'FindJObj'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_GVF'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Help'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Help', 'ExportFig'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Help', 'cprintf'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_ICP'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_ID19'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Imaging'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Indexter'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Maths')); addpath(fullfile(GT_MATLAB_HOME, 'zUtil_NoiseAnalysis'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_OAR'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Parameters'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Python'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Strain'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Strain2'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Taper'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Tests'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_TIFF'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_TomoUtils'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Twins'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_VTK'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_XML'));
addpath(fullfile(GT_MATLAB_HOME, 'FigureManagement'));
addpath(fullfile(GT_MATLAB_HOME, 'm2html'));
% matGeom toolbox
addpath(fullfile(GT_MATLAB_HOME, 'matGeom'));
% C Compiled code
addpath(fullfile(GT_MATLAB_HOME, 'bin', 'mex'));
disp('Loading configuration about external libraries from conf.xml');
load_conf()
disp('Finished adding.');
% Warning when launched on a Windows PC
if (ispc())
% Rendering: the default renderer may have to be changed
disp('If you are running the code on a Windows PC and experiencing')
disp('problems with colormaps or graphics resolution, you may have to')
disp('change the default graphics rendering mode to one of these:')
disp(' set(0, ''DefaultFigureRenderer'', ''opengl'')')
disp(' set(0, ''DefaultFigureRenderer'', ''zbuffer'')')
disp(' set(0, ''DefaultFigureRenderer'', ''painters'')')
end
disp(' ')
cd(fullfile(GT_MATLAB_HOME, 'matGeom'));
setupMatGeom();
disp(' ')
cd(current_dir);
if (exist('skip_functions_check', 'var') && skip_functions_check)
check_compiled_funcs = false;
elseif (verLessThan('MATLAB', '8.6.0'))
check_compiled_funcs = true;
else
check = inputwdefault('Do you want to check compiled functions? (might be very slow) [y/n]', 'n');
check_compiled_funcs = strcmpi(check, 'y');
end
if (check_compiled_funcs)
gtCheckCompiledFunctions()
end
defaultColor = sprintf(gtGetANSIColour());
boldColor = sprintf(gtGetANSIColour('bold'));
disp([boldColor 'To report a bug, create a ticket at https://sourceforge.net/p/dct/tickets' defaultColor]);
end
function load_conf()
global GT_MATLAB_HOME
global GT_DB;
default_dbconf = struct( ...
'name', 'graintracking', ...
'host', 'graindb.esrf.fr', ...
'user', 'gtadmin', ... 'password', 'gtadmin');
default_astra_paths = struct( ...
'tools', [GT_MATLAB_HOME '/astra/tools'], ...
'mex', [GT_MATLAB_HOME '/astra/mex'] );
try
xml_conf = gtConfLoadXML();
% File and dirs patterns
try
dbconf = gtConfGetField(xml_conf, 'database');
catch mexc
gtPrintException(mexc, ...
'"database" is not a valid field of the xml.conf file. Using defaults.')
dbconf = default_dbconf;
end
GT_DB = struct( ...
'name', dbconf.name, ...
'host', dbconf.host, ...
'user', dbconf.user, ...
'password', dbconf.password);
[~, hostname] = system('hostname');
if (verLessThan('matlab', '8.4.0') ...
&& any(~cellfun(@isempty, regexpi(hostname, {'rnice', 'crunch', 'gpu'}))))
% This fixes a few problems with rendering on the ESRF cluster
opengl('software');
end
% ASTRA toolkit
try
astra_mex_paths = gtConfGetField(xml_conf, 'astra.mex.path');
inCellForm = iscell(astra_mex_paths);
for n = 1:length(astra_mex_paths)
if (inCellForm)
tmp_path = astra_mex_paths{n};
else
tmp_path = astra_mex_paths(n);
end
tmp_path = gtConfFilterAttribute(tmp_path, 'hostname');
if (~isempty(tmp_path))
addpath(tmp_path);
end
end
catch mexc
gtPrintException(mexc, ...
'No Astra mex files configuration. Using hardcoded paths for Astra mex files');
addpath(default_astra_paths.tools);
addpath(default_astra_paths.tools);
end
% Check which version of matlab compiled the oar executables
try
matlabVersion = gtConfGetField(xml_conf, 'matlab.version');
currentMatlabRelease = version('-release');
if (~strcmpi(currentMatlabRelease, matlabVersion))
warning('MATLAB_COMPILED:version_mismatch', ...
['You are now running matlab "%s", but the matlab ' ...
'command specified in conf.xml is "%s".\nThere is no ' ...
'guarantee that OAR jobs will work'], ...
currentMatlabRelease, matlabVersion);
end
catch mexc
gtPrintException(mexc, ...
'Couldn''t find matlab version in conf.xml');
end catch mexc
gtPrintException(mexc, ...
'Couldn''t load configuration file, setting default conf.')
GT_DB = struct( ...
'name', default_dbconf.name, ...
'host', default_dbconf.host, ...
'user', default_dbconf.user, ...
'password', default_dbconf.password);
addpath(default_astra_paths.tools);
addpath(default_astra_paths.tools);
end
end