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function initialise_gt()
%% INITIALISE.M for Matlab installations on Windows, Macs, and Linux
% in process of being modified - Greg & Wolfgang, August 2005
% should probably change this to a function so that finishing the script
% automatically clears up the variables. Ugly at the moment
% 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
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%
% 2011-2012, Modified and improved by Nicola Vigano', vigano@esrf.fr
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
{'/parallel' },... % embarrasingly parallel matlab (ML and GJ)
{'/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
};
% {'/xml_toolbox' },... % XML read and write tools (Geodise Project)
% {'/compiled' },... % Tools for compiling matlab code
% {'/distortion' },... % ID17 distortion correction (PT et GJ)
current_dir=pwd;
prefix = '';
%%%%%%%%%%%%%%%%%%%%% DO NOT MODIFY BELOW THIS LINE %%%%%%%%%%%%%%%%%%%%%%%
disp('Graintracking settings in progress...');
% XXX - Kind of messy. Multi platform support should be handled in a better way.
disp(['Machine is: ', computer])
% Linux machines
if (exist('/data/id19/archive/matlab/') == 7)
prefix = '/data/id19/archive/matlab/';
else
disp('ERROR: No folder called: "/data/id19/archive/matlab/"')
return
end
% Adding paths
for n = 1:length(pathstruct)
switch size(pathstruct{n}, 2)
addpath(fullfile(prefix, pathstruct{n}{1}))
addpath(fullfile(prefix, pathstruct{n}{1}), pathstruct{n}{2})
otherwise
disp(['Wrong parameters number for entry "', n, '"(', pathstruct{n}{1} ,') of structure "pathstruct"'])
addpath(fullfile(prefix, pathstruct{n}{1}))
end
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% 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')
%set(0,'DefaultAxesFontName','Times')
%set(0,'DefaultAxesFontSize',12)
%set(0,'DefaultTextFontName','Times')
%set(0,'DefaultTextFontSize',12)
% disp('Enabling OpenGL graphics by default - may cause problems with old versions of XMing')
%set(0,'DefaultFigureRenderer','opengl'); % permit hardware acceleration if card exists
% 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')
disp(['Using the DCT code in directory ' current_dir])
global GT_MATLAB_HOME
GT_MATLAB_HOME = current_dir;
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, '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, '8_optimization'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_ART'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Condor'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Cryst'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Cryst', 'file_cif'));
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_ErrorHandling'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_EDF'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_ForwardProjection'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_GVF'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_GUI'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_GUI', 'GUILayout_v1p10'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_GUI', 'GUILayout_v1p10', 'layoutHelp'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_GUI', 'GUILayout_v1p10', 'Patch'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Help'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_ICP'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Imaging'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Imaging', 'pmedf'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Index'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Maths'));
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_Smoothing'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Strain'));
addpath(fullfile(GT_MATLAB_HOME, 'zUtil_XML'));
addpath(fullfile(GT_MATLAB_HOME, 'FigureManagement'));
addpath(fullfile(GT_MATLAB_HOME, 'orthogonal_slicer'));
addpath(fullfile(GT_MATLAB_HOME, 'm2html'));
Wolfgang Ludwig
committed
addpath('/scisoft/users/batenbur/gpu/matlab');
addpath('/scisoft/users/batenbur/gpu/matlab/algorithms');
disp('Finished adding')
cd( current_dir )
