Cleaned code

stabix · Nov 14, 2014 · 7edd106 · 7edd106
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commit 7edd106
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Showing 23 changed files with 237 additions and 102 deletions.
diff --git a/MTEX_functions/MTEX_getBX_misorientation.m b/MTEX_functions/MTEX_getBX_misorientation.m
@@ -1,5 +1,6 @@
 % Copyright 2013 Max-Planck-Institut für Eisenforschung GmbH
-function misorientation = MTEX_getBX_misorientation(ori_grainA, ori_grainB, varargin)
+function misorientation = ...
+    MTEX_getBX_misorientation(ori_grainA, ori_grainB, varargin)
 %% MTEX function used for the calculation of the misorientation between 2 grains in degrees
 % Cho J.-H. et al., "Determination of a Mean Orientation in Electron
 % Backscatter Diffraction Measurements", Met. & Mat. Trans. A, 2005, Vol.36A, pp. 3427.

diff --git a/MTEX_functions/MTEX_setBX_orientation.m b/MTEX_functions/MTEX_setBX_orientation.m
@@ -1,5 +1,6 @@
 % Copyright 2013 Max-Planck-Institut für Eisenforschung GmbH
-function ori_grain = MTEX_setBX_orientation(phase, ca_ratio, eulers_angle, varargin)
+function ori_grain = ...
+    MTEX_setBX_orientation(phase, ca_ratio, eulers_angle, varargin)
 %% Set orientation of a grain by using MTEX function
 % phase = Crystal Structure (CS for MTEX)
 % eulers_angle = Euler angles (Bunge) in degrees

diff --git a/YAML_functions/load_YAML_BX_example_config_file.m b/YAML_functions/load_YAML_BX_example_config_file.m
@@ -95,7 +95,9 @@
 end
 
 %% Set specific slips for grains A and B
-if (~isfield(GB_YAML, 'SlipA_norm') && ~isfield(GB_YAML, 'SlipA_dir')) && (~isfield(GB_YAML, 'SlipB_norm') && ~isfield(GB_YAML, 'SlipB_dir'))
+if (~isfield(GB_YAML, 'SlipA_norm') && ~isfield(GB_YAML, 'SlipA_dir')) ...
+        && (~isfield(GB_YAML, 'SlipB_norm') ...
+        && ~isfield(GB_YAML, 'SlipB_dir'))
     GB_YAML.SlipA_norm = {[0], [0], [0], [1]};
     GB_YAML.SlipA_dir  = {[2], [-1], [-1], [0]};
     GB_YAML.SlipB_norm = {[0], [0], [0], [1]};
@@ -116,8 +118,10 @@
 
 slipA_all_vect = slip_systems(GB_YAML.Phase_A, 9);
 slipB_all_vect = slip_systems(GB_YAML.Phase_B, 9);
-specific_slips_A = get_slip_indices(GB_YAML.slipA_str_dir, slipA_all_vect, 2);
-specific_slips_B = get_slip_indices(GB_YAML.slipB_str_dir, slipB_all_vect, 2);
+specific_slips_A = ...
+    get_slip_indices(GB_YAML.slipA_str_dir, slipA_all_vect, 2);
+specific_slips_B = ...
+    get_slip_indices(GB_YAML.slipB_str_dir, slipB_all_vect, 2);
 
 specific_slips_AB = [specific_slips_A, specific_slips_B];
 
@@ -151,4 +155,4 @@
 end
 clear Names;
 
-end
+end
diff --git a/coordinate_system/coordinate_convention.m b/coordinate_system/coordinate_convention.m
@@ -1,5 +1,6 @@
 % Copyright 2013 Max-Planck-Institut für Eisenforschung GmbH
-function coordinate_convention_matrix = coordinate_convention(coordinate_angle, varargin)
+function coordinate_convention_matrix = ...
+    coordinate_convention(coordinate_angle, varargin)
 % coordinate_angle: Angle to rotate coordinate system of EBSD system
 
 % Z out of the plane
@@ -53,4 +54,4 @@
     coordinate_convention_matrix;
 end
 
-end
+end
diff --git a/coordinate_system/coordinate_system_apply.m b/coordinate_system/coordinate_system_apply.m
@@ -1,11 +1,12 @@
 % Copyright 2013 Max-Planck-Institut für Eisenforschung GmbH
-function eulers_out = coordinate_system_apply(eulers_in, CCM, testFlag, varargin)
+function eulers_out = ...
+    coordinate_system_apply(eulers_in, CCM, testFlag, varargin)
 %% Function used to apply the user selected coordinate system to the orientation
 % eulers_in : Euler angles in degree before modification of the coordinates sytem
 % ccm (coordinate convention matrix): Results from the function coordinate_convention_matrix.m
 % testFlag: Flag to test the function (1 if the user want to test)
 
-% author: c.zambaldi@mpie.de / d.mercier@mpie.de
+% authors: c.zambaldi@mpie.de / d.mercier@mpie.de
 
 if nargin < 3
     testFlag = false;
@@ -33,8 +34,10 @@
 eulers_out = g2eulers(g_out);
 
 if testFlag
-    fprintf('Euler angles in : %.1f° %.1f° %.1f°\n',eulers_in(1),eulers_in(2),eulers_in(3));
-    fprintf('Euler angles out : %.1f° %.1f° %.1f°\n',eulers_out(1),eulers_out(2),eulers_out(3));
+    fprintf('Euler angles in : %.1f° %.1f° %.1f°\n', ...
+        eulers_in(1),eulers_in(2),eulers_in(3));
+    fprintf('Euler angles out : %.1f° %.1f° %.1f°\n', ...
+        eulers_out(1),eulers_out(2),eulers_out(3));
 end
 
 end
diff --git a/gui_preCPFE/abaqus/abaqus_bias.m b/gui_preCPFE/abaqus/abaqus_bias.m
@@ -68,7 +68,8 @@
 
 if testing
     % for p = 2, num_elem = 10 and length = 10
-    dist0 = [1.380, 1.278, 1.183, 1.095, 1.014, 0.94, 0.87, 0.81, 0.75, 0.69];
+    dist0 = [1.380, 1.278, 1.183, 1.095, 1.014, ...
+        0.94, 0.87, 0.81, 0.75, 0.69];
     if p == -2 || p == 0.5
         dist0 = fliplr(dist0);
     end

diff --git a/gui_preCPFE/marc_mentat/mentat_bias.m b/gui_preCPFE/marc_mentat/mentat_bias.m
@@ -41,7 +41,8 @@
 biased_elem(1) = t_true(1);
 for jj = 1:num_elements
     ratio(jj) = (t_star(jj+1)-t_star(jj))/(t(jj+1)-t(jj));
-    biased_elem(jj+1) = ratio(jj) * (t_true(jj+1)-t_true(jj)) + biased_elem(jj);
+    biased_elem(jj+1) = ratio(jj) * ...
+        (t_true(jj+1)-t_true(jj)) + biased_elem(jj);
 end
 
 if testing

diff --git a/gui_preCPFE/preCPFE_indentation_setting_BX.m b/gui_preCPFE/preCPFE_indentation_setting_BX.m
@@ -288,7 +288,8 @@
 gdata.variables_geom.top8121617_y(:) = gdata.variables.sample_coordy_rightface;
 
 %% Clear axes
-cla;shg
+cla;
+shg;
 
 %% Plot the sample mesh
 

diff --git a/gwyddion/read_gwyddion_ascii.m b/gwyddion/read_gwyddion_ascii.m
@@ -102,4 +102,4 @@
     topo_plot(topo)
     set(gcf,'name','original data');
 end
-return
+return
diff --git a/microstructure_generation/neighbooring_edge_of_2cells.m b/microstructure_generation/neighbooring_edge_of_2cells.m
@@ -17,7 +17,8 @@
 [v, reg] = voronoiDiagram(dt);
 if length(reg) ~= size(dt.X,1)
     % My 2012B might end up here, which I think is a bug (due to numerical errors)
-    disp('voronoiDiagram fails (bug)');
+    commandwindow;
+    error('voronoiDiagram fails (bug)');
     random_2D_microstructure_data;
 end
 K = dt.convexHull;
@@ -60,19 +61,21 @@
 
     % which edge is infinity
     edgeinf = edges(:,1)==1;
-    [~, locinf]=ismember(sort(ridx(:,edgeinf))',sort([K(1:end-1) K(2:end)],2),'rows');
+    [~, locinf] = ismember(sort(ridx(:,edgeinf))', ...
+        sort([K(1:end-1) K(2:end)],2),'rows');
     vx(1,edgeinf) = XInf(1,locinf);
     vy(1,edgeinf) = XInf(2,locinf);
 
     xr = x(ridx);
     yr = y(ridx);
 
     if flag
-        figure(1)
-        clf
-        plot(x,y,'r+',vx,vy,'b-o',xr,yr,'g')
-        axis equal
+        figure(1);
+        clf;
+        plot(x,y,'r+',vx,vy,'b-o',xr,yr,'g');
+        axis equal;
         axis([-0.5 1.5 -0.5 1.5]);
-        disp (ridx)
+        disp (ridx);
     end
+end
 end
diff --git a/microstructure_generation/random_2D_microstructure_data.m b/microstructure_generation/random_2D_microstructure_data.m
@@ -1,5 +1,6 @@
 % Copyright 2013 Max-Planck-Institut für Eisenforschung GmbH
-function rdm_microstructure_dataset = random_2D_microstructure_data (number_of_grains, resolution, varargin)
+function rdm_microstructure_dataset = ...
+    random_2D_microstructure_data(number_of_grains, resolution, varargin)
 %% Function used to create random EBSD data based on TSL files (GF Type2 and RB file)
 % number_of_grains : Number of grains for the Voronoi tesselation
 % resolution : resolution along x and y axis for generation of seeds file
@@ -48,12 +49,19 @@
 end
 
 % GBs endpoints coordinates
-[rdm_microstructure_dataset.GBvx, rdm_microstructure_dataset.GBvy, rdm_microstructure_dataset.GB2cells(:,:), rdm_microstructure_dataset.flag_VorFailed] = ...
-    neighbooring_edge_of_2cells(rdm_microstructure_dataset.x_positions', rdm_microstructure_dataset.y_positions');
+[rdm_microstructure_dataset.GBvx, ...
+    rdm_microstructure_dataset.GBvy, ...
+    rdm_microstructure_dataset.GB2cells(:,:), ...
+    rdm_microstructure_dataset.flag_VorFailed] = ...
+    neighbooring_edge_of_2cells(...
+    rdm_microstructure_dataset.x_positions', ...
+    rdm_microstructure_dataset.y_positions');
 
 % GBs coordinates
-GB(1,:) = rdm_microstructure_dataset.GBvx(2,:) - rdm_microstructure_dataset.GBvx(1,:);
-GB(2,:) = rdm_microstructure_dataset.GBvy(2,:) - rdm_microstructure_dataset.GBvy(1,:);
+GB(1,:) = rdm_microstructure_dataset.GBvx(2,:) - ...
+    rdm_microstructure_dataset.GBvx(1,:);
+GB(2,:) = rdm_microstructure_dataset.GBvy(2,:) - ...
+    rdm_microstructure_dataset.GBvy(1,:);
 GB(3,:) = zeros;
 
 % flag is to know if the voronoiDiagram fails (degenerated case?)
@@ -79,17 +87,21 @@
     rdm_microstructure_dataset.gb_length(1,ii) = norm(GB(ii));
 
     CosTheta = dot(GB(:,ii),[1,0,0])/(norm(GB(:,ii))*norm([1,0,0]));
-    rdm_microstructure_dataset.gb_trace_angle(1,ii) = acos(CosTheta)*180/pi;
+    rdm_microstructure_dataset.gb_trace_angle(1,ii) = ...
+        acos(CosTheta)*180/pi;
 end
 
 rdm_microstructure_dataset.GBvx = rdm_microstructure_dataset.GBvx';
 rdm_microstructure_dataset.GBvy = rdm_microstructure_dataset.GBvy';
 rdm_microstructure_dataset.GB2cells = rdm_microstructure_dataset.GB2cells';
 
-rdm_microstructure_dataset.confidence_index = ones((resolution*resolution), 1);
-rdm_microstructure_dataset.image_quality = ones((resolution*resolution), 1);
+rdm_microstructure_dataset.confidence_index = ...
+    ones((resolution*resolution), 1);
+rdm_microstructure_dataset.image_quality = ...
+    ones((resolution*resolution), 1);
 rdm_microstructure_dataset.phase_ang = ones((resolution*resolution), 1);
-rdm_microstructure_dataset.detector_intensity  = ones((resolution*resolution), 1);
+rdm_microstructure_dataset.detector_intensity = ...
+    ones((resolution*resolution), 1);
 rdm_microstructure_dataset.fit = ones((resolution*resolution), 1);
 
 rdm_microstructure_dataset.x_pixel_pos = 1:(resolution*resolution);

diff --git a/preCPFE_mesh_plot_finalize.m b/preCPFE_mesh_plot_finalize.m
@@ -1,8 +1,12 @@
+% Copyright 2013 Max-Planck-Institut für Eisenforschung GmbH
 function preCPFE_mesh_plot_finalize
-% Axis setting
+%% Axis setting
+
 axis tight; % Axis tight to the sample
 axis equal; % Axis aspect ratio
-grid off
-xyzlabel
-rotate3d on
-shg
+grid off;
+xyzlabel;
+rotate3d on;
+shg;
+
+end
diff --git a/tsl_oim/open_file_GF2.m b/tsl_oim/open_file_GF2.m
@@ -15,7 +15,9 @@ function open_file_GF2(starting_folder, varargin)
 % authors: c.zambaldi@mpie.de / d.mercier@mpie.de
 
 if nargin == 0
-    starting_folder = fullfile(getenv('SLIP_TRANSFER_TBX_ROOT'), 'gui_ebsd_map', 'EBSD_data_Examples');
+    starting_folder = ...
+        fullfile(get_stabix_root, ...
+        'gui_ebsd_map', 'EBSD_data_Examples');
 end
 
 %% Get data from the GUI
@@ -24,7 +26,9 @@ function open_file_GF2(starting_folder, varargin)
 cd(starting_folder);
 
 %% FileGF2 loading
-[filenameGF2, pathnameGF2] = uigetfile([gui.config_map.TSLOIM_data_path_GF2, '.txt'], 'Select the ''Grain File Type 2'' file');
+[filenameGF2, pathnameGF2] = ...
+    uigetfile([gui.config_map.TSLOIM_data_path_GF2, '.txt'], ...
+    'Select the ''Grain File Type 2'' file');
 % Handle canceled file selection
 if filenameGF2 == 0
     filenameGF2 = '';
@@ -51,6 +55,6 @@ function open_file_GF2(starting_folder, varargin)
 
 guidata(gcf, gui);
 
-cd(getenv('SLIP_TRANSFER_TBX_ROOT'));
+cd(get_stabix_root);
 
 end
diff --git a/tsl_oim/open_file_RB.m b/tsl_oim/open_file_RB.m
@@ -16,7 +16,8 @@ function open_file_RB(starting_folder, varargin)
 % authors: c.zambaldi@mpie.de / d.mercier@mpie.de
 
 if nargin == 0
-    starting_folder = fullfile(getenv('SLIP_TRANSFER_TBX_ROOT'), 'gui_ebsd_map', 'EBSD_data_Examples');
+    starting_folder = fullfile(get_stabix_root, ...
+        'gui_ebsd_map', 'EBSD_data_Examples');
 end
 
 %% Get data from the GUI
@@ -25,7 +26,9 @@ function open_file_RB(starting_folder, varargin)
 cd(starting_folder);
 
 %% FileRB loading
-[filenameRB, pathnameRB] = uigetfile([gui.config_map.TSLOIM_data_path_GF2, '.txt'], 'Select the ''Reconstructed Boundary'' file');
+[filenameRB, pathnameRB] = ...
+    uigetfile([gui.config_map.TSLOIM_data_path_GF2, '.txt'], ...
+    'Select the ''Reconstructed Boundary'' file');
 % Handle canceled file selection
 if filenameRB == 0
     filenameRB = '';
@@ -52,6 +55,6 @@ function open_file_RB(starting_folder, varargin)
 
 guidata(gcf, gui);
 
-cd(getenv('SLIP_TRANSFER_TBX_ROOT'));
+cd(get_stabix_root);
 
 end
diff --git a/tsl_oim/read_oim_grain_file_type2.m b/tsl_oim/read_oim_grain_file_type2.m
@@ -66,12 +66,14 @@
             DIAM_OK = true;
         end
     else
-        if ~(GRAIN_NUMBERS_OK && EULER_ANGLES_OK && AVG_POS_XY_OK && PHASE_OK)
+        if ~(GRAIN_NUMBERS_OK && EULER_ANGLES_OK && ...
+                AVG_POS_XY_OK && PHASE_OK)
             fclose(fid);
             error('Grain File Type 2 columns are wrong !')
         end
         if ~(EDGE_GRAIN_OK && DIAM_OK)
-            warning('Missing information if edge or interior grain, and diameter of grains !')
+            warning(['Missing information if edge or interior grain, ' ...
+                'and diameter of grains !'])
         end
         ii = ii + 1;
         data(ii,:) = sscanf(ln,'%f');

diff --git a/tsl_oim/read_oim_reconstructed_boundaries_file.m b/tsl_oim/read_oim_reconstructed_boundaries_file.m
@@ -1,5 +1,6 @@
 % Copyright 2013 Max-Planck-Institut für Eisenforschung GmbH
-function RB = read_oim_reconstructed_boundaries_file(fname, fpath, varargin)
+function RB = ...
+    read_oim_reconstructed_boundaries_file(fname, fpath, varargin)
 %% Function to read TSL-OIM reconstructed boundaries file
 % fname : Name of the reconstructed boundaries file
 % fpath : Path to the reconstructed boundaries file
@@ -48,10 +49,12 @@
     ln = fgetl(fid);
     if ln(1) == '#';
         header{end+1} = ln;
-        if strfind(ln, 'right hand average orientation (phi1, PHI, phi2 in radians)')
+        if strfind(ln, ['right hand average orientation ' ...
+                '(phi1, PHI, phi2 in radians)'])
             RIGHT_ORI_OK = true;
         end
-        if strfind(ln, 'left hand average orientation (phi1, PHI, phi2 in radians)')
+        if strfind(ln, ['left hand average orientation ' ...
+                '(phi1, PHI, phi2 in radians)'])
             LEFT_ORI_OK = true;
         end
         if strfind(ln, 'length (in microns)')
@@ -67,7 +70,8 @@
             ID_GRAINS_OK = true;
         end
     else
-        if ~(RIGHT_ORI_OK && LEFT_ORI_OK && GB_LENGTH_OK&& GB_TRACE_ANGLE_OK&& GB_ENDPOINTS_COORD_OK && ID_GRAINS_OK)
+        if ~(RIGHT_ORI_OK && LEFT_ORI_OK && GB_LENGTH_OK && ...
+                GB_TRACE_ANGLE_OK&& GB_ENDPOINTS_COORD_OK && ID_GRAINS_OK)
            fclose(fid);
            error('Reconstructed Boundaries File columns are wrong !')
         end
@@ -123,5 +127,4 @@
             col_idx.GRAIN_ID = idx;
         end
     end
-end
-
+end