ENH: Sevral changes and enhancements.

francopestilli · Sep 12, 2016 · 67e3b63 · 67e3b63
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commit 67e3b63
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Showing 34 changed files with 4 additions and 9 deletions.
diff --git a/.gitignore b/.gitignore
diff --git a/LICENSE b/LICENSE
diff --git a/README.md b/README.md
diff --git a/compute/mbaComputeFiberLengthDistribution.m b/compute/mbaComputeFiberLengthDistribution.m
diff --git a/compute/mbaComputeFibersCoordsDistribution.m b/compute/mbaComputeFibersCoordsDistribution.m
diff --git a/compute/mbaComputeFibersOutliers.m b/compute/mbaComputeFibersOutliers.m
diff --git a/compute/mbaRemoveFiberLengthOutliers.m b/compute/mbaRemoveFiberLengthOutliers.m
diff --git a/compute/mbaRemoveFibersCoordsDistributionOutlier.m b/compute/mbaRemoveFibersCoordsDistributionOutlier.m
diff --git a/display/mbaBuildFascicleFrame.m b/display/mbaBuildFascicleFrame.m
diff --git a/display/mbaDisplayBrainSlice.m b/display/mbaDisplayBrainSlice.m
@@ -1,4 +1,4 @@
-function h = mbaDisplayBrainSlice(nifti, slice, cmap, rescale,alpha)
+function h = mbaDisplayBrainSlice(nifti, slice, ax, cmap, rescale,alpha)
 % 
 % Add a slice from a nifti image to a matlab plot
 %
@@ -49,22 +49,22 @@
 if find(plane) == 1
     % Add the img to the current 3D plot
     z_dims = [z.min z.max; z.min z.max];
-    h = surf([x.min x.max],[y.min y.max],z_dims,...
+    h = surf(ax,[x.min x.max],[y.min y.max],z_dims,...
         image_rgb,'facecolor','texture','faceAlpha',alpha);
 elseif find(plane) == 2
     % The img dimensions must be permuted to match what is expected in
     % surf
     image_rgb = permute(image_rgb,[2 1 3]);
     % Add the img to the current 3D plot
     z_dims = [z.min z.min;   z.max z.max];
-    h = surf([x.min x.max],[y.min y.max],z_dims,...
+    h = surf(ax,[x.min x.max],[y.min y.max],z_dims,...
         image_rgb,'facecolor','texture','FaceAlpha',alpha);
 elseif find(plane) == 3
     % The img dimensions must be permuted to match what is expected in
     % surf
     image_rgb = permute(image_rgb,[2 1 3]);
     % Add the img to the current 3D plot
-    h = surf([x.min x.max],[y.min y.max],repmat(z.min, [2 2]),...
+    h = surf(ax, [x.min x.max],[y.min y.max],repmat(z.min, [2 2]),...
         image_rgb,'facecolor','texture','FaceAlpha',alpha);
 end
 

diff --git a/display/mbaDisplayConnectome.m b/display/mbaDisplayConnectome.m
@@ -25,10 +25,6 @@
 tic
 fprintf('[%s] Displaying connectome... ',mfilename);
 
-% Handling parallel processing
-poolwasopen=1; % if a matlabpool was open already we do not open nor close one
-if (matlabpool('size') == 0), matlabpool open; poolwasopen=0; end
-
 % Check if a fgure handle was passed in, otherwise open a figure
 if notDefined('figureHandle'), figureHandle = figure('Renderer','OpenGL');end
 
@@ -137,7 +133,6 @@
 % Done
 t = toc;
 fprintf('done in  %2.3f seconds at %2.3f ms/fiber.\n',t,(t/numFibers)*1000);
-	    keyboard
 
 end % end MAIN function
 

diff --git a/display/mbaDisplayFasciclesGroup.m b/display/mbaDisplayFasciclesGroup.m
diff --git a/display/mbaDisplayOverlay.m b/display/mbaDisplayOverlay.m
diff --git a/display/mbaFiberSplitLoops.m b/display/mbaFiberSplitLoops.m
diff --git a/externals/fs_annotationToLabelFiles.m b/externals/fs_annotationToLabelFiles.m
diff --git a/externals/fs_labelFileToNiftiRoi.m b/externals/fs_labelFileToNiftiRoi.m
diff --git a/externals/fs_loadCtab.m b/externals/fs_loadCtab.m
diff --git a/externals/fs_read_annotation.m b/externals/fs_read_annotation.m
diff --git a/t_mba_segment_tract.m b/t_mba_segment_tract.m
diff --git a/utilities/build3Dframe.m b/utilities/build3Dframe.m
diff --git a/utilities/frame.m b/utilities/frame.m
diff --git a/utilities/mbaBuild3Dframe.m b/utilities/mbaBuild3Dframe.m
diff --git a/utilities/mbaBuildSurfaceFromFrame.m b/utilities/mbaBuildSurfaceFromFrame.m
diff --git a/utilities/mbaCheckSlice.m b/utilities/mbaCheckSlice.m
diff --git a/utilities/mbaGetResizedSliceImage.m b/utilities/mbaGetResizedSliceImage.m
diff --git a/utilities/mbaGetSliceFromNifti.m b/utilities/mbaGetSliceFromNifti.m
diff --git a/utilities/mbaGetSliceView.m b/utilities/mbaGetSliceView.m
diff --git a/utilities/mbaImageHistogramClip.m b/utilities/mbaImageHistogramClip.m
diff --git a/utilities/mbaMakeImageFromNiftiSlice.m b/utilities/mbaMakeImageFromNiftiSlice.m
diff --git a/utilities/mbaMakeOverlay.m b/utilities/mbaMakeOverlay.m
diff --git a/utilities/mbaNormalize.m b/utilities/mbaNormalize.m
diff --git a/utilities/mbaResampleToNifti.m b/utilities/mbaResampleToNifti.m
diff --git a/utilities/mbaReslice.m b/utilities/mbaReslice.m
diff --git a/utilities/mbaXformAcpcSlice2ImageIndices.m b/utilities/mbaXformAcpcSlice2ImageIndices.m