diff --git a/.gitignore b/.gitignore index 5f73f9dcf7b0244f2e198b6df71c98db760ee3b4..1815c889fc495377b5897243f775097d13b88aa9 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,5 @@ Figures/ +data/Other/isoSurfaceGeneration/sepia/ *remoteDir.mat *deepLayerApicalDendrite* *layer2ApicalDendrite* diff --git a/code/+surface/+Scripts/sepia_writePLY.m b/code/+surface/+Scripts/sepia_writePLY.m new file mode 100644 index 0000000000000000000000000000000000000000..4f458b52caec0255cd6fb9eee1bb0dfd62b07900 --- /dev/null +++ b/code/+surface/+Scripts/sepia_writePLY.m @@ -0,0 +1,3 @@ + +p = surface.config_V2_ACC('sepia'); +surface.genIsosurface.fromVolumeTracing(p); \ No newline at end of file diff --git a/code/+surface/+genIsosurface/readVolume.m b/code/+surface/+genIsosurface/readVolume.m index b2fe8dbc690c43da658fae61133b7c191d3205d1..cf3871f27e575923a66cbc2e0747793544db1fdb 100644 --- a/code/+surface/+genIsosurface/readVolume.m +++ b/code/+surface/+genIsosurface/readVolume.m @@ -16,7 +16,7 @@ outdir = fullfile(volAnnotationDir,[volAnnotationFilename,'Raw']); if ~exist(outdir,'dir') util.mkdir(outdir) unzip(fullfile(volAnnotationDir,[volAnnotationFilename,'.zip']), outdir); - unzip(fullfile(outdir,'data'),outdir) + unzip(fullfile(outdir,'data_Volume'),outdir) end % WKW path of first magnification (highest resolution) diff --git a/code/+surface/config_V2_ACC.m b/code/+surface/config_V2_ACC.m index 34970000f8ce360c65845adf323835122a681489..2bb0d523ad1cab6d094d2e57954e70d88d5f5256 100644 --- a/code/+surface/config_V2_ACC.m +++ b/code/+surface/config_V2_ACC.m @@ -29,6 +29,17 @@ if strcmp(dataset,'acc') 'JO_ACC_Z_straightenedPosthoc_version'); p.volAnnotationName = 'ACC_volumeAnnotations'; end + + +if strcmp(dataset,'sepia') + p.raw.voxelSize = [11.24,11.24,30]; + p.bbox = {[0, 0, 0, 1100, 1100, 998]}; + p.treeNames = {'Segment 1'}; + + p.volAnnotationDir = fullfile(p.outputDirectory,... + 'alik_uct_HalfBrain_5_8um_50kV_Air_LE4'); + p.volAnnotationName = 'The_OL_volume'; +end p.bbox = cellfun(@Util.convertWebknossosToMatlabBbox,p.bbox,... 'UniformOutput',false);