=== creation history === {{{ make_one_nifti.py /l/aba/niis/ make_v3.py niis.npy ~/aba/try8/aba_annotation_ourctx.nii v3.npy norm_hv.py v3.npy gene_list.txt 0.01 norm_hv caret_command -depth-volume ~/aba/try9/aba_annotation_ourctx.nii ~/aba/try8_scaled/Mouse.aba.R.topology_file_367.OPEN.2007-08-28.23460.topo ~/aba/try8_scaled/Mouse.aba.R.coordinate_file_369.2007-08-28.23460.coord ~/aba/try8_scaled/depthVol.nii ~/aba/try8_scaled/tile1Vol.nii ~/aba/try8_scaled/tile2Vol.nii ~/aba/try8_scaled/tile3Vol.nii cd /l/aba/layers/100523_cityblockOverGenesEuclideanOverVoxels_noneighbors_6 find_layers_cluster.py 6 -n 0 ~/aba/norm_hv.npy ~/aba/try8_scaled/depths.npy ~/aba/try8_scaled/surfaceToVolume.p ~/aba/try8_scaled/neighbors.p layers | tee log.txt convert_voxelLayers_npy2nifti.py /l/aba/niis/0610007P14Rik_col8_right layers_4_5_voxelLayers ~/aba/try8/aba_annotation_ourctx cd ~/aba/try8_scaled voxelLayers2metric.py 23460 norm_hv_0.01.npy norm_hv_0.01_names.txt surfaceToVolume.p /l/aba/layers/100523_cityblockOverGenesEuclideanOverVoxels_noneighbors_6/layers_6_92_voxelLayers.npy composite_avgByLayer_try8 cp -i Mouse.aba.R.In.FLAT_CYCLE5.2007-08-28.23460.coord Mouse.aba.R.In.FLAT_CYCLE5.2007-08-28.23460_text.coord caret_file_convert -text Mouse.aba.R.In.FLAT_CYCLE5.2007-08-28.23460_text.coord perl -e 'undef $/; $file = <>; $file =~ s/.*EndHeader\n\d+\n//s; print $file' < Mouse.aba.R.In.FLAT_CYCLE5.2007-08-28.23460_text.coord > flat_cycle5.txt }}} Now, in Python, {{{ from numpy import * x = load('composite_avgByLayer_try8_scaled_avgByLayer.npy') y = empty((size(x,0), size(x,1)*size(x,2))) for gene in range(size(x,2)): for layer in range(size(x,1)): y[:,gene*size(x,1) + layer] = x[:,layer,gene] save('composite_avgByLayer_try8_scaled_interlace.npy',y) }}} Quit and reload to save memory, then savemat: {{{ from numpy import * y = load('composite_avgByLayer_try8_scaled_interlace.npy') from scipy import io io.savemat('composite_avgByLayer_try8_scaled.mat', {'A' : y}) }}} Now, in Octave, {{{ A = load('composite_avgByLayer_try8_scaled.mat'); sampleDist = 200; % microns flatcycle5 = load('flat_cycle5.txt'); [XI, YI, ZI] = my_griddata(flatcycle5(:,2),flatcycle5(:,3),flatcycle5(:,1),min(flatcycle5(:,2)):sampleDist:max(flatcycle5(:,2)),min(flatcycle5(:,3)):sampleDist:max(flatcycle5(:,3)),'nearest',sampleDist); % test D = A(ZI+1,1); D= reshape(D,size(ZI)); max(max(D - ZI)) %ans = 0 D= zeros([size(ZI) size(A,2)-1]); for gene=2:size(A,2) D(:,:,gene-1) = A(ZI + 1,gene); D(find(0 == ZI) + (gene-2).*prod(size(ZI))) = NaN; end % test im = D(:,:,1); im(isnan(im)) = 0; imagesc(flipud(im)) save -mat-binary 'data_try8_scaled_right_layerAvg.mat' D paintFile = load('paint.txt'); paint = paintFile(ZI + 1, 2); paint = reshape(paint, size(ZI)); paint(find(0 == ZI)) = NaN; % test im = paint; im(isnan(im)) = 0; imagesc(flipud(im)) % test for i=1:30 %printf('%d: %d\n', i, length(find(paint == i))) j(i) = length(find(paint == i)); end find(j == 0) %ans = % 9 10 11 clear i j save -mat-binary 'data_try8_scaled_right_layerAvg.mat' D notNaNIndices = find(~isnan(paint(:))); paint2 = paint(:); paint3 = paint2(notNaNIndices); save('-mat', 'paint.mat', 'paint', 'paint2', 'paint3') D2 = zeros(size(D,1)*size(D,2),size(D,3)); for i=1:size(D,3) dd = D(:,:,i); D2(:,i) = dd(:); %i end notNaNIndices = find(~isnan(D2(:,1))); D3 = D2(notNaNIndices,:); D_valid = ~isnan(D(:,:,1)); D_NaNs = isnan(D(:,:,1)).*D(:,:,1); D_NaNs_and_ones = D_NaNs + 1; D_vert = repmat((1:size(D,1))',1,size(D,2)) .* D_NaNs_and_ones; D_horiz = repmat((1:size(D,2)),size(D,1),1) .* D_NaNs_and_ones; D_vert2 = D_vert(:); D_horiz2 = D_horiz(:); % test max(find(~isnan(D_vert2)) - find(~isnan(D_horiz2))) % ans = 0 notNaNIndices = find(~isnan(D_vert2)); D_vert3 = D_vert2(notNaNIndices,:); D_horiz3 = D_horiz2(notNaNIndices,:); % test testColumn = D3(:,1); im = []; for i=1:size(testColumn,1) im(D_vert3(i),D_horiz3(i),:) = testColumn(i,:); end imagesc(flipud(im)) save ('-mat','data_try8_scaled_right_layerAvg_start.mat', 'D', 'D2', 'D3', 'D_valid', 'D_NaNs', 'D_NaNs_and_ones', 'D_vert', 'D_horiz', 'D_vert2', 'D_horiz2', 'D_vert3','D_horiz3') }}} See also [[Mouse.aba.R.In.FLAT_CYCLE5.2007-08-28.23460.coord]] ---- CategoryDataSetFile
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