data try8 scaled right layerAvg.mat

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