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Merge pull request #78 from MATLAB-Community-Toolboxes-at-INCF/wds_20…
…24_wrap readability improvements and bug fixes
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| @@ -0,0 +1,55 @@ | ||
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| % this script was made to explore the input/output requirements of the | ||
| % pretrained neuropixels network | ||
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| E = [[1:192]' [1:192]'+0.5]; % number electrodes by Y (whole number) and X 2*(mod 1) | ||
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| NP = repmat(E,1,1,500); % 500 frames of data | ||
| % now transpose to be the same as the expected neuropixels data | ||
| NP = permute(NP, [3 1 2]); | ||
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| nb_probes = 384; % Number of probes | ||
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| pre_post_omission = 3; % Number of frames omitted before and after the inferred frame | ||
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| pre_frame = 30; % Number of frames provided before the inferred frame | ||
| post_frame = 30; % Number of frames provided after the inferred frame | ||
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| batch_size = 100; | ||
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| start_frame = 100; | ||
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| end_frame = 200; | ||
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| input_full = single(zeros(batch_size, nb_probes, 2, pre_frame + post_frame)); | ||
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| for frame_index = start_frame:end_frame | ||
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| input_index = (frame_index - pre_frame - pre_post_omission) : (frame_index + post_frame + pre_post_omission ); | ||
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| input_index = input_index(input_index ~= frame_index); % drop the predicted frame | ||
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| for index_padding = 1: pre_post_omission % drop pre_post_omission number of frames surrounding the predicted frame | ||
| input_index = input_index(input_index ~= frame_index - index_padding); | ||
| input_index = input_index(input_index ~= frame_index + index_padding); | ||
| end | ||
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| data_img_input = ephys(input_index, :, :); | ||
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| data_img_input = permute(data_img_input,[2,3,1]); | ||
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| data_img_input = (single(data_img_input) - local_mean) / local_std; | ||
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| % alternating filling with zeros padding | ||
| odd = 1: 2: nb_probes; | ||
| even = odd + 1; | ||
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| input_full(frame_index-start_frame+1, odd, 1, :) = data_img_input(:, 1, :); | ||
| input_full(frame_index-start_frame+1, even, 2, :) = data_img_input(:, 2, :); | ||
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| end | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,58 @@ | ||
| function frame = checkerboard2NPframe(cb) | ||
| % CHECKERBOARD2NPFRAME - convert geometrically realistic matrix to raw Neuropixels Phase 3 format | ||
| % | ||
| % FRAME = CHECKERBOARD2NPFRAME(CB) | ||
| % | ||
| % Convert geometrically-realistic matrix data CB (384 x 2 x NSAMPLES) | ||
| % into a format that matches the raw data output of Neuropixels Phase 3 | ||
| % probes. CB is expected to reflect the checkerboard layout of electrodes, | ||
| % where every even linear index is 0. | ||
| % | ||
| % FRAME will be a 192 x 2 x NSAMPLES matrix. | ||
| % | ||
| % For example, the following single-frame example input where each data point has | ||
| % been set, for illustration purposes, to the electrode number (incremented by 0.25) | ||
| % would be transformed as follows: | ||
| % | ||
| % 1.0000 0 | ||
| % 0 1.2500 | ||
| % 2.0000 0 | ||
| % 0 2.2500 | ||
| % 3.0000 0 | ||
| % 0 3.2500 | ||
| % ... | ||
| % 190.0000 0 | ||
| % 0 190.2500 | ||
| % 191.0000 0 | ||
| % 0 191.2500 | ||
| % 192.0000 0 | ||
| % 0 192.2500 | ||
| % | ||
| % to | ||
| % | ||
| % 1.0000 1.2500 | ||
| % 2.0000 2.2500 | ||
| % 3.0000 3.2500 | ||
| % ... | ||
| % 189.0000 189.2500 | ||
| % 190.0000 190.2500 | ||
| % 191.0000 191.2500 | ||
| % 192.0000 192.2500 | ||
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| % Check input dimensions | ||
| if size(cb, 1) ~= 384 || size(cb, 2) ~= 2 | ||
| error('Input matrix CB must be 384 x 2 x NSAMPLES.'); | ||
| end | ||
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| frame = zeros(size(cb,1)/2, size(cb,2), size(cb,3)); | ||
| odd = 1:2:size(cb,1); | ||
| even = odd + 1; | ||
| frame(:,1,:) = cb(odd,1,:); | ||
| frame(:,2,:) = cb(even,2,:); | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,48 @@ | ||
| function cb = NPframe2checkerboard(frame) | ||
| % NPFRAME2CHECKERBOARD - convert raw Neuropixels Phase 3 to geometrically realistic matrix | ||
| % | ||
| % CB = NPframe2checkerboard(FRAME) | ||
| % | ||
| % Convert Neuropixels data frame data FRAME (192 x 2 x NSAMPLES) | ||
| % into a geometrically-realistic matrix that reflects the checkerboad | ||
| % layout of electrodes such as the Phase 3 version. | ||
| % | ||
| % CB will be a 384 x 2 x NSAMPLES matrix where every even linear index | ||
| % will be 0. | ||
| % | ||
| % For example, the following single-frame example input where each data point has | ||
| % been set, for illustration purposes, to the electrode number (incremented by 0.5) | ||
| % would be transformed as follows: | ||
| % | ||
| % 1.0000 1.5000 | ||
| % 2.0000 2.5000 | ||
| % 3.0000 3.5000 | ||
| % ... | ||
| % 189.0000 189.5000 | ||
| % 190.0000 190.5000 | ||
| % 191.0000 191.5000 | ||
| % | ||
| % to | ||
| % | ||
| % 1.0000 0 | ||
| % 0 1.5000 | ||
| % 2.0000 0 | ||
| % 0 2.5000 | ||
| % 3.0000 0 | ||
| % 0 3.5000 | ||
| %... | ||
| % 190.0000 0 | ||
| % 0 190.5000 | ||
| % 191.0000 0 | ||
| % 0 191.5000 | ||
| % 192.0000 0 | ||
| % 0 192.5000 | ||
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| cb = zeros(size(frame,1)*2,size(frame,2),size(frame,3)); | ||
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| odd = 1:2:size(frame,1)*2; | ||
| even = odd + 1; | ||
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| cb(odd,1,:) = frame(:,1,:); | ||
| cb(even,2,:) = frame(:,2,:); | ||
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