sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
2f8c1fc6cbe852ff384f7447bc0e223133c30128cb06defee06e1bc7f15eeeae | MATLAB | 484 | 19 | function imwritestack(stack, filename)
im = Tiff(filename, 'w');
infostruct.ImageLength = size(stack, 1);
infostruct.ImageWidth = size(stack, 2);
infostruct.Photometric = Tiff.Photometric.MinIsBlack;
infostruct.BitsPerSample =16;
infostruct.SampleFormat = Tiff.SampleFormat.UInt;
infostruct.PlanarConfiguration = Tiff.... |
6c09e147cba574be9cdfbc149f0575e9f0ad1c0a1c8d4e7d1702e7a5b063e87a | MATLAB | 492 | 17 | function [p_value, jack_se1,jack_se2] = compareHeritability(h2_1, se_1, h2_2, se_2)
n_fam = length(se_1);
A = (n_fam-1)/n_fam;
B1 = sum((se_1 - sum(se_1/n_fam)).^2);
h2_var1 = A*B1;
jack_se1 = sqrt(h2_var1);
B2 = sum((se_2 - sum(se_2/n_fam)).^2);
h2_var2 = A*B2;
jack_se2 = sqrt(h2_var2);
% Cal... |
38e67d170cf7aef85aed199168df602608472e15f1a6e704d05f666ef5b00837 | MATLAB | 498 | 11 | function binPixInd = mat2binInd(obj, matPixInd)
% mat2binInd(acq, ind) converts a Matlab-conventional index (into a movie
% frame) into an index that can be used with the column-major binary movie
% file.
% Assume all slices and Channels have same image size
movRows = obj.correctedMovies.slice(1).channel(1).size(1,1);... |
319d0237e1d2cd147cfa8fd374bbe5925ef2e2335a3ed92acc9d006edea96a37 | MATLAB | 501 | 13 | function window = getWindow(signal, center, window_size)
half_window = floor(window_size / 2);
start_idx = max(1, center - half_window);
end_idx = min(length(signal), center + half_window);
window = signal(start_idx:end_idx);
% Zero-pad if near edges
if length(window) < window_size
... |
762729f6692d6a30b005969012fe26fc19dea8370d914ca4996d33c7d42fe61b | MATLAB | 505 | 22 | function mov = translateAcq(mov, xShift, yShift, fillval)
if nargin < 4
fillval = nan;
end
[h, w, z] = size(mov);
referenceFrame = imref2d([h, w]);
parfor f = 1:z
% if mod(f,250)==0
% display(sprintf('Applying frame shift %d of %d',f,z)),
% end
tformMat = eye(3);
tformMat(3, 1) = xShift(... |
15d97ba8293e937540e5389ca878750535e636ac76571f2cc8ca0f7c67867bd6 | MATLAB | 519 | 18 | function grid = vector_to_symmetric_grid(vec,num_net)
% Initialize a matrix of zeros
grid = zeros(num_net, num_net);
% Index to keep track of the position in the vector
idx = 1;
% Fill in the upper triangle of the matrix, including the diagonal
for i = 1:num_net
for j = i:num_net
... |
e6014211e4a674f69878e8def8f679e3b32579cd15d0d542bc57ee48e5bd5e92 | MATLAB | 535 | 18 | folder = '\\harvey-rotScope-scanimage\C\data\Matthias\MM102\MM102_160730';
oldStr = 'MM102_160730_depthstart_00002';
newStr = 'MM102_160730_main_00001';
lst = dir(fullfile(folder, '*.tif'));
for f = lst(:)'
if isempty(strfind(f.name, oldStr))
continue
end
newName = strrep(f.name, oldStr, newStr);... |
c2567c57b20bb1d400152b47765ed11e5bc5e667ce7b76bb4f0a67493cef5361 | MATLAB | 536 | 16 | function cbKeypressTraceWin(sel, ~, evt)
%Allows for keypresses from the traces figures
switch evt.Key
case {'1', '2', '3', '4', '5', '6', '7', '8', '9'}
% cRoi is the unique number that the current ROI will get. It is
% not stored globally but always determined locally from the
% roiInfo s... |
e2ad72b9d9cac19bd9ab556aa8b6e6c2ab6b14afe371206a74558dac43d2410d | MATLAB | 547 | 13 | function y=generate_psf(gama,kernelRadius_user)
gama=gama/(2.335); % gama is fwhm, new gama is sigma
kernelRadius_default = ceil(gama* sqrt(-2* log(0.0002)))+1; % if the kernel radius is not defined instead of fwhm, use fw at 0.0002 of the maximum
if nargin == 1
kernelRadius = kernelRadius_default;
else
k... |
a0aee08ae67b8037d4b821dc46aa6cd6008f7944861300df96a1111c266c1ab6 | MATLAB | 554 | 13 | cd('Z:\Laura\code_workspace\LD187')
mouseDir = pwd;
sessionList = dir('LD*');
destDir = ['C:\DATA\Laura\code_workspace\' sessionList(1).name(1:5)];
for session = 7:9%:size(sessionList)
cd(fullfile(mouseDir,sessionList(session).name))
load(['selected_rois_' sessionList(session).name(1:12)],'acq')
if ~exist(f... |
4b9a7a7a8ea546c24b1a6fee4dda60949400db6be1fb4a61583b2ff76133a611 | MATLAB | 558 | 15 | function A = runningPrctile(A, winSize, prctile)
% runningPrctile(A, winSize, prctile)
assert(isvector(A), 'A must be a vector')
assert(winSize>=1 && winSize<=numel(A) && round(winSize)==winSize, ...
'winSize must be an integer between 1 and numel(A)');
assert(prctile>=0 && prctile <=100, 'prctile must be between ... |
815e7f14742af36666932f8912ecd98b4c43e85c4eea258d432e77722f2e40d0 | MATLAB | 566 | 16 | clearvars
mainpath = '/home/tud1006235/Documents/Simulated_Data/PxSize_100nm/10_Dens1000_sbr15vs5_nonst_otf2000_on20/Test/Noisy/';
[TifPaths, fileNames] = getTifFilePaths(mainpath, '*.tif');
Imax = 5000;
outpath = [fileparts(mainpath) 'N_max' num2str(Imax) '/'];
mkdir(outpath);
for nf = 1: numel(TifPaths)
imref = d... |
2f384a73824d49ec387045ae86ce888aec4a6d296519b910f07c046f0b3f50c8 | MATLAB | 591 | 21 | %% Pipeline for Concentric Circles
% nina fultz - february 24th
cd concentricCircles/
%% using inflow effect at 7T to make vessel mask
makingVesselfromT1.m
%% dilating vessels so that it hits the CSF signal scan
VesselDilatingwithBoundaries.m
%% manually correct those vessels
%% make concentric circles on all p... |
736be7292b69a41482dec5c8900f74e5a1f75bcb487c2b7fbfa86871576d8043 | MATLAB | 611 | 26 | function int = calculate_int(subj_data)
% Get the size of subj_data
[trs, vertices] = size(subj_data);
% Initialize INT array
int = zeros(vertices, 1);
% Calculate INT for each vertex and each subject
parfor v = 1:vertices
% Extract the BOLD time series for the kth vertex
bold_ts = squeeze(subj_data(:, v));... |
230aa44d663acfb129743fdcbb6c4ec7cd175089c8332d2697fe62b5b567e723 | MATLAB | 615 | 23 | %% segmenting t1s
clear;
%%
GENERALDIR = 'R:\- Gorter\- Personal folders\Fultz, N\csfdonuts_lydiane\'
addpath(genpath('R:\- Gorter\- Personal folders\Fultz, N\scripts\csfdonuts_lydiane\functions'));
allSubjects = dir([GENERALDIR '*20201014_Reconstruction']);
subjectNb = 1;
subject = allSubjects(subjectN... |
027b6f4f9bc7c072b7318fb57d5666e648d7b913ee5fa912b5e2a3d5a5cd055f | MATLAB | 626 | 23 | function anchor_starts = find_speed_crossings(speed, reset, threshold)
anchor_starts = [];
num_laps = length(reset) - 1;
for i = 1:num_laps
% Get current lap boundaries
start_idx = reset(i);
end_idx = reset(i+1) - 1;
% Extract lap speed data
lap_speed = speed(start_idx:end_idx);
%... |
3f95c11946a09a2d1048bf403cae9baa253ed262d4432a3519af7ab927402e48 | MATLAB | 655 | 35 | %% csf donuts plots
fig_crosssec_and_barplots.m
fig_violinplots.m
fig_violinplots_aca_m1_postm1.m
fig_violinplots_aca_m1_postm1_FA.m
fig_violinplots_b0.m
fig_violinplots_FA.m
doubledonuts_crosssec.m %fig 2k
%% creating the vectors
rgb_maps.m
just_vectors_not_rgb.m
%% physio retrospectiv... |
f6c882d4a9bac4d8f9aaf750aa5bf5c3f0047fb9e24f58247b9935efca464216 | MATLAB | 687 | 14 | function plotSubScatterFit(sel)
% Delete old line if applicable
if isfield(sel.disp,'subFitLine') && isvalid(sel.disp.subFitLine)
delete(sel.disp.subFitLine),
end
% Plot fit line
%xRange = [min(sel.disp.fNeuropil), max(sel.disp.fNeuropil)] - median(sel.disp.fNeuropil);
xRange = [min(sel.disp.fNeuropil), max(sel.d... |
c624f1b453a353286402c91ac980bf809c0c46bfe0992b4e36d76e71940ba6de | MATLAB | 697 | 19 | function addMovie(obj, pathToTiff)
%Function to add a file to the acquisition object, checking for errors
try Tiff(pathToTiff);
if sum(strcmp(pathToTiff,obj.Movies)) > 0
error('Duplicate'),
end
obj.Movies{end+1} = pathToTiff;
catch err
if strcmp(err.message,'Dupl... |
7d80890c32215af60adf38aa30908c4950f39c98da2d82fdf72a006c1d15ba12 | MATLAB | 719 | 28 | function run(ajp, isExitAfterOneJob)
% Runs a loop that loads acquisition objects and processes them.
if ~exist('isExitAfterOneJob', 'var') || isempty(isExitAfterOneJob)
isExitAfterOneJob = true;
end
nJobsDone = 0;
while ~ajp.flagStop
success = ajp.loadNextAcq;
if ~success && ~isExitAfterOneJob
... |
228226c4963ebb33d2405cfcf180e11c7512249c4c29ba44060fc8ecdb5a1026 | MATLAB | 800 | 31 | function subCoefScrollWheel(sel, ~, evt)
%Allows interactive adjustment of neuropil subtractive coefficient
if strcmpi(evt.Source.CurrentModifier,'control')
gain = 0.05;
elseif strcmpi(evt.Source.CurrentModifier,'shift')
gain = .5;
else
gain = 0.005;
end
switch sign(evt.VerticalScrollCount)
case -1 %... |
ed6ef20ba005cfaa026850295a2cfb30b1061d2301357d38d89552bdbd638815 | MATLAB | 837 | 26 | function saveCurrentAcq(ajp)
% Saves the current acq both in its default dir and in the inProgress dir.
try
% Rename acq object before saving:
if verLessThan('matlab', 'R2014a')
acqVarName = genvarname(ajp.currentAcq.acqName);
else
acqVarName = matlab.lang.makeValidName(ajp.currentAcq.acqNa... |
3d7fa9fd27c324b9c6a9ff9b465901b2623e4d7aba26ac4f644526610ef69b11 | MATLAB | 842 | 28 | cd('Z:\Laura\code_workspace\LD185')
mouseDir = pwd;
sessionList = dir('LD*');
for session = [36 8:34 37:size(sessionList,1)]
output_dir = fullfile('Z:\Laura\code_workspace\',...
sessionList(session).name(1:5),sessionList(session).name);
if ~exist(output_dir,'dir')
mkdir(output_dir)
end
cd(fullfile(mouseDir,ses... |
bf8053fd6f30c855f0333daed528ad3cdf185ccfee2f7e46bb54e1b2857df039 | MATLAB | 845 | 25 | function [plateau_starts, plateau_durations] = filterPlateausBySpeed(plateau_starts, plateau_durations, speed, speed_threshold)
% Filter plateaus by speed condition
valid = true(size(plateau_starts));
abs_threshold = abs(speed_threshold);
for i = 1:length(plateau_starts)
start_sample = plateau_starts(i);
end_... |
631a3ab28aa42a1354761e7b909fbda17ed9016156657a608294ae9ce9716a4d | MATLAB | 854 | 22 | function removeRoiList(acq)
% removeRoiList(acq) updates the way that ROI information is stored.
if isfield(acq.roiInfo.slice(1), 'roiList')
for sl = 1:numel(acq.roiInfo.slice)
roiInfoOld = acq.roiInfo.slice(sl);
for r = 1:numel(roiInfoOld.roi)
roiId = acq.roiInfo.slice(sl).roiL... |
129e59a51b652dfb92f98c44bd24b1e9e5b6512e105608f9623259210fdf99d5 | MATLAB | 855 | 22 | %% elastix registration
clear;
% goal: to register t1s to b0
% register t2 maps to the b0
%% Define project directory and subject code
project_directory = '/exports/gorter-hpc/users/ninafultz/';
project_name = 'csf_donut';
subject_code = 'csfdonut02_20191022';
%% Paths
t2maps_path = fullfile(project_d... |
2f2f3a58897e12430c805c76f689456f55dfab3312a036d5736b9cf1750f7d11 | MATLAB | 869 | 26 | cd('Z:\Laura\DATA\imaging\Current Imaging\LD169')
mouseDir = pwd;
sessionList = dir('LD*');
%
for session = 4:56%size(sessionList,1)
cd(fullfile(mouseDir,sessionList(session).name))
% acq = Acquisition2P([],@lnd_init);
% acq.motionCorrect;
output_dir = fullfile('Z:\Laura\code_workspace\',mouseDir(end-4:end),...
se... |
42e73f504a1dc9125d48664714c51801af9b6decc3b16a443f212c83cea33912 | MATLAB | 876 | 28 | function resultArray = runningPrctileMat(dataArray, winLength, nth)
runningWindow = sort(dataArray(1:winLength));
dataArrayLength = numel(dataArray);
resultArray = dataArray;
iWinInsert = floor(winLength/2);
for iWinStart = 1:(dataArrayLength-winLength)
iNextDataPoint = iWinStart + winLength;
resultArray(iWin... |
0380fb00048c3d0fffa45fc7cc63e164b3cda24eda089de51289234a0a65213e | MATLAB | 900 | 33 | function par2nifti(subjPath, parDir);
%% loading par file
cd(parDir)
[img_data, ~ ] = import_parrec_special_WT2_LH(1, '*'); % loads the raw data of all echoes (NOT YET MASKED!)
FA_map_avg = flipud(img_data);
img_data_flipped = permute(FA_map_avg,[3 1 2]); % Flips the first dimension (top-to-bottom)
%... |
d6161a5978091d9d2643e439afbc663c20003ab791c63ada833a5e38b3a5d614 | MATLAB | 900 | 25 | function r = detectFullframeRecursive(mov, idx)
% Recursive full-frame alignment code from:
% https://scanbox.wordpress.com/2014/03/20/recursive-image-alignment-and-statistics/
if(length(idx)==1)
A = mov(:, :, idx(1));
r.m = A; % mean
r.T = [0 0]; % no translation (identity)
r.n = 1; % # of frames... |
899431e5c1c8ceb742b2fd6a5a6febb55859508cf6852853b0117493dc5ec739 | MATLAB | 901 | 37 |
A= xlsread('1.xls');
Fs=2000;
peak=[];
k=1;mm=1;
figure
for i=1:size(A,2)
subplot(5,6,k)
temp=A(:,i);
time=(1:length(temp))/Fs;
% ÕÒÑ°10s-15sÖ®¼äµÄpeakÖµ
onset=10; % 10s
endset=15; % 15s
[peak(i,1),ind]=max(temp(onset*Fs:endset*Fs));
plot(time,temp)
hold on
... |
1ac02d12bedc2abfd0e8df92d64b5e70d439842a600c57a03e6b908a59833017 | MATLAB | 905 | 33 | function save(obj,writeDir,writeName,varName)
% Saves the acquisition object. By default uses defaultDir as writeDir and
% acqName as both writeName and varName
%
% save(obj,writeDir,writeName,varName)
%
% writeDir is the directory to save the acq in
% writeName is the filename to save the acq as
% varName is the var... |
ae3b664f2fb7c595357d158da5589a44874e6f9aeb2745966dc3473b7d8045e1 | MATLAB | 917 | 35 | function img = getOverviewImg(acq, altImg)
% Merges the anatomical and activity images into a nice overview image for
% selectRois
if nargin<2
altImg = [];
end
%% Get mean img:
mode = 'standard';
switch mode
case 'standard'
meanImg = acq.meanRef;
meanImg(meanImg<0) = 0;
meanImg(is... |
1e0a101a24b3cdcca6134e537a9034f677fd0b658ee5a6d43d56e4e5b662a6ce | MATLAB | 921 | 30 | function movInd = nh2movInd(sel, nhInd, nhCenter, nhSize)
% movInd = nh2movInd(sel, nhInd, nhCenter, nhSize) coverts linear indices
% into the covariance neighborhood region into linear indices into the
% whole movie frame.
if ~exist('nhCenter', 'var') || isempty(nhCenter)
nhCenter = sel.disp.currentPos;
end
if ~... |
2ffcd9754bcc1f4ae3bd82a05f2d188b2c2b37e2af1b0d0921fe0917d90d8f75 | MATLAB | 924 | 27 | cd('Z:\Laura\DATA\imaging\Current Imaging\LD169')
mouseDir = pwd;
sessionList = dir('LD*');
%
for session = [3:4 58:size(sessionList,1)-1]
cd(fullfile(mouseDir,sessionList(session).name))
% acq = Acquisition2P([],@lnd_init);
% acq.motionCorrect;
output_dir = fullfile('Z:\Laura\code_workspace\',mouseDir(end-4:end),...
... |
4e05db7cbe777497b27fc1a01e7d21307d7b3484c57234cd43e52283dea6834c | MATLAB | 926 | 28 | function [netIds, parcelColors] = processNetworkData(filePath, numParcels, networkNames)
% Function to process network data from a given file
fileID = fopen(filePath, 'r');
netIds = zeros(numParcels, 1);
parcelColors = zeros(numParcels, 4);
for i = 1:numParcels
% Read the netwo... |
8f30d4c70c3317da3de074076c674245426637aec101a8afc87cb6255544691d | MATLAB | 936 | 22 | function mergeCurrentROI(sel)
isMerging = strcmp('Select cluster to merge with', ...
get(get(sel.h.ax.cluster, 'Title'), 'string'));
if ~isMerging
sel.disp.clus2merge = sel.disp.currentClustInd;
title(sel.h.ax.cluster,'Select cluster to merge with'),
elseif isMerging
ind2merge = sel.disp.currentCluste... |
2685423cd67bba76b5d7d0c4a518caa3f8b2f372817f0567d27ac88f73c7bfe6 | MATLAB | 959 | 29 | %{
Initialize a batch of sessions for processing using Acq2p.
%}
%% Get session list:
dirRaw = '\\research.files.med.harvard.edu\Neurobio\HarveyLab\Matthias\data\imaging\raw';
mouse = 'MM112';
snList = dir(fullfile(dirRaw, mouse, 'MM*'));
snList = snList([snList.isdir]==1);
%% Initialize:
for i = 1:numel(snList)
... |
8a9545e5db3fd96914d5279c723c8b78da3559032103f36a0f3009f187bc5dbd | MATLAB | 970 | 31 | function mov = getRoiMovie(acq, roiNum)
% mov = getRoiMovie(acq, roiNum) returns a 3D mov stack of the image data
% in acq surrounding the roi roiNum.
h = acq.derivedData(1).size(1);
w = acq.derivedData(1).size(2);
nFramesTotal = cat(1, acq.derivedData.size);
nFramesTotal = sum(nFramesTotal(:, 3));
roiInd = acq.roiIn... |
2306bae69387e275bbc5a46d9028f48b7cdd213857525b5ed5ad07839a60b2ab | MATLAB | 973 | 54 |
% matlabpool('open',4);
%%
tic
load modeldata_12.mat
% load behMod.mat
% q_list=[1]';
parm_results=[];
% for qq=q_list;
% for qq=2
parfor qq=1:12
% parfor(qq=1:8,8)
ResModData=modeldata{qq,1};
results=[];
for parm1=[0.005 0.01 0.05 0.1 0.5]*10e7;% delta1
for parm2=[0.... |
4d2a5d9552ab714d6239ad9c8341e050ac26691663fe577f071e05cd7c4bb867 | MATLAB | 975 | 34 | function reorienting_t1(subjPath);
anatFolder = fullfile(subjPath, 'anat');
%% loading file
img_data = fullfile(anatFolder, '3dt1_0.9mm.nii');
img_data = niftiread(img_data);
ADC_map_avg = flipud(img_data);
ADC_map_avg = permute(ADC_map_avg,[3 2 1]); % Flips the first dimension (top-to-bott... |
8d1990e3282a0ee87a33cb792635a429e2bbfcafd6543dc533c8cf6ed63d0f64 | MATLAB | 996 | 28 | function trEdge = getEdgeTrace(acq)
% trEdge = getEdgeTrace(acq) returns the pixel values at the edge of the
% frame for each line independently.
h = acq.derivedData(1).size(1);
w = acq.derivedData(1).size(2);
nFramesTotal = cat(1, acq.derivedData.size);
nFramesTotal = sum(nFramesTotal(:, 3));
% Find edges:
colBright... |
613681c1b3b3b8eb63d59ee0c02b404cd7b000aba375b6dc115916bb3ae78bee | MATLAB | 1,002 | 35 | function ICC_2_k = ICC2K(T)
% T should be a table of the long format of the ratings with variables:
% T.rating : numeric rating
% T.soundID : categorical or numeric id for each sound (1..291)
% T.raterID : categorical or numeric id for each participant
%
% Example:
% T = table(ratingsVec, soundVec, rat... |
d1dfdd6ca7ef98437cdb8a3932a767632c2460f45203b8327e12e9216ff8c865 | MATLAB | 1,016 | 43 | function [loss,gradients,mseF1,mseF2,mseF3,mseF4,mseF5,f1,f2,f3,f4]=modelLoss(parameters,net1,CP,CB,CBIC,U0,dataInfer,w1,w2,w3,w4,w5)
net1.Learnables=parameters(1:6,:);
alpha=parameters(end,:).Value{1};
% make predictions
U=forward(net1,CP);
gradientsU=dlgradient(sum(U,"all"),CP,EnableHigherDerivatives=true... |
cb4b2c2ba11a221febd0bc0953cae46016cf2d7bace5853f8d687f881c857549 | MATLAB | 1,018 | 24 | function calcRoi(sel)
%Helper function that performs clustering using n simultaneous normcuts and
%updates cluster/ROI display accordingly
nCuts = sel.disp.clusterNum;
clusterMod = sel.disp.clusterMod;
[clusterIndex, clusterCentroid] = getClusters(sel, nCuts, nCuts+1+clusterMod);
clusterQual = mean(silhouette(sel.di... |
520e944e0fd722f62050be2f3a23a652d7fd84324baa3d1c0447bfb4ce331ab3 | MATLAB | 1,038 | 46 | function mask = computeicmask_v2(mag,phi,Parenchyma_Only)
% function mask = ComputeICMask(mag,phi,Parenchyma_Only)
% Changes
% 29/09/09: Initial release (JM)
% 30/09/09: Added Parenchyma_Only swith in order to include the skull
% when needed (JM)
if nargin==2
Parenchyma_Only = 1;
end
mask =... |
16fec541405e44d620351271cbe38ff8be3491443ee9ad63d4f3b582535a0f17 | MATLAB | 1,047 | 38 | function out = hanning3d( n_x, n_y, n_z, pad_array )
% Create 3d Hanning filter:
% out = hanning3d( n_x, [n_y, n_z])
% if only n_x is specified [n_x, n_y, n_z] is assumed
if (nargin == 1)
n_y = n_x;
n_z = n_x;
end
a = .25; %default hanning is 2
xx = linspace(-1,1,n_x).*(a/2);
yy = linspace(-1,... |
563d5843c62b7f183bdbed8cd9f3158b0ddd87dd1dd0ce96d57c8580f57ce6ff | MATLAB | 1,048 | 45 |
% spid=[];
% for j=1:1000
% a=(1:11)';
% spid=[spid;a];
% end
%
% simPostCNOAnimID=cell(1000,1);
% for i=1:1000
% x=spid(randperm(length(spid)));
% x=x(1:11);
% simPostCNOAnimID{i}=x;
% end
% save('simPostCNOAnimID','simPostCNOAnimID');
%%
load postlearnmodeldata.mat
load para... |
e352cc73a827b998652aea788e03d168278086e1f9ce4c2ba6eadaea88d045fc | MATLAB | 1,056 | 36 | %% csf mobility all subjects
%% purpose
% 1) plot average of ADC as it moves from 0 for different cross sectionals
% 2) bar plots for ratings
% 3) statistical comparison
clear;
% Define project parameters
project_directory = '/exports/gorter-hpc/users/ninafultz/';
project_name = 'csfdonuts_lydiane';
%fig = 'donut0... |
a7fd35e4bcd743ce2a42f3d5ac02d11080b6b47fb874e8a53097d92b2e6c36c5 | MATLAB | 1,066 | 34 | function [stimMov, dFmov] = getStimEvokedMovie(stimExpt, nROI, nTarg, winSize)
if nargin < 4
winSize = 30;
end
%
% if nargin < 3
% nTarg = nROI;
% end
% tV = stimExpt.tV;
mov = getRoiMovie(stimExpt.acq, stimExpt.cIds(nROI), winSize);
stimTimes = [];
for nBlock = 1:stimExpt.numStimBlocks
blockOffsetFrame ... |
079b8b18576a6cd54345d8969d255c7d46d4eb53e417d125dc8642f85d72e7a8 | MATLAB | 1,071 | 31 | function addCorrMovies(obj,nSlice,nChannel)
%Example of an Acq2P Initialization Function. Allows user selection of
%movies to form acquisition, sorts alphabetically, assigns an acquisition
%name and default directory, and assigns the object to a workspace variable
%named after the acquisition name
if ~exist('nSlice','... |
7a53916df5e8f334beaa6b5672e0eb29b71ef78a8f7af919cd86466289b0fc4a | MATLAB | 1,078 | 45 | function anchor_starts = find_speed_crossings_down(speed, reset, threshold)
if nargin < 3
threshold = 0.05;
end
% Handle reset vector
if nargin < 2 || isempty(reset)
reset = [1, length(speed)+1];
else
reset = unique(reset(:))';
if reset(1) ~= 1
reset = [1, reset];
end
if reset(end) <=... |
a36fc3d4b4bef491eb6052ee8de4933f0752f08afcb3734a9e7eb29d3ffae32a | MATLAB | 1,083 | 28 | function plotTwoDistributions(all1, short1, long1, all2, short2, long2, bin_size, bin_units, titles, main_title)
max_range = 1.2;
edges = -max_range:bin_size:max_range;
centers = (edges(1:end-1) + edges(2:end))/2;
xlabel_str = ['Distance from anchor (' bin_units ')'];
figure('Name', main_title,... |
5a8b24162a35235edf80e6b969d69d2fd1d6fe8d674c724680446c74794c49c5 | MATLAB | 1,097 | 26 | function addOverlayTrace(sel)
thisROIind = sel.nh2movInd(find(sel.disp.roiMask));
mov = sel.movMap.Data.mov;
thisROItrace = mean(mov(:, sel.acq.mat2binInd(thisROIind)), 2)';
smoothWin = gausswin(sel.disp.smoothWindow)/sum(gausswin(sel.disp.smoothWindow));
thisROItrace = conv(thisROItrace,smoothWin, 'valid');
xFrames =... |
4a0546afde2b0699ca9af4b177ae090ef923a22ca2760068ed05540ac97991f6 | MATLAB | 1,099 | 37 | function plotDonutBarPlots(filename, col_right, col_left, categories)
% Read the Excel file
data = readtable(filename, 'FileType', 'spreadsheet'); % Reads .xlsx file
% Extract columns
A1_right = data.(col_right);
A1_left = data.(col_left);
% Initialize counts
category_counts = zeros(1... |
29ed32ab14c2a3b60def1f121ae2e1fa6cd4a41a02f1271d9c01de1f57df64ef | MATLAB | 1,116 | 32 | function mov = getRoiMovie(acq, roiNum, winSize)
% mov = getRoiMovie(acq, roiNum) returns a 3D mov stack of the image data
% in acq surrounding the roi roiNum.
h = acq.correctedMovies.slice(1).channel(1).size(1,1);
w = acq.correctedMovies.slice(1).channel(1).size(1,2);
nFramesTotal = sum(acq.correctedMovies.slice(1).c... |
290f605c340ab9af4d625e88a8593fa953fd5c0e9b487f45f1e6a456f7ece98f | MATLAB | 1,129 | 30 | function deconvNmf(acq)
% Wrapper function for NMF-source deconvolution.
% Matthias-specific: Some acqs from MM102 and MM104 have fake SI metadata
% because the code hadn't been updated for SI2016. Detect that here and get
% real metadata:
if isfield(acq.metaDataSI, 'SI4') || isempty(acq.metaDataSI)
fPath = acq.Mo... |
63243e27677d46a78f37f72d63d5e2580fba493c0225f38f13be777b10220d94 | MATLAB | 1,155 | 35 | function splitCurrentROI(sel)
% Get Covariance Data for normCuts
[covMat, pxNeighbors] = sel.getCovData;
corrMat = corrcov(covMat, 1);
m = size(corrMat, 1);
offDiags = diag2full(ones(m, 4), [-sqrt(m) -1 1 sqrt(m)], m, m); % 4-connected
nhWeight = 0;
W = corrMat + nhWeight*offDiags;
% Select subset of W matrix corresp... |
b319095548e1d5358e5e8201629623b832c5b54b0f6f6fc1e2a179ebb207aac3 | MATLAB | 1,160 | 36 | function par2nifti(subjPath, parDir);
%% loading par file
cd(parDir)
[img_data, ~ ] = import_parrec_special_WT2_LH(1, '*'); % loads the raw data of all echoes (NOT YET MASKED!)
FA_map_avg = flipud(img_data);
img_data_flipped = permute(FA_map_avg,[3 1 2]); % Flips the first dimension (top-to-bottom)
%... |
09a11fcd6bc9bb543ccb04b3d345ff1891c3ed0ec76076eef0bf19efe4181b09 | MATLAB | 1,168 | 42 |
function [loss,gradients,mseF1,mseF2,mseF3,mseF4,mseF5]=modelLoss(parameters,net1,CP,CB1,CB2,xpin,w1,w2,w3,w4,w5)
net1.Learnables=parameters(1:end-1,:);
Gi=parameters(end,:).Value{1};
% make predictions
U=forward(net1,CP);
Ux=dlgradient(sum(U,"all"),CP,EnableHigherDerivatives=true);
Uxx=dlgradient(sum(Ux... |
90b0f00b937bd6466b5ba903b429b3c3961c1859a229de3c3ac97111659dac16 | MATLAB | 1,181 | 40 | %% loading mhd file and thresholding
GENERALDIR = 'R:\- Gorter\- Personal folders\Fultz, N\csfdonuts_lydiane\'
allSubjects = dir([GENERALDIR '*20201019_Reconstruction']);
subjectNb = 1;
subject = allSubjects(subjectNb);
disp(subject.name)
refScanTemp = dir([subject.folder '\' subject.name '\mhd\Scan*.mhd... |
03b675256172e90c1256079b94a607a9df9ea3e1d901db4670b5073a60b3e0c2 | MATLAB | 1,189 | 42 | classdef acq2pJobProcessor < handle
properties
debug = false;
dir
logFileName
currentAcq
currentAcqFileName
nameFunc
end
properties (Hidden = true, Access = protected)
flagStop = false;
end
methods
% Constructor:
... |
52816e14e8abc93525ce6700429889686a9c8c929fa5d914966257052fd1a28c | MATLAB | 1,205 | 40 | %% loading mhd file and thresholding
GENERALDIR = 'R:\- Gorter\- Personal folders\Fultz, N\csfdonuts_lydiane\'
allSubjects = dir([GENERALDIR '*20191022_Reconstruction']);
subjectNb = 1;
subject = allSubjects(subjectNb);
disp(subject.name)
refScanTemp = dir([subject.folder '\' subject.name '\mhd\Scan*.mhd... |
198a6f4dab4c82ba2234b474fe98d26b9ebf85caa307339326c24f02c61197f1 | MATLAB | 1,227 | 30 | function [plateau_starts, plateau_durations] = getPlateauInfo(plateaus, widPlat, min_plateau_duration_samples, plateau_grouping, group_num)
% Extract plateau starts and durations with optional group filtering
plateau_starts = find(diff(plateaus) == 1) + 1;
plateau_durations = widPlat;
% Filter by minimum duration
vali... |
aadbf16c29bc4b439b520d05f5ebd3b563b53c374b81dc0689f22591178d9cee | MATLAB | 1,262 | 44 | function anat_par2nifti(subjPath);
regDir = fullfile(subjPath , 'reg');
anat_dir = fullfile(subjPath, 'anat');
par_path = fullfile(subjPath, 'par');
%% saving T2* map
% Define the directory and file pattern
filePattern = fullfile(anat_dir, '*_3dt1_0.9mm*.nii.gz');
% Find matching files
matching... |
a5fa919a5e5eb80b6577ce4e41572ada5ce36b2cfb699f108019a28394bfe132 | MATLAB | 1,270 | 54 | function log(ajp, msg)
% Writes log message to the command line and to disk.
% Log if we're in debug mode:
if ajp.debug
msg = ['DEBUG MODE: ', msg];
end
% Log which computer we're on:
[~, host] = system('hostname');
host = strtrim(host);
% Combine information into tabular form:
msgFull = sprintf('%s\t%s\t%s\t%s\... |
8dc13d32ae20729a9043665d54e4df0ac6e7256a119f3a593eac75b78bfd156a | MATLAB | 1,277 | 38 | function doSubTracePlot(sel,~,~)
if ~isfield(sel.disp,'fBody')
return;
end
% Calculate corrected dF and plot
dF = sel.disp.fBody-sel.disp.fNeuropil*sel.disp.neuropilCoef(2);
dF = dF/sel.disp.f0Body;
dF = dF - median(dF);
movSizes = [sel.acq.correctedMovies.slice.channel.size];
nFramesComplete = sum(movSizes(:, 3... |
19c0a909aa36ed87cff5dca9cf6a0fbbdc48c2a3736f238c3c00daa95e31301b | MATLAB | 1,289 | 38 | function segmented_region = regiongrowing_v2(image, seed_point, seed_value, tolerance)
% Create a binary mask for the segmented region
[rows, cols] = size(image);
segmented_region = false(rows, cols);
region_pixels = false(rows, cols);
region_pixels(seed_point(1), seed_point(2)) = true;
segmente... |
3a87df23020e62df2ffe4979d5808804cdff8362c2ced380c4e33785b4d1fab5 | MATLAB | 1,299 | 32 | function [clusterIndex, clusterCentroid] = getClusters(sel, nCuts, nClusters)
% getClusters(sel, nCuts, nClusters) performs k-means clustering on the
% normcuts data. This function should be used wherever clustering is done,
% rather than using kmeans() separately in different places.
cutVecs = sel.disp.cutVecs(:,(1+s... |
2ca7341f75b3a45779c2c66a4149ecf82685003fe88d34b8f55d1cebd588d670 | MATLAB | 1,303 | 36 | function AJlk(obj)
%Example of an Acq2P Initialization Function. Allows user selection of
%movies to form acquisition, sorts alphabetically, assigns an acquisition
%name and default directory, and assigns the object to a workspace variable
%named after the acquisition name
%Initialize user selection of multiple tif fi... |
380e742b5b49e707163b151e4d30cc14f065667388bee9112a0efca1e823cec6 | MATLAB | 1,312 | 36 | function cbMousemove(sel, ~, ~)
% Give the figure focus when the mouse moves onto it:
if ~isequal(gcf, sel.h.fig.main)
figure(sel.h.fig.main)
end
% Do not change clusters based on mouse movement when a cell/neuropil pair
% has been selected (to prevent that the loaded pair is unloaded by
% accidentally moving acr... |
f87be0350ddfffc09e38ecd93a18b2448f36bcf9151051a983df91f6fcefd149 | MATLAB | 1,315 | 41 | function plot_voxel_t2_fit(echo_times, T2_map, goodnessFit, x, y, z)
%%
% Extract voxel data
voxel_data = squeeze(T2_map(x, y, z, :));
% Check if the voxel data is all zeros
if all(voxel_data == 0)
disp('The selected voxel data is all zeros.');
return;
end
%%
%%
... |
ed7e915d360dc09b32d0469b376129ca0f2dc8d218bf16c94b83a72ee16d8900 | MATLAB | 1,330 | 35 | function [p_values, actual_diffs,actual_diffs_perc] = computeNetworkHeritabilityPValues(movieNetHerit, restNetHerit, numPermutations)
numNetworks = 17;
numDays = 2;
p_values = zeros(numNetworks, numDays);
actual_diffs = zeros(numNetworks, numDays);
for day = 1:numDays
actual_diff = mean(movieNetHerit(:,:,day), 2)... |
5068015dec1c2a85383e2f1e2f2d223282eb7a61ebd17e2b519c69e7b17a1f01 | MATLAB | 1,356 | 41 | function pixCov = mmPixCov(mov, nh)
temporalBin = 8;
mov = mov(:,:,1:end-rem(end, temporalBin)); % Deal with movies that are not evenly divisible.
movSize = size(mov);
[h, w, z] = size(mov);
z = z/temporalBin;
mov = squeeze(sum(reshape(mov,movSize(1)*movSize(2),temporalBin,movSize(3)/temporalBin),2));
mov = bsxfun(@m... |
7a9308e65854383dbd88d60812923f410a46d299395126f52498999e283638bb | MATLAB | 1,361 | 43 | function lnd_init(acq)
movPath = pwd;
fileList = dir('LD*tif');
movNames = cell(1,10*floor(size(fileList,1)/10));%cell(1,size(fileList,1));%
for file = 1:10*floor(size(fileList,1)/10)%size(fileList,1)%
movNames{file} = fileList(file).name;
end
%Set default directory to folder location,
acq... |
e768f8d87059eca0fa51264aeec5be978d9892a96da5612b92072a762fd9e27b | MATLAB | 1,366 | 42 | function lnd_init_green(acq)
movPath = pwd;
fileList = dir('LD*tif');
movNames = cell(1,10*floor(size(fileList,1)/10));%cell(1,size(fileList,1));%
for file = 1:10*floor(size(fileList,1)/10)%size(fileList,1)%
movNames{file} = fileList(file).name;
end
%Set default directory to folder location... |
edb7dd224891e93bb56886f1418177d0d8ed437515a51df084f0d85970ee4525 | MATLAB | 1,366 | 40 | function echo_times = extract_echo_times(directory_path, common_prefix)
%%
% Find all NIfTI files matching the pattern
nifti_files = dir(fullfile(directory_path, [common_prefix '_e*_ph.nii']));
nifti_files = {nifti_files.name}; % Extract file names into a cell array
% Initialize array to store ech... |
70d3659f5c465f12b4aad62861562ed173494dcf636acbc8a9c63fa78452c4f5 | MATLAB | 1,368 | 50 | % From the paper of DBlink, a mithocondria simulator, dynamic part is
% integrated in blinkPSF function
% https://github.com/alonsaguy/DBlink/blob/main/demo/DataHandlers.py
% TU Delft
% Grussmayer Lab
%
% Miyase Tekpinar
%function mito_mask = mithocondria(pxnum, pxsize, num_of_mito, R_range, P_range)
pxnum = 500
pxsiz... |
e2e020eb91d0024e657ada9c9deed4577f2080ff19f6a96a5f67c626ae91b0d1 | MATLAB | 1,376 | 45 | function u=nagumo_implicit(u,xpt,dt,alpha,template,templatex);
dx=xpt(2)-xpt(1);
np=length(u)-1;
dudt=zeros(np+1,1);
u0=u;
while 1
ajac=sparse(np+1,np+1);
res=zeros(np+1,1);
% node 1
i=1;
res(i)=(u(i+1)-u(i))/dx^2+u(i).*(1-u(i)).*(u(i)-alpha)-(u(i)-u0(i))/dt;
ajac=ajac+spa... |
32c1ddc595d0532f52774ec7dd4a9a476aae2a239bbad82db91d154666708208 | MATLAB | 1,385 | 48 | function extractSources(acq,nSlice,data,initImages)
% Wrapper function for NMF-based source extraction.
if ~exist('nSlice','var') || isempty(nSlice)
nSlice = 1;
end
if ~exist('data','var')
data = [];
end
if ~exist('initImages','var')
initImages = [];
end
% NMF code requires syncInfo. Create minimal... |
e5e3577d6963221bc016a9e93b73ca0a1abf0be561d1ef2e69268a5a3bdc39db | MATLAB | 1,396 | 45 | function plotDonutM2onwardsrating(filename, col_right, col_left, categories);
%%
% Read the Excel file
data = readtable(filename, 'FileType', 'spreadsheet'); % Reads .xlsx file
% Initialize counts for each category
category_counts = zeros(1, length(categories));
% Process each subject
for i ... |
c67a1a35e274307d785fefd17a9bf0246769554d7fcc6134697b42847e520b79 | MATLAB | 1,401 | 58 | % SRHIST Generate a 2D histogram image from a set of x,y coordinates
%
% SYNOPSIS:
% histim=SRhist(xsz,ysz,xco,yco)
%
% INPUTS:
% xsz
% x dimension of the histogram image, in pixels
% ysz
% y dimension of the histogram image, in pixels
% xco
% x coordinates, in pixels
% yco
% ... |
e317ef75f6fa85ac8bda2aa0d632f94e65ed7e18421025afabb2c122be4b0bda | MATLAB | 1,413 | 41 | function success = loadNextAcq(ajp)
% Checks if there are new unprocessed acq2ps in the to-be-processed folder.
acqFileList = dir(fullfile(ajp.dir.jobs, '*.mat'));
% Go to next un-done job:
if isempty(acqFileList)
success = false;
return
end
ajp.currentAcqFileName = acqFileList(1).name;
nextFilePath = fullfil... |
4a41100ebeb9444287534cdd06d9daa3619a6ddaac9d0441b916981ae2700c68 | MATLAB | 1,414 | 43 | function fieldsPxCov(obj, movNums, radiusPxCov, temporalBin, sliceNum, channelNum, writeDir)
% Function to fill in acq2p object fields for a pixCov file
% Function mimics setup of calcPxCov and fields in fields as if function
% were called ordinarily
%% Input handling / Error Checking
if ~exist('sliceNum','var') || i... |
2f8ebfd871b7495cd5d40a4823cbd231a7206d0ce3a5e67efecb07ebdd78b99e | MATLAB | 1,427 | 46 | function setupGurobi()
% SETUPGUROBI - Automatically find and add Gurobi to MATLAB path
% Check if Gurobi is already in path
if ~isempty(which('gurobi'))
fprintf('Gurobi is already in MATLAB path.\n');
return;
end
% Common Gurobi installation locations
possible_paths = ... |
f2f36347773c8e6a34d8708d4e5e8f9e7ae830f787cf77e11882d77bfb0d493f | MATLAB | 1,428 | 53 | function success = acq2server(obj,fileDest,rawTransfer)
%Example auxilliary function to transfer all files in an acq's default
%directory to the server, perform motion correction, then transfer the
%acquisition and motion corrected data to the server
%
% acq2server(obj,fileDest,rawTransfer)
%
%obj is the acquisition ob... |
85de2bab0e0dbcd9488477250e681cabb015decde6508f66893fac405529398e | MATLAB | 1,430 | 43 | function addMovieSizes(acq)
% Function to find and store movie size information in old acquisition
% objects that did not calculate this info during motion correction.
if isfield(acq.correctedMovies.slice(1).channel(1), 'size')
warning('This acquisition already has size information. Will not change anything.');
en... |
6344984fd222d26a37f49e63bb2d63c28dc453192a2499ad306835acd5b2f4ac | MATLAB | 1,433 | 73 | numLayers = 3;
numNeurons=40;
layers=featureInputLayer(1);
for i=1:numLayers-1
layers = [layers
fullyConnectedLayer(numNeurons)
tanhLayer];
end
layers = [layers
fullyConnectedLayer(1)];
net1=dlnetwork(layers);
net1 = dlupdate(@double,net1);
% Collocation points
xpt=l... |
08e59be7a1fe5f9ae85469ac350265ab99d74bbdef8c04ac8944d5aea540d177 | MATLAB | 1,453 | 35 | function view_voxel_data(masked_par_data, T2_map, S0, goodnessFit)
% Display the 3D image using imshow3Dfull
figure;
imshow3Dfull(masked_par_data(:,:,:,2)); % Show data from the 2nd echo
% Set up the callback function for mouse click
set(gcf, 'WindowButtonDownFcn', @voxel_callback);
% ... |
ea652244810298d81dc2932a4fa787f4bd96823449833f9c0be3955191c1dc7d | MATLAB | 1,453 | 41 | function SCsc(obj)
%Example of an Acq2P Initialization Function. Allows user selection of
%movies to form acquisition, sorts alphabetically, assigns an acquisition
%name and default directory, and assigns the object to a workspace variable
%named after the acquisition name
%Initialize user selection of multiple tif fi... |
6187fcc628abad0af98525c8cdf845cb41c571c97177bdb797b65b0706af73f3 | MATLAB | 1,455 | 41 | function SC2Pinit(obj)
%Example of an Acq2P Initialization Function. Allows user selection of
%movies to form acquisition, sorts alphabetically, assigns an acquisition
%name and default directory, and assigns the object to a workspace variable
%named after the acquisition name
%Initialize user selection of multiple ti... |
4079124bab895be255db86264c27d2b7d01b1fe5090fc6ea9cbfc898cfe345fc | MATLAB | 1,460 | 55 |
addpath('/exports/gorter-hpc/users/ninafultz/scripts/spm12')
%%
% Define project path and subject
project_path = '/exports/gorter-hpc/users/ninafultz/highres_pvs/';
subject = '20240307_PVS3';
% Construct the full path to the functional directory
func_dir = fullfile(project_path, subject, 'func');
anat_dir = full... |
fc298e59c84286853b54fd4575a8ab718f3bdad3ebecd769c8f13ad7823fc26f | MATLAB | 1,466 | 60 | moving = [1 2; 0 0];
Dx = [1 -1; 0 0];
Dy = [0 0; 0 0];
D = cat(3, Dx, Dy);
disp(imwarp(moving, D))
%% Test it
img = double(imread('cameraman.tif'));
[x_orig, y_orig] = meshgrid((0:255)-255/2);
C_orig = cat(3, x_orig, y_orig);
figure(1)
imagesc(img)
title('Original')
% Create affine tform:
theta = 15;
tform = affin... |
f7b47c11a72e56287be6e1e763b6ed1d12dc508ef7ed78c85f72d76e04a8d09f | MATLAB | 1,467 | 39 | function outFile = ft_GlobalSurrogateAnalysis(subjList, freqLabel, varargin)
p = inputParser;
p.addParameter('BaseDir', pwd, @(x)ischar(x)||isstring(x));
p.addParameter('OutDir', '', @(x)ischar(x)||isstring(x));
p.addParameter('NPerm', 5000, @(x)isnumeric(x)&&isscalar(x)&&x>0);
p.parse(varargin{:});
opt = p.Results;
... |
3c397a1909cf8da2804b855f8511b1a6d230ace75e60466fe306b5155898a0bd | MATLAB | 1,477 | 39 | function acq2tempDir(acq, dirTemp)
% Switch the paths pointing to the pixcov and bin files to the local temp
% dir.
acq.defaultDir = dirTemp;
if isfield(acq.roiInfo.slice, 'covFile')
[~, filename, ext] = fileparts(acq.roiInfo.slice.covFile.fileName);
acq.roiInfo.slice.covFile.fileName = fullfile(dirTemp, [fil... |
9c5667a7b3c47c6129eebf06964e139740e4730d02a59b457c31ca8b5419e83b | MATLAB | 1,505 | 51 | function [out, swi_image] = my_unwrap2( in, x_f, y_f, z_f, twoD, create_SWI, swi_factor )
% Unwrap 3-D complex data using FFT approach
% function out = my_unwrap( in, x_f, y_f, z_f, twoD )
% A 3-D hanning filter is constructed and is used to highpass filter
% the complex data
% get rid of possible NaN's and repl... |
914030adc1e9bb39f77065743a50e854efbe443eb75abc329b1ab8d20c35b3fb | MATLAB | 1,518 | 42 | function SClk(obj)
%Example of an Acq2P Initialization Function. Allows user selection of
%movies to form acquisition, sorts alphabetically, assigns an acquisition
%name and default directory, and assigns the object to a workspace variable
%named after the acquisition name
%Initialize user selection of multiple tif fi... |
186da57b81e360aa714cbf789312ff406f78170d68cd62fa38bdfe6f45d823f6 | MATLAB | 1,526 | 57 | %{
This script creates a test environment to quickly test new or changed
motion correction functions.
%}
%% Load raw data:
a = MM102_160825_main;
acq = a.acq;
[mov, si] = tiffRead('\\research.files.med.harvard.edu\Neurobio\HarveyLab\Matthias\data\imaging\raw\MM102\MM102_160825\MM102_160825_MAIN_00001_00008.tif');
mov... |
174247199f2127aadc21ef9a3e54fd923bbb7256ec88347bda2ac7a05ba98f83 | MATLAB | 1,535 | 43 | function CAR2Pinit(obj)
%Example of an Acq2P Initialization Function. Allows user selection of
%movies to form acquisition, sorts alphabetically, assigns an acquisition
%name and default directory, and assigns the object to a workspace variable
%named after the acquisition name
%Initialize user selection of multiple t... |
dc3099d72b547e118fba794a77a2162538d8889a1c06f8bb0df27fd02153655c | MATLAB | 1,548 | 52 | function [loss,gradients,mseF1,mseF2,mseF3,mseF4,mseF5,mseF6]=modelLoss(parameters,net1,net2,CP,CB1,CB2,CBIC,CBt,U0,w1,w2,w3,w4,w5,w6,Y,Temp,dx)
net1.Learnables=parameters(1:8,:); net2.Learnables=parameters(9:end,:);
% make predictions
U=forward(net1,CP); AB=forward(net2,CBt);
gradientsU=dlgradient(sum(U,"all"),C... |
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