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values | md5 stringlengths 32 32 | text stringlengths 23 843k |
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github | drbenvincent/darc-experiments-matlab-master | plotDiscountSurface.m | .m | darc-experiments-matlab-master/darc-experiments/@Model_hyperbolic1ME_time/plotDiscountSurface.m | 3,941 | UNKNOWN | 5e5f8fc832f6a6154c0225d60dd272f9 | function plotDiscountSurface(obj, thetaStruct, varargin)
p = inputParser;
p.FunctionName = mfilename;
p.addRequired('thetaStruct',@isstruct);
p.addParameter('xScale','linear',@(x)any(strcmp(x,{'linear','log'})));
p.addParameter('data',[],@isstruct_or_table)
p.addParameter('pointEstimateType','mean',@isstr);
p.addParam... |
github | drbenvincent/darc-experiments-matlab-master | generate_designs.m | .m | darc-experiments-matlab-master/darc-experiments/response_error_types/@ChoiceFuncPsychometric/generate_designs.m | 9,159 | utf_8 | 76956e5e60901d47f17673051e41dc9a | function designs_allowed = generate_designs(obj, previous_designs, responses, thetas)
%generate_designs
%
% Create a matrix of possible designs. These will be considered by our
% optimization procedure.
%
% Inputs
%
% Outputs
% designs_allowed: A matrix of designs. Each column is one component of the
% design space.... |
github | drbenvincent/darc-experiments-matlab-master | SCRIPT_logk_comparison_of_methods.m | .m | darc-experiments-matlab-master/generate_figs_for_paper/SCRIPT_logk_comparison_of_methods.m | 3,145 | utf_8 | e64012ec647f029f09c5a77568cecc0c | function SCRIPT_logk_comparison_of_methods()
addpath('darc-experiments')
%% Sort figure and subpanel arrangement
fh = figure(56); clf, drawnow
set(fh, 'WindowStyle','normal')
nrows = 4;
subplot_handles = layout([1,2,3,4; 5,6,7,8; 9,10,11,12]');
drawnow
%% Load data for the 3 example participants
examples = makeExa... |
github | drbenvincent/darc-experiments-matlab-master | SCRIPT_logk_param_recovery_role_of_prior.m | .m | darc-experiments-matlab-master/generate_figs_for_paper/SCRIPT_logk_param_recovery_role_of_prior.m | 1,364 | utf_8 | 8356fade05ebefc58e78eb445bb1ed3a | function SCRIPT_logk_param_recovery_role_of_prior()
%% Setup
addpath('darc-experiments')
save_path = fullfile(pwd,'data');
logk_list = [-8:0.05:-1];
%% Run parameter sweeps
result_adaptive2 = parameter_sweep(logk_list, @param_recovery_adaptive_logk, 2);
result_adaptive4 = parameter_sweep(logk_list, @param_recovery... |
github | drbenvincent/darc-experiments-matlab-master | SCRIPT_logk_param_recovery.m | .m | darc-experiments-matlab-master/generate_figs_for_paper/SCRIPT_logk_param_recovery.m | 1,837 | utf_8 | 8cd207bb03305b7bd749d5315336357b | function SCRIPT_logk_param_recovery()
%% Setup
addpath('darc-experiments')
save_path = fullfile(pwd,'data');
logk_list = [-8:0.05:-1];
%% Run parameter sweeps
result_kirby = parameter_sweep(logk_list, @param_recovery_kirby_logk, 27);
result_koffarnus = parameter_sweep(logk_list, @param_recovery_koffarnus, 5);
res... |
github | drbenvincent/darc-experiments-matlab-master | SCRIPT_models_parameter_recovery.m | .m | darc-experiments-matlab-master/generate_figs_for_paper/SCRIPT_models_parameter_recovery.m | 4,615 | utf_8 | 1626fe0b1ac43a7f3a36ffd0fca2874a | function SCRIPT_models_parameter_recovery()
%% Setup
addpath('darc-experiments')
trials = 30; %30
K = 51; % 51
% CALCULATIONS: Do parameter recovery for all models ===========================
%% Hyperbolic discounting of time (with magnitude effect)
true_m_vec = linspace(-1, -0.5, K);
true_c_vec = linspace(-0.5, -... |
github | drbenvincent/darc-experiments-matlab-master | fig_darc_schematic.m | .m | darc-experiments-matlab-master/generate_figs_for_paper/fig_darc_schematic.m | 3,127 | utf_8 | 419ae13f8cc195dcb598b39ba7512225 | % fig_darc_schematic
% Create the basic structure of the figure to demonstrate the approaches:
% - Expected Utility Theory
% - Prospect Theory
% - Discounting
f = figure(1);
clf
h = layout([1, 2, 3; 4 5 6; 7 8 9]);
reward = linspace(-10,10,100);
probability = linspace(0,1,1000);
delays = linspace(0,365, 3650);
odds ... |
github | ajit2704/underwater-image-enhancement-master | vanherk.m | .m | underwater-image-enhancement-master/mat/vanherk.m | 4,841 | utf_8 | 5b0cf60c12e2432af9a978d4bad7ff3b | function Y = vanherk(X,N,TYPE,varargin)
% VANHERK Fast max/min 1D filter
%
% Y = VANHERK(X,N,TYPE) performs the 1D max/min filtering of the row
% vector X using a N-length filter.
% The filtering type is defined by TYPE = 'max' or 'min'. This function
% uses the van Herk algorithm for min/max filt... |
github | ajit2704/underwater-image-enhancement-master | maxfilt2.m | .m | underwater-image-enhancement-master/mat/maxfilt2.m | 1,849 | utf_8 | 45cc67fb2afee0dc77cfc7798629574f | function Y = maxfilt2(X,varargin)
% MAXFILT2 Two-dimensional max filter
%
% Y = MAXFILT2(X,[M N]) performs two-dimensional maximum
% filtering on the image X using an M-by-N window. The result
% Y contains the maximun value in the M-by-N neighborhood around
% each pixel in the original image. ... |
github | ajit2704/underwater-image-enhancement-master | bilateralFilter.m | .m | underwater-image-enhancement-master/mat/bilateralFilter.m | 6,703 | utf_8 | a76d6aab0840ad8b7e6e749526f36660 | %
% output = bilateralFilter( data, edge, ...
% edgeMin, edgeMax, ...
% sigmaSpatial, sigmaRange, ...
% samplingSpatial, samplingRange )
%
% Bilateral and Cross-Bilateral Filter using the Bilateral Grid.
%
% Bilaterally filters the image 'data' ... |
github | ajit2704/underwater-image-enhancement-master | autolevel.m | .m | underwater-image-enhancement-master/mat/autolevel.m | 2,027 | utf_8 | 42c51c0ef7df19d0766b3376c3b1500b | function imDst = autolevel(varargin)
[I,lowCut,highCut] =parse_inputs(varargin{:});
[hei,wid,~] = size(I);
PixelAmount = wid * hei;
if size(I,3)==3
[HistRed,~] = imhist(I(:,:,1));
[HistGreen,~] = imhist(I(:,:,2));
[HistBlue,~] = imhist(I(:,:,3));
CumRed = cumsum(HistRed);
CumGreen = cumsum(HistGreen)... |
github | ajit2704/underwater-image-enhancement-master | saliency_detection.m | .m | underwater-image-enhancement-master/mat/saliency_detection.m | 2,484 | utf_8 | d13d25afa6342e87bb05929451469b52 | %---------------------------------------------------------
% Copyright (c) 2009 Radhakrishna Achanta [EPFL]
% Contact: firstname.lastname@epfl.ch
%---------------------------------------------------------
% Citation:
% @InProceedings{LCAV-CONF-2009-012,
% author = {Achanta, Radhakrishna and Hemami, Sheila and E... |
github | ajit2704/underwater-image-enhancement-master | white_balance.m | .m | underwater-image-enhancement-master/mat/white_balance.m | 2,152 | utf_8 | 86ed46f043a7b9801c456cde675ebdda | %my own white-balance function, created by Qu Jingwei
function new_image = white_balance3(src_image)
[height,width,dim] = size(src_image);
temp = zeros(height,width);
%transform the RGB color space to YCbCr color space
ycbcr_image = rgb2ycbcr(src_image);
Y = ycbcr_image(:,:,1);
Cb = ycbcr_image(:,:,2);
Cr = yc... |
github | atdemarco/svrlsmgui-master | svrlsmgui.m | .m | svrlsmgui-master/svrlsmgui.m | 62,702 | utf_8 | 32070ab04e38ec6e5a30f181f8bf30c6 | function varargout = svrlsmgui(varargin)
% SVRLSMGUI MATLAB code for svrlsmgui.fig
% SVRLSMGUI, by itself, creates a new SVRLSMGUI or raises the existing
% singleton*.
%
% H = SVRLSMGUI returns the handle to a new SVRLSMGUI or the handle to
% the existing singleton*.
%
% SVRLSMGUI('CALLBACK',hO... |
github | atdemarco/svrlsmgui-master | lm2table.m | .m | svrlsmgui-master/functions/lm2table.m | 6,711 | utf_8 | 91866ec8af0be9264d12a99b61a74344 | function html = lm2table(mdl,caption)
%% Pretty css ...
% table {
% color: #333;
% font-family: Helvetica, Arial, sans-serif;
% width: 640px;
% /* Table reset stuff */
% border-collapse: collapse; border-spacing: 0;
% }
%
% td, th { border: 0 none; height: 30px; }
%
% th {
% /* Gradient Backgroun... |
github | atdemarco/svrlsmgui-master | step2_parallel.m | .m | svrlsmgui-master/functions/step2_parallel.m | 7,925 | utf_8 | 122e2f4b9e8fd73099f44977fe49aaaa | function [parameters,variables,thresholds] = step2_parallel(handles,parameters,variables,thresholds,all_perm_data)
handles = UpdateProgress(handles,'Sorting null betas for each lesioned voxel in the dataset (parallelized).',1);
L = length(variables.m_idx);
tail = parameters.tailshort; % so not a broadcast v... |
github | atdemarco/svrlsmgui-master | generic_hyperopts.m | .m | svrlsmgui-master/functions/generic_hyperopts.m | 4,224 | utf_8 | cb65bf7a69325a21821ec0c7ce414ec8 | function results = generic_hyperopts(parameters,variables)
% This attempts to optimize using matlab's default hyperparameter optimization options ...
% because it doesn't use bayesopt, it cannot update the progress bar (not output function)
% For clarity...
lesiondata = variables.lesion_dat;
beha... |
github | atdemarco/svrlsmgui-master | svrlsm_prepare_ica.m | .m | svrlsmgui-master/functions/svrlsm_prepare_ica.m | 7,989 | utf_8 | 1731883379f898e0e583d4ca6325a72e | function [parameters,variables] = svrlsm_prepare_ica(parameters,variables)
% We'll decompose the lesion data into ICs... and use percent damage to those ROIs as the lesion data values...
% Reread in each subject in the analysis, the mask, and make concatenated ICA file for fsl
for ni= 1 : variables.SubNum % numel(var... |
github | atdemarco/svrlsmgui-master | step1_notparallel_old.m | .m | svrlsmgui-master/functions/step1_notparallel_old.m | 5,199 | utf_8 | ab0fe65d23076e5b40c6aac94ecc66fd | function [handles,parameters] = step1_notparallel(handles,parameters,variables)
% This is where we'll save our GBs of permutation data output...
parameters.outfname_big = fullfile(variables.output_folder.clusterwise,['pmu_beta_maps_N_' num2str(parameters.PermNumVoxelwise) '.bin']);
%% Try to use cache ... |
github | atdemarco/svrlsmgui-master | step1_notparallel.m | .m | svrlsmgui-master/functions/step1_notparallel.m | 5,174 | utf_8 | f2d672f41a6a70b48e3d7ed78b5b812a | function [handles,parameters] = step1_notparallel(handles,parameters,variables)
% This is where we'll save our GBs of permutation data output...
parameters.outfname_big = fullfile(variables.output_folder.clusterwise,['pmu_beta_maps_N_' num2str(parameters.PermNumVoxelwise) '.bin']);
%% Try to use cache ... |
github | atdemarco/svrlsmgui-master | build_and_write_pmaps.m | .m | svrlsmgui-master/functions/build_and_write_pmaps.m | 10,054 | utf_8 | a98d12f50beab6567543d822657e3661 | function [thresholded,variables] = build_and_write_pmaps(options,parameters,variables,thresholds)
switch parameters.tailshort % parameters.tails
case 'pos' % options.hypodirection{1} % One-tailed positive tail... high scores BAD
[thresholded,variables] = write_p_maps_pos_tail(parameters,variable... |
github | atdemarco/svrlsmgui-master | svrlsm_bayesopt.m | .m | svrlsmgui-master/functions/svrlsm_bayesopt.m | 15,549 | utf_8 | 2215a0e43cc0ed243fb6b154de1f8378 | function results = svrlsm_bayesopt(parameters,variables)
% For clarity...
lesiondata = variables.lesion_dat;
behavdata = variables.one_score;
%% Which parameters to optimize and ranges to optim over
params = hyperparameters('fitrsvm',lesiondata,behavdata);
standrange = params(strcmp('Standardize',... |
github | atdemarco/svrlsmgui-master | svrlsm_waitbar.m | .m | svrlsmgui-master/functions/svrlsm_waitbar.m | 726 | utf_8 | 5732f213c7d380dbecbb6ffa4179a9d8 | function svrlsm_waitbar(waitbar_handles,newval,message)
if isempty(waitbar_handles)
return
end
% if numel(waitbar_handles) ~= 2 % < caused by multiple svrlsmgui's open at once
% error('Too many handles in input array')
% end
set_progress_percent(waitbar_handles(1),newval)
if narg... |
github | atdemarco/svrlsmgui-master | step1_parallel.m | .m | svrlsmgui-master/functions/step1_parallel.m | 8,340 | utf_8 | 9ce154f0ddd002dfff3717ec0effd46d | function [handles,parameters] = step1_parallel(handles,parameters,variables)
% This is where we'll save our GBs of permutation data output...
parameters.outfname_big = fullfile(variables.output_folder.clusterwise,['pmu_beta_maps_N_' num2str(parameters.PermNumVoxelwise) '.bin']);
%% Try to use cache to skip... |
github | atdemarco/svrlsmgui-master | build_and_write_beta_cutoffs.m | .m | svrlsmgui-master/functions/build_and_write_beta_cutoffs.m | 3,366 | utf_8 | f724334d6a434ee45dc9f8b9b64c223f | function [thresholded,variables] = build_and_write_beta_cutoffs(options,parameters,variables,thresholds,thresholded)
switch parameters.tailshort % parameters.tails
case 'pos' % One-tailed positive tail... high scores bad
[thresholded,variables] = write_beta_cutoff_pos_tail(variables,thresholds,... |
github | atdemarco/svrlsmgui-master | svrinteract.m | .m | svrlsmgui-master/functions/svrinteract.m | 10,295 | utf_8 | 844fdc5833c36244c16ecf3dc90d0faf | function varargout = svrinteract(varargin)
% SVRINTERACT MATLAB code for svrinteract.fig
% SVRINTERACT, by itself, creates a new SVRINTERACT or raises the existing
% singleton*.
%
% H = SVRINTERACT returns the handle to a new SVRINTERACT or the handle to
% the existing singleton*.
%
% SVRINTERA... |
github | atdemarco/svrlsmgui-master | optimalParameterReport.m | .m | svrlsmgui-master/functions/optimalParameterReport.m | 10,418 | utf_8 | f029005bdb9ec73ef901438e0e2fcdf8 | function variables = optimalParameterReport(parameters,variables)
mkdir(variables.output_folder.hyperparameterinfo)
%variables = optimalParameterReport(parameters,variables);
%variables.files_created.cfwerinfo = fullcfwerout;
% based on Zhang et al (2014)
% returns results for two measures of hyper... |
github | atdemarco/svrlsmgui-master | continuize_lesions.m | .m | svrlsmgui-master/functions/continuize_lesions.m | 3,445 | utf_8 | 4c8d28c69af12f9066e66e03d26ae518 | function variables = continuize_lesions(variables,parameters)
% 8/7/17 - added support for parallelization
% 8/7/17 - fixed bug - intercept term and adding its beta back into residuals
% 11/16/17 - added check for user interrupt
% 2/19/18 - added in-gui waitbar in parallelized and non-parallelized loop
% w... |
github | atdemarco/svrlsmgui-master | write_nifti_hdr.m | .m | svrlsmgui-master/functions/nifti/write_nifti_hdr.m | 2,762 | utf_8 | 82987cccd27d7f60b004bdbec61b6d24 | function write_nifti_hdr(h, fname)
% WRITE_NIFTI_HDR Write NIFTI header
%
% WRITE_NIFTI_HDR(H, FNAME) writes the header structure H into the file
% FNAME. The validity of H is not checked.
[pathstr, basename, ext] = fileparts(fname);
if strcmp(ext, '.img')
fname = fullfile(pathstr, [basename '.hdr']);
en... |
github | atdemarco/svrlsmgui-master | analyze_to_nifti.m | .m | svrlsmgui-master/functions/nifti/analyze_to_nifti.m | 1,235 | utf_8 | 18757b17671315605f0fda9ab06b7129 | function analyze_to_nifti(fname)
% ANALYZE_TO_NIFTI(FNAME)
%
% Converts the ANALYZE image FNAME to .nii (one file) format. If no FNAME
% is provided, converts every .img file in the current directory.
%
% The header information is set up based on what SPM5 does if you reslice.
% The origin is set to the center... |
github | atdemarco/svrlsmgui-master | nifti2jpg.m | .m | svrlsmgui-master/functions/nifti/nifti2jpg.m | 1,178 | utf_8 | 534ca9fc2dd45fab241045c7a7d29e53 | function nifti2jpg(fname, skip, flip)
if nargin < 2
skip = 1;
end
if nargin < 3
flip = [0 0 1; 1 0 1]; % works for NIC T1s after dicom2analyze
end
[hdr, img] = read_nifti(fname);
vals = img(:);
vals = sort(vals(1:10:end));
anatmin = vals(round(length(vals) * 10 / 100));
anatmax = vals(round(len... |
github | atdemarco/svrlsmgui-master | run_beta_PMU_old.m | .m | svrlsmgui-master/functions/unused/run_beta_PMU_old.m | 24,927 | utf_8 | 245c8f57bb62a9aebd3d04d065c89441 | function variables = run_beta_PMU(parameters, variables, cmd, beta_map,handles)
options = handles.options;
zerostemplate = zeros(variables.vo.dim(1:3)); % make a zeros template....
ori_beta_val = beta_map(variables.m_idx).'; % Original observed beta values.
tic;
if parameters.parallelize %... |
github | atdemarco/svrlsmgui-master | crossval_diagnostics.m | .m | svrlsmgui-master/functions/unused/crossval_diagnostics.m | 3,065 | utf_8 | 02ba5b4ce471ec375db0f8ee55bbdfad | function varargout = crossval_diagnostics(varargin)
% CROSSVAL_DIAGNOSTICS MATLAB code for crossval_diagnostics.fig
% CROSSVAL_DIAGNOSTICS, by itself, creates a new CROSSVAL_DIAGNOSTICS or raises the existing
% singleton*.
%
% H = CROSSVAL_DIAGNOSTICS returns the handle to a new CROSSVAL_DIAGNOSTICS or t... |
github | HelmchenLabSoftware/OCIA-master | eventDetector.m | .m | OCIA-master/caImgAnalysis/eventDetection/eventDetector.m | 15,135 | utf_8 | 64d69083f3f62775510da94cfc8f656b | function varargout = eventDetector(ROIStats, stim, ROISet, eventDetectMethod, frameRate, bpfilter, psConfig, saveName)
% event detection function - wrapper to different event detection algorithms
% input: structure created by GetRoiStats (*_RoiStats)
dbgLevel = 2;
% required folders
folderList = {'Projects/EventDetect'... |
github | HelmchenLabSoftware/OCIA-master | eventDetector_old.m | .m | OCIA-master/caImgAnalysis/eventDetection/eventDetector_old.m | 12,802 | utf_8 | ad7f17e5b4904c061333c7f354dac6c0 | function varargout = eventDetector(roiStats, eventDetectMethod)
% event detection function - wrapper to different event detection algorithms
% input: structure created by GetRoiStats (*_RoiStats)
dbgLevel = 2;
% required folders
folderList = {'Projects/EventDetect','Projects/TwoPhotonAnalyzer'};
addFolders2Path(folderL... |
github | HelmchenLabSoftware/OCIA-master | PeelingOptimizeSpikeTimesSaturation.m | .m | OCIA-master/caImgAnalysis/eventDetection/newPeeling/PeelingOptimizeSpikeTimesSaturation.m | 4,465 | utf_8 | 82892eced9f5fb70e0d8ad3f544df164 | function [spkTout,output] = PeelingOptimizeSpikeTimesSaturation(dff,spkTin,lowerT,upperT,...
ca_amp,ca_gamma,ca_onsettau,ca_rest, ca_kappas, kd, conc, dffmax, frameRate, dur, optimMethod,maxIter,doPlot)
% optimization of spike times found by Peeling algorithm
% minimize the sum of the residual squared
% while sever... |
github | HelmchenLabSoftware/OCIA-master | PeelingOptimizeSpikeTimes.m | .m | OCIA-master/caImgAnalysis/eventDetection/newPeeling/PeelingOptimizeSpikeTimes.m | 4,159 | utf_8 | 61e419a2e0808657c62b39f38bc0fb60 | function [spkTout,output] = PeelingOptimizeSpikeTimes(dff,spkTin,lowerT,upperT,...
rate,tauOn,A1,tau1,optimMethod,maxIter,doPlot)
% optimization of spike times found by Peeling algorithm
% minimize the sum of the residual squared
% while several optimization algorithms are implemented (see below), we have only used... |
github | HelmchenLabSoftware/OCIA-master | Peeling.m | .m | OCIA-master/caImgAnalysis/eventDetection/newPeeling/Peeling.m | 9,350 | utf_8 | feca5c14c59423537078bfaf885a57e7 | function [ca_p, peel_p, data] = Peeling(dff, rate, varargin)
% this is the main routine of the peeling algorithm
%
% Peeling algorithm was developed by Fritjof Helmchen
% Brain Research Institute
% University of Zurich
% Switzerland
%
% Matlab implementation and spike timing optimization by Henry Luetcke & Fritjof Helm... |
github | HelmchenLabSoftware/OCIA-master | CalciumDecay.m | .m | OCIA-master/caImgAnalysis/eventDetection/newPeeling/CalciumDecay.m | 1,116 | utf_8 | 67138b4224a9d6e8edefa5aa8b387b8e | function [t,X] = CalciumDecay(p_gamma,p_carest,p_cacurrent,p_kappas,p_kd,p_conc,tspan)
% Uses ODE45 to solve Single-compartment model differential equation
%
% Fritjof Helmchen (helmchen@hifo.uzh.ch)
% Brain Research Institute,University of Zurich, Switzerland
% created: 7.10.2013, last update: 25.10.2013 fh
options... |
github | HelmchenLabSoftware/OCIA-master | comparingReferences.m | .m | OCIA-master/caImgAnalysis/OCIA/misc/comparingReferences.m | 2,914 | utf_8 | fd9fe5ba3dd91c9f7ff76ab741405cee | function comparingReferences
load('refImg_fromMapping');
refImgMapping = refImg;
load('refImg');
load('ROIs');
figure('NumberTitle', 'off', 'Name', 'Reference compare', 'Position', [30, 80, 1850, 910], 'Color', 'white');
makeSubplot(1, refImg, 'Reference from session', ROIs, [-0.05, 1.05]); %#ok<*USENS,*NODEF>
makeS... |
github | HelmchenLabSoftware/OCIA-master | plotWideFieldMaps_old.m | .m | OCIA-master/caImgAnalysis/OCIA/misc/plotWideFieldMaps_old.m | 5,024 | utf_8 | df2406424fd659898e4fbbbb5e365bf9 | % plot Wide-Field maps
sessDirs = dir();
sessDirs(arrayfun(@(i) isempty(regexp(sessDirs(i).name, '^session\d\d_\d+$', 'once')), 1 : numel(sessDirs))) = [];
sessDirs = sessDirs([1, 2, 4 6]);
if ~exist('sessMat', 'var');
sessMat = struct();
sessMat(numel(sessDirs)) = struct();
end;
trialTypesRegexp = { 'hit',... |
github | HelmchenLabSoftware/OCIA-master | changing_frame_0_balazs.m | .m | OCIA-master/caImgAnalysis/OCIA/misc/changing_frame_0_balazs.m | 6,227 | utf_8 | 4da913c737f7e68564f0e3529a5fd541 | function changing_frame_0_balazs()
fr0 = [];
load('stimStartFrames');
load('trials_ind');
load('norm_frame');
load('rois_OCIA_old');
load('ROIs_registered');
fr2=57:58;
fr_dev2 = nan(size(fr_dev)); %#ok<*NODEF>
stimFrames = 59:68;
fixedStartFrame = max(stimStartFrame);
% trialTypes = { 'hit', 'CR' };
trialTypes = { ... |
github | HelmchenLabSoftware/OCIA-master | BEGetTrialInfo.m | .m | OCIA-master/caImgAnalysis/OCIA/@OCIA/BEGetTrialInfo.m | 2,254 | utf_8 | ecb6e0a8914941c49d705be87c4ca6df | %% #BEGetTrialInfo
function trialInfo = BEGetTrialInfo(this, iTrial)
% default is empty
freq = ''; spotIndex = ''; isTargetOrNTones = ''; resp = ''; respTime = ''; corr = ''; rew = '';
if iTrial > 0 && iTrial <= this.be.config.training.nTrials && isfield(this.be, 'stims');
if isfield(this.be, 'spotMatrix') &... |
github | HelmchenLabSoftware/OCIA-master | DWMatchBehavTrialsToImagingData.m | .m | OCIA-master/caImgAnalysis/OCIA/@OCIA/DWMatchBehavTrialsToImagingData.m | 6,399 | utf_8 | afd7fe9d63c0d81ca6439a845346cc6f | function DWMatchBehavTrialsToImagingData(this)
% DWMatchBehavTrialsToImagingData - [no description]
%
% DWMatchBehavTrialsToImagingData(this)
%
% [No description]
%
% 2013-2016 - Copyleft and programmed by Balazs Laurenczy (blaurenczy_at_gmail.com)
% match the behavior trials and the data files
% update the wait... |
github | HelmchenLabSoftware/OCIA-master | DWMatchBehavTrialsToImagingDataForSession.m | .m | OCIA-master/caImgAnalysis/OCIA/@OCIA/DWMatchBehavTrialsToImagingDataForSession.m | 16,055 | utf_8 | 3a28c46a1d44236c27a5d27a8ab6b9fb | %% - #DWMatchBehavTrialsToImagingDataForSession
function DWMatchBehavTrialsToImagingDataForSession(this, animalID, dayID, spotID, iSess, rowIndexes, locFilter)
% get the number of imaging trials found
nTrialsFound = size(rowIndexes, 1);
% abort if no trials
if ~nTrialsFound; return; end;
% find the right behavior ou... |
github | HelmchenLabSoftware/OCIA-master | INRunExp_standard.m | .m | OCIA-master/caImgAnalysis/OCIA/@OCIA/INRunExp_standard.m | 6,976 | utf_8 | 0ca07cd497925df810b83f5c082ea448 | function INRunExp_standard(this)
% INRunExp_standard - [no description]
%
% INRunExp_standard(this)
%
% [No description]
%
% 2013-2016 - Copyleft and programmed by Balazs Laurenczy (blaurenczy_at_gmail.com)
o('#%s ...', mfilename, 3, this.verb);
%% init
% extract the parameters structure
params = this.in.standa... |
github | HelmchenLabSoftware/OCIA-master | INSavePlot.m | .m | OCIA-master/caImgAnalysis/OCIA/@OCIA/INSavePlot.m | 3,579 | utf_8 | 4a457e0f84d96fe70d00758e8266075b | function INSavePlot(this, savePath, plotToSave, varargin)
% INSavePlot - [no description]
%
% INSavePlot(this, savePath, plotToSave, varargin)
%
% [No description]
%
% 2013-2016 - Copyleft and programmed by Balazs Laurenczy (blaurenczy_at_gmail.com)
% if no save path has been provided, create a dialog to request... |
github | HelmchenLabSoftware/OCIA-master | JTUpdateVirtualJoints.m | .m | OCIA-master/caImgAnalysis/OCIA/@OCIA/JTUpdateVirtualJoints.m | 5,706 | utf_8 | 72e85fec6b3a1f27b93113ed88dc6252 | function JTUpdateVirtualJoints(this, iFrame, iJointType)
% JTUpdateVirtualJoints - [no description]
%
% JTUpdateVirtualJoints(this, iFrame, iJointType)
%
% [No description]
%
% 2013-2016 - Copyleft and programmed by Balazs Laurenczy (blaurenczy_at_gmail.com)
% show debug plots of virtual joints
showDeb... |
github | HelmchenLabSoftware/OCIA-master | BELightPulse.m | .m | OCIA-master/caImgAnalysis/OCIA/@OCIA/BELightPulse.m | 1,073 | utf_8 | 7d7e8d6d47649bbc740a57b9bccf2f5e | function BELightPulse(this, pulseDur, IPI, nPulses)
% BELightPulse - [no description]
%
% BELightPulse(this, pulseDur, IPI, nPulses)
%
% [No description]
%
% 2013-2016 - Copyleft and programmed by Balazs Laurenczy (blaurenczy_at_gmail.com)
imagTTLState = get(this.GUI.handles.be.imagTTL, 'Value');
o('#%s(): pulse... |
github | HelmchenLabSoftware/OCIA-master | INTestStim.m | .m | OCIA-master/caImgAnalysis/OCIA/@OCIA/INTestStim.m | 3,097 | utf_8 | d3c965f0467534cb336f38b928666bc2 |
function INTestStim(this, ~, ~)
% INTestStim - [no description]
%
% INTestStim(this)
%
% [No description]
%
% 2013-2016 - Copyleft and programmed by Balazs Laurenczy (blaurenczy_at_gmail.com)
% update button
set(this.GUI.handles.in.testStimBut, 'Value', 1, 'Enable', 'off', 'BackgroundColor', 'yellow');
% disabl... |
github | HelmchenLabSoftware/OCIA-master | ANSavePlot.m | .m | OCIA-master/caImgAnalysis/OCIA/@OCIA/ANSavePlot.m | 6,041 | utf_8 | 3d1614ebf1f33d5130d6d4f323ecb622 | function ANSavePlot(this, savePath, varargin)
% ANSavePlot - [no description]
%
% ANSavePlot(this, savePath, varargin)
%
% [No description]
%
% 2013-2016 - Copyleft and programmed by Balazs Laurenczy (blaurenczy_at_gmail.com)
% if no save path has been provided, create a dialog to request one
if isempty(savePath... |
github | HelmchenLabSoftware/OCIA-master | DIUpdateGUI.m | .m | OCIA-master/caImgAnalysis/OCIA/@OCIA/DIUpdateGUI.m | 4,060 | utf_8 | 7053fe17121fcccefd4ec7791bf84fb4 | %% #DIUpdateGUI
function DIUpdateGUI(this, ~, ~)
o('#%s() ...', mfilename, 3, this.verb);
try % capture display errors
%% camera plot
try
currFrame = peekdata(this.GUI.di.camHandle, 1);
flushdata(this.GUI.di.camHandle);
currFrame(:, :, 2) = currFrame(:, :, 1);
currFrame(:, :, 3) = currFrame(:, :, 1)... |
github | HelmchenLabSoftware/OCIA-master | DWFilterTable.m | .m | OCIA-master/caImgAnalysis/OCIA/@OCIA/DWFilterTable.m | 9,418 | utf_8 | 0487d32d14dbf96aa9d050a83844249d | function [filtTable, filtTableIndexes] = DWFilterTable(this, filtText, tableToUse, tIDs)
% DWFilterTable - Filter the DataWatcher table and return the rows (and row indexes)
%
% [filtTable, filtTableIndexes] = DWFilterTable(this, filtText)
% [filtTable, filtTableIndexes] = DWFilterTable(this, filtText, tabl... |
github | HelmchenLabSoftware/OCIA-master | OCIACreateParamPanelControls.m | .m | OCIA-master/caImgAnalysis/OCIA/@OCIA/OCIACreateParamPanelControls.m | 26,865 | utf_8 | 96f2eed824df54d1d3e64fbb0b6a310d |
function OCIACreateParamPanelControls(this, modeID, varargin)
% OCIACreateParamPanelControls - Creates a parameter pannel menu
%
% OCIACreateParamPanelControls(this, modeID, optionalHandleOfNavButtons)
%
% Creates a parameter panel menu from a parameter panel configuration ("this.GUI.(modeID).paramPanConfig") an... |
github | HelmchenLabSoftware/OCIA-master | DIStartStopCamera.m | .m | OCIA-master/caImgAnalysis/OCIA/@OCIA/DIStartStopCamera.m | 1,247 | utf_8 | 72f49cb06536a9aff1927ea2ee8e228b | %% #DIStartStopCamera
function DIStartStopCamera(this, commandString)
o('#%s() ...', mfilename, 3, this.verb);
try % capture display errors
if strcmp(commandString, 'toggle') && strcmp(get(this.GUI.di.camHandle, 'Running'), 'on');
commandString = 'stop';
elseif strcmp(commandString, 'toggle') && strcmp(get(this.... |
github | HelmchenLabSoftware/OCIA-master | INRunExp_trigInTTLOut.m | .m | OCIA-master/caImgAnalysis/OCIA/@OCIA/INRunExp_trigInTTLOut.m | 5,723 | utf_8 | e2655bca7a3289d93c5abc75499bcb6b | function INRunExp_trigInTTLOut(this)
% INRunExp_trigInTTLOut - [no description]
%
% INRunExp_trigInTTLOut(this)
%
% [No description]
%
% 2013-2016 - Copyleft and programmed by Balazs Laurenczy (blaurenczy_at_gmail.com)
params = this.in.(this.in.expMode);
if this.in.TTLOutStr.isWorking; return; end;
if ~this.in.... |
github | HelmchenLabSoftware/OCIA-master | BERunTrial.m | .m | OCIA-master/caImgAnalysis/OCIA/@OCIA/BERunTrial.m | 41,549 | utf_8 | 0645e93632a4428e9495406823adfe13 | function BERunTrial(this)
% BERunTrial - [no description]
%
% BERunTrial(this)
%
% [No description]
%
% 2013-2016 - Copyleft and programmed by Balazs Laurenczy (blaurenczy_at_gmail.com)
% /!\ NOTE: all times are in seconds (with decimals though) since trial start or trial init
% init some variables
trainConf = ... |
github | HelmchenLabSoftware/OCIA-master | DWMatchROISetsToData.m | .m | OCIA-master/caImgAnalysis/OCIA/@OCIA/DWMatchROISetsToData.m | 7,461 | utf_8 | 7149efd47267f932563694835593decb | %% - #DWMatchROISetsToData
function DWMatchROISetsToData(this)
% update the wait bar
DWWaitBar(this, 0);
% get the list of all animals
uniqueAnimals = get(this, 'animal');
if ~isempty(uniqueAnimals) && ~iscell(uniqueAnimals); uniqueAnimals = { uniqueAnimals }; end;
if isempty(uniqueAnimals); uniqueAnimals = { '' }; e... |
github | HelmchenLabSoftware/OCIA-master | OCIA.m | .m | OCIA-master/caImgAnalysis/OCIA/@OCIA/OCIA.m | 77,388 | utf_8 | 77043c2f7b13e21ffd1f9a11c36961a1 | classdef OCIA < handle
% OCIA - Online Calcium Imaging Assistant
%
% this = OCIA()
% this = OCIA(configName)
% this = OCIA(configName, DWFilt)
%
% Returns an OCIA object 'this', using the configuration file specified by 'configName' using the syntax
% "OCIA_config_[configName].m". If no conf... |
github | HelmchenLabSoftware/OCIA-master | RDSelROI.m | .m | OCIA-master/caImgAnalysis/OCIA/@OCIA/RDSelROI.m | 3,644 | utf_8 | 0361eb322847a59f38e2c2b6c30702ff | %% #OCIA:RD:RDSelROI
function RDSelROI(this, varargin)
o('#RDSelROI()', 4, this.verb);
h = []; % no handle by default
% get the handle if there is any
if nargin > 1; h = varargin{1}; end;
% if change was requested by a number, overwrite the selection
if ~isempty(h) && isnumeric(h) && ~ishandle(h);
selROIs = h;
... |
github | HelmchenLabSoftware/OCIA-master | OCIA_genStimVect_fromAnalogInWideField.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/genStimVect/OCIA_genStimVect_fromAnalogInWideField.m | 15,569 | utf_8 | db650f76208ac994600bd0dc7f54800a | %% #OCIA:AN:OCIA_genStimVect_fromAnalogInWideField
function [isValid, unvalidReason] = OCIA_genStimVect_fromAnalogInWideField(this, iDWRow, varargin)
% get whether to do plots or not
if nargin > 2; doPlotsTrig = varargin{1}; doPlotsMicr = varargin{1}; doPlotsSummary = varargin{1}; %#ok<NASGU>
elseif nargin > 3; ... |
github | HelmchenLabSoftware/OCIA-master | OCIA_genStimVect_fromBehavTextFile.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/genStimVect/OCIA_genStimVect_fromBehavTextFile.m | 5,478 | utf_8 | 1379c5e1886d23dbf086cae8b1e60820 | %% #OCIA:AN:OCIA_genStimVect_fromBehavTextFile
function [isValid, unvalidReason] = OCIA_genStimVect_fromBehavTextFile(this, iDWRow, varargin)
% get whether to do plots or not
if nargin > 2; doDebugPlots = varargin{1};
else doDebugPlots = 0;
end;
rowID = DWGetRowID(this, iDWRow); % get the row ID ... |
github | HelmchenLabSoftware/OCIA-master | OCIA_genStimVect_noStim.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/genStimVect/OCIA_genStimVect_noStim.m | 882 | utf_8 | 03e130ba77be5a2d529963b4cd2fe64c | %% #OCIA:AN:OCIA_genStimVect_fromMicrAnalogIn
function [isValid, unvalidReason] = OCIA_genStimVect_noStim(this, iDWRow, varargin)
isValid = true; % by default, the row is valid
unvalidReason = ''; % by default no reason
%% init the stim vector
% get the number of skipped frames
nSkippedFrames = this.an.skipFrame.nFra... |
github | HelmchenLabSoftware/OCIA-master | OCIA_genStimVect_fromInputArgument.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/genStimVect/OCIA_genStimVect_fromInputArgument.m | 2,411 | utf_8 | 8cb502bb2a0dfe425818d1461d8d8ff5 | %% #OCIA:AN:OCIA_genStimVect_fromInputArgument
function [isValid, unvalidReason] = OCIA_genStimVect_fromInputArgument(this, iDWRow, stimVectCellArray, ...
stimTypesCellArray, nMaxStimTypesCellArray)
isValid = true; % by default, the row is valid
unvalidReason = ''; % by default no reason
o('#%s(): row num: %d ...... |
github | HelmchenLabSoftware/OCIA-master | OCIA_genStimVect_fromMicrAnalogIn.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/genStimVect/OCIA_genStimVect_fromMicrAnalogIn.m | 25,627 | utf_8 | 8fb42ab887a6a62a42ac00cb7eb1782b | %% #OCIA:AN:OCIA_genStimVect_fromMicrAnalogIn
function [isValid, unvalidReason] = OCIA_genStimVect_fromMicrAnalogIn(this, iDWRow, varargin)
% get whether to do plots or not
if nargin > 2; doPlotsYscan = varargin{1}; doPlotsMicr = varargin{1};
elseif nargin > 3; doPlotsYscan = varargin{1}; doPlotsMicr = varargin{... |
github | HelmchenLabSoftware/OCIA-master | OCIA_genStimVect_fromWhisker.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/genStimVect/OCIA_genStimVect_fromWhisker.m | 4,088 | utf_8 | b073f00c4f340f8c1ab5674eb41e5d5d | %% #OCIA:AN:OCIA_genStimVect_fromWhisker
function [isValid, unvalidReason] = OCIA_genStimVect_fromWhisker(this, iDWRow, varargin)
% get whether to do plots or not
if nargin > 2; doDebugPlots = varargin{1};
else doDebugPlots = 0;
end;
rowID = DWGetRowID(this, iDWRow); % get the row ID
isValid = t... |
github | HelmchenLabSoftware/OCIA-master | OCIA_startFunction_widefieldCreateAveragesForEachCondition.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/startFunctions/OCIA_startFunction_widefieldCreateAveragesForEachCondition.m | 9,795 | utf_8 | eef9147a9768002dbc4259deb36d33ff | function OCIA_startFunction_widefieldCreateAveragesForEachCondition(this)
% OCIA_startFunction_widefieldCreateAveragesForEachCondition - [no description]
%
% OCIA_startFunction_widefieldCreateAveragesForEachCondition(this)
%
% [No description]
%
% 2013-2016 - Copyleft and programmed by Balazs Laurenczy (blaurencz... |
github | HelmchenLabSoftware/OCIA-master | OCIA_analysis_wideField_drawCropRect.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/analysis/OCIA_analysis_wideField_drawCropRect.m | 820 | utf_8 | f4f3787ccee041fd8eb5d85d86bace20 | function OCIA_analysis_wideField_drawCropRect(this, ~, ~)
% OCIA_analysis_wideField_drawCropRect - [no description]
%
% OCIA_analysis_wideField_drawCropRect(this)
%
% [No description]
%
% 2013-2016 - Copyleft and programmed by Balazs Laurenczy (blaurenczy_at_gmail.com)
% remove previous rectangle
axeChilds = get... |
github | HelmchenLabSoftware/OCIA-master | OCIA_analysis_getROIStat.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/analysis/OCIA_analysis_getROIStat.m | 1,842 | utf_8 | 0108c7662da8e7c25a69f40e48834599 | % get the grouping from the different variables
function [ROIStat, description] = OCIA_analysis_getROIStat(ROIStatToCalc, respMethod, PSCaTracesStats, ...
stimIDIndexes, stimIDs)
% get the average responsiveness to all trials
ROIResps = reshape(nanmean(PSCaTracesStats.ROIRespTrial, 2), ...
size(PSCaTracesS... |
github | HelmchenLabSoftware/OCIA-master | OCIA_analysis_getWhiskVectors.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/analysis/OCIA_analysis_getWhiskVectors.m | 1,996 | utf_8 | a3c25dc726e7ecc35017c2d86ec7ff70 | %% #OCIA:AN:OCIA_analysis_caTraces_whiskvectors
function [WAEnvs, WAAmp, WASetP, WAExpWhisk, WAFovWhisk] = OCIA_analysis_getWhiskVectors(this, ...
rawWhiskTraces, whiskFrameRateCellArray)
nRuns = numel(rawWhiskTraces);
% define frequency bands
Expwhisk_low_frequ = 7; % Hz frequ. band for exploratory ... |
github | HelmchenLabSoftware/OCIA-master | OCIA_analysis_getGrouping.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/analysis/OCIA_analysis_getGrouping.m | 5,378 | utf_8 | 71ab6791a9546bb97c7e85f287c452c3 | % get the grouping from the different variables
function [grouping, groupLabels] = OCIA_analysis_getGrouping(this, iDWRows, stimIDIndexes, selDispStimIDs, groupBy, ROINames, ROIPhases)
% create the grouping variable
switch groupBy;
case 'ROI';
% remove the ROISet tag
cleanROINames = regexprep(ROIN... |
github | HelmchenLabSoftware/OCIA-master | OCIA_analysis_behav_getBehavVars.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/analysis/OCIA_analysis_behav_getBehavVars.m | 32,382 | utf_8 | 7db800f203bd40f7c6c94b65743f703a | function [behavVars, rowIDs, colIDs] = OCIA_analysis_behav_getBehavVars(this, allBehavStructs, ...
selectedLoadedBehavRows, includeEOTrials)
% OCIA_analysis_behav_getBehavVars - [no description]
%
% [behavVars, rowIDs, colIDs] = OCIA_analysis_behav_getBehavVars(this, allBehavStructs, ...
% ... |
github | HelmchenLabSoftware/OCIA-master | OCIA_parseNotebookFile_H45Balazs.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/parseNotebook/OCIA_parseNotebookFile_H45Balazs.m | 9,607 | utf_8 | 0c5a917a0ff89436458c3f52e1cb6233 | function notebookInfo = OCIA_parseNotebookFile_H45Balazs(notebookFilePath)
% written by B. Laurenczy - 2013/10/15
%% init variables
notebookInfo = cell(1, 14);
% notebookInfo = cell(1, 10);
iRow = 1;
skipLineRead = false;
% regular expression patterns
% mouseIDPattern = '^mou_[db]l_\d{6}_\d{2}$';
mouseIDPattern = '^\... |
github | HelmchenLabSoftware/OCIA-master | OCIA_parseNotebookFile_H37Alex.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/parseNotebook/OCIA_parseNotebookFile_H37Alex.m | 9,570 | utf_8 | b92b584eb116531a7c99ab7a809f163f | function notebookInfo = OCIA_parseNotebookFile_H37Alex(notebookFilePath)
% written by B. Laurenczy - 2013/10/15
%% init variables
notebookInfo = cell(1, 14);
% notebookInfo = cell(1, 10);
iRow = 1;
skipLineRead = false;
% regular expression patterns
% mouseIDPattern = '^mou_[db]l_\d{6}_\d{2}$';
mouseIDPattern = '^\w+... |
github | HelmchenLabSoftware/OCIA-master | OCIA_parseNotebookFile_default.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/parseNotebook/OCIA_parseNotebookFile_default.m | 9,500 | utf_8 | ed75ced6923a9b1d824192423aad1eb1 | function [infoTable, tIDs] = OCIA_parseNotebookFile_default(notebookFilePath)
% written by B. Laurenczy - 2014/02/11
%% init variables
infoTable = cell(1000, 9);
tIDs = { 'animal', 'spot', 'runType', 'comments', 'day', 'time', 'imType', 'imType2', 'dimNB'};
iRow = 1;
skipLineRead = false;
% regular expression pattern... |
github | HelmchenLabSoftware/OCIA-master | OCIA_dataWatcherProcess_fiberMovies.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/dataWatcherProcess/OCIA_dataWatcherProcess_fiberMovies.m | 3,029 | utf_8 | 998fce6c62245a138a9e85236238e151 | %% #OCIA_dataWatcherProcess_fiberMovies
function OCIA_dataWatcherProcess_fiberMovies(this, ~, ~)
%% initialize movie
% get the path of the selected movie
moviePath = DWGetFullPath(this, this.dw.selectedTableRows(1));
if regexp(moviePath, '\.avi$');
% get VideoReader object for the selected movie
vrHand = ... |
github | HelmchenLabSoftware/OCIA-master | OCIA_dataWatcherProcess_trackMovies.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/dataWatcherProcess/OCIA_dataWatcherProcess_trackMovies.m | 8,209 | utf_8 | fd53cc601f82c5641c2b56e69a35c184 | %% #OCIA_dataWatcherProcess_trackMovies
function OCIA_dataWatcherProcess_trackMovies(this, ~, ~)
% change mode
OCIAChangeMode(this, 'DataWatcher');
%% initialize movie
% get the path of the selected movie
moviePath = this.path.moviePath;
moviePathCropped = regexprep(moviePath, '\.avi', '_cropped.avi');
if... |
github | HelmchenLabSoftware/OCIA-master | OCIA_dataWatcherProcess_importIJROIs.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/dataWatcherProcess/OCIA_dataWatcherProcess_importIJROIs.m | 5,124 | utf_8 | 01dcc93b17c38d8516f53940750a8bb4 | %% #OCIA_dataWatcherProcess_importIJROIs
function OCIA_dataWatcherProcess_importIJROIs(this, ~, ~)
importIJROIsTic = tic; % for performance timing purposes
showMessage(this, 'Extracting and importing imageJ ROISet ...');
DWWaitBar(this, 0);
% get the index(es) of the ImageJ ROISet rows
ijROISetRows = DWFilterTable(t... |
github | HelmchenLabSoftware/OCIA-master | OCIA_dataWatcherProcess_onlineAnalysis.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/dataWatcherProcess/OCIA_dataWatcherProcess_onlineAnalysis.m | 2,959 | utf_8 | be69fc0cc3a327f294c91a3b3ba66d94 | function OCIA_dataWatcherProcess_onlineAnalysis(this, h, ~)
% OCIA_dataWatcherProcess_onlineAnalysis - [no description]
%
% OCIA_dataWatcherProcess_onlineAnalysis(this, h, ~)
%
% [No description]
%
% 2013-2016 - Copyleft and programmed by Balazs Laurenczy (blaurenczy_at_gmail.com)
localVerb = 2;
% check if the ... |
github | HelmchenLabSoftware/OCIA-master | OCIA_dataWatcherProcess_analyseRows_old.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/dataWatcherProcess/OCIA_dataWatcherProcess_analyseRows_old.m | 3,918 | utf_8 | 528fa9a37feb8773fc07c70a8c900e0e | %% #OCIA_dataWatcherProcess_analyseRows
function OCIA_dataWatcherProcess_analyseRows_old(this, ~, ~)
analyseRowsTic = tic; % for performance timing purposes
% store the selected rows so that even changing the selection in the DataWatcher mode does not affect the Analyser
this.an.selectedTableRows = this.dw.selectedTa... |
github | HelmchenLabSoftware/OCIA-master | OCIA_dataWatcherProcess_saveResults.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/dataWatcherProcess/OCIA_dataWatcherProcess_saveResults.m | 3,035 | utf_8 | 42d498164768321b83ac3e51df89af8c | %% #OCIA_dataWatcherProcess_saveResults
function OCIA_dataWatcherProcess_saveResults(this, ~, ~)
% get imaging rows
% imgRows = DWFindTableRows(this, 'imgData', '', '', '', '', '', '');
imgRows = this.dw.selectedTableRows;
% loop trough all rows
for iRow = 1 : numel(imgRows);
% get the run ID
rowID = spr... |
github | HelmchenLabSoftware/OCIA-master | OCIA_dataProcess_imgData_moDet.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/dataProcess/OCIA_dataProcess_imgData_moDet.m | 15,192 | utf_8 | 6feea3c4ee368f580b086b9938bd6a03 | %% #OCIA:OCIA_dataProcess_imgData_moDet
function [isValid, unvalidReason] = OCIA_dataProcess_imgData_moDet(this, iDWRow, varargin)
% by default, row is valid
isValid = true;
unvalidReason = '';
% get the selected processing steps and this row's processing state
selProcOpts = this.an.procOptions.id(get(this.GUI.handle... |
github | HelmchenLabSoftware/OCIA-master | OCIA_dataProcess_imgData_skipFrame.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/dataProcess/OCIA_dataProcess_imgData_skipFrame.m | 1,915 | utf_8 | e6b8685e6992028e7df3f99b7ba25864 | %% #OCIA:OCIA_dataProcess_imgData_skipFrame
function [isValid, unvalidReason] = OCIA_dataProcess_imgData_skipFrame(this, iDWRow, varargin)
% by default, row is valid
isValid = true;
unvalidReason = '';
% get the selected processing steps and this row's processing state
selProcOpts = this.an.procOptions.id(get(this.GU... |
github | HelmchenLabSoftware/OCIA-master | OCIA_dataProcess_imgData_moCorr_HMM.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/dataProcess/OCIA_dataProcess_imgData_moCorr_HMM.m | 994 | utf_8 | 14c90ea89a699cbba11589d9202ad1fd | %% #OCIA:OCIA_dataProcess_imgData_moCorr_HMM
function [isValid, unvalidReason] = OCIA_dataProcess_imgData_moCorr_HMM(this, iDWRow, varargin)
% by default, row is valid
isValid = true;
unvalidReason = '';
% get the selected processing steps and this row's processing state
selProcOpts = this.an.procOptions.id(get(this.... |
github | HelmchenLabSoftware/OCIA-master | OCIA_dataProcess_imgData.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/dataProcess/OCIA_dataProcess_imgData.m | 4,270 | utf_8 | 079515d1ffc08676c79160f68b6b1a54 | %% #OCIA:OCIA_dataProcess_imgData
function [isValid, unvalidReason] = OCIA_dataProcess_imgData(this, iDWRow)
% set a flag that tells whether this row is valid for processing or not
isValid = false;
% create a string holding the reason why this row was flagged as not valid
unvalidReason = 'unknown reason';
rowID = DWGe... |
github | HelmchenLabSoftware/OCIA-master | OCIA_dataProcess_imgData_moCorr.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/dataProcess/OCIA_dataProcess_imgData_moCorr.m | 1,449 | utf_8 | e046854327443ac0fc19c58b8212ce05 | %% #OCIA:OCIA_dataProcess_imgData_moCorr
function [isValid, unvalidReason] = OCIA_dataProcess_imgData_moCorr(this, iDWRow, varargin)
% check if the processing should be aborted
[doAbort, isValid, unvalidReason] = DWCheckProcessAbort(this, [], []); if doAbort; return; end;
% call the custom function f... |
github | HelmchenLabSoftware/OCIA-master | OCIA_dataProcess_imgData_genStimVect.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/dataProcess/OCIA_dataProcess_imgData_genStimVect.m | 1,875 | utf_8 | 6acd477616696fcc37880a714b4fb587 | %% #OCIA:OCIA_dataProcess_imgData_genStimVect
function [isValid, unvalidReason] = OCIA_dataProcess_imgData_genStimVect(this, iDWRow, varargin)
% by default, row is valid
isValid = true;
unvalidReason = '';
% get the selected processing steps and this row's processing state
selProcOpts = this.an.procOptions.id(get(thi... |
github | HelmchenLabSoftware/OCIA-master | OCIA_dataProcess_wfTr_genStimVect.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/dataProcess/OCIA_dataProcess_wfTr_genStimVect.m | 1,781 | utf_8 | 89ca04b9628644f1348a94b4b2c2f1e0 | %% #OCIA:OCIA_dataProcess_wfTr_genStimVect
function [isValid, unvalidReason] = OCIA_dataProcess_wfTr_genStimVect(this, iDWRow, varargin)
% by default, row is valid
isValid = true;
unvalidReason = '';
% get the selected processing steps and this row's processing state
selProcOpts = this.an.procOptions.id(get(this.GUI.... |
github | HelmchenLabSoftware/OCIA-master | OCIA_dataProcess_behavData.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/dataProcess/OCIA_dataProcess_behavData.m | 605 | utf_8 | 9558137229f20b8370a63ae3b653739e | %% #OCIA:OCIA_dataProcess_behavData
function [isValid, unvalidReason] = OCIA_dataProcess_behavData(this, iDWRow)
% set a flag that tells whether this row is valid for processing or not
isValid = false; %#ok<NASGU>
% create a string holding the reason why this row was flagged as not valid
unvalidReason = 'unknown reaso... |
github | HelmchenLabSoftware/OCIA-master | OCIA_dataProcess_imgData_fJitt.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/dataProcess/OCIA_dataProcess_imgData_fJitt.m | 13,736 | utf_8 | 9b86b78d25f09c9835279897968bf35c | %% #OCIA:OCIA_dataProcess_imgData_fJitt
function [isValid, unvalidReason] = OCIA_dataProcess_imgData_fJitt(this, iDWRow, varargin)
% by default, row is valid
isValid = true;
unvalidReason = '';
% get the selected processing steps and this row's processing state
selProcOpts = this.an.procOptions.id(get(this.GUI.handle... |
github | HelmchenLabSoftware/OCIA-master | OCIA_dataProcess_wfTr.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/dataProcess/OCIA_dataProcess_wfTr.m | 2,911 | utf_8 | 49ad001f1a3801e538d264c2d9197384 | %% #OCIA:OCIA_dataProcess_wfTr
function [isValid, unvalidReason] = OCIA_dataProcess_wfTr(this, iDWRow)
% set a flag that tells whether this row is valid for processing or not
isValid = false;
% create a string holding the reason why this row was flagged as not valid
unvalidReason = 'unknown reason';
rowID = DWGetRowID... |
github | HelmchenLabSoftware/OCIA-master | OCIA_dataProcess_imgData_moCorr_TurboReg.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/dataProcess/OCIA_dataProcess_imgData_moCorr_TurboReg.m | 20,402 | utf_8 | fd9b7d416c0cd89e92f898625045d53d | %% #OCIA:OCIA_dataProcess_imgData_moCorr_TurboReg
function [isValid, unvalidReason] = OCIA_dataProcess_imgData_moCorr_TurboReg(this, iDWRow, varargin)
% by default, row is valid
isValid = true;
unvalidReason = '';
% get the selected processing steps and this row's processing state
selProcOpts = this.an.procOptions.id... |
github | HelmchenLabSoftware/OCIA-master | OCIA_dataProcess_imgData_fShift.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/dataProcess/OCIA_dataProcess_imgData_fShift.m | 9,776 | utf_8 | 8bfdd6962d12089b5c936fcc3a0f0344 | %% #OCIA:OCIA_dataProcess_imgData_fShift
function [isValid, unvalidReason] = OCIA_dataProcess_imgData_fShift(this, iDWRow, varargin)
% by default, row is valid
isValid = true;
unvalidReason = '';
% get the selected processing steps and this row's processing state
selProcOpts = this.an.procOptions.id(get(this.GUI.hand... |
github | HelmchenLabSoftware/OCIA-master | OCIA_dataProcess_imgData_extrCaTraces.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/dataProcess/OCIA_dataProcess_imgData_extrCaTraces.m | 6,455 | utf_8 | 9a39a9a8f93fa8489347c130b681db3d | %% #OCIA:OCIA_dataProcess_imgData_extrCaTraces
function [isValid, unvalidReason] = OCIA_dataProcess_imgData_extrCaTraces(this, iDWRow, varargin)
% by default, row is valid
isValid = true;
unvalidReason = '';
% get the selected processing steps and this row's calcium data
selProcOpts = this.an.procOptions.id(get(this.... |
github | HelmchenLabSoftware/OCIA-master | OCIA_annotateTable_wenrui.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/annotates/OCIA_annotateTable_wenrui.m | 4,177 | utf_8 | 27e9a97bb43ff75be39b4648cc4c8d45 | function OCIA_annotateTable_wenrui(this)
% OCIA_annotateTable_wenrui - [no description]
%
% OCIA_annotateTable_wenrui(this)
%
% [No description]
%
% 2013-2016 - Copyleft and programmed by Balazs Laurenczy (blaurenczy_at_gmail.com)
% extract the depth from the spot IDs
depths = regexprep(this.dw.spotIDs, '^Spot\d... |
github | HelmchenLabSoftware/OCIA-master | OCIA_dataSaveConfig_img.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/others/OCIA_dataSaveConfig_img.m | 2,446 | utf_8 | 157a4a7a2ff2501ff296389c33bb3222 | function dataConf = OCIA_dataConfig_img(this, iDWRow, dataConf)
% generate a configuration that specifies how the data should be saved as a cell-array with 7 columns:
% { data field name, data to save set/get function, sub-cells save name, names of the attributes to save,
% attributes to save, display name, dat... |
github | HelmchenLabSoftware/OCIA-master | OCIA_dataSaveConfig_whisk.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/others/OCIA_dataSaveConfig_whisk.m | 1,026 | utf_8 | fe313ea9c3368232c2956634ebca3dbf | function dataConf = OCIA_dataConfig_whisk(this, iDWRow, dataConf)
% generate a configuration that specifies how the data should be saved as a cell-array with 7 columns:
% { data field name, data to save set/get function, sub-cells save name, names of the attributes to save, attributes to save,
% display name, dat... |
github | HelmchenLabSoftware/OCIA-master | OCIA_dataSaveConfig_behav.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/others/OCIA_dataSaveConfig_behav.m | 1,031 | utf_8 | 1350a4228175fd1cdd5c933e69c72029 | function dataConf = OCIA_dataSaveConfig_behav(this, iDWRow, dataConf)
% generate a configuration that specifies how the data should be saved as a cell-array with 7 columns:
% { data field name, data to save set/get function, sub-cells save name, names of the attributes to save, attributes to save,
% display name,... |
github | HelmchenLabSoftware/OCIA-master | DWMatchBehavTrialsToImagingDataShankar.m | .m | OCIA-master/caImgAnalysis/OCIA/custom/others/DWMatchBehavTrialsToImagingDataShankar.m | 6,333 | utf_8 | 68a4994114b2d05a5a911a375b5a86b6 | function DWMatchBehavTrialsToImagingDataShankar(this)
% DWMatchBehavTrialsToImagingDataShankar - [no description]
%
% DWMatchBehavTrialsToImagingDataShankar(this)
%
% Match the behavior trials and the data files.
% 2013-2016 - Copyleft and programmed by Balazs Laurenczy (blaurenczy_at_gmail.com)
% update the wa... |
github | HelmchenLabSoftware/OCIA-master | runExperiment.m | .m | OCIA-master/caImgAnalysis/caImgExperiment/@CaImgExperiment/runExperiment.m | 16,480 | utf_8 | 3ec18810499954502e465b6c620c9fb9 | function CaImgExp = runExperiment(CaImgExp, nRuns)
% runExperiment method for the CaImgExperiment class. Runs the calcium imaging experiment.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Originally created on 18 / 03 / 2012 %
% Written by B. Laurenczy (blaurenczy@gmail.com) %
... |
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