plateform stringclasses 1
value | repo_name stringlengths 13 113 | name stringlengths 3 74 | ext stringclasses 1
value | path stringlengths 12 229 | size int64 23 843k | source_encoding stringclasses 9
values | md5 stringlengths 32 32 | text stringlengths 23 843k |
|---|---|---|---|---|---|---|---|---|
github | HelmchenLabSoftware/OCIA-master | wt_rotate_coords.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_rotate_coords.m | 5,599 | utf_8 | 9e4a334eb51adfbc44014d732fd60204 | % WT_ROTATE_COORDS
%
% Transform coordinates of objects or whiskers between absolute and
% relative framework. A note on transformations:
% Absolute coordinates are in the framework of the actual image
% Relative coordinates are with respect to head position in the image
%
% Syntax: wt_rotate_coords(COORDS, DIR, RE... |
github | HelmchenLabSoftware/OCIA-master | wt_extrapolate_position.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_extrapolate_position.m | 4,880 | utf_8 | 86fd722243d9611965ccc5bd115194d2 | function mImgFilter = wt_extrapolate_position(mW0, mImg, mWA)
% WT_EXTRAPOLATE_POSITION
% Create an image-mask that will 'highlight' the likely position of the
% whisker in current frame, based on velocity information in previos
% frames.
%
% 1 - Linear interpolation of whisker shape in the X preceeding frames
% 2 ... |
github | HelmchenLabSoftware/OCIA-master | wt_calibration.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_calibration.m | 4,876 | utf_8 | a143e384f49f955761952d3ab551c926 | function wt_calibration(sOption)
% WT_CALIBRATION Calibrate and measure image regions
%
% wt_calibration('calibrate')
% wt_calibration('measure')
% wt_calibration('recalculate')
global g_tWT
switch lower(sOption)
case 'calibrate'
Calibrate
wt_display_frame
case 'calibrate-import-image'
... |
github | HelmchenLabSoftware/OCIA-master | wt_get_build_number.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_get_build_number.m | 511 | utf_8 | 4cd3f5ac2ca28358b6203bad67c583ad | % wt_get_build_number
function sBuild = wt_get_build_number
% Set paths
sWT_dir = which('wt');
sWT_dir = sWT_dir(1:findstr(sWT_dir, 'wt.m')-1);
% Get build number from SVN entries files
sBuild = 'Unknown';
if ispc, sSVNPath = [sWT_dir '.svn\' 'entries'];
else, sSVNPath = [sWT_dir '.svn/' 'entries']; end
if exist(sSVN... |
github | HelmchenLabSoftware/OCIA-master | wt_dump_screen.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_dump_screen.m | 1,849 | utf_8 | 375701158967ce6a3ae8cf1288e6e117 | %%%% WT_DUMP_SCREEN *****************************************
%
% Whisker Tracker (WT)
%
% Authors: Per Magne Knutsen, Dori Derdikman
%
% (c) Copyright 2004 Yeda Research and Development Company Ltd.,
% Rehovot, Israel
%
% This software is protected by copyright and patent law. Any unauthorized
% use, reproduction ... |
github | HelmchenLabSoftware/OCIA-master | wt_prep_gui.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_prep_gui.m | 20,021 | utf_8 | 00b3b9f97fec08f4c6ae1e7479c20136 | function wt_prep_gui
% WT_PREP_GUI
global g_tWT
hFrameWin = findobj('Tag', 'WTMainWindow');
set(hFrameWin, 'color', [.8 .8 .8])
figure(hFrameWin); clf; g_tWT.Handles.hSlider = [];
set(hFrameWin, 'NumberTitle', 'off', 'Name', ['WhiskerTracker (Revision ' wt_get_build_number ')'], ...
'resizeFcn', ['wt_resize_sli... |
github | HelmchenLabSoftware/OCIA-master | wt_mark_object.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_mark_object.m | 5,048 | utf_8 | c852ba81c9b336c1264876140284470d | function wt_mark_object(nWhisker, sOption, nLocation)
% WT_MARK_OBJECT
% Mark object. Accepts whisker ID as its single input parameter.
% Brings up a cross-hair to mark location in frame where whisker touches
% object. Only works in conjunction with the WT GUI.
% Syntax: wt_mark_object(ID)
global g_tWT
nCurrentFrame =... |
github | HelmchenLabSoftware/OCIA-master | wt_head_tracker.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_head_tracker.m | 7,494 | utf_8 | 8bb26b2011d840cf56a96a3ba9c0b063 | function bResult = wt_head_tracker(sFileName)
% WT_HEAD_TRACKER
% Track rat head movements
%
warning off MATLAB:divideByZero
warning off MATLAB:mir_warning_variable_used_as_function
global g_tWT
bResult = 1;
wt_toggle_display_mode(0)
g_tWT.MovieInfo.ImCropSize = round([g_tWT.MovieInfo.RadExt g_tWT.MovieInfo.EyeNoseA... |
github | HelmchenLabSoftware/OCIA-master | wt_plot_signal_noise.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_plot_signal_noise.m | 3,785 | utf_8 | 16ae4d2f5488b3e23f73a272f627ff86 | function bStop = wt_plot_signal_noise(vSR)
% WT_PLOT_SIGNAL_NOISE
% Plots the signal-to-noise ratio of the whisker against the background.
% The ratio itself is computed in the find_next_whisker.dll. This function
% just accepts the number(s) to plot. Adds a red, horizontal bar for
% setting the threshold at which trac... |
github | HelmchenLabSoftware/OCIA-master | wt_clear_selected_whisker.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_clear_selected_whisker.m | 2,251 | utf_8 | aba3a703c9cf0c5ea4afc2e0ca864686 | function wt_clear_selected_whisker()
% WT_CLEAR_SELECTED_WHISKER
% Delete all or parts of tracked data of selected whiskers, or delete all
% tracked whiskers.
global g_tWT
cIdents = {g_tWT.MovieInfo.WhiskerIdentity{:}};
nFontSize = 8;
nLinSep = 10;
vScrnSize = get(0, 'ScreenSize');
nFigHeight = (length(cIdents)-1) ... |
github | HelmchenLabSoftware/OCIA-master | wt_rotate_frame.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_rotate_frame.m | 993 | utf_8 | a92c107a47390dbb6d73e084fa620630 | % WT_ROTATE_FRAME
%
function wt_rotate_frame( nDir )
global g_tWT
% Display warning message
if ~isfield(g_tWT.MovieInfo, 'SplinePoints'), return, end
if ~isempty(g_tWT.MovieInfo.SplinePoints)
sQuestResp = questdlg('Changing the ROI will delete already marked whiskers. Continue?', 'Warning', 'Yes', 'No', 'Yes')... |
github | HelmchenLabSoftware/OCIA-master | wt_flip_frame.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_flip_frame.m | 866 | utf_8 | 9b7c021b84096aead6b9a000be27738e | %%%% WT_FLIP_FRAME %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Whisker Tracker (WT)
%
% Authors: Per Magne Knutsen, Dori Derdikman
%
% (c) Copyright 2004 Yeda Research and Development Company Ltd.,
% Rehovot, Israel
%
% This software is protected by copyright and patent law. Any unauthorized
% use, repr... |
github | HelmchenLabSoftware/OCIA-master | wt_create_filter.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_create_filter.m | 6,277 | utf_8 | 38d33983265ffab70c0fc85628361dbe | function tFilter = wt_create_filter(tDefaultFilter, sOption)
% Whisker Tracker (WT)
%
% Authors: Per Magne Knutsen, Dori Derdikman
%
% (c) Copyright 2004 Yeda Research and Development Company Ltd.,
% Rehovot, Israel
%
% This software is protected by copyright and patent law. Any unauthorized
% use, reproduction or ... |
github | HelmchenLabSoftware/OCIA-master | wt_crop_behaving_video.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_crop_behaving_video.m | 7,146 | utf_8 | 5176de9198f557e2304c65564f2de0a9 | % WT_CROP_BEHAVING_VIDEO
% Extract region of interest parallel to whisker-pad.
% wt_crop_behaving_video(M, C, HOR, RAD, METHOD), where
% M is the loaded frame
% C is a 3-by-2 vector containing X Y coordinates of right-eye, left-eye
% and nose.
% HOR is the length of the extracted region (anterior-posterior ax... |
github | HelmchenLabSoftware/OCIA-master | wt_subtract_bg_frame.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_subtract_bg_frame.m | 8,477 | utf_8 | aa677748a07abb05bd8819239e12c399 | % WT_SUBTRACT_BG_FRAME
% IMG_OUT = wt_subtract_bg_frame(IMG, F), where
% IMG is the frame from which to subtract the background frame
% F is the current frame number
% IMG_OUT is IMG minus the background
%
% Subtract background frame from passed image. The passed coordinates are
% used to select what portion of t... |
github | HelmchenLabSoftware/OCIA-master | wt_adjust_whisker_length.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_adjust_whisker_length.m | 2,894 | utf_8 | 390bc5df4dbfa6f89ebf615bca7636e6 | % WT_ADJUST_WHISKER_LENGTH
% Adjust whisker length to that of first known frame.
%
% Syntax: [vX, vY] = wt_adjust_whisker_length(I,X,Y), where
% I = I'th whisker
% X = vector of X splinepoints
% Y = vector of Y splinepoints
% Output variables:
% X = a... |
github | HelmchenLabSoftware/OCIA-master | wt_mark_whisker.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_mark_whisker.m | 9,460 | utf_8 | 4d40afc1c5ad815e172aff1e9cf8b192 | function wt_mark_whisker(varargin)
% WT_MARK_WHISKER
% Mark new whisker, or add/remove spline-points that define whiskerpoints.
% Syntax: wt_mark_whisker(OPT), where
% OPT is an optional string that runs one of the following
% subroutines:
% 'new' - mark a new whisker
% ... |
github | HelmchenLabSoftware/OCIA-master | wt_user_variables.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_user_variables.m | 2,835 | utf_8 | 74f02db2f7a53d0fb75ebcb184aaae2d | function wt_user_variables(varargin)
% Create and modify user-defined variables
% The purpose of this function is to provide the user with an easy way to
% store experiment variables inside the WT .mat file. These user variables
% can also be variables that are accessed from within scripts.
%
% Note that adding or modi... |
github | HelmchenLabSoftware/OCIA-master | wt_select_directory_tree.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_select_directory_tree.m | 2,153 | utf_8 | 417e8fdbcd1f4fd60f3f876e7994ed58 | function wt_select_directory_tree
% WT_SELECT_DIRECTORY_TREE
% Select all movies recursively from all sub-directories below a selected
% top-level directory.
%
% This function prompts the user to select a top-level directory and
% generates a list of all AVI movies, with complete paths, contained in the
% entire direct... |
github | HelmchenLabSoftware/OCIA-master | wt_set_last_frame.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_set_last_frame.m | 1,021 | utf_8 | 6199a5377c8aeda55264f84ac6b28483 | %%%% WT_SET_LAST_FRAME %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function wt_set_last_frame
% Set Last Frame for all Whiskers defined so far
% Must check for Cancel or eXit
%
% Whisker Tracker (WT)
%
% Authors: Per Magne Knutsen, Dori Derdikman
%
% (c) Copyright 2004 Yeda Research and Development Company Ltd.,
% ... |
github | HelmchenLabSoftware/OCIA-master | wt_create_outline.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_create_outline.m | 5,411 | utf_8 | 5fca5ab8f2f3db6a7d388de56b54c24c | function wt_create_outline(sOption, nOL)
% WT_CREATE_OUTLINE Mark lines that denote various axis in image
% This function allows points, lines, polygons etc. to be labelled for
% later data analysis. WT itself does not use either of these
%
% wt_create_outline('add', OL)
% wt_create_outline('draw', OL)
% wt_create_o... |
github | HelmchenLabSoftware/OCIA-master | wt_copy_paste_whisker.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_copy_paste_whisker.m | 2,350 | utf_8 | 1aa4c51e190eed32144a0a9ad9a72997 | function wt_copy_paste_whisker(sOption, nW)
% Copy/paste a selected whisker to/from clipoard
switch sOption
case 'copy'
CopyPasteWhisker(nW, 'copy');
case 'paste'
CopyPasteWhisker(nW, 'paste');
wt_display_frame;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%... |
github | HelmchenLabSoftware/OCIA-master | checkfilename.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/bin/checkfilename.m | 510 | utf_8 | 6739291d3d5ed243836882af670df101 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Converts between forward and backward slash on Windows and Linux filesystems
function sFilename = CheckFilename(sFilename)
if ispc
sFilename = strrep(sFilename, '/', '\');
sFilename = strrep(sFilename, '\\', '\');
elseif isun... |
github | HelmchenLabSoftware/OCIA-master | wt_create_filters.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/bin/wt_create_filters.m | 690 | utf_8 | 77a8b948154ca3fc7b9fcc69b7081298 | %%%% WT_CREATE_FILTERS %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% create a filter for each angle for checking "whiskeriness"
function filters_vec = wt_create_filters(whisker_width,whisker_length)
flt = zeros(whisker_length);
start_ind = ceil(whisker_length/2)-floor(3*whisker_width/2);
flt(start_ind:start_ind+3*whisker_widt... |
github | HelmchenLabSoftware/OCIA-master | ExportToExcel.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/bin/windows/ExportToExcel.m | 1,230 | utf_8 | 9a793be148c08ea1554add206bccaf28 | % ExportToExcel(cHeaders, cData)
% by Naama Rubin
function ExportToExcel(cHeaders, cData)
% Open new instance of Excel
Excel = actxserver('Excel.Application');
set(Excel, 'Visible', 1);
% Create new workbook
Workbooks = Excel.Workbooks;
Workbook = invoke(Workbooks, 'Add');
Sheets = Excel.ActiveWorkBook.Sheets;
% She... |
github | HelmchenLabSoftware/OCIA-master | concatanateSegmentsOriginalMovie.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/concatanate/concatanateSegmentsOriginalMovie.m | 1,415 | utf_8 | 9c753d4f1fb2ae25de3fc6958222f7a6 |
function f= concatanateSegments(dirname)
list = dir(dirname);
i=3;
oldExpName='Experiment';
whiskingAll = [];
mkdir(fullfile(dirname,'whiskByTrial'));
count = 0;
for i=3:length(list)
fname = list(i).name;
ind=strfind(fname,'_Whisker_Tracking');
if(~isempty(ind))
expname = fname(1:ind-1);
... |
github | HelmchenLabSoftware/OCIA-master | concatanateSegments.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/concatanate/concatanateSegments.m | 1,415 | utf_8 | f8c5c57461919a03ee74e82fcc5004ed |
function f= concatanateSegments(dirname)
list = dir(dirname);
i=3;
oldExpName='Experiment';
whiskingAll = [];
mkdir(fullfile(dirname,'whiskByTrial'));
count = 0;
for i=3:length(list)
fname = list(i).name;
ind=strfind(fname,'_Whisker_Tracking');
if(~isempty(ind))
expname = fname(1:ind-3);
... |
github | HelmchenLabSoftware/OCIA-master | makePureTone_new.m | .m | OCIA-master/other/functions_widefield/Iwen_auditory_functions/makePureTone_new.m | 1,496 | utf_8 | 680b0d87131bb0a6a09654fa8797c3c8 | function s = makePureTone_new(freqs,duration,varargin)
% generate a pure tone
% in1 ... carrier frequency in Hz
% in2 ... duration in s
% in3 ... sampling frequency in Hz {44100}
% in4 ... play tone {0}; 0 or 1
% in5 ... save wav file {[]}; filename of wav file
% out1 ... the sound vector s
% this file written by Henr... |
github | HelmchenLabSoftware/OCIA-master | TDMS_dataToGroupChanStruct_v4.m | .m | OCIA-master/other/functions_widefield/behavior_functions/import_lick_data/TDMS_dataToGroupChanStruct_v4.m | 2,718 | utf_8 | 0a6dab50f4d81124788a530edfe98382 | function output = TDMS_dataToGroupChanStruct_v4(inputStruct,varargin)
%TDMS_dataToGroupChanStruct_v4
%
% NOTE: This reproduces the data structure for the old lab functionality
% of the function getStructTDM
%
% See Also: TDMS_genvarname2, TDMS_readTDMSFile
REPLACE_STR = '_';
PREPEND_STR = 'p_';
PREPEND_GRP... |
github | HelmchenLabSoftware/OCIA-master | TDMS_dataToGroupChanStruct_v3.m | .m | OCIA-master/other/functions_widefield/behavior_functions/import_lick_data/TDMS_dataToGroupChanStruct_v3.m | 2,710 | utf_8 | 1ca966df0513a1925134cd2633570a53 | function output = TDMS_dataToGroupChanStruct_v3(inputStruct,varargin)
%TDMS_dataToGroupChanStruct_v3
%
% translates objects AND properties to valid field names
%
% Similar to TDMS_dataToGroupChanStruct_v1, but also translates
% properties
%
% output = TDMS_dataToGroupChanStruct_v3(inputStruct)
%
% OPTIONAL ... |
github | HelmchenLabSoftware/OCIA-master | TDMS_preprocessFile.m | .m | OCIA-master/other/functions_widefield/behavior_functions/import_lick_data/tdmsSubfunctions/TDMS_preprocessFile.m | 24,202 | utf_8 | 9027de756f8016d279addde445319f56 | function metaStruct = TDMS_preprocessFile(fid,tdmsFileName,params)
%TDMS_preprocessFile Populates props and gets segment information
%
% NOTE: This file shouldn't be called directly by the user
%
% metaStruct = TDMS_preprocessFile(fid,tdmsFileName,params)
%
% INPUTS
% ==========================================... |
github | HelmchenLabSoftware/OCIA-master | hanning.m | .m | OCIA-master/other/functions_slovin/spectogram_functions/hanning.m | 292 | utf_8 | 56fe015f155b73f7eb537f7a3093ead2 | function w = hanning(n)
if ~rem(n,2)
w = .5*(1 - cos(2*pi*(1:n/2)'/(n+1)));
w = [w; w(end:-1:1)];
else
w = .5*(1 - cos(2*pi*(1:(n+1)/2)'/(n+1)));
w = [w; w(end-1:-1:1)];
end
function myprintf(verbose, varargin)
if strcmpi(verbose, 'on')
fprintf(varargin{:});
end; |
github | HelmchenLabSoftware/OCIA-master | mtrainer_GUI_export.m | .m | OCIA-master/behavior/mtrainer_GUI_export.m | 57,797 | utf_8 | bb7ef417782c2fbef69065eee4adb42f | function varargout = mtrainer_GUI_export(varargin)
% TODO:
% - stopping the experiment: trial no 100 ? plot ? set buttons to stop ?
% - reward anyway system
% - forbid disconnecting HW or changing mouseID while experiment is running
% - lickThresh calibrator with setter
% - online lick ploting
% - online p... |
github | HelmchenLabSoftware/OCIA-master | daq_sessionInterfaceH45.m | .m | OCIA-master/behavior/daq/daq_sessionInterfaceH45.m | 4,666 | utf_8 | 4bfeda072efe6d1b8ef7c49d06067dcc | function [data, S, F, T, P] = daq_sessionInterfaceH45(dur, recordRate, condition, doPlot)
% s = daq.createSession('ni');
% s.Rate = 50;
% s.DurationInSeconds = 40;
% s.addAnalogInputChannel('Dev1','ai0', 'Voltage');
% s.Channels.InputType = 'SingleEnded';
% s.Channels.Range = [-10 10];
realTimePlot = 0;
recordChanNa... |
github | HelmchenLabSoftware/OCIA-master | daq_sessionInterfaceH30.m | .m | OCIA-master/behavior/daq/daq_sessionInterfaceH30.m | 6,252 | utf_8 | 0ea24a3bcc0b8963af28024c82ae66b6 | function [data, S, F, T, P] = daq_sessionInterfaceH30(dur, recordRate, condition, doPlot)
% s = daq.createSession('ni');
% s.Rate = 50;
% s.DurationInSeconds = 40;
% s.addAnalogInputChannel('Dev1','ai0', 'Voltage');
% s.Channels.InputType = 'SingleEnded';
% s.Channels.Range = [-10 10];
realTimePlot = 0;
% recordChan... |
github | HelmchenLabSoftware/OCIA-master | daq_sessionInterface.m | .m | OCIA-master/behavior/daq/daq_sessionInterface.m | 1,475 | utf_8 | 7db7e719bbb05c2ed3fc8276d2d00939 | function daq_sessionInterface(config)
% s = daq.createSession('ni');
% s.Rate = 50;
% s.DurationInSeconds = 40;
% s.addAnalogInputChannel('Dev1','ai0', 'Voltage');
% s.Channels.InputType = 'SingleEnded';
% s.Channels.Range = [-10 10];
% daqreset;
fprintf('Connecting hardware...\n');
s = daq.createSession(config.hardw... |
github | HelmchenLabSoftware/OCIA-master | daq_ni_usb6008.m | .m | OCIA-master/behavior/daq/daq_ni_usb6008.m | 2,637 | utf_8 | 8f4ab52789a17dc8daf2ef4e7fcd36ee | function daq_ni_usb6008
ai=analoginput('nidaq','Dev1');
ao=analogoutput('nidaq','Dev1');
dio=digitalio('nidaq','Dev1');
disp('done create device')
testMode = 'analogIn'; % analogOut or analogIn or digital
switch lower(testMode)
case 'analogin'
%% Collect analog input
% analog input channel
... |
github | HelmchenLabSoftware/OCIA-master | waitForExternalTrigger_H30.m | .m | OCIA-master/behavior/daq/waitForExternalTrigger_H30.m | 1,558 | utf_8 | 080163444a2aff0f5793c00952a3c729 | function status = waitForExternalTrigger_H30(timeout)
% input argument: timeout in seconds
% RETURNS:
% - status = 0 if waiting timed out
% - status = 1 if trigger was successfully received
% - status = 2 if could not connect to the nidaq analog input (or other error)
% created on 2014-02-01 by Balaz... |
github | HelmchenLabSoftware/OCIA-master | externalTrigger_nidaq.m | .m | OCIA-master/behavior/daq/externalTrigger_nidaq.m | 1,910 | utf_8 | 52a0ca32193ecd4ba0079915dae9e268 | function status = waitForExternalTrigger_H30(timeout)
% input argument: timeout in seconds
% RETURNS:
% - status = 0 if waiting timed out
% - status = 1 if trigger was successfully received
% - status = 2 if could not connect to the nidaq analog input
% this file written by Henry Luetcke (hluetck@gma... |
github | HelmchenLabSoftware/OCIA-master | analyseBehavPerf.m | .m | OCIA-master/behavior/perfAnalysis/analyseBehavPerf.m | 5,182 | utf_8 | 6051e144aa04de4837f45fd6cc287d3c | %% Function - analyseBehavPerf
function counts = analyseBehavPerf(respTypes, binWidthProp, binWidthCum, doBinCout)
dbgLvl = 0;
o(' #analyzeBehavPerf(): nTrials: %d.', size(respTypes, 2), 1, dbgLvl);
% transform the response types into sums
respTypeToRespCountTic = tic; % for performance timin... |
github | HelmchenLabSoftware/OCIA-master | mtrainerAnalyser_pooledPerformance_bins.m | .m | OCIA-master/behavior/mtrainer/mtrainerAnalyser_pooledPerformance_bins.m | 6,607 | utf_8 | 542605197d955dd0ad8e813ec2c311a0 | %% Function - mtrainerAnalyser_pooledPerformance
function figHand = mtrainerAnalyser_pooledPerformance_bins(outAll, titleStr, binWidth)
% dbgLevel = 2;
nTrials = length(outAll.respTypes);
% calculate number of bins, make sure that there is at least one
nBins = max(round(nTrials / binWidth), 1);
figName = titleStr;
... |
github | HelmchenLabSoftware/OCIA-master | mtrainer.m | .m | OCIA-master/behavior/mtrainer/mtrainer.m | 16,753 | utf_8 | f5cf1c7c0cf86007548ef75917035e5c | function mtrainer()
% main function for mtrainer experiment suite
% all times are in s!
% written by Henry Luetcke (hluetck@gmail.com)
% 2013-05-07
% modified by Balazs Laurenczy (blaurenczy@gmail.com)
% 2013-05-15
% modified by Balazs Laurenczy (blaurenczy@gmail.com)
% 2013-08-08
doEmptyWater = 0;
% doEmptyWater = 1... |
github | HelmchenLabSoftware/OCIA-master | mtrainerAnalyser_performance.m | .m | OCIA-master/behavior/mtrainer/mtrainerAnalyser_performance.m | 8,824 | utf_8 | 7c3efc292a98890cdd2df684966b8536 | %% Function - mtrainerAnalyser_performance
function mtrainerAnalyser_performance(varargin)
if nargin >= 1;
% for each trial: 1 = correct detect, 2 = correct reject, 3 = false alarm, 4 = miss, 5 = early
respTypes = varargin{1};
doSavePlots = 0;
savePath = '';
end;
if nargin >... |
github | HelmchenLabSoftware/OCIA-master | mtrainerAnalyser_loadAllFromFolder.m | .m | OCIA-master/behavior/mtrainer/mtrainerAnalyser_loadAllFromFolder.m | 11,698 | utf_8 | f65b08bd16909d18e68a76b009bf88ee | %% Function - mtrainerAnalyser_loadAllFromFolder
function outAll = mtrainerAnalyser_loadAllFromFolder(folderPath, skipIncomplete, doMakeConsistent, ...
doRemoveUnresponsive, doSavePlots)
%% Initialize variables
dbgLevel = 4;
% output structure for all data in the requested folder
outAll = struct();
% fields that... |
github | HelmchenLabSoftware/OCIA-master | mtrainerAnalyser_pooledPerformance.m | .m | OCIA-master/behavior/mtrainer/mtrainerAnalyser_pooledPerformance.m | 13,056 | utf_8 | b60d5cf1801f259ba926464fd19f619c | %% Function - mtrainerAnalyser_pooledPerformance
function mtrainerAnalyser_pooledPerformance(outAll, titleStr)
dbgLevel = 2;
uniqueDays = unique(cellstr(datestr(outAll.datesAsNum, 'yyyymmdd')));
nDays = numel(uniqueDays);
o('#mtrain...pooledPerf: %d trial(s) in %d day(s).', numel(outAll.respTypes), nDays, 1, dbgLevel... |
github | HelmchenLabSoftware/OCIA-master | mtrainerAnalyser_freqAnalysis_bins.m | .m | OCIA-master/behavior/mtrainer/mtrainerAnalyser_freqAnalysis_bins.m | 2,389 | utf_8 | e6cff6d257bc5bfe9d98519822f2e677 | %% Function - mtrainerAnalyser_pooledPerformance
function figHand = mtrainerAnalyser_freqAnalysis_bins(outAll, titleStr, binWidth)
dbgLevel = 2;
nFreqs = 5;
% for each trial: 1 = correct detect, 2 = correct reject, 3 = false alarm, 4 = miss, 5 = early
respTypes = outAll.respTypes(outAll.nFreqs == nFreqs);
freqs = ou... |
github | HelmchenLabSoftware/OCIA-master | mtrainer_oldversion_scheduledStarts.m | .m | OCIA-master/behavior/mtrainer/mtrainer_oldversion_scheduledStarts.m | 16,949 | utf_8 | cb689fcefe86d96085f1a191049aa7cd | function mtrainer()
% main function for mtrainer experiment suite
% all times are in s!
% written by Henry Luetcke (hluetck@gmail.com)
% 2013-05-07
% modified by Balazs Laurenczy (blaurenczy@gmail.com)
% 2013-05-15
doEmptyWater = 1;
automode = 1;
unsavedOut = struct();
mouseId = 'testing'; taskType = 'freqDiscrimina... |
github | HelmchenLabSoftware/OCIA-master | mtrainer_oldversion_legacyInterface.m | .m | OCIA-master/behavior/mtrainer/mtrainer_oldversion_legacyInterface.m | 8,514 | utf_8 | 745363c7c815304e2e4265dd8ef8ab38 | function mtrainer(varargin)
% main function for mtrainer experiment suite
% all times are in s!
% written by Henry Luetcke (hluetck@gmail.com)
% 2012-11-08
if ~nargin
% gui select mat-file with config structure
[FileName,PathName] = uigetfile('*.mat','Select configuration file');
S = load(fullfile(PathNam... |
github | HelmchenLabSoftware/OCIA-master | mtrainer_GUI.m | .m | OCIA-master/behavior/mtrainer/mtrainer_GUI.m | 34,409 | utf_8 | 3d5a15b6438819e18ebd58da906241e8 | function varargout = mtrainer_GUI(varargin)
% TODO:
% - stopping the experiment: trial no 100 ? plot ? set buttons to stop ?
% - reward anyway system
% - forbid disconnecting HW or changing mouseID while experiment is running
% - piezoThresh calibrator with setter
% - online lick ploting
% - online perform... |
github | PacktPublishing/ROS-Programming-Building-Powerful-Robots-master | teleop.m | .m | ROS-Programming-Building-Powerful-Robots-master/Module03/Chapter08/Matlab/teleop.m | 10,043 | utf_8 | 7f1f1a8bd40b2cbd4fb318fe3d696aa9 | function varargout = teleop(varargin)
%Before starting this code, you have to launch any robotic simulation on
%ROS PC or start a ROS robot
% For example, you can test it using turtlebot simulation
% You can launch turtlebot simulation using following command
% $ roslaunch turtlebot_gazebo turtlebot_world.launch
% R... |
github | thigiacmaytinh/FaceDetection-master | modelConvert.m | .m | FaceDetection-master/lib/opencv320/contrib/ximgproc/tutorials/scripts/modelConvert.m | 2,117 | utf_8 | dd8b0dc376b1da49ced7529a9e3a7723 | function modelConvert(model, outname)
%% script for converting Piotr's matlab model into YAML format
outfile = fopen(outname, 'w');
fprintf(outfile, '%%YAML:1.0\n\n');
fprintf(outfile, ['options:\n'...
' numberOfTrees: 8\n'...
' numberOfTreesToEvaluate: 4\n'...
... |
github | imistyrain/ssd-master | classification_demo.m | .m | ssd-master/matlab/demo/classification_demo.m | 5,412 | utf_8 | 8f46deabe6cde287c4759f3bc8b7f819 | function [scores, maxlabel] = classification_demo(im, use_gpu)
% [scores, maxlabel] = classification_demo(im, use_gpu)
%
% Image classification demo using BVLC CaffeNet.
%
% IMPORTANT: before you run this demo, you should download BVLC CaffeNet
% from Model Zoo (http://caffe.berkeleyvision.org/model_zoo.html)
%
% *****... |
github | LidkeLab/matlab-instrument-control-master | readH5File.m | .m | matlab-instrument-control-master/@MIC_H5/readH5File.m | 12,944 | utf_8 | 672b14572a6fdb018bd3c7db059ca5ae | function [H5Structure] = readH5File(FilePath, GroupName)
%Extracts contents of an h5 file into H5Structure.
% This method will extract the Data and Attributes from a group
% named GroupName in the .h5 file specified by FilePath.
% Examples:
% H5Structure = readH5File('C:\file.h5') will extract all
% contents of... |
github | LidkeLab/matlab-instrument-control-master | gui.m | .m | matlab-instrument-control-master/@MIC_GalvoDigital/gui.m | 7,602 | utf_8 | 8de2934750c217a43375207089f3210f | % gui: Graphical User Interface to MIC_GalvoDigital
%
% Functions: gui2properties, properties2gui, closeFigure, CalAngle,
% setAngle_Button, setParameters_Button, ToggleGalvo
%
% REQUIREMENTS:
% MIC_Abstract.m
% MATLAB NI-DAQmx driver installed via the Support Package Installer
%
% CITATION: Hanieh Maz... |
github | LidkeLab/matlab-instrument-control-master | errorcheck.m | .m | matlab-instrument-control-master/@MIC_MCLNanoDrive/errorcheck.m | 3,188 | utf_8 | 2abc63fb57985d22013e75228d9714dc | function varargout = errorcheck(obj,fname,varargin)
% certain errors throw variable error codes but are specific to axis controls, this is logical branch for that
if obj.LastError ~= obj.ErrorCode.MCL_SUCCESS
displayError(fname,varargin);
end
% Error check function for processing most of the MCL Nano Drive errors... |
github | LidkeLab/matlab-instrument-control-master | gui.m | .m | matlab-instrument-control-master/@MIC_SPTCollect/gui.m | 23,826 | utf_8 | efd104ecb8670653062f168d48d398c1 |
function gui(obj)
% GUI SRcollect Gui for TIRF microscope
% Detailed explanation goes here
h = findall(0,'tag','TIRF-SRcollect.gui');
if ~(isempty(h))
figure(h);
return;
end
%%
xsz=400;
ysz=1000;
xst=100;
yst=50;
pw=.95;
psep=.001;
staticst=10;
editst=110;
guiFig = figure('Units','pixels','Position',[xst y... |
github | LidkeLab/matlab-instrument-control-master | setCamProperties.m | .m | matlab-instrument-control-master/@MIC_AndorCamera/setCamProperties.m | 5,290 | utf_8 | 00353ba3ce9c36d6a6457121019fb226 | function setCamProperties(obj,CamSetting)
%SETCAMERAPROPERTIES Summary of this function goes here
% in: a duplicate CameraSetting structure to be checked and set
% this function sets the camera properties on the camera so that what you
% select on the gui is committed to the API
obj.ReadyForAcq=0;
%obj.CameraParamet... |
github | LidkeLab/matlab-instrument-control-master | gui.m | .m | matlab-instrument-control-master/@MIC_RB_PSFEng/gui.m | 17,913 | utf_8 | 3ffb4d357fa8f7872686a894b1cd3210 | function gui( obj )
%GUI Gui for MIC_RB_PSFEng class
% Detailed explanation goes here
%Prevent opening more than one figure for same instrument
if ishandle(obj.GuiFigure)
guiFig = obj.GuiFigure;
figure(obj.GuiFigure);
return
end
%Open figure
guiFig = figure('NumberTitle','off','Resize','off','Units','pi... |
github | LidkeLab/matlab-instrument-control-master | gui.m | .m | matlab-instrument-control-master/@MIC_TIRF_SRcollect/gui.m | 21,009 | utf_8 | 93650b7a3e977f739c1540ff8e7a8970 |
function gui(obj)
% GUI SRcollect Gui for TIRF microscope
% Detailed explanation goes here
h = findall(0,'tag','TIRF-SRcollect.gui');
if ~(isempty(h))
figure(h);
return;
end
%%
xsz=400;
ysz=1060;
xst=100;
yst=100;
pw=.95;
psep=.001;
staticst=10;
editst=110;
guiFig = figure('Units','pixels','Position',[xst ... |
github | vaibhavjoshi16/Matlab-solver-for-adaptive-two-phase-flows-master | coarsening.m | .m | Matlab-solver-for-adaptive-two-phase-flows-master/coarsening.m | 5,050 | utf_8 | 19e7e1fc6bd780ce0690c5302041ffbf | function [Sol,eta] = coarsening(Sol,eta,theta)
% COARSENING coarsens the current mesh
%
% USAGE
% [Sol,eta] = coarsening(Sol,eta,theta)
%
% INPUT
% Sol: current mesh data
% eta: error indicator for each triangle
% theta: parameter in (0,1).
% We mark minimal number of triangles M such th... |
github | vaibhavjoshi16/Matlab-solver-for-adaptive-two-phase-flows-master | bisection.m | .m | Matlab-solver-for-adaptive-two-phase-flows-master/bisection.m | 11,047 | utf_8 | 76f20349eeb792a7d8eaac98f42ee2a2 | function [Sol,eta] = bisection(Sol,eta,theta)
% BISECTION refines the triangulation using newest vertex bisection
%
% USAGE
% [Sol,eta] = bisection(Sol,eta,theta)
%
% INPUT
% Sol: current mesh data with all variable data
% eta: error indicator for each triangle
% theta: parameter in (0,1).
% ... |
github | zheng-da/incubator-mxnet-master | callmxnet.m | .m | incubator-mxnet-master/matlab/+mxnet/private/callmxnet.m | 1,666 | utf_8 | 23c3a6783ce55cb2598391d3aa27cf4e | % Licensed to the Apache Software Foundation (ASF) under one
% or more contributor license agreements. See the NOTICE file
% distributed with this work for additional information
% regarding copyright ownership. The ASF licenses this file
% to you under the Apache License, Version 2.0 (the
% "License"); you may not u... |
github | zheng-da/incubator-mxnet-master | parse_json.m | .m | incubator-mxnet-master/matlab/+mxnet/private/parse_json.m | 19,881 | utf_8 | 9cd6f452886def83ecf848d78f2e903a | % Licensed to the Apache Software Foundation (ASF) under one
% or more contributor license agreements. See the NOTICE file
% distributed with this work for additional information
% regarding copyright ownership. The ASF licenses this file
% to you under the Apache License, Version 2.0 (the
% "License"); you may not u... |
github | vladostan/pulse-master | pcamat.m | .m | pulse-master/ComponentAnalysis/FastICA/pcamat.m | 12,075 | utf_8 | bcb1117d4132558d0d54d8b7b616a902 | function [E, D] = pcamat(vectors, firstEig, lastEig, s_interactive, ...
s_verbose);
%PCAMAT - Calculates the pca for data
%
% [E, D] = pcamat(vectors, firstEig, lastEig, ...
% interactive, verbose);
%
% Calculates the PCA matrices for given data (row) vectors. Returns
% the eigenvector (E) and diag... |
github | vladostan/pulse-master | icaplot.m | .m | pulse-master/ComponentAnalysis/FastICA/icaplot.m | 13,259 | utf_8 | dde3e6d852f657a3c1eaacbd03f5dcc7 | function icaplot(mode, varargin);
%ICAPLOT - plot signals in various ways
%
% ICAPLOT is mainly for plottinf and comparing the mixed signals and
% separated ica-signals.
%
% ICAPLOT has many different modes. The first parameter of the function
% defines the mode. Other parameters and their order depends on the
% mode. ... |
github | taojiastanford/Automation-of-Calligraphy-master | SOMFn.m | .m | Automation-of-Calligraphy-master/TryAutoencoder/SOMFn.m | 842,616 | utf_8 | 2a3d050c1e1d69645129185dadd1a0c7 | function [Y,Xf,Af] = SOMFn(X,~,~)
%MYNEURALNETWORKFUNCTION neural network simulation function.
%
% Generated by Neural Network Toolbox function genFunction, 10-Dec-2016 10:17:26.
%
% [Y] = myNeuralNetworkFunction(X,~,~) takes these arguments:
%
% X = 1xTS cell, 1 inputs over TS timesteps
% Each X{1,ts} = 40... |
github | zhangchn/otx-master | PPCProcessor.m | .m | otx-master/src/source/Processors/PPCProcessor.m | 62,175 | utf_8 | 713d85183996bcd7d3f41e667af270b8 | /*
PPCProcessor.m
A subclass of ExeProcessor that handles PPC-specific issues.
This file is in the public domain.
*/
#import <Cocoa/Cocoa.h>
#import "PPCProcessor.h"
#import "ArchSpecifics.h"
#import "ListUtils.h"
#import "ObjcAccessors.h"
#import "ObjectLoader.h"
#import "Searchers.h"
#import "SyscallS... |
github | zhangchn/otx-master | Exe32Processor.m | .m | otx-master/src/source/Processors/Exe32Processor.m | 71,832 | utf_8 | fb7d3166b5926cb8213fe98a8dd69574 | /*
Exe32Processor.m
This file relies upon, and steals code from, the cctools source code
available from: http://www.opensource.apple.com/darwinsource/
This file is in the public domain.
*/
#import <Cocoa/Cocoa.h>
#import <mach/mach_time.h>
#import "Exe32Processor.h"
#import "ArchSpecifics.h"
#impor... |
github | zhangchn/otx-master | PPC64Processor.m | .m | otx-master/src/source/Processors/PPC64Processor.m | 74,333 | utf_8 | 6357b279a717e624564964c7ba8e1495 | /*
PPC64Processor.m
A subclass of Exe64Processor that handles PPC64-specific issues.
This file is in the public domain.
*/
#import <Cocoa/Cocoa.h>
#import "PPC64Processor.h"
#import "PPCProcessor.h"
#import "Arch64Specifics.h"
#import "List64Utils.h"
#import "Objc64Accessors.h"
#import "Object64Loader.h... |
github | amcorrigan/IA-Lab-master | choosePlanes.m | .m | IA-Lab-master/GUI/choosePlanes.m | 1,713 | utf_8 | 8b73f8946c63776dba8f7342c186874b | function zvalues = choosePlanes(IL,initSelection,parenth)
% choose selected z planes for modifying the import file.
zidx = find(strcmpi('zslice',IL.ChoiceStruct.Labels),1,'first');
origzvalues = IL.ChoiceStruct.Choices{zidx};
if nargin<3 || isempty(parenth)
parenth = gfigure();
end
set(parenth,'closere... |
github | amcorrigan/IA-Lab-master | chooseWells.m | .m | IA-Lab-master/GUI/chooseWells.m | 1,183 | utf_8 | db96ecfe82d88de9511f61be6874106f | function wellrowcol = chooseWells(IL,initSelection,parenth)
% find out what choices are available
wellidx = find(strcmpi('well',IL.ChoiceStruct.Labels),1,'first');
[r,c] = wellstr2rowcol(IL.ChoiceStruct.Choices{wellidx});
data = NaN*zeros(IL.PlateDimensions([2,1]));
data(amcSub2Ind(size(data),[r,c])) = 1;
... |
github | amcorrigan/IA-Lab-master | getStringGUI.m | .m | IA-Lab-master/GUI/getStringGUI.m | 1,184 | utf_8 | 5fc2dd0f88ca0bf52baa4d95bb53748c | function str = getStringGUI(title, msg, varargin)
% get the user to enter a string
if nargin<2 || isempty(msg)
msg = 'Enter some text:';
end
if nargin<1 || isempty(title)
title = 'Get text';
end
fig = gfigure('Name',title,'closerequestfcn',@closereqfun,varargin{:});... |
github | amcorrigan/IA-Lab-master | chooseFields.m | .m | IA-Lab-master/GUI/chooseFields.m | 1,820 | utf_8 | 8cff1357e138e3aeb7e124e10002eb05 | function fvalues = chooseFields(IL,initSelection,parenth)
% choose selected z planes for modifying the import file.
% This could be completely generalised, nothing field or z specific here
% apart from the choice of label
fidx = find(strcmpi('field',IL.ChoiceStruct.Labels),1,'first');
origfvalues = IL.ChoiceSt... |
github | amcorrigan/IA-Lab-master | prepareForExport.m | .m | IA-Lab-master/ExportClasses/prepareForExport.m | 2,849 | utf_8 | b51365d0b86be053e25c4b1c4fc72590 | function stats2 = prepareForExport(stats,include,exclude)
% prepare the statistics structure for export
%
% To export to a csv-type file, each of the fields should contain only
% scalars
% So go through the fields, and if there are non-scalars, replace the field
% with multiple fields, one for each element
... |
github | amcorrigan/IA-Lab-master | label2outline.m | .m | IA-Lab-master/Utilities/label2outline.m | 3,037 | utf_8 | 5ecb67916987dd5c80e4bee236a291db | function bordxy = label2outline(L,skip,interpfact)
% Currently the interpolation means that there is a bit of a discontinuity
% at the join, this needs tidying up by extending the range of the
% interpolation input
% no real logic behind choosing these factors, just whatever looks nice and
% retains the detail... |
github | amcorrigan/IA-Lab-master | expandCellIndices.m | .m | IA-Lab-master/Utilities/expandCellIndices.m | 800 | utf_8 | 88d51af88990f29b0c4028308028871a | function expandIdx = expandCellIndices(cellidx)
% expand the cell indices cellidx into a list of permutations
% use a recursive function?
expandIdx = recurseexpand(cellidx{1},cellidx(2:end));
end
function expandIdx = recurseexpand(currlist,remcellidx)
% for every element of currlist, combine with ea... |
github | amcorrigan/IA-Lab-master | matchLabels.m | .m | IA-Lab-master/Utilities/matchLabels.m | 865 | utf_8 | c436f156ccd8f0e0b607f5edd2c4847b | function [Lnew,probvals] = matchLabels(L2,Lseed)
% adjust the values in L2 so that they match those in the seed region.
% Try not to assume that the seed region will be wholely contained within
% L2, but that there is overlap.
%
% also, optionally check for confusion in which region is which, and flag
% this up... |
github | amcorrigan/IA-Lab-master | az_parseXML_ChannelColour_mes.m | .m | IA-Lab-master/Utilities/az_parseXML_ChannelColour_mes.m | 3,396 | utf_8 | d6908fa960c4fea024cc188e7a861100 | function o_struct = az_parseXML_ChannelColour_mes(i_fileName)
%
% i_fileName = '\\UK-Image-01\HCB\Technology Eval\Automated confocal\Yokogawa CV7000\CV7000 Demo Data\Corrected Images\Bead 96well_20140827_122725\AssayPlate_BD_#353219\JP_60x_beads_96w_4col.mes'
try
tree = xmlread(i_fileName);
catch... |
github | amcorrigan/IA-Lab-master | parseChildNodes.m | .m | IA-Lab-master/Utilities/parseChildNodes.m | 1,742 | utf_8 | aa71c09fe13a05a2507661f5a965daa6 | function children = parseChildNodes(theNode)
% Recurse over node children.
children = [];
if theNode.hasChildNodes
childNodes = theNode.getChildNodes;
numChildNodes = childNodes.getLength;
allocCell = cell(1, numChildNodes);
children = struct( ...
'Nam... |
github | amcorrigan/IA-Lab-master | savejson.m | .m | IA-Lab-master/Utilities/jsonlab/savejson.m | 19,584 | utf_8 | 116395347173d949bf39b82ac3bdd794 | function json=savejson(rootname,obj,varargin)
%
% json=savejson(rootname,obj,filename)
% or
% json=savejson(rootname,obj,opt)
% json=savejson(rootname,obj,'param1',value1,'param2',value2,...)
%
% convert a MATLAB object (cell, struct or array) into a JSON (JavaScript
% Object Notation) string
%
% author: Q... |
github | amcorrigan/IA-Lab-master | loadjson.m | .m | IA-Lab-master/Utilities/jsonlab/loadjson.m | 16,843 | ibm852 | 76e78ae4dcbb1c593583aa12596c6608 | function data = loadjson(fname,varargin)
%
% data=loadjson(fname,opt)
% or
% data=loadjson(fname,'param1',value1,'param2',value2,...)
%
% parse a JSON (JavaScript Object Notation) file or string
%
% authors:Qianqian Fang (fangq<at> nmr.mgh.harvard.edu)
% created on 2011/09/09, including previous works from ... |
github | amcorrigan/IA-Lab-master | loadubjson.m | .m | IA-Lab-master/Utilities/jsonlab/loadubjson.m | 13,774 | utf_8 | cf1ef9319b0f46d709ea706a0048f15d | function data = loadubjson(fname,varargin)
%
% data=loadubjson(fname,opt)
% or
% data=loadubjson(fname,'param1',value1,'param2',value2,...)
%
% parse a JSON (JavaScript Object Notation) file or string
%
% authors:Qianqian Fang (fangq<at> nmr.mgh.harvard.edu)
% created on 2013/08/01
%
% $Id$
%
% input:
... |
github | amcorrigan/IA-Lab-master | saveubjson.m | .m | IA-Lab-master/Utilities/jsonlab/saveubjson.m | 18,302 | utf_8 | 71eb65f95dee01aa2bf33ff80a5bf80d | function json=saveubjson(rootname,obj,varargin)
%
% json=saveubjson(rootname,obj,filename)
% or
% json=saveubjson(rootname,obj,opt)
% json=saveubjson(rootname,obj,'param1',value1,'param2',value2,...)
%
% convert a MATLAB object (cell, struct or array) into a Universal
% Binary JSON (UBJSON) binary string
%... |
github | amcorrigan/IA-Lab-master | AddTextToImageWithBorder.m | .m | IA-Lab-master/Utilities/textimage/AddTextToImageWithBorder.m | 2,034 | utf_8 | 98e36284eff76a81ec7ab9b7a1986c24 | function Image = AddTextToImageWithBorder(Image,String,Position,Color,Font,FontSize,BorderWidth,BorderColor)
% Image = AddTextToImage(Image,String,Position,Color,Font,FontSize,BorderWidth,BorderColor)
%
% Works as AddTextToImage, except also allows for a border of thickness
% BorderWidth pixels and color give... |
github | amcorrigan/IA-Lab-master | real2rgb.m | .m | IA-Lab-master/Utilities/sc/real2rgb.m | 4,918 | utf_8 | e3d94e10c8a2aca6dfbb6e867ed707bc | function [B lims map] = real2rgb(A, cmap, lims)
%REAL2RGB Converts a real-valued matrix into a truecolor image
%
% Examples:
% B = real2rgb(A, cmap);
% B = real2rgb(A, cmap, lims);
% [B lims map] = real2rgb(...);
%
% This function converts a real-valued matrix into a truecolor image (i.e.
% double array... |
github | amcorrigan/IA-Lab-master | imsc.m | .m | IA-Lab-master/Utilities/sc/imsc.m | 1,299 | utf_8 | 97cd4a988efe36fe0575539142fc605e | %IMSC Wrapper function to SC which replicates display behaviour of IMAGESC
%
% Examples:
% imsc(I, varargin)
% imsc(x, y, I, varargin)
% h = imsc(...)
%
% IN:
% x - 1x2 vector of x-axis bounds. If x(1) > x(2) the image is flipped
% left-right. Default: [1 size(I, 2)].
% y - 1x2 vector of y-... |
github | amcorrigan/IA-Lab-master | rescale.m | .m | IA-Lab-master/Utilities/sc/rescale.m | 1,613 | utf_8 | 427de5e2419533818c74ea0c8fd7f773 | function [B lims] = rescale(A, lims, out_lims)
%RESCALE Linearly rescale values in an array
%
% Examples:
% B = rescale(A)
% B = rescale(A, lims)
% B = rescale(A, lims, out_lims)
% [B lims] = rescale(A)
%
% Linearly rescales values in an array, saturating values outside limits.
%
% IN:
% A - Inpu... |
github | amcorrigan/IA-Lab-master | imdisp.m | .m | IA-Lab-master/Utilities/sc/imdisp.m | 19,654 | utf_8 | c97ad19a7be236223dde28b870a9b800 | function hIm = imdisp(I, varargin)
%IMDISP Display one or more images nicely
%
% Examples:
% imdisp
% imdisp(I)
% imdisp(I, map)
% imdisp(I, lims)
% imdisp(I, map, lims)
% imdisp(..., param1, value1, param2, value2, ...)
% h = imdisp(...)
%
% This function displays one or more images nicely. ... |
github | amcorrigan/IA-Lab-master | sc.m | .m | IA-Lab-master/Utilities/sc/sc.m | 31,219 | utf_8 | f247fe4402993a806f759a89a6ddf8a6 | function [I limits map] = sc(I, varargin)
%SC Display/output truecolor images with a range of colormaps
%
% Examples:
% sc(image)
% sc(image, limits)
% sc(image, map)
% sc(image, limits, map)
% sc(image, map, limits)
% sc(..., col1, mask1, col2, mask2,...)
% out = sc(...)
% [out clim map] = ... |
github | amcorrigan/IA-Lab-master | rescale.m | .m | IA-Lab-master/Utilities/sc/private/rescale.m | 1,613 | utf_8 | 427de5e2419533818c74ea0c8fd7f773 | function [B lims] = rescale(A, lims, out_lims)
%RESCALE Linearly rescale values in an array
%
% Examples:
% B = rescale(A)
% B = rescale(A, lims)
% B = rescale(A, lims, out_lims)
% [B lims] = rescale(A)
%
% Linearly rescales values in an array, saturating values outside limits.
%
% IN:
% A - Inpu... |
github | amcorrigan/IA-Lab-master | sfm_local_chanvese.m | .m | IA-Lab-master/ThirdParty/lanktonchanvese/sfm_local_chanvese.m | 2,172 | utf_8 | 3a6307d657f860fcd0f80de155397eb3 | % [seg Lz] = sfm_local_chanvese(img,mask,iterations,lambda,rad,display)
%
% img - any image (2D or 3D). color images will be
% converted to grayscale.
%
% mask - binary image representing initialization.
% (1's foreground, 0's background)
%
% iterations - number of iterations to run
%
% lam... |
github | amcorrigan/IA-Lab-master | fat_contour.m | .m | IA-Lab-master/ThirdParty/lanktonchanvese/fat_contour.m | 571 | utf_8 | d41a83dbdb50798bcf825109fc225bb8 | % FAT_CONTOUR draw a easily visible contour
function [h1 h2] = fat_contour(phi,dashed,c1)
%Coded by: Shawn Lankton
%Function: Display a contour
c2 = 'k';
if(~exist('c1','var')) c1 = 'r'; end
if(~exist('dashed','var')) dashed = false; end
t1 = 4;
t2 = 2;
hold on;
if(dashed)
h1 = conto... |
github | amcorrigan/IA-Lab-master | AboutWound.m | .m | IA-Lab-master/Examples/Pellet/AboutWound.m | 3,125 | utf_8 | e11339d283a2565d848bcb30104c1aa5 | function varargout = AboutWound(varargin)
% ABOUTWOUND MATLAB code for AboutWound.fig
% ABOUTWOUND, by itself, creates a new ABOUTWOUND or raises the existing
% singleton*.
%
% H = ABOUTWOUND returns the handle to a new ABOUTWOUND or the handle to
% the existing singleton*.
%
% ABOUTWOU... |
github | amcorrigan/IA-Lab-master | amcFillNaNs.m | .m | IA-Lab-master/Examples/Spheroid3D/utilities/amcFillNaNs.m | 1,083 | utf_8 | 58043bf2cbc8e1f285c575e09666201e | function outim = amcFillNaNs(im,blurScale,maxIts,initScale,epsilon)
% fill in NaNs by iteratively blurring from the edges
if nargin<2 || isempty(blurScale)
blurScale = max(1,0.01*min(size(im,1),size(im,2)));
end
if nargin<3 || isempty(maxIts)
maxIts = 40;
end
if nargin<4 || isempty(initScale)
... |
github | amcorrigan/IA-Lab-master | bwdistsc.m | .m | IA-Lab-master/Examples/Spheroid3D/utilities/bwdistsc.m | 18,385 | utf_8 | a8192c2781c7f03ef9cf7e9f0b91c769 | function D=bwdistsc(bw,aspect)
% D=BWDISTSC(BW,ASPECT)
% BWDISTSC computes Euclidean distance transform of the binary 3D image
% BW. For each pixel in BW, the distance transform assignes a number
% that is the distance between that pixel and the nearest nonzero pixel
% of BW. BW may be a single 2D image, 3D arra... |
github | amcorrigan/IA-Lab-master | nuclearPropertiesFunctionTest.m | .m | IA-Lab-master/Tests/nuclearPropertiesFunctionTest.m | 693 | utf_8 | ba0a6abfb01ff7b5766b72580e174ee8 | function tests = nuclearPropertiesFunctionTest
tests = functiontests(localfunctions);
end
function setupOnce(testCase)
parentfolder = fileparts(which('nuclearPropertiesWorkflow.m'));
parser = ParserYokogawa(fullfile(parentfolder,'AssayPlate'));
testCase.TestData.Workflow = nuclearPropertiesWorkflow('tempoutpu... |
github | amcorrigan/IA-Lab-master | YEAbout.m | .m | IA-Lab-master/YokoV2/YEAbout.m | 3,650 | utf_8 | 80021317baece190475f4d64bdddfe24 | function varargout = YEAbout(varargin)
% YEABOUT MATLAB code for YEAbout.fig
% YEABOUT, by itself, creates a new YEABOUT or raises the existing
% singleton*.
%
% H = YEABOUT returns the handle to a new YEABOUT or the handle to
% the existing singleton*.
%
% YEABOUT('CALLBACK',hObject,ev... |
github | amcorrigan/IA-Lab-master | gaussFiltND.m | .m | IA-Lab-master/Filters/gaussFiltND.m | 1,751 | utf_8 | 37578851d6366b2c6b5ba79f53e5a72c | function fim = gaussFiltND(im,frad,boundcon,relsiz)
% N-dimensional Gaussian filtering
% This works by permuting the image rather than the
% kernel so that the filtering is always done along the first dimension,
% which seems to be faster for some reason.
if nargin<4 || isempty(relsiz)
relsiz = 6; % size ... |
github | amcorrigan/IA-Lab-master | amcBilateral2D.m | .m | IA-Lab-master/Filters/amcBilateral2D.m | 5,348 | utf_8 | c9c7a1e74c52e78500f4ee6e81555d70 | function fim = amcBilateral2D(im,rdata,sxy,sr,rbins,xydsc)
% fast bilateral filtering, taking advantage of MATLAB's efficiency of
% array indexing
% Adam Corrigan
% if the normalization for r-binning is done only on rg without changing
% im, we don't have to scale then rescale at the end..
% first thing t... |
github | amcorrigan/IA-Lab-master | bwdistsc.m | .m | IA-Lab-master/Filters/bwdistsc.m | 18,385 | utf_8 | a8192c2781c7f03ef9cf7e9f0b91c769 | function D=bwdistsc(bw,aspect)
% D=BWDISTSC(BW,ASPECT)
% BWDISTSC computes Euclidean distance transform of the binary 3D image
% BW. For each pixel in BW, the distance transform assignes a number
% that is the distance between that pixel and the nearest nonzero pixel
% of BW. BW may be a single 2D image, 3D arra... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.