diff --git a/.gitignore b/.gitignore index 6146b2ba..c1db3745 100644 --- a/.gitignore +++ b/.gitignore @@ -23,8 +23,10 @@ tests/*.tsv* check_my_code_report.txt # jupyter notebook checkpoints -.ipynb_checkpoints -*/.ipynb_checkpoints/* +notebooks/.ipynb_checkpoints/* +notebooks/source/* +notebooks/output/* +notebooks/new_experiment/* # ignore node js files node_modules/* diff --git a/lib/utils/abspath.m b/lib/utils/abspath.m new file mode 100644 index 00000000..4376fc4f --- /dev/null +++ b/lib/utils/abspath.m @@ -0,0 +1,117 @@ +function fpath = abspath(fpath) +%ABSPATH Converts path to an absolute path +% +% Converts a relative path from the current working directory to an +% absolute path by glueing the pwd and the relative path together and +% eliminating relative references like '.' and '..'. If the provided path +% is already absolute, only the references like '.' and '..' are removed. +% +% Syntax: +% fpath = abspath(fpath) +% +% Input: +% fpath = path to be converted +% +% Output: +% fpath = absolute path +% +% Example +% fpath = abspath(fpath) +% +% See also + +%% Copyright notice +% -------------------------------------------------------------------- +% Copyright (C) 2010 Deltares +% Bas Hoonhout +% +% bas.hoonhout@deltares.nl +% +% Rotterdamseweg 185 +% 2629HD Delft +% +% This library is free software: you can redistribute it and/or +% modify it under the terms of the GNU Lesser General Public +% License as published by the Free Software Foundation, either +% version 2.1 of the License, or (at your option) any later version. +% +% This library is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +% Lesser General Public License for more details. +% +% You should have received a copy of the GNU Lesser General Public +% License along with this library. If not, see . +% -------------------------------------------------------------------- + +% This tool is part of OpenEarthTools. +% OpenEarthTools is an online collaboration to share and manage data and +% programming tools in an open source, version controlled environment. +% Sign up to recieve regular updates of this function, and to contribute +% your own tools. + +%% Version +% Created: 24 Nov 2010 +% Created with Matlab version: 7.9.0.529 (R2009b) + +% $Id$ +% $Date$ +% $Author$ +% $Revision$ +% $HeadURL$ +% $Keywords: $ + +%% convert to absolute path +% make sure fileseperators are right +fpath = fullfile(fpath, ''); + +% check if path is relative +isRelative = false; +if ispc() + if length(fpath) < 2 || ... + (fpath(2) ~= ':' && ~strcmpi(repmat(filesep,1,2), fpath(1:2))) + isRelative = true; + end +elseif isunix() + if ~any(strcmp(fpath(1), {filesep '~'})) + isRelative = true; + end +else + error('Unsupported operating system'); +end + +if isRelative + fpath = fullfile(pwd, fpath); +end + +if ispc() + root = fpath(1:2); + fpath = fpath(3:end); +elseif isunix() + root = fpath(1); + fpath = fpath(2:end); +end + +p = regexp(fpath, filesep, 'split'); + +% remove '.' elements +p = p(~strcmp(p, '.')); + +% replace relative references +i = 1; +while i <= length(p) + if strcmp(p{i}, '..') + p(i-1:i) = []; + i = i-2; + end + i = i+1; +end + +% glue path together +fpath = fullfile(root, p{:}, ''); + +% help unix users +if isunix && ... + (isempty(fpath) || ~strcmp(fpath(1), '~')) + fpath = [filesep fpath]; +end \ No newline at end of file diff --git a/notebooks/basic_usage.ipynb b/notebooks/basic_usage.ipynb index 595c05a8..47aca2e9 100644 --- a/notebooks/basic_usage.ipynb +++ b/notebooks/basic_usage.ipynb @@ -1,13 +1,21 @@ { "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Basic usage" + ] + }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ - "% add the relevant functions from the src folder\n", - "addpath(genpath(fullfile(pwd, '..', 'src')))" + "% add the relevant functions from the source and library folder\n", + "addpath(genpath(fullfile(pwd, '..', 'src')))\n", + "addpath(genpath(fullfile(pwd, '..', 'lib')))" ] }, { @@ -16,7 +24,7 @@ "source": [ "## Setting the parameters about our experiment\n", "\n", - "We need to define the configuration structure where we put all our information." + "We need to define the configuration structure where we put the information about the experiment." ] }, { @@ -28,41 +36,40 @@ "% define the folder where the data will be saved\n", "cfg.dir.output = fullfile(pwd, 'output');\n", "\n", + "cfg.verbose = 1;\n", + "\n", "% define the name of the task\n", "cfg.task.name = 'test task';\n", "\n", - "% can use the userInputs function to collect subject info\n", + "% We can use the userInputs function to collect subject info: this won't work in a jupyter notebook though\n", "% cfg = userInputs;\n", "\n", - "% Or we can add those information manually directly\n", + "% so we can add those information manually directly\n", "cfg.subject.subjectNb = 1;\n", "cfg.subject.runNb = 1;\n", "\n", "% if set to 'mri' then the data will be saved in the `func` folder\n", - "cfg.testingDevice = 'mri';\n", - "\n", - "% to keep things quiet\n", - "cfg.verbose = false;\n" + "cfg.testingDevice = 'mri';" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "If set to `eeg` then the data will be saved in the `eeg` folder\n", - "\n", - "```\n", - "cfg.testingDevice = 'eeg';\n", - "```\n", - "\n", - "By default we assume you are running things on a behavioral PC with no eyetracker.\n", + "By default we assume you are running a purely behavioral experiment with no eyetracker.\n", "\n", "```\n", "cfg.eyeTracker = false;\n", "cfg.testingDevice = 'pc';\n", "```\n", "\n", - "If the testing device is set to `pc` then the data will be saved in the `beh` folder" + "If the testing device is set to `pc` then the data will be saved in the `beh` folder\n", + "\n", + "If set to `eeg` then the data will be saved in the `eeg` folder\n", + "\n", + "```\n", + "cfg.testingDevice = 'eeg';\n", + "```" ] }, { @@ -74,110 +81,41 @@ "name": "stdout", "output_type": "stream", "text": [ - "cfg =\r\n", - "\r\n", - " scalar structure containing the fields:\r\n", - "\r\n", - " bids =\r\n", - "\r\n", - " scalar structure containing the fields:\r\n", - "\r\n", - " datasetDescription =\r\n", - "\r\n", - " scalar structure containing the fields:\r\n", - "\r\n", - " Acknowledgements: 0x0 sq_string\r\n", - " Authors: 1x1 cell\r\n", - " BIDSVersion: 0x0 sq_string\r\n", - " DatasetDOI: 0x0 sq_string\r\n", - " Funding: 1x1 cell\r\n", - " HowToAcknowledge: 0x0 sq_string\r\n", - " License: 0x0 sq_string\r\n", - " Name: 0x0 sq_string\r\n", - " ReferencesAndLinks: 1x1 cell\r\n", - "\r\n", - " mri =\r\n", - "\r\n", - " scalar structure containing the fields:\r\n", - "\r\n", - " Instructions: 0x0 sq_string\r\n", - " RepetitionTime: 0x0 matrix\r\n", - " SliceTiming: 0x0 matrix\r\n", - " TaskDescription: 0x0 sq_string\r\n", - " TaskName: 1x9 sq_string\r\n", - "\r\n", - " meg =\r\n", - "\r\n", - " scalar structure containing the fields:\r\n", - "\r\n", - " DewarPosition: 0x0 matrix\r\n", - " DigitizedHeadPoints: 0x0 matrix\r\n", - " DigitizedLandmarks: 0x0 matrix\r\n", - " PowerLineFrequency: 0x0 matrix\r\n", - " SamplingFrequency: 0x0 matrix\r\n", - " SoftwareFilters: 0x0 matrix\r\n", - " TaskName: 1x9 sq_string\r\n", - "\r\n", "\r\n", - " dir =\r\n", "\r\n", - " scalar structure containing the fields:\r\n", + "___________________________________________________\r\n", + "___________________________________________________\r\n", + " \r\n", + " ___ ___ ___ ___ ___ ___ ___ \r\n", + " / __| _ \\ _ \\ | _ )_ _| \\/ __|\r\n", + " | (__| _/ _/ | _ \\| || |) \\__ \\\r\n", + " \\___|_| |_| |___/___|___/|___/\r\n", + " \r\n", + "Thank you for using the CPP BIDS - version v1.0.0. \r\n", "\r\n", - " output = /home/remi/github/CPP_BIDS/notebooks/output\r\n", + "Current list of contributors includes:\r\n", + " Rémi Gau\r\n", + " Marco Barilari\r\n", + " Ceren Battal\r\n", + " Tomas Lenc\r\n", + "\b\r\n", "\r\n", - " eyeTracker =\r\n", + "Please cite using the following DOI: \r\n", + " https://doi.org/10.5281/zenodo.4007674\r\n", "\r\n", - " scalar structure containing the fields:\r\n", + "For bug report, suggestions or contributions see: \r\n", + " https://github.com/cpp-lln-lab/CPP_BIDS\r\n", "\r\n", - " do = 0\r\n", + "___________________________________________________\r\n", + "___________________________________________________\r\n", "\r\n", - " fileName =\r\n", - "\r\n", - " scalar structure containing the fields:\r\n", - "\r\n", - " task = testTask\r\n", - " zeroPadding = 3\r\n", - " dateFormat = yyyymmddHHMM\r\n", - "\r\n", - " mri =\r\n", - "\r\n", - " scalar structure containing the fields:\r\n", - "\r\n", - " acquisition = [](0x0)\r\n", - " contrastEnhancement = [](0x0)\r\n", - " echo = [](0x0)\r\n", - " phaseEncodingDirection = [](0x0)\r\n", - " reconstruction = [](0x0)\r\n", - " repetitionTime = [](0x0)\r\n", - "\r\n", - " subject =\r\n", - "\r\n", - " scalar structure containing the fields:\r\n", - "\r\n", - " askGrpSess =\r\n", - "\r\n", - " 1 1\r\n", - "\r\n", - " runNb = 1\r\n", - " sessionNb = 1\r\n", - " subjectGrp = \r\n", - " subjectNb = 1\r\n", - "\r\n", - " task =\r\n", - "\r\n", - " scalar structure containing the fields:\r\n", - "\r\n", - " name = test task\r\n", - "\r\n", - " testingDevice = mri\r\n", - " verbose = 0\r\n", "\r\n" ] } ], "source": [ "% We can then initialize all the other fields. The ones we have already filled in will not be overwritten\n", - "cfg = checkCFG(cfg)" + "cfg = checkCFG(cfg);" ] }, { @@ -195,7 +133,7 @@ "source": [ "% create the filenames: this include a step to check that all the information is there: createFilename calls \n", "% checkCFG before running\n", - "[cfg] = createFilename(cfg);" + "cfg = createFilename(cfg);" ] }, { @@ -220,12 +158,12 @@ "name": "stdout", "output_type": "stream", "text": [ - "ans = /home/remi/github/CPP_BIDS/notebooks/output/source/sub-001/ses-001\r\n" + "/home/remi/github/CPP_BIDS/notebooks/output/source/sub-001/ses-001\r\n" ] } ], "source": [ - "cfg.dir.outputSubject" + "disp(cfg.dir.outputSubject)" ] }, { @@ -248,12 +186,12 @@ "name": "stdout", "output_type": "stream", "text": [ - "ans = sub-001_ses-001_task-testTask_run-001_events_date-202008142236.tsv\r\n" + "sub-001_ses-001_task-testTask_run-001_events_date-202011171229.tsv\r\n" ] } ], "source": [ - "cfg.fileName.events" + "disp(cfg.fileName.events)" ] }, { @@ -272,15 +210,15 @@ "name": "stdout", "output_type": "stream", "text": [ - "ans = /home/remi/github/CPP_BIDS/notebooks/output/source/sub-001/ses-001/func/sub-001_ses-001_task-testTask_run-001_events_date-202008142236.tsv\r\n" + "/home/remi/github/CPP_BIDS/notebooks/output/source/sub-001/ses-001/func/sub-001_ses-001_task-testTask_run-001_events_date-202011171229.tsv\r\n" ] } ], "source": [ - "fullfile(...\n", + "disp(fullfile(...\n", " cfg.dir.outputSubject, ...\n", " cfg.fileName.modality, ...\n", - " cfg.fileName.events)" + " cfg.fileName.events))" ] }, { @@ -303,10 +241,12 @@ "metadata": {}, "outputs": [], "source": [ - "clear cfg\n", + "clear cfg logFile\n", "\n", "cfg.dir.output = fullfile(pwd, 'output');\n", "\n", + "cfg.verbose = 0;\n", + "\n", "cfg.task.name = 'test task';\n", "\n", "cfg.subject.subjectNb = 1;\n", @@ -314,13 +254,11 @@ "\n", "cfg.testingDevice = 'mri';\n", "\n", - "cfg.verbose = false;\n", - "\n", "% Create the filenames\n", "[cfg] = createFilename(cfg);\n", "\n", "% We can define what extra columns we want in our tsv file beyond the \n", - "% BIDS holy trinity ('onset', 'duration', 'trial_type')\n", + "% BIDS \"holy trinity\" ('onset', 'duration', 'trial_type')\n", "\n", "% Say we want to keep track of the type of target that what presented during a trial and of its position\n", "logFile.extraColumns = {'target_position', 'target_type'};\n" @@ -348,7 +286,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "This will initialize a structure for each extra column." + "This will initialize a structure for each extra column.\n" ] }, { @@ -362,7 +300,6 @@ "name": "stdout", "output_type": "stream", "text": [ - "ans =\r\n", "\r\n", " scalar structure containing the fields:\r\n", "\r\n", @@ -370,12 +307,12 @@ " Levels = \r\n", " LongName = \r\n", " TermURL = \r\n", - "\r\n" + " Units = \r\n" ] } ], "source": [ - "logFile.extraColumns.target_position.bids" + "disp(logFile.extraColumns.target_position.bids)" ] }, { @@ -394,7 +331,6 @@ "name": "stdout", "output_type": "stream", "text": [ - "ans =\r\n", "\r\n", " scalar structure containing the fields:\r\n", "\r\n", @@ -407,7 +343,7 @@ " }\r\n", " LongName = \r\n", " TermURL = \r\n", - "\r\n" + " Units = \r\n" ] } ], @@ -415,7 +351,7 @@ "logFile.extraColumns.target_position.bids.Description = 'Position of the target on the screen';\n", "logFile.extraColumns.target_position.bids.Levels = {'left', 'center', 'right'};\n", "\n", - "logFile.extraColumns.target_position.bids" + "disp(logFile.extraColumns.target_position.bids)" ] }, { @@ -471,33 +407,17 @@ "├── basic_usage.ipynb\r\n", "├── creating_BIDS_dataset.ipynb\r\n", "├── more_on_saving.ipynb\r\n", - "├── octave-workspace\r\n", "├── \u001b[01;34moutput\u001b[00m\r\n", - "│   ├── \u001b[01;34mrawdata\u001b[00m\r\n", - "│   │   ├── CHANGES\r\n", - "│   │   ├── dataset_description.json\r\n", - "│   │   ├── README\r\n", - "│   │   └── \u001b[01;34msub-001\u001b[00m\r\n", - "│   │   └── \u001b[01;34mses-001\u001b[00m\r\n", - "│   │   └── \u001b[01;34mfunc\u001b[00m\r\n", - "│   │   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_bold.json\r\n", - "│   │   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events.json\r\n", - "│   │   └── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events.tsv\r\n", "│   └── \u001b[01;34msource\u001b[00m\r\n", - "│   ├── CHANGES\r\n", - "│   ├── dataset_description.json\r\n", - "│   ├── README\r\n", "│   └── \u001b[01;34msub-001\u001b[00m\r\n", "│   └── \u001b[01;34mses-001\u001b[00m\r\n", "│   └── \u001b[01;34mfunc\u001b[00m\r\n", - "│   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_bold_date-202008090023.json\r\n", - "│   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008090023.json\r\n", - "│   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008090023.tsv\r\n", - "│   ├── sub-001_ses-001_task-testTask_run-001_events_date-202008142236.json\r\n", - "│   └── sub-001_ses-001_task-testTask_run-001_events_date-202008142236.tsv\r\n", - "└── README.md\r\n", + "│   ├── sub-001_ses-001_task-testTask_run-001_events_date-202011171229.json\r\n", + "│   └── sub-001_ses-001_task-testTask_run-001_events_date-202011171229.tsv\r\n", + "├── README.md\r\n", + "└── using_2_logfiles.ipynb\r\n", "\r\n", - "9 directories, 19 files\r\n", + "5 directories, 7 files\r\n", "\n" ] } @@ -531,7 +451,7 @@ "{\r\n", " \"onset\": {\r\n", " \"Description\": \"time elapsed since experiment start\",\r\n", - " \"Unit\": \"s\"\r\n", + " \"Units\": \"s\"\r\n", " },\r\n", " \"trial_type\": {\r\n", " \"Description\": \"types of trial\",\r\n", @@ -539,7 +459,7 @@ " },\r\n", " \"duration\": {\r\n", " \"Description\": \"duration of the event or the block\",\r\n", - " \"Unit\": \"s\"\r\n", + " \"Units\": \"s\"\r\n", " },\r\n", " \"target_position\": {\r\n", " \"Description\": \"Position of the target on the screen\",\r\n", @@ -549,13 +469,15 @@ " \"right\"\r\n", " ],\r\n", " \"LongName\": \"\",\r\n", - " \"TermURL\": \"\"\r\n", + " \"TermURL\": \"\",\r\n", + " \"Units\": \"\"\r\n", " },\r\n", " \"target_type\": {\r\n", " \"Description\": \"\",\r\n", " \"Levels\": \"\",\r\n", " \"LongName\": \"\",\r\n", - " \"TermURL\": \"\"\r\n", + " \"TermURL\": \"\",\r\n", + " \"Units\": \"\"\r\n", " }\r\n", "}\n" ] @@ -574,14 +496,18 @@ "name": "stdout", "output_type": "stream", "text": [ - "2.000000\t1.000000\tmotion_up\tleft\taudio\t\r\n", - "6.000000\t1.200000\tstatic\tright\tvisual\t\r\n" + "ans = 2\r\n", + "ans = 1\r\n", + "\r\n", + "ans = 6\r\n", + "ans = 1.2000\r\n", + "\r\n" ] } ], "source": [ "% The information about 2 events that we want to save\n", - "% NOTE : If the user DOES NOT provide `onset`, `trial_type`, this events will be skipped.\n", + "% NOTE : If the user DOES NOT provide `onset`, `duration`, this events will be skipped.\n", "\n", "% Trial one\n", "logFile(1,1).onset = 2;\n", @@ -618,10 +544,9 @@ "name": "stdout", "output_type": "stream", "text": [ - "warning: \r\n", - "Skipping saving this event.\r\n", + "warning: Skipping saving this event. \r\n", " onset: NaN \r\n", - " duration: NaN\r\n" + " duration: NaN \r\n" ] } ], @@ -649,11 +574,13 @@ "text": [ "warning: Missing some target_position data for this event.\r\n", "warning: called from\r\n", - " saveEventsFile>checkExtracolumns at line 219 column 13\r\n", - " saveEventsFile>checklLogFile at line 140 column 21\r\n", - " saveEventsFile>saveToLogFile at line 282 column 17\r\n", - " saveEventsFile at line 90 column 21\r\n", - "10.000000\t1.000000\tmotion_down\tn/a\taudio\t\r\n" + " saveEventsFile>checkExtracolumns at line 288 column 13\r\n", + " saveEventsFile>checklLogFile at line 173 column 21\r\n", + " saveEventsFile>saveToLogFile at line 351 column 17\r\n", + " saveEventsFile at line 123 column 21\r\n", + "ans = 10\r\n", + "ans = 1\r\n", + "\r\n" ] } ], @@ -679,22 +606,9 @@ "cell_type": "code", "execution_count": 18, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\r\n", - "Data were saved in this file:\r\n", - "\r\n", - "/home/remi/github/CPP_BIDS/notebooks/output/source/sub-001/ses-001/func/sub-001_ses-001_task-testTask_run-001_events_date-202008142236.tsv\r\n", - "\r\n" - ] - } - ], + "outputs": [], "source": [ "% close the file\n", - "cfg.verbose = true; % set verbose in true if you want to know where things are\n", "saveEventsFile('close', cfg, logFile);" ] }, diff --git a/notebooks/creating_BIDS_dataset.ipynb b/notebooks/creating_BIDS_dataset.ipynb index 9141308c..7cc44047 100644 --- a/notebooks/creating_BIDS_dataset.ipynb +++ b/notebooks/creating_BIDS_dataset.ipynb @@ -16,12 +16,20 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 33, + "metadata": {}, + "outputs": [], + "source": [ + "addpath(genpath(fullfile(pwd, '..', 'src')))\n", + "addpath(genpath(fullfile(pwd, '..', 'lib')))" + ] + }, + { + "cell_type": "code", + "execution_count": 34, "metadata": {}, "outputs": [], "source": [ - "addpath(genpath(fullfile(pwd, '..', 'src')));\n", - "\n", "cfg.dir.output = fullfile(pwd, 'output');\n", "\n", "cfg.task.name = 'test task';\n", @@ -33,14 +41,56 @@ "\n", "cfg.eyetracker.do = 1;\n", "\n", - "cfg.verbose = false;" + "cfg.verbose = 2;" ] }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 35, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\r\n", + "\r\n", + "___________________________________________________\r\n", + "___________________________________________________\r\n", + " \r\n", + " ___ ___ ___ ___ ___ ___ ___ \r\n", + " / __| _ \\ _ \\ | _ )_ _| \\/ __|\r\n", + " | (__| _/ _/ | _ \\| || |) \\__ \\\r\n", + " \\___|_| |_| |___/___|___/|___/\r\n", + " \r\n", + "Thank you for using the CPP BIDS - version v1.0.0. \r\n", + "\r\n", + "Current list of contributors includes:\r\n", + " Rémi Gau\r\n", + " Marco Barilari\r\n", + " Ceren Battal\r\n", + " Tomas Lenc\r\n", + "\b\r\n", + "\r\n", + "Please cite using the following DOI: \r\n", + " https://doi.org/10.5281/zenodo.4007674\r\n", + "\r\n", + "For bug report, suggestions or contributions see: \r\n", + " https://github.com/cpp-lln-lab/CPP_BIDS\r\n", + "\r\n", + "___________________________________________________\r\n", + "___________________________________________________\r\n", + "\r\n", + "\r\n", + "\r\n", + "Data will be saved in this directory:\r\n", + "\t/home/remi/github/CPP_BIDS/notebooks/output/source/sub-001/ses-001/func\r\n", + "\r\n", + "Data will be saved in this file:\r\n", + "\tsub-001_ses-001_task-testTask_run-001_events_date-202011171530.tsv\r\n" + ] + } + ], "source": [ "cfg.bids.datasetDescription.Name = 'my new bids data set';\n", "cfg.bids.datasetDescription.BIDSVersion = '1.3';\n", @@ -57,66 +107,41 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 36, "metadata": {}, "outputs": [], "source": [ - "mkdir(fullfile(cfg.dir.outputSubject, cfg.fileName.modality));\n", - "\n", "createDatasetDescription(cfg)" ] }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 37, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "\u001b[01;34m.\u001b[00m\r\n", - "├── basic_usage.ipynb\r\n", - "├── creating_BIDS_dataset.ipynb\r\n", - "├── more_on_saving.ipynb\r\n", - "├── octave-workspace\r\n", - "├── \u001b[01;34moutput\u001b[00m\r\n", - "│   ├── \u001b[01;34mrawdata\u001b[00m\r\n", - "│   │   ├── CHANGES\r\n", - "│   │   ├── dataset_description.json\r\n", - "│   │   ├── README\r\n", - "│   │   └── \u001b[01;34msub-001\u001b[00m\r\n", - "│   │   └── \u001b[01;34mses-001\u001b[00m\r\n", - "│   │   └── \u001b[01;34mfunc\u001b[00m\r\n", - "│   │   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_bold.json\r\n", - "│   │   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events.json\r\n", - "│   │   └── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events.tsv\r\n", - "│   └── \u001b[01;34msource\u001b[00m\r\n", - "│   ├── CHANGES\r\n", - "│   ├── dataset_description.json\r\n", - "│   ├── README\r\n", - "│   └── \u001b[01;34msub-001\u001b[00m\r\n", - "│   └── \u001b[01;34mses-001\u001b[00m\r\n", - "│   └── \u001b[01;34mfunc\u001b[00m\r\n", - "│   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_bold_date-202008090023.json\r\n", - "│   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008090023.json\r\n", - "│   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008090023.tsv\r\n", - "│   ├── sub-001_ses-001_task-testTask_run-001_events_date-202008142236.json\r\n", - "│   └── sub-001_ses-001_task-testTask_run-001_events_date-202008142236.tsv\r\n", - "└── README.md\r\n", + "\u001b[01;34moutput\u001b[00m\r\n", + "└── \u001b[01;34msource\u001b[00m\r\n", + " ├── dataset_description.json\r\n", + " └── \u001b[01;34msub-001\u001b[00m\r\n", + " └── \u001b[01;34mses-001\u001b[00m\r\n", + " └── \u001b[01;34mfunc\u001b[00m\r\n", "\r\n", - "9 directories, 19 files\r\n", + "4 directories, 1 file\r\n", "\n" ] } ], "source": [ - "!tree" + "!tree output" ] }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 38, "metadata": {}, "outputs": [ { @@ -162,42 +187,83 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 45, "metadata": {}, "outputs": [], "source": [ "cfg.mri.repetitionTime = 2.1;\n", - "cfg.mri.contrastEnhancement = [];\n", - "cfg.mri.phaseEncodingDirection = [];\n", - "cfg.mri.reconstruction = 'fast';\n", - "cfg.mri.echo = '1';\n", - "cfg.mri.acquisition = 'slow';" + "cfg.suffix.phaseEncodingDirection = 'i-';\n", + "cfg.suffix.reconstruction = 'motion correction';\n", + "cfg.suffix.echo = '1';\n", + "cfg.suffix.acquisition = 'slow';" ] }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 48, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\r\n", + "\r\n", + "___________________________________________________\r\n", + "___________________________________________________\r\n", + " \r\n", + " ___ ___ ___ ___ ___ ___ ___ \r\n", + " / __| _ \\ _ \\ | _ )_ _| \\/ __|\r\n", + " | (__| _/ _/ | _ \\| || |) \\__ \\\r\n", + " \\___|_| |_| |___/___|___/|___/\r\n", + " \r\n", + "Thank you for using the CPP BIDS - version v1.0.0. \r\n", + "\r\n", + "Current list of contributors includes:\r\n", + " Rémi Gau\r\n", + " Marco Barilari\r\n", + " Ceren Battal\r\n", + " Tomas Lenc\r\n", + "\b\r\n", + "\r\n", + "Please cite using the following DOI: \r\n", + " https://doi.org/10.5281/zenodo.4007674\r\n", + "\r\n", + "For bug report, suggestions or contributions see: \r\n", + " https://github.com/cpp-lln-lab/CPP_BIDS\r\n", + "\r\n", + "___________________________________________________\r\n", + "___________________________________________________\r\n", + "\r\n", + "\r\n", + "\r\n", + "Data will be saved in this directory:\r\n", + "\t/home/remi/github/CPP_BIDS/notebooks/output/source/sub-001/ses-001/func\r\n", + "\r\n", + "Data will be saved in this file:\r\n", + "\tsub-001_ses-001_task-testTask_run-001_events_date-202011171531.tsv\r\n" + ] + } + ], "source": [ "[cfg] = createFilename(cfg);" ] }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 47, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "ans = sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008142237.tsv\r\n" + "sub-001_ses-001_task-testTask_run-001_events_date-202011171531.tsv\r\n" ] } ], "source": [ - "cfg.fileName.events" + "disp(cfg.fileName.events)" ] }, { @@ -213,65 +279,43 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 51, "metadata": {}, "outputs": [], "source": [ - "createBoldJson(cfg)" + "createJson(cfg, 'func')" ] }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 52, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "\u001b[01;34m.\u001b[00m\r\n", - "├── basic_usage.ipynb\r\n", - "├── creating_BIDS_dataset.ipynb\r\n", - "├── more_on_saving.ipynb\r\n", - "├── octave-workspace\r\n", - "├── \u001b[01;34moutput\u001b[00m\r\n", - "│   ├── \u001b[01;34mrawdata\u001b[00m\r\n", - "│   │   ├── CHANGES\r\n", - "│   │   ├── dataset_description.json\r\n", - "│   │   ├── README\r\n", - "│   │   └── \u001b[01;34msub-001\u001b[00m\r\n", - "│   │   └── \u001b[01;34mses-001\u001b[00m\r\n", - "│   │   └── \u001b[01;34mfunc\u001b[00m\r\n", - "│   │   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_bold.json\r\n", - "│   │   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events.json\r\n", - "│   │   └── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events.tsv\r\n", - "│   └── \u001b[01;34msource\u001b[00m\r\n", - "│   ├── CHANGES\r\n", - "│   ├── dataset_description.json\r\n", - "│   ├── README\r\n", - "│   └── \u001b[01;34msub-001\u001b[00m\r\n", - "│   └── \u001b[01;34mses-001\u001b[00m\r\n", - "│   └── \u001b[01;34mfunc\u001b[00m\r\n", - "│   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_bold_date-202008090023.json\r\n", - "│   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_bold_date-202008142237.json\r\n", - "│   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008090023.json\r\n", - "│   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008090023.tsv\r\n", - "│   ├── sub-001_ses-001_task-testTask_run-001_events_date-202008142236.json\r\n", - "│   └── sub-001_ses-001_task-testTask_run-001_events_date-202008142236.tsv\r\n", - "└── README.md\r\n", + "\u001b[01;34moutput\u001b[00m\r\n", + "└── \u001b[01;34msource\u001b[00m\r\n", + " ├── dataset_description.json\r\n", + " └── \u001b[01;34msub-001\u001b[00m\r\n", + " └── \u001b[01;34mses-001\u001b[00m\r\n", + " └── \u001b[01;34mfunc\u001b[00m\r\n", + " ├── sub-001_ses-001_task-testTask_run-001_bold_date-202011171530.json\r\n", + " └── sub-001_ses-001_task-testTask_run-001_bold_date-202011171531.json\r\n", "\r\n", - "9 directories, 20 files\r\n", + "4 directories, 3 files\r\n", "\n" ] } ], "source": [ - "!tree" + "!tree output" ] }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 44, "metadata": {}, "outputs": [ { @@ -283,27 +327,6 @@ " \"RepetitionTime\": [],\r\n", " \"SliceTiming\": [],\r\n", " \"TaskDescription\": \"\",\r\n", - " \"TaskName\": \"test Task\",\r\n", - " \"timing\": {\r\n", - " \"IBI\": 5.4,\r\n", - " \"ISI\": 0.1,\r\n", - " \"onsetDelay\": 0.1,\r\n", - " \"endDelay\": 0.1,\r\n", - " \"eventDuration\": 0.8\r\n", - " },\r\n", - " \"dot\": {\r\n", - " \"speed\": 30,\r\n", - " \"coherence\": 1,\r\n", - " \"density\": 0.1,\r\n", - " \"lifeTime\": 10,\r\n", - " \"proportionKilledPerFrame\": 0,\r\n", - " \"size\": 1\r\n", - " }\r\n", - "}{\r\n", - " \"Instructions\": \"\",\r\n", - " \"RepetitionTime\": [],\r\n", - " \"SliceTiming\": [],\r\n", - " \"TaskDescription\": \"\",\r\n", " \"TaskName\": \"test Task\"\r\n", "}\n" ] @@ -326,7 +349,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 14, "metadata": {}, "outputs": [], "source": [ @@ -365,12 +388,12 @@ "metadata": {}, "outputs": [], "source": [ - "createBoldJson(cfg, parameters)" + "createJson(cfg, parameters)" ] }, { "cell_type": "code", - "execution_count": 14, + "execution_count": 15, "metadata": {}, "outputs": [ { @@ -382,43 +405,7 @@ " \"RepetitionTime\": [],\r\n", " \"SliceTiming\": [],\r\n", " \"TaskDescription\": \"\",\r\n", - " \"TaskName\": \"test Task\",\r\n", - " \"timing\": {\r\n", - " \"IBI\": 5.4,\r\n", - " \"ISI\": 0.1,\r\n", - " \"onsetDelay\": 0.1,\r\n", - " \"endDelay\": 0.1,\r\n", - " \"eventDuration\": 0.8\r\n", - " },\r\n", - " \"dot\": {\r\n", - " \"speed\": 30,\r\n", - " \"coherence\": 1,\r\n", - " \"density\": 0.1,\r\n", - " \"lifeTime\": 10,\r\n", - " \"proportionKilledPerFrame\": 0,\r\n", - " \"size\": 1\r\n", - " }\r\n", - "}{\r\n", - " \"Instructions\": \"\",\r\n", - " \"RepetitionTime\": [],\r\n", - " \"SliceTiming\": [],\r\n", - " \"TaskDescription\": \"\",\r\n", - " \"TaskName\": \"test Task\",\r\n", - " \"timing\": {\r\n", - " \"IBI\": 5.4,\r\n", - " \"ISI\": 0.1,\r\n", - " \"onsetDelay\": 0.1,\r\n", - " \"endDelay\": 0.1,\r\n", - " \"eventDuration\": 0.8\r\n", - " },\r\n", - " \"dot\": {\r\n", - " \"speed\": 30,\r\n", - " \"coherence\": 1,\r\n", - " \"density\": 0.1,\r\n", - " \"lifeTime\": 10,\r\n", - " \"proportionKilledPerFrame\": 0,\r\n", - " \"size\": 1\r\n", - " }\r\n", + " \"TaskName\": \"test Task\"\r\n", "}\n" ] } @@ -438,7 +425,7 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": 18, "metadata": {}, "outputs": [ { @@ -446,8 +433,17 @@ "output_type": "stream", "text": [ "onset\tduration\ttrial_type\ttarget_position\ttarget_type\n", - "2.000000\t1.000000\tmotion_up\tleft\taudio\t\n", - "6.000000\t1.200000\tstatic\tright\tvisual\t\n" + "ans = 2\n", + "2.000000\tans = 1\n", + "1.000000\tmotion_up\tleft\taudio\t\n", + "ans = 6\n", + "6.000000\tans = 1.2000\n", + "1.200000\tstatic\tright\tvisual\t\n", + "\n", + "Data were saved in this file:\n", + "\n", + "/home/remi/github/CPP_BIDS/notebooks/output/source/sub-001/ses-001/func/sub-001_ses-001_task-testTask_run-001_events_date-202011171307.tsv\n", + "\n" ] } ], @@ -455,6 +451,7 @@ "\n", "logFile.extraColumns = {'target_position', 'target_type'};\n", "\n", + "logFile = saveEventsFile('init', cfg, logFile);\n", "logFile = saveEventsFile('open', cfg, logFile);\n", "\n", "logFile(1,1).onset = 2;\n", @@ -476,7 +473,7 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": 53, "metadata": { "scrolled": false }, @@ -485,46 +482,22 @@ "name": "stdout", "output_type": "stream", "text": [ - "\u001b[01;34m.\u001b[00m\r\n", - "├── basic_usage.ipynb\r\n", - "├── creating_BIDS_dataset.ipynb\r\n", - "├── more_on_saving.ipynb\r\n", - "├── octave-workspace\r\n", - "├── \u001b[01;34moutput\u001b[00m\r\n", - "│   ├── \u001b[01;34mrawdata\u001b[00m\r\n", - "│   │   ├── CHANGES\r\n", - "│   │   ├── dataset_description.json\r\n", - "│   │   ├── README\r\n", - "│   │   └── \u001b[01;34msub-001\u001b[00m\r\n", - "│   │   └── \u001b[01;34mses-001\u001b[00m\r\n", - "│   │   └── \u001b[01;34mfunc\u001b[00m\r\n", - "│   │   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_bold.json\r\n", - "│   │   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events.json\r\n", - "│   │   └── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events.tsv\r\n", - "│   └── \u001b[01;34msource\u001b[00m\r\n", - "│   ├── CHANGES\r\n", - "│   ├── dataset_description.json\r\n", - "│   ├── README\r\n", - "│   └── \u001b[01;34msub-001\u001b[00m\r\n", - "│   └── \u001b[01;34mses-001\u001b[00m\r\n", - "│   └── \u001b[01;34mfunc\u001b[00m\r\n", - "│   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_bold_date-202008090023.json\r\n", - "│   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_bold_date-202008142237.json\r\n", - "│   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008090023.json\r\n", - "│   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008090023.tsv\r\n", - "│   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008142237.json\r\n", - "│   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008142237.tsv\r\n", - "│   ├── sub-001_ses-001_task-testTask_run-001_events_date-202008142236.json\r\n", - "│   └── sub-001_ses-001_task-testTask_run-001_events_date-202008142236.tsv\r\n", - "└── README.md\r\n", + "\u001b[01;34moutput\u001b[00m\r\n", + "└── \u001b[01;34msource\u001b[00m\r\n", + " ├── dataset_description.json\r\n", + " └── \u001b[01;34msub-001\u001b[00m\r\n", + " └── \u001b[01;34mses-001\u001b[00m\r\n", + " └── \u001b[01;34mfunc\u001b[00m\r\n", + " ├── sub-001_ses-001_task-testTask_run-001_bold_date-202011171530.json\r\n", + " └── sub-001_ses-001_task-testTask_run-001_bold_date-202011171531.json\r\n", "\r\n", - "9 directories, 22 files\r\n", + "4 directories, 3 files\r\n", "\n" ] } ], "source": [ - "!tree" + "!tree output" ] }, { @@ -540,7 +513,7 @@ }, { "cell_type": "code", - "execution_count": 17, + "execution_count": 20, "metadata": {}, "outputs": [], "source": [ @@ -549,7 +522,7 @@ }, { "cell_type": "code", - "execution_count": 18, + "execution_count": 21, "metadata": {}, "outputs": [ { @@ -559,34 +532,17 @@ "\u001b[01;34m.\u001b[00m\r\n", "├── basic_usage.ipynb\r\n", "├── creating_BIDS_dataset.ipynb\r\n", - "├── more_on_saving.ipynb\r\n", - "├── octave-workspace\r\n", "├── \u001b[01;34moutput\u001b[00m\r\n", - "│   ├── \u001b[01;34mrawdata\u001b[00m\r\n", + "│   ├── \u001b[01;34mraw\u001b[00m\r\n", "│   │   ├── CHANGES\r\n", "│   │   ├── dataset_description.json\r\n", "│   │   ├── README\r\n", - "│   │   ├── \u001b[01;34msource\u001b[00m\r\n", - "│   │   │   ├── CHANGES\r\n", - "│   │   │   ├── dataset_description.json\r\n", - "│   │   │   ├── README\r\n", - "│   │   │   └── \u001b[01;34msub-001\u001b[00m\r\n", - "│   │   │   └── \u001b[01;34mses-001\u001b[00m\r\n", - "│   │   │   └── \u001b[01;34mfunc\u001b[00m\r\n", - "│   │   │   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_bold_date-202008090023.json\r\n", - "│   │   │   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_bold_date-202008142237.json\r\n", - "│   │   │   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008090023.json\r\n", - "│   │   │   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008090023.tsv\r\n", - "│   │   │   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008142237.json\r\n", - "│   │   │   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008142237.tsv\r\n", - "│   │   │   ├── sub-001_ses-001_task-testTask_run-001_events_date-202008142236.json\r\n", - "│   │   │   └── sub-001_ses-001_task-testTask_run-001_events_date-202008142236.tsv\r\n", "│   │   └── \u001b[01;34msub-001\u001b[00m\r\n", "│   │   └── \u001b[01;34mses-001\u001b[00m\r\n", "│   │   └── \u001b[01;34mfunc\u001b[00m\r\n", - "│   │   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_bold.json\r\n", - "│   │   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events.json\r\n", - "│   │   └── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events.tsv\r\n", + "│   │   ├── sub-001_ses-001_task-testTask_run-001_bold.json\r\n", + "│   │   ├── sub-001_ses-001_task-testTask_run-001_events.json\r\n", + "│   │   └── sub-001_ses-001_task-testTask_run-001_events.tsv\r\n", "│   └── \u001b[01;34msource\u001b[00m\r\n", "│   ├── CHANGES\r\n", "│   ├── dataset_description.json\r\n", @@ -594,17 +550,15 @@ "│   └── \u001b[01;34msub-001\u001b[00m\r\n", "│   └── \u001b[01;34mses-001\u001b[00m\r\n", "│   └── \u001b[01;34mfunc\u001b[00m\r\n", - "│   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_bold_date-202008090023.json\r\n", - "│   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_bold_date-202008142237.json\r\n", - "│   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008090023.json\r\n", - "│   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008090023.tsv\r\n", - "│   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008142237.json\r\n", - "│   ├── sub-001_ses-001_task-testTask_acq-slow_rec-fast_run-001_echo-1_events_date-202008142237.tsv\r\n", - "│   ├── sub-001_ses-001_task-testTask_run-001_events_date-202008142236.json\r\n", - "│   └── sub-001_ses-001_task-testTask_run-001_events_date-202008142236.tsv\r\n", - "└── README.md\r\n", + "│   ├── sub-001_ses-001_task-testTask_run-001_bold_date-202011171307.json\r\n", + "│   ├── sub-001_ses-001_task-testTask_run-001_events_date-202011171307.json\r\n", + "│   └── sub-001_ses-001_task-testTask_run-001_events_date-202011171307.tsv\r\n", + "├── README.md\r\n", + "├── saving_arrays.ipynb\r\n", + "├── saving_stim_files.ipynb\r\n", + "└── using_2_logfiles.ipynb\r\n", "\r\n", - "13 directories, 33 files\r\n", + "9 directories, 18 files\r\n", "\n" ] } diff --git a/notebooks/demo_1_IoNS YRD_20201118.ipynb b/notebooks/demo_1_IoNS YRD_20201118.ipynb new file mode 100644 index 00000000..97b94de0 --- /dev/null +++ b/notebooks/demo_1_IoNS YRD_20201118.ipynb @@ -0,0 +1,179 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# CPP BIDS: quick demo 1" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "% add the relevant functions from the source and library folder\n", + "addpath(genpath(fullfile(pwd, '..', 'src')))\n", + "addpath(genpath(fullfile(pwd, '..', 'lib')))" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Simplest case: behavioral experiment" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Set up" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "scrolled": true + }, + "outputs": [], + "source": [ + "% clean up\n", + "clear cfg logFile\n", + "rmdir(fullfile(pwd, 'new_experiment'), 's');\n", + "\n", + "% Define where to save things, subject and run number, task name\n", + "cfg.dir.output = fullfile(pwd, 'new_experiment'); \n", + "\n", + "cfg.subject.subjectNb = 1;\n", + "cfg.subject.runNb = 1;\n", + "\n", + "cfg.task.name = 'test task';\n", + "\n", + "% to print some output to the prompt\n", + "cfg.verbose = 1;\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Initialize the output files" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "cfg = createFilename(cfg);\n", + "logFile = saveEventsFile('init', cfg);\n", + "logFile = saveEventsFile('open', cfg, logFile);" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Add content to the outpute file\n", + "\n", + "Append content to `logFile` and then save it." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "logFile(1, 1).onset = 2;\n", + "logFile(1, 1).trial_type = 'target';\n", + "logFile(1, 1).duration = 0.25;\n", + "\n", + "logFile(2, 1).onset = 5;\n", + "logFile(2, 1).trial_type = 'no_target';\n", + "logFile(2, 1).duration = 0.36;\n", + "\n", + "logFile = saveEventsFile('save', cfg, logFile);\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "% close the file\n", + "saveEventsFile('close', cfg, logFile);" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### check the output" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "scrolled": true + }, + "outputs": [], + "source": [ + "!tree new_experiment" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "!cat new_experiment/source/sub-001/ses-001/beh/sub-001_ses-001_task-testTask_run-001_events_date-*.tsv" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "!cat new_experiment/source/sub-001/ses-001/beh/sub-001_ses-001_task-testTask_run-001_events_date-*.json" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Octave", + "language": "octave", + "name": "octave" + }, + "language_info": { + "file_extension": ".m", + "help_links": [ + { + "text": "GNU Octave", + "url": "https://www.gnu.org/software/octave/support.html" + }, + { + "text": "Octave Kernel", + "url": "https://github.com/Calysto/octave_kernel" + }, + { + "text": "MetaKernel Magics", + "url": "https://metakernel.readthedocs.io/en/latest/source/README.html" + } + ], + "mimetype": "text/x-octave", + "name": "octave", + "version": "4.2.2" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/notebooks/demo_2_IoNS YRD_20201118.ipynb b/notebooks/demo_2_IoNS YRD_20201118.ipynb new file mode 100644 index 00000000..ee21c112 --- /dev/null +++ b/notebooks/demo_2_IoNS YRD_20201118.ipynb @@ -0,0 +1,325 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# CPP BIDS: quick demo 2" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "% add the relevant functions from the source and library folder\n", + "addpath(genpath(fullfile(pwd, '..', 'src')))\n", + "addpath(genpath(fullfile(pwd, '..', 'lib')))" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# fMRI experiment with eyetracking" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Set up" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "scrolled": true + }, + "outputs": [], + "source": [ + "% clean up\n", + "clear cfg logFile\n", + "\n", + "% Define where to save things, subject and run number, task name\n", + "cfg.dir.output = fullfile(pwd, 'new_experiment'); \n", + "\n", + "cfg.subject.subjectNb = 1;\n", + "cfg.subject.runNb = 1;\n", + "\n", + "cfg.task.name = 'test task';\n", + "\n", + "cfg.testingDevice = 'mri';\n", + "\n", + "cfg.eyeTracker.do = 1;\n", + "\n", + "% to print some output to the prompt\n", + "cfg.verbose = 1;\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Additional details about the experiment " + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "% other information to save in the TSV file\n", + "logFile.extraColumns = {'target_position', 'target_type'};\n", + "\n", + "% Time between events in seconds\n", + "parameters.timing.ISI = 0.1;\n", + "\n", + "% Number of seconds before the stimuli are presented\n", + "parameters.timing.onsetDelay = .1;\n", + "\n", + "% Event duration\n", + "parameters.timing.eventDuration = 0.8;\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## fMRI details" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "cfg.mri.repetitionTime = 2.1;\n", + "\n", + "cfg.suffix.phaseEncodingDirection = 'AP';\n", + "cfg.suffix.reconstruction = 'MoCo';\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Initialize the output files" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "cfg = createFilename(cfg);\n", + "\n", + "logFile = saveEventsFile('init', cfg, logFile);\n", + "logFile = saveEventsFile('open', cfg, logFile);" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Save metadata" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "createJson(cfg, 'func', parameters)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "!tree new_experiment" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Add content to the outpute file" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "logFile(1,1).onset = 2;\n", + "logFile(1,1).trial_type = 'motion_up';\n", + "logFile(1,1).duration = 1;\n", + "logFile(1,1).target_position = 'left';\n", + "logFile(1,1).target_type = 'audio';\n", + "\n", + "logFile(2,1).onset = 6;\n", + "logFile(2,1).trial_type = 'static';\n", + "logFile(2,1).duration = 1.2;\n", + "logFile(2,1).target_position = 'right';\n", + "logFile(2,1).target_type = 'visual';\n", + "\n", + "logFile = saveEventsFile('save', cfg, logFile);" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "% close the file\n", + "saveEventsFile('close', cfg, logFile);" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Content of the `events.tsv` file" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "scrolled": true + }, + "outputs": [], + "source": [ + "!cat new_experiment/source/sub-001/ses-001/func/sub-001_ses-001_task-*events*.tsv" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Content of the data dictionary `events.json` file" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "!cat new_experiment/source/sub-001/ses-001/func/sub-001_ses-001_task-*events*.json" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Content of the metadata `bold.json` file" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "scrolled": true + }, + "outputs": [], + "source": [ + "!cat new_experiment/source/sub-001/ses-001/func/sub-001_ses-001_task-*bold*.json" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Convert to a BIDS dataset" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Create a dataset description" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "scrolled": true + }, + "outputs": [], + "source": [ + "cfg.bids.datasetDescription.Name = 'A new BIDS dataset';\n", + "cfg.bids.datasetDescription.BIDSVersion = '1.3';\n", + "cfg.bids.datasetDescription.License = 'CC-BY';\n", + "cfg.bids.datasetDescription.Authors = {'IONS YRD 2020'};\n", + "cfg.bids.datasetDescription.Acknowledgements = '';\n", + "cfg.bids.datasetDescription.HowToAcknowledge = '';\n", + "cfg.bids.datasetDescription.Funding = {''};\n", + "cfg.bids.datasetDescription.ReferencesAndLinks = {''};\n", + "cfg.bids.datasetDescription.DatasetDOI = '';\n", + "\n", + "[cfg] = createFilename(cfg);\n", + "createDatasetDescription(cfg)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "convertSourceToRaw(cfg)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "!tree new_experiment" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Octave", + "language": "octave", + "name": "octave" + }, + "language_info": { + "file_extension": ".m", + "help_links": [ + { + "text": "GNU Octave", + "url": "https://www.gnu.org/software/octave/support.html" + }, + { + "text": "Octave Kernel", + "url": "https://github.com/Calysto/octave_kernel" + }, + { + "text": "MetaKernel Magics", + "url": "https://metakernel.readthedocs.io/en/latest/source/README.html" + } + ], + "mimetype": "text/x-octave", + "name": "octave", + "version": "4.2.2" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/notebooks/more_on_saving.ipynb b/notebooks/saving_arrays.ipynb similarity index 76% rename from notebooks/more_on_saving.ipynb rename to notebooks/saving_arrays.ipynb index b3c25aea..c3cb9fd0 100644 --- a/notebooks/more_on_saving.ipynb +++ b/notebooks/saving_arrays.ipynb @@ -4,17 +4,22 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "## Saving arrays in the tsv file" + "## Saving arrays in the tsv file\n", + "\n", + "It is possible to save several values at once in a tsv file." ] }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 16, "metadata": {}, "outputs": [], "source": [ + "clear cfg logFile\n", + "\n", "% add the relevant functions from the src folder\n", - "addpath(genpath(fullfile(pwd, '..', 'src')));\n", + "addpath(genpath(fullfile(pwd, '..', 'src')))\n", + "addpath(genpath(fullfile(pwd, '..', 'lib')))\n", "\n", "cfg.dir.output = fullfile(pwd, 'output');\n", "\n", @@ -25,7 +30,7 @@ "\n", "cfg.testingDevice = 'mri';\n", "\n", - "cfg.verbose = false;\n", + "cfg.verbose = 1;\n", "\n", "[cfg] = createFilename(cfg);\n", "\n", @@ -41,24 +46,7 @@ }, { "cell_type": "code", - "execution_count": 10, - "metadata": {}, - "outputs": [], - "source": [ - "logFile.extraColumns.target_position.length = 2;\n", - "logFile.extraColumns.target_type.length = 1;" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Note that it is also possible to directly open the file: things will be intialised automatically." - ] - }, - { - "cell_type": "code", - "execution_count": 11, + "execution_count": 23, "metadata": {}, "outputs": [ { @@ -70,6 +58,10 @@ } ], "source": [ + "logFile.extraColumns.target_position.length = 2;\n", + "logFile.extraColumns.target_type.length = 1;\n", + "\n", + "logFile = saveEventsFile('init', cfg, logFile);\n", "logFile = saveEventsFile('open', cfg, logFile);" ] }, @@ -82,7 +74,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 18, "metadata": { "scrolled": true }, @@ -91,7 +83,16 @@ "name": "stdout", "output_type": "stream", "text": [ - "2.000000\t1.000000\tmotion_up\tn/a\tn/a\tn/a\t2.000000\t1.000000\tvisual\t\r\n" + "ans = 2\r\n", + "ans = 1\r\n", + "ans = 2\r\n", + "ans = 1\r\n", + "\r\n", + "ans = 4\r\n", + "ans = 1\r\n", + "ans = 2\r\n", + "ans = 1\r\n", + "\r\n" ] } ], @@ -99,16 +100,16 @@ "% Trial one : missing duration value\n", "logFile(1,1).onset = 2;\n", "logFile(1,1).trial_type = 'motion_up';\n", - "logFile(1,1).duration = [];\n", + "logFile(1,1).duration = 1;\n", "logFile(1,1).target_position = [2, 1];\n", "logFile(1,1).target_type = 'visual';\n", "\n", "% Trial two\n", - "logFile(1,1).onset = 2;\n", - "logFile(1,1).trial_type = 'motion_up';\n", - "logFile(1,1).duration = 1;\n", - "logFile(1,1).target_position = [2, 1];\n", - "logFile(1,1).target_type = 'visual';\n", + "logFile(2,1).onset = 4;\n", + "logFile(2,1).trial_type = 'motion_up';\n", + "logFile(2,1).duration = 1;\n", + "logFile(2,1).target_position = [2, 1];\n", + "logFile(2,1).target_type = 'visual';\n", "\n", "logFile = saveEventsFile('save', cfg, logFile);" ] @@ -122,7 +123,7 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": 19, "metadata": {}, "outputs": [ { @@ -131,11 +132,14 @@ "text": [ "warning: Missing some target_position data for this event.\r\n", "warning: called from\r\n", - " saveEventsFile>checkExtracolumns at line 219 column 13\r\n", - " saveEventsFile>checklLogFile at line 140 column 21\r\n", - " saveEventsFile>saveToLogFile at line 282 column 17\r\n", - " saveEventsFile at line 90 column 21\r\n", - "6.000000\t1.200000\tstatic\tn/a\tn/a\tn/a\t3.000000\tn/a\taudio\t\r\n" + " saveEventsFile>checkExtracolumns at line 288 column 13\r\n", + " saveEventsFile>checklLogFile at line 173 column 21\r\n", + " saveEventsFile>saveToLogFile at line 351 column 17\r\n", + " saveEventsFile at line 123 column 21\r\n", + "ans = 6\r\n", + "ans = 1.2000\r\n", + "ans = 3\r\n", + "\r\n" ] } ], @@ -159,7 +163,7 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": 20, "metadata": {}, "outputs": [ { @@ -168,12 +172,16 @@ "text": [ "warning: A field for this event is longer than expected. Truncating the extra values.\r\n", "warning: called from\r\n", - " saveEventsFile>nanPadding at line 269 column 9\r\n", - " saveEventsFile>checkExtracolumns at line 214 column 14\r\n", - " saveEventsFile>checklLogFile at line 140 column 21\r\n", - " saveEventsFile>saveToLogFile at line 282 column 17\r\n", - " saveEventsFile at line 90 column 21\r\n", - "6.000000\t1.200000\tstatic\tn/a\tn/a\tn/a\t3.000000\t4.000000\ttouch\t\r\n" + " saveEventsFile>nanPadding at line 338 column 9\r\n", + " saveEventsFile>checkExtracolumns at line 283 column 14\r\n", + " saveEventsFile>checklLogFile at line 173 column 21\r\n", + " saveEventsFile>saveToLogFile at line 351 column 17\r\n", + " saveEventsFile at line 123 column 21\r\n", + "ans = 6\r\n", + "ans = 1.2000\r\n", + "ans = 3\r\n", + "ans = 4\r\n", + "\r\n" ] } ], @@ -190,7 +198,7 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": 21, "metadata": {}, "outputs": [ { @@ -200,7 +208,7 @@ "\r\n", "Data were saved in this file:\r\n", "\r\n", - "/home/remi/github/CPP_BIDS/notebooks/output/source/sub-001/ses-001/func/sub-001_ses-001_task-testTask_run-001_events_date-202008142241.tsv\r\n", + "/home/remi/github/CPP_BIDS/notebooks/output/source/sub-001/ses-001/func/sub-001_ses-001_task-testTask_run-001_events_date-202011171253.tsv\r\n", "\r\n" ] } @@ -222,7 +230,7 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": 22, "metadata": {}, "outputs": [ { @@ -245,15 +253,9 @@ "logFile.extraColumns.Speed.length = 12;\n", "\n", "% open the file\n", + "logFile = saveEventsFile('init', cfg, logFile);\n", "logFile = saveEventsFile('open', cfg, logFile);\n" ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Saving `_stim.tsv` files" - ] } ], "metadata": { diff --git a/notebooks/saving_stim_files.ipynb b/notebooks/saving_stim_files.ipynb new file mode 100644 index 00000000..320f0829 --- /dev/null +++ b/notebooks/saving_stim_files.ipynb @@ -0,0 +1,47 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Saving `_stim.tsv` files" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Octave", + "language": "octave", + "name": "octave" + }, + "language_info": { + "file_extension": ".m", + "help_links": [ + { + "text": "GNU Octave", + "url": "https://www.gnu.org/software/octave/support.html" + }, + { + "text": "Octave Kernel", + "url": "https://github.com/Calysto/octave_kernel" + }, + { + "text": "MetaKernel Magics", + "url": "https://metakernel.readthedocs.io/en/latest/source/README.html" + } + ], + "mimetype": "text/x-octave", + "name": "octave", + "version": "4.2.2" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/notebooks/using_2_logfiles.ipynb b/notebooks/using_2_logfiles.ipynb index 77f76f4d..ef29eddb 100644 --- a/notebooks/using_2_logfiles.ipynb +++ b/notebooks/using_2_logfiles.ipynb @@ -4,7 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# saving two `_events.tsv` for the same run\n", + "# Saving two `_events.tsv` for the same run\n", "\n", "This won't create BIDS valid output but this might help you organize some of your output in different TSV files.\n", "\n" @@ -17,18 +17,15 @@ "outputs": [], "source": [ "% add the relevant functions from the src folder\n", - "addpath(genpath(fullfile(pwd, '..', 'src')));\n", + "addpath(genpath(fullfile(pwd, '..', 'src')))\n", + "addpath(genpath(fullfile(pwd, '..', 'lib')))\n", "\n", "cfg.dir.output = fullfile(pwd, 'output');\n", "\n", "cfg.task.name = 'test task';\n", "\n", "cfg.subject.subjectNb = 1;\n", - "cfg.subject.runNb = 1;\n", - "\n", - "cfg.testingDevice = 'pc';\n", - "\n", - "cfg.verbose = true;" + "cfg.subject.runNb = 1;" ] }, { @@ -50,11 +47,34 @@ "output_type": "stream", "text": [ "\r\n", - "Data will be saved in this directory:\r\n", - "\t/home/remi/github/CPP_BIDS/notebooks/output/source/sub-001/ses-001/beh\r\n", "\r\n", - "Data will be saved in this file:\r\n", - "\tsub-001_ses-001_task-testTask_run-001_events_date-202010191603.tsv\r\n" + "___________________________________________________\r\n", + "___________________________________________________\r\n", + " \r\n", + " ___ ___ ___ ___ ___ ___ ___ \r\n", + " / __| _ \\ _ \\ | _ )_ _| \\/ __|\r\n", + " | (__| _/ _/ | _ \\| || |) \\__ \\\r\n", + " \\___|_| |_| |___/___|___/|___/\r\n", + " \r\n", + "Thank you for using the CPP BIDS - version v1.0.0. \r\n", + "\r\n", + "Current list of contributors includes:\r\n", + " Rémi Gau\r\n", + " Marco Barilari\r\n", + " Ceren Battal\r\n", + " Tomas Lenc\r\n", + "\b\r\n", + "\r\n", + "Please cite using the following DOI: \r\n", + " https://doi.org/10.5281/zenodo.4007674\r\n", + "\r\n", + "For bug report, suggestions or contributions see: \r\n", + " https://github.com/cpp-lln-lab/CPP_BIDS\r\n", + "\r\n", + "___________________________________________________\r\n", + "___________________________________________________\r\n", + "\r\n", + "\r\n" ] } ], @@ -77,6 +97,7 @@ } ], "source": [ + "logFile = saveEventsFile('init', cfg, logFile);\n", "logFile = saveEventsFile('open', cfg, logFile);" ] }, @@ -91,20 +112,7 @@ "cell_type": "code", "execution_count": 4, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\r\n", - "Data will be saved in this directory:\r\n", - "\t/home/remi/github/CPP_BIDS/notebooks/output/source/sub-001/ses-001/beh\r\n", - "\r\n", - "Data will be saved in this file:\r\n", - "\tsub-001_ses-001_task-testTask_acq-extraInfo_run-001_events_date-202010191603.tsv\r\n" - ] - } - ], + "outputs": [], "source": [ "% we use a copy of the configuration and we modify the 'acq' field in the BIDS naming convention\n", "cfg_2 = cfg;\n", @@ -128,6 +136,7 @@ } ], "source": [ + "logFile_2 = saveEventsFile('init', cfg_2, logFile_2);\n", "logFile_2 = saveEventsFile('open', cfg_2, logFile_2);\n", "clear cfg2 % we don't need it anymore as this was only need to create the new filename" ] @@ -150,12 +159,22 @@ "name": "stdout", "output_type": "stream", "text": [ - "2.000000\t0.500000\tmotion_up\t2.000000\tvisual\t\n", - "3.000000\t1.000000\tmotion_down\t1.000000\tvisual\t\n", + "ans = 2\n", + "ans = 0.50000\n", + "ans = 2\n", + "\n", + "ans = 3\n", + "ans = 1\n", + "ans = 1\n", "\n", "\n", - "2.000000\t0.500000\tmotion_up\tred\t\n", - "3.000000\t1.000000\tmotion_down\tblue\t\n" + "\n", + "ans = 2\n", + "ans = 0.50000\n", + "\n", + "ans = 3\n", + "ans = 1\n", + "\n" ] } ], @@ -198,24 +217,7 @@ "cell_type": "code", "execution_count": 7, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\n", - "Data were saved in this file:\n", - "\n", - "/home/remi/github/CPP_BIDS/notebooks/output/source/sub-001/ses-001/beh/sub-001_ses-001_task-testTask_run-001_events_date-202010191603.tsv\n", - "\n", - "\n", - "Data were saved in this file:\n", - "\n", - "/home/remi/github/CPP_BIDS/notebooks/output/source/sub-001/ses-001/beh/sub-001_ses-001_task-testTask_acq-extraInfo_run-001_events_date-202010191603.tsv\n", - "\n" - ] - } - ], + "outputs": [], "source": [ "saveEventsFile('close', cfg, logFile);\n", "saveEventsFile('close', cfg, logFile_2);" diff --git a/src/utils/checkCppBidsDependencies.m b/src/utils/checkCppBidsDependencies.m index 88cd1833..1bb82894 100644 --- a/src/utils/checkCppBidsDependencies.m +++ b/src/utils/checkCppBidsDependencies.m @@ -16,21 +16,23 @@ function checkCppBidsDependencies(cfg) if strcmp(GITHUB_WORKSPACE, '/github/workspace') pth = GITHUB_WORKSPACE; - addpath(fullfile(pth, 'lib', 'JSONio')); - addpath(fullfile(pth, 'lib', 'bids-matlab')); + addpath(genpath(fullfile(pth, 'lib'))); elseif isempty(GITHUB_WORKSPACE) % local pth = fullfile(fileparts(mfilename('fullpath')), '..', '..'); + addpath(fullfile(pth, 'lib', 'utils')); + + pth = fullfile(fileparts(mfilename('fullpath')), '..', '..'); + pth = abspath(pth); + checkSubmodule(fullfile(pth, 'lib', 'JSONio')); checkSubmodule(fullfile(pth, 'lib', 'bids-matlab')); - addpath(fullfile(pth, 'src', 'subfun')); + addpath(genpath(fullfile(pth, 'src'))); end - addpath(fullfile(pth, 'lib', 'utils')); - printCreditsCppBids(cfg); end diff --git a/src/utils/printCreditsCppBids.m b/src/utils/printCreditsCppBids.m index 46209414..e7547ce0 100644 --- a/src/utils/printCreditsCppBids.m +++ b/src/utils/printCreditsCppBids.m @@ -30,8 +30,9 @@ function printCreditsCppBids(cfg) contributors = { ... 'Rémi Gau', ... 'Marco Barilari', ... - 'Ceren Battal'}; - + 'Ceren Battal', ... + 'Tomas Lenc'}; + DOI_URL = 'https://doi.org/10.5281/zenodo.4007674'; repoURL = 'https://github.com/cpp-lln-lab/CPP_BIDS'; diff --git a/src/utils/utilsForTests/setUp.m b/src/utils/utilsForTests/setUp.m index 0f7cf9eb..ec282c03 100644 --- a/src/utils/utilsForTests/setUp.m +++ b/src/utils/utilsForTests/setUp.m @@ -2,7 +2,7 @@ function [cfg, logFile] = setUp() - cfg.verbose = true; + cfg.verbose = 2; cfg.subject.subjectNb = 1; cfg.subject.runNb = 1;