Merge pull request #70 from Remi-Gau/remi-tesing_20210303

[ENH] post tesing 20210303 update

Author: Remi-Gau

.all-contributorsrc

@@ -0,0 +1,71 @@
+{
+  "files": [
+    "README.md"
+  ],
+  "imageSize": 100,
+  "commit": false,
+  "contributors": [
+    {
+      "login": "mohmdrezk",
+      "name": "Mohamed Rezk",
+      "avatar_url": "https://avatars2.githubusercontent.com/u/9597815?v=4",
+      "profile": "https://github.com/mohmdrezk",
+      "contributions": [
+        "code",
+        "design",
+        "ideas"
+      ]
+    },
+    {
+      "login": "marcobarilari",
+      "name": "marcobarilari",
+      "avatar_url": "https://avatars3.githubusercontent.com/u/38101692?v=4",
+      "profile": "https://github.com/marcobarilari",
+      "contributions": [
+        "code",
+        "design",
+        "ideas",
+        "bug",
+        "userTesting",
+        "review",
+        "question",
+        "infra",
+        "maintenance"
+      ]
+    },
+    {
+      "login": "Remi-Gau",
+      "name": "Remi Gau",
+      "avatar_url": "https://avatars3.githubusercontent.com/u/6961185?v=4",
+      "profile": "https://remi-gau.github.io/",
+      "contributions": [
+        "code",
+        "design",
+        "ideas",
+        "bug",
+        "userTesting",
+        "review",
+        "question",
+        "infra",
+        "maintenance"
+      ]
+    },
+    {
+      "login": "CerenB",
+      "name": "CerenB",
+      "avatar_url": "https://avatars1.githubusercontent.com/u/10451654?v=4",
+      "profile": "https://github.com/CerenB",
+      "contributions": [
+        "bug",
+        "userTesting"
+      ]
+    }
+  ],
+  "contributorsPerLine": 7,
+  "projectName": "localizer_visual_motion",
+  "projectOwner": "cpp-lln-lab",
+  "repoType": "github",
+  "repoHost": "https://github.com",
+  "skipCi": false
+  "contributorsSortAlphabetically": true
+}

README.md

@@ -1,4 +1,7 @@
 [![](https://img.shields.io/badge/Octave-CI-blue?logo=Octave&logoColor=white)](https://github.com/cpp-lln-lab/localizer_visual_motion/actions)
+<!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
+[![All Contributors](https://img.shields.io/badge/all_contributors-4-orange.svg?style=flat-square)](#contributors-)
+<!-- ALL-CONTRIBUTORS-BADGE:END -->
 ![](https://github.com/cpp-lln-lab/localizer_visual_motion/workflows/CI/badge.svg)
 
 [![codecov](https://codecov.io/gh/cpp-lln-lab/localizer_visual_motion/branch/master/graph/badge.svg)](https://codecov.io/gh/cpp-lln-lab/localizer_visual_motion)
@@ -143,3 +146,25 @@ The `numEventsPerBlock` should be a multiple of the number of "base" listed in t
   - `-1` indicates static
 - `expParameters.designSpeeds` is an array `(nr_blocks, numEventsPerBlock) * speedEvent`
 - `expParameters.designFixationTargets` is an array `(nr_blocks, numEventsPerBlock)` showing for each event if it should be accompanied by a target
+
+## Contributors ✨
+
+Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)):
+
+<!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
+<!-- prettier-ignore-start -->
+<!-- markdownlint-disable -->
+<table>
+  <tr>
+    <td align="center"><a href="https://github.com/mohmdrezk"><img src="https://avatars2.githubusercontent.com/u/9597815?v=4" width="100px;" alt=""/><br /><sub><b>Mohamed Rezk</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/localizer_visual_motion/commits?author=mohmdrezk" title="Code">💻</a> <a href="#design-mohmdrezk" title="Design">🎨</a> <a href="#ideas-mohmdrezk" title="Ideas, Planning, & Feedback">🤔</a></td>
+    <td align="center"><a href="https://github.com/marcobarilari"><img src="https://avatars3.githubusercontent.com/u/38101692?v=4" width="100px;" alt=""/><br /><sub><b>marcobarilari</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/localizer_visual_motion/commits?author=marcobarilari" title="Code">💻</a> <a href="#design-marcobarilari" title="Design">🎨</a> <a href="#ideas-marcobarilari" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/cpp-lln-lab/localizer_visual_motion/issues?q=author%3Amarcobarilari" title="Bug reports">🐛</a> <a href="#userTesting-marcobarilari" title="User Testing">📓</a> <a href="https://github.com/cpp-lln-lab/localizer_visual_motion/pulls?q=is%3Apr+reviewed-by%3Amarcobarilari" title="Reviewed Pull Requests">👀</a> <a href="#question-marcobarilari" title="Answering Questions">💬</a> <a href="#infra-marcobarilari" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#maintenance-marcobarilari" title="Maintenance">🚧</a></td>
+    <td align="center"><a href="https://remi-gau.github.io/"><img src="https://avatars3.githubusercontent.com/u/6961185?v=4" width="100px;" alt=""/><br /><sub><b>Remi Gau</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/localizer_visual_motion/commits?author=Remi-Gau" title="Code">💻</a> <a href="#design-Remi-Gau" title="Design">🎨</a> <a href="#ideas-Remi-Gau" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/cpp-lln-lab/localizer_visual_motion/issues?q=author%3ARemi-Gau" title="Bug reports">🐛</a> <a href="#userTesting-Remi-Gau" title="User Testing">📓</a> <a href="https://github.com/cpp-lln-lab/localizer_visual_motion/pulls?q=is%3Apr+reviewed-by%3ARemi-Gau" title="Reviewed Pull Requests">👀</a> <a href="#question-Remi-Gau" title="Answering Questions">💬</a> <a href="#infra-Remi-Gau" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#maintenance-Remi-Gau" title="Maintenance">🚧</a></td>
+    <td align="center"><a href="https://github.com/CerenB"><img src="https://avatars1.githubusercontent.com/u/10451654?v=4" width="100px;" alt=""/><br /><sub><b>CerenB</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/localizer_visual_motion/issues?q=author%3ACerenB" title="Bug reports">🐛</a> <a href="#userTesting-CerenB" title="User Testing">📓</a></td>
+  </tr>
+</table>
+
+<!-- markdownlint-enable -->
+<!-- prettier-ignore-end -->
+<!-- ALL-CONTRIBUTORS-LIST:END -->
+
+This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!

lib/CPP_BIDS

@@ -11,16 +11,15 @@
     % setParamters.m file is
     % change that if you want the data to be saved somewhere else
     cfg.dir.output = fullfile( ...
-                              fileparts(mfilename('fullpath')), '..', ...
-                              'output');
+                              fileparts(mfilename('fullpath')), 'output');
 
     %% Debug mode settings
 
     cfg.debug.do = false; % To test the script out of the scanner, skip PTB sync
     cfg.debug.smallWin = false; % To test on a part of the screen, change to 1
     cfg.debug.transpWin = false; % To test with trasparent full size screen
 
-    cfg.verbose = 2;
+    cfg.verbose = 1;
 
     %% Engine parameters
 
@@ -64,7 +63,7 @@
     % IBI
     % block length = (cfg.eventDuration + cfg.ISI) * cfg.design.nbEventsPerBlock
 
-    cfg.timing.eventDuration = 0.8; % second
+    cfg.timing.eventDuration = 0.6; % second
 
     % Time between blocs in secs
     cfg.timing.IBI = 0;
@@ -79,7 +78,7 @@
     if cfg.pacedByTriggers.do
 
         cfg.pacedByTriggers.quietMode = true;
-        cfg.pacedByTriggers.nbTriggers = 1;
+        cfg.pacedByTriggers.nbTriggers = 5;
 
         cfg.timing.eventDuration = cfg.mri.repetitionTime / 2 - 0.04; % second
 
@@ -103,7 +102,7 @@
     % Number of dots per visual angle square.
     cfg.dot.density = 1;
     % Dot life time in seconds
-    cfg.dot.lifeTime = .4;
+    cfg.dot.lifeTime = 0.4;
     % proportion of dots killed per frame
     cfg.dot.proportionKilledPerFrame = 0;
     % Dot Size (dot width) in visual angles.
@@ -136,7 +135,7 @@
 
     cfg.extraColumns = { ...
                         'direction', ...
-                        'speed', ...
+                        'speedDegVA', ...
                         'target', ...
                         'event', ...
                         'block', ...
@@ -167,7 +166,7 @@
 function cfg = setMRI(cfg)
     % letter sent by the trigger to sync stimulation and volume acquisition
     cfg.mri.triggerKey = 't';
-    cfg.mri.triggerNb = 1;
+    cfg.mri.triggerNb = 5;
 
     cfg.mri.repetitionTime = 1.8;
 

lib/CPP_PTB

@@ -16,15 +16,12 @@
     thisEvent.fixationPosition = thisFixation.fixation.xDisplacement;
     thisEvent.aperturePosition = cfg.aperture.xPos * sign(cfg.aperture.xPosPix);
 
-    % % this value should be in degrees / second in the log file
-    % % highlights that the way speed is passed around could be
-    % % simplified.
-    % %
-    % thisEvent.speed
-    % %
+    thisEvent = pixToDeg('speedPix', thisEvent, cfg);
+    thisEvent.speedDegVA = thisEvent.speedDegVA * cfg.screen.monitorRefresh;
 
     % Save the events txt logfile
     % we save event by event so we clear this variable every loop
+    thisEvent.isStim = logFile.isStim;
     thisEvent.fileID = logFile.fileID;
     thisEvent.extraColumns = logFile.extraColumns;
 

setParameters.m

@@ -10,7 +10,7 @@
     % set direction, speed of that event and if it is a target
     thisEvent.trial_type = cfg.design.blockNames{iBlock};
     thisEvent.direction = cfg.design.directions(iBlock, iEvent);
-    thisEvent.speed = cfg.design.speeds(iBlock, iEvent);
+    thisEvent.speedPix = cfg.design.speeds(iBlock, iEvent);
     thisEvent.target = cfg.design.fixationTargets(iBlock, iEvent);
 
     % If this frame shows a target we change the color of the cross

subfun/preSaveSetup.m

@@ -17,6 +17,7 @@ function saveResponsesAndTriggers(responseEvents, cfg, logFile, triggerString)
             end
         end
 
+        responseEvents(1).isStim = logFile.isStim;
         responseEvents(1).fileID = logFile.fileID;
         responseEvents(1).extraColumns = logFile.extraColumns;
         saveEventsFile('save', cfg, responseEvents);

subfun/preTrialSetup.m

@@ -42,6 +42,7 @@
 
     % Prepare for the output logfiles with all
     logFile.extraColumns = cfg.extraColumns;
+    logFile = saveEventsFile('init', cfg, logFile);
     logFile = saveEventsFile('open', cfg, logFile);
 
     % prepare textures