added confirmation box

README.rst

@@ -0,0 +1,92 @@
+********
+Charlie2
+********
+
+:Version: 2.0
+:Author: Samuel R. Mathias
+:Contact: samuel.mathias@yale.edu
+:Github: http://github.com/sammosummo/Charlie2/
+:License: MIT
+
+Introduction
+============
+
+Charlie2 is a free, open-source, cross-platform neurocognitive test battery written in
+Python, with a focus on extendability. It will be used to collect data for one of our
+lab projects, but may be used freely by others.
+
+What does it do?
+================
+
+Like its predecessor, Charlie2 runs neurocognitive tests. There are currently 9 tests in
+the battery, taking ~30 minutes to complete per proband. Each test has a docstring with
+citations; have a look in the `charlie2/tests` folder to see what is available.
+
+Notable features
+================
+
+* Since Charlie2 is written in Python, it is cross-platform. I have had success running
+  it on various platforms, from tablets running Windows 10 to Raspberry Pis.
+
+* Charlie2 works especially well on touchscreen devices.
+
+* Charlie2 has a GUI which allows the user to store/view proband metadata (e.g., their
+  age, sex, and miscellaneous notes made before or after testing), run tests
+  individually or in pre-defined batches, and back up data to a remote storage server
+  such as Google Drive.
+
+* Modifying or adding new tests to Charlie2 is quick, easy and Pythonic.
+
+* Data are recorded after each trial. This means that you have access to trial-specific
+  data rather than just the summary data. It also means that the tests are resumable;
+  that is, the progress of each proband is retained. This prevents a proband from
+  performing a test twice, and allows them to pick up where they left off, if a test
+  gets interrupted.
+
+* Summary statistics are automatically computed after a proband completes a test. All of
+  the data (summary and trial-specific) are stored within various formats, including
+  human-readable csv files and Python pickles.
+
+What's changed
+==============
+
+Charlie2 has an entirely new code base. Below are the most significant changes.
+
+* Charlie2 is written in/for Python 3.6 or greater. It does not work with Python 2, and
+  probably won't work with earlier versions of Python 3.
+
+* Rather than relying on command-line arguments, Charlie2 is GUI-based.
+
+* Most of the heavy lifting is done by PyQt5, not pygame, which is no longer a
+  dependency.
+
+* Questionnaires have been completely removed.
+
+What (still) doesn't work
+=========================
+
+* Charlie2 is not stand-alone.
+
+* Charlie2 is **not** currently a regular Python package, so isn't installable via
+  `pip`. This probably won't ever happen.
+
+Installation and usage
+======================
+
+Charlie is simply a collection of Python scripts. All functionality is accessed from a
+PyQt5 application which is launched via `main.py`. If this is not enough information for
+you, I recommend performing the following steps:
+
+1. Download and install Miniconda for your platform from here: https://repo.continuum.io/miniconda/
+
+2. Create a new conda environment called `Charlie2` and `activate` it.
+
+3. Run these commands:
+   ::
+      conda update conda
+      conda install pip pyqt pandas
+      pip install google-api-python-client oauth2client
+
+4. Download Charlie2: https://github.com/sammosummo/Charlie2/archive/master.zip
+
+5. `cd` to the directory you saved Charlie2 and run `python main.py`.

charlie2/_scratch/_geometry.py

@@ -1,9 +1,8 @@
-import numpy as np
-import matplotlib.pyplot as plt
-from scipy import interpolate
 import cmocean
+import matplotlib.pyplot as plt
+import numpy as np
 from matplotlib import cm
-
+from scipy import interpolate
 
 cmap = cm.ScalarMappable(cmap=cmocean.cm.phase)
 cmap.to_rgba([0., 0.5, 1.])

charlie2/_scratch/_intersection.py

@@ -1,5 +1,6 @@
-import numpy as np
 import matplotlib.pyplot as plt
+import numpy as np
+
 
 """
 Sukhbinder

charlie2/_scratch/commandline.py

@@ -5,6 +5,7 @@
 """
 import argparse
 from argparse import ArgumentParser
+
 from .recipes import str2bool
 
 

charlie2/_scratch/event_tester.py

@@ -1,4 +1,5 @@
 from sys import argv, exit
+
 from PyQt5.QtCore import Qt
 from PyQt5.QtWidgets import QApplication, QMainWindow, QWidget
 

charlie2/_scratch/make_vwm.py

@@ -1,9 +1,11 @@
-from charlie2.tools.recipes import get_vwm_stimuli
 import wave
-from tqdm import tqdm
 from os import listdir
 
-if __name__ == '__main__':
+from tqdm import tqdm
+
+from charlie2.tools.recipes import get_vwm_stimuli
+
+if __name__ == "__main__":
     # sequences = [item for sublist in get_vwm_stimuli("en") for item in sublist]
     # s = "/Users/smathias/Documents/Charlie2/charlie2/stimuli/audio/verbalworkingmemory"
     # for sequence in sequences:
@@ -23,20 +25,15 @@
     #     output.close()
     p = "/Users/smathias/Documents/Charlie2/charlie2/stimuli/audio/verbalworkingmemory/"
     s = "/Users/smathias/Documents/Charlie2/charlie2/stimuli/audio/common/silence.wav"
-    s = wave.open(s, 'rb')
-    for f in [f for f in listdir(p) if '.wav' in f]:
-        w = wave.open(p + f, 'rb')
+    s = wave.open(s, "rb")
+    for f in [f for f in listdir(p) if ".wav" in f]:
+        w = wave.open(p + f, "rb")
         data = []
         data.append([s.getparams(), s.readframes(s.getnframes())])
         data.append([w.getparams(), w.readframes(w.getnframes())])
         w.close()
-        output = wave.open('tmp.wav', 'wb')
+        output = wave.open("tmp.wav", "wb")
         output.setparams(data[0][0])
         for i in range(2):
             output.writeframes(data[i][1])
         output.close()
-
-
-
-
-

charlie2/_scratch/quickstart.py

@@ -5,9 +5,10 @@
 the user has access to.
 """
 from __future__ import print_function
+
 from apiclient.discovery import build
 from httplib2 import Http
-from oauth2client import file, client, tools
+from oauth2client import client, file, tools
 
 # Setup the Drive v3 API
 SCOPES = [

charlie2/_scratch/tmp.py

@@ -798,14 +798,3 @@
 # def play_feedback_sound(self, correct):
 #     """Play either the correct sound if true or incorrect sound if false."""
 #     self.feedback_sounds[correct].play()
-
-
-
-
-
-
-
-
-
-
-

charlie2/_scratch/upload.py

@@ -5,14 +5,14 @@
 import datetime
 import hashlib
 import mimetypes
-import time
 import os
+import time
+
 import httplib2
 from apiclient import discovery
-from oauth2client import client
-from oauth2client import tools
-from oauth2client.file import Storage
 from apiclient.http import MediaFileUpload
+from oauth2client import client, tools
+from oauth2client.file import Storage
 
 # If modifying these scopes, delete your previously saved credentials
 # at ~/.credentials/drive-python-quickstart.json

charlie2/tests/digitsymbol.py

@@ -41,23 +41,21 @@
   814–823.
 
 """
-from sys import gettrace
-
-from charlie2.tools.stats import basic_summary
-
-__version__ = 2.0
-__author__ = "Sam Mathias"
-
-
 from logging import getLogger
-from typing import Dict, List, Union
+from typing import Dict, List
 
 from PyQt5.QtCore import Qt
 from PyQt5.QtGui import QKeyEvent
 
+from charlie2.tools.stats import basic_summary
+
 from ..tools.basetestwidget import BaseTestWidget
 from ..tools.recipes import digits, symbols
 
+__version__ = 2.0
+__author__ = "Sam Mathias"
+
+
 logger = getLogger(__name__)
 
 
@@ -71,10 +69,11 @@ def __init__(self, parent=None) -> None:
             3. Hide the mouse.
             4. Define x-positions of digits and symbols in the key.
             5. Load and hide the key.
+            6. Set a flag so that skipped trials are deleted rather than stored.
 
         """
         super(TestWidget, self).__init__(parent)
-        if gettrace() is None:
+        if self.debugging is False:
             self.block_deadline = 90 * 1000
         else:
             self.block_deadline = 4 * 1000
@@ -84,6 +83,7 @@ def __init__(self, parent=None) -> None:
         self.xs = range(-300, 350, 75)
         self.digit = None
         self.symbol = None
+        self.delete_skipped = True
 
     def make_trials(self) -> List[Dict[str, int]]:
         """Generates new trials.
@@ -161,11 +161,14 @@ def keyReleaseEvent_(self, event: QKeyEvent) -> None:
             self.symbol.deleteLater()
             self.digit.deleteLater()
             if t.practice:
+                self.performing_trial = False
                 s = self.instructions[7:9][not t.correct]
                 a = self.display_text(s, (0, -100))
+                self.play_feeback(t.correct)
                 self.sleep(1000)
                 a.hide()
                 a.deleteLater()
+                self._performing_trial = True
 
     def summarise(self) -> Dict[str, int]:
         """Summarises the data.

charlie2/tests/emotionrecognition.py

@@ -24,22 +24,19 @@
   Neurosci. Methods, 115:137–143.
 
 """
+from logging import getLogger
 from typing import Dict, List
 
+from PyQt5.QtCore import Qt
 from PyQt5.QtGui import QKeyEvent
 
+from charlie2.tools.basetestwidget import BaseTestWidget
 from charlie2.tools.stats import basic_summary
 
 __version__ = 2.0
 __author__ = "Sam Mathias"
 
 
-from logging import getLogger
-
-from PyQt5.QtCore import Qt
-
-from charlie2.tools.basetestwidget import BaseTestWidget
-
 logger = getLogger(__name__)
 
 
@@ -55,7 +52,10 @@ def __init__(self, parent=None) -> None:
         """
         super(TestWidget, self).__init__(parent)
         self.mouse_visible = False
-        self.block_deadline = 300 * 1000
+        if self.debugging:
+            self.block_deadline = 4 * 1000
+        else:
+            self.block_deadline = 240 * 1000
 
     def make_trials(self) -> List[Dict[str, int]]:
         """Generates new trials.
@@ -66,6 +66,7 @@ def make_trials(self) -> List[Dict[str, int]]:
                 2. `face` (:obj:`str`)
                 3. `emotion` (:obj:`str`)
         """
+
         def e(s):
             if "N" in s:
                 return "neutral"

charlie2/tests/facialmemory.py

@@ -25,23 +25,21 @@
   performance and ”effort”. Brain Cogn.,33, 388-414.
 
 """
+from logging import getLogger
 from sys import gettrace
 from typing import Dict, List
 
+from PyQt5.QtCore import Qt
 from PyQt5.QtGui import QKeyEvent
 
+from charlie2.tools.basetestwidget import BaseTestWidget
+
 from ..tools.stats import basic_summary
 
 __version__ = 2.0
 __author__ = "Sam Mathias"
 
 
-from logging import getLogger
-
-from PyQt5.QtCore import Qt
-
-from charlie2.tools.basetestwidget import BaseTestWidget
-
 logger = getLogger(__name__)
 
 
@@ -142,13 +140,16 @@ def block(self) -> None:
         """
         b = self.current_trial.block_number
         if b == 0:
-            if gettrace() is None:
+            if self.debugging is False:
                 self.trial_deadline = int(2.5 * 1000)
             else:
                 self.trial_deadline = 100
         else:
             self.trial_deadline = None
-            self.block_deadline = 300 * 1000
+            if self.debugging:
+                self.block_deadline = 4 * 1000
+            else:
+                self.block_deadline = 240 * 1000
         self.display_instructions_with_space_bar(self.instructions[4 + b])
 
     def trial(self) -> None:
@@ -192,6 +193,9 @@ def summarise(self) -> Dict[str, int]:
             dict: Summary statistics.
 
         """
-        trials = [t for t in self.procedure.completed_trials if
-                  t["block_type"] == "recognition"]
+        trials = [
+            t
+            for t in self.procedure.completed_trials
+            if t["block_type"] == "recognition"
+        ]
         return basic_summary(trials)