From 9a2547b6f6d9da919cc96d4eaea65bc48719d1a7 Mon Sep 17 00:00:00 2001
From: Maddy Cappelloni <mcappel3@u.rochester.edu>
Date: Mon, 9 Jul 2018 11:29:59 -0400
Subject: [PATCH 01/12] init commit

---
 expyfun/_experiment_controller.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/expyfun/_experiment_controller.py b/expyfun/_experiment_controller.py
index 50a3749c..24360b56 100644
--- a/expyfun/_experiment_controller.py
+++ b/expyfun/_experiment_controller.py
@@ -1105,6 +1105,9 @@ def _log_presses(self, pressed):
     def check_force_quit(self):
         """Check to see if any force quit keys were pressed."""
         self._response_handler.check_force_quit()
+    
+    def check_calibration(self):
+        """Check if calibration interrupt keys were pressed."""
 
     def text_input(self, stop_key='return', pos=[0, 0], color='white',
                    font_name='Arial', font_size=24, wrap=True, units='norm',

From 76c71a55449f7391df9bebe922b8dcdb23ffdc05 Mon Sep 17 00:00:00 2001
From: Maddy Cappelloni <mcappel3@u.rochester.edu>
Date: Thu, 12 Jul 2018 15:01:28 -0400
Subject: [PATCH 02/12] add check function

---
 expyfun/_eyelink_controller.py | 23 ++++++++++++++++++++++-
 1 file changed, 22 insertions(+), 1 deletion(-)

diff --git a/expyfun/_eyelink_controller.py b/expyfun/_eyelink_controller.py
index 7cfeafb7..a5a8b595 100644
--- a/expyfun/_eyelink_controller.py
+++ b/expyfun/_eyelink_controller.py
@@ -137,6 +137,8 @@ class EyelinkController(object):
         Sample rate to use. Must be one of [250, 500, 1000, 2000].
     verbose : bool, str, int, or None
         If not None, override default verbose level (see expyfun.verbose).
+    calbration_keys : list
+        Keys that will trigger recalibration when check_recalibration.
 
     Notes
     -----
@@ -144,7 +146,7 @@ class EyelinkController(object):
     If this was `None`, data will be saved to the current working dir.
     """
     @verbose_dec
-    def __init__(self, ec, link='default', fs=1000, verbose=None):
+    def __init__(self, ec, link='default', fs=1000, verbose=None, calibration_key=['c']):
         if link == 'default':
             link = get_config('EXPYFUN_EYELINK', None)
         if link is not None and pylink is None:
@@ -381,6 +383,25 @@ def calibrate(self, beep=False, prompt=True):
         self._start_recording()
         return fname
 
+    def check_recalibrate(self, keys=None):
+        """Compare key buffer to recalibration keys and calibrate if matched.
+
+        This function always uses the keyboard, so is part of abstraction.
+        """
+        if keys is None:
+            keys = self._ec._response_handler._retrieve_keyboard_events(self.calibration_key)
+        else:
+            if isinstance(keys, string_types):
+                keys = [keys]
+            if isinstance(keys, list):
+                keys = [k for k in keys if k in self.calibration_key]
+            else:
+                raise TypeError('Calibration checking requires a string or '
+                                ' list of strings, not a {}.'
+                                ''.format(type(keys)))
+        if len(keys):
+            self.calibrate(prompt=False)
+
     def _stamp_trial_id(self, ids):
         """Send trial id message
 

From 1c17e56a29c016bc595eacbb90e2fa6aceaef0b6 Mon Sep 17 00:00:00 2001
From: Maddy Cappelloni <mcappel3@u.rochester.edu>
Date: Mon, 30 Jul 2018 13:31:42 -0400
Subject: [PATCH 03/12] add call_on_every_wait

---
 expyfun/_experiment_controller.py | 26 ++++++++++++++++++++++++++
 expyfun/_eyelink_controller.py    |  3 ++-
 expyfun/_utils.py                 |  2 ++
 3 files changed, 30 insertions(+), 1 deletion(-)

diff --git a/expyfun/_experiment_controller.py b/expyfun/_experiment_controller.py
index 24360b56..83aac51f 100644
--- a/expyfun/_experiment_controller.py
+++ b/expyfun/_experiment_controller.py
@@ -139,6 +139,7 @@ def __init__(self, exp_name, audio_controller=None, response_device=None,
         # placeholder for extra actions to do on flip-and-play
         self._on_every_flip = []
         self._on_next_flip = []
+        self._on_every_wait = []
         self._on_trial_ok = []
         # placeholder for extra actions to run on close
         self._extra_cleanup_fun = []  # be aware of order when adding to this
@@ -680,6 +681,31 @@ def call_on_every_flip(self, function):
         else:
             self._on_every_flip = []
 
+    def call_on_every_wait(self, function):
+        """Add a function to be executed on every wait.
+
+        Parameters
+        ----------
+        function : function | None
+            The function to call. If ``None``, all the "on every flip"
+            functions will be cleared.
+
+        See Also
+        --------
+        ExperimentController.call_on_next_flip
+
+        Notes
+        -----
+        See `flip_and_play` for order of operations. Can be called multiple
+        times to add multiple functions to the queue. If the function must be
+        called with arguments, use `functools.partial` before passing to
+        `call_on_every_flip`.
+        """
+        if function is not None:
+            self._on_every_wait.append(function)
+        else:
+            self._on_every_wait = []
+
     def _convert_units(self, verts, fro, to):
         """Convert between different screen units"""
         check_units(to)
diff --git a/expyfun/_eyelink_controller.py b/expyfun/_eyelink_controller.py
index a5a8b595..1df73d8e 100644
--- a/expyfun/_eyelink_controller.py
+++ b/expyfun/_eyelink_controller.py
@@ -191,6 +191,7 @@ def __init__(self, ec, link='default', fs=1000, verbose=None, calibration_key=['
         self._current_open_file = None
         logger.debug('EyeLink: Setup complete')
         self._ec.flush()
+        self.calibration_key = calibration_key
 
     def _setup(self, fs=1000):
         """Start up Eyelink
@@ -400,7 +401,7 @@ def check_recalibrate(self, keys=None):
                                 ' list of strings, not a {}.'
                                 ''.format(type(keys)))
         if len(keys):
-            self.calibrate(prompt=False)
+            self.calibrate()
 
     def _stamp_trial_id(self, ids):
         """Send trial id message
diff --git a/expyfun/_utils.py b/expyfun/_utils.py
index 15544ec0..4aaa2217 100644
--- a/expyfun/_utils.py
+++ b/expyfun/_utils.py
@@ -749,6 +749,8 @@ def wait_secs(secs, ec=None):
             win.dispatch_events()
         if ec is not None:
             ec.check_force_quit()
+            for function in ec._on_every_wait:
+                function()
 
 
 def running_rms(signal, win_length):

From 387d7f52cac529ac92173dd36c4c78fd5b468709 Mon Sep 17 00:00:00 2001
From: Maddy Cappelloni <mcappel3@u.rochester.edu>
Date: Mon, 30 Jul 2018 13:47:15 -0400
Subject: [PATCH 04/12] PEP8 and extra lines

---
 expyfun/_experiment_controller.py | 3 ---
 expyfun/_eyelink_controller.py    | 6 ++++--
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/expyfun/_experiment_controller.py b/expyfun/_experiment_controller.py
index 83aac51f..f39c4559 100644
--- a/expyfun/_experiment_controller.py
+++ b/expyfun/_experiment_controller.py
@@ -1131,9 +1131,6 @@ def _log_presses(self, pressed):
     def check_force_quit(self):
         """Check to see if any force quit keys were pressed."""
         self._response_handler.check_force_quit()
-    
-    def check_calibration(self):
-        """Check if calibration interrupt keys were pressed."""
 
     def text_input(self, stop_key='return', pos=[0, 0], color='white',
                    font_name='Arial', font_size=24, wrap=True, units='norm',
diff --git a/expyfun/_eyelink_controller.py b/expyfun/_eyelink_controller.py
index 1df73d8e..90466345 100644
--- a/expyfun/_eyelink_controller.py
+++ b/expyfun/_eyelink_controller.py
@@ -146,7 +146,8 @@ class EyelinkController(object):
     If this was `None`, data will be saved to the current working dir.
     """
     @verbose_dec
-    def __init__(self, ec, link='default', fs=1000, verbose=None, calibration_key=['c']):
+    def __init__(self, ec, link='default', fs=1000, verbose=None,
+                 calibration_key=['c']):
         if link == 'default':
             link = get_config('EXPYFUN_EYELINK', None)
         if link is not None and pylink is None:
@@ -390,7 +391,8 @@ def check_recalibrate(self, keys=None):
         This function always uses the keyboard, so is part of abstraction.
         """
         if keys is None:
-            keys = self._ec._response_handler._retrieve_keyboard_events(self.calibration_key)
+            check = self.calibration_key
+            keys = self._ec._response_handler._retrieve_keyboard_events(check)
         else:
             if isinstance(keys, string_types):
                 keys = [keys]

From ada314dd518f4747ed3030ad42725bceda486a4d Mon Sep 17 00:00:00 2001
From: Maddy Cappelloni <mcappel3@u.rochester.edu>
Date: Fri, 3 Aug 2018 13:22:25 -0400
Subject: [PATCH 05/12] add tests

---
 expyfun/_eyelink_controller.py           | 4 ++--
 expyfun/tests/test_eyelink_controller.py | 6 +++++-
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/expyfun/_eyelink_controller.py b/expyfun/_eyelink_controller.py
index 90466345..871340a9 100644
--- a/expyfun/_eyelink_controller.py
+++ b/expyfun/_eyelink_controller.py
@@ -385,7 +385,7 @@ def calibrate(self, beep=False, prompt=True):
         self._start_recording()
         return fname
 
-    def check_recalibrate(self, keys=None):
+    def check_recalibrate(self, keys=None, prompt=True):
         """Compare key buffer to recalibration keys and calibrate if matched.
 
         This function always uses the keyboard, so is part of abstraction.
@@ -403,7 +403,7 @@ def check_recalibrate(self, keys=None):
                                 ' list of strings, not a {}.'
                                 ''.format(type(keys)))
         if len(keys):
-            self.calibrate()
+            self.calibrate(prompt=prompt)
 
     def _stamp_trial_id(self, ids):
         """Send trial id message
diff --git a/expyfun/tests/test_eyelink_controller.py b/expyfun/tests/test_eyelink_controller.py
index 87c08660..139a9492 100644
--- a/expyfun/tests/test_eyelink_controller.py
+++ b/expyfun/tests/test_eyelink_controller.py
@@ -2,7 +2,8 @@
 import warnings
 
 from expyfun import EyelinkController, ExperimentController
-from expyfun._utils import _TempDir, _hide_window, requires_opengl21
+from expyfun._utils import (_TempDir, _hide_window, requires_opengl21,
+                            fake_button_press)
 
 warnings.simplefilter('always')
 
@@ -46,6 +47,9 @@ def test_eyelink_methods():
         # run much of the calibration code, but don't *actually* do it
         el._fake_calibration = True
         el.calibrate(beep=False, prompt=False)
+        fake_button_press(ec, 'c')
+        el.check_recalibrate(prompt=False)
+        el.check_recalibrate('k', prompt=False)
         el._fake_calibration = False
         # missing el_id
         assert_raises(KeyError, ec.identify_trial, ec_id='foo', ttl_id=[0])

From 2d4d6e91e2f67962c7bc528ef9444caa95adc4a3 Mon Sep 17 00:00:00 2001
From: Maddy Cappelloni <mcappel3@u.rochester.edu>
Date: Fri, 3 Aug 2018 14:00:19 -0400
Subject: [PATCH 06/12] add test to wait_for_fix

---
 expyfun/_eyelink_controller.py | 19 ++++++++++++++++---
 1 file changed, 16 insertions(+), 3 deletions(-)

diff --git a/expyfun/_eyelink_controller.py b/expyfun/_eyelink_controller.py
index 871340a9..adc8bb6e 100644
--- a/expyfun/_eyelink_controller.py
+++ b/expyfun/_eyelink_controller.py
@@ -389,7 +389,15 @@ def check_recalibrate(self, keys=None, prompt=True):
         """Compare key buffer to recalibration keys and calibrate if matched.
 
         This function always uses the keyboard, so is part of abstraction.
+        
+        Parameters
+        ----------
+        keys : list or string
+            keys to check if prompt recalibration
+        prompt : bool
+            Whether to show the calibration prompt or not
         """
+        calibrate = False
         if keys is None:
             check = self.calibration_key
             keys = self._ec._response_handler._retrieve_keyboard_events(check)
@@ -404,6 +412,8 @@ def check_recalibrate(self, keys=None, prompt=True):
                                 ''.format(type(keys)))
         if len(keys):
             self.calibrate(prompt=prompt)
+            calibrate = True
+        return calibrate
 
     def _stamp_trial_id(self, ids):
         """Send trial id message
@@ -529,7 +539,7 @@ def wait_for_fix(self, fix_pos, fix_time=0., tol=100., max_wait=np.inf,
         """
         # initialize eye position to be outside of target
         fix_success = False
-
+        calibrate = False
         # sample eye position for el.fix_hold seconds
         time_in = time.time()
         time_out = time_in + max_wait
@@ -538,7 +548,7 @@ def wait_for_fix(self, fix_pos, fix_time=0., tol=100., max_wait=np.inf,
             raise ValueError('fix_pos must be a 2-element array-like vector')
         fix_pos = self._ec._convert_units(fix_pos[:, np.newaxis], units, 'pix')
         fix_pos = fix_pos[:, 0]
-        while (time.time() < time_out and not
+        while (time.time() < time_out and not calibrate and not
                (fix_success and time.time() - time_in >= fix_time)):
             # sample eye position
             eye_pos = self.get_eye_position()  # in pixels
@@ -549,7 +559,10 @@ def wait_for_fix(self, fix_pos, fix_time=0., tol=100., max_wait=np.inf,
                 time_in = time.time()
             self._ec._response_handler.check_force_quit()
             self._ec.wait_secs(check_interval)
-
+            calibrate = self.check_recalibrate()
+        # rerun wait_for_fix if recalibrated
+        if calibrate:
+            fix_success = False
         return fix_success
 
     def maintain_fix(self, fix_pos, check_duration, tol=100., period=.250,

From da1a8498d8eab4755eb1bbe8a0f0285059eeb3b1 Mon Sep 17 00:00:00 2001
From: Maddy Cappelloni <mcappel3@u.rochester.edu>
Date: Fri, 3 Aug 2018 15:01:49 -0400
Subject: [PATCH 07/12] fix docs

---
 expyfun/_experiment_controller.py        | 11 -----------
 expyfun/_eyelink_controller.py           |  2 +-
 expyfun/tests/test_eyelink_controller.py |  2 +-
 3 files changed, 2 insertions(+), 13 deletions(-)

diff --git a/expyfun/_experiment_controller.py b/expyfun/_experiment_controller.py
index f39c4559..60224c34 100644
--- a/expyfun/_experiment_controller.py
+++ b/expyfun/_experiment_controller.py
@@ -689,17 +689,6 @@ def call_on_every_wait(self, function):
         function : function | None
             The function to call. If ``None``, all the "on every flip"
             functions will be cleared.
-
-        See Also
-        --------
-        ExperimentController.call_on_next_flip
-
-        Notes
-        -----
-        See `flip_and_play` for order of operations. Can be called multiple
-        times to add multiple functions to the queue. If the function must be
-        called with arguments, use `functools.partial` before passing to
-        `call_on_every_flip`.
         """
         if function is not None:
             self._on_every_wait.append(function)
diff --git a/expyfun/_eyelink_controller.py b/expyfun/_eyelink_controller.py
index adc8bb6e..e5cfae5d 100644
--- a/expyfun/_eyelink_controller.py
+++ b/expyfun/_eyelink_controller.py
@@ -147,7 +147,7 @@ class EyelinkController(object):
     """
     @verbose_dec
     def __init__(self, ec, link='default', fs=1000, verbose=None,
-                 calibration_key=['c']):
+                 calibration_key=('c',):
         if link == 'default':
             link = get_config('EXPYFUN_EYELINK', None)
         if link is not None and pylink is None:
diff --git a/expyfun/tests/test_eyelink_controller.py b/expyfun/tests/test_eyelink_controller.py
index 139a9492..3d830b23 100644
--- a/expyfun/tests/test_eyelink_controller.py
+++ b/expyfun/tests/test_eyelink_controller.py
@@ -48,7 +48,7 @@ def test_eyelink_methods():
         el._fake_calibration = True
         el.calibrate(beep=False, prompt=False)
         fake_button_press(ec, 'c')
-        el.check_recalibrate(prompt=False)
+        assert el.check_recalibrate(prompt=False)
         el.check_recalibrate('k', prompt=False)
         el._fake_calibration = False
         # missing el_id

From 8503b5ee785f6b9c8f4620c13c5cf37c81db5417 Mon Sep 17 00:00:00 2001
From: Maddy Cappelloni <mcappel3@u.rochester.edu>
Date: Fri, 3 Aug 2018 15:28:28 -0400
Subject: [PATCH 08/12] very important missing paren

---
 expyfun/_eyelink_controller.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/expyfun/_eyelink_controller.py b/expyfun/_eyelink_controller.py
index e5cfae5d..cda48063 100644
--- a/expyfun/_eyelink_controller.py
+++ b/expyfun/_eyelink_controller.py
@@ -147,7 +147,7 @@ class EyelinkController(object):
     """
     @verbose_dec
     def __init__(self, ec, link='default', fs=1000, verbose=None,
-                 calibration_key=('c',):
+                 calibration_key=('c',)):
         if link == 'default':
             link = get_config('EXPYFUN_EYELINK', None)
         if link is not None and pylink is None:

From 1782482db4273473cb4af20ac98bd400930f8359 Mon Sep 17 00:00:00 2001
From: Maddy Cappelloni <mcappel3@u.rochester.edu>
Date: Fri, 3 Aug 2018 15:34:20 -0400
Subject: [PATCH 09/12] inevitable whitespace

---
 expyfun/_eyelink_controller.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/expyfun/_eyelink_controller.py b/expyfun/_eyelink_controller.py
index cda48063..85dbc110 100644
--- a/expyfun/_eyelink_controller.py
+++ b/expyfun/_eyelink_controller.py
@@ -389,7 +389,7 @@ def check_recalibrate(self, keys=None, prompt=True):
         """Compare key buffer to recalibration keys and calibrate if matched.
 
         This function always uses the keyboard, so is part of abstraction.
-        
+
         Parameters
         ----------
         keys : list or string

From 2863c807c8e7d34393ad828c11318a502aa2d9db Mon Sep 17 00:00:00 2001
From: Maddy Cappelloni <mcappel3@u.rochester.edu>
Date: Sun, 5 Aug 2018 12:00:43 -0400
Subject: [PATCH 10/12] better docs

---
 expyfun/_experiment_controller.py |  2 +-
 expyfun/_eyelink_controller.py    | 19 +++++++++++++------
 2 files changed, 14 insertions(+), 7 deletions(-)

diff --git a/expyfun/_experiment_controller.py b/expyfun/_experiment_controller.py
index 60224c34..78b53553 100644
--- a/expyfun/_experiment_controller.py
+++ b/expyfun/_experiment_controller.py
@@ -687,7 +687,7 @@ def call_on_every_wait(self, function):
         Parameters
         ----------
         function : function | None
-            The function to call. If ``None``, all the "on every flip"
+            The function to call. If ``None``, all the "on every wait"
             functions will be cleared.
         """
         if function is not None:
diff --git a/expyfun/_eyelink_controller.py b/expyfun/_eyelink_controller.py
index 85dbc110..e6b1d20e 100644
--- a/expyfun/_eyelink_controller.py
+++ b/expyfun/_eyelink_controller.py
@@ -137,8 +137,9 @@ class EyelinkController(object):
         Sample rate to use. Must be one of [250, 500, 1000, 2000].
     verbose : bool, str, int, or None
         If not None, override default verbose level (see expyfun.verbose).
-    calbration_keys : list
-        Keys that will trigger recalibration when check_recalibration.
+    calbration_key : iterable
+        Keys that can be pressed to trigger recalibration when
+        ``EyelinkController.check_recalibrate'' is called.
 
     Notes
     -----
@@ -388,14 +389,20 @@ def calibrate(self, beep=False, prompt=True):
     def check_recalibrate(self, keys=None, prompt=True):
         """Compare key buffer to recalibration keys and calibrate if matched.
 
-        This function always uses the keyboard, so is part of abstraction.
+        The function takes key presses from the key buffer and compares them
+        to EyelinkController 'calibration_keys'. If one of the calibration keys
+        has been pressed prior to calling this function, a new calibration will
+        start. Instead of using the key buffer, keys can also be manually input
+        into the function.
 
         Parameters
         ----------
-        keys : list or string
-            keys to check if prompt recalibration
+        keys : list or string or None
+            Keys to check against the set of calibration keys that trigger a
+            calibration. None if using keys from the key buffer.
         prompt : bool
-            Whether to show the calibration prompt or not
+            Whether to show the calibration prompt screen before starting the
+            calibation procedure,
         """
         calibrate = False
         if keys is None:

From d331f271b9a4091c5cafc6d31277efdd01ddcece Mon Sep 17 00:00:00 2001
From: Maddy Cappelloni <mcappel3@u.rochester.edu>
Date: Tue, 7 Aug 2018 13:51:19 -0400
Subject: [PATCH 11/12] add tests for call_on_every_wait

---
 expyfun/tests/test_experiment_controller.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/expyfun/tests/test_experiment_controller.py b/expyfun/tests/test_experiment_controller.py
index bc2df489..5df4fa6e 100644
--- a/expyfun/tests/test_experiment_controller.py
+++ b/expyfun/tests/test_experiment_controller.py
@@ -332,6 +332,10 @@ def test_ec(ac=None, rd=None):
         ec.stop()
         assert_true(ec._playing is False)
 
+        ec.call_on_every_wait(ec.write_data_line('waiting'))
+        ec.wait_secs(0.05)
+        ec.call_on_every_wait(None)
+
         ec.flip(-np.inf)
         assert_true(ec._playing is False)
         ec.estimate_screen_fs()

From 0a068d1552cc78821a737268283c8d66ea0f3518 Mon Sep 17 00:00:00 2001
From: Maddy Cappelloni <mcappel3@u.rochester.edu>
Date: Thu, 6 Sep 2018 11:55:59 -0400
Subject: [PATCH 12/12] fix coverage maybe

---
 expyfun/tests/test_experiment_controller.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/expyfun/tests/test_experiment_controller.py b/expyfun/tests/test_experiment_controller.py
index 5df4fa6e..a898b83e 100644
--- a/expyfun/tests/test_experiment_controller.py
+++ b/expyfun/tests/test_experiment_controller.py
@@ -332,7 +332,7 @@ def test_ec(ac=None, rd=None):
         ec.stop()
         assert_true(ec._playing is False)
 
-        ec.call_on_every_wait(ec.write_data_line('waiting'))
+        ec.call_on_every_wait(ec.check_force_quit)
         ec.wait_secs(0.05)
         ec.call_on_every_wait(None)