Clean-up Experiment dependencies inside Stimulus

stytra/stimulation/__init__.py

@@ -1,5 +1,6 @@
 import datetime
 from copy import deepcopy
+import warnings
 
 from PyQt5.QtCore import pyqtSignal, QTimer, QObject
 from stytra.stimulation.stimuli import Pause, DynamicStimulus
@@ -112,7 +113,12 @@ def update_protocol(self):
 
         # pass experiment to stimuli for calibrator and asset folders:
         for stimulus in self.stimuli:
-            stimulus.initialise_external(self.experiment)
+            try:
+                stimulus.initialise_external(self.experiment, self.experiment.calibrator)
+            except TypeError:
+                stimulus.initialise_external(self.experiment)
+                warnings.warn("Warning: 'initialise_external' will require a calibrator input from the new update!", FutureWarning)
+                warnings.warn("Warning: 'initialise_external' will require a calibrator input from the new update!", DeprecationWarning)
 
         if self.dynamic_log is None:
             self.dynamic_log = DynamicLog(self.stimuli, experiment=self.experiment)

stytra/stimulation/stimuli/conditional.py

@@ -36,9 +36,9 @@ def get_dynamic_state(self):
             state.update(self.active.get_dynamic_state())
         return state
 
-    def initialise_external(self, experiment):
-        super().initialise_external(experiment)
-        self.active.initialise_external(experiment)
+    def initialise_external(self, experiment, calibrator):
+        super().initialise_external(experiment, calibrator)
+        self.active.initialise_external(experiment, calibrator)
 
     def get_state(self):
         state = super().get_state()
@@ -157,10 +157,10 @@ def get_dynamic_state(self):
             state.update(self._stim_on.get_dynamic_state())
         return state
 
-    def initialise_external(self, experiment):
-        super().initialise_external(experiment)
-        self._stim_on.initialise_external(experiment)
-        self._stim_off.initialise_external(experiment)
+    def initialise_external(self, experiment, calibrator):
+        super().initialise_external(experiment, calibrator)
+        self._stim_on.initialise_external(experiment, calibrator)
+        self._stim_off.initialise_external(experiment, calibrator)
 
     def get_state(self):
         state = super().get_state()
@@ -271,7 +271,7 @@ def __init__(self, stimulus, *args, centering_stimulus=None, margin=45, **kwargs
 
     def check_condition_on(self):
         y, x, theta = self._experiment.estimator.get_position()
-        scale = self._experiment.calibrator.mm_px ** 2
+        scale = self._calibrator.mm_px ** 2 
         return (
             x > 0 and ((x - self.xc) ** 2 + (y - self.yc) ** 2) <= self.margin / scale
         )
@@ -324,14 +324,14 @@ def __init__(
 
     def check_condition_on(self):
         y, x, theta = self._experiment.estimator.get_position()
-        scale = self._experiment.calibrator.mm_px ** 2
+        scale = self._calibrator.mm_px ** 2
         return (not np.isnan(x)) and (
             (x - self.xc) ** 2 + (y - self.yc) ** 2 <= self.margin_in / scale
         )
 
     def check_condition_off(self):
         y, x, theta = self._experiment.estimator.get_position()
-        scale = self._experiment.calibrator.mm_px ** 2
+        scale = self._calibrator.mm_px ** 2
         return np.isnan(x) or (
             (x - self.xc) ** 2 + (y - self.yc) ** 2 > self.margin_out / scale
         )

stytra/stimulation/stimuli/external.py

@@ -42,7 +42,7 @@ def __init__(
         pulse_dur_str = str(pulse_dur_ms).zfill(3)
         self.mex = str("shock" + amp_dac + pulse_dur_str)
 
-    def initialise_external(self, experiment):
+    def initialise_external(self, experiment, calibrator):
         """
 
         Parameters

stytra/stimulation/stimuli/generic_stimuli.py

@@ -1,5 +1,6 @@
 import numpy as np
 import datetime
+import warnings
 
 
 class Stimulus:
@@ -66,6 +67,7 @@ def __init__(self, duration=0.0):
         self._elapsed = 0.0  # time from the beginning of the stimulus
         self.name = "undefined"
         self._experiment = None
+        self._calibrator = None
         self.real_time_start = None
         self.real_time_stop = None
 
@@ -111,7 +113,7 @@ def stop(self):
         """
         pass
 
-    def initialise_external(self, experiment):
+    def initialise_external(self, experiment, calibrator = -999):
         """ Make a reference to the Experiment class inside the Stimulus.
         This is required to access from inside the Stimulus class to the
         Calibrator, the Pyboard, the asset directories with movies or the motor
@@ -130,7 +132,18 @@ def initialise_external(self, experiment):
             None
 
         """
+
+        if calibrator == -999:
+            self._calibrator = self._experiment.calibrator
+            warnings.warn("Warning: 'initialise_external' will require a calibrator input from the new update!", FutureWarning)
+            warnings.warn("Warning: 'initialise_external' will require a calibrator input from the new update!", DeprecationWarning)
+        else:
+            self._calibrator = calibrator
+
+
         self._experiment = experiment
+
+
 
 
 class DynamicStimulus(Stimulus):
@@ -289,10 +302,10 @@ def update(self):
             s.update()
             s._elapsed = self._elapsed
 
-    def initialise_external(self, experiment):
-        super().initialise_external(experiment)
+    def initialise_external(self, experiment, calibrator):
+        super().initialise_external(experiment, calibrator)
         for s in self._stim_list:
-            s.initialise_external(experiment)
+            s.initialise_external(experiment, calibrator)
 
     @property
     def dynamic_parameter_names(self):

stytra/stimulation/stimuli/kinematograms.py

@@ -75,8 +75,8 @@ def get_dimensions(self):
         -------
         number of dots to display and the displacement amount in pixel coordinates
         """
-        if self._experiment.calibrator is not None:
-            mm_px = self._experiment.calibrator.mm_px
+        if self._calibrator is not None:
+            mm_px = self._calibrator.mm_px  
         else:
             mm_px = 1
 

stytra/stimulation/stimuli/visual.py

@@ -313,8 +313,8 @@ def get_tile_ranges(self, imw, imh, w, h, tr: QTransform):
         return range(x_start, x_end + 1), range(y_start, y_end + 1)
 
     def paint(self, p, w, h):
-        if self._experiment.calibrator is not None:
-            mm_px = self._experiment.calibrator.mm_px
+        if self._calibrator is not None: 
+            mm_px = self._calibrator.mm_px
         else:
             mm_px = 1
 
@@ -396,8 +396,8 @@ def __init__(self, *args, background, background_name=None, **kwargs):
                 self.background_name = "array {}x{}".format(*self._background.shape)
         self._qbackground = None
 
-    def initialise_external(self, experiment):
-        super().initialise_external(experiment)
+    def initialise_external(self, experiment, calibrator):
+        super().initialise_external(experiment, calibrator)
 
         # Get background image from folder:
         if isinstance(self._background, str):
@@ -468,7 +468,7 @@ def __init__(
     def create_pattern(self):
         l = max(
             2,
-            int(self.grating_period / (max(self._experiment.calibrator.mm_px, 0.0001))),
+            int(self.grating_period / (max(self._calibrator.mm_px, 0.0001))),
         )
         if self.wave_shape == "square":
             self._pattern = np.ones((l, 3), np.uint8) * self.color_1
@@ -483,8 +483,8 @@ def create_pattern(self):
                 + (1 - w[:, None]) * np.array(self.color_2)[None, :]
             ).astype(np.uint8)
 
-    def initialise_external(self, experiment):
-        super().initialise_external(experiment)
+    def initialise_external(self, experiment, calibrator):
+        super().initialise_external(experiment, calibrator)
         self.create_pattern()
         # Get background image from folder:
         self._qbackground = qimage2ndarray.array2qimage(self._pattern[None, :, :])
@@ -532,7 +532,7 @@ def get_unit_dims(self, w, h):
         #TODO what does this thing define?
         """
         return (
-            int(self.grating_period / (max(self._experiment.calibrator.mm_px, 0.0001))),
+            int(self.grating_period / (max(self._calibrator.mm_px, 0.0001))),
             self.barheight,
         )
 
@@ -547,7 +547,7 @@ def draw_block(self, p, point, w, h):
             point.y(),
             int(
                 self.grating_period
-                / (2 * max(self._experiment.calibrator.mm_px, 0.0001))
+                / (2 * max(self._calibrator.mm_px, 0.0001))
             ),
             self.barheight,
         )
@@ -654,7 +654,7 @@ def update(self):
 
     def paint(self, p, w, h):
         x, y = (
-            (np.arange(d) - d / 2) * self._experiment.calibrator.mm_px for d in (w, h)
+            (np.arange(d) - d / 2) * self._calibrator.mm_px for d in (w, h)
         )
         self.image = np.round(
             np.sin(
@@ -751,8 +751,8 @@ def create_pattern(self, side_len=500):
         self._pattern = W * self.color_1 + (1 - W) * self.color_2
         self._qbackground = qimage2ndarray.array2qimage(self._pattern)
 
-    def initialise_external(self, experiment):
-        super().initialise_external(experiment)
+    def initialise_external(self, experiment, calibrator):
+        super().initialise_external(experiment, calibrator)
         self.create_pattern()
 
     def draw_block(self, p, point, w, h):
@@ -933,8 +933,8 @@ def __init__(
     def paint(self, p, w, h):
         super().paint(p, w, h)
 
-        if self._experiment.calibrator is not None:
-            mm_px = self._experiment.calibrator.mm_px
+        if self._calibrator is not None:
+            mm_px = self._calibrator.mm_px
         else:
             mm_px = 1