Merge pull request #154 from DuguidLab/develop

Add viariable contrast gratings

.gitignore

@@ -137,3 +137,4 @@ dmypy.json
 .nova/
 
 /devices/
+visiomode_data/

README.md

@@ -80,6 +80,8 @@ If running over `ssh`, you will need to prepend `DISPLAY=:0` to the `visiomode`
 DISPLAY=:0 visiomode
 ```
 
+This will launch the behaviour window (what the animal sees). The web interface can be accessed from any machine connected on the same network as the Raspberry Pi running Visiomode at `http://<YOUR-PI-HOSTNAME>.local:5000`, where `<YOUR-PI-HOSTNAME>` is the hostname of your Raspberry Pi. If you're unsure on what this is, run `hostname` in a terminal window.
+
 
 ## Upgrading
 

src/visiomode/__init__.py

@@ -22,3 +22,7 @@
 def run():
     """Application entry point."""
     visiomode.core.Visiomode()
+
+
+if __name__ == "__main__":
+    run()

src/visiomode/config.py

@@ -40,3 +40,4 @@ def __init__(self, path=DEFAULT_PATH):
             path: Path to config YAML, defaults to DEFAULT_PATH. Only used if it exists.
         """
         self.load_yaml(path)
+        os.makedirs(self.data_dir, exist_ok=True)

src/visiomode/models.py

@@ -66,6 +66,7 @@ class Trial(Base):
     timestamp: str = datetime.datetime.now().isoformat()
     correction: bool = False
     response_time: int = -1
+    stimulus: dict = dataclasses.field(default_factory=dict)
 
     def __repr__(self):
         return "<Trial {}>".format(str(self.timestamp))

src/visiomode/protocols/__init__.py

@@ -224,6 +224,12 @@ def parse_trial(self, trial_start, outcome, response=None, response_time=-1):
             response_time=response_time,
             timestamp=trial_start,
             correction=self.correction_trial,
+            stimulus={
+                "target": self.target.get_details(),
+                "distractor": self.distractor.get_details()
+                if self.distractor
+                else None,
+            },
         )
         return trial
 

src/visiomode/protocols/gonogo.py

@@ -44,6 +44,7 @@ def __init__(self, target, distractor, corrections_enabled="false", **kwargs):
     def show_stimulus(self):
         if not self.correction_trial:
             self.current_stimulus = self.get_random_stimulus()
+            self.current_stimulus.generate_new_trial()
         self.current_stimulus.show()
 
     def hide_stimulus(self):

src/visiomode/protocols/tafc.py

@@ -49,6 +49,9 @@ def __init__(
 
     def show_stimulus(self):
         if not self.correction_trial:
+            self.target.generate_new_trial()
+            self.distractor.generate_new_trial()
+
             target_x, distr_x = self.shuffle_centerx()
             self.target.set_centerx(target_x)
             self.distractor.set_centerx(distr_x)

src/visiomode/protocols/target_only.py

@@ -26,6 +26,7 @@ def update_stimulus(self):
         self.target.update()
 
     def show_stimulus(self):
+        self.target.generate_new_trial()
         self.target.show()
 
     def hide_stimulus(self):

src/visiomode/stimuli/__init__.py

@@ -32,13 +32,13 @@ def load_image(name):
     return image, image.get_rect()
 
 
-def normalise_array(array, contrast=1.0):
+def normalise_array(array, contrast=1.0, background_px=127):
     """Cast array to a UINT8 image matrix."""
-    image = (
-        ((array - np.min(array)) / (np.max(array) - np.min(array)))
-        * 255
-        * float(contrast)
-    )
+    contrast_min = (1 - contrast) * background_px
+    contrast_max = (1 + contrast) * background_px
+
+    image = np.interp(array, (array.min(), array.max()), (contrast_min, contrast_max))
+
     return image.astype(np.uint8)
 
 
@@ -62,6 +62,7 @@ def __init__(self, background, **kwargs):
 
     def show(self):
         self.hidden = False
+
         self.screen.blit(self.image, self.rect)
 
     def draw(self):
@@ -83,5 +84,12 @@ def collision(self, x, y):
     def set_centerx(self, centerx):
         self.rect.centerx = centerx
 
+    def get_details(self):
+        """Returns a dictionary of stimulus attributes."""
+        return dict()
+
+    def generate_new_trial(self):
+        """Regenerate stimuli for a fresh trial"""
+
 
 plugins.load_modules_dir(__path__[0])

src/visiomode/stimuli/grating.py

@@ -11,17 +11,33 @@
 class Grating(stimuli.Stimulus):
     form_path = "stimuli/grating.html"
 
-    def __init__(self, background, period=20, contrast=1.0, **kwargs):
+    def __init__(self, background, period=30, contrast=1.0, **kwargs):
         super().__init__(background, **kwargs)
         self.period = int(period)
+        self.contrast = float(contrast)
 
-        grating = Grating.sinusoid(self.width, self.height, self.period, contrast)
+        grating = Grating.sinusoid(self.width, self.height, self.period, self.contrast)
         self.image = pg.surfarray.make_surface(grating)
         self.rect = self.image.get_rect()
         self.area = self.screen.get_rect()
 
     @classmethod
     def sinusoid(cls, width: int, height: int, period: int, contrast: float = 1.0):
+        sinusoid = Grating._sinusoid(width, height, period)
+        return stimuli.grayscale_array(sinusoid, contrast)
+
+    @classmethod
+    def _sinusoid(cls, width: int, height: int, period: int):
+        """Generate a sinusoid array in numpy.
+
+        Args:
+            width:
+            height:
+            period:
+
+        Returns:
+
+        """
         # generate 1-D sine wave of required period
         x = np.arange(height)
         y = np.sin(2 * np.pi * x / period)
@@ -31,4 +47,5 @@ def sinusoid(cls, width: int, height: int, period: int, contrast: float = 1.0):
 
         # create 2-D array of sine-wave
         sinusoid = np.array([[y[j] for j in range(height)] for i in range(width)])
-        return stimuli.grayscale_array(sinusoid, contrast)
+
+        return sinusoid

src/visiomode/stimuli/moving_grating.py

@@ -17,16 +17,16 @@ def __init__(self, background, period=20, freq=1.0, contrast=1.0, **kwargs):
         super().__init__(background, **kwargs)
 
         self.period = int(period)
+        self.contrast = float(contrast)
         self.frequency = float(freq)
         # Determine sign of direction based on frequency (negative => downwards, positive => upwards)
         self.direction = (lambda x: (-1, 1)[x < 0])(self.frequency)
         self.px_per_cycle = (
             self.direction * (self.period * abs(self.frequency)) / stimuli.config.fps
         )
-        print(self.px_per_cycle)
 
         grating = Grating.sinusoid(
-            self.width, self.height + (self.period * 2), self.period, contrast
+            self.width, self.height + (self.period * 2), self.period, self.contrast
         )
         self.image = pg.surfarray.make_surface(grating).convert(self.screen)
         self.rect = self.image.get_rect()

src/visiomode/stimuli/variable_contrast_grating.py

@@ -0,0 +1,34 @@
+#  This file is part of visiomode.
+#  Copyright (c) 2022 Constantinos Eleftheriou <[email protected]>
+#  Distributed under the terms of the MIT Licence.
+
+import random
+import pygame as pg
+
+import visiomode.stimuli as stimuli
+import visiomode.stimuli.grating as grating
+
+
+class VariableContrastGrating(grating.Grating):
+    form_path = ""
+
+    def __init__(self, background, contrasts=(0, 0.06, 0.12, 0.25, 0.5, 1.0), **kwargs):
+        super().__init__(background, **kwargs)
+
+        self.contrasts = contrasts
+        self.sinusoid_array = grating.Grating._sinusoid(
+            self.width, self.height, self.period
+        )
+
+        self.generate_new_trial()
+
+    def generate_new_trial(self):
+        self.trial_contrast = random.choice(self.contrasts)
+
+        _grating = stimuli.grayscale_array(self.sinusoid_array, self.trial_contrast)
+        self.image = pg.surfarray.make_surface(_grating)
+        self.rect = self.image.get_rect()
+        self.area = self.screen.get_rect()
+
+    def get_details(self):
+        return {"trial_contrast": self.trial_contrast}

src/visiomode/stimuli/variable_contrast_moving_grating.py

@@ -0,0 +1,35 @@
+#  This file is part of visiomode.
+#  Copyright (c) 2022 Constantinos Eleftheriou <[email protected]>
+#  Distributed under the terms of the MIT Licence.
+
+import random
+import pygame as pg
+
+import visiomode.stimuli as stimuli
+import visiomode.stimuli.grating as grating
+import visiomode.stimuli.moving_grating as moving_grating
+
+
+class VariableContrastMovingGrating(moving_grating.MovingGrating):
+    form_path = ""
+
+    def __init__(self, background, contrasts=(0, 0.06, 0.12, 0.25, 0.5, 1.0), **kwargs):
+        super().__init__(background, **kwargs)
+
+        self.contrasts = contrasts
+        self.sinusoid_array = grating.Grating._sinusoid(
+            self.width, self.height, self.period
+        )
+
+        self.generate_new_trial()
+
+    def generate_new_trial(self):
+        self.trial_contrast = random.choice(self.contrasts)
+
+        _grating = stimuli.grayscale_array(self.sinusoid_array, self.trial_contrast)
+        self.image = pg.surfarray.make_surface(_grating)
+        self.rect = self.image.get_rect()
+        self.area = self.screen.get_rect()
+
+    def get_details(self):
+        return {"trial_contrast": self.trial_contrast}

src/visiomode/webpanel/templates/stimuli/grating.html

@@ -2,7 +2,7 @@
     <div class="col">
         <label for="{{ idx or '' }}period">Period (cycles)</label>
         <input id="{{ idx or '' }}period" class="form-control mb-3"
-               type="number" value="20"
+               type="number" value="30"
                min="1" step="1">
     </div>
     <div class="col">

src/visiomode/webpanel/templates/stimuli/moving_grating.html

@@ -2,7 +2,7 @@
     <div class="col">
         <label for="{{ idx or ''}}period">Period (cycles)</label>
         <input id="{{ idx or ''}}period" class="form-control mb-3"
-               type="number" value="20"
+               type="number" value="30"
                min="1" step="1">
     </div>
     <div class="col">