Merge pull request #28 from computational-psychology/dev

Closing some smaller issues

docs/_templates/autosummary/noises.rst

@@ -60,7 +60,7 @@
    {% if functions %}
    Demos
    -----
-   :doc:`reference/demos/components/{{name}}`
+   :doc:`../../demos/noises/{{name}}`
 
    Functions
    ---------

docs/reference/demos/components/waves.md

@@ -39,7 +39,7 @@ w_height = iw.IntSlider(value=10, min=1, max=20, description="height [deg]")
 w_width = iw.IntSlider(value=10, min=1, max=20, description="width [deg]")
 w_ppd = iw.IntSlider(value=20, min=1, max=40, description="ppd")
 
-w_base_type = iw.Dropdown(value="horizontal", options=['horizontal','vertical','rotated','radial','cityblock','angular'], description="base_type")
+w_distance_metric = iw.Dropdown(value="horizontal", options=['horizontal','vertical','oblique','radial','rectilinear','angular'], description="distance_metric")
 w_freq = iw.FloatSlider(value=1, min=0, max=2, description="frequency [cpd]")
 w_phase = iw.FloatSlider(value=0, min=0, max=360, description="phase shift [deg]")
 w_rot = iw.FloatSlider(value=0, min=0, max=360, description="rotation [deg]")
@@ -54,7 +54,7 @@ w_mask = iw.ToggleButton(value=False, disabled=False, description="add mask")
 
 # Layout
 b_im_size = iw.HBox([w_height, w_width, w_ppd])
-b_geometry = iw.HBox([w_base_type, w_freq, w_phase, w_rot])
+b_geometry = iw.HBox([w_distance_metric, w_freq, w_phase, w_rot])
 b_intensities = iw.HBox([w_int1, w_int2])
 b_add = iw.HBox([w_ori, w_period, w_round, w_mask])
 ui = iw.VBox([b_im_size, b_geometry, b_intensities, b_add])
@@ -64,7 +64,7 @@ def show_sine(
     height=None,
     width=None,
     ppd=None,
-    base_type=None,
+    distance_metric=None,
     rotation=None,
     frequency=None,
     phase_shift=None,
@@ -78,7 +78,7 @@ def show_sine(
     stim = sine(
         visual_size=(height, width),
         ppd=ppd,
-        base_type=base_type,
+        distance_metric=distance_metric,
         rotation=rotation,
         frequency=frequency,
         phase_shift=phase_shift,
@@ -96,7 +96,7 @@ out = iw.interactive_output(
         "height": w_height,
         "width": w_width,
         "ppd": w_ppd,
-        "base_type": w_base_type,
+        "distance_metric": w_distance_metric,
         "rotation": w_rot,
         "frequency": w_freq,
         "phase_shift": w_phase,
@@ -124,7 +124,7 @@ w_height = iw.IntSlider(value=10, min=1, max=20, description="height [deg]")
 w_width = iw.IntSlider(value=10, min=1, max=20, description="width [deg]")
 w_ppd = iw.IntSlider(value=20, min=1, max=40, description="ppd")
 
-w_base_type = iw.Dropdown(value="horizontal", options=['horizontal','vertical','rotated','radial','cityblock','angular'], description="base_type")
+w_distance_metric = iw.Dropdown(value="horizontal", options=['horizontal','vertical','oblique','radial','rectilinear','angular'], description="distance_metric")
 w_freq = iw.FloatSlider(value=1, min=0, max=2, description="frequency [cpd]")
 w_phase = iw.FloatSlider(value=0, min=0, max=360, description="phase shift [deg]")
 w_rot = iw.FloatSlider(value=0, min=0, max=360, description="rotation [deg]")
@@ -139,7 +139,7 @@ w_mask = iw.ToggleButton(value=False, disabled=False, description="add mask")
 
 # Layout
 b_im_size = iw.HBox([w_height, w_width, w_ppd])
-b_geometry = iw.HBox([w_base_type, w_freq, w_phase, w_rot])
+b_geometry = iw.HBox([w_distance_metric, w_freq, w_phase, w_rot])
 b_intensities = iw.HBox([w_int1, w_int2])
 b_add = iw.HBox([w_ori, w_period, w_round, w_mask])
 ui = iw.VBox([b_im_size, b_geometry, b_intensities, b_add])
@@ -149,7 +149,7 @@ def show_square(
     height=None,
     width=None,
     ppd=None,
-    base_type=None,
+    distance_metric=None,
     rotation=None,
     frequency=None,
     phase_shift=None,
@@ -163,7 +163,7 @@ def show_square(
     stim = square(
         visual_size=(height, width),
         ppd=ppd,
-        base_type=base_type,
+        distance_metric=distance_metric,
         rotation=rotation,
         frequency=frequency,
         phase_shift=phase_shift,
@@ -181,7 +181,7 @@ out = iw.interactive_output(
         "height": w_height,
         "width": w_width,
         "ppd": w_ppd,
-        "base_type": w_base_type,
+        "distance_metric": w_distance_metric,
         "rotation": w_rot,
         "frequency": w_freq,
         "phase_shift": w_phase,
@@ -209,7 +209,7 @@ w_height = iw.IntSlider(value=10, min=1, max=20, description="height [deg]")
 w_width = iw.IntSlider(value=10, min=1, max=20, description="width [deg]")
 w_ppd = iw.IntSlider(value=20, min=1, max=40, description="ppd")
 
-w_base_type = iw.Dropdown(value="horizontal", options=['horizontal','vertical','rotated','radial','cityblock','angular'], description="base_type")
+w_distance_metric = iw.Dropdown(value="horizontal", options=['horizontal','vertical','oblique','radial','rectilinear','angular'], description="distance_metric")
 w_freq = iw.FloatSlider(value=0.5, min=0, max=2, description="frequency [cpd]")
 w_rot = iw.FloatSlider(value=0, min=0, max=360, description="rotation [deg]")
 w_phase = iw.FloatSlider(value=0, min=0, max=360, description="phase shift [deg]")
@@ -224,7 +224,7 @@ w_mask = iw.ToggleButton(value=False, disabled=False, description="add mask")
 
 # Layout
 b_im_size = iw.HBox([w_height, w_width, w_ppd])
-b_geometry = iw.HBox([w_base_type, w_freq, w_phase, w_rot])
+b_geometry = iw.HBox([w_distance_metric, w_freq, w_phase, w_rot])
 b_intensities = iw.HBox([w_int1, w_int2])
 b_add = iw.HBox([w_ori, w_period, w_round, w_mask])
 ui = iw.VBox([b_im_size, b_geometry, b_intensities, b_add])
@@ -234,7 +234,7 @@ def show_staircase(
     height=None,
     width=None,
     ppd=None,
-    base_type=None,
+    distance_metric=None,
     rotation=None,
     frequency=None,
     phase_shift=None,
@@ -248,7 +248,7 @@ def show_staircase(
     stim = staircase(
         visual_size=(height, width),
         ppd=ppd,
-        base_type=base_type,
+        distance_metric=distance_metric,
         rotation=rotation,
         frequency=frequency,
         phase_shift=phase_shift,
@@ -266,7 +266,7 @@ out = iw.interactive_output(
         "height": w_height,
         "width": w_width,
         "ppd": w_ppd,
-        "base_type": w_base_type,
+        "distance_metric": w_distance_metric,
         "rotation": w_rot,
         "frequency": w_freq,
         "int1": w_int1,

docs/reference/demos/stimuli/plaids.md

@@ -107,7 +107,7 @@ def show_plaid(
         "origin": origin,
         "round_phase_width": round_phase_width,
         "period": period,
-        "base_type": "rotated",
+        "distance_metric": "oblique",
     }
     
     p_grating1 = {

docs/reference/demos/stimuli/waves.md

@@ -126,9 +126,9 @@ display(ui, out)
 
 ## Square, radial
 
-## Sine, cityblock
+## Sine, rectilinear
 
-## Square, cityblock
+## Square, rectilinear
 
 ## Sine, angular
 

stimupy/components/__init__.py

@@ -5,6 +5,8 @@
 from stimupy.utils import resolution
 
 __all__ = [
+    "overview",
+    "plot_overview",
     "image_base",
     "draw_regions",
     "mask_elements",
@@ -46,14 +48,14 @@ def image_base(visual_size=None, shape=None, ppd=None, rotation=0.0, origin="mea
         "x", "y" : single axes
         "horizontal", "vertical" : numpy.ndarray of shape, with distance from origin,
         in deg. visual angle, at each pixel
-        "rotated" : numpy.ndarray of shape, with rotated distance from origin,
+        "oblique" : numpy.ndarray of shape, with oblique distance from origin,
         in deg. visual angle, at each pixel
         "radial" : numpyn.ndarray of shape, with radius from origin,
         in deg. visual angle, at each pixel
         "angular" : numpy.ndarray of shape, with angle relative to 3 o'clock,
         in rad, at each pixel
-        "cityblock" : numpy.ndarray of shape, with cityblock distance from origin,
-        in deg. visual angle ,at each pixel
+        "rectilinear" : numpy.ndarray of shape, with rectilinear/cityblock/Manhattan distance from origin,
+        in deg. visual angle, at each pixel
     """
 
     # Resolve resolution
@@ -77,8 +79,8 @@ def image_base(visual_size=None, shape=None, ppd=None, rotation=0.0, origin="mea
     # Linear distance image bases
     xx, yy = np.meshgrid(x, y)
 
-    # City-block distance (frames)
-    cityblock = np.maximum(np.abs(xx), np.abs(yy))
+    # Rectilinear distance (frames)
+    rectilinear = np.maximum(np.abs(xx), np.abs(yy))
 
     # Radial distance
     radial = np.sqrt(xx**2 + yy**2)
@@ -88,12 +90,12 @@ def image_base(visual_size=None, shape=None, ppd=None, rotation=0.0, origin="mea
     angular -= np.deg2rad(rotation + 90)
     angular %= 2 * np.pi
 
-    # Rotated
+    # Oblique
     alpha = [np.cos(np.deg2rad(rotation)), np.sin(np.deg2rad(rotation))]
-    rotated = alpha[0] * xx + alpha[1] * yy
+    oblique = alpha[0] * xx + alpha[1] * yy
 
     if origin == "corner":
-        rotated = rotated - rotated.min()
+        oblique = oblique - oblique.min()
 
     return {
         "visual_size": visual_size,
@@ -104,15 +106,15 @@ def image_base(visual_size=None, shape=None, ppd=None, rotation=0.0, origin="mea
         "y": y,
         "horizontal": xx,
         "vertical": yy,
-        "rotated": rotated,
-        "cityblock": cityblock,
+        "oblique": oblique,
+        "rectilinear": rectilinear,
         "radial": radial,
         "angular": angular,
     }
 
 
 def mask_elements(
-    orientation,
+    distance_metric,
     edges,
     shape=None,
     visual_size=None,
@@ -124,7 +126,7 @@ def mask_elements(
 
     Parameters
     ----------
-    orientation : any of keys in stimupy.components.image_base()
+    distance_metric : any of keys in stimupy.components.image_base()
         which dimension to mask over
     edges : Sequence[Number]
         upper-limit of each consecutive elements
@@ -152,7 +154,7 @@ def mask_elements(
     base = image_base(
         shape=shape, visual_size=visual_size, ppd=ppd, rotation=rotation, origin=origin
     )
-    distances = base[orientation]
+    distances = base[distance_metric]
     distances = np.round(distances, 8)
 
     # Mark elements with integer idx-value
@@ -164,7 +166,7 @@ def mask_elements(
     return {
         "mask": mask,
         "edges": edges,
-        "orientation": orientation,
+        "distance_metric": distance_metric,
         "rotation": base["rotation"],
         "shape": base["shape"],
         "visual_size": base["visual_size"],
@@ -208,17 +210,16 @@ def draw_regions(mask, intensities, intensity_background=0.5):
     return img
 
 
-from . import angulars, edges, frames, gaussians, lines, radials, shapes, waves
+from stimupy.components import angulars, edges, frames, gaussians, lines, radials, shapes, waves
 
 
-def create_overview():
-    """
-    Create dictionary with examples from all stimulus-components
+def overview(skip=False):
+    """Generate example stimuli from this module
 
     Returns
     -------
-    stims : dict
-        dict with all stimuli containing individual stimulus dicts.
+    dict[str, dict]
+        Dict mapping names to individual stimulus dicts
     """
 
     p = {
@@ -227,7 +228,7 @@ def create_overview():
     }
 
     # fmt: off
-    stims = {
+    stimuli = {
         # angulars
         "wedge": angulars.wedge(**p, width=30, radius=3),
         "angular_grating": angulars.grating(**p, n_segments=8),
@@ -262,12 +263,31 @@ def create_overview():
     }
     # fmt: on
 
-    return stims
+    # stimuli = {}
+    # for stimmodule_name in __all__:
+    #     if stimmodule_name in ["overview", "plot_overview"]:
+    #         pass
 
+    #     print(f"Generating stimuli from {stimmodule_name}")
+    #     # Get a reference to the actual module
+    #     stimmodule = globals()[stimmodule_name]
+    #     try:
+    #         stims = stimmodule.overview()
 
-def overview(mask=False, save=None, extent_key="shape"):
-    """
-    Plot overview with examples from all stimulus-components
+    #         # Accumulate
+    #         stimuli.update(stims)
+    #     except NotImplementedError as e:
+    #         if not skip:
+    #             raise e
+    #         # Skip stimuli that aren't implemented
+    #         print("-- not implemented")
+    #         pass
+
+    return stimuli
+
+
+def plot_overview(mask=False, save=None, extent_key="shape"):
+    """Plot overview of examples in this module (and submodules)
 
     Parameters
     ----------
@@ -284,7 +304,9 @@ def overview(mask=False, save=None, extent_key="shape"):
     """
     from stimupy.utils import plot_stimuli
 
-    stims = create_overview()
+    stims = overview(skip=True)
+    plot_stimuli(stims, mask=mask, extent_key=extent_key, save=save)
+
 
-    # Plotting
-    plot_stimuli(stims, mask=mask, save=save, extent_key=extent_key)
+if __name__ == "__main__":
+    plot_overview()

stimupy/components/angulars.py

@@ -46,7 +46,7 @@ def mask_angle(
     """
     stim = mask_elements(
         edges=np.deg2rad(angles),
-        orientation="angular",
+        distance_metric="angular",
         rotation=rotation,
         shape=shape,
         visual_size=visual_size,
@@ -178,7 +178,7 @@ def mask_segments(
         and additional keys containing stimulus parameters
     """
     stim = mask_elements(
-        orientation="angular",
+        distance_metric="angular",
         edges=np.deg2rad(edges),
         rotation=rotation,
         shape=shape,

stimupy/components/edges.py

@@ -1,4 +1,5 @@
 import copy
+
 import numpy as np
 
 from stimupy.components import gaussians, image_base
@@ -49,9 +50,9 @@ def step_edge(
     )
 
     img = np.ones(shape) * intensity_edges[0]
-    img = np.where(base["rotated"] < base["rotated"].mean(), img, intensity_edges[1])
+    img = np.where(base["oblique"] < base["oblique"].mean(), img, intensity_edges[1])
     mask = np.ones(shape)
-    mask = np.where(base["rotated"] < base["rotated"].mean(), mask, 2)
+    mask = np.where(base["oblique"] < base["oblique"].mean(), mask, 2)
 
     stim = {
         "img": img,
@@ -198,7 +199,7 @@ def cornsweet_edge(
     if ramp_width > max(base["visual_size"]) / 2:
         raise ValueError("ramp_width is too large")
 
-    dist = np.round(base["rotated"] / ramp_width, 6)
+    dist = np.round(base["oblique"] / ramp_width, 6)
     d1 = copy.deepcopy(dist)
     d2 = copy.deepcopy(dist) * (-1)
     d1[d1 < 0] = -1

stimupy/components/frames.py

@@ -38,7 +38,7 @@ def mask_frames(
         and additional keys containing stimulus parameters
     """
     stim = mask_elements(
-        orientation="cityblock",
+        distance_metric="rectilinear",
         edges=edges,
         rotation=0.0,
         shape=shape,