Update VariableView and analysis plotting apis (#268)

Update `VariableView` and analysis plotting apis

brainpy/analysis/__init__.py

@@ -22,6 +22,4 @@
 from .lowdim.lowdim_bifurcation import *
 
 from .constants import *
-from . import constants as C
-from . import stability
-from . import utils
+from . import constants as C, stability, plotstyle, utils

brainpy/analysis/lowdim/lowdim_bifurcation.py

@@ -8,7 +8,7 @@
 
 import brainpy.math as bm
 from brainpy import errors
-from brainpy.analysis import stability, utils, constants as C
+from brainpy.analysis import stability, plotstyle, utils, constants as C
 from brainpy.analysis.lowdim.lowdim_analyzer import *
 
 pyplot = None
@@ -79,8 +79,8 @@ def plot_bifurcation(self, with_plot=True, show=False, with_return=False,
         pyplot.figure(self.x_var)
         for fp_type, points in container.items():
           if len(points['x']):
-            plot_style = stability.plot_scheme[fp_type]
-            pyplot.plot(points['p'], points['x'], '.', **plot_style, label=fp_type)
+            plot_style = plotstyle.plot_schema[fp_type]
+            pyplot.plot(points['p'], points['x'], **plot_style, label=fp_type)
         pyplot.xlabel(self.target_par_names[0])
         pyplot.ylabel(self.x_var)
 
@@ -107,10 +107,11 @@ def plot_bifurcation(self, with_plot=True, show=False, with_return=False,
         ax = fig.add_subplot(projection='3d')
         for fp_type, points in container.items():
           if len(points['x']):
-            plot_style = stability.plot_scheme[fp_type]
+            plot_style = plotstyle.plot_schema[fp_type]
             xs = points['p0']
             ys = points['p1']
             zs = points['x']
+            plot_style.pop('linestyle')
             ax.scatter(xs, ys, zs, **plot_style, label=fp_type)
 
         ax.set_xlabel(self.target_par_names[0])
@@ -298,8 +299,8 @@ def plot_bifurcation(self, with_plot=True, show=False, with_return=False,
           pyplot.figure(var)
           for fp_type, points in container.items():
             if len(points['p']):
-              plot_style = stability.plot_scheme[fp_type]
-              pyplot.plot(points['p'], points[var], '.', **plot_style, label=fp_type)
+              plot_style = plotstyle.plot_schema[fp_type]
+              pyplot.plot(points['p'], points[var], **plot_style, label=fp_type)
           pyplot.xlabel(self.target_par_names[0])
           pyplot.ylabel(var)
 
@@ -330,10 +331,11 @@ def plot_bifurcation(self, with_plot=True, show=False, with_return=False,
           ax = fig.add_subplot(projection='3d')
           for fp_type, points in container.items():
             if len(points['p0']):
-              plot_style = stability.plot_scheme[fp_type]
+              plot_style = plotstyle.plot_schema[fp_type]
               xs = points['p0']
               ys = points['p1']
               zs = points[var]
+              plot_style.pop('linestyle')
               ax.scatter(xs, ys, zs, **plot_style, label=fp_type)
 
           ax.set_xlabel(self.target_par_names[0])

brainpy/analysis/lowdim/lowdim_phase_plane.py

@@ -6,7 +6,7 @@
 
 import brainpy.math as bm
 from brainpy import errors, math
-from brainpy.analysis import stability, constants as C, utils
+from brainpy.analysis import stability, plotstyle, constants as C, utils
 from brainpy.analysis.lowdim.lowdim_analyzer import *
 
 pyplot = None
@@ -107,8 +107,8 @@ def plot_fixed_point(self, show=False, with_plot=True, with_return=False):
     if with_plot:
       for fp_type, points in container.items():
         if len(points):
-          plot_style = stability.plot_scheme[fp_type]
-          pyplot.plot(points, [0] * len(points), '.', markersize=20, **plot_style, label=fp_type)
+          plot_style = plotstyle.plot_schema[fp_type]
+          pyplot.plot(points, [0] * len(points), **plot_style, label=fp_type)
       pyplot.legend()
       if show:
         pyplot.show()
@@ -248,9 +248,9 @@ def plot_nullcline(self, with_plot=True, with_return=False,
 
     if with_plot:
       if x_style is None:
-        x_style = dict(color='cornflowerblue', alpha=.7, )
-      fmt = x_style.pop('fmt', '.')
-      pyplot.plot(x_values_in_fx, y_values_in_fx, fmt, **x_style, label=f"{self.x_var} nullcline")
+        x_style = dict(color='cornflowerblue', alpha=.7, fmt='.')
+      line_args = (x_style.pop('fmt'), ) if 'fmt' in x_style else tuple()
+      pyplot.plot(x_values_in_fx, y_values_in_fx, *line_args, **x_style, label=f"{self.x_var} nullcline")
 
     # Nullcline of the y variable
     utils.output('I am computing fy-nullcline ...')
@@ -260,9 +260,9 @@ def plot_nullcline(self, with_plot=True, with_return=False,
 
     if with_plot:
       if y_style is None:
-        y_style = dict(color='lightcoral', alpha=.7, )
-      fmt = y_style.pop('fmt', '.')
-      pyplot.plot(x_values_in_fy, y_values_in_fy, fmt, **y_style, label=f"{self.y_var} nullcline")
+        y_style = dict(color='lightcoral', alpha=.7, fmt='.')
+      line_args = (y_style.pop('fmt'), ) if 'fmt' in y_style else tuple()
+      pyplot.plot(x_values_in_fy, y_values_in_fy, *line_args, **y_style, label=f"{self.y_var} nullcline")
 
     if with_plot:
       pyplot.xlabel(self.x_var)
@@ -349,8 +349,8 @@ def plot_fixed_point(self, with_plot=True, with_return=False, show=False,
     if with_plot:
       for fp_type, points in container.items():
         if len(points['x']):
-          plot_style = stability.plot_scheme[fp_type]
-          pyplot.plot(points['x'], points['y'], '.', markersize=20, **plot_style, label=fp_type)
+          plot_style = plotstyle.plot_schema[fp_type]
+          pyplot.plot(points['x'], points['y'], **plot_style, label=fp_type)
       pyplot.legend()
       if show:
         pyplot.show()

brainpy/analysis/plotstyle.py

@@ -0,0 +1,72 @@
+# -*- coding: utf-8 -*-
+
+
+__all__ = [
+  'plot_schema',
+  'set_plot_schema',
+]
+
+from .stability import (CENTER_MANIFOLD, SADDLE_NODE, STABLE_POINT_1D,
+                        UNSTABLE_POINT_1D, CENTER_2D, STABLE_NODE_2D,
+                        STABLE_FOCUS_2D, STABLE_STAR_2D, STABLE_DEGENERATE_2D,
+                        UNSTABLE_NODE_2D, UNSTABLE_FOCUS_2D, UNSTABLE_STAR_2D,
+                        UNSTABLE_DEGENERATE_2D, UNSTABLE_LINE_2D,
+                        STABLE_POINT_3D, UNSTABLE_POINT_3D, STABLE_NODE_3D, 
+                        UNSTABLE_SADDLE_3D, UNSTABLE_NODE_3D, STABLE_FOCUS_3D, 
+                        UNSTABLE_FOCUS_3D, UNSTABLE_CENTER_3D, UNKNOWN_3D)
+
+
+_markersize = 20
+
+plot_schema = {}
+
+plot_schema[CENTER_MANIFOLD] = {'color': 'orangered', 'markersize': _markersize, 'linestyle': 'None', 'marker': '.'}
+plot_schema[SADDLE_NODE] = {"color": 'tab:blue', 'markersize': _markersize, 'linestyle': 'None', 'marker': '.'}
+
+plot_schema[STABLE_POINT_1D] = {"color": 'tab:red', 'markersize': _markersize, 'linestyle': 'None', 'marker': '.'}
+plot_schema[UNSTABLE_POINT_1D] = {"color": 'tab:olive', 'markersize': _markersize, 'linestyle': 'None', 'marker': '.'}
+
+plot_schema.update({
+  CENTER_2D: {'color': 'lime', 'markersize': _markersize, 'linestyle': 'None', 'marker': '.'},
+  STABLE_NODE_2D: {"color": 'tab:red', 'markersize': _markersize, 'linestyle': 'None', 'marker': '.'},
+  STABLE_FOCUS_2D: {"color": 'tab:purple', 'markersize': _markersize, 'linestyle': 'None', 'marker': '.'},
+  STABLE_STAR_2D: {'color': 'tab:olive', 'markersize': _markersize, 'linestyle': 'None', 'marker': '.'},
+  STABLE_DEGENERATE_2D: {'color': 'blueviolet', 'markersize': _markersize, 'linestyle': 'None', 'marker': '.'},
+  UNSTABLE_NODE_2D: {"color": 'tab:orange', 'markersize': _markersize, 'linestyle': 'None', 'marker': '.'},
+  UNSTABLE_FOCUS_2D: {"color": 'tab:cyan', 'markersize': _markersize, 'linestyle': 'None', 'marker': '.'},
+  UNSTABLE_STAR_2D: {'color': 'green', 'markersize': _markersize, 'linestyle': 'None', 'marker': '.'},
+  UNSTABLE_DEGENERATE_2D: {'color': 'springgreen', 'markersize': _markersize, 'linestyle': 'None', 'marker': '.'},
+  UNSTABLE_LINE_2D: {'color': 'dodgerblue', 'markersize': _markersize, 'linestyle': 'None', 'marker': '.'},
+})
+
+
+plot_schema.update({
+  STABLE_POINT_3D: {'color': 'tab:gray', 'markersize': _markersize, 'linestyle': 'None', 'marker': '.'},
+  UNSTABLE_POINT_3D: {'color': 'tab:purple', 'markersize': _markersize, 'linestyle': 'None', 'marker': '.'},
+  STABLE_NODE_3D: {'color': 'tab:green', 'markersize': _markersize, 'linestyle': 'None', 'marker': '.'},
+  UNSTABLE_SADDLE_3D: {'color': 'tab:red', 'markersize': _markersize, 'linestyle': 'None', 'marker': '.'},
+  UNSTABLE_FOCUS_3D: {'color': 'tab:pink', 'markersize': _markersize, 'linestyle': 'None', 'marker': '.'},
+  STABLE_FOCUS_3D: {'color': 'tab:purple', 'markersize': _markersize, 'linestyle': 'None', 'marker': '.'},
+  UNSTABLE_NODE_3D: {'color': 'tab:orange', 'markersize': _markersize, 'linestyle': 'None', 'marker': '.'},
+  UNSTABLE_CENTER_3D: {'color': 'tab:olive', 'markersize': _markersize, 'linestyle': 'None', 'marker': '.'},
+  UNKNOWN_3D: {'color': 'tab:cyan', 'markersize': _markersize, 'linestyle': 'None', 'marker': '.'},
+})
+
+
+def set_plot_schema(fixed_point: str, **schema):
+  if not isinstance(fixed_point, str):
+    raise TypeError(f'Must instance of string, but we got {type(fixed_point)}: {fixed_point}')
+  if fixed_point not in plot_schema:
+    raise KeyError(f'Fixed point type {fixed_point} does not found in the built-in types. ')
+  plot_schema[fixed_point].update(**schema)
+
+
+def set_markersize(markersize):
+  if not isinstance(markersize, int):
+    raise TypeError(f"Must be an integer, but got {type(markersize)}: {markersize}")
+  global _markersize
+  __markersize = markersize
+  for key in tuple(plot_schema.keys()):
+    plot_schema[key]['markersize'] = markersize
+
+

brainpy/analysis/stability.py

@@ -6,7 +6,7 @@
   'get_1d_stability_types',
   'get_2d_stability_types',
   'get_3d_stability_types',
-  'plot_scheme',
+
 
   'stability_analysis',
 
@@ -27,17 +27,13 @@
   'UNSTABLE_LINE_2D',
 ]
 
-plot_scheme = {}
+
 
 SADDLE_NODE = 'saddle node'
 CENTER_MANIFOLD = 'center manifold'
-plot_scheme[CENTER_MANIFOLD] = {'color': 'orangered'}
-plot_scheme[SADDLE_NODE] = {"color": 'tab:blue'}
 
 STABLE_POINT_1D = 'stable point'
 UNSTABLE_POINT_1D = 'unstable point'
-plot_scheme[STABLE_POINT_1D] = {"color": 'tab:red'}
-plot_scheme[UNSTABLE_POINT_1D] = {"color": 'tab:olive'}
 
 CENTER_2D = 'center'
 STABLE_NODE_2D = 'stable node'
@@ -49,18 +45,7 @@
 UNSTABLE_STAR_2D = 'unstable star'
 UNSTABLE_DEGENERATE_2D = 'unstable degenerate'
 UNSTABLE_LINE_2D = 'unstable line'
-plot_scheme.update({
-  CENTER_2D: {'color': 'lime'},
-  STABLE_NODE_2D: {"color": 'tab:red'},
-  STABLE_FOCUS_2D: {"color": 'tab:purple'},
-  STABLE_STAR_2D: {'color': 'tab:olive'},
-  STABLE_DEGENERATE_2D: {'color': 'blueviolet'},
-  UNSTABLE_NODE_2D: {"color": 'tab:orange'},
-  UNSTABLE_FOCUS_2D: {"color": 'tab:cyan'},
-  UNSTABLE_STAR_2D: {'color': 'green'},
-  UNSTABLE_DEGENERATE_2D: {'color': 'springgreen'},
-  UNSTABLE_LINE_2D: {'color': 'dodgerblue'},
-})
+
 
 STABLE_POINT_3D = 'unclassified stable point'
 UNSTABLE_POINT_3D = 'unclassified unstable point'
@@ -71,17 +56,6 @@
 UNSTABLE_FOCUS_3D = 'unstable focus'
 UNSTABLE_CENTER_3D = 'unstable center'
 UNKNOWN_3D = 'unknown 3d'
-plot_scheme.update({
-  STABLE_POINT_3D: {'color': 'tab:gray'},
-  UNSTABLE_POINT_3D: {'color': 'tab:purple'},
-  STABLE_NODE_3D: {'color': 'tab:green'},
-  UNSTABLE_SADDLE_3D: {'color': 'tab:red'},
-  UNSTABLE_FOCUS_3D: {'color': 'tab:pink'},
-  STABLE_FOCUS_3D: {'color': 'tab:purple'},
-  UNSTABLE_NODE_3D: {'color': 'tab:orange'},
-  UNSTABLE_CENTER_3D: {'color': 'tab:olive'},
-  UNKNOWN_3D: {'color': 'tab:cyan'},
-})
 
 
 def get_1d_stability_types():

brainpy/dyn/rates/populations.py

@@ -180,8 +180,8 @@ def update(self, tdi, x=None):
     self.y.value = y
 
   def clear_input(self):
-    self.input[:] = 0.
-    self.input_y[:] = 0.
+    self.input.value = bm.zeros_like(self.input)
+    self.input_y.value = bm.zeros_like(self.input_y)
 
 
 class FeedbackFHN(RateModel):
@@ -375,8 +375,8 @@ def update(self, tdi, x=None):
     self.y.value = y
 
   def clear_input(self):
-    self.input[:] = 0.
-    self.input_y[:] = 0.
+    self.input.value = bm.zeros_like(self.input)
+    self.input_y.value = bm.zeros_like(self.input_y)
 
 
 class QIF(RateModel):
@@ -558,8 +558,8 @@ def update(self, tdi, x=None):
     self.y.value = y
 
   def clear_input(self):
-    self.input[:] = 0.
-    self.input_y[:] = 0.
+    self.input.value = bm.zeros_like(self.input)
+    self.input_y.value = bm.zeros_like(self.input_y)
 
 
 class StuartLandauOscillator(RateModel):
@@ -700,8 +700,8 @@ def update(self, tdi, x=None):
     self.y.value = y
 
   def clear_input(self):
-    self.input[:] = 0.
-    self.input_y[:] = 0.
+    self.input.value = bm.zeros_like(self.input)
+    self.input_y.value = bm.zeros_like(self.input_y)
 
 
 class WilsonCowanModel(RateModel):
@@ -857,8 +857,8 @@ def update(self, tdi, x=None):
     self.y.value = y
 
   def clear_input(self):
-    self.input[:] = 0.
-    self.input_y[:] = 0.
+    self.input.value = bm.zeros_like(self.input)
+    self.input_y.value = bm.zeros_like(self.input_y)
 
 
 class JansenRitModel(RateModel):
@@ -976,5 +976,5 @@ def update(self, tdi, x=None):
     self.i.value = bm.maximum(self.i + di * dt, 0.)
 
   def clear_input(self):
-    self.Ie[:] = 0.
-    self.Ii[:] = 0.
+    self.Ie.value = bm.zeros_like(self.Ie)
+    self.Ii.value = bm.zeros_like(self.Ii)

brainpy/math/delayvars.py

@@ -435,7 +435,7 @@ def update(self, value: Union[float, int, bool, JaxArray, jnp.DeviceArray]):
       self.idx.value = stop_gradient((self.idx + 1) % self.num_delay_step)
 
     elif self.update_method == CONCAT_UPDATING:
-      self.data.value = bm.concatenate([self.data[1:], bm.broadcast_to(value, self.delay_target_shape)], axis=0)
+      self.data.value = bm.vstack([self.data[1:], bm.broadcast_to(value,self.data.shape[1:])])
 
     else:
       raise ValueError(f'Unknown updating method "{self.update_method}"')