Merge pull request #42 from siftech/develop

v1.8.0

Author: danbryce

.gitignore

@@ -315,3 +315,7 @@ gmon.out
 unsat.core
 .gitignore
 core.dimacs
+notebooks/saved-results/out
+**/*.bbl
+**/*.blg
+**/*.out

README.md

@@ -1,4 +1,4 @@
 """Version information."""
 
 # The following line *must* be the last in the module, exactly as formatted:
-__version__ = "1.5.2"
+__version__ = "1.8.0"

auxiliary_packages/funman_benchmarks/src/funman_benchmarks/_version.py

@@ -1,4 +1,4 @@
 """Version information."""
 
 # The following line *must* be the last in the module, exactly as formatted:
-__version__ = "1.7.0"
+__version__ = "1.8.0"

auxiliary_packages/funman_demo/src/funman_demo/_version.py

@@ -10,7 +10,8 @@
     ParameterSynthesisScenario,
     ParameterSynthesisScenarioResult,
 )
-from funman.search import ResultCombinedHandler
+from funman.utils.handlers import ResultCombinedHandler
+
 
 from ..plot import plot_parameter_space
 

auxiliary_packages/funman_demo/src/funman_demo/example/__init__.py

@@ -0,0 +1,102 @@
+import logging
+import os
+from typing import List, Optional
+
+import matplotlib.animation as animation
+import matplotlib.pyplot as plt
+import numpy as np
+import pandas as pd
+import seaborn as sns
+from IPython.display import HTML
+from sklearn import preprocessing
+
+from funman.server.query import FunmanResults
+
+
+def animate_heat_map(my_df, frames):
+    fig = plt.figure()
+
+    vmin = my_df.min().min()
+    vmax = my_df.max().max()
+    # ax = sns.heatmap(data, vmin=0, vmax=1)
+    # fig, ax = plt.subplots()
+    # sns.heatmap(data, vmin=vmin, vmax=vmax, cmap="crest", ax=ax)
+
+    def init():
+        # plt.clf()
+        fig.clear()
+        data = my_df.loc[0, :]
+        ax = sns.heatmap(data, vmin=vmin, vmax=vmax, cmap="crest")
+        ax.set_xlabel(data.columns[0][0])
+        ax.set_ylabel(data.index.name)
+        ax.set_title(data.columns[0][0])
+
+    def animate(i):
+        # plt.clf()
+        fig.clear()
+        data = my_df.loc[i, :]
+        # ax.set_data(data)
+        ax = sns.heatmap(data, vmin=vmin, vmax=vmax, cmap="crest")
+        ax.set_xlabel(data.columns[0][0])
+        ax.set_ylabel(data.index.name)
+        ax.set_title(f"{data.columns[0][0]}: time = {i}")
+
+    anim = animation.FuncAnimation(
+        fig,
+        animate,
+        interval=1000,
+        frames=frames,
+        init_func=init,
+    )
+
+    return anim
+
+
+def plot_spatial_timeseries(
+    results: FunmanResults,
+    variables: Optional[List[str]] = None,
+    outdir=None,
+    fps=1,
+):
+    logging.getLogger("matplotlib.animation").setLevel(logging.ERROR)
+    logging.getLogger("matplotlib.colorbar").setLevel(logging.ERROR)
+
+    df = results.dataframe(points=[results.parameter_space.true_points()[-1]])
+    steps = len(df)
+    parameters = results.model._parameter_names()
+    vars = results.model._state_var_names()
+    to_drop = (
+        parameters
+        + ["id", "label"]
+        + [v for v in vars if variables is not None and v not in variables]
+    )
+    df = df.drop(columns=to_drop)
+
+    # x = df.values #returns a numpy array
+    # min_max_scaler = preprocessing.MinMaxScaler()
+    # standard_scaler = preprocessing.StandardScaler()
+    # x_scaled = min_max_scaler.fit_transform(x)
+    # # x_scaled = standard_scaler.fit_transform(x)
+    # df = pd.DataFrame(x_scaled, columns =df.columns)
+
+    df.columns = df.columns.str.split("_", expand=True)
+    df = df.stack([1])
+    df.index = df.index.set_names(["time"] + [df.columns[0][0]])
+
+    anim_h = animate_heat_map(df, steps)
+    if outdir:
+        anim_h.save(
+            os.path.join(outdir, "h.gif"),
+            writer=animation.PillowWriter(fps=fps),
+        )
+    hh = HTML(anim_h.to_jshtml())
+    dh = df.unstack().diff().fillna(0).stack([1]).rename(columns={"h": "dh"})
+    anim_dh = animate_heat_map(dh, steps)
+    if outdir:
+        anim_dh.save(
+            os.path.join(outdir, "dh.gif"),
+            writer=animation.PillowWriter(fps=fps),
+        )
+    hdh = HTML(anim_dh.to_jshtml())
+
+    return hh, hdh, anim_h, anim_dh

auxiliary_packages/funman_demo/src/funman_demo/example/pde.py

@@ -26,6 +26,7 @@ def __init__(
         alpha=0.2,
         plot_points=False,
         parameters=None,
+        dpi=100,
     ):
         if isinstance(parameter_space, ParameterSpace):
             self.ps = parameter_space
@@ -55,20 +56,30 @@ def __init__(
             Line2D([0], [0], color="g", lw=4, alpha=alpha),
             Line2D([0], [0], color="r", lw=4, alpha=alpha),
         ]
+        self.dpi = dpi
 
     def computeBounds(self, interval: Interval = Interval(lb=-2000, ub=2000)):
         box = Box(bounds={p: interval for p in self.parameters})
         return box
 
-    def initialize_figure(self):
+    def map_param_idx_to_plot_loc(self, i, j, plot_diagonal):
+        if plot_diagonal:
+            return i, j
+        elif i == 0 or j == self.dim - 1:
+            return None, None
+        else:
+            return i - 1, j
+
+    def initialize_figure(self, plot_diagonal):
         if self.dim == 0:
             return
 
+        dim_to_plot = self.dim if plot_diagonal else self.dim - 1
         fig, axs = plt.subplots(
-            self.dim,
-            self.dim,
+            dim_to_plot,
+            dim_to_plot,
             squeeze=False,
-            dpi=600,
+            dpi=self.dpi,
             figsize=(10, 10),
         )
         self.fig = fig
@@ -89,43 +100,74 @@ def initialize_figure(self):
 
         self.fig.tight_layout(pad=3.0)
         self.data = [[None] * self.dim] * self.dim
+
         for i in range(self.dim):
             for j in range(self.dim):
-                if j > i:
-                    axs[i, j].axis("off")
+                i_coord, j_coord = self.map_param_idx_to_plot_loc(
+                    i, j, plot_diagonal
+                )
+                if i_coord is None or j_coord is None:
+                    continue
+
+                if j_coord > i_coord:
+                    axs[i_coord, j_coord].axis("off")
                 else:
-                    (self.data[i][j],) = self.axs[i, j].plot([], [])
-                    axs[i, j].set_xlabel(f"{self.parameters[i]}")
-                    axs[i, j].set_ylabel(f"{self.parameters[j]}")
+                    (self.data[i][j],) = self.axs[i_coord, j_coord].plot(
+                        [], []
+                    )
+                    axs[i_coord, j_coord].set_xlabel(f"{self.parameters[i]}")
+                    axs[i_coord, j_coord].set_ylabel(f"{self.parameters[j]}")
         self.fig.suptitle(self.title)
         plt.legend(self.custom_lines, ["true", "false"])
 
-    def plot(self, show=False):
-        self.initialize_figure()
+    def plot(self, show=False, plot_diagonal=False):
+        self.initialize_figure(plot_diagonal)
         t = "true"
         f = "false"
         for b in self.ps.false_boxes:
-            self.plotNDBox(b, self.color_map[f])
+            self.plotNDBox(b, self.color_map[f], plot_diagonal=plot_diagonal)
         for b in self.ps.true_boxes:
-            self.plotNDBox(b, self.color_map[t])
+            self.plotNDBox(b, self.color_map[t], plot_diagonal=plot_diagonal)
         if self.plot_points:
             for p in self.ps.false_points():
-                self.plot_add_point(p, self.color_map[f], self.shape_map[f])
+                self.plot_add_point(
+                    p,
+                    self.color_map[f],
+                    self.shape_map[f],
+                    plot_diagonal=plot_diagonal,
+                )
             true_points = self.ps.true_points()
             for p in true_points:
-                self.plot_add_point(p, self.color_map[t], self.shape_map[t])
+                self.plot_add_point(
+                    p,
+                    self.color_map[t],
+                    self.shape_map[t],
+                    plot_diagonal=plot_diagonal,
+                )
         if show:
             plt.show(block=False)
 
-    def plot_add_point(self, point: Point, color="r", shape="x", alpha=0.9):
+    def plot_add_point(
+        self,
+        point: Point,
+        color="r",
+        shape="x",
+        alpha=0.9,
+        plot_diagonal=False,
+    ):
         for i in range(self.dim):
             for j in range(self.dim):
-                if i < j:
+                i_coord, j_coord = self.map_param_idx_to_plot_loc(
+                    i, j, plot_diagonal
+                )
+                if i_coord is None or j_coord is None:
+                    continue
+                if j_coord > i_coord:
                     continue
                 yval = (
                     point.values[self.parameters[j]] if self.dim > 1 else 0.0
                 )
-                self.axs[i, j].scatter(
+                self.axs[i_coord, j_coord].scatter(
                     point.values[self.parameters[i]],
                     yval,
                     color=color,
@@ -136,17 +178,23 @@ def plot_add_point(self, point: Point, color="r", shape="x", alpha=0.9):
                 # self.fig.canvas.draw()
                 # self.fig.canvas.flush_events()
 
-    def plotNDBox(self, box, color="g", alpha=0.2):
+    def plotNDBox(self, box, color="g", alpha=0.2, plot_diagonal=False):
         for i in range(self.dim):
             for j in range(self.dim):
-                if i < j:
+                i_coord, j_coord = self.map_param_idx_to_plot_loc(
+                    i, j, plot_diagonal
+                )
+                if i_coord is None or j_coord is None:
                     continue
+                if j_coord > i_coord:
+                    continue
+
                 x_limits = box.bounds[self.parameters[i]]
                 y_limits = box.bounds[self.parameters[j]]
 
                 if i == j:
                     # Plot a line segment
-                    self.axs[i, j].plot(
+                    self.axs[i_coord, j_coord].plot(
                         [x_limits.lb, x_limits.ub],
                         [x_limits.lb, x_limits.ub],
                         color=color,
@@ -162,7 +210,7 @@ def plotNDBox(self, box, color="g", alpha=0.2):
                         x = np.linspace(
                             float(x_limits.lb), float(x_limits.ub), 1000
                         )
-                        self.axs[i, j].fill_between(
+                        self.axs[i_coord, j_coord].fill_between(
                             x,
                             y_limits.lb,
                             y_limits.ub,

auxiliary_packages/funman_demo/src/funman_demo/parameter_space_plotter.py

@@ -1,11 +1,12 @@
 import json
 import logging
+from typing import Dict
 
 import matplotlib.pyplot as plt
 from IPython.display import clear_output
 from matplotlib.lines import Line2D
 
-from funman import Box, Point
+from funman import Box, Parameter, Point
 from funman.representation.parameter_space import ParameterSpace
 
 l = logging.getLogger(__file__)
@@ -65,3 +66,37 @@ def plot_cached_search(search_path, alpha: float = 0.2):
         ParameterSpace(true_boxes, false_boxes, true_points, false_points),
         alpha=alpha,
     )
+
+
+def summarize_results(variables, results, ylabel="Height"):
+    points = results.points()
+    boxes = results.parameter_space.boxes()
+
+    l.info("*" * 80)
+    l.info("*" * 80)
+    l.info("* Analysis Summary ")
+    l.info("*" * 80)
+    l.info(
+        f"{len(points)} Points (+:{len(results.parameter_space.true_points())}, -:{len(results.parameter_space.false_points())}), {len(boxes)} Boxes (+:{len(results.parameter_space.true_boxes)}, -:{len(results.parameter_space.false_boxes)})"
+    )
+    if points and len(points) > 0:
+        point: Point = points[-1]
+        parameters: Dict[Parameter, float] = results.point_parameters(point)
+        results.plot(
+            variables=variables,
+            label_marker={"true": ",", "false": ","},
+            xlabel="Time",
+            ylabel=ylabel,
+            legend=variables,
+            label_color={"true": "g", "false": "r"},
+        )
+        parameter_values = {p: point.values[p.name] for p in parameters}
+        l.info(f"Parameters = {parameter_values}")
+        l.info(parameters)
+        l.info(results.dataframe([point]))
+    else:
+        # if there are no points, then we have a box that we found without needing points
+        l.info(f"Found box with no points")
+        box = boxes[0]
+        l.info(json.dumps(box.explain(), indent=4))
+    l.info("*" * 80)

auxiliary_packages/funman_demo/src/funman_demo/plot.py

@@ -1,4 +1,4 @@
 """Version information."""
 
 # The following line *must* be the last in the module, exactly as formatted:
-__version__ = "1.7.0"
+__version__ = "1.8.0"