pyvale 2025.4.1__py3-none-any.whl → 2025.5.1__py3-none-any.whl

pyvale/simtools.py

@@ -0,0 +1,67 @@
+# ==============================================================================
+# pyvale: the python validation engine
+# License: MIT
+# Copyright (C) 2025 The Computer Aided Validation Team
+# ==============================================================================
+import numpy as np
+from pyvale.rendermesh import RenderMeshData
+
+class SimTools:
+    """Namespace for tools required for analysing simulation results.
+    """
+
+    @staticmethod
+    def centre_mesh_nodes(nodes: np.ndarray, spat_dim: int) -> np.ndarray:
+        """A method to centre the nodes of a mesh around the origin.
+
+        Parameters
+        ----------
+        nodes : np.ndarray
+            An array containing the node locations of the mesh.
+        spat_dim : int
+            The spatial dimension of the mesh.
+
+        Returns
+        -------
+        np.ndarray
+            An array containing the mesh node locations, but centred around
+            the origin.
+        """
+        max = np.max(nodes, axis=0)
+        min = np.min(nodes, axis=0)
+        middle = max - ((max - min) / 2)
+        if spat_dim == 3:
+            middle[2] = 0
+        centred = np.subtract(nodes, middle)
+        return centred
+
+    @staticmethod
+    def get_deformed_nodes(timestep: int,
+                           render_mesh: RenderMeshData) -> np.ndarray | None:
+        """A method to obtain the deformed locations of all the nodes at a given
+            timestep.
+
+        Parameters
+        ----------
+        timestep : int
+            The timestep at which to find the deformed nodes.
+        render_mesh: RenderMeshData
+            A dataclass containing the skinned mesh and simulation results.
+
+        Returns
+        -------
+        np.ndarray | None
+            An array containing the deformed values of all the components at
+            each node location. Returns None if there are no deformation values.
+        """
+        if render_mesh.fields_disp is None:
+            return None
+
+        added_disp = render_mesh.fields_disp[:, timestep]
+        if added_disp.shape[1] == 2:
+            added_disp = np.hstack((added_disp,np.zeros([added_disp.shape[0],1])))
+        coords = np.delete(render_mesh.coords, 3, axis=1)
+        deformed_nodes = coords + added_disp
+        return deformed_nodes
+
+

pyvale/visualexpplotter.py

@@ -1,17 +1,24 @@
-# ================================================================================
+# ==============================================================================
 # pyvale: the python validation engine
 # License: MIT
 # Copyright (C) 2025 The Computer Aided Validation Team
-# ================================================================================
+# ==============================================================================
+
+"""
+This module contains function for plotting virtuals sensor trace summary
+statistics and uncertainty bounds over simulated experiments.
+"""
 
 from typing import Any
 import numpy as np
 import matplotlib.pyplot as plt
+from pyvale.pyvaleexceptions import VisError
 from pyvale.visualopts import (PlotOptsGeneral,
-                                   TraceOptsExperiment)
+                               TraceOptsExperiment,
+                               EExpVisBounds,
+                               EExpVisCentre)
 from pyvale.experimentsimulator import ExperimentSimulator
 
-#TODO: Docstrings
 
 def plot_exp_traces(exp_sim: ExperimentSimulator,
                     component: str,
@@ -19,20 +26,56 @@ def plot_exp_traces(exp_sim: ExperimentSimulator,
                     sim_num: int,
                     trace_opts: TraceOptsExperiment | None = None,
                     plot_opts: PlotOptsGeneral | None = None) -> tuple[Any,Any]:
-
+    """Plots time traces for summary statistics of virtual sensor traces over
+    a series of virtual experiments.
+
+    Parameters
+    ----------
+    exp_sim : ExperimentSimulator
+        Experiment simulation object containing the set of virtual experiment to
+        be plotted.
+    component : str
+        String key for the field component to plot.
+    sens_array_num : int
+        List index for the sensor array to plot.
+    sim_num : int
+        Index for the simulation to plot.
+    trace_opts : TraceOptsExperiment | None, optional
+        Dataclass containing specific options for controlling the plot
+        appearance, by default None. If None the default options are used.
+    plot_opts : PlotOptsGeneral | None, optional
+        Dataclass containing general options for formatting plots and
+        visualisations, by default None. If None the default options are used.
+
+    Returns
+    -------
+    tuple[Any,Any]
+        A tuple containing a handle to the matplotlib figure and axis objects:
+        (fig,ax).
+
+    Raises
+    ------
+    VisError
+        There are no virtual experiments or virtuale experiment stats to plot in
+        the ExperimentSimulator object. Call 'run_experiments' and 'calc_stats'.
+    """
     if trace_opts is None:
         trace_opts = TraceOptsExperiment()
 
     if plot_opts is None:
         plot_opts = PlotOptsGeneral()
 
-    descriptor = exp_sim.sensor_arrays[sens_array_num].descriptor
-    comp_ind = exp_sim.sensor_arrays[sens_array_num].field.get_component_index(component)
-    samp_time = exp_sim.sensor_arrays[sens_array_num].get_sample_times()
-    num_sens = exp_sim.sensor_arrays[sens_array_num].get_measurement_shape()[0]
+    descriptor = exp_sim._sensor_arrays[sens_array_num].descriptor
+    comp_ind = exp_sim._sensor_arrays[sens_array_num].field.get_component_index(component)
+    samp_time = exp_sim._sensor_arrays[sens_array_num].get_sample_times()
+    num_sens = exp_sim._sensor_arrays[sens_array_num].get_measurement_shape()[0]
 
-    exp_data = exp_sim.get_data()
-    exp_stats = exp_sim.get_stats()
+    exp_data = exp_sim._exp_data
+    exp_stats = exp_sim._exp_stats
+
+    if exp_data is None or exp_stats is None:
+        raise VisError("Before visualising virtual experiment traces the " \
+        "virtual experiments must be run. exp_data or exp_stats is None.")
 
     if trace_opts.sensors_to_plot is None:
         sensors_to_plot = range(num_sens)
@@ -41,7 +84,7 @@ def plot_exp_traces(exp_sim: ExperimentSimulator,
 
     #---------------------------------------------------------------------------
     # Figure canvas setup
-    fig, ax = plt.subplots(figsize=plot_opts.single_fig_size_portrait,
+    fig, ax = plt.subplots(figsize=plot_opts.single_fig_size_landscape,
                            layout='constrained')
     fig.set_dpi(plot_opts.resolution)
 
@@ -49,66 +92,64 @@ def plot_exp_traces(exp_sim: ExperimentSimulator,
     # Plot all simulated experimental points
     if trace_opts.plot_all_exp_points:
         for ss in sensors_to_plot:
-            for ee in range(exp_sim.num_exp_per_sim):
+            for ee in range(exp_sim._num_exp_per_sim):
                 ax.plot(samp_time,
                         exp_data[sens_array_num][sim_num,ee,ss,comp_ind,:],
                         "+",
                         lw=plot_opts.lw,
                         ms=plot_opts.ms,
-                        color=plot_opts.colors[ss % plot_opts.n_colors])
+                        color=plot_opts.colors[ss % plot_opts.colors_num])
 
+    sensor_tags = descriptor.create_sensor_tags(num_sens)
+    lines = []
     for ss in sensors_to_plot:
-        if trace_opts.centre == "median":
-            ax.plot(samp_time,
-                    exp_stats[sens_array_num].median[sim_num,ss,comp_ind,:],
-                    trace_opts.exp_mean_line,
-                    lw=plot_opts.lw,
-                    ms=plot_opts.ms,
-                    color=plot_opts.colors[ss % plot_opts.n_colors])
+        if trace_opts.centre == EExpVisCentre.MEDIAN:
+            trace_centre = exp_stats[sens_array_num].med[sim_num,ss,comp_ind,:]
         else:
-            ax.plot(samp_time,
-                    exp_stats[sens_array_num].mean[sim_num,ss,comp_ind,:],
-                    trace_opts.exp_mean_line,
-                    lw=plot_opts.lw,
-                    ms=plot_opts.ms,
-                    color=plot_opts.colors[ss % plot_opts.n_colors])
-
-        if trace_opts is not None:
+            trace_centre = exp_stats[sens_array_num].mean[sim_num,ss,comp_ind,:]
+
+        line, = ax.plot(samp_time,
+                trace_centre,
+                trace_opts.exp_centre_line,
+                label=sensor_tags[ss],
+                lw=plot_opts.lw,
+                ms=plot_opts.ms,
+                color=plot_opts.colors[ss % plot_opts.colors_num])
+        lines.append(line)
+
+        if trace_opts.fill_between is not None:
             upper = np.zeros_like(exp_stats[sens_array_num].min)
             lower = np.zeros_like(exp_stats[sens_array_num].min)
 
-            if trace_opts.fill_between == 'max':
-                upper = exp_stats[sens_array_num].min
-                lower = exp_stats[sens_array_num].max
-
-            elif trace_opts.fill_between == 'quartile':
-                upper = exp_stats[sens_array_num].q25
-                lower = exp_stats[sens_array_num].q75
-
-            elif trace_opts.fill_between == '2std':
-                upper = exp_stats[sens_array_num].mean + \
-                        2*exp_stats[sens_array_num].std
-                lower = exp_stats[sens_array_num].mean - \
-                        2*exp_stats[sens_array_num].std
-
-            elif trace_opts.fill_between == '3std':
-                upper = exp_stats[sens_array_num].mean + \
-                        3*exp_stats[sens_array_num].std
-                lower = exp_stats[sens_array_num].mean - \
-                        3*exp_stats[sens_array_num].std
+            if trace_opts.fill_between == EExpVisBounds.MINMAX:
+                upper = trace_opts.fill_scale*exp_stats[sens_array_num].min
+                lower = trace_opts.fill_scale*exp_stats[sens_array_num].max
+            elif trace_opts.fill_between == EExpVisBounds.QUARTILE:
+                upper = trace_opts.fill_scale*exp_stats[sens_array_num].q25
+                lower = trace_opts.fill_scale*exp_stats[sens_array_num].q75
+            elif trace_opts.fill_between == EExpVisBounds.STD:
+                upper = trace_centre + \
+                        trace_opts.fill_scale*exp_stats[sens_array_num].std
+                lower = trace_centre - \
+                        trace_opts.fill_scale*exp_stats[sens_array_num].std
+            elif trace_opts.fill_between == EExpVisBounds.MAD:
+                upper = trace_centre + \
+                        trace_opts.fill_scale*exp_stats[sens_array_num].mad
+                lower = trace_centre - \
+                        trace_opts.fill_scale*exp_stats[sens_array_num].mad
 
             ax.fill_between(samp_time,
                 upper[sim_num,ss,comp_ind,:],
                 lower[sim_num,ss,comp_ind,:],
-                color=plot_opts.colors[ss % plot_opts.n_colors],
+                color=plot_opts.colors[ss % plot_opts.colors_num],
                 alpha=0.2)
 
     #---------------------------------------------------------------------------
     # Plot simulation and truth line
     if trace_opts.sim_line is not None:
-        sim_time = exp_sim.sensor_arrays[sens_array_num].field.get_time_steps()
-        sim_vals = exp_sim.sensor_arrays[sens_array_num].field.sample_field(
-                    exp_sim.sensor_arrays[sens_array_num].positions)
+        sim_time = exp_sim._sensor_arrays[sens_array_num].field.get_time_steps()
+        sim_vals = exp_sim._sensor_arrays[sens_array_num].field.sample_field(
+                    exp_sim._sensor_arrays[sens_array_num].positions)
 
         for ss in sensors_to_plot:
             ax.plot(sim_time,
@@ -118,14 +159,14 @@ def plot_exp_traces(exp_sim: ExperimentSimulator,
                     ms=plot_opts.ms)
 
     if trace_opts.truth_line is not None:
-        truth = exp_sim.sensor_arrays[sens_array_num].get_truth()
+        truth = exp_sim._sensor_arrays[sens_array_num].get_truth()
         for ss in sensors_to_plot:
             ax.plot(samp_time,
                     truth[ss,comp_ind,:],
                     trace_opts.truth_line,
                     lw=plot_opts.lw,
                     ms=plot_opts.ms,
-                    color=plot_opts.colors[ss % plot_opts.n_colors])
+                    color=plot_opts.colors[ss % plot_opts.colors_num])
 
     #---------------------------------------------------------------------------
     # Axis / legend labels and options
@@ -139,9 +180,10 @@ def plot_exp_traces(exp_sim: ExperimentSimulator,
     else:
         ax.set_xlim(trace_opts.time_min_max)
 
-    trace_opts.legend = False
-    if trace_opts.legend:
-        ax.legend(prop={"size":plot_opts.font_leg_size},loc='best')
+    if trace_opts.legend_loc is not None:
+        ax.legend(handles=lines,
+                  prop={"size":plot_opts.font_leg_size},
+                  loc=trace_opts.legend_loc)
 
     plt.grid(True)
     plt.draw()

pyvale/visualimagedef.py

@@ -1,8 +1,12 @@
-# ================================================================================
+# ==============================================================================
 # pyvale: the python validation engine
 # License: MIT
 # Copyright (C) 2025 The Computer Aided Validation Team
-# ================================================================================
+# ==============================================================================
+
+"""
+NOTE: this module is a feature under developement.
+"""
 
 import numpy as np
 import matplotlib.pyplot as plt
@@ -59,12 +63,12 @@ class ImageDefDiags:
         vector_map = "plasma"
 
         if def_mask is not None:
-            ImageDefDiags.plot_image('Def. Mask',def_mask,image_map)
+            ImageDefDiags.plot_speckle_image('Def. Mask',def_mask,image_map)
 
-        ImageDefDiags.plot_image('Subpx Def. Image',def_image_subpx,image_map)
-        ImageDefDiags.plot_image('Def. Image',def_image,image_map)
+        ImageDefDiags.plot_speckle_image('Subpx Def. Image',def_image_subpx,image_map)
+        ImageDefDiags.plot_speckle_image('Def. Image',def_image,image_map)
 
         ext = tuple(np.array([subpx_grid_xm.min(),subpx_grid_xm.max(),
                         subpx_grid_ym.min(),subpx_grid_ym.max()])*10**3)
-        ImageDefDiags.plot_image_xy('Sub Pixel Disp X',subpx_disp_x,ext,V_CMAP)
-        ImageDefDiags.plot_image_xy('Sub Pixel Disp Y',subpx_disp_y,ext,V_CMAP)
+        ImageDefDiags.plot_image_xy('Sub Pixel Disp X',subpx_disp_x,ext,vector_map)
+        ImageDefDiags.plot_image_xy('Sub Pixel Disp Y',subpx_disp_y,ext,vector_map)

pyvale/visualimages.py

@@ -1,8 +1,12 @@
-# ================================================================================
+# ==============================================================================
 # pyvale: the python validation engine
 # License: MIT
 # Copyright (C) 2025 The Computer Aided Validation Team
-# ================================================================================
+# ==============================================================================
+
+"""
+NOTE: this module is a feature under developement.
+"""
 
 from typing import Any
 import numpy as np
@@ -10,8 +14,6 @@ import matplotlib.pyplot as plt
 from pyvale.camera import CameraBasic2D
 from pyvale.visualopts import PlotOptsGeneral
 
-# NOTE: This module is a feature under developement.
-
 # TODO: this only works for a 2D camera, maybe this should be deprecated
 def plot_measurement_image(camera: CameraBasic2D,
                            component: str,