Demonstration using pyvista to create figures for cookbook documentation

cookbooks/convection-box/doc/plotting_scripts/plot_all_figures.sh

@@ -0,0 +1,5 @@
+# Run every python script in this directory to quickly regenerate all of the figures for this cookbook.
+
+python3 plot_visit0000.py;
+python3 plot_visit0001.py;
+

cookbooks/convection-box/doc/plotting_scripts/plot_visit0000.py

@@ -0,0 +1,68 @@
+import pyvista as pv
+import matplotlib.pyplot as plt
+from matplotlib.colors import ListedColormap
+from cmcrameri import cm # Fabio Crameri's color maps
+import numpy as np
+import os
+
+pv.set_plot_theme("document")
+plotter = pv.Plotter(off_screen=True)
+
+mesh = pv.read("../../output-convection-box/solution/solution-00000.pvtu")
+plot_spatial_bounds = [0, 1, 0, 1, 0, 0]
+mesh = mesh.clip_box(bounds=plot_spatial_bounds, invert=False)
+arrows = mesh.glyph(scale="velocity", factor=0.01,orient="velocity")
+
+# scale the meshes down to put the scale bar on the side (like in the docs)
+mesh = mesh.scale(0.75)
+arrows = arrows.scale(0.75)
+
+# Define properties for the scalar bar arguments
+sargs = dict(
+    width=0.2,
+    height=0.6,
+    title="T",
+    label_font_size=24,
+    title_font_size=32,
+    color="black",
+    position_x=0.0,
+    position_y=0.20,
+    vertical=True
+)
+
+mesh_actor = plotter.add_mesh(mesh, scalars="T", log_scale=False, scalar_bar_args=sargs,cmap=cm.vik)
+arrows_actor = plotter.add_mesh(arrows,color='white')
+plotter.view_xy()
+
+# Displace the meshes to make room for the scalar bar
+mesh_actor.position = (0.225,0.15,0)
+arrows_actor.position = (0.225,0.15,0)
+
+# shows the axes labels on the actual mesh (show_axes shows a widget in 3d space)
+plotter.show_bounds(
+use_3d_text=False,use_2d=True, # These parameters make it easier to plot 2D data
+axes_ranges=[0,1,0,1,0,0], # We displaced mesh_actor earler, so we need to reset the axes ranges
+grid='front',ticks='outside',location='outer',
+xtitle='X Axis',ytitle='Y Axis'# Model bounds are in meters, kilometers make the labels more readable
+)
+
+# Calculate Camera Position from Bounds
+bounds_array = np.array(plot_spatial_bounds)
+xmag = float(abs(bounds_array[1] - bounds_array[0]))
+ymag = float(abs(bounds_array[3] - bounds_array[2]))
+aspect_ratio = ymag / xmag
+# Multiplying the xmagnitude here results in an image with less white space.
+# Modifying plot_spatial_bounds directly will distort the actual pyvista mesh.
+aspect_ratio = ymag / (xmag*1.2) 
+plotter.window_size = (1024, int(1024 * aspect_ratio))
+xmid = xmag / 2 + bounds_array[0]  # X midpoint
+ymid = ymag / 2 + bounds_array[2]  # Y midpoint
+zoom = xmag * aspect_ratio * 1.875  # Zoom level - not sure why 1.875 works
+
+position = (xmid, ymid, zoom)
+focal_point = (xmid, ymid, 0)
+viewup = (0, 1, 0)
+camera = [position, focal_point, viewup]
+plotter.camera_position = camera
+plotter.camera_set = True
+plotter.screenshot("../visit0000.png")

cookbooks/convection-box/doc/plotting_scripts/plot_visit0001.py

@@ -0,0 +1,68 @@
+import pyvista as pv
+import matplotlib.pyplot as plt
+from matplotlib.colors import ListedColormap
+from cmcrameri import cm # Fabio Crameri's color maps
+import numpy as np
+import os
+
+pv.set_plot_theme("document")
+plotter = pv.Plotter(off_screen=True)
+
+mesh = pv.read("../../output-convection-box/solution/solution-00049.pvtu")
+plot_spatial_bounds = [0, 1, 0, 1, 0, 0]
+mesh = mesh.clip_box(bounds=plot_spatial_bounds, invert=False)
+arrows = mesh.glyph(scale="velocity", factor=0.001,orient="velocity")
+
+# scale the meshes down to put the scale bar on the side (like in the docs)
+mesh = mesh.scale(0.75)
+arrows = arrows.scale(0.75)
+
+# Define properties for the scalar bar arguments
+sargs = dict(
+    width=0.2,
+    height=0.6,
+    title="T",
+    label_font_size=24,
+    title_font_size=32,
+    color="black",
+    position_x=0.0,
+    position_y=0.20,
+    vertical=True
+)
+
+mesh_actor = plotter.add_mesh(mesh, scalars="T", log_scale=False, scalar_bar_args=sargs,cmap=cm.vik)
+arrows_actor = plotter.add_mesh(arrows,color='white')
+plotter.view_xy()
+
+# Displace the meshes to make room for the scalar bar
+mesh_actor.position = (0.225,0.15,0)
+arrows_actor.position = (0.225,0.15,0)
+
+# shows the axes labels on the actual mesh (show_axes shows a widget in 3d space)
+plotter.show_bounds(
+use_3d_text=False,use_2d=True, # These parameters make it easier to plot 2D data
+axes_ranges=[0,1,0,1,0,0], # We displaced mesh_actor earler, so we need to reset the axes ranges
+grid='front',ticks='outside',location='outer',
+xtitle='X Axis',ytitle='Y Axis'# Model bounds are in meters, kilometers make the labels more readable
+)
+
+# Calculate Camera Position from Bounds
+bounds_array = np.array(plot_spatial_bounds)
+xmag = float(abs(bounds_array[1] - bounds_array[0]))
+ymag = float(abs(bounds_array[3] - bounds_array[2]))
+
+# Multiplying the xmagnitude here results in an image with less white space.
+# Modifying plot_spatial_bounds directly will distort the actual pyvista mesh.
+aspect_ratio = ymag / (xmag*1.2) 
+plotter.window_size = (1024, int(1024 * aspect_ratio))
+xmid = xmag / 2 + bounds_array[0]  # X midpoint
+ymid = ymag / 2 + bounds_array[2]  # Y midpoint
+zoom = xmag * aspect_ratio * 1.875  # Zoom level - not sure why 1.875 works
+
+position = (xmid, ymid, zoom)
+focal_point = (xmid, ymid, 0)
+viewup = (0, 1, 0)
+camera = [position, focal_point, viewup]
+plotter.camera_position = camera
+plotter.camera_set = True
+plotter.screenshot("../visit0001.png")

cookbooks/crustal_deformation/pyvista_doc.py

@@ -0,0 +1,61 @@
+import pyvista as pv
+import matplotlib.pyplot as plt
+from matplotlib.colors import ListedColormap
+from cmcrameri import cm # Fabio Crameri's color maps
+import numpy as np
+import os
+
+timereader = pv.get_reader("./output-crustal_model_2D/solution.pvd")
+times = np.array(timereader.time_values) / 1e6  # convert yrs to Myrs
+
+pv.set_plot_theme("document")
+plotter = pv.Plotter(off_screen=True)
+
+mesh = pv.read("output-crustal_model_2D/solution/solution-00020.pvtu")
+plot_spatial_bounds = [0, 100e3, 0, 100e3, 0, 0]
+
+# Define properties for the scalar bar arguments
+sargs = dict(
+    width=0.6,
+    height=0.1,
+    title="Viscosity (Pa s)",
+    label_font_size=24,
+    title_font_size=32,
+    color="black",
+    position_x=0.20,
+    position_y=0.05,
+    n_labels=2,
+    vertical=False
+)
+
+mesh_actor = plotter.add_mesh(mesh, scalars="viscosity", log_scale=True, scalar_bar_args=sargs,cmap=cm.batlow_r)
+
+# Displace the mesh to make room for the scalar bar
+mesh_actor.position = (10e3,25e3,0)
+plotter.view_xy()
+
+plotter.show_bounds(
+use_3d_text=False,use_2d=True, # These parameters make it easier to plot 2D data
+axes_ranges=[0,80,0,16,0,0], # We displaced mesh_actor earler, so we need to reset the axes ranges
+grid='front',ticks='outside',location='outer',
+n_ylabels=3,n_xlabels=9,bold=False,
+xtitle='X Axis (km)',ytitle='Y Axis (km)'# Model bounds are in meters, kilometers make the labels more readable
+)
+
+# Calculate Camera Position from Bounds
+bounds_array = np.array(plot_spatial_bounds)
+xmag = float(abs(bounds_array[1] - bounds_array[0]))
+ymag = float(abs(bounds_array[3] - bounds_array[2]))
+aspect_ratio = ymag / xmag
+plotter.window_size = (1024, int(1024 * aspect_ratio))
+xmid = xmag / 2 + bounds_array[0]  # X midpoint
+ymid = ymag / 2 + bounds_array[2]  # Y midpoint
+zoom = xmag * aspect_ratio * 1.875  # Zoom level
+
+position = (xmid, ymid, zoom)
+focal_point = (xmid, ymid, 0)
+viewup = (0, 1, 0)
+camera = [position, focal_point, viewup]
+plotter.camera_position = camera
+plotter.camera_set = True
+plotter.screenshot("fig108.png")

doc/sphinx/environment.yml

@@ -11,3 +11,4 @@ dependencies:
   - pip:
     - sphinxcontrib-tikz
     - sphinxcontrib-svg2pdfconverter[CairoSVG]
+    - cmcrameri