Merge pull request mit-crpg#461 from GiudGiud/PR_plotter_fix

3D plot tests, plot test suite fixes and rcParams fix

openmoc/plotter.py

@@ -2,6 +2,7 @@
 import sys
 from numbers import Integral, Real
 from collections import Iterable
+import warnings
 
 import numpy as np
 import numpy.random
@@ -45,7 +46,7 @@
 plt.ioff()
 
 # Default matplotlib parameters to use in all plots
-matplotlib_rcparams = matplotlib.rcParamsDefault
+matplotlib_rcparams = matplotlib.rcParams
 matplotlib_rcparams['font.family'] = 'sans-serif'
 matplotlib_rcparams['font.weight'] = 'normal'
 matplotlib_rcparams['font.size'] = 15
@@ -61,6 +62,21 @@
  basestring = str
 
 
+def update_rc_param(curr_rc):
+ """Update matplotlib rcParams without triggering deprecation warnings.
+
+ Parameters
+ ----------
+ curr_rc : dictionary
+ A dictionary of matplotlib plotting parameters
+
+ """
+
+ with warnings.catch_warnings():
+ warnings.simplefilter("ignore", matplotlib.MatplotlibDeprecationWarning)
+ matplotlib.rcParams.update(curr_rc)
+
+
 def plot_tracks(track_generator, get_figure=False, plot_3D=False):
  """Plot the characteristic tracks from an OpenMOC simulation.
 
@@ -95,10 +111,8 @@ def plot_tracks(track_generator, get_figure=False, plot_3D=False):
  directory = openmoc.get_output_directory() + subdirectory
 
  # Ensure that normal settings are used even if called from ipython
- deprecated = ['text.latex.unicode', 'examples.directory']
- curr_rc = {k: matplotlib.rcParams[k] for k in matplotlib.rcParams.keys()
- if matplotlib.__version__[0] < '3.0' or k not in deprecated}
- matplotlib.rcParams.update(curr_rc)
+ curr_rc = matplotlib.rcParams.copy()
+ update_rc_param(curr_rc)
 
  # Make directory if it does not exist
  try:
@@ -112,6 +126,9 @@ def plot_tracks(track_generator, get_figure=False, plot_3D=False):
  vals_per_track = openmoc.NUM_VALUES_PER_RETRIEVED_TRACK
  num_azim = track_generator.getNumAzim()
  spacing = track_generator.getDesiredAzimSpacing()
+ if plot_3D and isinstance(track_generator, openmoc.TrackGenerator3D):
+ num_polar = track_generator.getNumPolar()
+ z_spacing = track_generator.getDesiredZSpacing()
  num_tracks = int(track_generator.getNumTracks())
  coords = track_generator.retrieveTrackCoords(num_tracks*vals_per_track)
 
@@ -140,21 +157,28 @@ def plot_tracks(track_generator, get_figure=False, plot_3D=False):
 
  title = 'Tracks for {0} angles and {1} cm spacing'\
  .format(num_azim, spacing)
+ if plot_3D and isinstance(track_generator, openmoc.TrackGenerator3D):
+ title = 'Tracks for {0}/{1} azimuthal/polar angles\n and {2}/{3} cm '\
+ 'azimuthal/axial spacings'.format(num_azim, num_polar, spacing,
+ z_spacing)
  plt.title(title)
 
  # Restore settings if called from ipython
- matplotlib.rcParams.update(curr_rc)
+ update_rc_param(curr_rc)
 
  # Save the figure to a file or return to user
  if track_generator.getGeometry().isRootDomain():
  if get_figure:
  return fig
  else:
  filename = \
- 'tracks-{1}-angles-{2}.png'.format(directory, num_azim,
+ 'tracks-{0}-angles-{1}.png'.format(num_azim,
  spacing)
- if plot_3D:
- filename = '3d-' + filename
+ if plot_3D and isinstance(track_generator, openmoc.TrackGenerator3D):
+ filename = '3d-tracks-{0}-azimuthal-{1}-polar-angles-{2}-'\
+ 'azimuthal-{3}-z-spacing.png'.format(num_azim, num_polar,
+ spacing, z_spacing)
+
  fig.savefig(directory+filename, bbox_inches='tight')
  plt.close(fig)
 
@@ -196,10 +220,8 @@ def plot_segments(track_generator, get_figure=False, plot_3D=False):
  directory = openmoc.get_output_directory() + subdirectory
 
  # Ensure that normal settings are used even if called from ipython
- deprecated = ['text.latex.unicode', 'examples.directory']
- curr_rc = {k: matplotlib.rcParams[k] for k in matplotlib.rcParams.keys()
- if matplotlib.__version__[0] < '3.0' or k not in deprecated}
- matplotlib.rcParams.update(curr_rc)
+ curr_rc = matplotlib.rcParams.copy()
+ update_rc_param(curr_rc)
 
  # Make directory if it does not exist
  try:
@@ -213,6 +235,9 @@ def plot_segments(track_generator, get_figure=False, plot_3D=False):
  vals_per_segment = openmoc.NUM_VALUES_PER_RETRIEVED_SEGMENT
  num_azim = track_generator.getNumAzim()
  spacing = track_generator.getDesiredAzimSpacing()
+ if plot_3D and isinstance(track_generator, openmoc.TrackGenerator3D):
+ num_polar = track_generator.getNumPolar()
+ z_spacing = track_generator.getDesiredZSpacing()
  num_segments = int(track_generator.getNumSegments())
  num_fsrs = int(track_generator.getGeometry().getNumTotalFSRs())
  coords = \
@@ -241,7 +266,7 @@ def plot_segments(track_generator, get_figure=False, plot_3D=False):
  numpy.random.shuffle(color_map)
 
  # Make figure of line segments for each track
- fig = plt.figure()
+ fig = plt.figure(constrained_layout=True)
  fig.patch.set_facecolor('none')
 
  # Create a color map corresponding to FSR IDs
@@ -266,12 +291,17 @@ def plot_segments(track_generator, get_figure=False, plot_3D=False):
 
  suptitle = 'Segments ({0} angles, {1} cm spacing)'.format(num_azim,
  spacing)
+ if plot_3D and isinstance(track_generator, openmoc.TrackGenerator3D):
+ suptitle = 'Segments ({0}/{1} azimuthal/polar angles\n and {2}/{3} cm '\
+ 'azimuthal/axial spacings'.format(num_azim, num_polar, spacing,
+ z_spacing)
  title = 'z = {0}'.format(z[0])
  plt.suptitle(suptitle)
- plt.title(title)
+ if not plot_3D:
+ plt.title(title)
 
  # Restore settings if called from ipython
- matplotlib.rcParams.update(curr_rc)
+ update_rc_param(curr_rc)
 
  if track_generator.getGeometry().isRootDomain():
  if get_figure:
@@ -280,8 +310,10 @@ def plot_segments(track_generator, get_figure=False, plot_3D=False):
  filename = 'segments-{0}-angles-{1}-spacing'.format(num_azim,
  spacing)
  filename = '{0}-z-{1}.png'.format(filename, z[0])
- if plot_3D:
- filename = '3d-' + filename
+ if plot_3D and isinstance(track_generator, openmoc.TrackGenerator3D):
+ filename = '3d-segments-{0}-azimuthal-{1}-polar-angles-{2}-'\
+ 'azimuthal-{3}-z-spacing.png'.format(num_azim, num_polar,
+ spacing, z_spacing)
  fig.savefig(directory+filename, bbox_inches='tight')
  plt.close(fig)
 
@@ -522,10 +554,10 @@ def plot_flat_source_regions(geometry, gridsize=250, xlim=None, ylim=None,
  cv.check_greater_than('marker_size', marker_size, 0)
 
  if geometry.getNumTotalFSRs() == 0:
- py_printf('ERROR', 'Unable to plot the flat source regions ' +
+ py_printf('ERROR', 'Unable to plot the source regions ' +
  'since no tracks have been generated.')
 
- py_printf('NORMAL', 'Plotting the flat source regions...')
+ py_printf('NORMAL', 'Plotting the source regions...')
 
  global subdirectory, matplotlib_rcparams
  directory = openmoc.get_output_directory() + subdirectory
@@ -544,31 +576,31 @@ def plot_flat_source_regions(geometry, gridsize=250, xlim=None, ylim=None,
  plot_params.zlim = zlim
  plot_params.plane = plane
  plot_params.offset = offset
- plot_params.suptitle = 'Flat Source Regions'
+ plot_params.suptitle = 'Source Regions'
  if plane == 'xy':
  plot_params.title = 'z = {0}'.format(plot_params.offset)
- plot_params.filename = 'flat-source-regions-z-{0}'\
+ plot_params.filename = 'source-regions-z-{0}'\
  .format(plot_params.offset)
  elif plane == 'xz':
  plot_params.title = 'y = {0}'.format(plot_params.offset)
- plot_params.filename = 'flat-source-regions-y-{0}'\
+ plot_params.filename = 'source-regions-y-{0}'\
  .format(plot_params.offset)
  elif plane == 'yz':
  plot_params.title = 'x = {0}'.format(plot_params.offset)
- plot_params.filename = 'flat-source-regions-x-{0}'\
+ plot_params.filename = 'source-regions-x-{0}'\
  .format(plot_params.offset)
  plot_params.interpolation = 'nearest'
  plot_params.vmin = 0
  plot_params.vmax = num_fsrs
 
- # Plot a 2D color map of the flat source regions
+ # Plot a 2D color map of the source regions
  figures = plot_spatial_data(fsrs_to_fsrs, plot_params, get_figure=True)
 
  if plot_params.geometry.isRootDomain():
 
  fig = figures[0]
 
- # Plot centroids on top of 2D flat source region color map
+ # Plot centroids on top of source region color map
  if centroids:
 
  # Populate a NumPy array with the FSR centroid coordinates
@@ -849,7 +881,7 @@ def plot_energy_fluxes(solver, fsrs, group_bounds=None, norm=True,
  group_bounds : Iterable of Real or None, optional
  The bounds of the energy groups
  norm : bool, optional
- Whether to normalize the fluxes (True by default)
+ Whether to normalize the fluxes to a unity flux sum (True by default)
  loglog : bool
  Whether to use a log scale on the x- and y-axes (True by default)
  get_figure : bool
@@ -894,10 +926,8 @@ def plot_energy_fluxes(solver, fsrs, group_bounds=None, norm=True,
  directory = openmoc.get_output_directory() + subdirectory
 
  # Ensure that normal settings are used even if called from ipython
- deprecated = ['text.latex.unicode', 'examples.directory']
- curr_rc = {k: matplotlib.rcParams[k] for k in matplotlib.rcParams.keys()
- if matplotlib.__version__[0] < '3.0' or k not in deprecated}
- matplotlib.rcParams.update(curr_rc)
+ curr_rc = matplotlib.rcParams.copy()
+ update_rc_param(curr_rc)
 
  # Make directory if it does not exist
  try:
@@ -913,7 +943,7 @@ def plot_energy_fluxes(solver, fsrs, group_bounds=None, norm=True,
  # Initialize an empty list of Matplotlib figures if requestd by the user
  figures = []
 
- # Iterate over all flat source regions
+ # Iterate over all source regions
  for fsr in fsrs:
 
  # Allocate memory for an array of this FSR's fluxes
@@ -967,7 +997,7 @@ def plot_energy_fluxes(solver, fsrs, group_bounds=None, norm=True,
  plt.close(fig)
 
  # Restore settings if called from ipython
- matplotlib.rcParams.update(curr_rc)
+ update_rc_param(curr_rc)
 
  # Return the figures if requested by user
  if get_figure:
@@ -992,7 +1022,7 @@ def plot_fission_rates(solver, nu=False, norm=False, transparent_zeros=True,
  Whether use the nu-fission rates instead of the fission rates
  (False by default)
  norm : bool
- Whether to normalize the fission rates (False by default)
+ Whether to normalize the fission rates to the mean (False by default)
  transparent_zeros : bool
  Whether to make all non-fissionable FSRs transparent (True by default)
  gridsize : Integral, optional
@@ -1028,7 +1058,7 @@ def plot_fission_rates(solver, nu=False, norm=False, transparent_zeros=True,
  global solver_types
  cv.check_type('solver', solver, solver_types)
 
- py_printf('NORMAL', 'Plotting the flat source region fission rates...')
+ py_printf('NORMAL', 'Plotting the source region fission rates...')
 
  # Compute the volume-weighted fission rates for each FSR
  geometry = solver.getGeometry()
@@ -1045,7 +1075,7 @@ def plot_fission_rates(solver, nu=False, norm=False, transparent_zeros=True,
  plot_params.zlim = zlim
  plot_params.plane = plane
  plot_params.offset = offset
- plot_params.suptitle = 'Flat Source Region Fission Rates'
+ plot_params.suptitle = 'Source Region Fission Rates'
  if plane == 'xy':
  plot_params.title = 'z = {0}'.format(offset)
  plot_params.filename = 'fission-rates-z-{0}.png'.format(offset)
@@ -1290,9 +1320,11 @@ def plot_spatial_data(domains_to_data, plot_params, get_figure=False):
  # Reshape data to 2D array for Matplotlib image plot
  surface.shape = (plot_params.gridsize, plot_params.gridsize)
 
- # Normalize data to maximum if requested
+ # Normalize data to average if requested
  if plot_params.norm:
- surface /= np.max(surface)
+ if np.nanmean(surface) == 0:
+ py_printf('WARNING', "Normalizing plot colormap by 0.")
+ surface /= np.nanmean(surface)
 
  # Set zero data entries to NaN so Matplotlib will make them transparent
  if plot_params.transparent_zeros:
@@ -1326,13 +1358,10 @@ def plot_spatial_data(domains_to_data, plot_params, get_figure=False):
  else:
 
  # Ensure that normal settings are used even if called from ipython
- deprecated = ['text.latex.unicode', 'examples.directory']
- curr_rc = {k: matplotlib.rcParams[k] for k in
- matplotlib.rcParams.keys() if matplotlib.__version__[0]
- < '3.0' or k not in deprecated}
- matplotlib.rcParams.update(curr_rc)
+ curr_rc = matplotlib.rcParams.copy()
+ update_rc_param(curr_rc)
 
- fig = plt.figure()
+ fig = plt.figure(constrained_layout=True)
  fig.patch.set_facecolor('none')
  plt.imshow(np.flipud(surface), extent=coords['bounds'],
  interpolation=plot_params.interpolation,
@@ -1366,7 +1395,7 @@ def plot_spatial_data(domains_to_data, plot_params, get_figure=False):
  plt.close()
 
  # Restore settings if called from ipython
- matplotlib.rcParams.update(curr_rc)
+ update_rc_param(curr_rc)
 
  # Return Matplotlib figures if requested by user
  if get_figure:
@@ -1411,10 +1440,8 @@ def plot_quadrature(solver, get_figure=False):
  directory = openmoc.get_output_directory() + subdirectory
 
  # Ensure that normal settings are used even if called from ipython
- deprecated = ['text.latex.unicode', 'examples.directory']
- curr_rc = {k: matplotlib.rcParams[k] for k in matplotlib.rcParams.keys()
- if matplotlib.__version__[0] < '3.0' or k not in deprecated}
- matplotlib.rcParams.update(curr_rc)
+ curr_rc = matplotlib.rcParams.copy()
+ update_rc_param(curr_rc)
 
  # Make directory if it does not exist
  try:
@@ -1497,7 +1524,7 @@ def plot_quadrature(solver, get_figure=False):
  plt.title(title)
 
  # Restore settings if called from ipython
- matplotlib.rcParams.update(curr_rc)
+ update_rc_param(curr_rc)
 
  # Save the figure or return to user
  if track_generator.getGeometry().isRootDomain():

tests/input_set.py

@@ -12,10 +12,11 @@ class InputSet(object):
 
  __metaclass__ = ABCMeta
 
- def __init__(self, num_dimensions=2):
+ def __init__(self, num_dimensions=2, small=False):
  self.materials = {}
  self.geometry = None
  self.dimensions = num_dimensions
+ self.small = small
 
  @abstractmethod
  def create_materials(self):
@@ -416,7 +417,6 @@ def create_geometry(self):
  super(SimpleLatticeInput, self).create_geometry()
 
 
-
 class PwrAssemblyInput(InputSet):
  """A 17x17 pin cell lattice problem from sample-input/ipython-notebook."""
 
@@ -569,7 +569,8 @@ def create_materials(self):
  directory='../../sample-input/')
 
  def create_geometry(self):
- """Instantiate a 4x4 non-uniform simple lattice Geometry."""
+ """Instantiate a 4x4 non-uniform simple lattice Geometry.
+ Lower left is at [0, 0, 0] and width is [2.62, 2.62, 2.5]"""
 
  fuel_rings = 1
  moderator_rings = 1
@@ -804,8 +805,11 @@ def create_geometry(self):
 
  lower_left = [0.,0.,0.]
  # set the XYZ widths of non-uniform lattice
+ n_z = 20
+ if self.small:
+ n_z = 5
  width = ([gap_size,pin_pitch,pin_pitch,gap_size],
- [gap_size,pin_pitch,pin_pitch,gap_size], [1.0]*20)
+ [gap_size,pin_pitch,pin_pitch,gap_size], [1.0]*n_z)
  lattice = openmoc.Lattice(name='lattice with gap')
  lattice.setWidths(width[0], width[1], width[2])
  lattice.setOffset(lower_left[0]+sum(width[0])/2.,
@@ -817,7 +821,7 @@ def create_geometry(self):
  [g,f,f,g],
  [g,f,f,g],
  [g,g,g,g]])
- fill_universes = numpy.tile(a,(20,1,1))
+ fill_universes = numpy.tile(a,(n_z,1,1))
 
  # make the geometry axially heterogeneous
  fill_universes[2][1][1] = g