Merge pull request #197 from prabhuramachandran/misc-viewer-improvements

Misc viewer improvements

docs/source/tutorial/circular_patch_simple.rst

@@ -370,22 +370,22 @@ interpreter with a few useful objects available.  These are::
     >>> dir()
     ['__builtins__', '__doc__', '__name__', 'interpolator', 'mlab',
      'particle_arrays', 'scene', 'self', 'viewer']
-    >>> len(particle_arrays)
-    1
-    >>> particle_arrays[0].name
+    >>> particle_arrays['fluid'].name
     'fluid'
 
-The ``particle_arrays`` object is a list of **ParticleArrayHelpers** which is
-available in :py:class:`pysph.tools.mayavi_viewer.ParticleArrayHelper`. The
+The ``particle_arrays`` object is a dictionary of **ParticleArrayHelpers**
+which is available in
+:py:class:`pysph.tools.mayavi_viewer.ParticleArrayHelper`. The
 ``interpolator`` is an instance of
 :py:class:`pysph.tools.mayavi_viewer.InterpolatorView` that is used by the
 viewer. The other objects can be used to script the user interface if desired.
+Note that the ``particle_arrays`` can be indexed by array name or index.
 
 Here is an example of scripting the viewer. Let us say we have two particle
 arrays, `'boundary'` and `'fluid'` in that order. Let us say, we wish to make
 the boundary translucent, then we can write the following::
 
-   b = particle_arrays[0]
+   b = particle_arrays['boundary']
    b.plot.actor.property.opacity = 0.2
 
 This does require some knowledge of Mayavi_ and scripting with it. The `plot`
@@ -394,6 +394,14 @@ a `Glyph` instance from Mayavi_. It is useful to use the `record feature
 <http://docs.enthought.com/mayavi/mayavi/mlab_changing_object_looks.html#changing-object-properties-interactively>`_
 of Mayavi to learn more about how best to script the view.
 
+The viewer will always look for a ``mayavi_config.py`` script inside the
+output directory to setup the visualization parameters. This file can be
+created by overriding the :py:class:`pysph.solver.application.Application`
+object's ``customize_output`` method. See the `dam break 3d
+<https://github.com/pypr/pysph/blob/master/pysph/examples/dam_break_3d.py>`_
+example to see this being used. Of course, this file can also be created
+manually.
+
 
 Loading output data files
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^

pysph/examples/dam_break_3d.py

@@ -74,6 +74,14 @@ def configure_scheme(self):
     def create_particles(self):
         return self.geom.create_particles()
 
+    def customize_output(self):
+        self._mayavi_config('''
+        viewer.scalar = 'u'
+        b = particle_arrays['boundary']
+        b.plot.actor.mapper.scalar_visibility = False
+        b.plot.actor.property.opacity = 0.1
+        ''')
+
 
 if __name__ == '__main__':
     app = DamBreak3D()

pysph/examples/sphysics/case5.py

@@ -114,7 +114,15 @@ def create_particles(self):
         self.scheme.setup_properties([f, b])
         return [f, b]
 
+    def customize_output(self):
+        self._mayavi_config('''
+        viewer.scalar = 'vmag'
+        b = particle_arrays['boundary']
+        b.plot.actor.mapper.scalar_visibility = False
+        b.plot.actor.property.opacity = 0.1
+        ''')
+
 
 if __name__ == '__main__':
     app = Case5()
-    app.run()
+    app.run()

pysph/examples/sphysics/dam_break.py

@@ -102,7 +102,15 @@ def create_particles(self):
         self.scheme.setup_properties([f, b])
         return [f, b]
 
+    def customize_output(self):
+        self._mayavi_config('''
+        viewer.scalar = 'vmag'
+        b = particle_arrays['boundary']
+        b.plot.actor.mapper.scalar_visibility = False
+        b.plot.actor.property.opacity = 0.15
+        ''')
+
 
 if __name__ == '__main__':
     app = DamBreak()
-    app.run()
+    app.run()

pysph/solver/application.py

@@ -1,14 +1,15 @@
 # Standard imports.
+from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter
 import glob
 import inspect
 import json
 import logging
 import os
-from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter
 from os.path import (abspath, basename, dirname, isdir, join, realpath,
                      splitext)
 import socket
 import sys
+from textwrap import dedent
 import time
 import numpy as np
 import warnings
@@ -124,7 +125,9 @@ def create_scheme(self):
     10. :py:meth:`create_tools()`: Add any ``pysph.solver.tools.Tool``
         instances.
 
-    Additionally, as the appliction runs there are several convenient optional
+    11. :py:meth:`customize_output()`: Customize the output visualization.
+
+    Additionally, as the application runs there are several convenient optional
     callbacks setup:
 
     1. :py:meth:`pre_step`: Called before each time step.
@@ -1379,6 +1382,17 @@ def _log_solver_info(self, solver):
             eqn_info = equations
         logger.info('Using equations:\n%s\n%s\n%s', sep, eqn_info, sep)
 
+    def _mayavi_config(self, code):
+        """Write out the given code to a `mayavi_config.py` in the output
+        directory.
+
+        Note that this will call `textwrap.dedent` on the code.
+        """
+        cfg = os.path.join(self.output_dir, 'mayavi_config.py')
+        if not os.path.exists(cfg):
+            with open(cfg, 'w') as fp:
+                fp.write(dedent(code))
+
     ######################################################################
     # Public interface.
     ######################################################################
@@ -1471,6 +1485,8 @@ def run(self, argv=None):
             self._message("Setup took: %.5f secs" % (setup_duration))
             self._write_info(self.info_filename, completed=False, cpu_time=0)
 
+        self.customize_output()
+
         start_time = time.time()
         self.solver.solve(not self.options.quiet)
         end_time = time.time()
@@ -1652,6 +1668,18 @@ def create_tools(self):
         """
         return []
 
+    def customize_output(self):
+        """Customize the output file visualization by adding any files.
+
+        For example, the pysph view command will look for a
+        ``mayavi_config.py`` file that can be used to script the viewer. You
+        can use self._mayavi_config('code') to add a default customization
+        here.
+
+        Note that this is executed before the simulation starts.
+        """
+        pass
+
     def pre_step(self, solver):
         """If overloaded, this is called automatically before each integrator
         step.  The method is passed the solver instance.

pysph/tools/mayavi_viewer.py

@@ -210,9 +210,11 @@ def _update_plot(self):
 
             if self.plot is None:
                 if interp.dim == 3:
-                    plot = mlab.pipeline.scalar_cut_plane(src)
+                    plot = mlab.pipeline.scalar_cut_plane(
+                        src, colormap='viridis'
+                    )
                 else:
-                    plot = mlab.pipeline.surface(src)
+                    plot = mlab.pipeline.surface(src, colormap='viridis')
                 self.plot = plot
                 scm = plot.module_manager.scalar_lut_manager
                 scm.set(show_legend=self.show_legend,
@@ -399,7 +401,9 @@ def _particle_array_changed(self, old, pa):
             old_empty = len(old_x) == 0
         if p is None and not empty:
             src = mlab.pipeline.scalar_scatter(x, y, z, s)
-            p = mlab.pipeline.glyph(src, mode='point', scale_mode='none')
+            p = mlab.pipeline.glyph(
+                src, mode='point', scale_mode='none', colormap='viridis'
+            )
             p.actor.property.point_size = 6
             scm = p.module_manager.scalar_lut_manager
             scm.set(show_legend=self.show_legend,
@@ -505,7 +509,8 @@ def _show_vectors_changed(self, value):
             pv = self.scene.mlab.pipeline.vectors(
                 self.plot.mlab_source.m_data,
                 mask_points=self.mask_on_ratio,
-                scale_factor=self.scale_factor
+                scale_factor=self.scale_factor,
+                colormap='viridis'
             )
             self.plot_vectors = pv
 
@@ -1010,7 +1015,11 @@ def _shell_fired(self):
         obj.edit_traits()
 
     def _get_shell_namespace(self):
-        return dict(viewer=self, particle_arrays=self.particle_arrays,
+        pas = {}
+        for i, x in enumerate(self.particle_arrays):
+            pas[i] = x
+            pas[x.name] = x
+        return dict(viewer=self, particle_arrays=pas,
                     interpolator=self.interpolator, scene=self.scene,
                     mlab=self.scene.mlab)
 
@@ -1024,6 +1033,9 @@ def _directory_changed(self, d):
             self.file_count = min(self.file_count, len(files))
         else:
             pass
+        config_file = os.path.join(d, 'mayavi_config.py')
+        if os.path.exists(config_file):
+            self.run_script(config_file)
 
     def _live_mode_changed(self, value):
         if value:
@@ -1168,6 +1180,9 @@ def main(args=None):
                 if len(_files) == 0:
                     _files = glob.glob(os.path.join(arg, '*.npz'))
                 files.extend(_files)
+                config_file = os.path.join(arg, 'mayavi_config.py')
+                if os.path.exists(config_file):
+                    scripts.append(config_file)
                 continue
             else:
                 usage()