/[escript]/trunk/doc/user/pyvisi.tex

Diff of /trunk/doc/user/pyvisi.tex

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-revision 1963 by ksteube,
Thu Sep 25 23:11:13 2008 UTC
+revision 1964 by caltinay,
Wed Nov  5 03:21:31 2008 UTC
 Line 18
  \modulesynopsis{Python Visualization Interface}
  \section{Introduction}
- \pyvisi is a Python module that is used to generate 2D and 3D visualization
+ \pyvisi is a Python module that is used to generate 2D and 3D visualizations
- for escript and its PDE solvers: finley and bruce. This module provides
+ for escript and its PDE solvers finley and bruce. The module provides
- an easy to use interface to the \VTK library (\VTKUrl). Pyvisi can be used to
+ an easy to use interface to the \VTK library (\VTKUrl) to render (generate)
- render (generate) surface maps and contours for scalar fields, arrows and
+ surface maps and contours for scalar fields, arrows and streamlines for vector
- streamlines for vector fields, and ellipsoids for tensor fields.
+ fields, and ellipsoids for tensor fields. There are three approaches for
- There are three
+ rendering an object. (1) Online - object is rendered on-screen with
- approaches for rendering an object. (1) Online - object is rendered on-screen
+ interaction capability (i.e. zoom and rotate), (2) Offline - object is
- with interaction capability (i.e. zoom and rotate), (2) Offline - object is
+ rendered off-screen (no pop-up window) and (3) Display - object is rendered
- rendered off-screen (no pop-up window) and (3) Display - object is rendered
+ on-screen but with no interaction capability (on-the-fly animation). All three
- on-screen but with no interaction capability (on-the-fly
+ approaches have the option to save the rendered object as an image (e.g. jpeg)
- animation). All three approaches have the option to save the rendered object
+ and subsequently converting a series of images into a movie (mpeg).
- as an image (i.e. jpg) and subsequently converting a series of images into a
- movie (.mpg).
  The following outlines the general steps to use Pyvisi:
  \begin{enumerate}
- \item Create a \Scene instance - a window in which objects are to be
+ \item Create a \Scene instance - a window in which objects will be rendered on.
- rendered on.
  \item Create a data input instance (i.e. \DataCollector or \ImageReader) -
- reads and loads the source data for visualization.
+ reads the source data for visualization.
- \item Create a data visualization instance (i.e. \Map, \Velocity, \Ellipsoid,
+ \item Create a data visualization object (i.e. \Map, \Velocity, \Ellipsoid,
- \Contour, \Carpet, \StreamLine or \Image) -  processes and manipulates
+ \Contour, \Carpet, \StreamLine, etc.) - creates a visual representation of
  the source data.
  \item Create a \Camera or \Light instance - controls the viewing angle and
  lighting effects.
  \item Render the object - using either the Online, Offline or Display approach.
- \item Generate movie - converts a series of images into a movie.
+ \item Generate movie - converts a series of images into a movie. (optional)
  \end{enumerate}
  \begin{center}
  \begin{math}
-Line 64 
 full details.
+Line 61 
 full details.
  \subsection{Scene Classes}
- This subsection details the instances used to setup the viewing environment.
+ This section details the instances used to setup the viewing environment.
  \subsubsection{\Scene class}
-Line 103 
 Set the position of the camera.
+Line 100 
 Set the position of the camera.
  \end{methoddesc}
  \begin{methoddesc}[Camera]{azimuth}{angle}
- Rotate the camera to the left and right.
+ Rotate the camera to the left and right. The angle parameter is in degrees.
  \end{methoddesc}
  \begin{methoddesc}[Camera]{elevation}{angle}
- Rotate the camera to the top and bottom (only between -90 and 90).
+ Rotate the camera up and down (angle must be between -90 and 90).
  \end{methoddesc}
  \begin{methoddesc}[Camera]{backView}{}
-Line 131 
 Rotate the camera to view the right side
+Line 128 
 Rotate the camera to view the right side
  \end{methoddesc}
  \begin{methoddesc}[Camera]{isometricView}{}
- Rotate the camera to view the isometric angle of the rendered object.
+ Rotate the camera to view an isometric projection of the rendered object.
  \end{methoddesc}
  \begin{methoddesc}[Camera]{dolly}{distance}
  Move the camera towards (greater than 1) the rendered object. However,
- the camera is unable to be moved away from the rendered object.
+ it is not possible to move the camera away from the rendered object with this
+ method.
  \end{methoddesc}
  \subsubsection{\Light class}
  \begin{classdesc}{Light}{scene, viewport = Viewport.SOUTH_WEST}
- A light controls the lighting effect for the rendered object and works in
+ A light controls the lighting effect for the rendered object and is set up in
  a similar way to \Camera.
  \end{classdesc}
-Line 160 
 Set the position of the light.
+Line 158 
 Set the position of the light.
  \end{methoddesc}
  \begin{methoddesc}[Light]{setAngle}{elevation = 0, azimuth = 0}
- An alternative to set the position and focal point of the light by using the
+ An alternative to set the position and focal point of the light by using
  elevation and azimuth.
  \end{methoddesc}
-Line 175 
 for visualization.
+Line 173 
 for visualization.
  \subsubsection{\DataCollector class}
  \begin{classdesc}{DataCollector}{source = Source.XML}
- A data collector is used to read data either from a XML file (using
+ A data collector is used to read data either from an XML file (using
  \texttt{setFileName()}) or from an escript object directly (using
- \texttt{setData()}). Writing XML files are expensive, but this approach has
+ \texttt{setData()}). Writing XML files is expensive but has the advantage
- the advantage given that the results can be analyzed easily after the
+ that the results can be analyzed easily after the simulation has completed.
- simulation has completed.
  \end{classdesc}
  The following are some of the methods available:
-Line 189 
 Set the XML file name to read.
+Line 186 
 Set the XML file name to read.
  \begin{methoddesc}[DataCollector]{setData}{**args}
  Create data using the \textless name\textgreater=\textless data\textgreater
- pairing. Assumption is made that the data will be given in the
+ pairing. The method assumes that the data is given in the appropriate format.
- appropriate format.
  \end{methoddesc}
  \begin{methoddesc}[DataCollector]{setActiveScalar}{scalar}
-Line 211 
 Specify the tensor field to load.
+Line 207 
 Specify the tensor field to load.
  An image reader is used to read data from an image in a variety of formats.
  \end{classdesc}
- The following are some of the methods available:
+ The following is one of the methods available:
  \begin{methoddesc}[ImageReader]{setImageName}{image_name}
- Set the image name to be read.
+ Set the filename of the image to be loaded.
  \end{methoddesc}
  \subsubsection{\TextTwoD class}
  \begin{classdesc}{Text2D}{scene, text, viewport = Viewport.SOUTH_WEST}
- A two-dimensional text is used to annotate the rendered object
+ This class is used to insert two-dimensional text for annotations
- (i.e. inserting titles, authors and labels).
+ (e.g. titles, authors and labels).
  \end{classdesc}
  The following are some of the methods available:
-Line 229 
 Set the 2D text size.
+Line 225 
 Set the 2D text size.
  \end{methoddesc}
  \begin{methoddesc}[Text2D]{boldOn}{}
- Bold the 2D text.
+ Use bold font style for the text.
  \end{methoddesc}
  \begin{methoddesc}[Text2D]{setColor}{color}
-Line 245 
 Including methods from \ActorTwoD.
+Line 241 
 Including methods from \ActorTwoD.
  \subsection{Data Visualization Classes}
  \label{DATAVIS SEC}
  This subsection details the instances used to process and manipulate the source
- data. The typical usage of some of the classes are also shown.
+ data. The typical usage of some of the classes is also shown. See \Sec{SAMPLEOUTPUT SEC} for sample images generated with these classes.
  One point to note is that the source can either be point or cell data. If the
  source is cell data, a conversion to point data may or may not be
  required, in order for the object to be rendered correctly.
  If a conversion is needed, the 'cell_to_point' flag (see below) must
- be set to 'True', otherwise 'False' (which is the default). On occasions, an
+ be set to 'True', otherwise to 'False' (which is the default). On occasions, an
  inaccurate object may be rendered from cell data even after conversion.
  \subsubsection{\Map class}
-Line 329 
 s.render(image_name = os.path.join(PYVIS
+Line 325 
 s.render(image_name = os.path.join(PYVIS
  \begin{classdesc}{MapOnPlaneCut}{scene, data_collector,
  viewport = Viewport.SOUTH_WEST, lut = Lut.COLOR, cell_to_point = False,
  outline = True}
- This class works in a similar way to \Map, except that it shows a scalar
+ This class works in a similar way to \Map, except that the result is a slice of
- field cut using a plane. The plane can be translated and rotated along the
+ the scalar field produced by cutting the map with a plane. The plane can be
- X, Y and Z axes.
+ translated and rotated to its desired position.
  \end{classdesc}
  The following are some of the methods available:\\
-Line 342 
 Methods from \ActorThreeD, \Transform an
+Line 338 
 Methods from \ActorThreeD, \Transform an
  \begin{classdesc}{MapOnPlaneClip}{scene, data_collector,
  viewport = Viewport.SOUTH_WEST, lut = Lut.COLOR, cell_to_point = False,
  outline = True}
- This class works in a similar way to \MapOnPlaneCut, except that it shows a
+ This class works in a similar way to \MapOnPlaneCut, except that the defined
- scalar field clipped using a plane.
+ plane is used to clip the scalar field.
  \end{classdesc}
  The following are some of the methods available:\\
-Line 354 
 Methods from \ActorThreeD, \Transform, \
+Line 350 
 Methods from \ActorThreeD, \Transform, \
  \begin{classdesc}{MapOnScalarClip}{scene, data_collector,
  viewport = Viewport.SOUTH_WEST, lut = Lut.COLOR, cell_to_point = False,
  outline = True}
- This class works in a similar way to \Map, except that it shows a scalar
+ This class works in a similar way to \Map, except that it only shows parts of
- field clipped using a scalar value.
+ the scalar field matching a scalar value.
  \end{classdesc}
  The following are some of the methods available:\\
-Line 367 
 Methods from \ActorThreeD, \Clipper and
+Line 363 
 Methods from \ActorThreeD, \Clipper and
  viewport = Viewport.SOUTH_WEST, lut = Lut.COLOR, cell_to_point = False}
  This class works in a similar way to \Map except that it
  shows a 2D scalar field clipped using a scalar value and subsequently
- rotated around the z-axis to create a  3D looking effect. This class should
+ rotated around the z-axis to create a 3D looking effect. This class should
  only be used with 2D data sets and NOT 3D.
  \end{classdesc}
-Line 379 
 Methods from \ActorThreeD, \Clipper, \Ro
+Line 375 
 Methods from \ActorThreeD, \Clipper, \Ro
  \begin{classdesc}{Velocity}{scene, data_collector, arrow = Arrow.TWO_D,
  color_mode = ColorMode.VECTOR, viewport = Viewport.SOUTH_WEST,
  lut = Lut.COLOR, cell_to_point = False, outline = True}
- Class that shows a vector field using arrows. The arrows can either be
+ This class is used to display a vector field using arrows. The arrows can
- color or gray-scale, depending on the lookup table used. If the arrows
+ either be color or gray-scale, depending on the lookup table used. If the
- are colored, there are two possible coloring modes, either using vector data or
+ arrows are colored, there are two possible coloring modes, either using vector
- scalar data. Similarly, there are two possible types of arrows, either
+ data or scalar data. Similarly, there are two possible types of arrows, either
- using two-dimensional or three-dimensional.
+ two-dimensional or three-dimensional.
  \end{classdesc}
  The following are some of the methods available:\\
-Line 395 
 Methods from \ActorThreeD, \GlyphThreeD,
+Line 391 
 Methods from \ActorThreeD, \GlyphThreeD,
  arrow = Arrow.TWO_D, color_mode = ColorMode.VECTOR,
  viewport = Viewport.SOUTH_WEST, lut = Lut.COLOR,
  cell_to_point = False, outline = True}
- This class works in a similar way to \MapOnPlaneCut, except that
+ This class works in a similar way to \MapOnPlaneCut, except that it shows a
- it shows a vector field using arrows cut using a plane.
+ vector field using arrows cut using a plane.
  \end{classdesc}
  The following are some of the methods available:\\
-Line 560 
 s.render(image_name = os.path.join(PYVIS
+Line 556 
 s.render(image_name = os.path.join(PYVIS
  \begin{classdesc}{Contour}{scene, data_collector,
  viewport = Viewport.SOUTH_WEST, lut = Lut.COLOR, cell_to_point = False,
  outline = True}
- Class that shows a scalar field using contour surfaces. The contour surfaces can
+ Class that shows a scalar field using contour surfaces. The contour surfaces
- either be color or gray-scale, depending on the lookup table used. This
+ can either be color or gray-scale, depending on the lookup table used. This
- class can also be used to generate iso surfaces.
+ class can also be used to generate isosurfaces.
  \end{classdesc}
  The following are some of the methods available:\\
-Line 599 
 dc1 = DataCollector(source = Source.XML)
+Line 595 
 dc1 = DataCollector(source = Source.XML)
  dc1.setFileName(file_name = os.path.join(PYVISI_EXAMPLE_MESHES_PATH, FILE_3D))
  dc1.setActiveScalar(scalar = SCALAR_FIELD_POINT_DATA)
- # Create a Contour.
+ # Create three contours.
  ctr1 = Contour(scene = s, data_collector = dc1, viewport = Viewport.SOUTH_WEST,
          lut = Lut.COLOR, cell_to_point = False, outline = True)
  ctr1.generateContours(contours = 3)
-Line 682 
 s = Scene(renderer = JPG_RENDERER, num_v
+Line 678 
 s = Scene(renderer = JPG_RENDERER, num_v
  dc1 = DataCollector(source = Source.XML)
  dc1.setFileName(file_name = os.path.join(PYVISI_EXAMPLE_MESHES_PATH, FILE_3D))
- # Create a Streamline.
+ # Create streamlines.
  sl1 = StreamLine(scene = s, data_collector = dc1,
          viewport = Viewport.SOUTH_WEST, color_mode = ColorMode.SCALAR,
          lut = Lut.COLOR, cell_to_point = False, outline = True)
-Line 851 
 s.render(image_name = os.path.join(PYVIS
+Line 847 
 s.render(image_name = os.path.join(PYVIS
  \begin{classdesc}{Logo}{scene, image_reader, viewport = Viewport.SOUTH_WEST}
  Class that displays a static image, in particular a logo
- (i.e. company symbol) and has NO interaction capability. The position and size
+ (e.g. company symbol) and has NO interaction capability. The position and size
  of the logo can be specified.
  \end{classdesc}
-Line 861 
 Methods from \ImageReslice and \ActorTwo
+Line 857 
 Methods from \ImageReslice and \ActorTwo
  \subsubsection{\Movie class}
  \begin{classdesc}{Movie}{parameter_file = "make_movie"}
- Class that creates a file called 'make_movie' by default (if a parameter
+ This class is used to create movies out of a series of images. The parameter
- file name is not specified) which contains a list of parameters required
+ specifies the name of a file that will contain the required information for the
- by the 'ppmtompeg' command to generate a movie from a series of images.
+ 'ppmtompeg' command which is used to generate the movie.
  \end{classdesc}
  The following are some of the methods available:\\
  \begin{methoddesc}[Movie]{imageRange}{input_directory, first_image, last_image}
- The image range from which the movie is to be generated from.
+ Use this method to specify that the movie is to be generated from image files
+ with filenames in a certain range (e.g. 'image000.jpg' to 'image050.jpg').
  \end{methoddesc}
  \begin{methoddesc}[Movie]{imageList}{input_directory, image_list}
- The image list from which the movie is to be generated from.
+ Use this method to specify a list of arbitrary image filenames from which the
+ movie is to be generated.
  \end{methoddesc}
  \begin{methoddesc}[Movie]{makeMovie}{movie}
- Generate the movie.
+ Generate the movie with the specified filename.
  \end{methoddesc}
  A typical usage of \Movie is shown below.
-Line 900 
 Y_SIZE = 800
+Line 898 
 Y_SIZE = 800
  SCALAR_FIELD_POINT_DATA = "temp"
  FILE_2D = "tempvel-"
  IMAGE_NAME = "movie"
- JPG_RENDERER = Renderer.ONLINE_JPG
+ JPG_RENDERER = Renderer.OFFLINE_JPG
  # Create a Scene.
  s = Scene(renderer = JPG_RENDERER, num_viewport = 1, x_size = X_SIZE,
-Line 920 
 cam1 = Camera(scene = s, viewport = View
+Line 918 
 cam1 = Camera(scene = s, viewport = View
  # Create a movie.
  mov = Movie()
- #lst = []
+ lst = []
  # Read in one file one after another and render the object.
  for i in range(938, 949):
-Line 928 
 for i in range(938, 949):
+Line 926 
 for i in range(938, 949):
              FILE_2D + "%06d.vtu") % i)
      s.render(image_name = os.path.join(PYVISI_EXAMPLE_IMAGES_PATH, \
-             IMAGE_NAME + "%06d.jpg") % i)
+             IMAGE_NAME + "%06d.jpg" % i))
-     #lst.append(IMAGE_NAME + "%06d.jpg" % i)
+     lst.append(IMAGE_NAME + "%06d.jpg" % i)
  # Images (first and last inclusive) from which the movie is to be generated.
  mov.imageRange(input_directory = PYVISI_EXAMPLE_IMAGES_PATH,
-Line 949 
 mov.makeMovie(os.path.join(PYVISI_EXAMPL
+Line 947 
 mov.makeMovie(os.path.join(PYVISI_EXAMPL
  \subsection{Coordinate Classes}
- This subsection details the instances used to position the rendered object.
+ This subsection details the instances used to position rendered objects.
  \subsubsection{\LocalPosition class}
  \begin{classdesc}{LocalPosition}{x_coor, y_coor}
- Class that defines the local positioning (X and Y) coordinate system (2D).
+ Class that defines a position (X and Y) in the local 2D coordinate system.
  \end{classdesc}
  \subsubsection{\GlobalPosition class}
  \begin{classdesc}{GlobalPosition}{x_coor, y_coor, z_coor}
- Class that defines the global positioning (X, Y and Z) coordinate system (3D).
+ Class that defines a position (X, Y and Z) in the global 3D coordinate system.
  \end{classdesc}
-Line 969 
 Class that defines the global positionin
+Line 967 
 Class that defines the global positionin
  \subsection{Supporting Classes}
  This subsection details the supporting classes and their corresponding methods
- inherited by the input (see Section \ref{INPUT SEC}) and data
+ inherited by the input (see \Sec{INPUT SEC}) and data
- visualization classes (see Section \ref{DATAVIS SEC}).
+ visualization classes (see \Sec{DATAVIS SEC}).
  \subsubsection{\ActorThreeD class}
  Class that defines a 3D actor. \\
-Line 1024 
 The following are some of the methods av
+Line 1022 
 The following are some of the methods av
  \begin{methoddesc}[ContourModule]{generateContours}{contours = None,
  lower_range = None, upper_range = None}
  Generate the specified number of contours within the specified range.
- In order to generate an iso surface, the 'lower_range' and 'upper_range'
+ In order to generate a single isosurface, the 'lower_range' and 'upper_range'
- must be equal.
+ must be set to the same value.
  \end{methoddesc}
  \subsubsection{\GlyphThreeD class}
-Line 1059 
 Set the maximum allowable scale factor f
+Line 1057 
 Set the maximum allowable scale factor f
  \end{methoddesc}
  \subsubsection{\PlaneSource class}
- Class that defines a plane source.  A plane source is defined by an origin
+ Class that defines a plane source. A plane source is defined by an origin
  and two other points, which form the axes (X and Y). \\
  The following are some of the methods available:
+ \begin{methoddesc}[PlaneSource]{setOrigin}{position}
+ Set the origin of the plane source.
+ \end{methoddesc}
  \begin{methoddesc}[PlaneSource]{setPoint1}{position}
  Set the first point from the origin of the plane source.
  \end{methoddesc}
-Line 1128 
 Translate the rendered object along the
+Line 1130 
 Translate the rendered object along the
  \end{methoddesc}
  \begin{methoddesc}[Transform]{rotateX}{angle}
- Rotate the plane along the x-axis.
+ Rotate the plane around the x-axis.
  \end{methoddesc}
  \begin{methoddesc}[Transform]{rotateY}{angle}
- Rotate the plane along the y-axis.
+ Rotate the plane around the y-axis.
  \end{methoddesc}
  \begin{methoddesc}[Transform]{rotateZ}{angle}
- Rotate the plane along the z-axis.
+ Rotate the plane around the z-axis.
  \end{methoddesc}
  \begin{methoddesc}[Transform]{setPlaneToXY}{offset = 0}
-Line 1178 
 Set the displacement scale factor.
+Line 1180 
 Set the displacement scale factor.
  \end{methoddesc}
  \subsubsection{\MaskPoints class}
- Class that defines the masking of points
+ Class that defines masking of points. This is useful to prevent the
- every n'th point.  This is useful to prevent the rendered object
+ rendered object from being cluttered with arrows or ellipsoids. \\
- from being cluttered with arrows or ellipsoids. \\
  The following are some of the methods available:
-Line 1189 
 Mask every n'th point.
+Line 1190 
 Mask every n'th point.
  \end{methoddesc}
  \begin{methoddesc}[MaskPoints]{randomOn}{}
- Enables the randomization of the points selected for masking.
+ Enables randomization of the points selected for masking.
  \end{methoddesc}
  \subsubsection{\ScalarBar class}
-Line 1230 
 Set the color of the scalar bar's title.
+Line 1231 
 Set the color of the scalar bar's title.
  \end{methoddesc}
  \subsubsection{\ImageReslice class}
- Class that defines an image reslice used to resize static
+ Class that defines an image reslice which is used to resize static
  (no interaction capability) images (i.e. logo). \\
  The following are some of the methods available:
  \begin{methoddesc}[ImageReslice]{setSize}{size}
- Set the size of the image (logo in particular), between 0 and 2. Size 1 (one)
+ Set the size factor of the image. The value must be between 0 and 2.
- displays the image in its original size (which is the default).
+ Size 1 (one) keeps the image in its original size (which is the default).
  \end{methoddesc}
  \subsubsection{\DataSetMapper class}
-Line 1283 
 The following are some of the methods av
+Line 1284 
 The following are some of the methods av
  \begin{methoddesc}[Rotation]{setResolution}{resolution}
  Set the resolution of the sweep for the rotation, which controls the
- number of intermediate points
+ number of intermediate points.
  \end{methoddesc}
  \begin{methoddesc}[Rotation]{setAngle}{angle}
-Line 1295 
 Set the angle of rotation.
+Line 1296 
 Set the angle of rotation.
  \section{More Examples}
- This section shows more examples.
+ This section provides examples for some common tasks.
- \textsf{Reading A Series of Files}
+ \subsection{Reading a Series of Files}
+ The following script shows how to generate images from a time series using
+ two data sources.
  \begin{python}
  """
-Line 1325 
 JPG_RENDERER = Renderer.ONLINE_JPG
+Line 1328 
 JPG_RENDERER = Renderer.ONLINE_JPG
  s = Scene(renderer = JPG_RENDERER, num_viewport = 1, x_size = X_SIZE,
          y_size = Y_SIZE)
- # Create a DataCollector reading from a XML file.
+ # Create a DataCollector reading from an XML file.
  dc1 = DataCollector(source = Source.XML)
  dc1.setActiveScalar(scalar = SCALAR_FIELD_POINT_DATA_1)
-Line 1349 
 mosc2.generateContours(0)
+Line 1352 
 mosc2.generateContours(0)
  # Create a Camera.
  cam1 = Camera(scene = s, viewport = Viewport.SOUTH_WEST)
- # Read in one file one after another and render the object.
+ # Read in one file after another and render the object.
  for i in range(99, 104):
      dc1.setFileName(file_name =  os.path.join(PYVISI_EXAMPLE_MESHES_PATH, \
              FILE_2D + "%04d.vtu") % i)
-Line 1360 
 for i in range(99, 104):
+Line 1363 
 for i in range(99, 104):
              IMAGE_NAME + "%04d.jpg") % i)
  \end{python}
- \textsf{Manipulating A Single File with A Series of Translation}
+ \subsection{Creating Slices of a Data Source}
+ The following script shows how to save a series of images that slice the
+ data at different points by gradually translating the cut plane.
  \begin{python}
  """
-Line 1386 
 JPG_RENDERER = Renderer.ONLINE_JPG
+Line 1391 
 JPG_RENDERER = Renderer.ONLINE_JPG
  s = Scene(renderer = JPG_RENDERER, num_viewport = 1, x_size = X_SIZE,
          y_size = Y_SIZE)
- # Create a DataCollector reading from a XML file.
+ # Create a DataCollector reading from an XML file.
  dc1 = DataCollector(source = Source.XML)
  dc1.setFileName(file_name = os.path.join(PYVISI_EXAMPLE_MESHES_PATH, FILE_3D))
  dc1.setActiveScalar(scalar = SCALAR_FIELD_POINT_DATA)
-Line 1401 
 mopc1.setPlaneToYZ(offset = 0.1)
+Line 1406 
 mopc1.setPlaneToYZ(offset = 0.1)
  c1 = Camera(scene = s, viewport = Viewport.SOUTH_WEST)
  c1.isometricView()
- # Render the object with multiple cuts using a series of translation.
+ # Render the object with multiple cuts using a series of translations.
  for i in range(0, 5):
      s.render(image_name = os.path.join(PYVISI_EXAMPLE_IMAGES_PATH, IMAGE_NAME +
              "%02d.jpg") % i)
      mopc1.translate(0.6,0,0)
  \end{python}
- \textsf{Reading Data Directly from Escript Objects}
+ \subsection{Reading Data Directly from escript Objects}
+ The following script shows how to combine Pyvisi code with escript code to
+ generate visualizations on the fly.
  \begin{python}
  """
-Line 1430 
 Y_SIZE = 400
+Line 1437 
 Y_SIZE = 400
  JPG_RENDERER = Renderer.ONLINE_JPG
  #... set some parameters ...
- xc=[0.02,0.002]
+ xc = [0.02,0.002]
- r=0.001
+ r = 0.001
- qc=50.e6
+ qc = 50.e6
- Tref=0.
+ Tref = 0.
- rhocp=2.6e6
+ rhocp = 2.6e6
- eta=75.
+ eta = 75.
- kappa=240.
+ kappa = 240.
- tend=5.
+ tend = 5.
- # ... time, time step size and counter ...
+ # initialize time, time step size and counter ...
  t=0
  h=0.1
  i=0
- #... generate domain ...
+ # generate domain ...
- mydomain = Rectangle(l0=0.05,l1=0.01,n0=250, n1=50)
+ mydomain = Rectangle(l0=0.05, l1=0.01, n0=250, n1=50)
- #... open PDE ...
+ # open PDE ...
- mypde=LinearPDE(mydomain)
+ mypde = LinearPDE(mydomain)
  mypde.setSymmetryOn()
- mypde.setValue(A=kappa*kronecker(mydomain),D=rhocp/h,d=eta,y=eta*Tref)
+ mypde.setValue(A=kappa*kronecker(mydomain), D=rhocp/h, d=eta, y=eta*Tref)
- # ... set heat source: ....
+ # set heat source: ...
- x=mydomain.getX()
+ x = mydomain.getX()
- qH=qc*whereNegative(length(x-xc)-r)
+ qH = qc*whereNegative(length(x-xc)-r)
- # ... set initial temperature ....
+ # set initial temperature ....
  T=Tref
  # Create a Scene.
-Line 1469 
 m = Map(scene = s, data_collector = dc,
+Line 1477 
 m = Map(scene = s, data_collector = dc,
  # Create a Camera.
  c = Camera(scene = s, viewport = Viewport.SOUTH_WEST)
- # ... start iteration:
+ # start iteration
- while t<0.4:
+ while t < 0.4:
-       i+=1
+       i += 1
-       t+=h
+       t += h
        mypde.setValue(Y=qH+rhocp/h*T)
-       T=mypde.getSolution()
+       T = mypde.getSolution()
        dc.setData(temp = T)
-Line 1486 
 while t<0.4:
+Line 1494 
 while t<0.4:
  \newpage
  \section{Useful Keys}
- This section shows some of the useful keys when interacting with the rendered
+ This section lists keyboard shortcuts available when interacting with rendered
- object (in the Online approach).
+ objects using the Online approach.
  \begin{table}[ht]
  \begin{center}
-Line 1516 
 Keypress 'w' & Modify the representation
+Line 1524 
 Keypress 'w' & Modify the representation
  Keypress 'r' & Reset the position of the rendered object to the center.
  \\ \hline
  \end{tabular}
- \caption{Useful keys}
+ \caption{Useful keys in Online render mode}
  \end{center}
  \end{table}
-Line 1525 
 Keypress 'r' & Reset the position of the
+Line 1533 
 Keypress 'r' & Reset the position of the
  \newpage
+ \renewcommand{\textfraction}{0.06} % force first table to stay with the text
  \section{Sample Output}
- This section displays some of the sample output by Pyvisi.
+ \label{SAMPLEOUTPUT SEC}
+ This section shows sample images produced with the various classes of Pyvisi.
- \begin{table}[ht]
+ The source code to produce these images is included in the Pyvisi distribution.
+ %
+ \begin{table}[hb]
  \begin{tabular}{c c c}
  \includegraphics[width=\thumbnailwidth]{figures/Map} &
  \includegraphics[width=\thumbnailwidth]{figures/MapOnPlaneCut} &
  \includegraphics[width=\thumbnailwidth]{figures/MapOnPlaneClip} \\
  Map & MapOnPlaneCut & MapOnPlaneClip \\
  \includegraphics[width=\thumbnailwidth]{figures/MapOnScalarClip} &
  \includegraphics[width=\thumbnailwidth]{figures/MapOnScalarClipWithRotation} &
- \includegraphics[width=\thumbnailwidth]{figures/Velocity} \\
+ \includegraphics[width=\thumbnailwidth]{figures/StreamLine} \\
- MapOnScalarClip & MapOnScalarClipWithRotation & Velocity \\ \\ \\ \\
+ MapOnScalarClip & MapOnScalarClipWithRotation & Streamline \\ \\ \\
- \includegraphics[width=\thumbnailwidth]{figures/VelocityOnPlaneCut} &
+ \includegraphics[width=\thumbnailwidth]{figures/Velocity} &
- \includegraphics[width=\thumbnailwidth]{figures/VelocityOnPlaneClip} &
+ \includegraphics[width=\thumbnailwidth]{figures/VelocityOnPlaneCut} &
- \includegraphics[width=\thumbnailwidth]{figures/Ellipsoid} \\
+ \includegraphics[width=\thumbnailwidth]{figures/VelocityOnPlaneClip} \\
- VelocityOnPlaneCut & VelocityOnPlaneClip & Ellipsoid \\ \\ \\ \\
+ Velocity & VelocityOnPlaneCut & VelocityOnPlaneClip \\ \\ \\
- \includegraphics[width=\thumbnailwidth]{figures/EllipsoidOnPlaneCut} &
+ \includegraphics[width=\thumbnailwidth]{figures/Ellipsoid} &
- \includegraphics[width=\thumbnailwidth]{figures/EllipsoidOnPlaneClip} \\
+ \includegraphics[width=\thumbnailwidth]{figures/EllipsoidOnPlaneCut} &
- EllipsoidOnPlaneCut & EllipsoidOnPlaneClip \\ \\ \\ \\
+ \includegraphics[width=\thumbnailwidth]{figures/EllipsoidOnPlaneClip} \\
+ Ellipsoid & EllipsoidOnPlaneCut & EllipsoidOnPlaneClip \\ \\
  \end{tabular}
- \caption{Sample output}
+ %\caption{Sample output}
  \end{table}
+ %
+ \newpage
+ %
  \begin{table}[t]
  \begin{tabular}{c c c}
  \includegraphics[width=\thumbnailwidth]{figures/Contour} &
  \includegraphics[width=\thumbnailwidth]{figures/ContourOnPlaneCut} &
  \includegraphics[width=\thumbnailwidth]{figures/ContourOnPlaneClip} \\
- Contour & ContourOnPlaneCut & ContourOnPlaneClip\\ \\
+ Contour & ContourOnPlaneCut & ContourOnPlaneClip \\ \\ \\
- \includegraphics[width=\thumbnailwidth]{figures/StreamLine} &
+ \includegraphics[width=\thumbnailwidth]{figures/Carpet} &
- \includegraphics[width=\thumbnailwidth]{figures/Carpet} &
+ \includegraphics[width=\thumbnailwidth]{figures/Rectangle} &
- \includegraphics[width=\thumbnailwidth]{figures/Rectangle} \\
+ \includegraphics[width=\thumbnailwidth]{figures/Image} \\
- Streamline & Carpet & Rectangle \\ \\ \\
+ Carpet & Rectangle & Image \\ \\ \\ \\ \\
  \includegraphics[width=\thumbnailwidth]{figures/Text} &
  \includegraphics[width=\thumbnailwidth]{figures/Logo} &
- \includegraphics[width=\thumbnailwidth]{figures/Image} \\
- Text & Logo & Image \\ \\
  \includegraphics[width=\thumbnailwidth]{figures/Legend} \\
- Legend \\ \\
+ Text & Logo & Legend \\ \\
  \end{tabular}
- \caption{Sample Output}
+ %\caption{Sample Output (continued)}
  \end{table}

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