--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/add_surface_field_from_expression.py	Sat Nov 14 14:14:45 2015 -0500
@@ -0,0 +1,53 @@
+#!/usr/bin/env python
+import argparse
+import shutil
+
+import icqsol_utils
+from icqsol.shapes.icqShapeManager import ShapeManager
+
+# Parse Command Line.
+parser = argparse.ArgumentParser()
+parser.add_argument( '--input', dest='input', help='Shape dataset selected from history' )
+parser.add_argument( '--field_name', dest='field_name', help='Surface field name' )
+parser.add_argument( '--expression', dest='expression', help='Expression for applying surface field to shape' )
+parser.add_argument( '--time_point', dest='time_points', type=float, action='append', nargs=1, help='Points in time' )
+parser.add_argument( '--output', dest='output', help='Output dataset' )
+parser.add_argument( '--output_format_and_type', dest='output_format_and_type', help='Output file format and type' )
+
+args = parser.parse_args()
+
+valid_field_name = args.field_name.replace( ' ', '_' )
+tmp_dir = icqsol_utils.get_temp_dir()
+shape_mgr = ShapeManager()
+
+# Get the shape from the input dataset.
+shape = shape_mgr.load(args.input)
+# Get the points from the shape.
+pdata = shape_mgr.shapeToVTKPolyData(shape)
+points = pdata.GetPoints()
+num_points = points.GetNumberOfPoints()
+# Define the data.
+data = vtk.vtkDoubleArray()
+data.SetName(valid_field_name)
+# Handle time points.
+time_points = [ '%.1f' % tp for tp in args.time_points ]
+num_time_points = len(time_points)
+# Update the data.
+data.SetNumberOfComponents(num_time_points)
+data.SetNumberOfTuples(num_points)
+# Add the surface field.
+for i in range(num_points):
+    x, y, z = points.GetPoint(i)
+    for j in range(num_time_points):
+        t = time_points[ j ]
+        field_value = eval(args.expression)
+        data.SetComponent(i, j, field_value)
+pdata.GetPointData().SetScalars(data)
+
+# Define the output file format and type.
+output_format, output_file_type = icqsol_utils.get_format_and_type( args.output_format_and_type )
+tmp_output_path = icqsol_utils.get_temporary_file_path( tmp_dir, output_format )
+
+# Save the output.
+shape_mgr.save( composite_shape, file_name=tmp_output_path, file_format=output_format, file_type=output_file_type )
+shutil.move( tmp_output_path, args.output )

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/icqsol_add_surface_field_from_expression.py	Sat Nov 14 14:14:45 2015 -0500
@@ -0,0 +1,57 @@
+#!/usr/bin/env python
+import argparse
+import shutil
+
+import icqsol_utils
+from icqsol.shapes.icqShapeManager import ShapeManager
+
+# Parse Command Line.
+parser = argparse.ArgumentParser()
+parser.add_argument( '--input', dest='input', help='Shape dataset selected from history' )
+parser.add_argument( '--input_file_format_and_type', dest='input_file_format_and_type', help='Input file format and type' )
+parser.add_argument( '--input_dataset_type', dest='input_dataset_type', help='Input dataset_type' )
+parser.add_argument( '--field_name', dest='field_name', help='Surface field name' )
+parser.add_argument( '--location', dest='location', help='Location of field within cell, either point or cell' )
+parser.add_argument( '--expression', dest='expression', help='Expression for applying surface field to shape' )
+parser.add_argument( '--time_point', dest='time_points', type=float, action='append', nargs=1, help='Points in time' )
+parser.add_argument( '--max_edge_length', dest='max_edge_length', type=float, default='0', help='Maximum edge length' )
+parser.add_argument( '--output', dest='output', help='Output dataset' )
+parser.add_argument( '--output_vtk_type', dest='output_vtk_type', help='Output VTK type' )
+
+args = parser.parse_args()
+
+input_format, input_file_type = icqsol_utils.get_format_and_type( args.input_file_format_and_type )
+time_points = [ tp[0] for tp in args.time_points ]
+tmp_dir = icqsol_utils.get_temp_dir()
+
+# Instantiate a ShapeManager for loading the input.
+if input_format == 'vtk':
+    shape_mgr = ShapeManager( file_format=input_format, vtk_dataset_type=args.input_dataset_type )
+else:
+    shape_mgr = ShapeManager( file_format=input_format )
+
+# Get the shape from the input dataset.
+shp = shape_mgr.loadAsShape(args.input)
+
+max_edge_length = float('inf')
+if args.max_edge_length > 0:
+    max_edge_length = args.max_edge_length
+
+# Add surface field to shape data.
+vtk_poly_data = shape_mgr.addSurfaceFieldFromExpressionToShape(shp,
+                                                               args.field_name,
+                                                               args.expression,
+                                                               time_points,
+                                                               max_edge_length,
+                                                               args.location)
+
+# Define the output file format and type (the outpur_format can only be 'vtk').
+output_format, output_file_type = icqsol_utils.get_format_and_type( args.output_vtk_type )
+tmp_output_path = icqsol_utils.get_temporary_file_path( tmp_dir, output_format )
+
+# Make sure the ShapeManager's writer is vtk.
+shape_mgr.setWriter( file_format='vtk', vtk_dataset_type=icqsol_utils.POLYDATA )
+
+# Save the output.
+shape_mgr.saveVtkPolyData( vtk_poly_data=vtk_poly_data, file_name=tmp_output_path, file_type=output_file_type)
+shutil.move( tmp_output_path, args.output )

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/icqsol_add_surface_field_from_expression.xml	Sat Nov 14 14:14:45 2015 -0500
@@ -0,0 +1,94 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="icqsol_add_surface_field_from_expression" name="Add surface field" version="1.0.0">
+    <description>from expression</description>
+    <macros>
+        <import>icqsol_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command>
+<![CDATA[
+    python $__tool_directory__/icqsol_add_surface_field_from_expression.py
+    --input "$input"
+    --input_file_format_and_type $input.ext
+    --input_dataset_type $input.metadata.dataset_type
+    --field_name "$field_name"
+    --location $location
+    --expression "$expression"
+    #for $tp in $time_points:
+        --time_point ${tp.time_point}
+    #end for
+    #if $refine_shape_cond.refine_shape == "yes":
+        --max_edge_length $refine_shape_cond.max_edge_length
+    #end if
+    --output "$output"
+    --output_vtk_type $output_vtk_type
+]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="plyascii,plybinary,vtkascii,vtkbinary" label="Shape">
+            <validator type="dataset_ok_validator" />
+        </param>
+        <param name="field_name" type="text" value="surface_field" label="Surface field name" help="Spaces will be converted to underscore character."/>
+        <param name="location" type="select" label="Location of field" help="Field values vary linearly between nodes when visualizing fields located at points, while each triangle is assigned a single value with fields located at cells.">
+            <option value="cell" selected="True">Cell</option>
+            <option value="point">Point</option>
+        </param>
+        <param name="expression" type="text" value="(x**2 * sin(y*pi) + z**4) * exp(t)" label="Expression" help="Legal variables are x,y,z (point coordinates) and t (time)."/>
+        <repeat name="time_points" title="Points in time" min="1" help="Provides snapshots of surface field over time sequence.">
+            <param name="time_point" type="float" value="0" label="Time point" help="Floating point number"/>
+        </repeat>
+        <conditional name="refine_shape_cond">
+            <param name="refine_shape" type="select" label="Refine shape?" help="Points will be added to the shape's edges restricting their length to the maximum.">
+                <option value="no" selected="True">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <param name="max_edge_length" type="float" value="0" label="Maximum edge length" help="Floating point number, 0 results in no refinement."/>
+            </when>
+        </conditional>
+        <expand macro="output_vtk_type_params" />
+    </inputs>
+    <outputs>
+        <data name="output" format="vtkascii" label="${tool.name} ${on_string}">
+            <actions>
+                <action type="format">
+                    <option type="from_param" name="output_vtk_type" />
+                </action>
+            </actions>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="box.vtkascii" ftype="vtkascii" />
+            <param name="input_file_format_and_type" value="vtkascii" />
+            <param name="input_dataset_type" value="POLYDATA" />
+            <param name="field_name" value="surface_field" />
+            <param name="expression" value="(x**2 * sin(y*pi) + z**4) * exp(t)" />
+            <repeat name="time_points">
+                <param name="time_point" value="0.1" />
+            </repeat>
+            <output name="output" file="box_with_surface_field.vtkascii" ftype="vtkascii" />
+            <param name="output_vtk_type" value="vtkascii" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+<![CDATA[
+
+Adds a surface field to a selected shape based on a given mathematical expression consisting of
+variables x, y, z (shape point coordinates) and t (time).  This tool will generate VTK POLYDATA
+files, so input PLY files or VTK files with a different dataset type will automatically be converted
+to VTK POLYDATA during tool execution.
+
+* **Shape** - Shape to which a surface field will be added.
+* **Surface field name** - Name of the surface field to be added to the shape.
+* **Expression** - Mathematical expression consisting of variables x, y, z (shape point coordinates) and t (time) that defines the surface field.
+* **Time point** - A floating point value that defines a time point where multiple time points define a sequence of time snapshots for the surface field.
+* **Refine shape** - Select yes to refine the shape by shortening the edge lengths to a defined maximum.
+* **Maximum edge length** - Points are added to the shape's edges that are longer than the defined maximum length.
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/icqsol_macros.xml	Sat Nov 14 14:14:45 2015 -0500
@@ -0,0 +1,115 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="1.0">icqsol</requirement>
+        </requirements>
+    </xml>
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:"/>
+            <exit_code range=":-1"/>
+            <regex match="Error:"/>
+            <regex match="Exception:"/>
+        </stdio>
+    </xml>
+    <!-- TODO: place this in colormaps_conf.xml -->
+    <xml name="color_map_param">
+        <param name="color_map" type="select" label="Color map">
+            <option value="hot" selected="True">Hot</option>
+            <option value="cold">Cold</option>
+            <option value="blackbody">Blackbody</option>
+            <option value="gnu">Gnu</option>
+        </param>
+    </xml>
+    <xml name="output_vtk_type_params">
+        <param name="output_vtk_type" type="select" label="Output file type">
+            <option value="vtkascii" selected="True">Vtk-ascii</option>
+            <option value="vtkbinary">Vtk-binary</option>
+        </param>
+    </xml>
+    <token name="@origin_cmd_args@">
+        --origin_x $create_process_cond.shape_cond.origin_x
+        --origin_y $create_process_cond.shape_cond.origin_y
+        --origin_z $create_process_cond.shape_cond.origin_z
+    </token>
+    <xml name="origin_params">
+        <param name="origin_x" type="float" value="0.0" label="X coordinate of origin" help="Floating point number"/>
+        <param name="origin_y" type="float" value="0.0" label="Y coordinate of origin" help="Floating point number"/>
+        <param name="origin_z" type="float" value="0.0" label="Z coordinate of origin" help="Floating point number"/>
+    </xml>
+    <token name="@lengths_cmd_args@">
+        --length_x $create_process_cond.shape_cond.length_x
+        --length_y $create_process_cond.shape_cond.length_y
+        --length_z $create_process_cond.shape_cond.length_z
+    </token>
+    <xml name="lengths_params">
+        <!-- At least one of these lengths must be greater than zero, but we have no validator for this. -->
+        <param name="length_x" type="float" value="1.0" label="Length in the X direction" help="Floating point number">
+            <validator type="in_range" min="0" exclude_min="false" />
+        </param>
+        <param name="length_y" type="float" value="0.0" label="Length in the Y direction" help="Floating point number">
+            <validator type="in_range" min="0" exclude_min="false" />
+        </param>
+        <param name="length_z" type="float" value="0.0" label="Length in the Z direction" help="Floating point number">
+            <validator type="in_range" min="0" exclude_min="false" />
+        </param>
+    </xml>
+    <xml name="lengths_exclude_min_params">
+        <param name="length_x" type="float" value="1.0" label="Length in the X direction" help="Floating point number">
+            <validator type="in_range" min="0" exclude_min="true" />
+        </param>
+        <param name="length_y" type="float" value="1.0" label="Length in the Y direction" help="Floating point number">
+            <validator type="in_range" min="0" exclude_min="true" />
+        </param>
+        <param name="length_z" type="float" value="1.0" label="Length in the Z direction" help="Floating point number">
+            <validator type="in_range" min="0" exclude_min="true" />
+        </param>
+    </xml>
+    <token name="@radius_cmd_args@">
+        --radius $create_process_cond.shape_cond.radius
+    </token>
+    <xml name="radius_params">
+        <param name="radius" type="float" value="1.0" label="Radius" help="Floating point number">
+            <validator type="in_range" min="0" exclude_min="True" />
+        </param>
+    </xml>
+    <token name="@n_theta_cmd_args@">
+        --n_theta $create_process_cond.shape_cond.n_theta
+    </token>
+    <xml name="n_theta_params">
+        <param name="n_theta" type="integer" value="16" label="Number of slices" help="Controls the tessellation along the longitude direction">
+            <validator type="in_range" min="0" exclude_min="False" />
+        </param>
+    </xml>
+    <token name="@n_phi_cmd_args@">
+        --n_phi $create_process_cond.shape_cond.n_phi
+    </token>
+    <xml name="n_phi_params">
+        <param name="n_phi" type="integer" value="8" label="Number of stacks" help="Controls the tessellation along the latitude direction">
+            <validator type="in_range" min="0" exclude_min="False" />
+        </param>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @unpublished{None,
+                author = {None},
+                title = {None},
+                year = {None},
+                eprint = {None},
+                url = {https://github.com/gregvonkuster/galaxy-csg}
+            }</citation>
+            <citation type="bibtex">
+                @misc(Schroeder-Martin-Lorensen2006,
+                author = "Will Schroeder and 
+                          Ken Martin and
+                          Bill Lorensen",
+                year = "2006",
+                title = "The Visualization Toolkit (4th ed.)",
+                publisher =  "Kitware",
+                url = "https://en.wikipedia.org/wiki/Special:BookSources/978-1-930934-19-1")
+            </citation>
+        </citations>
+    </xml>
+</macros>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/icqsol_utils.py	Sat Nov 14 14:14:45 2015 -0500
@@ -0,0 +1,59 @@
+import os
+import sys
+import tempfile
+
+POLYDATA='POLYDATA'
+
+def asbool( val ):
+    return str( val ).lower() in [ 'yes', 'true' ]
+
+def get_format_and_type( galaxy_ext ):
+    # Define the output file format and type.
+    format = None
+    datatype = None
+    if galaxy_ext in [ 'vtkascii', 'vtkbinary' ]:
+        format = 'vtk'
+    elif galaxy_ext in [ 'plyascii', 'plybinary' ]:
+        format = 'ply'
+    if galaxy_ext in [ 'vtkascii', 'plyascii' ]:
+        datatype = 'ascii'
+    elif galaxy_ext in [ 'vtkbinary', 'plybinary' ]:
+        datatype = 'binary'
+    return format, datatype
+
+def get_input_file_path( tmp_dir, input_file, format ):
+    """
+    iCqSol uses file extensions (e.g., .ply, .vtk) when reading and
+    writing files, so the Galaxy dataset naming convention of
+    setting all file extensions as .dat must be handled.
+    """
+    file_path = get_temporary_file_path( tmp_dir, format )
+    # Remove the file so we can create a symlink.
+    os.remove( file_path )
+    os.symlink( input_file, file_path )
+    return file_path
+
+def get_temp_dir( prefix='tmp-vtk-', dir=None ):
+    """
+    Return a temporary directory.
+    """
+    return tempfile.mkdtemp( prefix=prefix, dir=dir )
+
+def get_tempfilename( dir=None, suffix=None ):
+    """
+    Return a temporary file name.
+    """
+    fd, name = tempfile.mkstemp( suffix=suffix, dir=dir )
+    os.close( fd )
+    return name
+
+def get_temporary_file_path( tmp_dir, file_extension ):
+    """
+    Return the path to a temporary file with a valid VTK format
+    file extension.
+    """
+    return get_tempfilename( tmp_dir, file_extension )
+
+def stop_err( msg ):
+    sys.stderr.write( "%s\n" % msg )
+    sys.exit()

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/box.vtkascii	Sat Nov 14 14:14:45 2015 -0500
@@ -0,0 +1,16 @@
+# vtk DataFile Version 3.0
+vtk output
+ASCII
+DATASET POLYDATA
+POINTS 8 float
+0 0 0 0 0 1 0 1 1 
+0 1 0 1 0 0 1 1 0 
+1 1 1 1 0 1 
+POLYGONS 6 30
+4 0 1 2 3 
+4 4 5 6 7 
+4 0 4 7 1 
+4 3 2 6 5 
+4 0 3 5 4 
+4 1 7 6 2 
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/box_with_surface_field.vtkascii	Sat Nov 14 14:14:45 2015 -0500
@@ -0,0 +1,44 @@
+# vtk DataFile Version 3.0
+vtk output
+ASCII
+DATASET POLYDATA
+POINTS 24 float
+0 0 0 0 0 1 0 1 1 
+0 1 0 1 0 0 1 1 0 
+1 1 1 1 0 1 0 0 0 
+0 0 0 0 0 1 0 0 1 
+0 1 1 0 1 1 0 1 0 
+0 1 0 1 0 0 1 0 0 
+1 1 0 1 1 0 1 1 1 
+1 1 1 1 0 1 1 0 1 
+
+POLYGONS 12 48
+3 3 0 1 
+3 1 2 3 
+3 7 4 5 
+3 5 6 7 
+3 10 8 16 
+3 16 22 10 
+3 18 14 12 
+3 12 20 18 
+3 17 9 15 
+3 15 19 17 
+3 13 11 23 
+3 23 21 13 
+
+POINT_DATA 24
+SCALARS surface_field double
+LOOKUP_TABLE default
+0 1.10517 1.10517 0 0 1.35344e-16 1.10517 1.10517 0 
+0 1.10517 1.10517 1.10517 1.10517 0 0 0 0 
+1.35344e-16 1.35344e-16 1.10517 1.10517 1.10517 1.10517 
+NORMALS Normals float
+-1 0 0 -1 0 0 -1 0 0 
+-1 0 0 1 0 0 1 0 0 
+1 0 0 1 0 0 0 -1 0 
+0 0 -1 0 -1 0 0 0 1 
+0 1 0 0 0 1 0 1 0 
+0 0 -1 0 -1 0 0 0 -1 
+0 1 0 0 0 -1 0 1 0 
+0 0 1 0 -1 0 0 0 1 
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Sat Nov 14 14:14:45 2015 -0500
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="icqsol" version="1.0">
+        <repository changeset_revision="a357536fb363" name="package_icqsol_1_0" owner="greg" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>