Mercurial > repos > greg > icqsol_create_shape

changeset 0:d1d206669437 draft

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Uploaded
author greg
date Sat, 14 Nov 2015 13:57:09 -0500
parents
children e683e75d905d
files icqsol_create_shape.py icqsol_create_shape.xml icqsol_macros.xml icqsol_utils.py test-data/head.vtkascii test-data/notch1.vtkascii test-data/notch2.vtkascii test-data/shaft.vtkascii tool_dependencies.xml
diffstat 9 files changed, 706 insertions(+), 0 deletions(-) [+]
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line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/icqsol_create_shape.py	Sat Nov 14 13:57:09 2015 -0500
@@ -0,0 +1,86 @@
+#!/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( '--create_process', dest='create_process', help='Shape creation process (create or clone)' )
+parser.add_argument( '--shape_input', dest='shape_input', default=None, help='Shape file if create_process is clone' )
+parser.add_argument( '--shape', dest='shape', default=None, help='Shape if create_process is create' )
+parser.add_argument( '--origin_x', dest='origin_x', type=float, default=None, help='X coordinate of origin' )
+parser.add_argument( '--origin_y', dest='origin_y', type=float, default=None, help='Y coordinate of origin' )
+parser.add_argument( '--origin_z', dest='origin_z', type=float, default=None, help='Z coordinate of origin' )
+parser.add_argument( '--length_x', dest='length_x', type=float, default=None, help='X coordinate of end' )
+parser.add_argument( '--length_y', dest='length_y', type=float, default=None, help='Y coordinate of end' )
+parser.add_argument( '--length_z', dest='length_z', type=float, default=None, help='Z coordinate of end' )
+parser.add_argument( '--angle', dest='angle', type=float, default=None, help='Angle' )
+parser.add_argument( '--radius', dest='radius', type=float, default=None, help='Radius' )
+parser.add_argument( '--n_theta', dest='n_theta', type=int, default=0, help='Number of slices' )
+parser.add_argument( '--n_phi', dest='n_phi', type=int, default=0, help='Number of stacks' )
+parser.add_argument( '--rotate', dest='rotate', help='Rotate cloned shape' )
+parser.add_argument( '--rotation_axis_x', dest='rotation_axis_x', type=float, default=None, help='X component of rotation axis' )
+parser.add_argument( '--rotation_axis_y', dest='rotation_axis_y', type=float, default=None, help='Y component of rotation axis' )
+parser.add_argument( '--rotation_axis_z', dest='rotation_axis_z', type=float, default=None, help='Z component of rotation axis' )
+parser.add_argument( '--rotation_degree', dest='rotation_degree', type=float, default=None, help='Degree of rotation around axis' )
+parser.add_argument( '--translate', dest='translate', help='Translate cloned shape' )
+parser.add_argument( '--output', dest='output', default=None, help='Output dataset' )
+parser.add_argument( '--output_vtk_type', dest='output_vtk_type', help='Output file format and type' )
+
+args = parser.parse_args()
+
+if args.origin_x is not None and args.origin_y is not None and args.origin_z is not None:
+    origin = [ args.origin_x, args.origin_y, args.origin_z ]
+if args.length_x is not None and args.length_y is not None and args.length_z is not None:
+    lengths = [ args.length_x, args.length_y, args.length_z ]
+if args.rotation_axis_x is not None and args.rotation_axis_y is not None and args.rotation_axis_z is not None:
+    rotation_axis = [ args.rotation_axis_x, args.rotation_axis_y, args.rotation_axis_z ]
+
+# Define the output file format and type.
+format, file_type = icqsol_utils.get_format_and_type( args.output_vtk_type )
+tmp_dir = icqsol_utils.get_temp_dir()
+cloning = True if args.create_process == 'clone' else False
+
+# TODO: fix this to handle inputPLY files for cloning, but producing VTK POLYDATA.
+shape_mgr = ShapeManager(file_format=format, vtk_dataset_type=icqsol_utils.POLYDATA)
+
+if cloning:
+    # We're cloning an existing shape selected from the history.
+    tmp_input_path = icqsol_utils.get_input_file_path( tmp_dir, args.shape_input, '.%s' % format )
+    shape_to_clone = shape_mgr.loadAsShape( tmp_input_path )
+    new_shape = shape_mgr.cloneShape( shape_to_clone )
+    if icqsol_utils.asbool( args.rotate ):
+        shape_mgr.rotateShape( new_shape, axis=rotation_axis, angleDeg=args.rotation_degree )
+    if icqsol_utils.asbool( args.translate ):
+        shape_mgr.translateShape( new_shape, disp=origin )
+else:
+    # Create the primitive shape.
+    if args.shape == 'box':
+        new_shape = shape_mgr.createShape( 'box',
+                                           origin=origin,
+                                           lengths=lengths )
+    elif args.shape == 'cone':
+        new_shape = shape_mgr.createShape( 'cone',
+                                           radius=args.radius,
+                                           origin=origin,
+                                           lengths=lengths,
+                                           n_theta=args.n_theta )
+    elif args.shape == 'cylinder':
+        new_shape = shape_mgr.createShape( 'cylinder',
+                                           radius=args.radius,
+                                           origin=origin,
+                                           lengths=lengths,
+                                           n_theta=args.n_theta )
+    elif args.shape == 'sphere':
+        new_shape = shape_mgr.createShape( 'sphere',
+                                           radius=args.radius,
+                                           origin=origin,
+                                           n_theta=args.n_theta,
+                                           n_phi=args.n_phi )
+
+# Save the output.
+tmp_output_path = icqsol_utils.get_temporary_file_path( tmp_dir, '.%s' % format )
+shape_mgr.saveShape( shape=new_shape, file_name=tmp_output_path, file_type=file_type )
+shutil.move( tmp_output_path, args.output )
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/icqsol_create_shape.xml	Sat Nov 14 13:57:09 2015 -0500
@@ -0,0 +1,206 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="icqsol_create_shape" name="Create 3D shape" version="1.0.0">
+    <description></description>
+    <macros>
+        <import>icqsol_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command>
+<![CDATA[
+    python $__tool_directory__/icqsol_create_shape.py
+    --create_process $create_process_cond.create_process
+    #if $create_process_cond.create_process == 'create':
+        --shape $create_process_cond.shape_cond.shape
+        #if $create_process_cond.shape_cond.shape == 'box':
+            @origin_cmd_args@
+            @lengths_cmd_args@
+        #else if $create_process_cond.shape_cond.shape == 'cone':
+            @radius_cmd_args@
+            @origin_cmd_args@
+            @lengths_cmd_args@
+            @n_theta_cmd_args@
+        #else if $create_process_cond.shape_cond.shape == 'cylinder':
+            @radius_cmd_args@
+            @origin_cmd_args@
+            @lengths_cmd_args@
+            @n_theta_cmd_args@
+        #else if $create_process_cond.shape_cond.shape == 'sphere':
+            @radius_cmd_args@
+            @origin_cmd_args@
+            @n_theta_cmd_args@
+            @n_phi_cmd_args@
+        #end if
+        --output_vtk_type $create_process_cond.output_vtk_type
+        --output "$output_create"
+    #else:
+        --shape_input "$create_process_cond.shape_input"
+        --rotate $create_process_cond.rotate_cond.rotate
+        #if $create_process_cond.rotate_cond.rotate == 'yes':
+            --rotation_axis_x $create_process_cond.rotate_cond.rotation_axis_x
+            --rotation_axis_y $create_process_cond.rotate_cond.rotation_axis_y
+            --rotation_axis_z $create_process_cond.rotate_cond.rotation_axis_z
+            --rotation_degree $create_process_cond.rotate_cond.rotation_degree
+        #end if
+        #if $create_process_cond.translate_cond.translate == 'yes':
+            --translate $create_process_cond.translate_cond.translate
+            --origin_x $create_process_cond.translate_cond.translate_origin_x
+            --origin_y $create_process_cond.translate_cond.translate_origin_y
+            --origin_z $create_process_cond.translate_cond.translate_origin_z
+        #end if
+        --output_vtk_type $create_process_cond.shape_input.ext
+        --output "$output_clone"
+    #end if
+]]>
+    </command>
+    <inputs>
+        <conditional name="create_process_cond">
+            <param name="create_process" type="select" label="Create or clone?" help="Create a new shape or clone a shape in your history.">
+                <option value="create" selected="True">Create a shape</option>
+                <option value="clone">Clone a shape in your history</option>
+            </param>
+            <when value="create">
+                <conditional name="shape_cond">
+                    <param name="shape" type="select" label="Select shape">
+                        <option value="box" selected="True">Box</option>
+                        <option value="cone">Cone</option>
+                        <option value="cylinder">Cylinder</option>
+                        <option value="sphere">Sphere</option>
+                    </param>
+                    <when value="box">
+                        <expand macro="origin_params" />
+                        <expand macro="lengths_exclude_min_params" />
+                    </when>
+                    <when value="cone">
+                        <expand macro="radius_params" />
+                        <expand macro="origin_params" />
+                        <expand macro="lengths_params" />
+                        <expand macro="n_theta_params" />
+                    </when>
+                    <when value="cylinder">
+                        <expand macro="radius_params" />
+                        <expand macro="origin_params" />
+                        <expand macro="lengths_params" />
+                        <expand macro="n_theta_params" />
+                    </when>
+                    <when value="sphere">
+                        <expand macro="radius_params" />
+                        <expand macro="origin_params" />
+                        <expand macro="n_theta_params" />
+                        <expand macro="n_phi_params" />
+                    </when>
+                </conditional>
+                <expand macro="output_vtk_type_params" />
+            </when>
+            <when value="clone">
+                <param name="shape_input" type="data" format="plyascii,plybinary,vtkascii,vtkbinary" label="Shape to clone" help="Select shape for cloning.">
+                    <validator type="dataset_ok_validator" />
+                </param>
+                <conditional name="rotate_cond">
+                    <param name="rotate" type="select" label="Rotate cloned shape?">
+                        <option value="no" selected="True">No</option>
+                        <option value="yes">Yes</option>
+                    </param>
+                    <when value="no"/>
+                    <when value="yes">
+                        <param name="rotation_axis_x" type="float" value="0.0" label="X component of rotation axis" help="Floating point number"/>
+                        <param name="rotation_axis_y" type="float" value="0.0" label="Y component of rotation axis" help="Floating point number"/>
+                        <param name="rotation_axis_z" type="float" value="0.0" label="Z component of rotation axis" help="Floating point number"/>
+                        <param name="rotation_degree" type="float" value="0.0" label="Degree of rotation" help="Floating point number"/>
+                    </when>
+                </conditional>
+                <conditional name="translate_cond">
+                    <param name="translate" type="select" label="Translate cloned shape?">
+                        <option value="no" selected="True">No</option>
+                        <option value="yes">Yes</option>
+                    </param>
+                    <when value="no"/>
+                    <when value="yes">
+                        <param name="translate_origin_x" type="float" value="0.0" label="X coordinate of new origin" help="Floating point number"/>
+                        <param name="translate_origin_y" type="float" value="0.0" label="Y coordinate of new origin" help="Floating point number"/>
+                        <param name="translate_origin_z" type="float" value="0.0" label="Z coordinate of new origin" help="Floating point number"/>
+                    </when>
+                </conditional>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="output_create" format="vtkascii" label="${tool.name} ${on_string}: ${create_process_cond.shape_cond.shape}">
+            <filter>create_process_cond['create_process'] == "create"</filter>
+            <actions>
+                <action type="format">
+                    <option type="from_param" name="create_process_cond.output_vtk_type" />
+                </action>
+            </actions>
+        </data>
+        <data name="output_clone" format_source="shape_input" label="${tool.name}: Cloned ${on_string}">
+            <filter>create_process_cond['create_process'] == "clone"</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="shape" value="cone" />
+            <param name="radius" value="0.25" />
+            <param name="origin_x" value="-0.06" />
+            <param name="length_x" value="0.14" />
+            <param name="output_vtk_type" value="vtkascii" />
+            <output name="output" file="head.vtkascii" />
+        </test>
+        <test>
+            <param name="shape" value="box" />
+            <param name="origin_x" value="-0.06" />
+            <param name="origin_y" value="-0.015" />
+            <param name="origin_z" value="-0.15" />
+            <param name="length_x" value="0.03" />
+            <param name="length_y" value="0.03" />
+            <param name="length_z" value="0.30" />
+            <param name="output_vtk_type" value="vtkascii" />
+            <output name="output" file="notch1.vtkascii" />
+        </test>
+        <test>
+            <param name="shape" value="cylinder" />
+            <param name="radius" value="0.1" />
+            <param name="origin_x" value="0.0" />
+            <param name="origin_y" value="0.0" />
+            <param name="origin_z" value="0.0" />
+            <param name="length_x" value="1.0" />
+            <param name="length_y" value="0.0" />
+            <param name="length_z" value="0.0" />
+            <param name="n_theta" value="16" />
+            <param name="output_vtk_type" value="vtkascii" />
+            <output name="output" file="shaft.vtkascii" />
+        </test>
+        <test>
+            <param name="create_process" value="clone" />
+            <param name="shape_input" value="notch1.vtkascii" ftype="vtkascii" />
+            <param name="rotate" value="yes" />
+            <param name="rotation_axis_x" value="1.0" />
+            <param name="rotation_degree" value="90.0" />
+            <output name="output" file="notch2.vtkascii" ftype="vtkascii" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+**Create a shape** - creates a selected primitive shape where shapes are Box, Cone, Cylinder and Sphere.
+
+- **Origin X,Y,Z** - Origin coordinate for all shapes.
+- **Lengths X,Y,Z** - Edge lengths for Box, Cone and Cylinder.
+- **Radius** - Radius length for Cone, Cylinder and Sphere.
+- **Number of slices** - Controls the tessellation along the longitude direction for all shapes.
+- **Number of stacks** - Controls the tessellation along the latitude direction for all shapes.
+- **Output format and file type** - Choose the output format **ply** or **vtk** and file type **ascii** or **binary**.
+
+-----
+
+**Clone a shape from your history** - creates a new copy of a shape selected from your history.
+
+- **Shape to clone** - Shape selected from your history for cloning.
+- **Rotate cloned shape** - Enables rotation of the cloned shape around a defined axis.
+- **Rotation axis X,Y,Z?** - The axis of rotation for the cloned shape.
+- **Degree of rotation** - The degree of rotation around the axis.
+- **Translate cloned shape?** - Enables resetting the origin of the cloned shape, moving the shape.
+- **New origin X,Y,Z** - Translated origin of cloned shape.
+
+    </help>
+    <expand macro="citations" />
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/icqsol_macros.xml	Sat Nov 14 13:57:09 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 13:57:09 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/head.vtkascii	Sat Nov 14 13:57:09 2015 -0500
@@ -0,0 +1,65 @@
+# vtk DataFile Version 3.0
+vtk output
+ASCII
+DATASET POLYDATA
+POINTS 34 float
+-0.06 0 0 -0.06 0 -0.25 -0.06 -0.0956709 -0.23097 
+0.08 0 0 -0.06 -0.176777 -0.176777 -0.06 -0.23097 -0.0956709 
+-0.06 -0.25 -1.53081e-17 -0.06 -0.23097 0.0956709 -0.06 -0.176777 0.176777 
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/notch1.vtkascii	Sat Nov 14 13:57:09 2015 -0500
@@ -0,0 +1,33 @@
+# vtk DataFile Version 3.0
+vtk output
+ASCII
+DATASET POLYDATA
+POINTS 24 float
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+
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+
+POINT_DATA 24
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+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/notch2.vtkascii	Sat Nov 14 13:57:09 2015 -0500
@@ -0,0 +1,33 @@
+# vtk DataFile Version 3.0
+vtk output
+ASCII
+DATASET POLYDATA
+POINTS 24 float
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+
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+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/shaft.vtkascii	Sat Nov 14 13:57:09 2015 -0500
@@ -0,0 +1,103 @@
+# vtk DataFile Version 3.0
+vtk output
+ASCII
+DATASET POLYDATA
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Sat Nov 14 13:57:09 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>