Mercurial > repos > greg > icqsol_color_surface_field

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/icqsol_color_surface_field.py	Sat Nov 14 14:16:53 2015 -0500
@@ -0,0 +1,45 @@
+#!/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='Field name' )
+parser.add_argument( '--field_component_index', dest='field_component_index', type=int, help='Index of field component' )
+parser.add_argument( '--color_map', dest='color_map', help='Color map' )
+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()
+
+tmp_dir = icqsol_utils.get_temp_dir()
+input_format, input_file_type = icqsol_utils.get_format_and_type( args.input_file_format_and_type )
+
+# Instantiate a ShapeManager for loading the input.
+shape_mgr = ShapeManager( file_format='vtk', vtk_dataset_type=args.input_dataset_type )
+
+# Get the vtkPolyData from the input dataset.
+vtk_poly_data = shape_mgr.loadAsVtkPolyData(args.input)
+# Add color to the data.
+# TODO: Fix the following when we have this working.
+colored_vtk_poly_data = shape_mgr.colorSurfaceField(vtk_poly_data=vtk_poly_data,
+                                                    color_map=args.color_map,
+                                                    field_name=args.field_name,
+                                                    field_component=args.field_component_index)
+
+# Define the output file format and type.
+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 POLYDATA.
+shape_mgr.setWriter( file_format='vtk', vtk_dataset_type=icqsol_utils.POLYDATA )
+
+# Save the output.
+shape_mgr.saveVtkPolyData( vtk_poly_data=colored_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_color_surface_field.xml	Sat Nov 14 14:16:53 2015 -0500
@@ -0,0 +1,73 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="icqsol_color_surface_field" name="Color surface field" version="1.0.0">
+    <description></description>
+    <macros>
+        <import>icqsol_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command>
+<![CDATA[
+    python $__tool_directory__/icqsol_color_surface_field.py
+    --input "$input"
+    --input_file_format_and_type $input.ext
+    --input_dataset_type $input.metadata.dataset_type
+    --field_name $field_name
+    --field_component_index $field_component_index
+    --color_map $color_map
+    --output "$output"
+    --output_vtk_type $output_vtk_type
+]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="vtkascii,vtkbinary" label="Shape with uncolored surface field">
+            <validator type="expression" message="Shape must have an uncolored surface field.">value is not None and len(value.metadata.field_names) > 0</validator>
+        </param>
+        <param name="field_name" type="select" label="Field name" refresh_on_change="True">
+            <options>
+                <filter type="data_meta" ref="input" key="field_names"/>
+                <validator type="no_options" message="The selected shape has no uncolored surface fields." />
+            </options>
+        </param>
+        <param name="field_component_index" type="select" label="Field component index" dynamic_options="get_field_components_options(input, field_name=field_name)" help="Color will be applied to the selected field's component associated with this index." />
+        <expand macro="color_map_param" />
+        <expand macro="output_vtk_type_params" />
+    </inputs>
+    <outputs>
+        <data name="output" format_source="input" label="${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_with_surface_field.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="field_component_index" value="0" />
+            <param name="color_map" value="hot" />
+            <param name="output_vtk_type" value="vtkascii" />
+            <output name="output" file="box_with_surface_field_colored.vtkascii" ftype="vtkascii" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+<![CDATA[
+
+Colors a shape's selected surface field using a selected color map.  This tool will restrict selected
+input shapes to only those that have at least one surface field.
+
+* **Shape** - Shape containing a surface field to be colored.
+* **Field name for coloring** - Name of the surface field to be colored.
+* **Color map** - Color map to be used when coloring the surface field.
+
+]]>
+    </help>
+    <code file="icqsol_tool_form_utils.py" />
+    <options refresh="True" />
+    <expand macro="citations" />
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/icqsol_macros.xml	Sat Nov 14 14:16:53 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_tool_form_utils.py	Sat Nov 14 14:16:53 2015 -0500
@@ -0,0 +1,21 @@
+
+def get_field_components_options( dataset, **kwd ):
+    field_name = kwd.get( 'field_name', None )
+    options = []
+    if dataset.metadata is None:
+        return options
+    if not hasattr( dataset.metadata, 'field_names' ):
+        return options
+    if dataset.metadata.field_names is None:
+        return options
+    if field_name is None:
+        # The expression validator that helps populate the select list of input
+        # datsets in the icqsol_color_surface_field tool does not filter out
+        # datasets with no field field_names, so we need this check.
+        if len( dataset.metadata.field_names ) == 0:
+            return options
+        field_name = dataset.metadata.field_names[0]
+    field_components = dataset.metadata.field_components.get( field_name, [] )
+    for i, field_component in enumerate( field_components ):
+        options.append( ( field_component, field_component, i == 0 ) )
+    return options
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/icqsol_utils.py	Sat Nov 14 14:16:53 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_with_surface_field.vtkascii	Sat Nov 14 14:16:53 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/test-data/box_with_surface_field_colored.vtkascii	Sat Nov 14 14:16:53 2015 -0500
@@ -0,0 +1,52 @@
+# 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
+COLOR_SCALARS Colors 3
+0 0 1 1 0 0 1 0 0
+0 0 1 0 0 1
+0 0 1 1 0 0
+1 0 0 0 0 1
+0 0 1 1 0 0
+1 0 0 1 0 0
+1 0 0 0 0 1
+0 0 1 0 0 1
+0 0 1 0 0 1
+0 0 1 1 0 0
+1 0 0 1 0 0
+1 0 0
+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 14:16:53 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>