Mercurial > repos > iuc > icqsol_color_surface_field

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/icqsol_color_surface_field.py	Tue Aug 23 14:57:59 2016 -0400
@@ -0,0 +1,47 @@
+#!/usr/bin/env python
+import argparse
+import shutil
+
+import icqsol_utils
+
+# 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 = icqsol_utils.get_shape_manager(icqsol_utils.VTK, args.input_dataset_type)
+
+# Get the vtkPolyData from the input dataset.
+vtk_poly_data = shape_mgr.loadAsVtkPolyData(args.input)
+# Add color to the data.
+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)
+
+# Write min/max field values.
+minVal, maxVal = shape_mgr.getFieldRange(vtk_poly_data, args.field_name, args.field_component_index)
+print 'component {2} min/max values of field {3}: {0}/{1}'.format(minVal, maxVal, args.field_component_index, args.field_name)
+
+# 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=icqsol_utils.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	Tue Aug 23 14:57:59 2016 -0400
@@ -0,0 +1,70 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="icqsol_color_surface_field" name="Color" version="@WRAPPER_VERSION@.0">
+    <description>field</description>
+    <macros>
+        <import>icqsol_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <code file="icqsol_tool_form_utils.py" />
+    <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">
+            <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**
+
+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>
+    <options refresh="True" />
+    <expand macro="citations" />
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/icqsol_macros.xml	Tue Aug 23 14:57:59 2016 -0400
@@ -0,0 +1,116 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<macros>
+    <token name="@WRAPPER_VERSION@">1.0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="0.3.26">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	Tue Aug 23 14:57:59 2016 -0400
@@ -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	Tue Aug 23 14:57:59 2016 -0400
@@ -0,0 +1,86 @@
+import os
+import sys
+import tempfile
+
+from icqsol.shapes.icqShapeManager import ShapeManager
+from icqsol.bem.icqLaplaceSolver import LaplaceSolver
+
+PLY = 'ply'
+POLYDATA = 'POLYDATA'
+VTK = 'vtk'
+
+
+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_laplace_solver(shape_data, max_edge_length=float('inf')):
+    return LaplaceSolver(shape_data, max_edge_length=max_edge_length)
+
+
+def get_shape_manager(format=None, dataset_type=None):
+    # Instantiate a ShapeManager.
+    return ShapeManager(file_format=format, vtk_dataset_type=dataset_type)
+
+
+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.
+    """
+    if suffix is None:
+        s = None
+    elif suffix.startswith('.'):
+        s = suffix
+    else:
+        s = '.%s' % suffix
+    fd, name = tempfile.mkstemp(suffix=s, 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	Tue Aug 23 14:57:59 2016 -0400
@@ -0,0 +1,44 @@
+# vtk DataFile Version 4.0
+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
+
+CELL_DATA 12
+FIELD FieldData 1
+surface_field 1 12 double
+0.0136441 0.218305 0.97075 1.17541 0.0136441 0.218305 0.0136441 0.218305 0.106345
+0.42538 1.21152 1.53055
+POINT_DATA 24
+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	Tue Aug 23 14:57:59 2016 -0400
@@ -0,0 +1,47 @@
+# vtk DataFile Version 4.0
+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
+
+CELL_DATA 12
+COLOR_SCALARS Colors 3
+0 0 1 0.0431373 0.168627 0.956863 0.698039 0.839216 0.301961
+0.870588 0.45098 0.129412 0 0 1
+0.0431373 0.168627 0.956863 0 0 1
+0.0431373 0.168627 0.956863 0.00784314 0.0352941 0.992157
+0.172549 0.568627 0.827451 0.894118 0.376471 0.105882
+1 0 0
+POINT_DATA 24
+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
+