changeset 0:2294ae1842d5 draft default tip

Uploaded
author iuc
date Tue, 23 Aug 2016 15:04:45 -0400
parents
children
files icqsol_macros.xml icqsol_solve_laplace.py icqsol_solve_laplace.xml icqsol_utils.py test-data/sphere.vtkbinary test-data/sphere_electric_field.vtkascii
diffstat 6 files changed, 1885 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/icqsol_macros.xml	Tue Aug 23 15:04:45 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_solve_laplace.py	Tue Aug 23 15:04:45 2016 -0400
@@ -0,0 +1,51 @@
+#!/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('--input_potential_name', dest='input_potential_name', default='', help='Input surface potential field name.')
+parser.add_argument('--output_jump_electric_field_name', dest='output_jump_electric_field_name', default='jump_normal_electric_field', help='Set the name of the output field name.')
+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)
+tmp_dir = icqsol_utils.get_temp_dir()
+
+# Instantiate the shape manager.
+shape_mgr = icqsol_utils.get_shape_manager(input_format, args.input_dataset_type)
+
+# Get the vtk polydata from the input dataset.
+vtk_poly_data = shape_mgr.loadAsVtkPolyData(args.input)
+
+# Instantiate the Laplace solver.
+solver = icqsol_utils.get_laplace_solver(vtk_poly_data)
+
+# Set the output field names.
+solver.setResponseFieldName(args.output_jump_electric_field_name)
+
+# In place operation, vtk_poly_data will be modified.
+solver.setSourceFieldName(args.input_potential_name)
+normalEJump = solver.computeResponseField()
+surfIntegral = shape_mgr.integrateSurfaceField(solver.getVtkPolyData(), args.output_jump_electric_field_name)
+print 'Surface integral of normal electric field jump: {0}'.format(surfIntegral)
+minVal, maxVal = shape_mgr.getFieldRange(solver.getVtkPolyData(), args.output_jump_electric_field_name)
+print 'min/max values of normal electric field jump: {0}/{1}'.format(minVal, maxVal)
+
+# Define the output file format and type (the output_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=icqsol_utils.VTK, vtk_dataset_type=icqsol_utils.POLYDATA)
+
+# Save the output.
+shape_mgr.saveVtkPolyData(vtk_poly_data=solver.getVtkPolyData(), 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_solve_laplace.xml	Tue Aug 23 15:04:45 2016 -0400
@@ -0,0 +1,67 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="icqsol_solve_laplace" name="Solve Laplace equation" version="@WRAPPER_VERSION@.0">
+    <description>- computes the jump of normal electric field</description>
+    <macros>
+        <import>icqsol_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command>
+        <![CDATA[
+            python $__tool_directory__/icqsol_solve_laplace.py
+            --input "$input"
+            --input_file_format_and_type $input.ext
+            --input_dataset_type $input.metadata.dataset_type
+            --input_potential_name "$input_potential_name"
+            --output_jump_electric_field_name "$output_jump_electric_field_name"
+            --output "$output"
+            --output_vtk_type $output_vtk_type
+        ]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="vtkascii,vtkbinary" label="Shape" help="Format can be vtkascii or vtkbinary." />
+        <param name="input_potential_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 surface fields." />
+            </options>
+        </param>
+        <param name="output_jump_electric_field_name" type="text" value="jumpEn" label="Output flux field name" help="Name of the jump of normal electric field in the output file." />
+        <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="sphere.vtkbinary" ftype="vtkbinary" />
+            <param name="input_file_format_and_type" value="vtkbinary" />
+            <param name="input_dataset_type" value="POLYDATA" />
+            <param name="input_potential_name" value="v" />
+            <param name="output_jump_electric_field_name" value="E_normal_jump" />
+            <output name="output" file="sphere_electric_field.vtkascii" ftype="vtkascii" />
+            <param name="output_vtk_type" value="vtkascii" />
+        </test>
+    </tests>
+    <help>
+
+**What it does**
+
+Computes the jump in flux-like (Neumann) boundary conditions given prescribed Dirichlet boundary
+conditions by using the boundary element method.  Depending on the problem, the jump can be the
+surface flux or the normal electric field in electrostatic problems. The Dirichlet field is often
+called the potential (e.g. electrostatic potential). When the domain extends from the object to
+infinity and the interior of the object is perfectly conducting, the jump corresponds to the normal
+electric field just outside the object.
+
+* **Shape** - Shape whose surface contains a potential field.
+* **Output flux field name** - Name of the jump of normal electric field name in the output file.
+
+    </help>
+    <expand macro="citations" />
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/icqsol_utils.py	Tue Aug 23 15:04:45 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()
Binary file test-data/sphere.vtkbinary has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sphere_electric_field.vtkascii	Tue Aug 23 15:04:45 2016 -0400
@@ -0,0 +1,1565 @@
+# vtk DataFile Version 4.0
+vtk output
+ASCII
+DATASET POLYDATA
+POINTS 482 float
+0 1 0 0.191342 0.980785 0.0380602 0.19509 0.980785 0 
+0.37533 0.92388 0.0746578 0.382683 0.92388 0 0.544895 0.83147 0.108386 
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