# HG changeset patch
# User iuc
# Date 1471979085 14400
# Node ID 2294ae1842d52dd311e8ae33649917d11c782261
Uploaded
diff -r 000000000000 -r 2294ae1842d5 icqsol_macros.xml
--- /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 @@
+
+
+ 1.0
+
+
+ icqsol
+
+
+
+
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+
+
+
+
+
+
+
+
+
+
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+
+
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+
+
+ --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
+
+
+
+
+
+
+
+ --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
+
+
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+
+
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+
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+
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+
+
+
+ --radius $create_process_cond.shape_cond.radius
+
+
+
+
+
+
+
+ --n_theta $create_process_cond.shape_cond.n_theta
+
+
+
+
+
+
+
+ --n_phi $create_process_cond.shape_cond.n_phi
+
+
+
+
+
+
+
+
+
+ @unpublished{None,
+ author = {None},
+ title = {None},
+ year = {None},
+ eprint = {None},
+ url = {https://github.com/gregvonkuster/galaxy-csg}
+ }
+
+ @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")
+
+
+
+
diff -r 000000000000 -r 2294ae1842d5 icqsol_solve_laplace.py
--- /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)
diff -r 000000000000 -r 2294ae1842d5 icqsol_solve_laplace.xml
--- /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 @@
+
+
+ - computes the jump of normal electric field
+
+ icqsol_macros.xml
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**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.
+
+
+
+
diff -r 000000000000 -r 2294ae1842d5 icqsol_utils.py
--- /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()
diff -r 000000000000 -r 2294ae1842d5 test-data/sphere.vtkbinary
Binary file test-data/sphere.vtkbinary has changed
diff -r 000000000000 -r 2294ae1842d5 test-data/sphere_electric_field.vtkascii
--- /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
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