# HG changeset patch
# User iuc
# Date 1471978968 14400
# Node ID f63d4da328a3fd77af0d6f98bf4c1a91a0972487
Uploaded
diff -r 000000000000 -r f63d4da328a3 icqsol_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/icqsol_macros.xml Tue Aug 23 15:02:48 2016 -0400
@@ -0,0 +1,116 @@
+
+
+ 1.0
+
+
+ icqsol
+
+
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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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+ --radius $create_process_cond.shape_cond.radius
+
+
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+
+
+
+
+ --n_theta $create_process_cond.shape_cond.n_theta
+
+
+
+
+
+
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+ --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+ @unpublished{None,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 f63d4da328a3 icqsol_rotate_shape.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/icqsol_rotate_shape.py Tue Aug 23 15:02:48 2016 -0400
@@ -0,0 +1,45 @@
+#!/usr/bin/env python
+import argparse
+import shutil
+import operator
+
+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('--rotation_degrees', dest='rotation_degrees', type=float, default=0.0, help='Rotation angle in degrees')
+parser.add_argument('--rotation_axis_x', dest='rotation_axis_x', type=float, default=1.0, help='X coordinate of rotation axis')
+parser.add_argument('--rotation_axis_y', dest='rotation_axis_y', type=float, default=0.0, help='Y coordinate of rotation axis')
+parser.add_argument('--rotation_axis_z', dest='rotation_axis_z', type=float, default=0.0, help='Z coordinate of rotation axis')
+parser.add_argument('--output', dest='output', help='Output file name')
+parser.add_argument('--output_vtk_type', dest='output_vtk_type', default='ascii', help='Output VTK type')
+
+args = parser.parse_args()
+
+# Get the format of the input - either vtk or ply.
+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 a ShapeManager for loading the input.
+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)
+
+# Only rotate if the axis has some non-zero coordinates.
+# FIXME: this should be handled in a Galaxy tool validator.
+axis = (args.rotation_axis_x, args.rotation_axis_y, args.rotation_axis_z)
+if reduce(operator.mul, axis) != 0.0:
+ # Rotate (in place operation).
+ shape_mgr.rotateVtkPolyData(vtk_poly_data, angleDeg=args.rotation_degrees, axis=axis)
+
+output_format, output_file_type = icqsol_utils.get_format_and_type(args.output_vtk_type)
+
+# Save the output.
+tmp_dir = icqsol_utils.get_temp_dir()
+tmp_output_path = icqsol_utils.get_temporary_file_path(tmp_dir, icqsol_utils.VTK)
+shape_mgr.saveVtkPolyData(vtk_poly_data, file_name=tmp_output_path, file_type=output_file_type)
+shutil.move(tmp_output_path, args.output)
diff -r 000000000000 -r f63d4da328a3 icqsol_rotate_shape.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/icqsol_rotate_shape.xml Tue Aug 23 15:02:48 2016 -0400
@@ -0,0 +1,65 @@
+
+
+
+
+ icqsol_macros.xml
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
+
+
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+
+
+
+
+
+
+
+
+
+**What it does**
+
+Applies a rotation to a shape by a given angle about an arbitrary axis.
+
+* **Shape** - Shape to be rotated.
+* **Rotation axis X,Y,Z** - The axis of rotation.
+* **Degree of rotation** - The degree of rotation around the axis.
+
+
+
+
diff -r 000000000000 -r f63d4da328a3 icqsol_utils.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/icqsol_utils.py Tue Aug 23 15:02:48 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 f63d4da328a3 test-data/cylinder_with_field.vtkascii
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cylinder_with_field.vtkascii Tue Aug 23 15:02:48 2016 -0400
@@ -0,0 +1,129 @@
+# vtk DataFile Version 3.0
+vtk output
+ASCII
+DATASET POLYDATA
+POINTS 66 float
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+
+POLYGONS 64 256
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+POINT_DATA 66
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+
+FIELD FieldData 1
+my_field 1 66 double
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+0.681662 1.0824 0.902456
diff -r 000000000000 -r f63d4da328a3 test-data/rotated_cylinder_with_field.vtkascii
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rotated_cylinder_with_field.vtkascii Tue Aug 23 15:02:48 2016 -0400
@@ -0,0 +1,129 @@
+# vtk DataFile Version 4.0
+vtk output
+ASCII
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+POINTS 66 float
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+
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