# HG changeset patch # User iuc # Date 1471978887 14400 # Node ID d543f7bbe8da5e5ffb46999486d6e212712ec730 Uploaded diff -r 000000000000 -r d543f7bbe8da icqsol_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/icqsol_macros.xml Tue Aug 23 15:01:27 2016 -0400 @@ -0,0 +1,116 @@ + + + 1.0 + + + icqsol + + + + + + + + + + + + + + + + + + + + + + + + + + + --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 + + + + + + + + + + + + + + + + + + + + + + + + + + --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+ + + + + + + + --n_phi $create_process_cond.shape_cond.n_phi + + + + + + + + + + @unpublished{None, + author = {None}, + title = {None}, + year = {None}, + eprint = {None}, + url = {https://github.com/gregvonkuster/galaxy-csg} + } + +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 d543f7bbe8da icqsol_refine_shape.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/icqsol_refine_shape.py Tue Aug 23 15:01:27 2016 -0400 @@ -0,0 +1,39 @@ +#!/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('--max_edge_length', dest='max_edge_length', type=float, help='Maximum edge length') +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 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) + +# Refine the shape if requested. +vtk_poly_data = shape_mgr.refineVtkPolyData(vtk_poly_data, max_edge_length=args.max_edge_length) + +# 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=vtk_poly_data, file_name=tmp_output_path, file_type=output_file_type) +shutil.move(tmp_output_path, args.output) diff -r 000000000000 -r d543f7bbe8da icqsol_refine_shape.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/icqsol_refine_shape.xml Tue Aug 23 15:01:27 2016 -0400 @@ -0,0 +1,57 @@ + + + + + icqsol_macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +Refines a shape by limiting all edges to a specified length, resulting in a more detailed shape. + +* **Shape** - Shape to be refined. +* **Maximum edge length** - The shape's edges are smoothed by adding points to its edges that are longer than the defined maximum length. + + + + diff -r 000000000000 -r d543f7bbe8da icqsol_utils.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/icqsol_utils.py Tue Aug 23 15:01:27 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 d543f7bbe8da test-data/box_refined.vtkascii --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/box_refined.vtkascii Tue Aug 23 15:01:27 2016 -0400 @@ -0,0 +1,2803 @@ +# vtk DataFile Version 4.0 +vtk output +ASCII +DATASET POLYDATA +POINTS 1062 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 +0 0.9 0 0 0.8 0 0 0.7 0 +0 0.6 0 0 0.5 0 0 0.4 0 +0 0.3 0 0 0.2 0 0 0.1 0 +0 0 0.1 0 0 0.2 0 0 0.3 +0 0 0.4 0 0 0.5 0 0 0.6 +0 0 0.7 0 0 0.8 0 0 0.9 +0 0.0666667 0.933333 0 0.133333 0.866667 0 0.2 0.8 +0 0.266667 0.733333 0 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+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 +