# HG changeset patch
# User iuc
# Date 1471978444 14400
# Node ID e12b55e960de974ec4ecaa65081734517b6ba7d5
Uploaded
diff -r 000000000000 -r e12b55e960de icqsol_add_surface_field_from_expression.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/icqsol_add_surface_field_from_expression.py Tue Aug 23 14:54:04 2016 -0400
@@ -0,0 +1,55 @@
+#!/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='Surface field name')
+parser.add_argument('--location', dest='location', help='Location of field within cell, either point or cell')
+parser.add_argument('--expression', dest='expression', help='Expression for applying surface field to shape')
+parser.add_argument('--time_point', dest='time_points', type=float, action='append', nargs=1, help='Points in time')
+parser.add_argument('--max_edge_length', dest='max_edge_length', type=float, default=float('inf'), 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)
+time_points = [tp[0] for tp in args.time_points]
+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 vtkPolyData object.
+pdata = shape_mgr.loadAsVtkPolyData(args.input)
+
+# Add surface field to shape data.
+vtk_poly_data = shape_mgr.addSurfaceFieldFromExpressionToVtkPolyData(pdata,
+ args.field_name,
+ args.expression,
+ time_points,
+ args.max_edge_length,
+ args.location)
+
+# Write min/max field values and surface integral.
+for comp in range(len(time_points)):
+ minVal, maxVal = shape_mgr.getFieldRange(vtk_poly_data, args.field_name, comp)
+ surfIntegral = shape_mgr.integrateSurfaceField(vtk_poly_data, args.field_name, comp)
+ print 'component {2} min/max values of {3}: {0}/{1} surf integral: {4}'.format(minVal, maxVal, comp, args.field_name, surfIntegral)
+
+# Define the output file format and type (the outpur_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 e12b55e960de icqsol_add_surface_field_from_expression.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/icqsol_add_surface_field_from_expression.xml Tue Aug 23 14:54:04 2016 -0400
@@ -0,0 +1,95 @@
+
+
+ from expression
+
+ icqsol_macros.xml
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+**What it does**
+
+Adds a surface field to a selected shape based on a given mathematical expression consisting of
+variables x, y, z (shape point coordinates) and t (time). This tool will generate VTK POLYDATA
+files, so input PLY files or VTK files with a different dataset type will automatically be converted
+to VTK POLYDATA during tool execution.
+
+* **Shape** - Shape to which a surface field will be added.
+* **Surface field name** - Name of the surface field to be added to the shape.
+* **Expression** - Mathematical expression consisting of variables x, y, z (shape point coordinates) and t (time) that defines the surface field.
+* **Time point** - A floating point value that defines a time point where multiple time points define a sequence of time snapshots for the surface field.
+* **Refine shape** - Select yes to refine the shape by shortening the edge lengths to a defined maximum.
+* **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 e12b55e960de icqsol_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/icqsol_macros.xml Tue Aug 23 14:54:04 2016 -0400
@@ -0,0 +1,116 @@
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+ 1.0
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+ 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
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+
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+ --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
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+ @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 e12b55e960de icqsol_utils.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/icqsol_utils.py Tue Aug 23 14:54:04 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 e12b55e960de test-data/box.vtkascii
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/box.vtkascii Tue Aug 23 14:54:04 2016 -0400
@@ -0,0 +1,16 @@
+# vtk DataFile Version 3.0
+vtk output
+ASCII
+DATASET POLYDATA
+POINTS 8 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
+POLYGONS 6 30
+4 0 1 2 3
+4 4 5 6 7
+4 0 4 7 1
+4 3 2 6 5
+4 0 3 5 4
+4 1 7 6 2
+
diff -r 000000000000 -r e12b55e960de test-data/box_with_surface_field.vtkascii
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/box_with_surface_field.vtkascii Tue Aug 23 14:54:04 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
+