# HG changeset patch
# User greg
# Date 1447528485 18000
# Node ID d59a9d960f67bc38cfe4146a15302dd29c1e6eaa
Uploaded
diff -r 000000000000 -r d59a9d960f67 add_surface_field_from_expression.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/add_surface_field_from_expression.py Sat Nov 14 14:14:45 2015 -0500
@@ -0,0 +1,53 @@
+#!/usr/bin/env python
+import argparse
+import shutil
+
+import icqsol_utils
+from icqsol.shapes.icqShapeManager import ShapeManager
+
+# Parse Command Line.
+parser = argparse.ArgumentParser()
+parser.add_argument( '--input', dest='input', help='Shape dataset selected from history' )
+parser.add_argument( '--field_name', dest='field_name', help='Surface field name' )
+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( '--output', dest='output', help='Output dataset' )
+parser.add_argument( '--output_format_and_type', dest='output_format_and_type', help='Output file format and type' )
+
+args = parser.parse_args()
+
+valid_field_name = args.field_name.replace( ' ', '_' )
+tmp_dir = icqsol_utils.get_temp_dir()
+shape_mgr = ShapeManager()
+
+# Get the shape from the input dataset.
+shape = shape_mgr.load(args.input)
+# Get the points from the shape.
+pdata = shape_mgr.shapeToVTKPolyData(shape)
+points = pdata.GetPoints()
+num_points = points.GetNumberOfPoints()
+# Define the data.
+data = vtk.vtkDoubleArray()
+data.SetName(valid_field_name)
+# Handle time points.
+time_points = [ '%.1f' % tp for tp in args.time_points ]
+num_time_points = len(time_points)
+# Update the data.
+data.SetNumberOfComponents(num_time_points)
+data.SetNumberOfTuples(num_points)
+# Add the surface field.
+for i in range(num_points):
+ x, y, z = points.GetPoint(i)
+ for j in range(num_time_points):
+ t = time_points[ j ]
+ field_value = eval(args.expression)
+ data.SetComponent(i, j, field_value)
+pdata.GetPointData().SetScalars(data)
+
+# Define the output file format and type.
+output_format, output_file_type = icqsol_utils.get_format_and_type( args.output_format_and_type )
+tmp_output_path = icqsol_utils.get_temporary_file_path( tmp_dir, output_format )
+
+# Save the output.
+shape_mgr.save( composite_shape, file_name=tmp_output_path, file_format=output_format, file_type=output_file_type )
+shutil.move( tmp_output_path, args.output )
diff -r 000000000000 -r d59a9d960f67 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 Sat Nov 14 14:14:45 2015 -0500
@@ -0,0 +1,57 @@
+#!/usr/bin/env python
+import argparse
+import shutil
+
+import icqsol_utils
+from icqsol.shapes.icqShapeManager import ShapeManager
+
+# 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='0', 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.
+if input_format == 'vtk':
+ shape_mgr = ShapeManager( file_format=input_format, vtk_dataset_type=args.input_dataset_type )
+else:
+ shape_mgr = ShapeManager( file_format=input_format )
+
+# Get the shape from the input dataset.
+shp = shape_mgr.loadAsShape(args.input)
+
+max_edge_length = float('inf')
+if args.max_edge_length > 0:
+ max_edge_length = args.max_edge_length
+
+# Add surface field to shape data.
+vtk_poly_data = shape_mgr.addSurfaceFieldFromExpressionToShape(shp,
+ args.field_name,
+ args.expression,
+ time_points,
+ max_edge_length,
+ args.location)
+
+# 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='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 d59a9d960f67 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 Sat Nov 14 14:14:45 2015 -0500
@@ -0,0 +1,94 @@
+
+
+ from expression
+
+ icqsol_macros.xml
+
+
+
+
+
+
+
+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+
+
+
+
diff -r 000000000000 -r d59a9d960f67 icqsol_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/icqsol_macros.xml Sat Nov 14 14:14:45 2015 -0500
@@ -0,0 +1,115 @@
+
+
+
+
+ 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
+
+
+
+
+
+
+
+ --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 d59a9d960f67 icqsol_utils.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/icqsol_utils.py Sat Nov 14 14:14:45 2015 -0500
@@ -0,0 +1,59 @@
+import os
+import sys
+import tempfile
+
+POLYDATA='POLYDATA'
+
+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_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.
+ """
+ fd, name = tempfile.mkstemp( suffix=suffix, 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 d59a9d960f67 test-data/box.vtkascii
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/box.vtkascii Sat Nov 14 14:14:45 2015 -0500
@@ -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 d59a9d960f67 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 Sat Nov 14 14:14:45 2015 -0500
@@ -0,0 +1,44 @@
+# vtk DataFile Version 3.0
+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
+
+POINT_DATA 24
+SCALARS surface_field double
+LOOKUP_TABLE default
+0 1.10517 1.10517 0 0 1.35344e-16 1.10517 1.10517 0
+0 1.10517 1.10517 1.10517 1.10517 0 0 0 0
+1.35344e-16 1.35344e-16 1.10517 1.10517 1.10517 1.10517
+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
+
diff -r 000000000000 -r d59a9d960f67 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Sat Nov 14 14:14:45 2015 -0500
@@ -0,0 +1,6 @@
+
+
+
+
+
+