# HG changeset patch # User greg # Date 1447528613 18000 # Node ID 6a5b5cc5b88504fe0cc336d3d2eab792dcd4087f Uploaded diff -r 000000000000 -r 6a5b5cc5b885 icqsol_color_surface_field.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/icqsol_color_surface_field.py Sat Nov 14 14:16:53 2015 -0500 @@ -0,0 +1,45 @@ +#!/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='Field name' ) +parser.add_argument( '--field_component_index', dest='field_component_index', type=int, help='Index of field component' ) +parser.add_argument( '--color_map', dest='color_map', help='Color map' ) +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() + +tmp_dir = icqsol_utils.get_temp_dir() +input_format, input_file_type = icqsol_utils.get_format_and_type( args.input_file_format_and_type ) + +# Instantiate a ShapeManager for loading the input. +shape_mgr = ShapeManager( file_format='vtk', vtk_dataset_type=args.input_dataset_type ) + +# Get the vtkPolyData from the input dataset. +vtk_poly_data = shape_mgr.loadAsVtkPolyData(args.input) +# Add color to the data. +# TODO: Fix the following when we have this working. +colored_vtk_poly_data = shape_mgr.colorSurfaceField(vtk_poly_data=vtk_poly_data, + color_map=args.color_map, + field_name=args.field_name, + field_component=args.field_component_index) + +# Define the output file format and type. +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 POLYDATA. +shape_mgr.setWriter( file_format='vtk', vtk_dataset_type=icqsol_utils.POLYDATA ) + +# Save the output. +shape_mgr.saveVtkPolyData( vtk_poly_data=colored_vtk_poly_data, file_name=tmp_output_path, file_type=output_file_type) +shutil.move( tmp_output_path, args.output ) diff -r 000000000000 -r 6a5b5cc5b885 icqsol_color_surface_field.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/icqsol_color_surface_field.xml Sat Nov 14 14:16:53 2015 -0500 @@ -0,0 +1,73 @@ + + + + + icqsol_macros.xml + + + + + + + + value is not None and len(value.metadata.field_names) > 0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + + + + + + + diff -r 000000000000 -r 6a5b5cc5b885 icqsol_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/icqsol_macros.xml Sat Nov 14 14:16:53 2015 -0500 @@ -0,0 +1,115 @@ + + + + + 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 6a5b5cc5b885 icqsol_tool_form_utils.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/icqsol_tool_form_utils.py Sat Nov 14 14:16:53 2015 -0500 @@ -0,0 +1,21 @@ + +def get_field_components_options( dataset, **kwd ): + field_name = kwd.get( 'field_name', None ) + options = [] + if dataset.metadata is None: + return options + if not hasattr( dataset.metadata, 'field_names' ): + return options + if dataset.metadata.field_names is None: + return options + if field_name is None: + # The expression validator that helps populate the select list of input + # datsets in the icqsol_color_surface_field tool does not filter out + # datasets with no field field_names, so we need this check. + if len( dataset.metadata.field_names ) == 0: + return options + field_name = dataset.metadata.field_names[0] + field_components = dataset.metadata.field_components.get( field_name, [] ) + for i, field_component in enumerate( field_components ): + options.append( ( field_component, field_component, i == 0 ) ) + return options diff -r 000000000000 -r 6a5b5cc5b885 icqsol_utils.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/icqsol_utils.py Sat Nov 14 14:16:53 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 6a5b5cc5b885 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 14:16:53 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 6a5b5cc5b885 test-data/box_with_surface_field_colored.vtkascii --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/box_with_surface_field_colored.vtkascii Sat Nov 14 14:16:53 2015 -0500 @@ -0,0 +1,52 @@ +# 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 +COLOR_SCALARS Colors 3 +0 0 1 1 0 0 1 0 0 +0 0 1 0 0 1 +0 0 1 1 0 0 +1 0 0 0 0 1 +0 0 1 1 0 0 +1 0 0 1 0 0 +1 0 0 0 0 1 +0 0 1 0 0 1 +0 0 1 0 0 1 +0 0 1 1 0 0 +1 0 0 1 0 0 +1 0 0 +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 6a5b5cc5b885 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sat Nov 14 14:16:53 2015 -0500 @@ -0,0 +1,6 @@ + + + + + +