# HG changeset patch # User iuc # Date 1471978679 14400 # Node ID aceda40ef31193d662b1d7bbdf913e2da2c11808 Uploaded diff -r 000000000000 -r aceda40ef311 icqsol_color_surface_field.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/icqsol_color_surface_field.py Tue Aug 23 14:57:59 2016 -0400 @@ -0,0 +1,47 @@ +#!/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='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 = icqsol_utils.get_shape_manager(icqsol_utils.VTK, args.input_dataset_type) + +# Get the vtkPolyData from the input dataset. +vtk_poly_data = shape_mgr.loadAsVtkPolyData(args.input) +# Add color to the data. +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) + +# Write min/max field values. +minVal, maxVal = shape_mgr.getFieldRange(vtk_poly_data, args.field_name, args.field_component_index) +print 'component {2} min/max values of field {3}: {0}/{1}'.format(minVal, maxVal, args.field_component_index, args.field_name) + +# 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=icqsol_utils.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 aceda40ef311 icqsol_color_surface_field.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/icqsol_color_surface_field.xml Tue Aug 23 14:57:59 2016 -0400 @@ -0,0 +1,70 @@ + + + field + + icqsol_macros.xml + + + + + + + + + value is not None and len(value.metadata.field_names) > 0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +Colors a shape's selected surface field using a selected color map. This tool will restrict selected +input shapes to only those that have at least one surface field. + +* **Shape** - Shape containing a surface field to be colored. +* **Field name for coloring** - Name of the surface field to be colored. +* **Color map** - Color map to be used when coloring the surface field. + + + + + diff -r 000000000000 -r aceda40ef311 icqsol_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/icqsol_macros.xml Tue Aug 23 14:57:59 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 aceda40ef311 icqsol_tool_form_utils.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/icqsol_tool_form_utils.py Tue Aug 23 14:57:59 2016 -0400 @@ -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 aceda40ef311 icqsol_utils.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/icqsol_utils.py Tue Aug 23 14:57:59 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 aceda40ef311 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 14:57:59 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 + diff -r 000000000000 -r aceda40ef311 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 Tue Aug 23 14:57:59 2016 -0400 @@ -0,0 +1,47 @@ +# 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 +COLOR_SCALARS Colors 3 +0 0 1 0.0431373 0.168627 0.956863 0.698039 0.839216 0.301961 +0.870588 0.45098 0.129412 0 0 1 +0.0431373 0.168627 0.956863 0 0 1 +0.0431373 0.168627 0.956863 0.00784314 0.0352941 0.992157 +0.172549 0.568627 0.827451 0.894118 0.376471 0.105882 +1 0 0 +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 +