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icqsol_add_surface_field_from_expression.py icqsol_add_surface_field_from_expression.xml icqsol_macros.xml icqsol_utils.py test-data/box.vtkascii test-data/box_with_surface_field.vtkascii |
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| 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 |
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| @@ -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) |
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| 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 |
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| @@ -0,0 +1,95 @@ +<?xml version='1.0' encoding='UTF-8'?> +<tool id="icqsol_add_surface_field_from_expression" name="Add surface field" version="@WRAPPER_VERSION@.0"> + <description>from expression</description> + <macros> + <import>icqsol_macros.xml</import> + </macros> + <expand macro="requirements" /> + <command> + <![CDATA[ + python $__tool_directory__/icqsol_add_surface_field_from_expression.py + --input "$input" + --input_file_format_and_type $input.ext + --input_dataset_type $input.metadata.dataset_type + --field_name "$field_name" + --location $location + --expression "$expression" + #for $tp in $time_points: + --time_point ${tp.time_point} + #end for + #if $refine_shape_cond.refine_shape == "yes": + --max_edge_length $refine_shape_cond.max_edge_length + #end if + --output "$output" + --output_vtk_type $output_vtk_type + ]]> + </command> + <inputs> + <param name="input" type="data" format="plyascii,plybinary,vtkascii,vtkbinary" label="Shape"> + <validator type="dataset_ok_validator" /> + </param> + <param name="field_name" type="text" value="surface_field" label="Surface field name" help="Spaces will be converted to underscore character."/> + <param name="location" type="select" label="Location of field" help="Field values vary linearly between nodes when visualizing fields located at points, while each triangle is assigned a single value with fields located at cells."> + <option value="cell" selected="True">Cell</option> + <option value="point">Point</option> + </param> + <param name="expression" type="text" value="(x**2 * sin(y*pi) + z**4) * exp(t)" label="Expression" help="Legal variables are x,y,z (point coordinates) and t (time)."/> + <repeat name="time_points" title="Points in time" min="1" help="Provides snapshots of surface field over time sequence."> + <param name="time_point" type="float" value="0" label="Time point" help="Floating point number"/> + </repeat> + <conditional name="refine_shape_cond"> + <param name="refine_shape" type="select" label="Refine shape?" help="Points will be added to the shape's edges restricting their length to the maximum."> + <option value="no" selected="True">No</option> + <option value="yes">Yes</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="max_edge_length" type="float" value="0.1" label="Maximum edge length" help="Refine shape by restricting edges to this length."> + <validator type="in_range" min="0" exclude_min="true" /> + </param> + </when> + </conditional> + <expand macro="output_vtk_type_params" /> + </inputs> + <outputs> + <data name="output" format="vtkascii"> + <actions> + <action type="format"> + <option type="from_param" name="output_vtk_type" /> + </action> + </actions> + </data> + </outputs> + <tests> + <test> + <param name="input" value="box.vtkascii" ftype="vtkascii" /> + <param name="input_file_format_and_type" value="vtkascii" /> + <param name="input_dataset_type" value="POLYDATA" /> + <param name="field_name" value="surface_field" /> + <param name="location" value="cell" /> + <param name="expression" value="(x**2 * sin(y*pi) + z**4) * exp(t)" /> + <repeat name="time_points"> + <param name="time_point" value="0.1" /> + </repeat> + <output name="output" file="box_with_surface_field.vtkascii" ftype="vtkascii" /> + <param name="output_vtk_type" value="vtkascii" /> + </test> + </tests> + <help> +**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. + + </help> + <expand macro="citations" /> +</tool> |
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| 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 |
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| @@ -0,0 +1,116 @@ +<?xml version='1.0' encoding='UTF-8'?> +<macros> + <token name="@WRAPPER_VERSION@">1.0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.3.26">icqsol</requirement> + </requirements> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:"/> + <exit_code range=":-1"/> + <regex match="Error:"/> + <regex match="Exception:"/> + </stdio> + </xml> + <!-- TODO: place this in colormaps_conf.xml --> + <xml name="color_map_param"> + <param name="color_map" type="select" label="Color map"> + <option value="hot" selected="True">Hot</option> + <option value="cold">Cold</option> + <option value="blackbody">Blackbody</option> + <option value="gnu">Gnu</option> + </param> + </xml> + <xml name="output_vtk_type_params"> + <param name="output_vtk_type" type="select" label="Output file type"> + <option value="vtkascii" selected="True">Vtk-ascii</option> + <option value="vtkbinary">Vtk-binary</option> + </param> + </xml> + <token name="@origin_cmd_args@"> + --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 + </token> + <xml name="origin_params"> + <param name="origin_x" type="float" value="0.0" label="X coordinate of origin" help="Floating point number"/> + <param name="origin_y" type="float" value="0.0" label="Y coordinate of origin" help="Floating point number"/> + <param name="origin_z" type="float" value="0.0" label="Z coordinate of origin" help="Floating point number"/> + </xml> + <token name="@lengths_cmd_args@"> + --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 + </token> + <xml name="lengths_params"> + <!-- At least one of these lengths must be greater than zero, but we have no validator for this. --> + <param name="length_x" type="float" value="1.0" label="Length in the X direction" help="Floating point number"> + <validator type="in_range" min="0" exclude_min="false" /> + </param> + <param name="length_y" type="float" value="0.0" label="Length in the Y direction" help="Floating point number"> + <validator type="in_range" min="0" exclude_min="false" /> + </param> + <param name="length_z" type="float" value="0.0" label="Length in the Z direction" help="Floating point number"> + <validator type="in_range" min="0" exclude_min="false" /> + </param> + </xml> + <xml name="lengths_exclude_min_params"> + <param name="length_x" type="float" value="1.0" label="Length in the X direction" help="Floating point number"> + <validator type="in_range" min="0" exclude_min="true" /> + </param> + <param name="length_y" type="float" value="1.0" label="Length in the Y direction" help="Floating point number"> + <validator type="in_range" min="0" exclude_min="true" /> + </param> + <param name="length_z" type="float" value="1.0" label="Length in the Z direction" help="Floating point number"> + <validator type="in_range" min="0" exclude_min="true" /> + </param> + </xml> + <token name="@radius_cmd_args@"> + --radius $create_process_cond.shape_cond.radius + </token> + <xml name="radius_params"> + <param name="radius" type="float" value="1.0" label="Radius" help="Floating point number"> + <validator type="in_range" min="0" exclude_min="True" /> + </param> + </xml> + <token name="@n_theta_cmd_args@"> + --n_theta $create_process_cond.shape_cond.n_theta + </token> + <xml name="n_theta_params"> + <param name="n_theta" type="integer" value="16" label="Number of slices" help="Controls the tessellation along the longitude direction"> + <validator type="in_range" min="0" exclude_min="False" /> + </param> + </xml> + <token name="@n_phi_cmd_args@"> + --n_phi $create_process_cond.shape_cond.n_phi + </token> + <xml name="n_phi_params"> + <param name="n_phi" type="integer" value="8" label="Number of stacks" help="Controls the tessellation along the latitude direction"> + <validator type="in_range" min="0" exclude_min="False" /> + </param> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @unpublished{None, + author = {None}, + title = {None}, + year = {None}, + eprint = {None}, + url = {https://github.com/gregvonkuster/galaxy-csg} + }</citation> + <citation type="bibtex"> + @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") + </citation> + </citations> + </xml> +</macros> |
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| 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 |
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| @@ -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() |
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| 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 |
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| @@ -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 + |
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| 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 |
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| @@ -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 + |