# HG changeset patch
# User iuc
# Date 1471978752 14400
# Node ID 1574fdcc16dfcfa772ff35955c27a99b584d89f0
Uploaded
diff -r 000000000000 -r 1574fdcc16df icqsol_compose_shapes.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/icqsol_compose_shapes.py Tue Aug 23 14:59:12 2016 -0400
@@ -0,0 +1,43 @@
+#!/usr/bin/env python
+import argparse
+import shutil
+
+import icqsol_utils
+
+# Parse Command Line.
+parser = argparse.ArgumentParser()
+parser.add_argument('--expression', dest='expression', help='Composition expression')
+parser.add_argument('--shape_dataset', dest='shape_datasets', action='append', nargs=4, help='Shape datasets selected from history')
+parser.add_argument('--output', dest='output', help='Output dataset')
+parser.add_argument('--output_vtk_type', dest='output_vtk_type', help='Output file format and type')
+
+args = parser.parse_args()
+
+tmp_dir = icqsol_utils.get_temp_dir()
+shape_tuples = []
+shape_mgr = icqsol_utils.get_shape_manager()
+
+# Load the shapes.
+for (expression_var, dataset_path, galaxy_ext, vtk_dataset_type) in args.shape_datasets:
+ # Define the file format and type.
+ format, file_type = icqsol_utils.get_format_and_type(galaxy_ext)
+ if format == icqsol_utils.VTK:
+ shape_mgr.setReader(file_format=format, vtk_dataset_type=vtk_dataset_type)
+ else:
+ shape_mgr.setReader(file_format=format)
+ icqsol_path = icqsol_utils.get_input_file_path(tmp_dir, dataset_path, format)
+ shape_tuple = (expression_var, shape_mgr.loadAsShape(icqsol_path))
+ shape_tuples.append(shape_tuple)
+
+# 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)
+
+shape_mgr.setWriter(file_format=output_format, vtk_dataset_type=icqsol_utils.POLYDATA)
+
+# Compose the shapes.
+composite_shape = shape_mgr.composeShapes(shape_tuples, args.expression)
+
+# Save the output.
+shape_mgr.saveShape(shape=composite_shape, file_name=tmp_output_path, file_type=output_file_type)
+shutil.move(tmp_output_path, args.output)
diff -r 000000000000 -r 1574fdcc16df icqsol_compose_shapes.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/icqsol_compose_shapes.xml Tue Aug 23 14:59:12 2016 -0400
@@ -0,0 +1,74 @@
+
+
+
+
+ icqsol_macros.xml
+
+
+
+
+
+
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+
+
+**What it does**
+
+Creates a shape composed of any number of selected shapes where the composition is based on a mathematical
+expression consisting of **+**, **-** and ***** operations. The **+** results in a union of shapes, the
+**-** operator removes a shape and the ***** operator results in an intersection of shapes.
+
+For example, if the **Composition expression** is **A + B - C - D**, selecting 4 shapes from your history
+and associating each shape with a variable from the expression will result in a shape composed of the shapes
+associated with A and B, but eliminating the shapes associated with C and D.
+
+
+
+
diff -r 000000000000 -r 1574fdcc16df icqsol_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/icqsol_macros.xml Tue Aug 23 14:59:12 2016 -0400
@@ -0,0 +1,116 @@
+
+
+ 1.0
+
+
+ icqsol
+
+
+
+
+
+
+
+
+
+
+
+
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+
+
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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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+
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+
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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 1574fdcc16df icqsol_utils.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/icqsol_utils.py Tue Aug 23 14:59:12 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 1574fdcc16df test-data/head.vtkascii
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/head.vtkascii Tue Aug 23 14:59:12 2016 -0400
@@ -0,0 +1,65 @@
+# vtk DataFile Version 4.0
+vtk output
+ASCII
+DATASET POLYDATA
+POINTS 34 float
+-0.06 0 0 -0.06 0 -0.25 -0.06 -0.0956709 -0.23097
+0.08 0 0 -0.06 -0.176777 -0.176777 -0.06 -0.23097 -0.0956709
+-0.06 -0.25 0 -0.06 -0.23097 0.0956709 -0.06 -0.176777 0.176777
+-0.06 -0.0956709 0.23097 -0.06 0 0.25 -0.06 0.0956709 0.23097
+-0.06 0.176777 0.176777 -0.06 0.23097 0.0956709 -0.06 0.25 0
+-0.06 0.23097 -0.0956709 -0.06 0.176777 -0.176777 -0.06 0.0956709 -0.23097
+-0.06 0 -0.25 -0.06 -0.0956709 -0.23097 -0.06 -0.176777 -0.176777
+-0.06 -0.23097 -0.0956709 -0.06 -0.25 0 -0.06 -0.23097 0.0956709
+-0.06 -0.176777 0.176777 -0.06 -0.0956709 0.23097 -0.06 0 0.25
+-0.06 0.0956709 0.23097 -0.06 0.176777 0.176777 -0.06 0.23097 0.0956709
+-0.06 0.25 0 -0.06 0.23097 -0.0956709 -0.06 0.176777 -0.176777
+-0.06 0.0956709 -0.23097
+POLYGONS 32 128
+3 0 1 2
+3 18 3 19
+3 0 2 4
+3 19 3 20
+3 0 4 5
+3 20 3 21
+3 0 5 6
+3 21 3 22
+3 0 6 7
+3 22 3 23
+3 0 7 8
+3 23 3 24
+3 0 8 9
+3 24 3 25
+3 0 9 10
+3 25 3 26
+3 0 10 11
+3 26 3 27
+3 0 11 12
+3 27 3 28
+3 0 12 13
+3 28 3 29
+3 0 13 14
+3 29 3 30
+3 0 14 15
+3 30 3 31
+3 0 15 16
+3 31 3 32
+3 0 16 17
+3 32 3 33
+3 0 17 1
+3 33 3 18
+
+POINT_DATA 34
+NORMALS Normals float
+-1 0 0 -1 0 0 -1 0 0
+1 2.30575e-08 6.43464e-09 -1 0 0 -1 0 0
+-1 0 0 -1 0 0 -1 0 0
+-1 0 0 -1 0 0 -1 0 0
+-1 0 0 -1 0 0 -1 0 0
+-1 0 0 -1 0 0 -1 0 0
+0.872506 0 -0.488603 0.872506 -0.18698 -0.451411 0.872506 -0.345495 -0.345495
+0.872506 -0.451411 -0.18698 0.872506 -0.488603 0 0.872506 -0.451411 0.18698
+0.872506 -0.345495 0.345495 0.872506 -0.18698 0.451411 0.872506 0 0.488603
+0.872506 0.18698 0.451411 0.872506 0.345495 0.345495 0.872506 0.451411 0.18698
+0.872506 0.488603 0 0.872506 0.451411 -0.18698 0.872506 0.345495 -0.345495
+0.872506 0.18698 -0.451411
diff -r 000000000000 -r 1574fdcc16df test-data/notch1.vtkascii
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/notch1.vtkascii Tue Aug 23 14:59:12 2016 -0400
@@ -0,0 +1,33 @@
+# vtk DataFile Version 4.0
+vtk output
+ASCII
+DATASET POLYDATA
+POINTS 24 float
+-0.06 -0.015 -0.15 -0.06 -0.015 0.15 -0.06 0.015 0.15
+-0.06 0.015 -0.15 -0.03 -0.015 -0.15 -0.03 0.015 -0.15
+-0.03 0.015 0.15 -0.03 -0.015 0.15 -0.06 -0.015 -0.15
+-0.06 -0.015 -0.15 -0.06 -0.015 0.15 -0.06 -0.015 0.15
+-0.06 0.015 0.15 -0.06 0.015 0.15 -0.06 0.015 -0.15
+-0.06 0.015 -0.15 -0.03 -0.015 -0.15 -0.03 -0.015 -0.15
+-0.03 0.015 -0.15 -0.03 0.015 -0.15 -0.03 0.015 0.15
+-0.03 0.015 0.15 -0.03 -0.015 0.15 -0.03 -0.015 0.15
+
+POLYGONS 6 30
+4 0 1 2 3
+4 4 5 6 7
+4 8 16 22 10
+4 14 12 20 18
+4 9 15 19 17
+4 11 23 21 13
+
+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 1574fdcc16df test-data/notch2.vtkascii
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/notch2.vtkascii Tue Aug 23 14:59:12 2016 -0400
@@ -0,0 +1,33 @@
+# vtk DataFile Version 4.0
+vtk output
+ASCII
+DATASET POLYDATA
+POINTS 24 float
+-0.06 -0.15 0.015 -0.06 0.15 0.015 -0.06 0.15 -0.015
+-0.06 -0.15 -0.015 -0.03 -0.15 0.015 -0.03 -0.15 -0.015
+-0.03 0.15 -0.015 -0.03 0.15 0.015 -0.06 -0.15 0.015
+-0.06 -0.15 0.015 -0.06 0.15 0.015 -0.06 0.15 0.015
+-0.06 0.15 -0.015 -0.06 0.15 -0.015 -0.06 -0.15 -0.015
+-0.06 -0.15 -0.015 -0.03 -0.15 0.015 -0.03 -0.15 0.015
+-0.03 -0.15 -0.015 -0.03 -0.15 -0.015 -0.03 0.15 -0.015
+-0.03 0.15 -0.015 -0.03 0.15 0.015 -0.03 0.15 0.015
+
+POLYGONS 6 30
+4 0 1 2 3
+4 4 5 6 7
+4 8 16 22 10
+4 14 12 20 18
+4 9 15 19 17
+4 11 23 21 13
+
+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 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 0 1 0
+
diff -r 000000000000 -r 1574fdcc16df test-data/philips_bolt.vtkascii
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/philips_bolt.vtkascii Tue Aug 23 14:59:12 2016 -0400
@@ -0,0 +1,586 @@
+# vtk DataFile Version 4.0
+vtk output
+ASCII
+DATASET POLYDATA
+POINTS 432 float
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diff -r 000000000000 -r 1574fdcc16df test-data/shaft.vtkascii
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/shaft.vtkascii Tue Aug 23 14:59:12 2016 -0400
@@ -0,0 +1,103 @@
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