Mercurial > repos > greg > icqsol_solve_laplace

comparison icqsol_utils.py @ 0:e04795a38512 draft

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author greg
date Mon, 11 Jan 2016 08:55:00 -0500
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children 4fc22a63a17e
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-1:000000000000 0:e04795a38512
1 import os
2 import sys
3 import tempfile
4
5 from icqsol.shapes.icqShapeManager import ShapeManager
6 from icqsol.bem.icqLaplaceMatrices import LaplaceMatrices
7
8 PLY = 'ply'
9 POLYDATA = 'POLYDATA'
10 VTK = 'vtk'
11
12
13 def asbool(val):
14 return str(val).lower() in ['yes', 'true']
15
16
17 def get_format_and_type(galaxy_ext):
18 # Define the output file format and type.
19 format = None
20 datatype = None
21 if galaxy_ext in ['vtkascii', 'vtkbinary']:
22 format = VTK
23 elif galaxy_ext in ['plyascii', 'plybinary']:
24 format = PLY
25 if galaxy_ext in ['vtkascii', 'plyascii']:
26 datatype = 'ascii'
27 elif galaxy_ext in ['vtkbinary', 'plybinary']:
28 datatype = 'binary'
29 return format, datatype
30
31
32 def get_input_file_path(tmp_dir, input_file, format):
33 """
34 iCqSol uses file extensions (e.g., .ply, .vtk) when reading and
35 writing files, so the Galaxy dataset naming convention of
36 setting all file extensions as .dat must be handled.
37 """
38 file_path = get_temporary_file_path(tmp_dir, format)
39 # Remove the file so we can create a symlink.
40 os.remove(file_path)
41 os.symlink(input_file, file_path)
42 return file_path
43
44
45 def get_laplace_solver(shape_data, max_edge_length=float('inf')):
46 return LaplaceMatrices(shape_data, max_edge_length=max_edge_length)
47
48
49 def get_shape_manager(format, dataset_type):
50 # Instantiate a ShapeManager.
51 if format == VTK:
52 return ShapeManager(file_format=format, vtk_dataset_type=dataset_type)
53 else:
54 return ShapeManager(file_format=format)
55
56
57 def get_temp_dir(prefix='tmp-vtk-', dir=None):
58 """
59 Return a temporary directory.
60 """
61 return tempfile.mkdtemp(prefix=prefix, dir=dir)
62
63
64 def get_tempfilename(dir=None, suffix=None):
65 """
66 Return a temporary file name.
67 """
68 if suffix is None:
69 s = None
70 elif suffix.startswith('.'):
71 s = suffix
72 else:
73 s = '.%s' % suffix
74 fd, name = tempfile.mkstemp(suffix=s, dir=dir)
75 os.close(fd)
76 return name
77
78
79 def get_temporary_file_path(tmp_dir, file_extension):
80 """
81 Return the path to a temporary file with a valid VTK format
82 file extension.
83 """
84 return get_tempfilename(tmp_dir, file_extension)
85
86
87 def stop_err(msg):
88 sys.stderr.write("%s\n" % msg)
89 sys.exit()