[cig-commits] r4233 - mc/3D/CitcomS/trunk/visual

[tan2 at geodynamics.org]

Author: tan2
Date: 2006-08-04 17:14:39 -0700 (Fri, 04 Aug 2006)
New Revision: 4233

Added:
   mc/3D/CitcomS/trunk/visual/h52combined.py
Log:
Added a script to convert the HDF5 output file to the ASCII combined file, using PyTables extension package.


Added: mc/3D/CitcomS/trunk/visual/h52combined.py
===================================================================
--- mc/3D/CitcomS/trunk/visual/h52combined.py	2006-08-04 23:37:46 UTC (rev 4232)
+++ mc/3D/CitcomS/trunk/visual/h52combined.py	2006-08-05 00:14:39 UTC (rev 4233)
@@ -0,0 +1,152 @@
+#!/usr/bin/env python
+#
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+#
+#<LicenseText>
+#
+# CitcomS.py by Eh Tan, Eun-seo Choi, and Pururav Thoutireddy.
+# Copyright (C) 2002-2005, California Institute of Technology.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+#
+#</LicenseText>
+#
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+'''Convert the HDF5 output file to ASCII file(s), with the same format as the
+combined file
+
+usage: h52combined.py h5file step1 [step2 [...] ]
+'''
+
+import tables
+
+
+def find_prefix(h5file):
+    suffix = '.h5'
+
+    if h5file.endswith(suffix):
+        prefix = h5file[:-len(suffix)]
+    else:
+        prefix = h5file
+
+    return prefix
+
+
+
+def convert(h5file, prefix, record):
+    print 'in convert():', h5file, prefix, record
+
+    f = tables.openFile(h5file)
+
+    try:
+        # loop through all the caps
+        for cap in range(12):
+            cap_no = 'cap%02d' % cap
+
+            # get 'cap_no' group, if no such group, return None
+            group = _get_hdf_group(f.root, cap_no)
+            print repr(group)
+            if group is None:
+                break
+
+            x = group.coord
+            v = group.velocity[record,:]
+            t = group.temperature[record,:]
+            visc = group.viscosity[record,:]
+
+            # TODO: map record -> step
+            outputfile = '%s.%s.%d' % (prefix, cap_no, record)
+            #print outputfile
+
+            output(outputfile, x, v, t, visc)
+
+
+
+    finally:
+        f.close()
+
+    return outputfile
+
+
+
+def output(outputfile, x, v, t, visc):
+    out = file(outputfile, 'w')
+    try:
+        # write header (shape of the arrays)
+        nx, ny, nz = t.shape[:3]
+        header = '%d x %d x %d\n' % (nx, ny, nz)
+        out.write(header)
+
+        # write data
+        for i in range(ny):
+            for j in range(nx):
+                for k in range(nz):
+                    #n = k + j*nz + i*nz*nx
+                    xx = x[j, i, k, :]
+                    vv = v[j, i, k, :]
+                    tt = t[j, i, k]
+                    hh = visc[j, i, k]
+                    format = '%.6e '*7 + '%.6e\n'
+                    line = format % (
+                        xx[0], xx[1], xx[2],
+                        vv[0], vv[1], vv[2],
+                        tt, hh )
+                    out.write(line)
+
+    finally:
+        out.close()
+
+
+
+def _get_hdf_group(base, child):
+    try:
+        return base._f_getChild(child)
+    except tables.exceptions.NoSuchNodeError:
+        return None
+
+
+
+def make_general(outputfile):
+    import os
+
+    path = os.path.dirname(__file__)
+    cmd = '%s/dxgeneral.sh %s' % (path, outputfile)
+    #print cmd
+    os.system(cmd)
+
+
+
+if __name__ == '__main__':
+    import sys
+
+    if len(sys.argv) < 3:
+        print __doc__
+        sys.exit(1)
+
+
+    h5file = sys.argv[1]
+    file_prefix = find_prefix(h5file)
+
+    steps = [ int(x) for x in sys.argv[2:] ]
+
+
+    for step in steps:
+        # write to outputfile
+        outputfile = convert(h5file, file_prefix, step)
+
+        # generate header file for OpenDX
+        make_general(outputfile)
+


Property changes on: mc/3D/CitcomS/trunk/visual/h52combined.py
___________________________________________________________________
Name: svn:executable
   + *