From 6eb111dc7c112de63bddfcab06c5cef58111270e Mon Sep 17 00:00:00 2001
From: chen <chenzhang8722@gamil.com>
Date: Sun, 9 Oct 2016 19:01:38 -0400
Subject: [PATCH] add script convert ASCII table to HDF5

using H5Table
---
 processing/post/ascii2hdf5.py | 80 +++++++++++++++++++++++++++++++++++
 1 file changed, 80 insertions(+)
 create mode 100644 processing/post/ascii2hdf5.py

diff --git a/processing/post/ascii2hdf5.py b/processing/post/ascii2hdf5.py
new file mode 100644
index 000000000..c679d7741
--- /dev/null
+++ b/processing/post/ascii2hdf5.py
@@ -0,0 +1,80 @@
+#!/usr/bin/env python2.7
+# -*- coding: UTF-8 no BOM -*-
+
+# ------------------------------------------------------------------- #
+# NOTE:                                                               #
+#   1. Not all output is defined in the DS_HDF5.xml, please add new   #
+#      new one to the system wide definition file                     #
+#             <DAMASK_ROOT>/lib/damask/DS_HDF5.xml                    #
+#      or specify your own when initializing HDF5 class               #
+# ------------------------------------------------------------------- #
+
+import os
+import damask
+from optparse import OptionParser
+
+scriptName = os.path.splitext(os.path.basename(__file__))[0]
+scriptID   = ' '.join([scriptName,damask.version])
+
+# --------------------------------------------------------------------
+#                                MAIN
+# --------------------------------------------------------------------
+
+desp_msg = "Convert DAMASK ascii table to HDF5 file"
+parser = OptionParser(option_class=damask.extendableOption,
+                      usage='%prog options [file[s]]',
+                      description = desp_msg,
+                      version = scriptID)
+parser.add_option('-D', '--DefinitionFile',
+                  dest = 'storage definition file',
+                  type = 'string',
+                  metavar = 'string',
+                  help = 'definition file for H5 data storage')
+parser.add_option('-d','--debug',
+                  dest = 'debug output toggle',
+                  type = 'boolean',
+                  metavar = 'boolean',
+                  help = 'toggle on debug output')  # not necessary for now
+
+parser.set_defaults(debug=False,
+                    DefinitionFile='default')
+
+(options,filenames) = parser.parse_args()
+
+if options.DefinitionFile == 'default':
+    defFile = None
+else:
+    defFile = options.DefinitionFile
+
+# ----- read in data using DAMASK ASCII table class ----- #
+asciiTable = damask.ASCIItable(name=filenames, buffered=False)
+asciiTable.head_read()
+asciiTable.data_readArray()
+incNum = int(asciiTable.data[asciiTable.label_index('inc'), 0])
+allData = np.copy(asciiTable.data)  # deep copy all data, just to be safe
+featuresDim = [labels_idx[i+1] - labels_idx[i] for i in xrange(len(labels)-1)]
+featuresDim.append(fullTable.shape[1] - labels_idx[-1])
+
+# ----- create a new HDF5 file and save the data -----#
+# Will overwrite existing HDF5 file with the same name
+
+h5f = damask.H5Table(filenames.replace(".txt", ".h5"),
+                     new_file=True,
+                     dsXMLFile=defFile)
+# adding increment number as root level attributes
+h5f.add_attr('inc', incNum)
+for fi in xrange(len(labels)):
+    featureName = labels[fi]
+    if featureName == 'inc': continue
+    # remove trouble maker "("" and ")"
+    if "(" in featureName: featureName = featureName.replace("(", "")
+    if ")" in featureName: featureName = featureName.replace(")", "")
+    featureIdx = labels_idx[fi]
+    featureDim = featuresDim[fi]
+    # grab the data hook
+    dataset = fullTable[:, featureIdx:featureIdx+featureDim]
+    # reshape tensor to 3x3 --> just make life slightly easier
+    if dataset.shape[1] == 9:
+        dataset = dataset.reshape((dataset.shape[0], 3, 3))
+    # write out data
+    h5f.add_data(featureName, dataset)