Merge pull request #33 from prjemian/development

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prjemian · Jan 27, 2015 · a5e9252 · a5e9252
2 parents 08df563 + 3bbd438
commit a5e9252
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Showing 3 changed files with 62 additions and 58 deletions.
diff --git a/CHANGES.rst b/CHANGES.rst
@@ -7,6 +7,7 @@ Change History
 Production
 **********
 
+:2015.0127.0: ignore bad data lines
 :2015.0125.0: change handling of #L & #X, refactor detection of scanNum and scanCmd
 :2015.0113.0: dropped requirement of *lxml* package
 :2014.1228.1: build mne:name cross-references for counters and positioners

diff --git a/src/spec2nexus/__init__.py b/src/spec2nexus/__init__.py
@@ -1,52 +1,52 @@
-# -*- coding: iso-8859-1 -*-
-
-'''command-line tool to convert SPEC data files to NeXus HDF5'''
-
-#-----------------------------------------------------------------------------
-# :author:    Pete R. Jemian
-# :email:     prjemian@gmail.com
-# :copyright: (c) 2014-2015, Pete R. Jemian
-#
-# Distributed under the terms of the Creative Commons Attribution 4.0 International Public License.
-#
-# The full license is in the file LICENSE.txt, distributed with this software.
-#-----------------------------------------------------------------------------
-
-__version__   = '2015.0125.0'
-__release__   = __version__
-__author__    = 'Pete R. Jemian'
-__email__     = 'prjemian@gmail.com'
-__copyright__ = '2015, Pete R. Jemian'
-
-__package_name__ = 'spec2nexus'
-__license_url__  = 'http://creativecommons.org/licenses/by/4.0/deed.en_US'
-__license__      = 'Creative Commons Attribution 4.0 International Public License (see LICENSE file)'
-__description__  = 'Converts SPEC data files and scans into NeXus HDF5 files'
-__author_name__  = __author__
-__author_email__ = __email__
-__url__          = u'http://spec2nexus.readthedocs.org'
-__download_url__ = u'https://github.com/prjemian/spec2nexus/tarball/' + __version__
-__keywords__     = ['SPEC', 'diffraction', 'data acquisition', 'NeXus', 'HDF5']
-
-__install_requires__ = ('h5py','numpy', )
-__classifiers__ = [
-     'Development Status :: 5 - Production/Stable',
-     'Environment :: Console',
-     'Intended Audience :: Science/Research',
-     'License :: Freely Distributable',
-     'License :: Public Domain',
-     'Programming Language :: Python',
-     'Programming Language :: Python :: 2',
-     'Programming Language :: Python :: 2.7',
-     'Topic :: Scientific/Engineering',
-     'Topic :: Scientific/Engineering :: Astronomy',
-     'Topic :: Scientific/Engineering :: Bio-Informatics',
-     'Topic :: Scientific/Engineering :: Chemistry',
-     'Topic :: Scientific/Engineering :: Information Analysis',
-     'Topic :: Scientific/Engineering :: Interface Engine/Protocol Translator',
-     'Topic :: Scientific/Engineering :: Mathematics',
-     'Topic :: Scientific/Engineering :: Physics',
-     'Topic :: Scientific/Engineering :: Visualization',
-     'Topic :: Software Development',
-     'Topic :: Utilities',
-   ]
+# -*- coding: iso-8859-1 -*-
+
+'''command-line tool to convert SPEC data files to NeXus HDF5'''
+
+#-----------------------------------------------------------------------------
+# :author:    Pete R. Jemian
+# :email:     prjemian@gmail.com
+# :copyright: (c) 2014-2015, Pete R. Jemian
+#
+# Distributed under the terms of the Creative Commons Attribution 4.0 International Public License.
+#
+# The full license is in the file LICENSE.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
+__version__   = '2015.0127.0'
+__release__   = __version__
+__author__    = 'Pete R. Jemian'
+__email__     = 'prjemian@gmail.com'
+__copyright__ = '2014-2015, Pete R. Jemian'
+
+__package_name__ = 'spec2nexus'
+__license_url__  = 'http://creativecommons.org/licenses/by/4.0/deed.en_US'
+__license__      = 'Creative Commons Attribution 4.0 International Public License (see LICENSE file)'
+__description__  = 'Converts SPEC data files and scans into NeXus HDF5 files'
+__author_name__  = __author__
+__author_email__ = __email__
+__url__          = u'http://spec2nexus.readthedocs.org'
+__download_url__ = u'https://github.com/prjemian/spec2nexus/tarball/' + __version__
+__keywords__     = ['SPEC', 'diffraction', 'data acquisition', 'NeXus', 'HDF5']
+
+__install_requires__ = ('h5py','numpy', )
+__classifiers__ = [
+     'Development Status :: 5 - Production/Stable',
+     'Environment :: Console',
+     'Intended Audience :: Science/Research',
+     'License :: Freely Distributable',
+     'License :: Public Domain',
+     'Programming Language :: Python',
+     'Programming Language :: Python :: 2',
+     'Programming Language :: Python :: 2.7',
+     'Topic :: Scientific/Engineering',
+     'Topic :: Scientific/Engineering :: Astronomy',
+     'Topic :: Scientific/Engineering :: Bio-Informatics',
+     'Topic :: Scientific/Engineering :: Chemistry',
+     'Topic :: Scientific/Engineering :: Information Analysis',
+     'Topic :: Scientific/Engineering :: Interface Engine/Protocol Translator',
+     'Topic :: Scientific/Engineering :: Mathematics',
+     'Topic :: Scientific/Engineering :: Physics',
+     'Topic :: Scientific/Engineering :: Visualization',
+     'Topic :: Software Development',
+     'Topic :: Utilities',
+   ]
diff --git a/src/spec2nexus/plugins/spec_common_spec2nexus.py b/src/spec2nexus/plugins/spec_common_spec2nexus.py
@@ -131,7 +131,7 @@ def process(self, text, scan, *args, **kws):
 
     def writer(self, h5parent, writer, scan, *args, **kws):
         '''Describe how to store this data in an HDF5 NeXus file'''
-        write_dataset(h5parent, "comments", '\n'.join(scan.comments))
+        write_dataset(h5parent, "comments", '\n'.join(map(str, scan.comments)))
 
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 
@@ -1005,11 +1005,14 @@ def data_lines_postprocessing(scan):
             mca_spectrum = map(float, values[2:].split())
             scan.data['_mca_'].append(mca_spectrum)
         else:
-            buf = scan._interpret_data_row(values)
-            if len(buf) == num_columns:
-                # only keep complete rows
-                for label, val in buf.items():
-                    scan.data[label].append(val)
+            try:
+                buf = scan._interpret_data_row(values)
+                if len(buf) == num_columns:
+                    # only keep complete rows
+                    for label, val in buf.items():
+                        scan.data[label].append(val)
+            except ValueError, exc:
+                pass    # ignore bad data lines (could save it as such ...)
     scan.addH5writer('scan data', data_lines_writer)