Merge branch 'master' of https://github.com/prjemian/spec2nexus.git

CHANGES.rst

@@ -7,6 +7,7 @@ Change History
 Production
 **********
 
+:2016.0216.0: `issue #36 <https://github.com/prjemian/spec2nexus/issues/36>`_: identify NIAC2014-compliant NeXus files
 :2016.0210.0: bugfix: eznx.makeGroup() now correctly sets attributes on new group + documentation for NIAC2014 attributes
 :2016.0204.0: (`#45 <https://github.com/prjemian/spec2nexus/issues/45>`_) handle case when no data points in scan , 
               (`#46 <https://github.com/prjemian/spec2nexus/issues/46>`_) spec.getScan() ensures argument is used as ``str``

src/spec2nexus/dev_h5toText.py

@@ -28,6 +28,8 @@
 # sys.argv.append('6')
 # sys.argv.append(os.path.join(testpath, 'data', 'writer_1_3.h5'))
 sys.argv.append(os.path.join(testpath, 'data', 'Data_Q.h5'))
+# sys.argv.append(os.path.join(testpath, 'data', 'compression.h5'))
+# sys.argv.append(os.path.join(testpath, 'data', 'writer_1_3.h5'))
 # sys.argv.append(os.path.join(os.environ['HOMEPATH'], 'Desktop', 'thau_1.nxs.hdf'))
 
 

src/spec2nexus/h5toText.py

@@ -249,6 +249,113 @@ def isNeXusFile(filename):
     '''
     is `filename` is a NeXus HDF5 file?
     
+    Tests if ``filename`` adheres to either
+    "Associating plottable data using attributes applied to the **NXdata** group" 
+    (needs URL - NeXus manual is not yet ready to provide it)
+    or
+    "Associating plottable data by name using the ``axes`` attribute"
+    (needs URL - again, from NeXus manual)
+    or
+    "Associating plottable data by dimension number using the ``axis`` attribute"
+    (needs URL - again, from NeXus manual)
+    '''
+    if not os.path.exists(filename):
+        return None
+    m1 = isNeXusFile_ByNXdataAttrs
+    m2 = isNeXusFile_ByAxes
+    m3 = isNeXusFile_ByAxisAttr
+    # shorter method names to make next line readable
+    return m1(filename) or m2(filename) or m3(filename)
+
+
+def _get_group_niac2014(parent, attribute, nxclass_name):
+    '''
+    supports the NIAC2014method:
+    
+    Search parent for the group named by the attribute
+    (with fallback if the attribute is not defined to picking *any*
+    group that has the same nxclass_name).
+    '''
+    group = parent.attrs.get(attribute, None)
+    if group is None:
+        # Expect that some data files will not write these attributes.
+        # Find *any* HDF5 group that has its @NX_class attribute set to ``nxclass_name``.
+        for node0 in parent.values():
+            # TODO: verify
+            # Does this search ALL POSSIBLE {nxclass_name} groups for 
+            # at least one compliance or just the first one it finds?
+            if isNeXusGroup(node0, nxclass_name):
+                group = node0
+                break
+        if group is None:
+            return False
+    if not isNeXusGroup(group, nxclass_name):
+        return False
+    return group
+
+def isNeXusFile_ByNXdataAttrs(filename):
+    '''
+    is `filename` is a NeXus HDF5 file?
+    
+    This is the "NIAC2014" method.
+    In short, verify these NeXus classpaths exist::
+    
+        /@default={entry_group}
+        /{entry_group}:NXentry/@default={data_group}
+        /{entry_group}:NXentry/{data_group}:NXdata
+        /{entry_group}:NXentry/{data_group}:NXdata/@signal={signal_dataset}
+        /{entry_group}:NXentry/{data_group}:NXdata/{signal_dataset}
+        /{entry_group}:NXentry/{data_group}:NXdata/@axes=["{axes_dataset1}", ...]
+        /{entry_group}:NXentry/{data_group}:NXdata/@{axes_dataset1}_indices=int[]
+        ...
+    
+    where curly braces (``{`` and ``}``) denote that the enclosed name
+    is defined in the data file.
+    '''
+    try:
+        f = h5py.File(filename, 'r')
+        if not isHdf5File(f):
+            f.close()
+            return False
+
+        # find the NXentry group
+        nxentry = _get_group_niac2014(f, 'default', 'NXentry')
+        if nxentry is None:
+            return False
+
+        # find the NXdata group
+        nxdata = _get_group_niac2014(nxentry, 'default', 'NXdata')
+        if nxdata is None:
+            return False        # no compliant NXdata group identified
+
+        # find the signal dataset
+        signal = nxdata.attrs.get('signal', None)
+        if signal is None:
+            return False        # no signal attribute
+        if isinstance(signal, numpy.ndarray):
+            signal = signal[0]
+        if signal not in nxdata:
+            return False        # no signal dataset
+        ds_signal = nxdata[signal]
+        if not isNeXusDataset(ds_signal):
+            return False        # that HDF5 object is not a NeXus dataset
+
+        # Tests for nxdata.attrs['axes'] and nxdata.attrs['{axisname}_indices'] 
+        # cannot be robust since we expect some clients simply will not write these.
+
+        f.close()
+        return True
+    except Exception, _exc:
+        pass    # ignore any Exceptions, they mean that result stays "False"
+    return False
+
+
+def isNeXusFile_ByAxes(filename):
+    '''
+    is `filename` is a NeXus HDF5 file?
+
+    This has been, to date, the most common method in NeXus to define the default plot.
+    
     In short, verify this NeXus classpath exists::
     
         /NXentry/NXdata/dataset/@signal=1
@@ -283,6 +390,17 @@ def isNeXusFile(filename):
     return False
 
 
+def isNeXusFile_ByAxisAttr(filename):
+    '''
+    is `filename` is a NeXus HDF5 file?
+    
+    This is the oldest method in NeXus to define the default plot.
+    
+    NOTE: **Not implemented yet!**
+    '''
+    return False    # TODO: implement this method
+
+
 def isNeXusGroup(obj, NXtype):
     '''is `obj` a NeXus group?'''
     nxclass = None