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MNT #3 more concise code
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@prjemian
prjemian committed Jan 22, 2020
1 parent fbee7f3 commit 5381505
Showing 1 changed file with 39 additions and 123 deletions.
162 changes: 39 additions & 123 deletions critique.py
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Original file line number Diff line number Diff line change
@@ -1,13 +1,33 @@
#!/usr/bin/env python

'''
describe NeXus compliance of files in this repository
tests all files in this repo for basic compliance with the NeXus standard (per 2016 NIAC)
to update the compliance report in this repo, run this command::
USAGE
To update the compliance report in this repo::
./critique.py | tee critique.md
note: This code is compliant with both python 2 and python 3
Notes:
* This code is compliant with both python 2 and python 3
* This code does not perform a full validation of NeXus data files.
It only checks that a given file can be opened by h5py
and has at least one *NXentry* group.
Tests for this structure
(exact name of *entry01* is not required)::
<file_root>:
entry01 (NXentry)
... # content not checked at this level
... # additional content not checked at this level
:see: http://wiki.nexusformat.org/2014_How_to_find_default_data
:see: https://www.nexusformat.org/NIAC2016Minutes.html#nxdata
'''


Expand All @@ -16,19 +36,13 @@
import numpy
import pyRestTable
import os
import six
import sys


def isHdf5Group(obj):
"""is `obj` an HDF5 Group?"""
return isinstance(obj, h5py.Group)


def isNeXusGroup(obj, NXtype):
"""is `obj` a NeXus group?"""
nxclass = None
if isHdf5Group(obj):
if isinstance(obj, h5py.Group):
if "NX_class" not in obj.attrs:
return False
try:
Expand All @@ -39,16 +53,11 @@ def isNeXusGroup(obj, NXtype):
if isinstance(nxclass, numpy.ndarray):
nxclass = nxclass[0]

if six.PY3:
if isinstance(nxclass, bytes):
if isinstance(nxclass, bytes) and not isinstance(nxclass, str):
nxclass = nxclass.decode()
return nxclass == NXtype


def is_spec_file(fullname):
return False # see spec2nexus.spec.is_spec_file()


class Critic(object):
'''
describe a file in terms of NeXus compliance
Expand All @@ -59,9 +68,8 @@ class Critic(object):
def __init__(self, path, fname):
self.path = None
self.fname = None
self.hdf5 = None
self.NXentry_nodes = []
self.isNeXus = False
self.filetype = "not HDF5 file"

# can the file be found?
fullname = os.path.join(path, fname)
Expand All @@ -75,129 +83,37 @@ def __init__(self, path, fname):
# ok, passes basic qualifications, proceed
self.path = path
self.fname = fname

# alternative to find_self.NXentry_NXdata_nodes(), deeper analysis
# this code only checks for NXentry/NXdata/<data>/@signal=1
self.isNeXus = self.isHDF5(fullname) and self.niac2014Compliance(fullname)

# is it an HDF5 file?
if not self.openHDF5(fullname):
return

# TODO: make lists of
# all field names
# group names
# nx_class types
# TODO: check all field names
# field names for fit to the regexp
# field names for correct codepage
# strings for correct codepage
try:
with h5py.File(fullname, mode="r") as root:
self.filetype = "HDF5 file"
self.NXentry_nodes = self.find_NX_class_nodes(root, "NXentry")
if len(self.NXentry_nodes) > 0:
self.filetype = "NeXus HDF5 file"
except IOError:
pass # cannot open with HDF5

# finally: close the HDF5 file
self.hdf5.close()
# no deeper validation of the NeXus data file

def describe_file(self):
s = 'HDF5 file'
if self.hdf5 is None:
return 'not ' + s
if self.isNeXus:
s = 'NeXus ' + s
s = self.filetype
if len(self.NXentry_nodes) > 0:
s += ', %d **NXentry** group' % len(self.NXentry_nodes)
if len(self.NXentry_nodes) > 1:
s += 's'
return s

def __str__(self, *args, **kwargs):
return self.describe_file()

def isHDF5(self, fname):
'''is this an HDF5 file?'''
if not self.openHDF5(fname):
return False
self.hdf5.close()
return True

def openHDF5(self, fname):
'''try to open the file as HDF5'''
try:
self.hdf5 = h5py.File(fname, 'r')
except IOError:
return False
return True
return self.describe_file()

def find_NX_class_nodes(self, parent = None, nx_class = 'NXentry'):
def find_NX_class_nodes(self, parent, nx_class = 'NXentry'):
'''identify the NXentry (or as specified) nodes'''
parent = parent or self.hdf5
parent = parent
node_list = []
for node in parent.values():
if isNeXusGroup(node, nx_class):
node_list.append(node)
return node_list

def niac2014Compliance(self, fullname):
'''
tests file for compliance with NIAC2014 agreement on how to find the plottable data
.. note:: This test is not robust.
* It does not test every NXdata group for compliance
with the **NIAC2014** method.
* It does not test each NXentry for at least one NXdata
group compliant with the **NIAC2014** method.
* It does not detect a file with mixed structure,
both ``signal=1`` and **NIAC2014** methods.
Tests data file for this structure (as agreed at 2014 NIAC meeting)::
<file_root>:
@default = "entry01" (only needed to resolve ambiguity)
entry01 (NXentry)
@default = "data02" (only needed to resolve ambiguity)
data01 (NXdata)
...
data02 (NXdata)
@signal = "data1"
data1
data2
entry02 (NXentry)
...
:see: http://wiki.nexusformat.org/2014_How_to_find_default_data
'''
#------------------------------------------
def get_default(group, subgroupclass):
subgroups = self.find_NX_class_nodes(group, nx_class = subgroupclass)

# MUST have at least one of subgroupclass
if len(subgroups) > 0:

# if "default" attribute is supplied
if 'default' in group.attrs:
subgroupname = group.attrs['default']
if subgroupname in group:
return group[subgroupname]

# fallback case, 'default' attribute is optional
if len(subgroups) == 1:
return subgroups[0]

return False
#------------------------------------------
# TODO: make test more robust
compliance = False
if self.openHDF5(fullname):
entry = get_default(self.hdf5, 'NXentry')
if entry:
compliance = True
# data = get_default(entry, 'NXdata')
# if data:
# if 'signal' in data.attrs:
# signalname = data.attrs['signal']
# compliance = data.get(signalname) is not None
self.hdf5.close()

return compliance


class Registrar(object):
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