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Py2/3 MetaArray adjustments, first pass

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Paul B. Manis 2018-07-24 20:01:27 -04:00 committed by Ogi Moore
parent c0ae44bc2d
commit ae61d3582e
1 changed files with 33 additions and 9 deletions
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40
pyqtgraph/metaarray/MetaArray.py
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@ -26,6 +26,8 @@ except:
USE_HDF5 = False USE_HDF5 = False
HAVE_HDF5 = False HAVE_HDF5 = False
if HAVE_HDF5:
import h5py.highlevel
def axis(name=None, cols=None, values=None, units=None): def axis(name=None, cols=None, values=None, units=None):
"""Convenience function for generating axis descriptions when defining MetaArrays""" """Convenience function for generating axis descriptions when defining MetaArrays"""
@ -102,7 +104,7 @@ class MetaArray(object):
since the actual values are described (name and units) in the column info for the first axis. since the actual values are described (name and units) in the column info for the first axis.
""" """
version = '2' version = u'2'
# Default hdf5 compression to use when writing # Default hdf5 compression to use when writing
# 'gzip' is widely available and somewhat slow # 'gzip' is widely available and somewhat slow
@ -740,7 +742,7 @@ class MetaArray(object):
## decide which read function to use ## decide which read function to use
with open(filename, 'rb') as fd: with open(filename, 'rb') as fd:
magic = fd.read(8) magic = fd.read(8)
if magic == '\x89HDF\r\n\x1a\n': if magic == b'\x89HDF\r\n\x1a\n':
fd.close() fd.close()
self._readHDF5(filename, **kwargs) self._readHDF5(filename, **kwargs)
self._isHDF = True self._isHDF = True
@ -765,7 +767,7 @@ class MetaArray(object):
"""Read meta array from the top of a file. Read lines until a blank line is reached. """Read meta array from the top of a file. Read lines until a blank line is reached.
This function should ideally work for ALL versions of MetaArray. This function should ideally work for ALL versions of MetaArray.
""" """
meta = '' meta = u''
## Read meta information until the first blank line ## Read meta information until the first blank line
while True: while True:
line = fd.readline().strip() line = fd.readline().strip()
@ -776,6 +778,20 @@ class MetaArray(object):
#print ret #print ret
return ret return ret
def fix_info(self, info):
"""
Recursive version
"""
if isinstance(info, list):
for i in range(len(info)):
info[i] = self.fix_info(info[i])
elif isinstance(info, dict):
for k in info.keys():
info[k] = self.fix_info(info[k])
elif isinstance(info, bytes): # change all bytestrings to string and remove internal quotes
info = info.decode('utf-8').replace("\'", '')
return info
def _readData1(self, fd, meta, mmap=False, **kwds): def _readData1(self, fd, meta, mmap=False, **kwds):
## Read array data from the file descriptor for MetaArray v1 files ## Read array data from the file descriptor for MetaArray v1 files
## read in axis values for any axis that specifies a length ## read in axis values for any axis that specifies a length
@ -786,7 +802,7 @@ class MetaArray(object):
frameSize *= ax['values_len'] frameSize *= ax['values_len']
del ax['values_len'] del ax['values_len']
del ax['values_type'] del ax['values_type']
self._info = meta['info'] self._info = self.fix_info(meta['info'])
if not kwds.get("readAllData", True): if not kwds.get("readAllData", True):
return return
## the remaining data is the actual array ## the remaining data is the actual array
@ -814,7 +830,7 @@ class MetaArray(object):
frameSize *= ax['values_len'] frameSize *= ax['values_len']
del ax['values_len'] del ax['values_len']
del ax['values_type'] del ax['values_type']
self._info = meta['info'] self._info = self.fix_info(meta['info'])
if not kwds.get("readAllData", True): if not kwds.get("readAllData", True):
return return
@ -901,7 +917,7 @@ class MetaArray(object):
del ax['values_type'] del ax['values_type']
#subarr = subarr.view(subtype) #subarr = subarr.view(subtype)
#subarr._info = meta['info'] #subarr._info = meta['info']
self._info = meta['info'] self._info = self.fix_info(meta['info'])
self._data = subarr self._data = subarr
#raise Exception() ## stress-testing #raise Exception() ## stress-testing
#return subarr #return subarr
@ -934,10 +950,14 @@ class MetaArray(object):
f = h5py.File(fileName, mode) f = h5py.File(fileName, mode)
ver = f.attrs['MetaArray'] ver = f.attrs['MetaArray']
try:
ver = ver.decode('utf-8')
except:
pass
if ver > MetaArray.version: if ver > MetaArray.version:
print("Warning: This file was written with MetaArray version %s, but you are using version %s. (Will attempt to read anyway)" % (str(ver), str(MetaArray.version))) print("Warning: This file was written with MetaArray version %s, but you are using version %s. (Will attempt to read anyway)" % (str(ver), str(MetaArray.version)))
meta = MetaArray.readHDF5Meta(f['info']) meta = MetaArray.readHDF5Meta(f['info'])
self._info = meta self._info = self.fix_info(meta)
if writable or not readAllData: ## read all data, convert to ndarray, close file if writable or not readAllData: ## read all data, convert to ndarray, close file
self._data = f['data'] self._data = f['data']
@ -962,7 +982,7 @@ class MetaArray(object):
MetaArray._h5py_metaarray = proc._import('pyqtgraph.metaarray') MetaArray._h5py_metaarray = proc._import('pyqtgraph.metaarray')
ma = MetaArray._h5py_metaarray.MetaArray(file=fileName) ma = MetaArray._h5py_metaarray.MetaArray(file=fileName)
self._data = ma.asarray()._getValue() self._data = ma.asarray()._getValue()
self._info = ma._info._getValue() self._info = self.fix_info(ma._info._getValue())
#print MetaArray._hdf5Process #print MetaArray._hdf5Process
#import inspect #import inspect
#print MetaArray, id(MetaArray), inspect.getmodule(MetaArray) #print MetaArray, id(MetaArray), inspect.getmodule(MetaArray)
@ -1010,6 +1030,10 @@ class MetaArray(object):
data[k] = val data[k] = val
typ = root.attrs['_metaType_'] typ = root.attrs['_metaType_']
try:
typ = typ.decode('utf-8')
except:
pass
del data['_metaType_'] del data['_metaType_']
if typ == 'dict': if typ == 'dict':