Py2/3 MetaArray adjustments, first pass

This commit is contained in:
Paul B. Manis 2018-07-24 20:01:27 -04:00 committed by Ogi Moore
parent c0ae44bc2d
commit ae61d3582e

View File

@ -26,6 +26,8 @@ except:
USE_HDF5 = False
HAVE_HDF5 = False
if HAVE_HDF5:
import h5py.highlevel
def axis(name=None, cols=None, values=None, units=None):
"""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.
"""
version = '2'
version = u'2'
# Default hdf5 compression to use when writing
# 'gzip' is widely available and somewhat slow
@ -740,7 +742,7 @@ class MetaArray(object):
## decide which read function to use
with open(filename, 'rb') as fd:
magic = fd.read(8)
if magic == '\x89HDF\r\n\x1a\n':
if magic == b'\x89HDF\r\n\x1a\n':
fd.close()
self._readHDF5(filename, **kwargs)
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.
This function should ideally work for ALL versions of MetaArray.
"""
meta = ''
meta = u''
## Read meta information until the first blank line
while True:
line = fd.readline().strip()
@ -776,6 +778,20 @@ class MetaArray(object):
#print 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):
## Read array data from the file descriptor for MetaArray v1 files
## read in axis values for any axis that specifies a length
@ -786,7 +802,7 @@ class MetaArray(object):
frameSize *= ax['values_len']
del ax['values_len']
del ax['values_type']
self._info = meta['info']
self._info = self.fix_info(meta['info'])
if not kwds.get("readAllData", True):
return
## the remaining data is the actual array
@ -814,7 +830,7 @@ class MetaArray(object):
frameSize *= ax['values_len']
del ax['values_len']
del ax['values_type']
self._info = meta['info']
self._info = self.fix_info(meta['info'])
if not kwds.get("readAllData", True):
return
@ -901,7 +917,7 @@ class MetaArray(object):
del ax['values_type']
#subarr = subarr.view(subtype)
#subarr._info = meta['info']
self._info = meta['info']
self._info = self.fix_info(meta['info'])
self._data = subarr
#raise Exception() ## stress-testing
#return subarr
@ -934,10 +950,14 @@ class MetaArray(object):
f = h5py.File(fileName, mode)
ver = f.attrs['MetaArray']
try:
ver = ver.decode('utf-8')
except:
pass
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)))
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
self._data = f['data']
@ -962,7 +982,7 @@ class MetaArray(object):
MetaArray._h5py_metaarray = proc._import('pyqtgraph.metaarray')
ma = MetaArray._h5py_metaarray.MetaArray(file=fileName)
self._data = ma.asarray()._getValue()
self._info = ma._info._getValue()
self._info = self.fix_info(ma._info._getValue())
#print MetaArray._hdf5Process
#import inspect
#print MetaArray, id(MetaArray), inspect.getmodule(MetaArray)
@ -1010,6 +1030,10 @@ class MetaArray(object):
data[k] = val
typ = root.attrs['_metaType_']
try:
typ = typ.decode('utf-8')
except:
pass
del data['_metaType_']
if typ == 'dict':