def __init__(self, filename, dataset=0):
"""
Arguments:
filename : the filename
dataset: points to a specific dataset in the .kwik and .raw.kwd file,
however this can be an issue to change in e.g. OpenElectrophy or Spykeviewer
"""
BaseIO.__init__(self)
self._filename = filename
self._path, file = os.path.split(filename)
self._kwik = h5py.File(filename, 'r')
self._dataset = dataset
try:
rawfile = self._kwik['recordings'][str(
self._dataset
)]['raw'].attrs[
'hdf5_path'] # klustakwik/phy and newest version of open ephys
rawfile = rawfile.split('/')[0]
except:
rawfile = file.split(
'.')[0] + '_100.raw.kwd' # first version of open ephys files
self._kwd = h5py.File(self._path + os.sep + rawfile, 'r')
self._attrs = {}
self._attrs['kwik'] = self._kwik['recordings'][str(
self._dataset)].attrs
self._attrs['kwd'] = self._kwd['recordings'][str(self._dataset)].attrs
self._attrs['shape'] = self._kwd['recordings'][str(
self._dataset)]['data'].shape
try:
self._attrs['app_data'] = self._kwd['recordings'][str(
self._dataset
)]['application_data'].attrs # TODO: find bitvolt conversion in phy generated data
except:
self._attrs['app_data'] = False
def __init__(self, filename, mode="rw"):
"""
Initialise IO instance and NIX file.
:param filename: Full path to the file
"""
if not HAVE_NIX:
raise Exception("Failed to import NIX. "
"The NixIO requires the Python bindings for NIX "
"(nixio on PyPi). Try `pip install nixio`.")
BaseIO.__init__(self, filename)
self.filename = filename
if mode == "ro":
filemode = nix.FileMode.ReadOnly
elif mode == "rw":
filemode = nix.FileMode.ReadWrite
elif mode == "ow":
filemode = nix.FileMode.Overwrite
else:
raise ValueError("Invalid mode specified '{}'. "
"Valid modes: 'ro' (ReadOnly)', 'rw' (ReadWrite),"
" 'ow' (Overwrite).".format(mode))
self.nix_file = nix.File.open(self.filename, filemode, backend="h5py")
self._neo_map = dict()
self._nix_map = dict()
self._lazy_loaded = list()
self._object_hashes = dict()
self._block_read_counter = 0
self._path_map = dict()
def __init__(self, filename):
if not HAVE_H5PY:
raise ImportError("h5py is not available")
BaseIO.__init__(self, filename=filename)
self._data = h5py.File(filename, 'r')
self.object_refs = {}
self._lazy = False
def __init__(self, filename=None):
"""
Arguments:
filename : the filename
"""
BaseIO.__init__(self, filename)
def __init__(self, filename):
if not HAVE_H5PY:
raise ImportError("h5py is not available")
BaseIO.__init__(self, filename=filename)
self._data = h5py.File(filename, 'r')
self.object_refs = {}
self._lazy = False
def __init__(self, filename, dataset=0) :
"""
Arguments:
filename : the filename
dataset: points to a specific dataset in the .kwik and .raw.kwd file,
however this can be an issue to change in e.g. OpenElectrophy or Spykeviewer
"""
BaseIO.__init__(self)
self._filename = filename
self._path, file = os.path.split(filename)
self._kwik = h5py.File(filename, 'r')
self._dataset = dataset
try:
rawfile = self._kwik['recordings'][str(self._dataset)]['raw'].attrs['hdf5_path'] # klustakwik/phy and newest version of open ephys
rawfile = rawfile.split('/')[0]
except:
rawfile = file.split('.')[0] + '_100.raw.kwd' # first version of open ephys files
self._kwd = h5py.File(self._path + os.sep + rawfile, 'r')
self._attrs = {}
self._attrs['kwik'] = self._kwik['recordings'][str(self._dataset)].attrs
self._attrs['kwd'] = self._kwd['recordings'][str(self._dataset)].attrs
self._attrs['shape'] = self._kwd['recordings'][str(self._dataset)]['data'].shape
try:
self._attrs['app_data'] = self._kwd['recordings'][str(self._dataset)]['application_data'].attrs # TODO: find bitvolt conversion in phy generated data
except:
self._attrs['app_data'] = False
def __init__(self, filename, dataset=0):
"""
Arguments:
filename : the filename
dataset: points to a specific dataset in the .kwik and .raw.kwd file,
however this can be an issue to change in e.g. OpenElectrophy or Spykeviewer
"""
BaseIO.__init__(self)
self._filename = filename
self._path, file = os.path.split(filename)
self._kwik = h5py.File(filename, "r")
self._dataset = dataset
try:
rawfile = self._kwik["recordings"][str(self._dataset)]["raw"].attrs[
"hdf5_path"
] # klustakwik/phy and newest version of open ephys
rawfile = rawfile.split("/")[0]
except:
rawfile = file.split(".")[0] + "_100.raw.kwd" # first version of open ephys files
self._kwd = h5py.File(self._path + os.sep + rawfile, "r")
self._attrs = {}
self._attrs["kwik"] = self._kwik["recordings"][str(self._dataset)].attrs
self._attrs["kwd"] = self._kwd["recordings"][str(self._dataset)].attrs
self._attrs["shape"] = self._kwd["recordings"][str(self._dataset)]["data"].shape
try:
self._attrs["app_data"] = self._kwd["recordings"][str(self._dataset)][
"application_data"
].attrs # TODO: find bitvolt conversion in phy generated data
except:
self._attrs["app_data"] = False
def __init__(self, filename, mode="rw"):
"""
Initialise IO instance and NIX file.
:param filename: Full path to the file
"""
if not HAVE_NIX:
raise Exception("Failed to import NIX. "
"The NixIO requires the Python bindings for NIX "
"(nixio on PyPi). Try `pip install nixio`.")
BaseIO.__init__(self, filename)
self.filename = filename
if mode == "ro":
filemode = nix.FileMode.ReadOnly
elif mode == "rw":
filemode = nix.FileMode.ReadWrite
elif mode == "ow":
filemode = nix.FileMode.Overwrite
else:
raise ValueError("Invalid mode specified '{}'. "
"Valid modes: 'ro' (ReadOnly)', 'rw' (ReadWrite),"
" 'ow' (Overwrite).".format(mode))
self.nix_file = nix.File.open(self.filename, filemode, backend="h5py")
self._object_map = dict()
self._lazy_loaded = list()
self._object_hashes = dict()
self._block_read_counter = 0
self._path_map = dict()
def __init__(self, filename=None):
"""
Parameters
----------
filename: string, default=None
The filename.
"""
BaseIO.__init__(self, filename=filename)
def __init__(self, filename=None):
"""
This class read a abf file.
Arguments:
filename : the filename to read
"""
BaseIO.__init__(self)
self.filename = filename
def __init__(self, filename=None):
"""
Parameters
----------
filename: string, default=None
The filename.
"""
BaseIO.__init__(self, filename=filename)
def __init__(self, filename=None):
"""
This class read a smr file.
Arguments:
filename : the filename
"""
BaseIO.__init__(self)
self.filename = filename
def __init__(self, filename=None):
"""
Arguments:
filename : the .map Alpha Omega file name
"""
BaseIO.__init__(self)
self.filename = filename
def __init__(self, filename=None):
"""
Arguments:
filename: the filename
"""
BaseIO.__init__(self)
self._path = filename
self._filename = os.path.basename(filename)
self._fsrc = None
def __init__(self , filename = '', dllname = '') :
"""
Arguments:
filename: the file to read
ddlname: the name of neuroshare dll to be used for this file
"""
BaseIO.__init__(self)
self.dllname = dllname
self.filename = filename
def __init__(self, filename=None):
"""
This class read/write a elan based file.
**Arguments**
filename : the filename to read or write
"""
BaseIO.__init__(self)
self.filename = filename
def __init__(self, filename=None):
'''
Arguments:
filename: the filename
'''
BaseIO.__init__(self)
self._path = filename
self._filename = os.path.basename(filename)
self._fsrc = None
def __init__(self, filename='', dllname=''):
"""
Arguments:
filename: the file to read
ddlname: the name of neuroshare dll to be used for this file
"""
BaseIO.__init__(self)
self.dllname = dllname
self.filename = filename
def __init__(self , filename = None) :
"""
Arguments:
filename : the .map Alpha Omega file name
"""
BaseIO.__init__(self)
self.filename = filename
def __init__(self, filename=None):
"""
This class read/write a elan based file.
**Arguments**
filename : the filename to read or write
"""
BaseIO.__init__(self)
self.filename = filename
def __init__(self, filename=None):
"""
This class read a micromed TRC file.
Arguments:
filename : the filename to read
"""
BaseIO.__init__(self)
self.filename = filename
def __init__(self , filename = None) :
"""
This class read a WinEDR file.
Arguments:
filename : the filename
"""
BaseIO.__init__(self)
self.filename = filename
def __init__(self, filename=None, **kwargs):
if not HAVE_TABLES:
raise TABLES_ERR
BaseIO.__init__(self, filename=filename)
self.connected = False
self.objects_by_ref = {} # Loaded objects by reference id
self.parent_paths = {} # Tuples of (Segment, other parent) paths
self.name_indices = {}
if filename:
self.connect(filename=filename)
def __init__(self, filename=None, **kwargs):
if not HAVE_TABLES:
raise TABLES_ERR
BaseIO.__init__(self, filename=filename)
self.connected = False
self.objects_by_ref = {} # Loaded objects by reference id
self.parent_paths = {} # Tuples of (Segment, other parent) paths
self.name_indices = {}
if filename:
self.connect(filename=filename)
def __init__(self, filename=None):
"""
This class read a WinWCP wcp file.
Arguments:
filename : the filename to read
"""
BaseIO.__init__(self)
self.filename = filename
def __init__(self, filename):
"""
"""
BaseIO.__init__(self)
# remove extension because there is bunch of files : nev, ns1, ..., ns5, nsf
for ext in self.extensions:
if filename.endswith('.' + ext):
filename = filename.strip('.' + ext)
self.filename = filename
def __init__(self, filename) :
"""
"""
BaseIO.__init__(self)
# remove extension because there is bunch of files : nev, ns1, ..., ns5, nsf
for ext in self.extensions:
if filename.endswith('.'+ext):
filename = filename.strip('.'+ext)
self.filename = filename
def __init__(self, filename):
"""
Arguments:
filename : the filename
"""
BaseIO.__init__(self)
self.filename = os.path.abspath(filename)
model = kwik.KwikModel(self.filename) # TODO this group is loaded twice
self.models = [kwik.KwikModel(self.filename, channel_group=grp)
for grp in model.channel_groups]
def __init__(self , filename = None) :
"""
This class read a nex file.
Arguments:
filename : the filename to read you can pu what ever it do not read anythings
"""
BaseIO.__init__(self)
self.filename = filename
def __init__(self, filename) :
"""
Arguments:
filename : the filename
"""
BaseIO.__init__(self, filename)
self._extension_dir = tempfile.mkdtemp()
extension_file = join(self._extension_dir, "nwb_neo_extension.py")
with open(extension_file, "w") as fp:
fp.write(str(neo_extension))
self.extensions = [extension_file]
def __init__(self , filename = None) :
"""
This class read a plx file.
Arguments:
filename : the filename
load_spike_waveform : load or not waveform of spikes (default True)
"""
BaseIO.__init__(self)
self.filename = filename
def __init__(self, filename=None):
"""
This class read/write neo objects in matlab 5 to 7.2 format.
Arguments:
filename : the filename to read
"""
if not HAVE_SCIPY:
raise SCIPY_ERR
BaseIO.__init__(self)
self.filename = filename
def __init__(self , filename = None) :
"""
This class read a binary file.
**Arguments**
filename : the filename to read
"""
BaseIO.__init__(self)
self.filename = filename
def __init__(self, filename=None):
"""
This class read/write AnalogSignal in a text file.
Each signal is a column.
One of the column can be the time vector
Arguments:
filename : the filename to read/write
"""
BaseIO.__init__(self)
self.filename = filename
def __init__(self, filename=None):
"""
This class read a nex file.
Arguments:
filename : the filename to read you can pu what ever it do not read anythings
"""
BaseIO.__init__(self)
self.filename = filename
def __init__(self, filename=None):
"""
This class read a binary file.
**Arguments**
filename : the filename to read
"""
BaseIO.__init__(self)
self.filename = filename
def __init__(self, filename=None):
"""
This class read/write neo objects in matlab 5 to 7.2 format.
Arguments:
filename : the filename to read
"""
if not HAVE_SCIPY:
raise SCIPY_ERR
BaseIO.__init__(self)
self.filename = filename
def __init__(self, filename=None):
"""
This class read/write AnalogSignal in a text file.
Each signal is a column.
One of the column can be the time vector
Arguments:
filename : the filename to read/write
"""
BaseIO.__init__(self)
self.filename = filename
def __init__(self, filename=None):
"""
This class read a plx file.
Arguments:
filename : the filename
load_spike_waveform : load or not waveform of spikes (default True)
"""
BaseIO.__init__(self)
self.filename = filename
def __init__(self, filename, full_range=8192.*pq.mV) :
"""Initialize Blackrock reader.
**Arguments**
filename: string, the filename to read
full_range: Quantity, the full-scale analog range of the data.
This is set by your digitizing hardware. It should be in
volts or millivolts.
"""
BaseIO.__init__(self)
self.filename = filename
self.full_range = full_range
def __init__(self, filename, readonly=False):
"""
Initialize new IO instance.
If the file does not exist, it will be created.
This I/O works in a detached mode.
:param filename: full path to the file (like '/tmp/foo.h5')
"""
BaseIO.__init__(self, filename=filename)
self.f = FileHandler(filename)
self.readonly = readonly
def __init__(self, filename=None):
"""
This class read/write SpikeTrains in a text file.
Each row is a spiketrain.
**Arguments**
filename : the filename to read/write
"""
BaseIO.__init__(self)
self.filename = filename
def __init__(self, filename, full_range=8192.*pq.mV) :
"""Initialize Blackrock reader.
**Arguments**
filename: string, the filename to read
full_range: Quantity, the full-scale analog range of the data.
This is set by your digitizing hardware. It should be in
volts or millivolts.
"""
BaseIO.__init__(self)
self.filename = filename
self.full_range = full_range
def __init__(self , dirname=None) :
"""
**Arguments**
Arguments:
dirname: path of the TDT tank (a directory)
"""
BaseIO.__init__(self)
self.dirname = dirname
if self.dirname.endswith('/'):
self.dirname = self.dirname[:-1]
def __init__(self, dirname=None):
"""
**Arguments**
Arguments:
dirname: path of the TDT tank (a directory)
"""
BaseIO.__init__(self)
self.dirname = dirname
if self.dirname.endswith('/'):
self.dirname = self.dirname[:-1]
def __init__(self, filename=None):
"""
This class read/write SpikeTrains in a text file.
Each row is a spiketrain.
**Arguments**
filename : the filename to read/write
"""
BaseIO.__init__(self)
self.filename = filename
def __init__(self, filename):
"""
Arguments:
filename : the filename
"""
BaseIO.__init__(self)
self.filename = os.path.abspath(filename)
model = kwik.KwikModel(
self.filename) # TODO this group is loaded twice
self.models = [
kwik.KwikModel(self.filename, channel_group=grp)
for grp in model.channel_groups
]
def __init__(self , dirname = None) :
"""
This class read a WinEDR wcp file.
**Arguments**
Arguments:
dirname: path of the TDT tank (a directory)
"""
BaseIO.__init__(self)
self.dirname = dirname
if self.dirname.endswith('/'):
self.dirname = self.dirname[:-1]
def __init__(self, filename, mode='r'):
"""
Arguments:
filename : the filename
"""
if not have_pynwb:
raise Exception("Please install the pynwb package to use NWBIO")
if not have_hdmf:
raise Exception("Please install the hdmf package to use NWBIO")
BaseIO.__init__(self, filename=filename)
self.filename = filename
self.blocks_written = 0
self.nwb_file_mode = mode
def __init__(self , dirname = None) :
"""
This class read a WinEDR wcp file.
**Arguments**
Arguments:
dirname: path of the TDT tank (a directory)
"""
BaseIO.__init__(self)
self.dirname = dirname
if self.dirname.endswith('/'):
self.dirname = self.dirname[:-1]
def __init__(self, filename, print_diagnostic=False):
"""
Initialize the UAModel class and associate it to a file.
"""
self.associated = False
# Call base constructor
BaseIO.__init__(self)
# Remember choice whether to print diagnostic messages or not
self._print_diagnostic = print_diagnostic
# Associate to the session
self._associate(filename=filename)
# For consistency with baseio
self.filename = filename
def __init__(self, filename=None, ced_units=False):
"""
This class read a smr file.
Arguments:
filename : the filename
ced_units: whether a spike trains should be added for each unit
as determined by Spike2's spike sorting (True), or if a spike
channel should be considered a single unit and will ignore
Spike2's spike sorting (False). Defaults to False.
"""
BaseIO.__init__(self)
self.filename = filename
self.ced_units = ced_units
def __init__(self,
filename=None,
delimiter='\t',
usecols=None,
skiprows=0,
timecolumn=None,
sampling_rate=1.0 * pq.Hz,
t_start=0.0 * pq.s,
units=pq.V,
time_units=pq.s,
method='genfromtxt',
signal_group_mode='split-all',
metadata_filename=None):
"""
This class read/write AnalogSignal in a text file.
Each signal is a column.
One of the columns can be the time vector.
Arguments:
filename : the filename to read/write
"""
# todo: allow units to be a list/array (e.g. current and voltage in the same file)
BaseIO.__init__(self)
self.filename = filename
self.metadata_filename = metadata_filename
metadata = self.read_metadata()
self.delimiter = metadata.get("delimiter", delimiter)
self.usecols = metadata.get("usecols", usecols)
self.skiprows = metadata.get("skiprows", skiprows)
self.timecolumn = metadata.get("timecolumn", timecolumn)
self.sampling_rate = metadata.get("sampling_rate", sampling_rate)
self.time_units = metadata.get("time_units", time_units)
if self.time_units is not None:
self.time_units = pq.Quantity(1, self.time_units)
self.t_start = metadata.get("t_start", t_start)
if not isinstance(t_start, pq.Quantity):
if not isinstance(self.time_units, pq.Quantity):
raise ValueError("Units of t_start not specified")
self.t_start *= self.time_units
self.units = metadata.get("units", pq.Quantity(1, units))
self.method = metadata.get("method", method)
if not (self.method in ('genfromtxt', 'csv', 'homemade')
or callable(self.method)):
raise ValueError(
"method must be one of 'genfromtxt', 'csv', 'homemade', or a function"
)
self.signal_group_mode = metadata.get("signal_group_mode",
signal_group_mode)
def __init__(self, filename, dataset=0):
"""
Arguments:
filename : the filename
dataset : dataset number
experimentNum : experiment number
"""
BaseIO.__init__(self)
self._filename = filename
self._path, file = os.path.split(filename)
self._dataset = dataset
if int(file[-5]) > 1:
xmlfile = 'settings_' + file[-5] + '.xml'
else:
xmlfile = 'settings.xml'
tree = ET.parse(self._path + os.sep + xmlfile)
root = tree.getroot()
nodes = {}
for processor in root.iter('PROCESSOR'):
processorName = processor.attrib['name'].split('/')
node_info = {}
if processorName[0] == 'Sources':
if processorName[1] == 'OSC Port':
oscInfo = processor.findall('EDITOR')
osc = oscInfo[0].findall('OSCNODE')
node_info['address'] = osc[0].get('address')
node_info['NodeId'] = processor.attrib['NodeId']
elif processorName[1] == 'Rhythm FPGA':
chanInfo = processor.findall('CHANNEL_INFO')[0]
chan = [a.get('name') for a in chanInfo.findall('CHANNEL')]
node_info['chanNames'] = chan
node_info['NodeId'] = processor.attrib['NodeId']
else:
node_info['NodeId'] = processor.attrib['NodeId']
if processorName[1] in nodes.keys():
nodes[processorName[1]] += [node_info]
else:
nodes[processorName[1]] = [node_info]
self._nodes = nodes
rawfile = file.split(
'.')[0] + '_' + nodes['Rhythm FPGA'][0]['NodeId'] + '.raw.kwd'
self._kwe = h5py.File(filename, 'r')
self._kwd = h5py.File(self._path + os.sep + rawfile, 'r')
self._attrs = {}
self._attrs['kwe'] = self._kwe['recordings'][str(self._dataset)].attrs
self._attrs['kwd'] = self._kwd['recordings'][str(self._dataset)].attrs
self._attrs['shape'] = self._kwd['recordings'][str(
self._dataset)]['data'].shape
self._attrs['app_data'] = self._kwd['recordings'][str(
self._dataset)]['application_data'].attrs
def __init__(self, filename=None, ced_units=False):
"""
This class reads an smr file.
Arguments:
filename : the filename
ced_units: whether a spike trains should be added for each unit
as determined by Spike2's spike sorting (True), or if a spike
channel should be considered a single unit and will ignore
Spike2's spike sorting (False). Defaults to False.
"""
BaseIO.__init__(self)
self.filename = filename
self.ced_units = ced_units
def __init__(self, filename=None, parse_notes=None) :
"""
Arguments:
filename: the filename
parse_notes: (optional) A function which will parse the 'notes'
field in the file header and return a dictionary which will be
added to the object annotations.
"""
BaseIO.__init__(self)
self.filename = filename
self.parse_notes = parse_notes
def __init__(self,filename = './test_data/CEN184/THL_2012-03-21_18-40-42_000.dat'):
BaseIO.__init__(self)
self.filename = filename
f = open(filename)
#create a bundle header object with the file
head = BundleHeader(f)
#load the file
head.load(f)
#get the .pgf and .pul items in the file
for bi in head.oBundleItems:
if str(bi.oExtension)[0:4] == '.pgf':
self.pgf = PGFFile(f,bi)
if str(bi.oExtension)[0:4] == '.pul':
self.pul = PULFile(f,bi)
f.close()
def __init__(self , filename = None) :
"""
Arguments:
filename : the filename
Note:
- filename is here just for exampe because it will not be take in account
- if mode=='dir' the argument should be dirname (See TdtIO)
"""
BaseIO.__init__(self)
self.filename = filename
# Seed so all instances can return the same values
np.random.seed(1234)