/usr/share/pyshared/neo/io/baseio.py is in python-neo 0.2.0-1.
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"""
baseio
======
Classes
-------
BaseIO - abstract class which should be overridden, managing how a file will load/write
its data
If you want a model for developing a new IO start from exampleIO.
"""
from ..core import *
from .tools import create_many_to_one_relationship
read_error = "This type is not supported by this file format for reading"
write_error = "This type is not supported by this file format for writing"
class BaseIO(object):
"""
Generic class to handle all the file read/write methods for the key objects of the
core class. This template is file-reading/writing oriented but it can also handle data
read from/written to a database such as TDT sytem tanks or SQLite files.
This is an abstract class that will be subclassed for each format
The key methods of the class are:
- ``read()`` - Read the whole object structure, return the object at the highest level in the hierarchy
- ``read_block(lazy=True, cascade=True, **params)`` - Read Block object from file with some parameters
- ``read_segment(lazy=True, cascade=True, **params)`` - Read Segment object from file with some parameters
- ``read_spiketrainlist(lazy=True, cascade=True, **params)`` - Read SpikeTrainList object from file with some parameters
- ``write()`` - Write the whole object structure
- ``write_block(**params)`` - Write Block object to file with some parameters
- ``write_segment(**params)`` - Write Segment object to file with some parameters
- ``write_spiketrainlist(**params)`` - Write SpikeTrainList object to file with some parameters
The class can also implement these methods:
- ``read_XXX(lazy=True, cascade=True, **params)``
- ``write_XXX(**params)``
where XXX could be one one the object supported by the IO
Each class is able to declare what can be accessed or written directly discribed by **readable_objects** and **readable_objects**.
The object types can be one of the classes defined in neo.core (Block, Segment, AnalogSignal, ...)
Each class do not necessary support all the whole neo hierarchy but part of it.
This is discribe with **supported_objects**.
All IOs must support at least Block with a read_block()
** start a new IO **
If you want to implement your own file format, you should create a class that will
inherit from this BaseFile class and implement the previous methods.
See ExampleIO in exampleio.py
"""
is_readable = False
is_writable = False
supported_objects = []
readable_objects = []
writeable_objects = []
has_header = False
is_streameable = False
read_params = {}
write_params = {}
name = 'BaseIO'
description = 'This IO does not read or write anything'
extentions = [ ]
mode = 'file' # or 'fake' or 'dir' or 'database'
def __init__(self, filename=None, **kargs):
self.filename = filename
######## General read/write methods #######################
def read(self, lazy = False, cascade = True, **kargs):
if Block in self.readable_objects:
return self.read_block(lazy = lazy, cascade = cascade, **kargs)
elif Segment in self.readable_objects:
bl = Block(name = 'One segment only')
if not cascade:
return bl
seg = self.read_segment(lazy = lazy, cascade = cascade, **kargs)
bl.segments.append(seg)
create_many_to_one_relationship(bl)
return bl
else:
raise NotImplementedError
def write(self, bl, **kargs):
if Block in self.writeable_objects:
self.write_block(bl, **kargs)
elif Segment in self.writeable_objects:
assert len(bl.segments) == 1, '%s is based on segment so if you try to write a block it must contain only one Segment'% self.__class__.__name__
self.write_segment(bl.segments[0], **kargs)
else:
raise NotImplementedError
######## All individual read methods #######################
def read_block(self, **kargs):
assert(Block in self.readable_objects), read_error
def read_segment(self, **kargs):
assert(Segment in self.readable_objects), read_error
def read_unit(self, **kargs):
assert(Unit in self.readable_objects), read_error
def read_spiketrain(self, **kargs):
assert(SpikeTrain in self.readable_objects), read_error
def read_spike(self, **kargs):
assert(Spike in self.readable_objects), read_error
def read_analogsignal(self, **kargs):
assert(AnalogSignal in self.readable_objects), read_error
def read_irregularlysampledsignal(self, **kargs):
assert(IrregularlySampledSignal in self.readable_objects), read_error
def read_analogsignalarray(self, **kargs):
assert(AnalogSignalArray in self.readable_objects), read_error
def read_recordingchannelgroup(self, **kargs):
assert(RecordingChannelGroup in self.readable_objects), read_error
def read_recordingchannel(self, **kargs):
assert(RecordingChannel in self.readable_objects), read_error
def read_event(self, **kargs):
assert(Event in self.readable_objects), read_error
def read_eventarray(self, **kargs):
assert(EventArray in self.readable_objects), read_error
def read_epoch(self, **kargs):
assert(Epoch in self.readable_objects), read_error
def read_epocharray(self, **kargs):
assert(EpochArray in self.readable_objects), read_error
######## All individual write methods #######################
def write_block(self, bl, **kargs):
assert(Block in self.writeable_objects), write_error
def write_segment(self, seg, **kargs):
assert(Segment in self.writeable_objects), write_error
def write_unit(self, ut, **kargs):
assert(Unit in self.writeable_objects), write_error
def write_spiketrain(self,sptr, **kargs):
assert(SpikeTrain in self.writeable_objects), write_error
def write_spike(self, sp, **kargs):
assert(Spike in self.writeable_objects), write_error
def write_analogsignal(self, anasig, **kargs):
assert(AnalogSignal in self.writeable_objects), write_error
def write_irregularlysampledsignal(self,irsig, **kargs):
assert(IrregularlySampledSignal in self.writeable_objects), write_error
def write_analogsignalarray(self, anasigar, **kargs):
assert(AnalogSignalArray in self.writeable_objects), write_error
def write_recordingchannelgroup(self, rcg, **kargs):
assert(RecordingChannelGroup in self.writeable_objects), write_error
def write_recordingchannel(self, rc, **kargs):
assert(RecordingChannel in self.writeable_objects), write_error
def write_event(self,ev, **kargs):
assert(Event in self.writeable_objects), write_error
def write_eventarray(self, ea, **kargs):
assert(EventArray in self.writeable_objects), write_error
def write_epoch(self, ep, **kargs):
assert(Epoch in self.writeable_objects), write_error
def write_epocharray(self, epa, **kargs):
assert(EpochArray in self.writeable_objects), write_error
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