CLASS ndr.reader.intan_rhd¶
NDR_READER_INTAN_RHD - Reader class for Intan Technologies .RHD
file
This class reads data from Intan Technologies .RHD file format.
Intan Technologies: http://intantech.com
Superclasses¶
Properties¶
none
Methods¶
| Method | Description |
|---|---|
| canbereadtogether | can the channels in a channel struct be read in a single function call? |
| daqchannels2internalchannels | Convert a set of DAQ channel |
| epochclock | return the ndr.time.clocktype objects for an epoch |
| filenamefromepochfiles | Return the file name that corresponds to the .RHD file, or directory in case of directory |
| getchannelsepoch | List the channels that are available on this Intan |
| intan_rhd | Create a new Neuroscience Data Reader object |
| intananychannelname2intanchanneltype | Converts a channel bank from Intan native format or relative format to the appropriate Intan channel type |
| intanchanneltype2mfdaqchanneltype | Convert the channel type to generic format of multifuncdaqchannel |
| intanheadertype2mfdaqchanneltype | Convert between Intan headers and the ndr.ndr.reader.mfdaq channel types |
| intanname2mfdaqname | Converts a channel name from Intan native format to ndr.ndr.reader.mfdaq format |
| mfdaq_channeltypes | channel types for ndi.daq.system.mfdaq objects |
| mfdaq_prefix | Give the channel prefix for a channel type |
| mfdaq_type | Give the preferred long channel type for a channel type |
| mfdaqchanneltype2intanchanneltype | Convert the channel type from generic format of multifuncdaqchannel |
| mfdaqchanneltype2intanfreqheader | Return header name with frequency information for channel type |
| mfdaqchanneltype2intanheadertype | Convert between the ndr.ndr.reader.mfdaq channel types and Intan headers |
| readchannels_epochsamples | Read the data based on specified channels |
| readevents_epochsamples_native | read events or markers of specified channels for a specified epoch |
| samplerate | Get the sample rate for specific channel |
| t0_t1 | Return the beginning and end epoch times for an |
| underlying_datatype | get the underlying data type for a channel in an epoch |
Methods help¶
canbereadtogether - can the channels in a channel struct be read in a single function call?
[B,ERRORMSG] = CANBEREADTOGETHER(NDR_READER_BASE_OBJ, CHANNELSTRUCT)
Returns 1 if the NDR_READER_BASE_OBJ can read all of the channels in
CHANNELSTRUCT with a single function call. If they cannot be read together,
a description is provided in ERRORMSG.
In the abstract class, this returns 1 if all of the samplerate values are
the same and none are NaNs.
CHANNELSTRUCT is a structure with the following fields:
------------------------------------------------------------------------------
| Parameter | Description |
|-----------------------------|----------------------------------------------|
| internal_type | Internal channel type; the type of channel as|
| | it is known to the device. |
| internal_number | Internal channel number, as known to device |
| internal_channelname | Internal channel name, as known to the device|
| ndr_type | The NDR type of channel; should be one of the|
| | types returned by |
| | ndr.reader.base.mfdaq_type |
| samplerate | The sampling rate of this channel, or NaN if |
| | not applicable.
------------------------------------------------------------------------------
in the abstract class, this returns 1 if all the samplerates are the same
and none are NaNs
Help for ndr.reader.intan_rhd/canbereadtogether is inherited from superclass ndr.reader.base
daqchannels2internalchannels - Convert a set of DAQ channel
prefixes and channel numbers to an internal structure to pass to
internal reading functions
CHANNELSTRUCT = DAQCHANNELS2INTERNALCHANNELS(INTAN_RHD_OBJ, ...
CHANNELPREFIX, CHANNELNUMBERS, EPOCHSTREAMS, EPOCH_SELECT)
Inputs:
For a set of CHANNELPREFIX (cell array of channel prefixes that
describe channels for this device) and CHANNELNUMBER (array of
of channel numbers, 1 for each entry in CHANNELPREFIX), and for
a given recording epoch (specified by EPOCHSTREAMS and
EPOCH_SELECT), this function returns a structure CHANNELSTRUCT
describing the channel information that should be passed to
READCHANNELS_EPOCHSAMPLES or READEVENTS_EPOCHSAMPLES.
EPOCHSTREAMS is a cell array of full path file names or remote
access streams that comprise the epoch of data.
EPOCH_SELECT allows one to choose which epoch in the file one
wants to access, if the file(s) has more than epoch contained.
For most devices, EPOCH_SELECT is always 1.
Output: CHANNELSTRUCT is a structure with the following fields:
------------------------------------------------------------------------------
| Parameter | Description |
|-----------------------------|----------------------------------------------|
| internal_type | Internal channel type; the type of channel as|
| | it is known to the device. This is the type|
| | that readepoch_samples takes |
| internal_number | Internal channel number, as known to device |
| internal_channelname | Internal channel name, as known to the device|
| ndr_type | The NDR type of channel; should be one of the|
| | types returned by |
| | ndr.reader.base.mfdaq_type |
| samplerate | The sampling rate of this channel, or NaN if |
| | not applicable. |
------------------------------------------------------------------------------
Examples for Intan. Channels can be specified by either absolute reference
(for example, A-000 means the first channel in bank A) or in relative reference
(for example, ai1 means the first channel that was turned on; the one that appears
first in the header file).
Example:
% absolute reference
channelstruct_1 = daqchannels2internalchannels(intan_rhd_obj, 'A', 0, epochstreams, epoch_select)
% channelstruct_1.internal_type = 'ai';
% channelstruct_1.internal_number = 1; % assuming A-000 is the first channel acquired
% channelstruct_1.internal_channelname = 'A-000';
% channelstruct_1.ndr_type = 'ai'; % analog input
% channelstruct_1.samplerate = 20000;
% relative reference
channelstruct_2 = daqchannels2internalchannels(intan_rhd_obj, 'ai', 1, epochstreams, epoch_select)
% channelstruct_2.internal_type = 'ai';
% channelstruct_2.internal_number = 1; % we asked for the first internal/relative channel
% channelstruct_2.internal_channelname = 'A-000'; % assuming A-000 is the first channel acquired
% channelstruct_2.ndr_type = 'ai'; % analog input
% channelstruct_2.samplerate = 20000;
epochclock - return the ndr.time.clocktype objects for an epoch
EC = EPOCHCLOCK(NDR_READER_BASE_OBJ, EPOCHSTREAMS, EPOCH_SELECT)
Return the clock types available for this epoch as a cell array
of ndr.time.clocktype objects (or sub-class members).
For the generic ndr.reader.base, this returns a single clock
type 'dev_local'time';
See also: ndr.time.clocktype
Help for ndr.reader.intan_rhd/epochclock is inherited from superclass ndr.reader.base
filenamefromepochfiles - Return the file name that corresponds to the .RHD file, or directory in case of directory
[FILENAME, PARENTDIR, ISDIRECTORY] = FILENAMEFROMEPOCHFILES(NDR_NDRREADER_INTANREADER_OBJ, FILENAME_ARRAY)
Examines the list of filenames in FILENAME_ARRAY (cell array of full path file strings) and determines which
one is an .RHD data file. If the 1-file-per-channel mode is used, then PARENTDIR is the name of the directory
that holds the data files and ISDIRECTORY is 1.
getchannelsepoch - List the channels that are available on this Intan
device for a given set of files
CHANNELS = GETCHANNELSEPOCH(INTANREADER_OBJ, EPOCHSTREAMS, EPOCH_SELECT)
Returns the channel list of acquired channels in this epoch.
CHANNELS is a structure list of all channels with fields:
---------------------------------------------------------
'name' | The name of the channel (e.g., 'ai1')
'type' | The type of data store in the channel
| (e.g., 'analogin', 'digitalin', 'image', 'timestamp')
intan_rhd - Create a new Neuroscience Data Reader object
INTAN_RHD_OBJ = INTAN_RHD()
Creates a Neuroscience Data Reader object of the Intan
Technologies .RHD file format.
Documentation for ndr.reader.intan_rhd/intan_rhd
doc ndr.reader.intan_rhd
intananychannelname2intanchanneltype - Converts a channel bank from Intan native format or relative format to the appropriate Intan channel type
[INTANCHANNELTYPE,ABSOLUTE] = INTANANYCHANNELNAME2INTANCHANNELTYPE(INTANANYCHANNELNAME)
Converts any channel name into the type needed to call ndr.format.intan.readfile. If the channel was specified
as an absolute reference (that is, 'A', 'B', etc), then ABSOLUTE is 1. Otherwise, if the reference is relative,
then ABSOLUTE is 0.
Examples:
intanchanneltype = ndr.reader.intan_rhd.intananychannelname2intanchanneltype('ai') % returns 'amp', 0
intanchanneltype = ndr.reader.intan_rhd.intananychannelname2intanchanneltype('A') % returns 'amp', 1
intanchanneltype = ndr.reader.intan_rhd.intananychannelname2intanchanneltype('DIN') % returns 'din', 0
intanchanneltype2mfdaqchanneltype - Convert the channel type to generic format of multifuncdaqchannel
from the specific Intan channel type
INTANCHANNELTYPE = MFDAQCHANNELTYPE2INTANCHANNELTYPE(CHANNELTYPE)
The intanchanneltype is a string of the specific channel type for Intan.
intanheadertype2mfdaqchanneltype - Convert between Intan headers and the ndr.ndr.reader.mfdaq channel types
CHANNELTYPE = INTANHEADERTYPE2MFDAQCHANNELTYPE(INTANCHANNELTYPE)
Given an Intan header file type, returns the standard ndi.ndr.reader.mfdaq channel type.
intanname2mfdaqname - Converts a channel name from Intan native format to ndr.ndr.reader.mfdaq format
[CHANNAME] = INTANNAME2MFDAQNAME(NDR_NDRREADER_INTANREADER_OBJ, TYPE, NAME)
Given an Intan native channel name (e.g., 'A-000') in NAME and an
ndr.ndr.reader.mfdaq channel type string (see NDI_DEVICE_MFDAQ), this function
produces an ndr.ndr.reader.mfdaq channel name (e.g., 'ai1').
mfdaq_channeltypes - channel types for ndi.daq.system.mfdaq objects
CT = MFDAQ_CHANNELTYPES - channel types for ndi.daq.system.mfdaq objects
Returns a cell array of strings of supported channels of the
ndi.daq.system.mfdaq class. These are the following:
Channel type: | Description:
-------------------------------------------------------------
analog_in | Analog input channel
aux_in | Auxiliary input
analog_out | Analog output channel
digital_in | Digital input channel
digital_out | Digital output channel
marker |
See also: ndi.daq.system.mfdaq/MFDAQ_TYPE
Help for ndr.reader.intan_rhd.mfdaq_channeltypes is inherited from superclass ndr.reader.base
mfdaq_prefix - Give the channel prefix for a channel type
PREFIX = MFDAQ_PREFIX(CHANNELTYPE)
Produces the channel name prefix for a given CHANNELTYPE.
Channel type: | MFDAQ_PREFIX:
---------------------------------------------------------
'analog_in', 'ai' | 'ai'
'analog_out', 'ao' | 'ao'
'digital_in', 'di' | 'di'
'digital_out', 'do' | 'do'
'time','timestamp','t' | 't'
'auxiliary','aux','ax', | 'ax'
'auxiliary_in' |
'mark', 'marker', or 'mk' | 'mk'
'text' | 'text'
'event' or 'e' | 'e'
'metadata' or 'md' | 'md'
'digital_in_event', 'de', | 'dep'
'digital_in_event_pos','dep'|
'digital_in_event_neg','den'| 'den'
'digital_in_mark','dimp', | 'dimp'
'digital_in_mark_pos','dim' |
'digital_in_mark_neg','dimn'| 'dimn'
See also: ndi.daq.system.mfdaq/MFDAQ_TYPE
Help for ndr.reader.intan_rhd.mfdaq_prefix is inherited from superclass ndr.reader.base
mfdaq_type - Give the preferred long channel type for a channel type
TYPE = MFDAQ_TYPE(CHANNELTYPE)
Produces the preferred long channel type name for a given CHANNELTYPE.
Channel type: | MFDAQ_TYPE:
---------------------------------------------------------
'analog_in', 'ai' | 'analog_in'
'analog_out', 'ao' | 'analog_out'
'digital_in', 'di' | 'digital_in'
'digital_out', 'do' | 'digital_out'
'time','timestamp','t' | 'time'
'auxiliary','aux','ax', | 'auxiliary'
'auxiliary_in' |
'mark', 'marker', or 'mk' | 'mark'
'event' or 'e' | 'event'
See also: ndi.daq.system.mfdaq/MFDAQ_PREFIX
Help for ndr.reader.intan_rhd.mfdaq_type is inherited from superclass ndr.reader.base
mfdaqchanneltype2intanchanneltype - Convert the channel type from generic format of multifuncdaqchannel
to the specific Intan channel type
INTANCHANNELTYPE = MFDAQCHANNELTYPE2INTANCHANNELTYPE(CHANNELTYPE)
The intanchanneltype is a string of the specific channel type for Intan.
mfdaqchanneltype2intanfreqheader - Return header name with frequency information for channel type
HEADERNAME = MFDAQCHANNELTYPE2INTANFREQHEADER(CHANNELTYPE)
Given an ndr.ndr.mfdaq channel type string, this function returns the associated fieldname.
mfdaqchanneltype2intanheadertype - Convert between the ndr.ndr.reader.mfdaq channel types and Intan headers
INTANCHANHEADERTYPE = MFDAQCHANNELTYPE2INTANHEADERTYPE(CHANNELTYPE)
Given a standard ndr.ndr.reader.mfdaq channel type, returns the name of the type as
indicated in Intan header files.
readchannels_epochsamples - Read the data based on specified channels
DATA = READCHANNELS_EPOCHSAMPLES(INTANREADER_OBJ, CHANNELTYPE, CHANNEL, EPOCH, S0, S1)
CHANNELTYPE is the type of channel to read (single text string,
such as 'ai','analog_input','time')
CHANNEL is a vector of the channel numbers to read, beginning
from 1.
EPOCH is the epoch number to read from.
DATA will have one column per channel.
readevents_epochsamples_native - read events or markers of specified channels for a specified epoch
[DATA] = READEVENTS_EPOCHSAMPLES_NATIVE(NDR_READER_BASE_OBJ, CHANNELTYPE, CHANNEL, EPOCHFILES, T0, T1)
CHANNELTYPE is the type of channel to read
('event','marker', etc). It must be a string (not a cell array of strings).
CHANNEL is a vector with the identity of the channel(s) to be read.
EPOCH is the epoch number or epochID
DATA is a two-column vector; the first column has the time of the event. The second
column indicates the marker code. In the case of 'events', this is just 1. If more than one channel
is requested, DATA is returned as a cell array, one entry per channel.
TIMEREF is an ndi.time.timereference with the NDI_CLOCK of the device, referring to epoch N at time 0 as the reference.
Help for ndr.reader.intan_rhd/readevents_epochsamples_native is inherited from superclass ndr.reader.base
samplerate - Get the sample rate for specific channel
SR = SAMPLERATE(INTANREADER_OBJ, EPOCHSTREAMS, EPOCH_SELECT, CHANNELTYPE, CHANNEL)
SR is an array of sample rates from the specified channels.
CHANNELTYPE can be either a string or a cell array of strings
the same length as the vector CHANNEL.
If CHANNELTYPE is a single string, then it is assumed that that
CHANNELTYPE applies to every entry of CHANNEL.
t0_t1 - Return the beginning and end epoch times for an
epoch
T0T1 = T0_T1(INTAN_RHD_OBJ, EPOCHSTREAMS, EPOCH_SELECT)
Return the beginning (t0) and end (t1) times of the epoch
EPOCH_NUMBER in the same units as the ndr.time.clocktype objects
returned by EPOCH_NUMBER.
The abstract class always return {[NaN NaN]}.
See also: ndr.time.clocktype, EPOCHCLOCK
underlying_datatype - get the underlying data type for a channel in an epoch
[DATATYPE,P,DATASIZE] = UNDERLYING_DATATYPE(INTANREADER_OBJ, EPOCHSTREAMS, EPOCH_SELECT, CHANNELTYPE, CHANNEL)
Return the underlying datatype for the requested channel.
DATATYPE is a type that is suitable for passing to FREAD or FWRITE
(e.g., 'float64', 'uint16', etc. See help fread.)
P is a polynomial that converts between the double data that is returned by
READCHANNEL. RETURNED_DATA = (RAW_DATA+P(1))*P(2)+(RAW_DATA+P(1))*P(3) ...
DATASIZE is the sample size in bits.
CHANNELTYPE must be a string. It is assumed that
that CHANNELTYPE applies to every entry of CHANNEL.