McsPyDataTools API Reference¶

McsPy¶

McsPy is a Python module/package to read, handle and operate on HDF5-based raw data files converted from recordings of devices of the Multi Channel Systems MCS GmbH.

copyright:	2018 by Multi Channel Systems MCS GmbH
license:	see LICENSE for more details

class McsPy.McsHdf5Protocols[source]¶

Class of supported MCS-HDF5 protocol types and version ranges

Entry: (Protocol Type Name => Tuple of supported version range from (including) the first version entry up to (including) the second version entry)

classmethod check_protocol_type_version(protocol_type_name, version)[source]¶

Check if the given version of a protocol is supported by the implementation

Parameters:	protocol_type_name – name of the protocol that is tested version – version number that should be checked
Returns:	is true if the given protocol and version is supported

class McsPy.McsHdf5Types[source]¶

Class of supported MCS-HDF5 file structure types and version ranges

Entry: (Protocol TypeID => Tuple of supported version range from (including) the first version entry up to (including) the second version entry)

classmethod check_type_version(typeID, version)[source]¶

Check if the given version of a type is supported by the implementation

Parameters:	protocol_type_name – name of the protocol that is tested version – version number that should be checked
Returns:	is true if the given type and version is supported

classmethod get_mcs_class_name(typeID, version=None)[source]¶

Returns the McsPy class name, that corresponds to a given Mcs HDF5 file structure type. The function also checks if the requested class supports the Mcs HDF5 file structure type version

Parameters:	typeID – name of the type that is tested version – version number that should be checked
Returns:	a McsCMOSMEA class if the given type and version is supported

The ‘’McsData’’ module¶

class McsPy.McsData.RawData(raw_data_path)[source]¶

This class holds the information of a complete MCS raw data file

recordings¶: Access recordings

class McsPy.McsData.Recording(recording_grp)[source]¶

Container class for one recording

Provides the content of the HDF5 Folder “Recording_x” in Python.

analog_streams¶: Access all analog streams - collection of AnalogStream objects

frame_streams¶: Access all frame streams - collection of FrameStream objects

event_streams¶: Access event streams - collection of EventStream objects

segment_streams¶: Access segment streams - - collection of SegementStream objects

timestamp_streams¶: Access timestamp streams - collection of TimestampStream objects

duration_time¶: Duration of the recording

Data-Stream-Structures containing the data¶

class McsPy.McsData.Stream(stream_grp, info_type_name=None)[source]¶: Base class for all stream types

class McsPy.McsData.AnalogStream(stream_grp)[source]¶

Container class for one analog stream of several channels. Description for each channel is provided by a channel-associated object of ChannelInfo

Provides the content of the HDF5 Sub-folder “Stream_x” of “AnalogStream” in Python.

get_channel_in_range(channel_id, idx_start, idx_end)[source]¶

Get the signal of the given channel over the curse of time and in its measured range.

Parameters:	channel_id – ID of the channel idx_start – index of the first sampled signal value that should be returned (0 <= idx_start < idx_end <= count samples) idx_end – index of the last sampled signal value that should be returned (0 <= idx_start < idx_end <= count samples)
Returns:	Tuple (vector of the signal, unit of the values)

get_channel_sample_timestamps(channel_id, idx_start, idx_end)[source]¶

Get the timestamps of the sampled values.

Parameters:	channel_id – ID of the channel idx_start – index of the first signal timestamp that should be returned (0 <= idx_start < idx_end <= count samples) idx_end – index of the last signal timestamp that should be returned (0 <= idx_start < idx_end <= count samples)
Returns:	Tuple (vector of the timestamps, unit of the timestamps)

class McsPy.McsData.FrameStream(stream_grp)[source]¶

Container class for one frame stream with different entities

Provides the content of the HDF5 Subfolder “Stream_x” of “FrameStream” in Python.

class McsPy.McsData.FrameEntity(frame_entity_group, frame_info)[source]¶

Contains the stream of a specific frame entity. Meta-Information for this entity is available via an associated object of FrameEntityInfo

Provides the content of the HDF5 Subfolder “Stream_x” of “FrameStream” and Subfolder “FrameDataEntity_x” in Python.

get_sensor_signal(sensor_x, sensor_y, idx_start, idx_end)[source]¶

Get the signal of a single sensor over the curse of time and in its measured range.

Parameters:	sensor_x – x coordinate of the sensor sensor_y – y coordinate of the sensor idx_start – index of the first sampled frame that should be returned (0 <= idx_start < idx_end <= count frames) idx_end – index of the last sampled frame that should be returned (0 <= idx_start < idx_end <= count frames)
Returns:	Tuple (vector of the signal, unit of the values)

get_frame_timestamps(idx_start, idx_end)[source]¶

Get the timestamps of the sampled frames.

Parameters:	idx_start – index of the first sampled frame that should be returned (0 <= idx_start < idx_end <= count frames) idx_end – index of the last sampled frame that should be returned (0 <= idx_start < idx_end <= count frames)
Returns:	Tuple (vector of the timestamps, unit of the timestamps)

class McsPy.McsData.EventStream(stream_grp)[source]¶

Container class for one event stream with different entities

Provides the content of the HDF5 Subfolder “Stream_x” of “EventStream” in Python.

class McsPy.McsData.EventEntity(event_data, event_info)[source]¶

Contains the event data of a specific entity. Meta-Information for this entity is available via an associated object of EventEntityInfo

Maps data event entity content of the HDF5 Subfolder “Stream_x” of “EventStream” to Python structures.

count¶: Number of contained events

get_events(idx_start=None, idx_end=None)[source]¶

Get all n events of this entity of the given index range (idx_start <= idx < idx_end)

Parameters:	idx_start – start index of the range (including), if nothing is given -> 0 idx_end – end index of the range (excluding, if nothing is given -> last index
Returns:	Tuple of (2 x n matrix of timestamp (1. row) and duration (2. row), Used unit of time)

get_event_timestamps(idx_start=None, idx_end=None)[source]¶

Get all n event timestamps of this entity of the given index range

Parameters:	idx_start – start index of the range, if nothing is given -> 0 idx_end – end index of the range, if nothing is given -> last index
Returns:	Tuple of (n-length array of timestamps, Used unit of time)

get_event_durations(idx_start=None, idx_end=None)[source]¶

Get all n event durations of this entity of the given index range

Parameters:	idx_start – start index of the range, if nothing is given -> 0 idx_end – end index of the range, if nothing is given -> last index
Returns:	Tuple of (n-length array of duration, Used unit of time)

class McsPy.McsData.SegmentStream(stream_grp)[source]¶

Container class for one segment stream of different segment entities

Provides the content of the HDF5 Subfolder “Stream_x” of “SegmentStream” in Python.

class McsPy.McsData.SegmentEntity(segment_data, segment_ts, segment_info)[source]¶

Segment entity class, Meta-Information for this entity is available via an associated object of SegmentEntityInfo

DataSybType != Average → Maps segement entity content of the HDF5 Subfolder “Stream_x” of “SegmentStream” to Python structures.

segment_sample_count¶: Number of contained samples of segments (2d) or multi-segments (3d)

segment_count¶: Number of segments that are sampled for one time point (2d) -> 1 and (3d) -> n

get_segment_in_range(segment_id, flat=False, idx_start=None, idx_end=None)[source]¶

Get the a/the segment signals in its measured range.

Parameters:

segment_id – id resp. number of the segment (0 if only one segment is present or the index inside the multi-segment collection)
flat – true -> one-dimensional vector of the sequentially ordered segments, false -> k x n matrix of the n segments of k sample points
idx_start – index of the first segment that should be returned (0 <= idx_start < idx_end <= count segments)
idx_end – index of the last segment that should be returned (0 <= idx_start < idx_end <= count segments)

Returns:

Tuple (of a flat vector of the sequentially ordered segments or a k x n matrix of the n segments of k sample points depending on the value of flat , and the unit of the values)

get_segment_sample_timestamps(segment_id, flat=False, idx_start=None, idx_end=None)[source]¶

Get the timestamps of the sample points of the measured segment.

Parameters:

segment_id – id resp. number of the segment (0 if only one segment is present or the index inside the multi-segment collection)
flat – true -> one-dimensional vector of the sequentially ordered segment timestamps, false -> k x n matrix of the k timestamps of n segments
idx_start – index of the first segment for that timestamps should be returned (0 <= idx_start < idx_end <= count segments)
idx_end – index of the last segment for that timestamps should be returned (0 <= idx_start < idx_end <= count segments)

Returns:

Tuple (of a flat vector of the sequentially ordered segments or a k x n matrix of the n segments of k sample points depending on the value of flat , and the unit of the values)

class McsPy.McsData.AverageSegmentTuple(mean, std_dev, time_tick_unit, signal_unit)¶

Named tuple that describe one or more average segments (mean, std_dev, time_tick_unit, signal_unit).

Note

mean - mean signal values
std_dev - standard deviation of the signal value (it is 0 if there was only one sample segment)
time_tick_unit - sampling interval with time unit
signal_unit - measured unit of the signal

mean¶: Alias for field number 0

signal_unit¶: Alias for field number 3

std_dev¶: Alias for field number 1

time_tick_unit¶: Alias for field number 2

class McsPy.McsData.AverageSegmentEntity(segment_average_data, segment_average_annotation, segment_info)[source]¶

Contains a number of signal segments that are calcualted as averages of number of segments occured in a given time range. Meta-Information for this entity is available via an associated object of SegmentEntityInfo

DataSybType == Average → Maps segment entity content of the HDF5 DataSubType-Average: Subfolder “Stream_x” of “SegmentStream” to Python structures.

number_of_averages¶: Number of average segments inside this average entity

sample_length¶: Number of sample points of an average segment

time_ranges()[source]¶

List of time range tuples for all contained average segments

Returns:	List of tuple with start and end time point

time_range(average_segment_idx)[source]¶

Get the time range for that the average segment was calculated

Parameters:	average_segment_idx – index resp. number of the average segment
Returns:	Tuple with start and end time point

average_counts()[source]¶

List of counts of samples for all contained average segments

Parameters:	average_segment_idx – id resp. number of the average segment
Returns:	sample count

average_count(average_segment_idx)[source]¶

Count of samples that were used to calculate the average

Parameters:	average_segment_idx – id resp. number of the average segment
Returns:	sample count

get_scaled_average_segments()[source]¶

Get all contained average segments in its measured physical range.

Returns:	`AverageSegmentTuple` containing the k x n matrices for mean and standard deviation of all contained average segments n with the associated sampling and measuring information

get_scaled_average_segment(average_segment_idx)[source]¶

Get the selected average segment in its measured physical range.

Parameters:	segment_idx – index resp. number of the average segment
Returns:	`AverageSegmentTuple` containing the mean and standard deviation vector of the average segment with the associated sampling and measuring information

get_average_segments()[source]¶

Get all contained average segments AD-offset in ADC values with its measuring conditions

Returns:	`AverageSegmentTuple` containing the mean and standard deviation vector of the average segment in ADC steps with sampling tick and ADC-Step definition

get_average_segment(average_segment_idx)[source]¶

Get the AD-offset corrected average segment in ADC values with its measuring conditions

Parameters:	segment_id – id resp. number of the segment
Returns:	`AverageSegmentTuple` containing the k x n matrices for mean and standard deviation of all contained average segments in ADC steps with sampling tick and ADC-Step definition

class McsPy.McsData.TimeStampStream(stream_grp)[source]¶

Container class for one timestamp stream with different entities

Provides the content of the HDF5 Subfolder “Stream_x” of “TimeStampStream” in Python.

class McsPy.McsData.TimeStampEntity(timestamp_data, timestamp_info)[source]¶

Time-Stamp entity class, Meta-Information for this entity is available via an associated object of TimestampEntityInfo

Maps data timestamp entity data of the HDF5 Subfolder “Stream_x” of “TimeStampStream” to Python structures.

count¶: Number of contained timestamps

get_timestamps(idx_start=None, idx_end=None)[source]¶

Get all n time stamps of this entity of the given index range (idx_start <= idx < idx_end)

Parameters:	idx_start – start index of the range (including), if nothing is given -> 0 idx_end – end index of the range (excluding, if nothing is given -> last index
Returns:	Tuple of (n-length array of timestamps, Used unit of time)

Info-Classes containing Meta-Information for the data¶

class McsPy.McsData.Info(info_data)[source]¶

Base class of all info classes

Derived classes contain meta information for data structures and fields.

get_field(name)[source]¶: Get the field with that name -> access to the raw info array

group_id¶: Get the id of the group that the objects belongs to

label¶: Label of this object

data_type¶: Raw data type of this object

class McsPy.McsData.ChannelInfo(info_version, info)[source]¶

Contains all describing meta data for one sampled channel

channel_id¶: Get the ID of the channel

row_index¶: Get the index of the row that contains the associated channel data inside the data matrix

adc_step¶: Size and unit of one ADC step for this channel

version¶: Version number of the Type-Definition

class McsPy.McsData.InfoSampledData(info)[source]¶

Base class of all info classes for evenly sampled data

sampling_frequency¶: Get the used sampling frequency in Hz

sampling_tick¶: Get the used sampling tick

class McsPy.McsData.EventEntityInfo(info_version, info)[source]¶

Contains all meta data for one event entity

id¶: Event ID

raw_data_bytes¶: Lenght of raw data in bytes

source_channel_ids¶: ID’s of all channels that were involved in the event generation.

source_channel_labels¶: Labels of the channels that were involved in the event generation.

version¶: Version number of the Type-Definition

class McsPy.McsData.SegmentEntityInfo(info_version, info, source_channel_infos)[source]¶

Contains all meta data for one segment entity

id¶: Segment ID

pre_interval¶: Interval [start of the segment <- defining event timestamp]

post_interval¶: Interval [defining event timestamp -> end of the segment]

type¶: Type of the segment like ‘Average’ or ‘Cutout’

count¶: Count of segments inside the segment entity

version¶: Version number of the Type-Definition

class McsPy.McsData.TimeStampEntityInfo(info_version, info)[source]¶

Contains all meta data for one timestamp entity

id¶: Timestamp entity ID

unit¶: Unit in which the timestamps are measured

exponent¶: Exponent for the unit in which the timestamps are measured

measuring_unit¶: Unit in which the timestamp entity was measured

data_type¶: DataType for the timestamps

source_channel_ids¶: ID’s of all channels that were involved in the timestamp generation.

source_channel_labels¶: Labels of the channels that were involved in the timestamp generation.

version¶: Version number of the Type-Definition

The ‘’McsCMOS’’ module¶

McsCMOS¶

Wrapper and Helper to access MCS CMOS Data within H5 Files

copyright:	2018 by Multi Channel Systems MCS GmbH
license:	see LICENSE for more details

class McsPy.McsCMOS.CMOSConvProxy(parent)[source]¶

Private Class, should be embedded within a CMOSData Object. A proxy that transparently converts raw data to calibrated data.

shape¶: Shape of the data

class McsPy.McsCMOS.CMOSData(path)[source]¶: Wrapper for a HDF5 File containing CMOS Data

class McsPy.McsCMOS.CMOSSpikes(path)[source]¶: Wrapper for a HDF5 File containing CMOS Spike Data. Spike Information is accessible through the .spike Member, Waveform Information (if available) through the .waveforms Member.