Internal API¶

Subpackages¶

Submodules¶

nixio.block module¶

class nixio.block.Block(nixfile, nixparent, h5group, compression=<Compression.Auto: 'Auto'>)¶

Bases: nixio.entity.Entity

create_data_array(name='', array_type='', dtype=None, shape=None, data=None, compression=<Compression.Auto: 'Auto'>, copy_from=None, keep_copy_id=True, label=None, unit=None)¶

Create/copy a new data array for this block. Either shape or data must be given. If both are given their shape must agree. If dtype is not specified it will default to 64-bit floating points.

Parameters:	name (str) – The name of the data array to create/copy. array_type (str) – The type of the data array. dtype (`numpy.dtype`) – Which data-type to use for storage shape (tuple of int or long) – Layout (dimensionality and extent) data (array-like data) – Data to write after storage has been created compression (`Compression`) – En-/disable dataset compression. copy_from (nixio.DataArray) – The DataArray to be copied, None in normal mode keep_copy_id (bool) – Specify if the id should be copied in copy mode label (str) – The label, defaults to None. unit (str) – The unit of the stored data. Defaults to None.
Returns:	The newly created data array.
Return type:	`DataArray`

create_data_frame(name='', type_='', col_dict=None, col_names=None, col_dtypes=None, data=None, compression=<Compression.No: 'None'>, copy_from=None, keep_copy_id=True)¶

Create/copy a new data frame for this block. Either col_dict or col_name and col_dtypes must be given. If both are given, col_dict will be used.

Parameters:	name (str) – The name of the data frame to create/copy. type (str) – The type of the data frame. col_dict (dict or OrderedDict of {str: type}) – The dictionary that specifies column names and data type in each column col_names (tuples or list or np.array of string) – The collection of name of all columns in order col_dtypes (tuples or list or np.array of type) – The collection of data type of all columns in order data (array-like data with compound data type as specified in the columns) – Data to write after storage has been created compression (`Compression`) – En-/disable dataset compression. copy_from (nixio.DataFrame) – The DataFrame to be copied, None in normal mode keep_copy_id (bool) – Specify if the id should be copied in copy mode
Returns:	The newly created data frame.
Return type:	`DataFrame`

create_group(name, type_)¶

Create a new group on this block.

Parameters:	name (str) – The name of the group to create. type (str) – The type of the group.
Returns:	The newly created group.
Return type:	nixio.Group

create_multi_tag(name='', type_='', positions=None, extents=None, copy_from=None, keep_copy_id=True)¶

Create/copy a new multi tag for this block.

Parameters:	name (str) – The name of the tag to create/copy. type (str) – The type of tag. positions (nixio.DataArray) – A data array defining all positions of the tag. copy_from (nixio.MultiTag) – The MultiTag to be copied, None in normal mode keep_copy_id (bool) – Specify if the id should be copied in copy mode
Returns:	The newly created tag.
Return type:	nixio.MultiTag

classmethod create_new(nixparent, h5parent, name, type_, compression)¶

create_source(name, type_)¶

Create a new source on this block.

Parameters:	name (str) – The name of the source to create. type (str) – The type of the source.
Returns:	The newly created source.
Return type:	nixio.Source

create_tag(name='', type_='', position=0, copy_from=None, keep_copy_id=True)¶

Create/copy a new tag for this block.

Parameters:	name (str) – The name of the tag to create/copy. type (str) – The type of tag. position – Coordinates of the start position in units of the respective data dimension. copy_from (nixio.Tag) – The Tag to be copied, None in normal mode keep_copy_id (bool) – Specify if the id should be copied in copy mode
Returns:	The newly created tag.
Return type:	nixio.Tag

data_arrays¶: A property containing all data arrays of a block. DataArray entities can be obtained via their index or by their id. Data arrays can be deleted from the list. Adding a data array is done using the Blocks create_data_array method. This is a read only attribute.

data_frames¶

find_sources(filtr=<function Block.<lambda>>, limit=None)¶

Get all sources in this block recursively.

This method traverses the tree of all sources in the block. The traversal is accomplished via breadth first and can be limited in depth. On each node or source a filter is applied. If the filter returns true the respective source will be added to the result list. By default a filter is used that accepts all sources.

Parameters:	filtr (function) – A filter function limit (int) – The maximum depth of traversal
Returns:	A list containing the matching sources.
Return type:	list of nixio.Source

groups¶: A property containing all groups of a block. Group entities can be obtained via their index or by their id. Groups can be deleted from the list. Adding a Group is done using the Blocks create_group method. This is a read only attribute.

metadata¶

Associated metadata of the entity. Sections attached to the entity via this attribute can provide additional annotations. This is an optional read-write property, and can be None if no metadata is available.

Type:	nixio.Section

multi_tags¶: A property containing all multi tags of a block. MultiTag entities can be obtained via their index or by their id. Tags can be deleted from the list. Adding tags is done using the Blocks create_multi_tag method. This is a read only attribute.

pprint(indent=2, max_length=120, extra=True, start_depth=0)¶

Pretty Printing the Data and MetaData Tree of the whole File

Parameters:	indent (int) – The length of one indentation space max_length (int) – Maximum length of each line of output extra (bool) – True to print extra information of Entities start_depth (int) – Starting depth of indentation

sources¶: A property containing all sources of a block. Sources can be obtained via their index or by their id. Sources can be deleted from the list. Adding sources is done using the Blocks create_source method. This is a read only attribute.

tags¶: A property containing all tags of a block. Tag entities can be obtained via their index or by their id. Tags can be deleted from the list. Adding tags is done using the Blocks create_tag method. This is a read only attribute.

nixio.compression module¶

class nixio.compression.Compression¶

Bases: enum.Enum

An enumeration.

Auto = 'Auto'¶

DeflateNormal = 'DeflateNormal'¶

No = 'None'¶

nixio.container module¶

class nixio.container.Container(name, nixfile, parent, itemclass)¶

Bases: object

Container acts as an interface to container groups in the backend. In the case of HDF5, this is a group that is used as a container for other groups.

Examples of Containers:: Block.data_arrays Block.tags Block.multi_tags Source.sources

Parameters:	name – Name of the container parent – Parent NIX object where this container will be created itemclass – The class of the objects this container holds (for

checking and instantiations)

items()¶

class nixio.container.LinkContainer(name, parent, itemclass, itemstore)¶

Bases: nixio.container.Container

A LinkContainer acts as an interface to container groups in the backend that hold links to objects already contained in a Container.

Objects are added to a LinkContainer using the ‘append’ method, as opposed to Containers which get populated by the parent object ‘create’ methods.

An important difference between a LinkContainer and a Container is that links to objects are indexed by their ‘id’ whereas objects in Containers are indexed by ‘name’.

Examples of LinkContainers:: Group.data_arrays Group.tags Group.multi_tags

Parameters:	name – Name of the container parent – Parent H5Group where this container will be created itemclass – The class of the objects this container holds (for checking and instantiations) itemstore – The location (Container) where the original objects are stored and linked to.

append(item)¶

extend(items)¶

class nixio.container.SectionContainer(name, nixfile, parent, itemclass)¶

Bases: nixio.container.Container

SectionContainer extends Container with a new __delitem__ method. When a Section is deleted, all child sections need to be deleted individually to make sure all their references are removed.

class nixio.container.SourceContainer(name, nixfile, parent, itemclass)¶

Bases: nixio.container.Container

SourceContainer extends Container with a new __delitem__ method. When a Source is deleted, all child sources need to be deleted individually to make sure all their references are removed.

nixio.data_array module¶

class nixio.data_array.DataArray(nixfile, nixparent, h5group)¶

Bases: nixio.entity.Entity, nixio.data_set.DataSet

append_range_dimension(ticks=None, label=None, unit=None)¶

Append a new RangeDimension to the list of existing dimension descriptors.

Parameters:	ticks (list of float) – The ticks of the RangeDimension to create.
Returns:	The newly created RangeDimension.
Return type:	nixio.RangeDimension

append_range_dimension_using_self(index=None)¶

Convenience function to append a new RangeDimension to the list of existing dimensions that uses the DataArray itself as provider for the ticks. This is a replacement for rdim = array.append_range_dimension() rdim.link_data_array(self, index)

Parameters:	index – The slice of the DataArray that contains the tick values. This must be a vector of the data. Defaults to [-1], i.e. the full first dimension.
Type:	list of int
Returns:	the newly created nixio.RangeDimension
Return type:	nixio.RangeDimension

append_sampled_dimension(sampling_interval, label=None, unit=None, offset=None)¶

Append a new SampledDimension to the list of existing dimension descriptors.

Parameters:	sampling_interval (float) – The sampling interval of the SetDimension to create.
Returns:	The newly created SampledDimension.
Return type:	nixio.SampledDimension

append_set_dimension(labels=None)¶

Append a new SetDimension to the list of existing dimension descriptors.

Returns:	The newly created SetDimension.
Return type:	nixio.SetDimension

classmethod create_new(nixfile, nixparent, h5parent, name, type_, data_type, shape, compression)¶

data¶

DEPRECATED DO NOT USE ANYMORE! Returns self

Type:	`DataArray`

delete_dimensions()¶: Delete all the dimension descriptors for this DataArray.

dimensions¶

A property containing all dimensions of a DataArray. Dimensions can be obtained via their index. Adding dimensions is done using the respective append methods for dimension descriptors. This is a read only attribute.

Type:	Container of dimension descriptors.

dtype¶

The data type of the data stored in the DataArray. This is a read only property.

Returns:	The data type
Return type:	nixio.DataType

expansion_origin¶

The expansion origin of the calibration polynomial. This is a read-write property and can be set to None. The default value is 0.

Type:	float

get_slice(positions, extents=None, mode=<DataSliceMode.Index: 1>)¶

Reads a slice of the data. The slice can be specified either in indices or in data coordinates. For example, if the DataArray stores 1D data spanning one second in time sampled with 1kHz (1000 data points). If one wants to read the data of the interval 0.25 to 0.5 seconds, one can use either of the following statements:

```: interval_data = data_array.get_slice([250], [500], mode=DataSliceMode.Index)[:] interval_data = data_array.get_slice([0.25],[0.25], mode=DataSliceMode.Data)[:]

```

Note: The extents are not the end positions but the extent of the slice!

Parameters:	positions (list length must match dimensionality of the data.) – Specifies the start of the data slice. List of either indices or data positions depending on the DataSliceMode. extents (list, defaults to None) – Specifies the extents of the slice for each dimension. mode (nixio.DataSliceMode) – Specifies how positions and extents are interpreted, they are either treated as indices (DataSliceMode.Index) or as positions in data coordinates (DataSliceMode.Data), Defaults to nixio.DataSliceMode.Index.
Raises:	nixio.IncompatibleDimensions: if length of positions or, if given, extents does not match the rank of the data.
Raises:	ValueError: if an invalid slice mode is given
Returns:	A nixio.DataView object
Return type:	nixio.DataView

iter_dimensions()¶: 1-based index dimension iterator. The method returns a generator which returns the index starting from one and the dimensions.

label¶

The label of the DataArray. The label corresponds to the label of the x-axis of a plot. This is a read-write property and can be set to None.

Type:	str

metadata¶

Associated metadata of the entity. Sections attached to the entity via this attribute can provide additional annotations. This is an optional read-write property, and can be None if no metadata is available.

Type:	nixio.Section

polynom_coefficients¶

The polynomial coefficients for the calibration. By default this is set to a {0.0, 1.0} for a linear calibration with zero offset. This is a read-write property and can be set to None

Return type:	list of float

sources¶: A property containing all Sources referenced by the DataArray. Sources can be obtained by index or their id. Sources can be removed from the list, but removing a referenced Source will not remove it from the file. New Sources can be added using the append method of the list. This is a read only attribute.

unit¶

The unit of the values stored in the DataArray. This is a read-write property and can be set to None.

Type:	str

class nixio.data_array.DataSliceMode¶

Bases: enum.Enum

An enumeration.

Data = 2¶

Index = 1¶

nixio.data_frame module¶

class nixio.data_frame.DataFrame(nixfile, nixparent, h5group)¶

Bases: nixio.entity.Entity, nixio.data_set.DataSet

append_column(column, name, datatype=None)¶

Append a new column to the DataFrame In case of string, it will be better to set explicitly the datatype.

Parameters:	column (array-like data) – The new column name (str) – The name of new column datatype (nixio.DataType) – The DataType of new column

append_rows(data)¶

Append a new row to the DataFrame. The data supplied must be iterable.

Parameters:	data (array-like data) – The new row

column_names¶

The dtype is the list of names of all columns in the DatFrame. This is a read only property.

Type:	list of str

columns¶

The dtype is the list of names and data types of all columns in the DatFrame. This is a read only property.

Type:	list of tuples

classmethod create_new(nixfile, nixparent, h5parent, name, type_, shape, col_dtype, compression)¶

df_shape¶

The df_shape is the shape of the DataFrame in (number of rows, number of columns) format. This is a read only property.

Type:	tuple

dtype¶

The dtype is the list of DataTypes of all columns in the DatFrame. This is a read only property.

Type:	list of DataType

metadata¶

Associated metadata of the entity. Sections attached to the entity via this attribute can provide additional annotations. This is an optional read-write property, and can be None if no metadata is available.

Type:	nixio.Section

print_table(row_sl=None, col_sl=None)¶

Print the whole DataFrame as a table

Parameters:	row_sl (slice or iterable of int) – Rows to be printed; None for printing all rows col_sl (slice or iterable of int) – Columns to be printed; None for printing all columns

read_cell(position=None, col_name=None, row_idx=None)¶

Read a cell in the DataFrame

Parameters:	position (tuple or list or array with length 2) – Position of the targeted cell col_name (str) – The column name in which the targeted cell belongs to row_idx (list of int) – A length 1 list that specify on which row the targeted cell is located

read_columns(index=None, name=None, slc=None, group_by_cols=False)¶

Read one or multiple (part of) column(s) in the DataFrame

Parameters:	index (list of int) – Index of column(s) to be returned name (list of str) – Name of column(s) to be returned slc (slice) – The part of each column to be returned group_by_cols (bool) – True for group return values by columns, False for group by rows. Only applicable for reading multiple columns

read_rows(index)¶

Read one or multiple row(s) in the DataFrame

Parameters:	index (list of int) – Index of row(s) to be returned

row_count()¶: Return the total number of rows

units¶

The unit of the values stored in the DataFrame. This is a read-write property and can be set to None.

Type:	array of str

write_cell(cell, position=None, col_name=None, row_idx=None)¶

Overwrite a cell in the DataFrame

Parameters:	cell (same type as the specified column) – The new cell position (tuple or list or array with length 2) – Position of the targeted cell col_name (str) – The column name in which the targeted cell belongs to row_idx (list of int) – A length 1 list that specify on which row the targeted cell is located

write_column(column, index=None, name=None)¶

Overwrite an existing column. Either index or name of the column should be provided.

Parameters:	column (array-like data) – The new column index (string) – The index of the column that is written to name (str) – The name of the column that is written to

write_rows(rows, index)¶

Overwrite one or multiple existing row(s)

Parameters:	rows ((nested) array-like data) – The new rows(s) and their data index (list of int) – Index of rows(s) to be overwritten

write_to_csv(filename, mode='w')¶

Export the whole DataFrame to a CSV file

Parameters:	filename (str) – The resulted/ targeted CSV file to write to/ create mode (str) – The column name in which the targeted cell belongs to

nixio.data_set module¶

class nixio.data_set.DataSet¶

Bases: object

Data IO object for DataArray.

append(data, axis=0)¶

Append data to the DataSet along the axis specified.

Parameters:	data – The data to append. Shape must agree except for the specified axis axis – Along which axis to append the data to

data_extent¶

The size of the data.

Type:	tuple of int

data_type¶

The data type of the data stored in the DataArray. This is a read only property.

Type:	nixio.DataType

dtype¶

Type:	`numpy.dtype` object holding type information about the data stored in the DataSet.

len()¶

Length of the first dimension. Equivalent to DataSet.shape[0].

Type:	int or long

read_direct(data)¶

Directly read all data stored in the DataSet into data. The supplied data must be a numpy.ndarray that matches the DataSet’s shape, must have C-style contiguous memory layout and must be writeable (see numpy.ndarray.flags and ndarray for more information).

Parameters:	data (`numpy.ndarray`) – The array where data is being read into

shape¶

Type:	tuple of data array dimensions.

size¶

Number of elements in the DataSet, i.e. the product of the elements in shape.

Type:	int

write_direct(data)¶

Directly write all of data to the DataSet. The supplied data must be a numpy.ndarray that matches the DataSet’s shape and must have C-style contiguous memory layout (see numpy.ndarray.flags and ndarray for more information).

Parameters:	data (`numpy.ndarray`) – The array which contents is being written

nixio.data_view module¶

class nixio.data_view.DataView(da, slices)¶

Bases: nixio.data_set.DataSet

data_extent¶

The size of the data.

Type:	tuple of int

data_type¶

The data type of the data stored in the DataArray. This is a read only property.

Type:	nixio.DataType

nixio.datatype module¶

class nixio.datatype.DataType¶

Bases: object

Bool¶: alias of numpy.bool_

Double¶: alias of numpy.float64

Float¶: alias of numpy.float32

FloatTypes = (<class 'numpy.float32'>, <class 'numpy.float64'>)¶

Int16¶: alias of numpy.int16

Int32¶: alias of numpy.int32

Int64¶: alias of numpy.int64

Int8¶: alias of numpy.int8

IntTypes = (<class 'numpy.int8'>, <class 'numpy.int16'>, <class 'numpy.int32'>, <class 'numpy.int64'>, <class 'numpy.uint8'>, <class 'numpy.uint16'>, <class 'numpy.uint32'>, <class 'numpy.uint64'>)¶

String¶: alias of numpy.str_

UInt16¶: alias of numpy.uint16

UInt32¶: alias of numpy.uint32

UInt64¶: alias of numpy.uint64

UInt8¶: alias of numpy.uint8

classmethod get_dtype(value)¶

classmethod is_numeric_dtype(dtype)¶

nixio.dimension_type module¶

class nixio.dimension_type.DimensionType¶

Bases: enum.Enum

An enumeration.

Range = 'range'¶

Sample = 'sample'¶

Set = 'set'¶

nixio.dimensions module¶

class nixio.dimensions.Dimension(nixfile, data_array, index)¶

Bases: object

dimension_link¶: If the dimension has a DimensionLink to a data object, returns the DimensionLink object, otherwise returns None.

dimension_type¶

has_link¶: Return True if this Dimension links to a data object (DataArray or DataFrame). Read-only property.

index¶

link_data_array(data_array, index)¶

link_data_frame(data_frame, index)¶

remove_link()¶

class nixio.dimensions.DimensionContainer(name, nixfile, parent, itemclass)¶

Bases: nixio.container.Container

DimensionContainer extends Container to support returning different types of Dimension classes on return.

class nixio.dimensions.DimensionLink(nixfile, nixparent, h5group)¶

Bases: object

Links a Dimension to a data object (DataArray or DataFrame).

A single vector of values from the underlying data object must be specified to serve as the ticks or labels for the associated Dimension.

A single vector of a DataArray.
A single column of a DataFrame.

classmethod create_new(nixfile, nixparent, h5parent, dataobj, dotype, index)¶

file¶

id¶

index¶

label¶: Returns the label of the linked data object: For DataArray links, returns the label. For DataFrame links, returns the name of the column specified by the LinkDimension’s index.

linked_data¶

unit¶: Returns the unit from the linked data object (DataArray or DataFrame) specified by the LinkDimension’s index.

values¶: Returns the values (vector or column) from the linked data object (DataArray or DataFrame) specified by the LinkDimension’s index.

class nixio.dimensions.IndexMode¶

Bases: enum.Enum

IndexMode is used to define the behaviour of the index_of() methods.

GEQ = 'geq'¶

GreaterOrEqual = 'geq'¶

LEQ = 'leq'¶

Less = 'less'¶

LessOrEqual = 'leq'¶

class nixio.dimensions.RangeDimension(data_array, index)¶

Bases: nixio.dimensions.Dimension

axis(count, start=0)¶

Get an axis as defined by this range dimension.

Parameters:	count – A positive integer specifying the length of the axis (no of points). start – positive integer, indicates the starting tick.
Returns:	The created axis
Return type:	list

classmethod create_new(data_array, index, ticks)¶

index_of(position, mode=<IndexMode.LessOrEqual: 'leq'>)¶

Returns the index of a certain position in the dimension. Raises IndexError if the position is out of bounds (depending on mode).

Parameters:	position – The position. mode – The IndexMode to use (default LessOrEqual). The default value (LessOrEqual) will return the index of the position that matches a tick if it matches a dimension tick exactly. If it does not match a tick, the previous index is returned. If the mode is Less, the previous index of the matching tick is always returned. If the mode is GreaterOrEqual and the position does not match a tick exactly, the next index is returned.
Returns:	The matching index
Return type:	int

is_alias¶

In versions < 1.5 a RangeDimension that was referring to the DataArray it describes was called an AliasRangeDimension. This has been made more flexible by allowing to link to any DataArray or DataFrame. For downward compatibility this method has been re-introduced in 1.5.1.

Returns:	True, if this dimension links to a DataArray, False otherwise
Return type:	bool

label¶

link_data_array(data_array, index)¶

link_data_frame(data_frame, index)¶

tick_at(index)¶

Returns the tick at the given index. Will throw an Exception if the index is out of bounds.

Parameters:	index – The index.
Returns:	The corresponding position.
Return type:	double

ticks¶

unit¶

class nixio.dimensions.SampledDimension(data_array, index)¶

Bases: nixio.dimensions.Dimension

axis(count, start=None, start_position=None)¶

Get an axis as defined by this nixio.SampledDimension. It either starts at the offset of the dimension, a number of sample points later, or at a given position. The latter must not be less than the offset. If start and start_position are given, start takes precedence.

Parameters:	count (int) – A positive integer specifying the length of the axis (no of samples). start (int) – positive integer, indicates the starting sample. Defaults to None. Precedes over the start_position. start_position (double) – The start position of the axis. Defaults to None.
Raises:	ValueError if start is negative or if the start_position is given and is less than offset.
Returns:	The created axis
Return type:	tuple

classmethod create_new(data_array, index, sample)¶

index_of(position, mode=<IndexMode.LessOrEqual: 'leq'>)¶

Returns the index of a certain position in the dimension. Raises IndexError if the position is out of bounds (depending on mode).

Parameters:	position – The position. mode – The IndexMode to use (default LessOrEqual). The default value (LessOrEqual) will return the index of the position calculated based on the dimension offset and sampling_interval if it matches a dimension tick exactly. If it does not match a tick, the previous index is returned. If the mode is Less, the previous index of the calculated position is always returned. If the mode is GreaterOrEqual and the calculated position does not match a tick exactly, the next index is returned.
Returns:	The matching index.
Return type:	int

label¶

link_data_array(*_)¶

link_data_frame(*_)¶

offset¶

position_at(index)¶

Returns the position corresponding to a given index.

Parameters:	index – A positive integer.
Returns:	The position matching to the index.
Return type:	float

sampling_interval¶

unit¶

class nixio.dimensions.SetDimension(data_array, index)¶

Bases: nixio.dimensions.Dimension

classmethod create_new(data_array, index)¶

index_of(position, mode=<IndexMode.LessOrEqual: 'leq'>)¶

Returns the index of a certain position in the dimension. Raises IndexError if the position is out of bounds (depending on mode and number of labels).

Parameters:	position – The position. mode – The IndexMode to use (default LessOrEqual). The modes LessOrEqual and GreaterOrEqual will return the integer representation of the position if it is equal to the nearest integer. If the position is not an integer (or is not equal to the nearest integer), then the value is rounded down (for LessOrEqual) or rounded up (for GreaterOrEqual). If the mode is Less, the previous integer is always returned.
Returns:	The matching index
Return type:	int

labels¶

nixio.entity module¶

class nixio.entity.Entity(nixfile, nixparent, h5group)¶

Bases: object

classmethod create_new(nixfile, nixparent, h5parent, name=None, type_=None)¶

created_at¶

The creation time of the entity. This is a read-only property. Use force_created_at in order to change the creation time.

Return type:	int

definition¶

The definition of the entity. The definition can contain a textual description of the entity. This is an optional read-write property, and can be None if no definition is available.

Type:	str

file¶

Reference to the NIX File object. This is a read-only property.

Return type:	nixio.File

force_created_at(time=None)¶

Sets the creation time created_at to the given time (default: current time).

Parameters:	time (int) – The time to set.

force_updated_at(time=None)¶

Sets the update time updated_at to the given time. (default: current time)

Parameters:	time (int) – The time to set.

id¶

A property providing the ID of the Entity. The id is generated automatically, therefore the property is read-only.

Return type:	str

name¶

The name of an entity. The name serves as a human readable identifier. This is a read-only property; entities cannot be renamed.

Type:	str

type¶

The type of the entity. The type is used in order to add semantic meaning to the entity. This is a read-write property, but it can’t be set to None.

Type:	str

updated_at¶

The time of the last update of the entity. This is a read-only property. Use force_updated_at in order to change the update time.

Return type:	int

nixio.feature module¶

class nixio.feature.Feature(nixfile, nixparent, h5group)¶

Bases: object

classmethod create_new(nixfile, nixparent, h5parent, data, link_type)¶

created_at¶

The creation time of the entity. This is a read-only property. Use force_created_at in order to change the creation time.

Return type:	int

data¶

file¶

id¶

link_type¶

updated_at¶

The time of the last update of the entity. This is a read-only property. Use force_updated_at in order to change the update time.

Return type:	int

nixio.file module¶

class nixio.file.File(path, mode='a', compression=<Compression.Auto: 'Auto'>, auto_update_timestamps=True)¶

Bases: object

auto_update_timestamps¶

If enabled, automatically updates the ‘updated_at’ attribute when an object’s data or attributes are changed.

Type:	bool

blocks¶: A property containing all blocks of a file. Blocks can be obtained by their name, id or index. Blocks can be deleted from the list, when a block is deleted all its content (data arrays, tags and sources) will be also deleted from the file. Adding new Block is done via the create_block method of File. This is a read-only attribute.

close()¶: Closes an open file.

copy_section(obj, children=True, keep_id=True, name='')¶

Copy a section to the file.

Parameters:	obj (nixio.Section) – The Section to be copied children (bool) – Specify if the copy should be recursive keep_id (bool) – Specify if the id should be kept name (str) – Name of copied section, Default is name of source section
Returns:	The copied section
Return type:	nixio.Section

create_block(name='', type_='', compression=<Compression.Auto: 'Auto'>, copy_from=None, keep_copy_id=True)¶

Create a new block inside the file.

Parameters:	name (str) – The name of the block to create. type (str) – The type of the block. compression – No, DeflateNormal, Auto (default: Auto) copy_from (nixio.Block) – The Block to be copied, None in normal mode keep_copy_id (bool) – Specify if the id should be copied in copy mode
Returns:	The newly created block.
Return type:	nixio.Block

create_section(name, type_='undefined', oid=None)¶

Create a new metadata section inside the file.

Parameters:	name (str) – The name of the section to create. type (str) – The type of the section. oid (str) – object id, UUID string as specified in RFC 4122. If no id is provided, an id will be generated and assigned.
Returns:	The newly created section.
Return type:	nixio.Section

created_at¶

The creation time of the file. This is a read-only property. Use force_created_at in order to change the creation time.

Return type:	int

find_sections(filtr=<function File.<lambda>>, limit=None)¶

Get all sections and their child sections recursively.

This method traverses the trees of all sections. The traversal is accomplished via breadth first and can be limited in depth. On each node or section a filter is applied. If the filter returns true the respective section will be added to the result list. By default a filter is used that accepts all sections.

Parameters:	filtr (function) – A filter function limit (int) – The maximum depth of traversal
Returns:	A list containing the matching sections.
Return type:	list of nixio.Section

flush()¶

force_created_at(time=None)¶

Sets the creation time created_at to the given time (default: current time).

Parameters:	time (int) – The time to set

force_updated_at(time=None)¶

Sets the update time updated_at to the given time. (default: current time)

Parameters:	time (int) – The time to set (default: now)

format¶

The format of the file. This read only property should always have the value ‘nix’.

Type:	str

id¶

is_open()¶

Checks whether a file is open or closed.

Returns:	True if the file is open, False otherwise.
Return type:	bool

classmethod open(path, mode='a', compression=<Compression.Auto: 'Auto'>, backend=None, auto_update_timestamps=True)¶

Open a NIX file, or create it if it does not exist.

Parameters:	path – Path to file mode – FileMode ReadOnly, ReadWrite, or Overwrite. (default: ReadWrite) compression – No, DeflateNormal, Auto (default: Auto) auto_update_timestamps – Enable/disable automatic updating of ‘updated_at’ timestamp. (default: True)
Returns:	nixio.File object

pprint(indent=2, max_length=120, extra=True, max_depth=3)¶

Pretty Printing the Data and MetaData Tree of the whole File

Parameters:	indent (int) – The length of one indentation space max_length (int) – Maximum length of each line of output extra (bool) – True to print extra information of Entities max_depth (int) – Maximum recursion being printed in MetaData tree

sections¶: A property containing all root Sections of a file. Specific root Sections can be obtained by their name, id or index. Sections can be deleted from this list. Notice: when a section is deleted all its child section and properties will be removed too. Adding a new Section is done via the crate_section method of File. This is a read-only property.

updated_at¶

The time of the last update of the file. This is a read-only property. Use force_updated_at in order to change the update time.

Return type:	int

validate()¶

version¶

The file format version.

Type:	tuple

class nixio.file.FileMode¶

Bases: object

Overwrite = 'w'¶

ReadOnly = 'r'¶

ReadWrite = 'a'¶

nixio.file.can_read(nixfile)¶

nixio.file.can_write(nixfile)¶

nixio.file.make_fapl()¶

nixio.file.make_fcpl()¶

nixio.file.map_file_mode(mode)¶

nixio.group module¶

class nixio.group.Group(nixfile, nixparent, h5group)¶

Bases: nixio.entity.Entity

classmethod create_new(nixfile, nixparent, h5parent, name, type_)¶

data_arrays¶: A property containing all data arrays referenced by the group. Referenced data arrays can be obtained by index or their id. References can be removed from the list, removing a referenced DataArray will not remove it from the file. New references can be added using the append method of the list. This is a read only attribute.

data_frames¶: A property containing all data frames referenced by the group. Referenced data frames can be obtained by index or their id. References can be removed from the list, removing a referenced DataFrame will not remove it from the file. New references can be added using the append method of the list. This is a read only attribute.

metadata¶

Associated metadata of the entity. Sections attached to the entity via this attribute can provide additional annotations. This is an optional read-write property, and can be None if no metadata is available.

Type:	nixio.Section

multi_tags¶: A property containing all MultiTags referenced by the group. MultiTags can be obtained by index or their id. MultiTags can be removed from the list, removing a referenced MultiTag will not remove it from the file. New MultiTags can be added using the append method of the list. This is a read only attribute.

sources¶: A property containing all Sources referenced by the Group. Sources can be obtained by index or their id. Sources can be removed from the list, but removing a referenced Source will not remove it from the file. New Sources can be added using the append method of the list. This is a read only attribute.

tags¶: A property containing all tags referenced by the group. Tags can be obtained by index or their id. Tags can be removed from the list, removing a referenced Tag will not remove it from the file. New Tags can be added using the append method of the list. This is a read only attribute.

nixio.info module¶

nixio.link_type module¶

class nixio.link_type.LinkType¶

Bases: enum.Enum

An enumeration.

Indexed = 'indexed'¶

Tagged = 'tagged'¶

Untagged = 'untagged'¶

nixio.multi_tag module¶

class nixio.multi_tag.MultiTag(nixfile, nixparent, h5group)¶

Bases: nixio.tag.BaseTag

classmethod create_new(nixfile, nixparent, h5parent, name, type_, positions)¶

extents¶

The extents defined by the tag. This is an optional read-write property and may be set to None.

Type:	nixio.DataArray or None

feature_data(posidx, featidx, stop_rule=<SliceMode.Exclusive: 'exclusive'>)¶

metadata¶

Associated metadata of the entity. Sections attached to the entity via this attribute can provide additional annotations. This is an optional read-write property, and can be None if no metadata is available.

Type:	nixio.Section

positions¶

The positions defined by the tag. This is a read-write property.

Type:	nixio.DataArray

references¶

A property containing all data arrays referenced by the tag. Referenced data arrays can be obtained by index or their id. References can be removed from the list, removing a referenced DataArray will not remove it from the file. New references can be added using the append method of the list. This is a read only attribute.

Type:	nixio.LinkContainer of nixio.DataArray

retrieve_data(posidx, refidx)¶

retrieve_feature_data(posidx, featidx)¶

sources¶: A property containing all Sources referenced by the MultiTag. Sources can be obtained by index or their id. Sources can be removed from the list, but removing a referenced Source will not remove it from the file. New Sources can be added using the append method of the list. This is a read only attribute.

tagged_data(posidx, refidx, stop_rule=<SliceMode.Exclusive: 'exclusive'>)¶

nixio.property module¶

class nixio.property.OdmlType¶

Bases: enum.Enum

OdmlType provides all types currently supported by the odML data format. It provides additional information about the nature of the values of an odML Property.

Boolean = 'boolean'¶

Date = 'date'¶

Datetime = 'datetime'¶

Float = 'float'¶

Int = 'int'¶

Person = 'person'¶

String = 'string'¶

Text = 'text'¶

Time = 'time'¶

URL = 'url'¶

compatible(value)¶

compatible returns True or False depending on whether a passed value can be mapped to an OdmlType or not.

Parameters:	value – Any single value
Returns:	Boolean

get_odml_type = <bound method OdmlType.get_odml_type of <enum 'OdmlType'>>¶

class nixio.property.Property(nixfile, nixparent, h5dataset)¶

Bases: nixio.entity.Entity

An odML Property

classmethod create_new(nixfile, nixparent, h5parent, name, dtype, shape=None, oid=None)¶

data_type¶

definition¶

The definition of the entity. The definition can contain a textual description of the entity. This is an optional read-write property, and can be None if no definition is available.

Type:	str

delete_values()¶

dependency¶

dependency_value¶

extend_values(data)¶: Extends values to existing data. Suitable when new data is nested or original data is long.

name¶

The name of an entity. The name serves as a human readable identifier. This is a read-only property; entities cannot be renamed.

Type:	str

odml_type¶

pprint(indent=2, max_length=80, current_depth=-1)¶: Pretty print method. Method is called in Section.pprint()

reference¶

uncertainty¶

unit¶

value_origin¶

values¶

nixio.section module¶

class nixio.section.S(section_type, section=None)¶: Bases: object

class nixio.section.Section(nixfile, nixparent, h5group)¶

Bases: nixio.entity.Entity

copy_section(obj, children=True, keep_id=True, name='')¶

Copy a section to the section.

Parameters:	obj (nixio.Section) – The Section to be copied children (bool) – Specify if the copy should be recursive keep_id (bool) – Specify if the id should be kept name (str) – Name of copied section, Default is name of source section
Returns:	The copied section
Return type:	nixio.Section

classmethod create_new(nixfile, nixparent, h5parent, name, type_, oid=None)¶

create_property(name='', values_or_dtype=0, oid=None, copy_from=None, keep_copy_id=True)¶

Add a new property to the section.

Parameters:	name (str) – The name of the property to create/copy. values_or_dtype (list of values or a nixio.DataType) – The values of the property or a valid DataType. oid (str) – object id, UUID string as specified in RFC 4122. If no id is provided, an id will be generated and assigned. copy_from (nixio.Property) – The Property to be copied, None in normal mode keep_copy_id (bool) – Specify if the id should be copied in copy mode
Returns:	The newly created property.
Return type:	nixio.Property

create_section(name, type_='undefined', oid=None)¶

Creates a new subsection that is a child of this section entity.

Parameters:	name (str) – The name of the section to create. type (str) – The type of the section. oid (str) – object id, UUID string as specified in RFC 4122. If no id is provided, an id will be generated and assigned.
Returns:	The newly created section.
Return type:	nixio.Section

find_related(filtr=<function Section.<lambda>>)¶

Get all related sections of this section.

The result can be filtered. On each related section a filter is applied. If the filter returns true the respective section will be added to the result list. By default a filter is used that accepts all sections.

Parameters:	filtr (function) – A filter function
Returns:	A list containing the matching related sections.
Return type:	list of nixio.Section

find_sections(filtr=<function Section.<lambda>>, limit=None)¶

Get all child sections recursively. This method traverses the trees of all sections. The traversal is accomplished via breadth first and can be limited in depth. On each node or section a filter is applied. If the filter returns true the respective section will be added to the result list. By default a filter is used that accepts all sections.

Parameters:	filtr (function) – A filter function limit (int) – The maximum depth of traversal
Returns:	A list containing the matching sections.
Return type:	list of nixio.Section

inherited_properties()¶

items()¶

link¶

Link to another section. If a section is linked to another section, the linking section inherits all properties from the target section. This is an optional read-write property and may be set to None.

Type:	nixio.Section

parent¶

The parent section. This is a read-only property. For root sections this property is always None.

Accessing this property can be slow when the metadata tree is large.

Type:	nixio.Section

pprint(indent=2, max_depth=1, max_length=80, current_depth=0)¶

Pretty print method.

Parameters:	indent (int) – The number of indentation spaces per recursion max_depth (int) – The maximum times of recursion max_length (int) – The maximum length of each line of output current_depth (int) – The current times of recursion

props¶

A property containing all Property entities associated with the section. Properties can be accessed by name, index, or id. Properties can be deleted from the list. Adding new Properties is done using the create_property method. This is a read-only attribute.

Type:	Container of nixio.Property

reference¶

referring_blocks¶

referring_data_arrays¶

referring_groups¶

referring_multi_tags¶

referring_objects¶

referring_sources¶

referring_tags¶

repository¶

URL to the terminology repository the section is associated with. This is an optional read-write property and may be set to None.

Type:	str

sections¶

A property providing all child Sections of a Section. Child sections can be accessed by name, index, or id. Sections can also be deleted: if a Section is deleted, all its properties and child Sections are removed from the file too. Adding new Sections is achieved using the create_section method. This is a read-only attribute.

Type:	Container of nixio.Section

nixio.source module¶

class nixio.source.Source(nixfile, nixparent, h5group)¶

Bases: nixio.entity.Entity

classmethod create_new(nixfile, nixparent, h5parent, name, type_)¶

create_source(name, type_)¶

Create a new source as a child of the current Source.

Parameters:	name (str) – The name of the source to create. type (str) – The type of the source.
Returns:	The newly created source.
Return type:	nixio.Source

find_sources(filtr=<function Source.<lambda>>, limit=None)¶

Get all child sources of this source recursively.

This method traverses the tree of all sources. The traversal is accomplished via breadth first and can be limited in depth. On each node or source a filter is applied. If the filter returns true the respective source will be added to the result list. By default a filter is used that accepts all sources.

Parameters:	filtr (function) – A filter function limit (int) – The maximum depth of traversal
Returns:	A list containing the matching sources.
Return type:	list of nixio.Source

metadata¶

Associated metadata of the entity. Sections attached to the entity via this attribute can provide additional annotations. This is an optional read-write property, and can be None if no metadata is available.

Type:	nixio.Section

parent_block¶

Returns the block this source is contained in.

Returns:	the Block containing this source
Return type:	nixio.Block

parent_source¶

Get the parent source of this source. If this source is at the root, None will be returned

Returns:	the parent source
Return type:	Source or None

referring_data_arrays¶

Returns all DataArray entities linking to this source.

Returns:	all DataArrays referring to this source.
Return type:	list

referring_multi_tags¶

Returns all MultiTag entities linking to this source.

Returns:	all MultiTags referring to this source.
Return type:	list

referring_objects¶

Returns the list of entities that link to this source.

Returns:	all objects referring to this source.
Return type:	list

referring_tags¶

Returns all Tag entities linking to this source.

Returns:	all Tags referring to this source.
Return type:	list

sources¶: A property containing child sources of a Source. Sources can be obtained via their name, index, id. Sources can be deleted from the list. Adding sources is done using the Blocks create_source method. This is a read only attribute.

nixio.source_link_container module¶

class nixio.source_link_container.SourceLinkContainer(parent)¶

Bases: nixio.container.LinkContainer

append(item)¶

nixio.tag module¶

class nixio.tag.BaseTag(nixfile, nixparent, h5group)¶

Bases: nixio.entity.Entity

Base class for Tag and MultiTag

create_feature(data, link_type)¶

Create a new feature.

Parameters:	data (nixio.DataArray) – The data array of this feature. link_type (nixio.LinkType) – The link type of this feature.
Returns:	The created feature object.
Return type:	nixio.Feature

features¶

A property containing all features. Features can be obtained via their index or their ID. Features can be deleted from the list. Adding new features is done using the create_feature method. This is a read only attribute.

Type:	Container of nixio.Feature.

units¶

Property containing the units of the tag. The tag must provide a unit for each dimension of the position or extent vector. This is a read-write property.

Type:	list of str

class nixio.tag.FeatureContainer(name, nixfile, parent, itemclass)¶

Bases: nixio.container.Container

The FeatureContainer has one minor difference from the regular Container: A Feature can be retrieved by the ID or name of the linked DataArray as well as the ID of the feature itself.

class nixio.tag.SliceMode¶

Bases: enum.Enum

An enumeration.

Exclusive = 'exclusive'¶

Inclusive = 'inclusive'¶

to_index_mode()¶

class nixio.tag.Tag(nixfile, nixparent, h5group)¶

Bases: nixio.tag.BaseTag

classmethod create_new(nixfile, nixparent, h5parent, name, type_, position)¶

extent¶

The extent defined by the tag. This is an optional read-write property and may be set to None.

Type:	list of float

feature_data(featidx, stop_rule=<SliceMode.Exclusive: 'exclusive'>)¶

metadata¶

Associated metadata of the entity. Sections attached to the entity via this attribute can provide additional annotations. This is an optional read-write property, and can be None if no metadata is available.

Type:	nixio.Section

position¶

The position defined by the tag. This is a read-write property.

Type:	list of float

references¶

A property containing all data arrays referenced by the tag. Referenced data arrays can be obtained by index or their id. References can be removed from the list, removing a referenced DataArray will not remove it from the file. New references can be added using the append method of the list. This is a read only attribute.

Type:	Container of nixio.DataArray

retrieve_data(refidx)¶

retrieve_feature_data(featidx)¶

sources¶: A property containing all Sources referenced by the Tag. Sources can be obtained by index or their id. Sources can be removed from the list, but removing a referenced Source will not remove it from the file. New Sources can be added using the append method of the list. This is a read only attribute.

tagged_data(refidx, stop_rule=<SliceMode.Exclusive: 'exclusive'>)¶

nixio.validator module¶

class nixio.validator.ValidationError¶

Bases: object

Static class for defining validation error messages

DataFrameMismatch = 'referenced data frame for dimension {} does not have the same row count as the data array'¶

DimensionMismatch = 'data dimensionality does not match number of defined dimensions'¶

DimensionTypeMismatch = 'dimension_type attribute for dimension {} does not match Dimension object type'¶

ExtentDimensionMismatch = 'number of entries in extent does not match number of dimensions in all referenced DataArrays'¶

ExtentsDimensionMismatch = 'number of entries (in 2nd dim) in extents does not match number of dimensions in all referenced DataArrays'¶

IncorrectDimensionIndex = 'index for dimension {} is set to incorrect value {}'¶

InvalidDimensionIndex = 'index for dimension {} is not set to a valid value (index > 0)'¶

InvalidDimensionUnit = 'unit for dimension {} is set but it is not an atomic SI unit (Note: composite units are not supported)'¶

InvalidSamplingInterval = 'sampling interval for dimension {} is not valid (interval > 0)'¶

InvalidUnit = 'unit is invalid: not an atomic SI (Note: composite units are not supported)'¶

NoData = 'data is not set'¶

NoDataType = 'data type is not set'¶

NoDate = 'date is not set'¶

NoID = 'no ID set'¶

NoLinkType = 'link_type is not set'¶

NoName = 'no name set'¶

NoPosition = 'position is not set'¶

NoPositions = 'positions are not set'¶

NoSamplingInterval = 'sampling interval for dimension {} is not set'¶

NoTicks = 'ticks for dimension {} are not set'¶

NoType = 'no type set'¶

PositionDimensionMismatch = 'number of entries in position does not match number of dimensions in all referenced DataArrays'¶

PositionExtentMismatch = 'number of entries in position and extent do not match'¶

PositionsDimensionMismatch = 'number of entries (in 2nd dim) in positions does not match number of dimensions in all referenced DataArrays'¶

PositionsExtentsMismatch = 'number of entries in positions and extents do not match'¶

RangeDimTicksMismatch = 'number of ticks in RangeDimension ({}) differs from the number of data entries along the corresponding data dimension'¶

ReferenceUnitsIncompatible = "some of the referenced DataArrays' dimensions have units that are not convertible to the units set in the Tag (Note: composite units are not supported)"¶

ReferenceUnitsMismatch = "some of the referenced DataArrays' dimensions don't have units where the Tag has; make sure that all references have the same number of dimensions as the Tag has units and that each dimension has a unit set"¶

SetDimLabelsMismatch = 'number of labels in SetDimension ({}) differs from the number of data entries along the corresponding data dimension'¶

UnsortedTicks = 'ticks for dimension {} are not sorted'¶

class nixio.validator.ValidationWarning¶

Bases: object

InvalidUnit = 'unit is not SI or composite of SI units'¶

NoExpansionOrigin = 'polynomial coefficients for calibration are set, but expansion origin is missing'¶

NoFileID = 'file ID is not set'¶

NoFormat = 'format is not set'¶

NoPolynomialCoefficients = 'expansion origin for calibration is set, but polynomial coefficients are missing'¶

NoUnit = 'unit is not set'¶

NoVersion = 'version is not set'¶

OffsetNoUnit = 'offset for dimension {} is set, but no valid unit is set'¶

nixio.validator.check_block(block)¶

Validate a Block and return all errors and warnings for the block and each individual contained object.

Returns:	A list of ‘errors’ and a list of ‘warnings’

nixio.validator.check_data_array(da)¶

Validate a DataArray and its Dimensions and return all errors and warnings. Errors and warnings about Dimension objects are included in the DataArray errors and warnings lists.

Returns:	A list of ‘errors’ and a list of ‘warnings’

nixio.validator.check_entity(entity)¶: General NIX entity validator

nixio.validator.check_feature(feat, idx)¶

Validate a Feature and return all errors.

Returns:	A list of ‘errors’

nixio.validator.check_file(nixfile)¶

Validate a NIX file and all contained objects and return all errors and warnings for each individual object.

Returns:	A nested dictionary of errors and warnings. Each subdictionary

is indexed by the object with values describing the error or warning. :rtype: Dictionary

nixio.validator.check_group(group)¶

Validate a Group and return all errors and warnings. Does not check contained objects.

Returns:	A list of ‘errors’ and a list of ‘warnings’

nixio.validator.check_multi_tag(mtag)¶

Validate a MultiTag and its Features and return all errors and warnings. Errors and warnings about Features are included in the MultiTag errors and warnings lists.

For Features, only the basic Entity requirements, LinkType, and the existence of a referenced DataArray are checked. The linked DataArray is not checked for validity (see check_data_array() for those validation checks).

Returns:	A list of ‘errors’ and a list of ‘warnings’

nixio.validator.check_property(prop, idx)¶

Validate a Property and return all errors.

Returns:	A list of ‘errors’ and ‘warnings’

nixio.validator.check_range_dimension(dim, idx)¶

Validate a RangeDimension and return all errors and warnings.

Returns:	A list of ‘errors’ and a list of ‘warnings’

nixio.validator.check_sampled_dimension(dim, idx)¶

Validate a SampledDimension and return all errors and warnings.

Returns:	A list of ‘errors’ and a list of ‘warnings’

nixio.validator.check_section(section)¶

Validate a Section and its Properties return all errors and warnings.

Errors and warnings about Properties are included in the Section errors and warnings lists.

Returns:	A list of ‘errors’ and a list of ‘warnings’

nixio.validator.check_set_dimension()¶

Validate a SetDimension and return all errors and warnings.

Returns:	A list of ‘errors’ and a list of ‘warnings’

nixio.validator.check_source(source)¶

Validate a Source and return all errors and warnings.

Returns:	A list of ‘errors’ and a list of ‘warnings’

nixio.validator.check_tag(tag)¶

Validate a Tag and its Features and return all errors and warnings. Errors and warnings about Features are included in the Tag errors and warnings lists.

For Features, only the basic Entity requirements, LinkType, and the existence of a referenced DataArray are checked. The linked DataArray is not checked for validity (see check_data_array() for those validation checks).

Returns:	A list of ‘errors’ and a list of ‘warnings’

nixio.validator.get_dim_units(data_array)¶: Helper function to collect the units of the dimensions of a data array

nixio.validator.tag_units_match_refs_units(tag_units, refs_units)¶

Module contents¶

class nixio.File(path, mode='a', compression=<Compression.Auto: 'Auto'>, auto_update_timestamps=True)¶

Bases: object

auto_update_timestamps¶

If enabled, automatically updates the ‘updated_at’ attribute when an object’s data or attributes are changed.

Type:	bool

blocks¶: A property containing all blocks of a file. Blocks can be obtained by their name, id or index. Blocks can be deleted from the list, when a block is deleted all its content (data arrays, tags and sources) will be also deleted from the file. Adding new Block is done via the create_block method of File. This is a read-only attribute.

close()¶: Closes an open file.

copy_section(obj, children=True, keep_id=True, name='')¶

Copy a section to the file.

Parameters:	obj (nixio.Section) – The Section to be copied children (bool) – Specify if the copy should be recursive keep_id (bool) – Specify if the id should be kept name (str) – Name of copied section, Default is name of source section
Returns:	The copied section
Return type:	nixio.Section

create_block(name='', type_='', compression=<Compression.Auto: 'Auto'>, copy_from=None, keep_copy_id=True)¶

Create a new block inside the file.

Parameters:	name (str) – The name of the block to create. type (str) – The type of the block. compression – No, DeflateNormal, Auto (default: Auto) copy_from (nixio.Block) – The Block to be copied, None in normal mode keep_copy_id (bool) – Specify if the id should be copied in copy mode
Returns:	The newly created block.
Return type:	nixio.Block

create_section(name, type_='undefined', oid=None)¶

Create a new metadata section inside the file.

Parameters:	name (str) – The name of the section to create. type (str) – The type of the section. oid (str) – object id, UUID string as specified in RFC 4122. If no id is provided, an id will be generated and assigned.
Returns:	The newly created section.
Return type:	nixio.Section

created_at¶

The creation time of the file. This is a read-only property. Use force_created_at in order to change the creation time.

Return type:	int

find_sections(filtr=<function File.<lambda>>, limit=None)¶

Get all sections and their child sections recursively.

This method traverses the trees of all sections. The traversal is accomplished via breadth first and can be limited in depth. On each node or section a filter is applied. If the filter returns true the respective section will be added to the result list. By default a filter is used that accepts all sections.

Parameters:	filtr (function) – A filter function limit (int) – The maximum depth of traversal
Returns:	A list containing the matching sections.
Return type:	list of nixio.Section

flush()¶

force_created_at(time=None)¶

Sets the creation time created_at to the given time (default: current time).

Parameters:	time (int) – The time to set

force_updated_at(time=None)¶

Sets the update time updated_at to the given time. (default: current time)

Parameters:	time (int) – The time to set (default: now)

format¶

The format of the file. This read only property should always have the value ‘nix’.

Type:	str

id¶

is_open()¶

Checks whether a file is open or closed.

Returns:	True if the file is open, False otherwise.
Return type:	bool

classmethod open(path, mode='a', compression=<Compression.Auto: 'Auto'>, backend=None, auto_update_timestamps=True)¶

Open a NIX file, or create it if it does not exist.

Parameters:	path – Path to file mode – FileMode ReadOnly, ReadWrite, or Overwrite. (default: ReadWrite) compression – No, DeflateNormal, Auto (default: Auto) auto_update_timestamps – Enable/disable automatic updating of ‘updated_at’ timestamp. (default: True)
Returns:	nixio.File object

pprint(indent=2, max_length=120, extra=True, max_depth=3)¶

Pretty Printing the Data and MetaData Tree of the whole File

Parameters:	indent (int) – The length of one indentation space max_length (int) – Maximum length of each line of output extra (bool) – True to print extra information of Entities max_depth (int) – Maximum recursion being printed in MetaData tree

sections¶: A property containing all root Sections of a file. Specific root Sections can be obtained by their name, id or index. Sections can be deleted from this list. Notice: when a section is deleted all its child section and properties will be removed too. Adding a new Section is done via the crate_section method of File. This is a read-only property.

updated_at¶

The time of the last update of the file. This is a read-only property. Use force_updated_at in order to change the update time.

Return type:	int

validate()¶

version¶

The file format version.

Type:	tuple

class nixio.Block(nixfile, nixparent, h5group, compression=<Compression.Auto: 'Auto'>)¶

Bases: nixio.entity.Entity

create_data_array(name='', array_type='', dtype=None, shape=None, data=None, compression=<Compression.Auto: 'Auto'>, copy_from=None, keep_copy_id=True, label=None, unit=None)¶

Create/copy a new data array for this block. Either shape or data must be given. If both are given their shape must agree. If dtype is not specified it will default to 64-bit floating points.

Parameters:	name (str) – The name of the data array to create/copy. array_type (str) – The type of the data array. dtype (`numpy.dtype`) – Which data-type to use for storage shape (tuple of int or long) – Layout (dimensionality and extent) data (array-like data) – Data to write after storage has been created compression (`Compression`) – En-/disable dataset compression. copy_from (nixio.DataArray) – The DataArray to be copied, None in normal mode keep_copy_id (bool) – Specify if the id should be copied in copy mode label (str) – The label, defaults to None. unit (str) – The unit of the stored data. Defaults to None.
Returns:	The newly created data array.
Return type:	`DataArray`

create_data_frame(name='', type_='', col_dict=None, col_names=None, col_dtypes=None, data=None, compression=<Compression.No: 'None'>, copy_from=None, keep_copy_id=True)¶

Create/copy a new data frame for this block. Either col_dict or col_name and col_dtypes must be given. If both are given, col_dict will be used.

Parameters:	name (str) – The name of the data frame to create/copy. type (str) – The type of the data frame. col_dict (dict or OrderedDict of {str: type}) – The dictionary that specifies column names and data type in each column col_names (tuples or list or np.array of string) – The collection of name of all columns in order col_dtypes (tuples or list or np.array of type) – The collection of data type of all columns in order data (array-like data with compound data type as specified in the columns) – Data to write after storage has been created compression (`Compression`) – En-/disable dataset compression. copy_from (nixio.DataFrame) – The DataFrame to be copied, None in normal mode keep_copy_id (bool) – Specify if the id should be copied in copy mode
Returns:	The newly created data frame.
Return type:	`DataFrame`

create_group(name, type_)¶

Create a new group on this block.

Parameters:	name (str) – The name of the group to create. type (str) – The type of the group.
Returns:	The newly created group.
Return type:	nixio.Group

create_multi_tag(name='', type_='', positions=None, extents=None, copy_from=None, keep_copy_id=True)¶

Create/copy a new multi tag for this block.

Parameters:	name (str) – The name of the tag to create/copy. type (str) – The type of tag. positions (nixio.DataArray) – A data array defining all positions of the tag. copy_from (nixio.MultiTag) – The MultiTag to be copied, None in normal mode keep_copy_id (bool) – Specify if the id should be copied in copy mode
Returns:	The newly created tag.
Return type:	nixio.MultiTag

classmethod create_new(nixparent, h5parent, name, type_, compression)¶

create_source(name, type_)¶

Create a new source on this block.

Parameters:	name (str) – The name of the source to create. type (str) – The type of the source.
Returns:	The newly created source.
Return type:	nixio.Source

create_tag(name='', type_='', position=0, copy_from=None, keep_copy_id=True)¶

Create/copy a new tag for this block.

Parameters:	name (str) – The name of the tag to create/copy. type (str) – The type of tag. position – Coordinates of the start position in units of the respective data dimension. copy_from (nixio.Tag) – The Tag to be copied, None in normal mode keep_copy_id (bool) – Specify if the id should be copied in copy mode
Returns:	The newly created tag.
Return type:	nixio.Tag

data_arrays¶: A property containing all data arrays of a block. DataArray entities can be obtained via their index or by their id. Data arrays can be deleted from the list. Adding a data array is done using the Blocks create_data_array method. This is a read only attribute.

data_frames¶

find_sources(filtr=<function Block.<lambda>>, limit=None)¶

Get all sources in this block recursively.

This method traverses the tree of all sources in the block. The traversal is accomplished via breadth first and can be limited in depth. On each node or source a filter is applied. If the filter returns true the respective source will be added to the result list. By default a filter is used that accepts all sources.

Parameters:	filtr (function) – A filter function limit (int) – The maximum depth of traversal
Returns:	A list containing the matching sources.
Return type:	list of nixio.Source

groups¶: A property containing all groups of a block. Group entities can be obtained via their index or by their id. Groups can be deleted from the list. Adding a Group is done using the Blocks create_group method. This is a read only attribute.

metadata¶

Associated metadata of the entity. Sections attached to the entity via this attribute can provide additional annotations. This is an optional read-write property, and can be None if no metadata is available.

Type:	nixio.Section

multi_tags¶: A property containing all multi tags of a block. MultiTag entities can be obtained via their index or by their id. Tags can be deleted from the list. Adding tags is done using the Blocks create_multi_tag method. This is a read only attribute.

pprint(indent=2, max_length=120, extra=True, start_depth=0)¶

Pretty Printing the Data and MetaData Tree of the whole File

Parameters:	indent (int) – The length of one indentation space max_length (int) – Maximum length of each line of output extra (bool) – True to print extra information of Entities start_depth (int) – Starting depth of indentation

sources¶: A property containing all sources of a block. Sources can be obtained via their index or by their id. Sources can be deleted from the list. Adding sources is done using the Blocks create_source method. This is a read only attribute.

tags¶: A property containing all tags of a block. Tag entities can be obtained via their index or by their id. Tags can be deleted from the list. Adding tags is done using the Blocks create_tag method. This is a read only attribute.

class nixio.Group(nixfile, nixparent, h5group)¶

Bases: nixio.entity.Entity

classmethod create_new(nixfile, nixparent, h5parent, name, type_)¶

data_arrays¶: A property containing all data arrays referenced by the group. Referenced data arrays can be obtained by index or their id. References can be removed from the list, removing a referenced DataArray will not remove it from the file. New references can be added using the append method of the list. This is a read only attribute.

data_frames¶: A property containing all data frames referenced by the group. Referenced data frames can be obtained by index or their id. References can be removed from the list, removing a referenced DataFrame will not remove it from the file. New references can be added using the append method of the list. This is a read only attribute.

metadata¶

Associated metadata of the entity. Sections attached to the entity via this attribute can provide additional annotations. This is an optional read-write property, and can be None if no metadata is available.

Type:	nixio.Section

multi_tags¶: A property containing all MultiTags referenced by the group. MultiTags can be obtained by index or their id. MultiTags can be removed from the list, removing a referenced MultiTag will not remove it from the file. New MultiTags can be added using the append method of the list. This is a read only attribute.

sources¶: A property containing all Sources referenced by the Group. Sources can be obtained by index or their id. Sources can be removed from the list, but removing a referenced Source will not remove it from the file. New Sources can be added using the append method of the list. This is a read only attribute.

tags¶: A property containing all tags referenced by the group. Tags can be obtained by index or their id. Tags can be removed from the list, removing a referenced Tag will not remove it from the file. New Tags can be added using the append method of the list. This is a read only attribute.

class nixio.DataArray(nixfile, nixparent, h5group)¶

Bases: nixio.entity.Entity, nixio.data_set.DataSet

append_range_dimension(ticks=None, label=None, unit=None)¶

Append a new RangeDimension to the list of existing dimension descriptors.

Parameters:	ticks (list of float) – The ticks of the RangeDimension to create.
Returns:	The newly created RangeDimension.
Return type:	nixio.RangeDimension

append_range_dimension_using_self(index=None)¶

Convenience function to append a new RangeDimension to the list of existing dimensions that uses the DataArray itself as provider for the ticks. This is a replacement for rdim = array.append_range_dimension() rdim.link_data_array(self, index)

Parameters:	index – The slice of the DataArray that contains the tick values. This must be a vector of the data. Defaults to [-1], i.e. the full first dimension.
Type:	list of int
Returns:	the newly created nixio.RangeDimension
Return type:	nixio.RangeDimension

append_sampled_dimension(sampling_interval, label=None, unit=None, offset=None)¶

Append a new SampledDimension to the list of existing dimension descriptors.

Parameters:	sampling_interval (float) – The sampling interval of the SetDimension to create.
Returns:	The newly created SampledDimension.
Return type:	nixio.SampledDimension

append_set_dimension(labels=None)¶

Append a new SetDimension to the list of existing dimension descriptors.

Returns:	The newly created SetDimension.
Return type:	nixio.SetDimension

classmethod create_new(nixfile, nixparent, h5parent, name, type_, data_type, shape, compression)¶

data¶

DEPRECATED DO NOT USE ANYMORE! Returns self

Type:	`DataArray`

delete_dimensions()¶: Delete all the dimension descriptors for this DataArray.

dimensions¶

A property containing all dimensions of a DataArray. Dimensions can be obtained via their index. Adding dimensions is done using the respective append methods for dimension descriptors. This is a read only attribute.

Type:	Container of dimension descriptors.

dtype¶

The data type of the data stored in the DataArray. This is a read only property.

Returns:	The data type
Return type:	nixio.DataType

expansion_origin¶

The expansion origin of the calibration polynomial. This is a read-write property and can be set to None. The default value is 0.

Type:	float

get_slice(positions, extents=None, mode=<DataSliceMode.Index: 1>)¶

Reads a slice of the data. The slice can be specified either in indices or in data coordinates. For example, if the DataArray stores 1D data spanning one second in time sampled with 1kHz (1000 data points). If one wants to read the data of the interval 0.25 to 0.5 seconds, one can use either of the following statements:

```: interval_data = data_array.get_slice([250], [500], mode=DataSliceMode.Index)[:] interval_data = data_array.get_slice([0.25],[0.25], mode=DataSliceMode.Data)[:]

```

Note: The extents are not the end positions but the extent of the slice!

Parameters:	positions (list length must match dimensionality of the data.) – Specifies the start of the data slice. List of either indices or data positions depending on the DataSliceMode. extents (list, defaults to None) – Specifies the extents of the slice for each dimension. mode (nixio.DataSliceMode) – Specifies how positions and extents are interpreted, they are either treated as indices (DataSliceMode.Index) or as positions in data coordinates (DataSliceMode.Data), Defaults to nixio.DataSliceMode.Index.
Raises:	nixio.IncompatibleDimensions: if length of positions or, if given, extents does not match the rank of the data.
Raises:	ValueError: if an invalid slice mode is given
Returns:	A nixio.DataView object
Return type:	nixio.DataView

iter_dimensions()¶: 1-based index dimension iterator. The method returns a generator which returns the index starting from one and the dimensions.

label¶

The label of the DataArray. The label corresponds to the label of the x-axis of a plot. This is a read-write property and can be set to None.

Type:	str

metadata¶

Associated metadata of the entity. Sections attached to the entity via this attribute can provide additional annotations. This is an optional read-write property, and can be None if no metadata is available.

Type:	nixio.Section

polynom_coefficients¶

The polynomial coefficients for the calibration. By default this is set to a {0.0, 1.0} for a linear calibration with zero offset. This is a read-write property and can be set to None

Return type:	list of float

sources¶: A property containing all Sources referenced by the DataArray. Sources can be obtained by index or their id. Sources can be removed from the list, but removing a referenced Source will not remove it from the file. New Sources can be added using the append method of the list. This is a read only attribute.

unit¶

The unit of the values stored in the DataArray. This is a read-write property and can be set to None.

Type:	str

class nixio.DataFrame(nixfile, nixparent, h5group)¶

Bases: nixio.entity.Entity, nixio.data_set.DataSet

append_column(column, name, datatype=None)¶

Append a new column to the DataFrame In case of string, it will be better to set explicitly the datatype.

Parameters:	column (array-like data) – The new column name (str) – The name of new column datatype (nixio.DataType) – The DataType of new column

append_rows(data)¶

Append a new row to the DataFrame. The data supplied must be iterable.

Parameters:	data (array-like data) – The new row

column_names¶

The dtype is the list of names of all columns in the DatFrame. This is a read only property.

Type:	list of str

columns¶

The dtype is the list of names and data types of all columns in the DatFrame. This is a read only property.

Type:	list of tuples

classmethod create_new(nixfile, nixparent, h5parent, name, type_, shape, col_dtype, compression)¶

df_shape¶

The df_shape is the shape of the DataFrame in (number of rows, number of columns) format. This is a read only property.

Type:	tuple

dtype¶

The dtype is the list of DataTypes of all columns in the DatFrame. This is a read only property.

Type:	list of DataType

metadata¶

Associated metadata of the entity. Sections attached to the entity via this attribute can provide additional annotations. This is an optional read-write property, and can be None if no metadata is available.

Type:	nixio.Section

print_table(row_sl=None, col_sl=None)¶

Print the whole DataFrame as a table

Parameters:	row_sl (slice or iterable of int) – Rows to be printed; None for printing all rows col_sl (slice or iterable of int) – Columns to be printed; None for printing all columns

read_cell(position=None, col_name=None, row_idx=None)¶

Read a cell in the DataFrame

Parameters:	position (tuple or list or array with length 2) – Position of the targeted cell col_name (str) – The column name in which the targeted cell belongs to row_idx (list of int) – A length 1 list that specify on which row the targeted cell is located

read_columns(index=None, name=None, slc=None, group_by_cols=False)¶

Read one or multiple (part of) column(s) in the DataFrame

Parameters:	index (list of int) – Index of column(s) to be returned name (list of str) – Name of column(s) to be returned slc (slice) – The part of each column to be returned group_by_cols (bool) – True for group return values by columns, False for group by rows. Only applicable for reading multiple columns

read_rows(index)¶

Read one or multiple row(s) in the DataFrame

Parameters:	index (list of int) – Index of row(s) to be returned

row_count()¶: Return the total number of rows

units¶

The unit of the values stored in the DataFrame. This is a read-write property and can be set to None.

Type:	array of str

write_cell(cell, position=None, col_name=None, row_idx=None)¶

Overwrite a cell in the DataFrame

Parameters:	cell (same type as the specified column) – The new cell position (tuple or list or array with length 2) – Position of the targeted cell col_name (str) – The column name in which the targeted cell belongs to row_idx (list of int) – A length 1 list that specify on which row the targeted cell is located

write_column(column, index=None, name=None)¶

Overwrite an existing column. Either index or name of the column should be provided.

Parameters:	column (array-like data) – The new column index (string) – The index of the column that is written to name (str) – The name of the column that is written to

write_rows(rows, index)¶

Overwrite one or multiple existing row(s)

Parameters:	rows ((nested) array-like data) – The new rows(s) and their data index (list of int) – Index of rows(s) to be overwritten

write_to_csv(filename, mode='w')¶

Export the whole DataFrame to a CSV file

Parameters:	filename (str) – The resulted/ targeted CSV file to write to/ create mode (str) – The column name in which the targeted cell belongs to

class nixio.Tag(nixfile, nixparent, h5group)¶

Bases: nixio.tag.BaseTag

classmethod create_new(nixfile, nixparent, h5parent, name, type_, position)¶

extent¶

The extent defined by the tag. This is an optional read-write property and may be set to None.

Type:	list of float

feature_data(featidx, stop_rule=<SliceMode.Exclusive: 'exclusive'>)¶

metadata¶

Associated metadata of the entity. Sections attached to the entity via this attribute can provide additional annotations. This is an optional read-write property, and can be None if no metadata is available.

Type:	nixio.Section

position¶

The position defined by the tag. This is a read-write property.

Type:	list of float

references¶

A property containing all data arrays referenced by the tag. Referenced data arrays can be obtained by index or their id. References can be removed from the list, removing a referenced DataArray will not remove it from the file. New references can be added using the append method of the list. This is a read only attribute.

Type:	Container of nixio.DataArray

retrieve_data(refidx)¶

retrieve_feature_data(featidx)¶

sources¶: A property containing all Sources referenced by the Tag. Sources can be obtained by index or their id. Sources can be removed from the list, but removing a referenced Source will not remove it from the file. New Sources can be added using the append method of the list. This is a read only attribute.

tagged_data(refidx, stop_rule=<SliceMode.Exclusive: 'exclusive'>)¶

class nixio.MultiTag(nixfile, nixparent, h5group)¶

Bases: nixio.tag.BaseTag

classmethod create_new(nixfile, nixparent, h5parent, name, type_, positions)¶

extents¶

The extents defined by the tag. This is an optional read-write property and may be set to None.

Type:	nixio.DataArray or None

feature_data(posidx, featidx, stop_rule=<SliceMode.Exclusive: 'exclusive'>)¶

metadata¶

Associated metadata of the entity. Sections attached to the entity via this attribute can provide additional annotations. This is an optional read-write property, and can be None if no metadata is available.

Type:	nixio.Section

positions¶

The positions defined by the tag. This is a read-write property.

Type:	nixio.DataArray

references¶

A property containing all data arrays referenced by the tag. Referenced data arrays can be obtained by index or their id. References can be removed from the list, removing a referenced DataArray will not remove it from the file. New references can be added using the append method of the list. This is a read only attribute.

Type:	nixio.LinkContainer of nixio.DataArray

retrieve_data(posidx, refidx)¶

retrieve_feature_data(posidx, featidx)¶

sources¶: A property containing all Sources referenced by the MultiTag. Sources can be obtained by index or their id. Sources can be removed from the list, but removing a referenced Source will not remove it from the file. New Sources can be added using the append method of the list. This is a read only attribute.

tagged_data(posidx, refidx, stop_rule=<SliceMode.Exclusive: 'exclusive'>)¶

class nixio.Source(nixfile, nixparent, h5group)¶

Bases: nixio.entity.Entity

classmethod create_new(nixfile, nixparent, h5parent, name, type_)¶

create_source(name, type_)¶

Create a new source as a child of the current Source.

Parameters:	name (str) – The name of the source to create. type (str) – The type of the source.
Returns:	The newly created source.
Return type:	nixio.Source

find_sources(filtr=<function Source.<lambda>>, limit=None)¶

Get all child sources of this source recursively.

This method traverses the tree of all sources. The traversal is accomplished via breadth first and can be limited in depth. On each node or source a filter is applied. If the filter returns true the respective source will be added to the result list. By default a filter is used that accepts all sources.

Parameters:	filtr (function) – A filter function limit (int) – The maximum depth of traversal
Returns:	A list containing the matching sources.
Return type:	list of nixio.Source

metadata¶

Associated metadata of the entity. Sections attached to the entity via this attribute can provide additional annotations. This is an optional read-write property, and can be None if no metadata is available.

Type:	nixio.Section

parent_block¶

Returns the block this source is contained in.

Returns:	the Block containing this source
Return type:	nixio.Block

parent_source¶

Get the parent source of this source. If this source is at the root, None will be returned

Returns:	the parent source
Return type:	Source or None

referring_data_arrays¶

Returns all DataArray entities linking to this source.

Returns:	all DataArrays referring to this source.
Return type:	list

referring_multi_tags¶

Returns all MultiTag entities linking to this source.

Returns:	all MultiTags referring to this source.
Return type:	list

referring_objects¶

Returns the list of entities that link to this source.

Returns:	all objects referring to this source.
Return type:	list

referring_tags¶

Returns all Tag entities linking to this source.

Returns:	all Tags referring to this source.
Return type:	list

sources¶: A property containing child sources of a Source. Sources can be obtained via their name, index, id. Sources can be deleted from the list. Adding sources is done using the Blocks create_source method. This is a read only attribute.

class nixio.Section(nixfile, nixparent, h5group)¶

Bases: nixio.entity.Entity

copy_section(obj, children=True, keep_id=True, name='')¶

Copy a section to the section.

Parameters:	obj (nixio.Section) – The Section to be copied children (bool) – Specify if the copy should be recursive keep_id (bool) – Specify if the id should be kept name (str) – Name of copied section, Default is name of source section
Returns:	The copied section
Return type:	nixio.Section

classmethod create_new(nixfile, nixparent, h5parent, name, type_, oid=None)¶

create_property(name='', values_or_dtype=0, oid=None, copy_from=None, keep_copy_id=True)¶

Add a new property to the section.

Parameters:	name (str) – The name of the property to create/copy. values_or_dtype (list of values or a nixio.DataType) – The values of the property or a valid DataType. oid (str) – object id, UUID string as specified in RFC 4122. If no id is provided, an id will be generated and assigned. copy_from (nixio.Property) – The Property to be copied, None in normal mode keep_copy_id (bool) – Specify if the id should be copied in copy mode
Returns:	The newly created property.
Return type:	nixio.Property

create_section(name, type_='undefined', oid=None)¶

Creates a new subsection that is a child of this section entity.

Parameters:	name (str) – The name of the section to create. type (str) – The type of the section. oid (str) – object id, UUID string as specified in RFC 4122. If no id is provided, an id will be generated and assigned.
Returns:	The newly created section.
Return type:	nixio.Section

find_related(filtr=<function Section.<lambda>>)¶

Get all related sections of this section.

The result can be filtered. On each related section a filter is applied. If the filter returns true the respective section will be added to the result list. By default a filter is used that accepts all sections.

Parameters:	filtr (function) – A filter function
Returns:	A list containing the matching related sections.
Return type:	list of nixio.Section

find_sections(filtr=<function Section.<lambda>>, limit=None)¶

Get all child sections recursively. This method traverses the trees of all sections. The traversal is accomplished via breadth first and can be limited in depth. On each node or section a filter is applied. If the filter returns true the respective section will be added to the result list. By default a filter is used that accepts all sections.

Parameters:	filtr (function) – A filter function limit (int) – The maximum depth of traversal
Returns:	A list containing the matching sections.
Return type:	list of nixio.Section

inherited_properties()¶

items()¶

link¶

Link to another section. If a section is linked to another section, the linking section inherits all properties from the target section. This is an optional read-write property and may be set to None.

Type:	nixio.Section

parent¶

The parent section. This is a read-only property. For root sections this property is always None.

Accessing this property can be slow when the metadata tree is large.

Type:	nixio.Section

pprint(indent=2, max_depth=1, max_length=80, current_depth=0)¶

Pretty print method.

Parameters:	indent (int) – The number of indentation spaces per recursion max_depth (int) – The maximum times of recursion max_length (int) – The maximum length of each line of output current_depth (int) – The current times of recursion

props¶

A property containing all Property entities associated with the section. Properties can be accessed by name, index, or id. Properties can be deleted from the list. Adding new Properties is done using the create_property method. This is a read-only attribute.

Type:	Container of nixio.Property

reference¶

referring_blocks¶

referring_data_arrays¶

referring_groups¶

referring_multi_tags¶

referring_objects¶

referring_sources¶

referring_tags¶

repository¶

URL to the terminology repository the section is associated with. This is an optional read-write property and may be set to None.

Type:	str

sections¶

A property providing all child Sections of a Section. Child sections can be accessed by name, index, or id. Sections can also be deleted: if a Section is deleted, all its properties and child Sections are removed from the file too. Adding new Sections is achieved using the create_section method. This is a read-only attribute.

Type:	Container of nixio.Section

class nixio.S(section_type, section=None)¶: Bases: object

class nixio.Feature(nixfile, nixparent, h5group)¶

Bases: object

classmethod create_new(nixfile, nixparent, h5parent, data, link_type)¶

created_at¶

The creation time of the entity. This is a read-only property. Use force_created_at in order to change the creation time.

Return type:	int

data¶

file¶

id¶

link_type¶

updated_at¶

The time of the last update of the entity. This is a read-only property. Use force_updated_at in order to change the update time.

Return type:	int

class nixio.Property(nixfile, nixparent, h5dataset)¶

Bases: nixio.entity.Entity

An odML Property

classmethod create_new(nixfile, nixparent, h5parent, name, dtype, shape=None, oid=None)¶

data_type¶

definition¶

The definition of the entity. The definition can contain a textual description of the entity. This is an optional read-write property, and can be None if no definition is available.

Type:	str

delete_values()¶

dependency¶

dependency_value¶

extend_values(data)¶: Extends values to existing data. Suitable when new data is nested or original data is long.

name¶

The name of an entity. The name serves as a human readable identifier. This is a read-only property; entities cannot be renamed.

Type:	str

odml_type¶

pprint(indent=2, max_length=80, current_depth=-1)¶: Pretty print method. Method is called in Section.pprint()

reference¶

uncertainty¶

unit¶

value_origin¶

values¶

class nixio.OdmlType¶

Bases: enum.Enum

OdmlType provides all types currently supported by the odML data format. It provides additional information about the nature of the values of an odML Property.

Boolean = 'boolean'¶

Date = 'date'¶

Datetime = 'datetime'¶

Float = 'float'¶

Int = 'int'¶

Person = 'person'¶

String = 'string'¶

Text = 'text'¶

Time = 'time'¶

URL = 'url'¶

compatible(value)¶

compatible returns True or False depending on whether a passed value can be mapped to an OdmlType or not.

Parameters:	value – Any single value
Returns:	Boolean

get_odml_type = <bound method OdmlType.get_odml_type of <enum 'OdmlType'>>¶

class nixio.SampledDimension(data_array, index)¶

Bases: nixio.dimensions.Dimension

axis(count, start=None, start_position=None)¶

Get an axis as defined by this nixio.SampledDimension. It either starts at the offset of the dimension, a number of sample points later, or at a given position. The latter must not be less than the offset. If start and start_position are given, start takes precedence.

Parameters:	count (int) – A positive integer specifying the length of the axis (no of samples). start (int) – positive integer, indicates the starting sample. Defaults to None. Precedes over the start_position. start_position (double) – The start position of the axis. Defaults to None.
Raises:	ValueError if start is negative or if the start_position is given and is less than offset.
Returns:	The created axis
Return type:	tuple

classmethod create_new(data_array, index, sample)¶

index_of(position, mode=<IndexMode.LessOrEqual: 'leq'>)¶

Returns the index of a certain position in the dimension. Raises IndexError if the position is out of bounds (depending on mode).

Parameters:	position – The position. mode – The IndexMode to use (default LessOrEqual). The default value (LessOrEqual) will return the index of the position calculated based on the dimension offset and sampling_interval if it matches a dimension tick exactly. If it does not match a tick, the previous index is returned. If the mode is Less, the previous index of the calculated position is always returned. If the mode is GreaterOrEqual and the calculated position does not match a tick exactly, the next index is returned.
Returns:	The matching index.
Return type:	int

label¶

link_data_array(*_)¶

link_data_frame(*_)¶

offset¶

position_at(index)¶

Returns the position corresponding to a given index.

Parameters:	index – A positive integer.
Returns:	The position matching to the index.
Return type:	float

sampling_interval¶

unit¶

class nixio.RangeDimension(data_array, index)¶

Bases: nixio.dimensions.Dimension

axis(count, start=0)¶

Get an axis as defined by this range dimension.

Parameters:	count – A positive integer specifying the length of the axis (no of points). start – positive integer, indicates the starting tick.
Returns:	The created axis
Return type:	list

classmethod create_new(data_array, index, ticks)¶

index_of(position, mode=<IndexMode.LessOrEqual: 'leq'>)¶

Returns the index of a certain position in the dimension. Raises IndexError if the position is out of bounds (depending on mode).

Parameters:	position – The position. mode – The IndexMode to use (default LessOrEqual). The default value (LessOrEqual) will return the index of the position that matches a tick if it matches a dimension tick exactly. If it does not match a tick, the previous index is returned. If the mode is Less, the previous index of the matching tick is always returned. If the mode is GreaterOrEqual and the position does not match a tick exactly, the next index is returned.
Returns:	The matching index
Return type:	int

is_alias¶

In versions < 1.5 a RangeDimension that was referring to the DataArray it describes was called an AliasRangeDimension. This has been made more flexible by allowing to link to any DataArray or DataFrame. For downward compatibility this method has been re-introduced in 1.5.1.

Returns:	True, if this dimension links to a DataArray, False otherwise
Return type:	bool

label¶

link_data_array(data_array, index)¶

link_data_frame(data_frame, index)¶

tick_at(index)¶

Returns the tick at the given index. Will throw an Exception if the index is out of bounds.

Parameters:	index – The index.
Returns:	The corresponding position.
Return type:	double

ticks¶

unit¶

class nixio.SetDimension(data_array, index)¶

Bases: nixio.dimensions.Dimension

classmethod create_new(data_array, index)¶

index_of(position, mode=<IndexMode.LessOrEqual: 'leq'>)¶

Returns the index of a certain position in the dimension. Raises IndexError if the position is out of bounds (depending on mode and number of labels).

Parameters:	position – The position. mode – The IndexMode to use (default LessOrEqual). The modes LessOrEqual and GreaterOrEqual will return the integer representation of the position if it is equal to the nearest integer. If the position is not an integer (or is not equal to the nearest integer), then the value is rounded down (for LessOrEqual) or rounded up (for GreaterOrEqual). If the mode is Less, the previous integer is always returned.
Returns:	The matching index
Return type:	int

labels¶

class nixio.FileMode¶

Bases: object

Overwrite = 'w'¶

ReadOnly = 'r'¶

ReadWrite = 'a'¶

class nixio.DataSliceMode¶

Bases: enum.Enum

An enumeration.

Data = 2¶

Index = 1¶

class nixio.DataType¶

Bases: object

Bool¶: alias of numpy.bool_

Double¶: alias of numpy.float64

Float¶: alias of numpy.float32

FloatTypes = (<class 'numpy.float32'>, <class 'numpy.float64'>)¶

Int16¶: alias of numpy.int16

Int32¶: alias of numpy.int32

Int64¶: alias of numpy.int64

Int8¶: alias of numpy.int8

IntTypes = (<class 'numpy.int8'>, <class 'numpy.int16'>, <class 'numpy.int32'>, <class 'numpy.int64'>, <class 'numpy.uint8'>, <class 'numpy.uint16'>, <class 'numpy.uint32'>, <class 'numpy.uint64'>)¶

String¶: alias of numpy.str_

UInt16¶: alias of numpy.uint16

UInt32¶: alias of numpy.uint32

UInt64¶: alias of numpy.uint64

UInt8¶: alias of numpy.uint8

classmethod get_dtype(value)¶

classmethod is_numeric_dtype(dtype)¶

class nixio.DimensionType¶

Bases: enum.Enum

An enumeration.

Range = 'range'¶

Sample = 'sample'¶

Set = 'set'¶

class nixio.LinkType¶

Bases: enum.Enum

An enumeration.

Indexed = 'indexed'¶

Tagged = 'tagged'¶

Untagged = 'untagged'¶

class nixio.Compression¶

Bases: enum.Enum

An enumeration.

Auto = 'Auto'¶

DeflateNormal = 'DeflateNormal'¶

No = 'None'¶

class nixio.SliceMode¶

Bases: enum.Enum

An enumeration.

Exclusive = 'exclusive'¶

Inclusive = 'inclusive'¶

to_index_mode()¶

class nixio.IndexMode¶

Bases: enum.Enum

IndexMode is used to define the behaviour of the index_of() methods.

GEQ = 'geq'¶

GreaterOrEqual = 'geq'¶

LEQ = 'leq'¶

Less = 'less'¶

LessOrEqual = 'leq'¶