High Level API Reference¶

File¶

A File represents a specific data source of a NIX back-end for example an NIX HDF5 file. All entities of the nix data model must exist in the context of an open File object. Therefore NIX entities can’t be initialized via their constructors but only through the factory methods of their respective parent entity.

Working with files¶

file = File.open("test.h5", FileMode.ReadWrite)
# do some work
file.close()

File open modes¶

class nixio.FileMode¶

Overwrite = 'w'¶

ReadOnly = 'r'¶

ReadWrite = 'a'¶

File API¶

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

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

Block¶

The Block entity is a top-level, summarizing element that allows to group the other data entities belonging for example to the same recording session. All data entities such as Source, DataArray, DataFrame, Tag and MultiTag have to be associated with one Block.

Create a new Block¶

A block can only be created on an existing file object. Do not use the blocks constructors for this purpose.

block = file.create_block("session one", "recordingsession");

Working with blocks¶

After a block was created it can be used to create further entities. See the documentation of Source, DataArray, DataFrame, Tag and MultiTag for more information. The next example shows how some properties of a block can be accessed.

block = file.blocks[some_id]

# add metadata to a block
section = file.sections[sec_id]
block.metadata = section

# get associated metadata from a block
block.metadata

# remove associated metadata from a block
block.metadata = None

Deleting a block¶

When a block is deleted from a file all contained data e.g. sources, data arrays and tags will be removed too.

del file.blocks[some_id]

Block API¶

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

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

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_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¶

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

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

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.

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.

id¶

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

Return 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

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.

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

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.

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

DataArray¶

The DataArray is the core entity of the NIX data model, its purpose is to store arbitrary n-dimensional data. In addition to the common fields id, name, type, and definition the DataArray stores sufficient information to understand the physical nature of the stored data.

A guiding principle of the data model is provides enough information to create a plot of the stored data. In order to do so, the DataArray defines a property dataType which provides the physical type of the stored data (for example 16 bit integer or double precision IEEE floatingpoint number). The property unit specifies the SI unit of the values stored in the DataArray whereas the label defines what is given in this units. Together, both specify what corresponds to the the y-axis of a plot.

In some cases it is much more efficient or convenient to store data not as floating point numbers but rather as (16 bit) integer values as, for example read from a data acquisition board. In order to convert such data to the correct values, we follow the approach taken by the comedi data-acquisition library (http://www.comedi.org) and provide polynomCoefficients and an expansionOrigin.

Create and delete a DataArray¶

A DataArray can only be created at an existing block. Do not use the DataArrays constructors for this purpose.

data_array = block.crate_data_array("matrix", "data");
del block.data_arrays[data_array]

DataArray API¶

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

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

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)¶

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¶

DEPRECATED DO NOT USE ANYMORE! Returns self

Type:	`DataArray`

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

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_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

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.

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

id¶

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

Return type:	str

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

len()¶

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

Type:	int or long

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

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

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

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

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.

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

unit¶

The unit of the values stored in the DataArray. This is a read-write property and can 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

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

DataSet¶

The DataSet object is used for data input/output to the underlying storage.

class nixio.data_array.DataSet¶

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

DataFrame¶

The DataFrame presents data in a rows-and-columns format.

Create and delete a DataFrame¶

data_array = block.create_data_frame("table", "df", col_dict={}, data=[]);
del block.data_frames[data_frame]

DataFrame API¶

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

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

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)¶

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_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

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

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

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

len()¶

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

Type:	int or long

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

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

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_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

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

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

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

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

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

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_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

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

Tags¶

Besides the DataArray the tag entities can be considered as the other core entities of the data model. They are meant to attach annotations directly to the data and to establish meaningful links between different kinds of stored data. Most importantly tags allow the definition of points or regions of interest in data that is stored in other DataArray entities. The data array entities the tag applies to are defined by its property references.

Further the referenced data is defined by an origin vector called position and an optional extent vector that defines its size. Therefore position and extent of a tag, together with the references field defines a group of points or regions of interest collected from a subset of all available DataArray entities.

Further tags have a field called features which makes it possible to associate other data with the tag. Semantically a feature of a tag is some additional data that contains additional information about the points of hyperslabs defined by the tag. This could be for example data that represents a stimulus (e.g. an image or a signal) that was applied in a certain interval during the recording.

Tag API¶

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

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

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

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

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'>)¶

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.

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

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

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

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'>)¶

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

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

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

MultiTag API¶

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

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

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

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

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'>)¶

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.

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

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

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

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'>)¶

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

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

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

Source¶

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

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

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

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

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

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

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

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.

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

Group¶

Groups establish a simple way of grouping entities that in some way belong together. The Group exists inside a Block and can contain (link) DataArrays, Tags, and MultiTags. As any other nix-entity, the Groups is named, has a type, and a definition property. Additionally, it contains data_arrays, tags, and multi_tags lists. As indicated before, the group does only link the entities. Thus, deleting elements from the lists does not remove them from file, it merely removes the link from the group.

data_array = block.create_data_array("matrix", "data");
tag = block.create_tag("a tag", "event", [0.0, 1.0])
group = block.create_group("things that belong together", "group")
group.tags.append(tag)
group.data_arrays.append(data_array)

del group.data_arrays[data_array]
del group.tags[tag]

Group API¶

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

classmethod create_new(nixfile, nixparent, h5parent, name, 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_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.

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

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.

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

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.

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

Section¶

Metadata stored in a NIX file can be accessed directly from an open file.

Create and delete sub sections¶

sub = section.create_section("a name", "type")
del section.sections[sub]

Add and remove properties¶

Properties can be created using the create_property method. Existing properties can be accessed and deleted directly from the respective section.

section.create_property("one", [1])
section.create_property("two", [2])

# iterate over properties
for p in section:
   print(p)

# access by name
one = section["one"]

# convert properties into a dict
dct = dict(section.items())

# delete properties
del section["one"]
del section["two"]

Section API¶

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

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

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

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

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

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

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

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

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

Property¶

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

An odML Property

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

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.

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

odml_type¶

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

reference¶

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

uncertainty¶

unit¶

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

value_origin¶

values¶