8.6.4. pymodaq_data.data module

Created the 28/10/2022

@author: Sebastien Weber

exception pymodaq_data.data.DataDimError[source]: Bases: Exception

exception pymodaq_data.data.DataDimWarning[source]: Bases: Warning

exception pymodaq_data.data.DataIndexWarning[source]: Bases: Warning

exception pymodaq_data.data.DataLengthError[source]: Bases: Exception

exception pymodaq_data.data.DataShapeError[source]: Bases: Exception

exception pymodaq_data.data.DataSizeWarning[source]: Bases: Warning

exception pymodaq_data.data.DataTypeWarning[source]: Bases: Warning

exception pymodaq_data.data.DataUnitError[source]: Bases: Exception

pymodaq_data.data.warning: alias of DataSizeWarning

class pymodaq_data.data.AxesManagerBase(data_shape, axes, nav_indexes=None, sig_indexes=None, **kwargs)[source]

Bases: object

Attributes:

axes
nav_axes
nav_indexes
nav_shape
shape
sig_indexes
sig_shape

Methods

`get_axes_index`()	Get the index list from the axis objects
`get_axis_from_index_spread`(index, spread_order)	Only valid for Spread data
`get_nav_axes`()	Get the navigation axes corresponding to the data
`get_shape_from_index`(index)	Get the data shape at the given index
`get_sorted_index`([axis_index, spread_index])	Get the index to sort the specified axis
`is_axis_navigation`(axis)	Check if an axis is considered signal or navigation
`is_axis_signal`(axis)	Check if an axis is considered signal or navigation

append_axis
compute_shape_from_axes
compute_sig_indexes
get_axis_from_index
get_signal_axes

append_axis(axis)[source]

abstractmethod compute_shape_from_axes()[source]

compute_sig_indexes()[source]

get_axes_index()[source]

Get the index list from the axis objects

Return type:: List[int]

abstractmethod get_axis_from_index(index, create=False)[source]

Return type:: List[Axis]

get_axis_from_index_spread(index, spread_order)[source]

Only valid for Spread data

Return type:: Axis

get_nav_axes()[source]

Get the navigation axes corresponding to the data

Use get_axis_from_index for all index in self.nav_indexes, but in spread distribution, one index may correspond to multiple nav axes, see Spread data distribution

Return type:: List[Axis]

abstractmethod get_shape_from_index(index)[source]

Get the data shape at the given index

Return type:: int

get_signal_axes()[source]

abstractmethod get_sorted_index(axis_index=0, spread_index=0)[source]

Get the index to sort the specified axis

Parameters:

axis_index (int) – The index along which one should sort the data
spread_index (int) – for spread data only, specifies which spread axis to use

Return type:

Tuple[ndarray, Tuple[slice]]

Returns:

np.ndarray (the sorted index from the specified axis)
tuple of slice – used to slice the underlying data

is_axis_navigation(axis)[source]

Check if an axis is considered signal or navigation

Return type:: bool

is_axis_signal(axis)[source]

Check if an axis is considered signal or navigation

Return type:: bool

property axes

property nav_axes: List[int]

property nav_indexes: Iterable[int]

property nav_shape: tuple

property shape: Tuple[int]

property sig_indexes: Iterable[int]

property sig_shape: tuple

class pymodaq_data.data.AxesManagerSpread(*args, **kwargs)[source]

Bases: AxesManagerBase

For this particular data category, some explanation is needed, see example below:

Examples

One take images data (20x30) as a function of 2 parameters, say xaxis and yaxis non-linearly spaced on a regular grid.

data.shape = (150, 20, 30) data.nav_indexes = (0,)

The first dimension (150) corresponds to the navigation (there are 150 non uniform data points taken) The second and third could correspond to signal data, here an image of size (20x30) so: * nav_indexes is (0, ) * sig_indexes are (1, 2)

xaxis = Axis(name=xaxis, index=0, data…) length 150 yaxis = Axis(name=yaxis, index=0, data…) length 150

In fact from such a data shape the number of navigation axes in unknown . In our example, they are 2. To somehow keep track of some ordering in these navigation axes, one adds an attribute to the Axis object: the spread_order xaxis = Axis(name=xaxis, index=0, spread_order=0, data…) length 150 yaxis = Axis(name=yaxis, index=0, spread_order=1, data…) length 150

Methods

`compute_shape_from_axes`()	Get data shape from axes
`get_axis_from_index`(index[, create])	in spread mode, different nav axes have the same index (but not the same spread_order integer value) so may return multiple axis
`get_axis_from_index_spread`(index, spread_order)
`get_shape_from_index`(index)	Get the data shape at the given index
`get_sorted_index`([axis_index, spread_index])	Get the index to sort the specified axis

compute_shape_from_axes()[source]

Get data shape from axes

First get the nav length from one of the navigation axes Then check for signal axes

get_axis_from_index(index, create=False)[source]

in spread mode, different nav axes have the same index (but not the same spread_order integer value) so may return multiple axis

No possible “linear” creation in this mode except if the index is a signal index

Return type:: List[Axis]

get_axis_from_index_spread(index, spread_order)[source]

Return type:: Axis

get_shape_from_index(index)[source]

Get the data shape at the given index

Return type:: int

get_sorted_index(axis_index=0, spread_index=0)[source]

Get the index to sort the specified axis

Parameters:

axis_index (int) – The index along which one should sort the data
spread_index (int) – for spread data only, specifies which spread axis to use

Return type:

Tuple[ndarray, Tuple[slice]]

Returns:

np.ndarray (the sorted index from the specified axis)
tuple of slice – used to slice the underlying data

class pymodaq_data.data.AxesManagerUniform(*args, **kwargs)[source]

Bases: AxesManagerBase

Methods

`get_axis_from_index`(index[, create])	Get the axis referred by a given data dimensionality index
`get_axis_from_index_spread`(index, spread_order)	in spread mode, different nav axes have the same index (but not the same spread_order integer value)
`get_shape_from_index`(index)	Get the data shape at the given index
`get_sorted_index`([axis_index, spread_index])	Get the index to sort the specified axis

compute_shape_from_axes

compute_shape_from_axes()[source]

get_axis_from_index(index, create=False)[source]

Get the axis referred by a given data dimensionality index

If the axis is absent, create a linear one to fit the data shape if parameter create is True

Parameters:

index (int) – The index referring to the data ndarray shape
create (bool) – If True and the axis referred by index has not been found in axes, create one

Returns:

List[Axis] or None

Return type:

List[Axis]

See also

Axis.create_linear_data()

get_axis_from_index_spread(index, spread_order)[source]

in spread mode, different nav axes have the same index (but not the same spread_order integer value)

Return type:: Axis

get_shape_from_index(index)[source]

Get the data shape at the given index

Return type:: int

get_sorted_index(axis_index=0, spread_index=0)[source]

Get the index to sort the specified axis

Parameters:

axis_index (int) – The index along which one should sort the data
spread_index (int) – for spread data only, specifies which spread axis to use

Return type:

Tuple[ndarray, Tuple[slice]]

Returns:

np.ndarray (the sorted index from the specified axis)
tuple of slice – used to slice the underlying data

class pymodaq_data.data.Axis(label='', units='', data=None, index=0, scaling=None, offset=None, size=None, spread_order=0)[source]

Bases: SerializableBase

Object holding info and data about physical axis of some data

In case the axis’s data is linear, store the info as a scale and offset else store the data

Parameters:

label (str) – The label of the axis, for instance ‘time’ for a temporal axis
units (str) – The units of the data in the object, for instance ‘s’ for seconds
data (ndarray) – A 1D ndarray holding the data of the axis
index (int) – an integer representing the index of the Data object this axis is related to
scaling (float) – The scaling to apply to a linspace version in order to obtain the proper scaling
offset (float) – The offset to apply to a linspace/scaled version in order to obtain the proper axis
size (int) – The size of the axis array (to be specified if data is None)
spread_order (int) – An integer needed in the case where data has a spread DataDistribution. It refers to the index along the data’s spread_index dimension

Examples

>>> axis = Axis('myaxis', units='seconds', data=np.array([1,2,3,4,5]), index=0)

Attributes:

data: np.ndarray: get/set the data of Axis
index: int: get/set the index this axis corresponds to in a DataWithAxis object
label: str: get/set the label of this axis
offset
scaling
size: int: get/set the size/length of the 1D ndarray
units: str: get/set the units for this axis without conversion (equivalent to

Methods

`create_linear_data`(nsteps)	replace the axis data with a linear version using scaling and offset
`deserialize`(bytes_str)	Convert bytes into an Axis object
`find_index`(threshold)	find the index of the threshold value within the axis
`flip`()	flip the direction of the axis
`force_units`(units)	Change immediately the units to whatever else.
`get_data`()	Convenience method to obtain the axis data (usually None because scaling and offset are used)
`get_data_at`(indexes)	Get data at specified indexes
`get_quantity`()	Convenience method to obtain the numerical data as a quantity array
`get_scale_offset_from_data`([data])	Get the scaling and offset from the axis's data
`serialize`(axis)	Convert an Axis object into a bytes message together with the info to convert it back

as_dwa
copy
create_simple_linear_data
find_indexes
from_quantity
is_axis_linear
max
mean
min
to_base_units
to_reduced_units
units_as

static create_simple_linear_data(nsteps)[source]

static deserialize(bytes_str)[source]

Convert bytes into an Axis object

Convert the first bytes into an Axis reading first information about the Axis

Return type:

Tuple[Axis, bytes]

Returns:

Axis (the decoded Axis)
bytes (the remaining bytes string if any)

static from_quantity(quantity, label='axis', index=0)[source]

static serialize(axis)[source]

Convert an Axis object into a bytes message together with the info to convert it back

Parameters:: axis (Axis)
Returns:: bytes
Return type:: the total bytes message to serialize the Axis

Notes

The bytes sequence is constructed as:

serialize the axis label
serialize the axis units
serialize the axis array
serialize the axis
serialize the axis spread_order

as_dwa(set_itself_as_axis=False)[source]

Return type:: DataWithAxes

copy()[source]

create_linear_data(nsteps)[source]: replace the axis data with a linear version using scaling and offset

find_index(threshold)[source]

find the index of the threshold value within the axis

Return type:: int

find_indexes(thresholds)[source]

Return type:: Iterable[int]

flip()[source]: flip the direction of the axis

force_units(units)[source]: Change immediately the units to whatever else. Use this with care!

get_data()[source]

Convenience method to obtain the axis data (usually None because scaling and offset are used)

Return type:: ndarray

get_data_at(indexes)[source]

Get data at specified indexes

Parameters:: indexes (Union[int, Iterable, slice])
Return type:: ndarray

get_quantity()[source]

Convenience method to obtain the numerical data as a quantity array

Return type:: Quantity

get_scale_offset_from_data(data=None)[source]

Get the scaling and offset from the axis’s data

If data is not None, extract the scaling and offset

Parameters:: data (ndarray)

is_axis_linear(data=None)[source]

max()[source]

mean()[source]

min()[source]

to_base_units(inplace=False)[source]

to_reduced_units(inplace=False)[source]

units_as(units, inplace=True, context=None, **context_kwargs)[source]

base_type = 'Axis'

property data

get/set the data of Axis

Type:: np.ndarray

property index: int

get/set the index this axis corresponds to in a DataWithAxis object

Type:: int

property label: str

get/set the label of this axis

Type:: str

property offset

property scaling

property size: int

get/set the size/length of the 1D ndarray

Type:: int

property units: str

get/set the units for this axis without conversion (equivalent to force_units)

Type:: str

class pymodaq_data.data.DataBase(name, source=None, dim=None, distribution=DataDistribution.uniform, data=None, labels=None, origin='', units='', **kwargs)[source]

Bases: DataLowLevel, NDArrayOperatorsMixin

Base object to store homogeneous data and metadata generated by pymodaq’s objects.

To be inherited for real data

Parameters:

name (str) – the identifier of these data
source (DataSource) – Enum specifying if data are raw or processed (for instance from roi)
dim (DataDim) – The identifier of the data type
distribution (DataDistribution) – The distribution type of the data: uniform if distributed on a regular grid or spread if on specific unordered points
data (List[ndarray]) – The data the object is storing. In case of Quantities, the object units attribute will be forced to the unit of this quantity, ignoring the units argument.
labels (List[str]) – The labels of the data nd-arrays
origin (str) – An identifier of the element where the data originated, for instance the DAQ_Viewer’s name. Used when appending DataToExport in DAQ_Scan to disintricate from which origin data comes from when scanning multiple detectors.
units (str) – A unit string identifier as specified in the UnitRegistry of the pint module
kwargs (named parameters) – All other parameters are stored dynamically using the name/value pair. The name of these extra parameters are added into the extra_attributes attribute

name

the identifier of these data

Type:: str

source

Enum specifying if data are raw or processed (for instance from roi)

Type:: DataSource or str

dim

The identifier of the data type

Type:: DataDim or str

distribution

The distribution type of the data: uniform if distributed on a regular grid or spread if on specific unordered points

Type:: DataDistribution or str

data

The data the object is storing

Type:: list of ndarray

labels

The labels of the data nd-arrays

Type:: list of str

origin

An identifier of the element where the data originated, for instance the DAQ_Viewer’s name. Used when appending DataToExport in DAQ_Scan to disintricate from which origin data comes from when scanning multiple detectors.

Type:: str

shape

The shape of the underlying data

Type:: Tuple[int]

size

The size of the ndarrays stored in the object

Type:: int

length

The number of ndarrays stored in the object

Type:: int

extra_attributes

list of string giving identifiers of the attributes added dynamically at the initialization (for instance to save extra metadata using the DataSaverLoader

Type:: List[str]

See also

DataWithAxes, DataFromPlugins, DataRaw, DataSaverLoader

Examples

>>> import numpy as np
>>> from pymodaq.utils.data import DataBase, DataSource, DataDim, DataDistribution
>>> data = DataBase('mydata', source=DataSource['raw'], dim=DataDim['Data1D'],     distribution=DataDistribution.uniform, data=[np.array([1.,2.,3.]), np.array([4.,5.,6.])],    labels=['channel1', 'channel2'], origin='docutils code')
>>> data.dim
<DataDim.Data1D: 1>
>>> data.source
<DataSource.raw: 0>
>>> data.shape
(3,)
>>> data.length
2
>>> data.size
3

Attributes:

data: List[np.ndarray]: get/set (and check) the data the object is storing
dim: DataDim: the enum representing the dimensionality of the stored data
distribution: DataDistribution: the enum representing the distribution of the stored data
labels
length: The length of data.
quantities: Get the arrays as pint quantities (with units)
shape: The shape of the nd-arrays
size: The size of the nd-arrays
source: DataSource: the enum representing the source of the data
units

Methods

`abs`()	Take the absolute value of itself
`angle`()	Take the phase value of itself
`append`(data)	Append data content if the underlying arrays have the same shape and compatible units
`as_dte`([name])	Convenience method to wrap the DataWithAxes object into a DataToExport
`average`(other, weight)	Compute the weighted average between self and other DataBase
`fliplr`()	Reverse the order of elements along axis 1 (left/right)
`flipud`()	Reverse the order of elements along axis 0 (up/down)
`force_units`(units)	Change immediately the units to whatever else.
`get_data_index`([index])	Get the data by its index in the list, same as self[index]
`get_dim_from_data`(data)	Get the dimensionality DataDim from data
`get_full_name`()	Get the data ful name including the origin attribute into the returned value
`imag`()	Take the imaginary part of itself
`pop`(index)	Returns a copy of self but with data taken at the specified index
`real`()	Take the real part of itself
`set_dim`(dim)	Addhoc modification of dim independantly of the real data shape, should be used with extra care
`stack_as_array`([axis, dtype])	Stack all data arrays in a single numpy array
`to_dB`()	Get a new data object in decibels
`to_dict`()	Get the data arrays into dictionary whose keys are the labels
`units_as`(units[, inplace, context])	Set the object units to the new one (if possible)
`unwrap`()	unwrap the underlying array (should be angles otherwise meaningless)
`value`([units])	Returns the underlying float value (of the first elt in the data list) if this data holds only a float otherwise returns a mean of the underlying data
`values`([units])	Returns the underlying float value (for each data array in the data list) if this data holds only a float otherwise returns a mean of the underlying data

add_extra_attribute
check_shape_from_data
deepcopy
to_base_units

abs()[source]: Take the absolute value of itself

add_extra_attribute(**kwargs)[source]

angle()[source]: Take the phase value of itself

append(data)[source]: Append data content if the underlying arrays have the same shape and compatible units

as_dte(name='mydte')[source]

Convenience method to wrap the DataWithAxes object into a DataToExport

Return type:: DataToExport

average(other, weight)[source]

Compute the weighted average between self and other DataBase

Parameters:

other_data (DataBase)
weight (int) – The weight the ‘other’ holds with respect to self

Returns:

DataBase

Return type:

DataBase

check_shape_from_data(data)[source]

deepcopy()[source]

fliplr()[source]: Reverse the order of elements along axis 1 (left/right)

flipud()[source]: Reverse the order of elements along axis 0 (up/down)

force_units(units)[source]: Change immediately the units to whatever else. Use this with care!

get_data_index(index=0)[source]

Get the data by its index in the list, same as self[index]

Return type:: ndarray

get_dim_from_data(data)[source]: Get the dimensionality DataDim from data

get_full_name()[source]

Get the data ful name including the origin attribute into the returned value

Returns:: str
Return type:: str

Examples

d0 = DataBase(name=’datafromdet0’, origin=’det0’)

imag()[source]: Take the imaginary part of itself

pop(index)[source]

Returns a copy of self but with data taken at the specified index

Return type:: DataBase

real()[source]: Take the real part of itself

set_dim(dim)[source]: Addhoc modification of dim independantly of the real data shape, should be used with extra care

stack_as_array(axis=0, dtype=None)[source]

Stack all data arrays in a single numpy array

Parameters:

axis (int) – The new stack axis index, default 0
dtype (str or np.dtype) – the dtype of the stacked array

Return type:

ndarray

See also

np.stack()

to_base_units()[source]

to_dB()[source]

Get a new data object in decibels

new in 4.3.0

Return type:: DataBase

to_dict()[source]: Get the data arrays into dictionary whose keys are the labels

units_as(units, inplace=True, context=None, **context_kwargs)[source]

Set the object units to the new one (if possible)

Parameters:

units (str) – The new unit to convert the data to
inplace (bool) – default True. If True replace the data’s arrays by array in the new units If False, return a new data object
context (str) – See pint documentation

Return type:

DataBase

unwrap()[source]: unwrap the underlying array (should be angles otherwise meaningless)

value(units=None)[source]

Returns the underlying float value (of the first elt in the data list) if this data holds only a float otherwise returns a mean of the underlying data

Parameters:: units (str) – if unit is compatible with self.units, convert the data to these new units before getting the value
Return type:: float

values(units=None)[source]

Returns the underlying float value (for each data array in the data list) if this data holds only a float otherwise returns a mean of the underlying data

Return type:: List[float]

base_type = 'Data'

property data: List[ndarray]

get/set (and check) the data the object is storing

Type:: List[np.ndarray]

property dim

the enum representing the dimensionality of the stored data

Type:: DataDim

property distribution

the enum representing the distribution of the stored data

Type:: DataDistribution

property labels

property length: The length of data. This is the length of the list containing the nd-arrays

property quantities: list[Quantity]: Get the arrays as pint quantities (with units)

property shape: The shape of the nd-arrays

property size: The size of the nd-arrays

property source

the enum representing the source of the data

Type:: DataSource

property units

class pymodaq_data.data.DataCalculated(name, dim=None, distribution=DataDistribution.uniform, data=None, labels=None, origin='', units='', axes=[], nav_indexes=(), errors=None, **kwargs)[source]

Bases: DataWithAxes

Specialized DataWithAxes set with source as ‘calculated’. To be used for processed/calculated data

class pymodaq_data.data.DataDim(*values)[source]

Bases: BaseEnum

Enum for dimensionality representation of data

static from_data_array(data_array)[source]

Data0D = 0

Data1D = 1

Data2D = 2

DataND = 3

property dim_index

class pymodaq_data.data.DataDistribution(*values)[source]

Bases: BaseEnum

Enum for distribution of data

spread = 1

uniform = 0

class pymodaq_data.data.DataFromRoi(name, dim=None, distribution=DataDistribution.uniform, data=None, labels=None, origin='', units='', axes=[], nav_indexes=(), errors=None, **kwargs)[source]

Bases: DataCalculated

Specialized DataWithAxes set with source as ‘calculated’. To be used for processed data from region of interest

class pymodaq_data.data.DataLowLevel(name)[source]

Bases: object

Abstract object for all Data Object

Parameters:: name (str) – the identifier of the data

name

Type:: str

timestamp

Time in seconds since epoch. See method time.time()

Type:: float

Attributes:

name: Get/Set the identifier of the data
timestamp: Get/Set the timestamp of when the object has been created

property name: Get/Set the identifier of the data

property timestamp: Get/Set the timestamp of when the object has been created

class pymodaq_data.data.DataRaw(name, dim=None, distribution=DataDistribution.uniform, data=None, labels=None, origin='', units='', axes=[], nav_indexes=(), errors=None, **kwargs)[source]

Bases: DataWithAxes

Specialized DataWithAxes set with source as ‘raw’. To be used for raw data

class pymodaq_data.data.DataSource(*values)[source]

Bases: BaseEnum

Enum for source of data

calculated = 1

raw = 0

class pymodaq_data.data.DataToExport(name, data=[], **kwargs)[source]

Bases: DataLowLevel, SerializableBase

Object to store all raw and calculated DataWithAxes data for later exporting, saving, sending signal…

Includes methods to retrieve data from dim, source… Stored data have a unique identifier their name. If some data is appended with an existing name, it will replace the existing data. So if you want to append data that has the same name

Parameters:

name (str) – The identifier of the exporting object
data (List[DataWithAxes]) – All the raw and calculated data to be exported

name

timestamp

data

Attributes:

data: List[DataWithAxes]: get the data contained in the object

Methods

`affect_name_to_origin_if_none`()	Affect self.name to all DataWithAxes children's attribute origin if this origin is not defined
`average`(other, weight)	Compute the weighted average between self and other DataToExport and attributes it to self
`deserialize`(bytes_str)	Convert bytes into a DataToExport object
`get_data_from_Naxes`(Naxes[, deepcopy])	Get the data matching the given number of axes
`get_data_from_attribute`(attribute, ...[, ...])	Get the data matching a given attribute value
`get_data_from_dim`(dim[, deepcopy, sort_by_name])	Get the data matching the given DataDim
`get_data_from_dims`(dims[, deepcopy, ...])	Get the data matching the given DataDim
`get_data_from_full_name`(full_name[, deepcopy])	Get the DataWithAxes with matching full name
`get_data_from_missing_attribute`(attribute[, ...])	Get the data matching a given attribute value
`get_data_from_name`(name)	Get the data matching the given name
`get_data_from_name_origin`(name[, origin])	Get the data matching the given name and the given origin
`get_data_from_sig_axes`(Naxes[, deepcopy])	Get the data matching the given number of signal axes
`get_data_from_source`(source[, deepcopy, ...])	Get the data matching the given DataSource
`get_data_with_naxes_lower_than`([n_axes, ...])	Get the data with n axes lower than the given number
`get_full_names`([dim])	Get the ful names including the origin attribute into the returned value, eventually filtered by dim
`get_names`([dim])	Get the names of the stored DataWithAxes, eventually filtered by dim
`get_origins`([dim])	Get the origins of the underlying data into the returned value, eventually filtered by dim
`index`(data)	Here use a comparison to assert data is equal to one element in the list
`index_from_name_origin`(name[, origin])	Get the index of a given DataWithAxes within the list of data
`merge_as_dwa`(dim[, name])	attempt to merge filtered dwa into one
`plot`([plotter_backend])	Call a plotter factory and its plot method over the actual data
`pop`(index)	return and remove the DataWithAxes referred by its index
`remove`(dwa)	Use the DataWithAxes object comparison __eq__ to retrieve the elt to remove
`serialize`(dte)	Convert a DataToExport into a bytes string

add_extra_attribute
append
deepcopy
get_data_from_full_names
get_data_from_names
get_dim_presents

classmethod deserialize(bytes_str)[source]

Convert bytes into a DataToExport object

Convert the first bytes into a DataToExport reading first information about the underlying data

Return type:

Tuple[DataToExport, bytes]

Returns:

DataToExport (the decoded DataToExport)
bytes (the remaining bytes if any)

static serialize(dte)[source]

Convert a DataToExport into a bytes string

Parameters:: dte (DataToExport)
Returns:: bytes
Return type:: the total bytes message to serialize the DataToExport

Notes

The bytes sequence is constructed as:

serialize the string type: ‘DataToExport’
serialize the timestamp: float
serialize the name
serialize the list of DataWithAxes

add_extra_attribute(**kwargs)[source]

affect_name_to_origin_if_none()[source]: Affect self.name to all DataWithAxes children’s attribute origin if this origin is not defined

average(other, weight)[source]

Compute the weighted average between self and other DataToExport and attributes it to self

Parameters:

other (DataToExport)
weight (int) – The weight the ‘other_data’ holds with respect to self

Return type:

DataToExport

deepcopy()[source]

get_data_from_Naxes(Naxes, deepcopy=False)[source]

Get the data matching the given number of axes

Parameters:: Naxes (int) – Number of axes in the DataWithAxes objects
Returns:: DataToExport
Return type:: DataToExport

get_data_from_attribute(attribute, attribute_value, deepcopy=False, sort_by_name=False)[source]

Get the data matching a given attribute value

Parameters:

attribute (str) – The name of the attribute to sort data with
attribute_value (Any) – The value of the attribute
deepcopy (bool) – If True, the returned data are deepcopied from the original
sort_by_name (bool) – If True the returned data are sorted alphabetically using their name, default is False

Returns:

DataToExport

Return type:

DataToExport

get_data_from_dim(dim, deepcopy=False, sort_by_name=False)[source]

Get the data matching the given DataDim

Returns:: DataToExport
Return type:: DataToExport

get_data_from_dims(dims, deepcopy=False, sort_by_name=False)[source]

Get the data matching the given DataDim

Returns:: DataToExport
Return type:: DataToExport

get_data_from_full_name(full_name, deepcopy=False)[source]

Get the DataWithAxes with matching full name

Return type:: DataWithAxes

get_data_from_full_names(full_names, deepcopy=False)[source]

Return type:: DataToExport

get_data_from_missing_attribute(attribute, deepcopy=False)[source]

Get the data matching a given attribute value

Parameters:

attribute (str) – a string of a possible attribute
deepcopy (bool) – if True the returned DataToExport will contain deepcopies of the DataWithAxes

Returns:

DataToExport

Return type:

DataToExport

get_data_from_name(name)[source]

Get the data matching the given name

Return type:: DataWithAxes

get_data_from_name_origin(name, origin='')[source]

Get the data matching the given name and the given origin

Return type:: DataWithAxes

get_data_from_names(names)[source]

Return type:: DataToExport

get_data_from_sig_axes(Naxes, deepcopy=False)[source]

Get the data matching the given number of signal axes

Parameters:: Naxes (int) – Number of signal axes in the DataWithAxes objects
Returns:: DataToExport
Return type:: DataToExport

get_data_from_source(source, deepcopy=False, sort_by_name=False)[source]

Get the data matching the given DataSource

Returns:: DataToExport
Return type:: DataToExport

get_data_with_naxes_lower_than(n_axes=2, deepcopy=False)[source]

Get the data with n axes lower than the given number

Parameters:: Naxes (int) – Number of axes in the DataWithAxes objects
Returns:: DataToExport
Return type:: DataToExport

get_dim_presents()[source]

Return type:: List[str]

get_full_names(dim=None)[source]

Get the ful names including the origin attribute into the returned value, eventually filtered by dim

Parameters:: dim (DataDim)
Returns:: list of str
Return type:: the names of the (filtered) DataWithAxes data constructed as : origin/name

Examples

d0 = DataWithAxes(name=’datafromdet0’, origin=’det0’)

get_names(dim=None)[source]

Get the names of the stored DataWithAxes, eventually filtered by dim

Parameters:: dim (DataDim)
Returns:: list of str
Return type:: List[str]

get_origins(dim=None)[source]

Get the origins of the underlying data into the returned value, eventually filtered by dim

Parameters:: dim (DataDim)
Returns:: list of str
Return type:: the origins of the (filtered) DataWithAxes data

Examples

d0 = DataWithAxes(name=’datafromdet0’, origin=’det0’)

index(data)[source]

Here use a comparison to assert data is equal to one element in the list

But the __eq__ method is not checking the name while it is the main issue for elt finding Hence here I’m doing both checks

index_from_name_origin(name, origin='')[source]

Get the index of a given DataWithAxes within the list of data

Return type:: List[DataWithAxes]

merge_as_dwa(dim, name=None)[source]

attempt to merge filtered dwa into one

Only possible if all filtered dwa and underlying data have same shape

Parameters:

dim (Union[str, DataDim]) – will only try to merge dwa having this dimensionality
name (str) – The new name of the returned dwa

Return type:

DataRaw

plot(plotter_backend='matplotlib', *args, **kwargs)[source]: Call a plotter factory and its plot method over the actual data

pop(index)[source]

return and remove the DataWithAxes referred by its index

Parameters:: index (int) – index as returned by self.index_from_name_origin

See also

index_from_name_origin

Return type:: DataWithAxes

remove(dwa)[source]

Use the DataWithAxes object comparison __eq__ to retrieve the elt to remove

Parameters:: dwa (DataWithAxes) – The da to remove from the list

append: Dispatch methods based on type signature

See also

Dispatcher

property data: List[DataWithAxes]

get the data contained in the object

Type:: List[DataWithAxes]

class pymodaq_data.data.DataWithAxes(name, source=None, dim=None, distribution=DataDistribution.uniform, data=None, labels=None, origin='', units='', axes=[], nav_indexes=(), errors=None, **kwargs)[source]

Bases: DataBase, SerializableBase

Data object with Axis objects corresponding to underlying data nd-arrays

Parameters:

axes (List[Axis]) – the list of Axis object for proper plotting, calibration …
nav_indexes (Tuple[int]) – highlight which Axis in axes is Signal or Navigation axis depending on the content: For instance, nav_indexes = (2,), means that the axis with index 2 in a at least 3D ndarray data is the first navigation axis For instance, nav_indexes = (3,2), means that the axis with index 3 in a at least 4D ndarray data is the first navigation axis while the axis with index 2 is the second navigation Axis. Axes with index 0 and 1 are signal axes of 2D ndarray data
errors (Iterable[ndarray]) – The list should match the length of the data attribute while the ndarrays should match the data ndarray

Attributes:

axes: convenience property to fetch attribute from axis_manager
errors: Get/Set the errors bar values as a list of np.ndarray
n_axes: Get the number of axes (even if not specified)
nav_indexes: convenience property to fetch attribute from axis_manager
sig_indexes: convenience property to fetch attribute from axis_manager

Methods

`axes_limits`([axes_indexes])	Get the limits of specified axes (all if axes_indexes is None)
`check_axes_linear`([axes])	Check if any axis may be non linear
`create_missing_axes`()	Check if given the data shape, some axes are missing to properly define the data (especially for plotting)
`deepcopy_with_new_data`([data, ...])	deepcopy without copying the initial data (saving memory)
`deserialize`(bytes_str)	Convert bytes into a DataWithAxes object
`errors_as_dwa`()	Get a dwa from self replacing the data content with the error attribute (if not None)
`find_peaks`([height, threshold])	Apply the scipy find_peaks method to 1D data
`fit`(function, initial_guess[, data_index, ...])	Apply 1D curve fitting using the scipy optimization package
`ft`([axis, axis_label, axis_units, labels])	Process the Fourier Transform of the data on the specified axis and returns the new data
`get_axis_from_label`(label)	Get the axis referred by a given label
`get_axis_indexes`()	Get all present different axis indexes
`get_data_as_dwa`([index])	Get the underlying data selected from the list at index, returned as a DataWithAxes
`get_dim_from_data_axes`()	Get the dimensionality DataDim from data taking into account nav indexes
`get_error`(index)	Get a particular error ndarray at the given index in the list
`get_nav_axes_with_data`()	Get the data's navigation axes making sure there is data in the data field
`ift`([axis, axis_label, axis_units, labels])	Process the inverse Fourier Transform of the data on the specified axis and returns the new data
`interp`(new_axis_data, **kwargs)	Performs linear interpolation for 1D data only.
`mean`([axis])	Process the mean of the data on the specified axis and returns the new data
`moment`()	returns the two first moments of the data over the axis
`pad`(pad_width, **kwargs)	Pad the data arrays using the numpy pad function
`plot`([plotter_backend, viewer])	Call a plotter factory and its plot method over the actual data
`rot90`([k, axes])	Rotate an array by 90 degrees in the plane specified by axes.
`serialize`(dwa)	Convert a DataWithAxes into a bytes string
`sort_data`([axis_index, spread_index, inplace])	Sort data along a given axis, default is 0
`sum`([axis])	Process the sum of the data on the specified axis and returns the new data
`transpose`()	replace the data by their transposed version

check_squeeze
crop_at_along
get_axis_from_index
get_axis_from_index_spread
get_data_dimension
get_nav_axes
get_sig_index
set_axes_manager

classmethod deserialize(bytes_str)[source]

Convert bytes into a DataWithAxes object

Convert the first bytes into a DataWithAxes reading first information about the underlying data

Return type:

Tuple[DataWithAxes, bytes]

Returns:

DataWithAxes (the decoded DataWithAxes)
bytes (the remaining bytes string if any)

static serialize(dwa)[source]

Convert a DataWithAxes into a bytes string

Parameters:: dwa (DataWithAxes)
Returns:: bytes
Return type:: the total bytes message to serialize the DataWithAxes

Notes

The bytes sequence is constructed as:

serialize the timestamp: float
serialize the name
serialize the source enum as a string
serialize the dim enum as a string
serialize the distribution enum as a string
serialize the list of numpy arrays
serialize the list of labels
serialize the origin
serialize the nav_index tuple as a list of int
serialize the list of axis
serialize the errors attributes (None or list(np.ndarray))
serialize the list of names of extra attributes
serialize the extra attributes

axes_limits(axes_indexes=None)[source]

Get the limits of specified axes (all if axes_indexes is None)

Return type:: List[Tuple[float, float]]

check_axes_linear(axes=None)[source]

Check if any axis may be non linear

Should trigger a spread like distribution except id dim is Data1D, in which cas, it doesn’t matter

Return type:: bool

check_squeeze(total_slices, is_navigation)[source]

create_missing_axes()[source]: Check if given the data shape, some axes are missing to properly define the data (especially for plotting)

crop_at_along(coordinates_tuple)[source]

deepcopy_with_new_data(data=None, remove_axes_index=None, source=DataSource.calculated, keep_dim=False)[source]

deepcopy without copying the initial data (saving memory)

The new data, may have some axes stripped as specified in remove_axes_index

Parameters:

data (List[ndarray]) – The new data
remove_axes_index (Union[int, List[int]]) – indexes of the axis to be removed
source (DataSource)
keep_dim (bool) – if False (the default) will calculate the new dim based on the data shape else keep the same (be aware it could lead to issues)

Return type:

DataWithAxes

errors_as_dwa()[source]

Get a dwa from self replacing the data content with the error attribute (if not None)

New in 4.2.0

find_peaks(height=None, threshold=None, **kwargs)[source]

Apply the scipy find_peaks method to 1D data

Parameters:

height (number or ndarray or sequence, optional)
threshold (number or ndarray or sequence, optional)
kwargs (dict) – extra named parameters applied to the find_peaks scipy method

Return type:

DataToExport

See also

find_peaks()

fit(function, initial_guess, data_index=None, axis_index=0, **kwargs)[source]

Apply 1D curve fitting using the scipy optimization package

Parameters:

function (Callable) – a callable to be used for the fit
initial_guess (Iterable) – The initial parameters for the fit
data_index (int) – The index of the data over which to do the fit, if None apply the fit to all
axis_index (int) – the axis index to use for the fit (if multiple) but there should be only one
kwargs (dict) – extra named parameters applied to the curve_fit scipy method

Return type:

DataCalculated

See also

curve_fit()

ft(axis=0, axis_label=None, axis_units=None, labels=None)[source]

Process the Fourier Transform of the data on the specified axis and returns the new data

Parameters:

axis (int) – Apply the FT on this axis index
axis_label (str) – A new label for the FT computed axis
axis_units (str) – New units (without conversion on top of the one from the FT) for the computed axis
labels (List[str]) – list of string for new labels

Return type:

DataWithAxes

See also

ft(), fft()

get_axis_from_index(index, create=False)[source]

get_axis_from_index_spread(index, spread)[source]

get_axis_from_label(label)[source]

Get the axis referred by a given label

Parameters:: label (str) – The label of the axis
Returns:: Axis or None
Return type:: Axis

get_axis_indexes()[source]

Get all present different axis indexes

Return type:: List[int]

get_data_as_dwa(index=0)[source]

Get the underlying data selected from the list at index, returned as a DataWithAxes

Return type:: DataWithAxes

get_data_dimension()[source]

Return type:: str

get_dim_from_data_axes()[source]

Get the dimensionality DataDim from data taking into account nav indexes

Return type:: DataDim

get_error(index)[source]

Get a particular error ndarray at the given index in the list

new in 4.2.0

get_nav_axes()[source]

Return type:: List[Axis]

get_nav_axes_with_data()[source]

Get the data’s navigation axes making sure there is data in the data field

Return type:: List[Axis]

get_sig_index()[source]

Return type:: List[Axis]

ift(axis=0, axis_label=None, axis_units=None, labels=None)[source]

Process the inverse Fourier Transform of the data on the specified axis and returns the new data

Parameters:

axis (int)
axis_label (str) – A new label for the FT computed axis
axis_units (str) – New units (without conversion on top of the one from the FT) for the computed axis
labels (List[str]) – list of string for new labels

Return type:

DataWithAxes

See also

ift(), ifft()

interp(new_axis_data, **kwargs)[source]

Performs linear interpolation for 1D data only.

For more complex ones, see scipy.interpolate()

Parameters:

new_axis_data (Union[Axis, ndarray]) – The coordinates over which to do the interpolation
kwargs (dict) – extra named parameters to be passed to the interp() method

Return type:

DataWithAxes

See also

interp(), interpolate()

mean(axis=0)[source]

Process the mean of the data on the specified axis and returns the new data

Parameters:: axis (int)
Return type:: DataWithAxes

moment()[source]

returns the two first moments of the data over the axis

only valid for Data1D data

Return type:

Tuple[DataWithAxes, DataWithAxes]

Returns:

DataCalculated (containing the moment of order 0 (mean))
DataCalculated (containing the moment of order 1 (std))

pad(pad_width, **kwargs)[source]

Pad the data arrays using the numpy pad function

The accepted pad_witdh type is the same than the numpy pad function

see numpy.pad method for the signature and possible named arguments

plot(plotter_backend='matplotlib', *args, viewer=None, **kwargs)[source]: Call a plotter factory and its plot method over the actual data

rot90(k=1, axes=(0, 1))[source]

Rotate an array by 90 degrees in the plane specified by axes.

Valid only for 2D data

set_axes_manager(data_shape, axes, nav_indexes, **kwargs)[source]

sort_data(axis_index=0, spread_index=0, inplace=False)[source]

Sort data along a given axis, default is 0

Parameters:

axis_index (int) – The index along which one should sort the data
spread_index (int) – for spread data only, specifies which spread axis to use
inplace (bool) – modify in place or not the data (and its axes)

Return type:

DataWithAxes

sum(axis=0)[source]

Process the sum of the data on the specified axis and returns the new data

Parameters:: axis (int)
Return type:: DataWithAxes

transpose()[source]

replace the data by their transposed version

Valid only for 2D data

property axes: convenience property to fetch attribute from axis_manager

property errors

Get/Set the errors bar values as a list of np.ndarray

new in 4.2.0

property n_axes: Get the number of axes (even if not specified)

property nav_indexes: convenience property to fetch attribute from axis_manager

property sig_indexes: convenience property to fetch attribute from axis_manager

class pymodaq_data.data.DwaType(*values)[source]

Bases: BaseEnum

Different types of DataWithAxes.

DataActuator = 2

DataCalculated = 4

DataFromPlugins = 3

DataRaw = 1

DataWithAxes = 0

class pymodaq_data.data.NavAxis(*args, **kwargs)[source]

Bases: Axis

iaxis: Axis

vaxis: Axis

pymodaq_data.data.check_units(units)[source]

pymodaq_data.data.squeeze(data_array, do_squeeze=True, squeeze_indexes=None)[source]

Squeeze numpy arrays return at least 1D arrays except if do_squeeze is False

Return type:: ndarray