8.3.1. Hdf5 module and classes

8.3.1.1. Hdf5 backends

The H5Backend is a wrapper around three hdf5 python packages: pytables, h5py and h5pyd. It allows seamless integration of any of these with PyMoDAQ features.

class pymodaq.utils.h5modules.backends.H5Backend(backend='tables')[source]

Attributes

filename
h5file

Methods

`add_group`(group_name, group_type, where[, ...])	Add a node in the h5 file tree of the group type :param group_name: :type group_name: (str) a custom name for this group :param group_type: one of the possible values of GroupType :type group_type: str or GroupType enum :param where: :type where: (str or node) parent node where to create the new group :param metadata: :type metadata: (dict) extra metadata to be saved with this new group node
`close_file`()	Flush data and close the h5file
`create_earray`(where, name, dtype[, ...])	create enlargeable arrays from data with a given shape and of a given type.
`create_vlarray`(where, name, dtype[, title])	create variable data length and type and enlargeable 1D arrays
`define_compression`(compression, compression_opts)	Define cmpression library and level of compression :param compression: but zlib is used by pytables while gzip is used by h5py :type compression: (str) either gzip and zlib are supported here as they are compatible :param compression_opts (int): :type compression_opts (int): 0 to 9 0: None, 9: maximum compression
`get_children`(where)	Get a dict containing all children node hanging from where with their name as keys and types among Node, CARRAY, EARRAY, VLARRAY or StringARRAY
`get_node_name`(node)	return node name :param node (str or node instance): :param see h5py and pytables documentation on nodes:
`get_node_path`(node)	return node path :param node (str or node instance): :param see h5py and pytables documentation on nodes:
`get_set_group`(where, name[, title])	Retrieve or create (if absent) a node group Get attributed to the class attribute `current_group`
`is_node_in_group`(where, name)	Check if a given node with name is in the group defined by where (comparison on lower case strings) :param where: path or parent node instance :type where: (str or node) :param name: group node name :type name: (str)

create_carray
flush
get_attr
get_group_by_title
get_node
get_parent_node
has_attr
isopen
open_file
read
root
save_file_as
set_attr
walk_groups
walk_nodes

add_group(group_name, group_type: GroupType, where, title='', metadata={}) → GROUP[source]

Add a node in the h5 file tree of the group type :param group_name: :type group_name: (str) a custom name for this group :param group_type: one of the possible values of GroupType :type group_type: str or GroupType enum :param where: :type where: (str or node) parent node where to create the new group :param metadata: :type metadata: (dict) extra metadata to be saved with this new group node

Returns: (node)
Return type: newly created group node

close_file()[source]: Flush data and close the h5file

create_earray(where, name, dtype, data_shape=None, title='')[source]: create enlargeable arrays from data with a given shape and of a given type. The array is enlargeable along the first dimension

create_vlarray(where, name, dtype, title='')[source]

create variable data length and type and enlargeable 1D arrays

Parameters

where ((str) group location in the file where to create the array node) –
name ((str) name of the array) –
dtype ((dtype) numpy dtype style, for particular case of strings, use dtype='string') –
title ((str) node title attribute (written in capitals)) –

Return type

array

define_compression(compression, compression_opts)[source]: Define cmpression library and level of compression :param compression: but zlib is used by pytables while gzip is used by h5py :type compression: (str) either gzip and zlib are supported here as they are compatible :param compression_opts (int): :type compression_opts (int): 0 to 9 0: None, 9: maximum compression

get_children(where)[source]

Get a dict containing all children node hanging from where with their name as keys and types among Node, CARRAY, EARRAY, VLARRAY or StringARRAY

Parameters: instance) (where (str or node) – see h5py and pytables documentation on nodes, and Node objects of this module
Returns: dict
Return type: keys are children node names, values are the children nodes

See also

GROUP.children_name()

get_node_name(node)[source]

return node name :param node (str or node instance): :param see h5py and pytables documentation on nodes:

Returns: str
Return type: name of the node

get_node_path(node)[source]

return node path :param node (str or node instance): :param see h5py and pytables documentation on nodes:

Returns: str
Return type: full path of the node

get_set_group(where, name, title='')[source]

Retrieve or create (if absent) a node group Get attributed to the class attribute current_group

Parameters

where (str or node) – path or parent node instance
name (str) – group node name
title (str) – node title

Returns

group

Return type

group node

is_node_in_group(where, name)[source]

Check if a given node with name is in the group defined by where (comparison on lower case strings) :param where: path or parent node instance :type where: (str or node) :param name: group node name :type name: (str)

Returns: True if node exists, False otherwise
Return type: bool

8.3.1.2. Low Level saving

H5SaverBase and H5Saver classes are a help to save data in a hierachical hdf5 binary file through the H5Backend object and allowing integration in the PyMoDAQ Framework. These objects allows the creation of a file, of the various nodes necessary to save PyMoDAQ’s data. The saving functionalities are divided in two objects: H5SaverBase and H5Saver. H5SaverBase contains everything needed for saving, while H5Saver, inheriting H5SaverBase, add Qt functionality such as emitted signals. However, these are not specific of PyMoDAQ’s data types. To save and load data, one should use higher level objects, see High Level saving/loading.

Created the 15/11/2022

@author: Sebastien Weber

class pymodaq.utils.h5modules.saving.H5Saver(*args, **kwargs)[source]

status_sig: Signal: emits a signal of type Threadcommand in order to senf log information to a main UI
new_file_sig: Signal: emits a boolean signal to let the program know when the user pressed the new file button on the UI

emit_new_file(status)[source]

Emits the new_file_sig

Parameters: status (bool) – emits True if a new file has been asked by the user pressing the new file button on the UI

class pymodaq.utils.h5modules.saving.H5SaverBase(save_type='scan', backend='tables')[source]

Object containing all methods in order to save datas in a hdf5 file with a hierarchy compatible with the H5Browser. The saving parameters are contained within a Parameter object: self.settings that can be displayed on a UI using the widget self.settings_tree. At the creation of a new file, a node group named Raw_datas and represented by the attribute raw_group is created and set with a metadata attribute:

‘type’ given by the save_type class parameter

The root group of the file is then set with a few metadata:

‘pymodaq_version’ the current pymodaq version, e.g. 1.6.2
‘file’ the file name
‘date’ the current date
‘time’ the current time

All datas will then be saved under this node in various groups

See also

H5Browser

Parameters

h5_file (pytables hdf5 file) – object used to save all datas and metadas
h5_file_path (str or Path) – Signal signal represented by a float. Is emitted each time the hardware reached the target position within the epsilon precision (see comon_parameters variable)
save_type (str) – an element of the enum module attribute SaveType * ‘scan’ is used for DAQScan module and should be used for similar application * ‘detector’ is used for DAQ_Viewer module and should be used for similar application * ‘custom’ should be used for customized applications

settings

Parameter instance (pyqtgraph) containing all settings (could be represented using the settings_tree widget)

Type: Parameter

settings_tree

Widget representing as a Tree structure, all the settings defined in the class preamble variable params

Type: ParameterTree

classmethod find_part_in_path_and_subpath(base_dir, part='', create=False, increment=True)[source]

Find path from part time.

Parameters	Type	Description
base_dir	Path object	The directory to browse
part	string	The date of the directory to find/create
create	boolean	Indicate the creation flag of the directory

Returns: found path from part
Return type: Path object

get_last_scan()[source]

Gets the last scan node within the h5_file and under the raw_group

Returns: scan_group
Return type: pytables group or None

get_scan_index()[source]: return the scan group index in the “scan templating”: Scan000, Scan001 as an integer

init_file(update_h5=False, custom_naming=False, addhoc_file_path=None, metadata={})[source]

Initializes a new h5 file. Could set the h5_file attributes as:

a file with a name following a template if custom_naming is False and addhoc_file_path is None
a file within a name set using a file dialog popup if custom_naming is True
a file with a custom name if addhoc_file_path is a Path object or a path string

Parameters

update_h5 (bool) – create a new h5 file with name specified by other parameters if false try to open an existing file and will append new data to it
custom_naming (bool) – if True, a selection file dialog opens to set a new file name
addhoc_file_path (Path or str) – supplied name by the user for the new file
metadata (dict) – dictionnary with pair of key, value that should be saved as attributes of the root group

Returns

update_h5 – True if new file has been created, False otherwise

Return type

bool

load_file(base_path=None, file_path=None)[source]

Opens a file dialog to select a h5file saved on disk to be used

Parameters

base_path –
file_path –

See also

init_file()

classmethod set_current_scan_path(base_dir, base_name='Scan', update_h5=False, next_scan_index=0, create_scan_folder=False, create_dataset_folder=True, curr_date=None, ind_dataset=None)[source]

Parameters

base_dir –
base_name –
update_h5 –
next_scan_index –
create_scan_folder –
create_dataset_folder –

update_file_paths(update_h5=False)[source]

Parameters

update_h5 (bool) – if True, will increment the file name and eventually the current scan index if False, get the current scan index in the h5 file

Returns

scan_path (Path)
current_filename (str)
dataset_path (Path)

value_changed(param)[source]

Non-mandatory method to be subclassed for actions to perform (methods to call) when one of the param’s value in self._settings is changed

Parameters: param (Parameter) – the parameter whose value just changed

Examples

>>> if param.name() == 'do_something':
>>>     if param.value():
>>>         print('Do something')
>>>         self.settings.child('main_settings', 'something_done').setValue(False)

They both inherits from the ParameterManager MixIn class that deals with Parameter and ParameterTree, see saving_settings_fig.

8.3.1.3. High Level saving/loading

Each PyMoDAQ’s data type: Axis, DataWithAxes, DataToExport (see What is PyMoDAQ’s Data?) is associated with its saver/loader counterpart. These objects ensures that all metadata necessary for an exact regeneration of the data is being saved at the correct location in the hdf5 file hierarchy. The AxisSaverLoader, DataSaverLoader, DataToExportSaver all derive from an abstract class: DataManagement allowing the manipulation of the nodes and making sure the data type is defined.

8.3.1.3.1. Base data class saver/loader

Created the 21/11/2022

@author: Sebastien Weber

class pymodaq.utils.h5modules.data_saving.AxisSaverLoader(*args, **kwargs)[source]

Specialized Object to save and load Axis object to and from a h5file

Parameters: h5saver (H5Saver) –

data_type

The enum for this type of data, here ‘axis’

Type: DataType

add_axis(where: Union[Node, str], axis: Axis, enlargeable=False)[source]

Write Axis info at a given position within a h5 file

Parameters

where (Union[Node, str]) – the path of a given node or the node itself
axis (Axis) – the Axis object to add as a node in the h5file
enlargeable (bool) – Specify if the underlying array will be enlargebale

get_axes(where: Union[Node, str]) → List[Axis][source]

Return a list of Axis objects from the Axis Nodes hanging from (or among) a given Node

Parameters: where (Union[Node, str]) – the path of a given node or the node itself
Returns: List[Axis]
Return type: the list of all Axis object

load_axis(where: Union[Node, str]) → Axis[source]

create an Axis object from the data and metadata at a given node if of data_type: ‘axis

Parameters: where (Union[Node, str]) – the path of a given node or the node itself
Return type: Axis

class pymodaq.utils.h5modules.data_saving.DataManagement(*args, **kwargs)[source]

Base abstract class to be used for all specialized object saving and loading data to/from a h5file

data_type

The enum for this type of data, here abstract and should be redefined

Type: DataType

get_last_node_name(where: Union[str, Node]) → Optional[str][source]

Get the last node name among the ones already saved

Parameters: where (Union[Node, str]) – the path of a given node or the node itself
Returns: str
Return type: the name of the last saved node or None if none saved

class pymodaq.utils.h5modules.data_saving.DataSaverLoader(*args, **kwargs)[source]

Specialized Object to save and load DataWithAxes object to and from a h5file

Parameters: h5saver (H5Saver or Path or str) –

data_type

The enum for this type of data, here ‘data’

Type: DataType

add_data(where: Union[Node, str], data: DataWithAxes, save_axes=True, **kwargs)[source]

Adds Array nodes to a given location adding eventually axes as others nodes and metadata

Parameters

where (Union[Node, str]) – the path of a given node or the node itself
data (DataWithAxes) –
save_axes (bool) –

get_axes(where: Union[Node, str]) → List[Axis][source]

Parameters: where (Union[Node, str]) – the path of a given node or the node itself

get_data_arrays(where: Union[Node, str], with_bkg=False, load_all=False) → List[ndarray][source]

Parameters

where (Union[Node, str]) – the path of a given node or the node itself
with_bkg (bool) – If True try to load background node and return the array with background subtraction
load_all (bool) – If True load all similar nodes hanging from a parent

Return type

list of ndarray

isopen() → bool[source]: Get the opened status of the underlying hdf5 file

load_data(where, with_bkg=False, load_all=False) → DataWithAxes[source]

Return a DataWithAxes object from the Data and Axis Nodes hanging from (or among) a given Node

Does not include navigation axes stored elsewhere in the h5file. The node path is stored in the DatWithAxis using the attribute path

Parameters

where (Union[Node, str]) – the path of a given node or the node itself
with_bkg (bool) – If True try to load background node and return the data with background subtraction
load_all (bool) – If True, will load all data hanging from the same parent node

See also

load_data

class pymodaq.utils.h5modules.data_saving.DataToExportSaver(h5saver: Union[H5Saver, Path, str])[source]

Object used to save DataToExport object into a h5file following the PyMoDAQ convention

Parameters: h5saver (H5Saver) –

add_data(where: Union[Node, str], data: DataToExport, settings_as_xml='', metadata=None, **kwargs)[source]

Parameters

where (Union[Node, str]) – the path of a given node or the node itself
data (DataToExport) –
settings_as_xml (str) – The settings parameter as an XML string
metadata (dict) – all extra metadata to be saved in the group node where data will be saved

static channel_formatter(ind: int)[source]: All DataWithAxes included in the DataToExport will be saved into a channel group indexed and formatted as below

isopen() → bool[source]: Get the opened status of the underlying hdf5 file

8.3.1.3.2. Specific data class saver/loader

Some more dedicated objects are derived from the objects above. They allow to add background data, Extended arrays (arrays that will be populated after creation, for instance for a scan) and Enlargeable arrays (whose final length is not known at the moment of creation, for instance when logging or continuously saving)

Created the 21/11/2022

@author: Sebastien Weber

class pymodaq.utils.h5modules.data_saving.BkgSaver(*args, **kwargs)[source]

Specialized Object to save and load DataWithAxes background object to and from a h5file

Parameters: hsaver (H5Saver) –

data_type

The enum for this type of data, here ‘bkg’

Type: DataType

class pymodaq.utils.h5modules.data_saving.DataEnlargeableSaver(*args, **kwargs)[source]

Specialized Object to save and load enlargeable DataWithAxes saved object to and from a h5file

Particular case of DataND with a single nav_indexes parameter will be appended as chunks of signal data

Parameters: h5saver (H5Saver) –

data_type

The enum for this type of data, here ‘data_enlargeable’

Type: DataType

Notes

To be used to save data from a timed logger (DAQViewer continuous saving or DAQLogger extension) or from an adaptive scan where the final shape is unknown or other module that need this feature

add_data(where: Union[Node, str], data: DataWithAxes, axis_values: Optional[Iterable[float]] = None)[source]

Append data to an enlargeable array node

Data of dim (0, 1 or 2) will be just appended to the enlargeable array.

Uniform DataND with one navigation axis of length (Lnav) will be considered as a collection of Lnav signal data of dim (0, 1 or 2) and will therefore be appended as Lnav signal data

Parameters

where (Union[Node, str]) – the path of a given node or the node itself
data (DataWithAxes) –
axis_values (optional, list of floats) – the new spread axis values added to the data if None the axes are not added to the h5 file

class pymodaq.utils.h5modules.data_saving.DataExtendedSaver(*args, **kwargs)[source]

Specialized Object to save and load DataWithAxes saved object to and from a h5file in extended arrays

Parameters

h5saver (H5Saver) –
extended_shape (Tuple[int]) – the extra shape compared to the data the h5array will have

data_type

The enum for this type of data, here ‘data’

Type: DataType

add_data(where: Union[Node, str], data: DataWithAxes, indexes: List[int], distribution=DataDistribution.uniform)[source]

Adds given DataWithAxes at a location within the initialized h5 array

Parameters

where (Union[Node, str]) – the path of a given node or the node itself
data (DataWithAxes) –
indexes (Iterable[int]) – indexes where to save data in the init h5array (should have the same length as extended_shape and with values coherent with this shape

class pymodaq.utils.h5modules.data_saving.DataToExportEnlargeableSaver(h5saver: H5Saver, enl_axis_names: Optional[Iterable[str]] = None, enl_axis_units: Optional[Iterable[str]] = None, axis_name: str = 'nav axis', axis_units: str = '')[source]

Generic object to save DataToExport objects in an enlargeable h5 array

The next enlarged value should be specified in the add_data method

Parameters

h5saver (H5Saver) –
enl_axis_names (Iterable[str]) – The names of the enlargeable axis, default [‘nav_axis’]
enl_axis_units (Iterable[str]) – The names of the enlargeable axis, default [‘’]
axis_name (str, deprecated use enl_axis_names) – the name of the enlarged axis array
axis_units (str, deprecated use enl_axis_units) – the units of the enlarged axis array

add_data(where: Union[Node, str], data: DataToExport, axis_values: Optional[List[Union[float, ndarray]]] = None, axis_value: Optional[Union[float, ndarray]] = None, settings_as_xml='', metadata=None)[source]

Parameters

where (Union[Node, str]) – the path of a given node or the node itself
data (DataToExport) – The data to be saved into an enlargeable array
axis_values (iterable float or np.ndarray) – The next value (or values) of the enlarged axis
axis_value (float or np.ndarray #deprecated in 4.2.0, use axis_values) – The next value (or values) of the enlarged axis
settings_as_xml (str) – The settings parameter as an XML string
metadata (dict) – all extra metadata to be saved in the group node where data will be saved

class pymodaq.utils.h5modules.data_saving.DataToExportExtendedSaver(h5saver: H5Saver, extended_shape: Tuple[int])[source]

Object to save DataToExport at given indexes within arrays including extended shape

Mostly used for data generated from the DAQScan

Parameters

h5saver (H5Saver) –
extended_shape (Tuple[int]) – the extra shape compared to the data the h5array will have

add_data(where: Union[Node, str], data: DataToExport, indexes: Iterable[int], distribution=DataDistribution.uniform, settings_as_xml='', metadata={})[source]

Parameters

where (Union[Node, str]) – the path of a given node or the node itself
data (DataToExport) –
indexes (List[int]) – indexes where to save data in the init h5array (should have the same length as extended_shape and with values coherent with this shape
settings_as_xml (str) – The settings parameter as an XML string
metadata (dict) – all extra metadata to be saved in the group node where data will be saved

add_nav_axes(where: Union[Node, str], axes: List[Axis])[source]

Used to add navigation axes related to the extended array

Notes

For instance the scan axes in the DAQScan

class pymodaq.utils.h5modules.data_saving.DataToExportTimedSaver(h5saver: H5Saver)[source]

Specialized DataToExportEnlargeableSaver to save data as a function of a time axis

Only one element ca be added at a time, the time axis value are enlarged using the data to be added timestamp

Notes

This object is made for continuous saving mode of DAQViewer and logging to h5file for DAQLogger

add_data(where: Union[Node, str], data: DataToExport, settings_as_xml='', metadata=None, **kwargs)[source]

Parameters

where (Union[Node, str]) – the path of a given node or the node itself
data (DataToExport) – The data to be saved into an enlargeable array
axis_values (iterable float or np.ndarray) – The next value (or values) of the enlarged axis
axis_value (float or np.ndarray #deprecated in 4.2.0, use axis_values) – The next value (or values) of the enlarged axis
settings_as_xml (str) – The settings parameter as an XML string
metadata (dict) – all extra metadata to be saved in the group node where data will be saved

8.3.1.4. Specialized loading

Data saved from a DAQ_Scan will naturally include navigation axes shared between many different DataWithAxes (as many as detectors/channels/ROIs). They are therefore saved at the root of the scan node and cannot be retrieved using the standard data loader. Hence this DataLoader object.

class pymodaq.utils.h5modules.data_saving.DataLoader(h5saver: Union[H5Saver, Path])[source]

Specialized Object to load DataWithAxes object from a h5file

On the contrary to DataSaverLoader, does include navigation axes stored elsewhere in the h5file (for instance if saved from the DAQ_Scan)

Parameters

h5saver (H5Saver) –

Attributes

h5saver

Methods

`get_nav_group`(where)	param where the path of a given node or the node itself
`get_node`(where[, name])	Convenience method to get node
`load_data`(where[, with_bkg, load_all])	Load data from a node (or channel node)
`walk_nodes`([where])	Return a Node generator iterating over the h5file content

close_file
load_all

get_nav_group(where: Union[Node, str]) → Optional[Node][source]

Parameters

where (Union[Node, str]) – the path of a given node or the node itself

Returns

GROUP (returns the group named SPECIAL_GROUP_NAMES[‘nav_axes’] holding all NavAxis for)
those data

See also

SPECIAL_GROUP_NAMES

get_node(where: Union[Node, str], name: Optional[str] = None) → Node[source]: Convenience method to get node

load_data(where: Union[Node, str], with_bkg=False, load_all=False) → DataWithAxes[source]

Load data from a node (or channel node)

Loaded data contains also nav_axes if any and with optional background subtraction

Parameters

where (Union[Node, str]) – the path of a given node or the node itself
with_bkg (bool) – If True will attempt to substract a background data node before loading
load_all (bool) – If True, will load all data hanging from the same parent node

walk_nodes(where: Union[str, Node] = '/')[source]: Return a Node generator iterating over the h5file content

8.3.1.5. Browsing Data

Using the H5Backend it is possible to write scripts to easily access a hdf5 file content. However, PyMoDAQ includes a dedicated hdf5 viewer understanding dedicated metadata and therefore displaying nicely the content of the file, see H5Browser. Two objects can be used to browse data: H5BrowserUtil and H5Browser. H5BrowserUtil gives you methods to quickly (in a script) get info and data from your file while the H5Browser adds a UI to interact with the hdf5 file.

Created the 15/11/2022

@author: Sebastien Weber

class pymodaq.utils.h5modules.browsing.H5Browser(parent: QMainWindow, h5file=None, h5file_path=None, backend='tables')[source]

UI used to explore h5 files, plot and export subdatas

Parameters

parent (QtWidgets container) – either a QWidget or a QMainWindow
h5file (h5file instance) – exact type depends on the backend
h5file_path (str or Path) – if specified load the corresponding file, otherwise open a select file dialog
backend (str) – either ‘tables, ‘h5py’ or ‘h5pyd’

See also

H5Backend, H5Backend

add_comments(status: bool, comment='')[source]

Add comments to a node

Parameters

status (bool) –
comment (str) – The comment to be added in a comment attribute to the current node path

See also

current_node_path

check_version()[source]: Check version of PyMoDAQ to assert if file is compatible or not with the current version of the Browser

export_data()[source]: Opens a dialog to export data

See also

H5BrowserUtil.export_data

get_tree_node_path()[source]: Get the node path of the currently selected node in the UI

populate_tree()[source]: Init the ui-tree and store data into calling the h5_tree_to_Qtree convertor method

See also

h5tree_to_QTree, update_status

quit_fun()[source]

setup_actions()[source]

Method where to create actions to be subclassed. Mandatory

Examples

>>> self.add_action('Quit', 'close2', "Quit program")
>>> self.add_action('Grab', 'camera', "Grab from camera", checkable=True)
>>> self.add_action('Load', 'Open', "Load target file (.h5, .png, .jpg) or data from camera", checkable=False)
>>> self.add_action('Save', 'SaveAs', "Save current data", checkable=False)

See also

ActionManager.add_action

show_h5_data(item, with_bkg=False, plot_all=False)[source]

Parameters

item –
with_bkg –
plot_all –

class pymodaq.utils.h5modules.browsing.H5BrowserUtil(backend='tables')[source]

Utility object to interact and get info and data from a hdf5 file

Inherits H5Backend and all its functionalities

Parameters: backend (str) – The used hdf5 backend: either tables, h5py or h5pyd

export_data(node_path='/', filesavename: str = 'datafile.h5', filter=None)[source]: Initialize the correct exporter and export the node

get_h5_attributes(node_path)[source]

get_h5file_scans(where='/')[source]

Get the list of the scan nodes in the file

Parameters: where (str) – the path in the file
Returns: dict with keys: scan_name, path (within the file) and data (the live scan png image)
Return type: list of dict

8.3.1.6. Module savers

Created the 23/11/2022

@author: Sebastien Weber

class pymodaq.utils.h5modules.module_saving.ActuatorSaver(*args, **kwargs)[source]

Implementation of the ModuleSaver class dedicated to DAQ_Move modules

Parameters

h5saver –
module –

class pymodaq.utils.h5modules.module_saving.DetectorEnlargeableSaver(*args, **kwargs)[source]

Implementation of the ModuleSaver class dedicated to DAQ_Viewer modules in order to save enlargeable data

Parameters: module –

class pymodaq.utils.h5modules.module_saving.DetectorExtendedSaver(*args, **kwargs)[source]

Implementation of the ModuleSaver class dedicated to DAQ_Viewer modules in order to save enlargeable data

Parameters: module –

class pymodaq.utils.h5modules.module_saving.DetectorSaver(*args, **kwargs)[source]

Implementation of the ModuleSaver class dedicated to DAQ_Viewer modules

Parameters: module –

add_bkg(where: Union[Node, str], data_bkg: DataToExport)[source]

Adds a DataToExport as a background node in the h5file

Parameters

where (Union[Node, str]) – the path of a given node or the node itself
data_bkg (DataToExport) – The data to be saved as background

class pymodaq.utils.h5modules.module_saving.LoggerSaver(*args, **kwargs)[source]

Implementation of the ModuleSaver class dedicated to H5Logger module

H5Logger is the special logger to h5file of the DAQ_Logger extension

Parameters

h5saver –
module –

add_data(dte: DataToExport)[source]

Add data to it’s corresponding control module

The name of the control module is the DataToExport name attribute

class pymodaq.utils.h5modules.module_saving.ModuleSaver(*args, **kwargs)[source]

Abstract base class to save info and data from main modules (DAQScan, DAQViewer, DAQMove, …)

flush()[source]: Flush the underlying file

get_last_node(where: Optional[Union[Node, str]] = None)[source]

Get the last node corresponding to this particular Module instance

Parameters

where (Union[Node, str]) – the path of a given node or the node itself
new (bool) – if True force the creation of a new indexed node of this class type if False return the last node (or create one if None)

Returns

GROUP

Return type

the Node associated with this module which should be a GROUP node

get_set_node(where: Optional[Union[Node, str]] = None, name: Optional[str] = None) → GROUP[source]

Get or create the node corresponding to this particular Module instance

Parameters

where (Union[Node, str]) – the path of a given node or the node itself
new (bool) – if True force the creation of a new indexed node of this class type if False return the last node (or create one if None)

Returns

GROUP

Return type

the Node associated with this module which should be a GROUP node

class pymodaq.utils.h5modules.module_saving.ScanSaver(*args, **kwargs)[source]

Implementation of the ModuleSaver class dedicated to DAQScan module

Parameters

h5saver –
module –

get_set_node(where: Optional[Union[Node, str]] = None, new=False) → GROUP[source]

Get the last group scan node

Get the last Scan Group or create one get the last Scan Group if: * there is one already created * new is False

Parameters

where (Union[Node, str]) – the path of a given node or the node itself
new (bool) –

Returns

GROUP

Return type

the GROUP associated with this module