8.5.2.3. pymodaq_gui.h5modules.saving module

Created the 15/11/2022

@author: Sebastien Weber

class pymodaq_gui.h5modules.saving.H5Saver(*args, **kwargs)

Bases: H5SaverBase, QObject

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

Methods

emit_new_file(status)

Emits the new_file_sig

close
new_file_sig
show_file_content
status_sig

close()

emit_new_file(status)

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

show_file_content()

class pymodaq_gui.h5modules.saving.H5SaverBase(save_type='scan', backend='tables')

Bases: H5SaverLowLevel, ParameterManager

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_data 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

• ‘pymodaq_data_version’ the current pymodaq_data version, e.g. 0.0.1

• ‘file’ the file name

• ‘date’ the current date

• ‘time’ the current time

All data 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

Methods

find_part_in_path_and_subpath(base_dir[, ...])	Find path from part time.
get_last_scan()	Gets the last scan node within the h5_file and under the raw_group
get_scan_index()	return the scan group index in the "scan templating": Scan000, Scan001 as an integer
init_file([update_h5, custom_naming, ...])	Initializes a new h5 file.
load_file([base_path, file_path])	Opens a file dialog to select a h5file saved on disk to be used
set_current_scan_path(base_dir[, base_name, ...])
update_file_paths([update_h5])
value_changed(param)

get_params_for_save_type
get_scan_groups
save_file
show_settings
update_status

classmethod find_part_in_path_and_subpath(base_dir, part='', create=False, increment=True)

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

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)

Parameters:

• base_dir

• base_name

• update_h5

• next_scan_index

• create_scan_folder

• create_dataset_folder

static get_params_for_save_type(type)

get_last_scan()

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_groups()

get_scan_index()

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={})

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)

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

Parameters:

• base_path

• file_path

See also

init_file()

save_file(filename=None)

show_settings(show=True)

update_file_paths(update_h5=False)

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)

update_status(status)

value_changed(param)

params = [{'limits': ['scan', 'detector', 'logger', 'custom', 'actuator', 'optimizer'], 'name': 'save_type', 'readonly': True, 'title': 'Save type:', 'type': 'list'}, {'name': 'save_2D', 'title': 'Save 2D datas and above:', 'type': 'bool', 'value': True}, {'name': 'save_raw_only', 'title': 'Save raw datas only:', 'tooltip': 'if True, will not save extracted ROIs used to do live plotting, only raw datas will be saved', 'type': 'bool', 'value': True}, {'default': False, 'name': 'do_save', 'title': 'Do Save:', 'type': 'bool', 'value': False}, {'default': 0, 'name': 'N_saved', 'title': 'N saved:', 'type': 'int', 'value': 0, 'visible': False}, {'children': [{'limits': ['tables', 'h5py'], 'name': 'backend_type', 'readonly': True, 'title': 'Backend type:', 'type': 'list'}, {'children': [{'name': 'endpoint', 'readonly': False, 'title': 'Endpoint:', 'type': 'str', 'value': 'http://hsds.sebastienweber.fr'}, {'name': 'user', 'readonly': False, 'title': 'User:', 'type': 'str', 'value': 'pymodaq_user'}, {'name': 'password', 'readonly': False, 'title': 'password:', 'type': 'str', 'value': 'pymodaq'}], 'name': 'hsds_options', 'title': 'HSDS Server:', 'type': 'group', 'visible': False}], 'name': 'backend', 'title': 'Backend:', 'type': 'group'}, {'default': False, 'name': 'custom_name', 'title': 'custom_name?:', 'type': 'bool', 'value': False}, {'default': False, 'name': 'show_file', 'title': 'show file content?', 'type': 'bool_push', 'value': False}, {'filetype': False, 'name': 'base_path', 'readonly': True, 'title': 'Base path:', 'type': 'browsepath', 'value': 'C:\\Data'}, {'name': 'base_name', 'readonly': True, 'title': 'Base name:', 'type': 'str', 'value': 'Scan'}, {'name': 'current_scan_name', 'readonly': True, 'title': 'Current scan:', 'type': 'str', 'value': ''}, {'name': 'current_scan_path', 'readonly': True, 'title': 'Current path:', 'type': 'text', 'value': 'C:\\Data', 'visible': False}, {'name': 'current_h5_file', 'readonly': True, 'title': 'h5file:', 'type': 'text', 'value': ''}, {'name': 'new_file', 'title': 'New file', 'type': 'action'}, {'children': [{'limits': ['zlib', 'gzip'], 'name': 'h5comp_library', 'title': 'Compression library:', 'type': 'list', 'value': 'zlib'}, {'max': 9, 'min': 0, 'name': 'h5comp_level', 'title': 'Compression level:', 'type': 'int', 'value': 5}], 'name': 'compression_options', 'title': 'Compression options:', 'type': 'group'}]

settings_name = 'h5saver_settings'