pymodaq 3.6.12__py3-none-any.whl → 4.0.1__py3-none-any.whl

pymodaq/daq_utils/h5modules.py

@@ -1,1559 +0,0 @@
-# Standard imports
-import os
-import sys
-from collections import OrderedDict
-import warnings
-import logging
-import copy
-from pathlib import Path
-import importlib
-
-# 3rd party imports
-from qtpy import QtGui, QtCore, QtWidgets
-from qtpy.QtCore import Qt, QObject, Signal, QByteArray
-import numpy as np
-import datetime
-
-# Project imports
-import pymodaq.daq_utils.parameter.ioxml
-from pyqtgraph.parametertree import Parameter, ParameterTree
-from pymodaq.daq_utils.config import Config
-from pymodaq.daq_utils.parameter import utils as putils
-from pymodaq.daq_utils.tree_layout.tree_layout_main import Tree_layout
-from pymodaq.daq_utils.gui_utils.utils import h5tree_to_QTree, pngbinary2Qlabel
-from pymodaq.daq_utils.gui_utils.file_io import select_file
-from pymodaq.daq_utils.gui_utils.dock import DockArea
-from pymodaq.daq_utils.gui_utils.utils import dashboard_submodules_params
-from pymodaq.daq_utils.plotting.data_viewers.viewerND import ViewerND
-from pymodaq.daq_utils.abstract.logger import AbstractLogger
-from pymodaq.daq_utils.h5backend import H5Backend, backends_available, Node
-from pymodaq.daq_utils.h5exporters import ExporterFactory
-from pymodaq.daq_utils.h5utils import get_h5_data_from_node
-from pymodaq.daq_utils.exceptions import InvalidSave, InvalidGroupDataType, InvalidDataDimension, \
-    InvalidDataType, InvalidScanType, InvalidGroupType
-
-from pymodaq.daq_utils import daq_utils as utils
-from pymodaq.daq_utils.scanner import SCAN_TYPES as stypes
-
-from dateutil import parser
-from packaging import version as version_mod
-
-config = Config()
-
-logger = utils.set_logger(utils.get_module_name(__file__))
-
-version = '0.0.1'
-save_types = ['scan', 'detector', 'logger', 'custom']
-group_types = ['raw_datas', 'scan', 'detector', 'move', 'data', 'ch', '', 'external_h5']
-group_data_types = ['data0D', 'data1D', 'data2D', 'dataND']
-data_types = ['data', 'axis', 'live_scan', 'navigation_axis', 'external_h5', 'strings', 'bkg']
-data_dimensions = ['0D', '1D', '2D', 'ND']
-scan_types = ['']
-scan_types.extend(stypes)
-
-
-class H5LogHandler(logging.StreamHandler):
-    def __init__(self, h5saver):
-        super().__init__()
-        self.h5saver = h5saver
-        formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
-        self.setFormatter(formatter)
-
-    def emit(self, record):
-        msg = self.format(record)
-        self.h5saver.add_log(msg)
-
-
-class H5SaverBase(H5Backend):
-    """Object containing all methods in order to save datas in a *hdf5 file* with a hierachy 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 list module attribute save_types = ['scan', 'detector', 'custom']
-               * 'scan' is used for DAQ_Scan 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
-
-    Attributes
-    ----------
-
-    settings: Parameter
-               Parameter instance (pyqtgraph) containing all settings (can be represented with the settings_tree widget)
-
-    settings_tree: ParameterTree
-                   Widget representing a Tree structure, all settings are defined in the class variable ``params``
-
-    """
-
-    params = [
-                 {'title': 'Save type:', 'name': 'save_type', 'type': 'list', 'limits': save_types, 'readonly': True},
-             ] + dashboard_submodules_params + \
-             [{'title': 'Backend:', 'name': 'backend', 'type': 'group', 'children': [
-                 {'title': 'Backend type:', 'name': 'backend_type', 'type': 'list', 'limits': backends_available,
-                  'readonly': True},
-                 {'title': 'HSDS Server:', 'name': 'hsds_options', 'type': 'group', 'visible': False, 'children': [
-                     {'title': 'Endpoint:', 'name': 'endpoint', 'type': 'str',
-                      'value': config('data_saving', 'hsds', 'root_url'), 'readonly': False},
-                     {'title': 'User:', 'name': 'user', 'type': 'str',
-                      'value': config('data_saving', 'hsds', 'username'), 'readonly': False},
-                     {'title': 'password:', 'name': 'password', 'type': 'str',
-                      'value': config('data_saving', 'hsds', 'pwd'), 'readonly': False},
-                 ]},
-             ]},
-
-              {'title': 'custom_name?:', 'name': 'custom_name', 'type': 'bool', 'default': False, 'value': False},
-              {'title': 'show file content?', 'name': 'show_file', 'type': 'bool_push', 'default': False,
-               'value': False},
-              {'title': 'Base path:', 'name': 'base_path', 'type': 'browsepath',
-               'value': config('data_saving', 'h5file', 'save_path'), 'filetype': False, 'readonly': True, },
-              {'title': 'Base name:', 'name': 'base_name', 'type': 'str', 'value': 'Scan', 'readonly': True},
-              {'title': 'Current scan:', 'name': 'current_scan_name', 'type': 'str', 'value': '', 'readonly': True},
-              {'title': 'Current path:', 'name': 'current_scan_path', 'type': 'text',
-               'value': config('data_saving', 'h5file', 'save_path'), 'readonly': True, 'visible': False},
-              {'title': 'h5file:', 'name': 'current_h5_file', 'type': 'text', 'value': '', 'readonly': True},
-              {'title': 'New file', 'name': 'new_file', 'type': 'action'},
-              {'title': 'Saving dynamic', 'name': 'dynamic', 'type': 'list',
-               'limits': config('data_saving', 'data_type', 'dynamics'),
-               'value': config('data_saving', 'data_type', 'dynamic')},
-              {'title': 'Compression options:', 'name': 'compression_options', 'type': 'group', 'children': [
-                  {'title': 'Compression library:', 'name': 'h5comp_library', 'type': 'list', 'value': 'zlib',
-                   'limits': ['zlib', 'gzip']},
-                  {'title': 'Compression level:', 'name': 'h5comp_level', 'type': 'int',
-                   'value': config('data_saving', 'h5file', 'compression_level'), 'min': 0, 'max': 9},
-              ]},
-              ]
-
-    def __init__(self, save_type='scan', backend='tables'):
-        """
-
-        Parameters
-        ----------
-        save_type (str): one of ['scan', 'detector', 'logger', 'custom']
-        backend (str): either 'tables' for pytables backend, 'h5py' for h5py backends or 'h5pyd' for HSDS backend
-
-        See Also
-        --------
-        https://github.com/HDFGroup/hsds
-        """
-        H5Backend.__init__(self, backend)
-        if save_type not in save_types:
-            raise InvalidSave('Invalid saving type')
-
-        self.h5_file_path = None
-        self.h5_file_name = None
-        self.logger_array = None
-        self.file_loaded = False
-
-        self.current_group = None
-        self.current_scan_group = None
-        self.current_scan_name = None
-        self.raw_group = None
-
-        self.settings = Parameter.create(title='Saving settings', name='save_settings', type='group',
-                                         children=self.params)
-        self.settings.child(('save_type')).setValue(save_type)
-
-        # self.settings.child('saving_options', 'save_independent').show(save_type == 'scan')
-        # self.settings.child('saving_options', 'do_save').show(not save_type == 'scan')
-        # self.settings.child('saving_options', 'current_scan_name').show(save_type == 'scan')
-
-        self.settings.sigTreeStateChanged.connect(
-            self.parameter_tree_changed)  # any changes on the settings will update accordingly the detector
-
-    @property
-    def h5_file(self):
-        return self._h5file
-
-    def init_file(self, update_h5=False, custom_naming=False, addhoc_file_path=None, metadata=dict([]),
-                  raw_group_name='Raw_datas'):
-        """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: bool
-                   True if new file has been created, False otherwise
-        """
-        datetime_now = datetime.datetime.now()
-
-        if addhoc_file_path is None:
-            if not os.path.isdir(self.settings.child('base_path').value()):
-                os.mkdir(self.settings.child('base_path').value())
-
-            # set the filename and path
-            base_name = self.settings.child('base_name').value()
-
-            if not custom_naming:
-                custom_naming = self.settings.child('custom_name').value()
-
-            if not custom_naming:
-                scan_type = self.settings.child('save_type').value() == 'scan'
-                scan_path, current_scan_name, save_path = self.update_file_paths(update_h5)
-                self.current_scan_name = current_scan_name
-                self.settings.child('current_scan_name').setValue(current_scan_name)
-                self.settings.child('current_scan_path').setValue(str(scan_path))
-
-                if not scan_type:
-                    self.h5_file_path = save_path.parent  # will remove the dataset part used for DAQ_scan datas
-                    self.h5_file_name = base_name + datetime_now.strftime('_%Y%m%d_%H_%M_%S.h5')
-                else:
-                    self.h5_file_name = save_path.name + ".h5"
-                    self.h5_file_path = save_path.parent
-
-            else:
-                self.h5_file_name = select_file(start_path=base_name, save=True, ext='h5')
-                self.h5_file_path = self.h5_file_name.parent
-
-        else:
-            if isinstance(addhoc_file_path, str):
-                addhoc_file_path = Path(addhoc_file_path)
-            self.h5_file_path = addhoc_file_path.parent
-            self.h5_file_name = addhoc_file_path.name
-
-        fullpathname = str(self.h5_file_path.joinpath(self.h5_file_name))
-        self.settings.child('current_h5_file').setValue(fullpathname)
-
-        if update_h5:
-            self.current_scan_group = None
-
-        scan_group = None
-        if self.current_scan_group is not None:
-            scan_group = self.get_node_name(self.current_scan_group)
-
-        if update_h5:
-            self.close_file()
-            self.open_file(fullpathname, 'w', title='PyMoDAQ file')
-
-        else:
-            self.close_file()
-            self.open_file(fullpathname, 'a', title='PyMoDAQ file')
-
-        self.raw_group = self.get_set_group(self.root(), raw_group_name, title='Data from PyMoDAQ modules')
-        self.get_set_logger(self.raw_group)
-
-        if scan_group is not None:
-            self.current_scan_group = self.get_set_group(self.raw_group, scan_group)
-        else:
-            self.current_scan_group = self.get_last_scan()
-
-        self.raw_group.attrs['type'] = self.settings.child(
-            ('save_type')).value()  # first possibility to set a node attribute
-        self.root().set_attr('file', self.h5_file_name)  # second possibility
-        if update_h5:
-            self.set_attr(self.root(), 'date', datetime_now.date().isoformat())
-            self.set_attr(self.root(), 'time', datetime_now.time().isoformat())
-            for metadat in metadata:
-                self.raw_group.attrs[metadat] = metadata[metadat]
-        return update_h5
-
-    def add_scan_group(self, title='', settings_as_xml='', metadata=dict([])):
-        """
-        Add a new group of type scan
-        See Also
-        -------
-        add_incremental_group
-        """
-        if self.current_scan_group is not None:
-            if len(self.get_children(self.current_scan_group)) == 0:
-                new_scan = False
-            else:
-                new_scan = True
-        else:
-            new_scan = True
-        if new_scan:
-            self.current_scan_group = self.add_incremental_group('scan', self.raw_group, title, settings_as_xml,
-                                                                 metadata)
-            self.set_attr(self.current_scan_group, 'description', '')
-            self.settings.child(('current_scan_name')).setValue(self.get_node_name(self.current_scan_group))
-
-        return self.current_scan_group
-
-    def update_file_paths(self, 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
-
-        """
-
-        try:
-            # set the filename and path
-            base_path = self.settings.child(('base_path')).value()
-            base_name = self.settings.child(('base_name')).value()
-            current_scan = self.settings.child(('current_scan_name')).value()
-            scan_type = self.settings.child(('save_type')).value() == 'scan'
-            ind_dataset = None
-            if current_scan == '' or update_h5:
-                next_scan_index = 0
-                update_h5 = True  # just started the main program so one should create a new h5
-                self.file_loaded = False
-            else:
-                next_scan_index = self.get_scan_index()
-            if self.file_loaded:
-                ind_dataset = int(os.path.splitext(self.h5_file_name)[0][-3:])
-                try:
-                    curr_date = datetime.date.fromisoformat(self.get_attr(self.root(), 'date'))
-                except ValueError:
-                    curr_date = parser.parse(self.get_attr(self.root(), 'date')).date()
-            else:
-                curr_date = datetime.date.today()
-
-            scan_path, current_filename, dataset_path = self.set_current_scan_path(base_path, base_name, update_h5,
-                                                                                   next_scan_index,
-                                                                                   create_dataset_folder=False,
-                                                                                   curr_date=curr_date,
-                                                                                   ind_dataset=ind_dataset)
-            self.settings.child(('current_scan_path')).setValue(str(dataset_path))
-
-            return scan_path, current_filename, dataset_path
-
-        except Exception as e:
-            logger.exception(str(e))
-
-    @classmethod
-    def find_part_in_path_and_subpath(cls, 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
-        -------
-        Path object
-            found path from part
-        """
-        found_path = None
-        if part in base_dir.parts:  # check if current year is in the given base path
-            if base_dir.name == part:
-                found_path = base_dir
-            else:
-                for ind in range(len(base_dir.parts)):
-                    tmp_path = base_dir.parents[ind]
-                    if tmp_path.name == part:
-                        found_path = base_dir.parents[ind]
-                        break
-        else:  # if not check if year is in the subfolders
-            subfolders_year_name = [x.name for x in base_dir.iterdir() if x.is_dir()]
-            subfolders_found_path = [x for x in base_dir.iterdir() if x.is_dir()]
-            if part not in subfolders_year_name:
-                if increment:
-                    found_path = base_dir.joinpath(part)
-                else:
-                    found_path = base_dir
-                if create:
-                    found_path.mkdir()
-            else:
-                ind_path = subfolders_year_name.index(part)
-                found_path = subfolders_found_path[ind_path]
-        return found_path
-
-    @classmethod
-    def set_current_scan_path(cls, 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
-
-        Returns
-        -------
-
-        """
-        base_dir = Path(base_dir)
-        if curr_date is None:
-            curr_date = datetime.date.today()
-
-        year_path = cls.find_part_in_path_and_subpath(base_dir, part=str(curr_date.year),
-                                                      create=True)  # create directory of the year if it doen't exist and return it
-        day_path = cls.find_part_in_path_and_subpath(year_path, part=curr_date.strftime('%Y%m%d'),
-                                                     create=True)  # create directory of the day if it doen't exist and return it
-        dataset_base_name = curr_date.strftime('Dataset_%Y%m%d')
-        dataset_paths = sorted([path for path in day_path.glob(dataset_base_name + "*" + ".h5") if path.is_file()])
-
-        if ind_dataset is None:
-            if dataset_paths == []:
-
-                ind_dataset = 0
-            else:
-                if update_h5:
-                    ind_dataset = int(dataset_paths[-1].stem.partition(dataset_base_name + "_")[2]) + 1
-                else:
-                    ind_dataset = int(dataset_paths[-1].stem.partition(dataset_base_name + "_")[2])
-
-        dataset_path = cls.find_part_in_path_and_subpath(day_path,
-                                                         part=dataset_base_name + "_{:03d}".format(ind_dataset),
-                                                         create=False, increment=True)
-        scan_paths = sorted([path for path in dataset_path.glob(base_name + '*') if path.is_dir()])
-        # if scan_paths==[]:
-        #     ind_scan=0
-        # else:
-        #     if list(scan_paths[-1].iterdir())==[]:
-        #         ind_scan=int(scan_paths[-1].name.partition(base_name)[2])
-        #     else:
-        #         ind_scan=int(scan_paths[-1].name.partition(base_name)[2])+1
-        ind_scan = next_scan_index
-        #
-        # scan_path = cls.find_part_in_path_and_subpath(dataset_path, part=base_name + '{:03d}'.format(ind_scan),
-        #                                               create=create_scan_folder)
-        scan_path = ''
-        return dataset_path, base_name + '{:03d}'.format(ind_scan), dataset_path
-
-    def get_last_scan(self):
-        """Gets the last scan node within the h5_file and under the the **raw_group**
-
-        Returns
-        -------
-        scan_group: pytables group or None
-
-
-        """
-        groups = [group for group in list(self.get_children(self.raw_group)) if 'Scan' in group]
-        groups.sort()
-        if len(groups) != 0:
-            scan_group = self.get_node(self.raw_group, groups[-1])
-        else:
-            scan_group = None
-        return scan_group
-
-    def get_scan_index(self):
-        """ return the scan group index in the "scan templating": Scan000, Scan001 as an integer
-        """
-        try:
-            if self.current_scan_group is None:
-                return 0
-            else:
-
-                groups = [group for group in self.get_children(self.raw_group) if 'Scan' in group]
-                groups.sort()
-                flag = False
-                if len(groups) != 0:
-                    if 'scan_done' in self.get_attr(self.get_node(self.raw_group, groups[-1])):
-                        if self.get_attr(self.get_node(self.raw_group, groups[-1]), 'scan_done'):
-                            return len(groups)
-                        return len(groups) - 1
-                    return len(groups) - 1
-                return 0
-
-        except Exception as e:
-            logger.exception(str(e))
-
-    def load_file(self, 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
-        --------
-        :py:meth:`init_file`
-
-        """
-        if base_path is None:
-            base_path = self.settings.child('base_path').value()
-            if not os.path.isdir(base_path):
-                base_path = None
-
-        if file_path is None:
-            file_path = select_file(base_path, save=False, ext='h5')
-
-        if not (file_path is None or file_path == ''):
-            if not isinstance(file_path, Path):
-                file_path = Path(file_path)
-
-            if 'h5' not in file_path.suffix:
-                raise IOError('Invalid file type, should be a h5 file')
-
-            self.init_file(addhoc_file_path=file_path)
-            self.file_loaded = True
-
-    def save_file(self, filename=None):
-        if filename is None:
-            filename = select_file(None, save=True, ext='h5')
-        if filename != '':
-            super().save_file_as(filename)
-
-    def get_set_logger(self, where):
-        """ Retrieve or create (if absent) a logger enlargeable array to store logs
-        Get attributed to the class attribute ``logger_array``
-        Parameters
-        ----------
-        where: node
-               location within the tree where to save or retrieve the array
-
-        Returns
-        -------
-        logger_array: vlarray
-                      enlargeable array accepting strings as elements
-        """
-        if isinstance(where, Node):
-            where = where.node
-        logger = 'Logger'
-        if logger not in list(self.get_children(where)):
-            # check if logger node exist
-            self.logger_array = self.add_string_array(where, logger)
-            self.logger_array.attrs['type'] = 'log'
-        else:
-            self.logger_array = self.get_node(where, name=logger)
-        return self.logger_array
-
-    def add_log(self, msg):
-        self.logger_array.append(msg)
-
-    def add_data_group(self, where, group_data_type, title='', settings_as_xml='', metadata=dict([])):
-        """Creates a group node at given location in the tree
-
-        Parameters
-        ----------
-        where: group node
-               where to create data group
-        group_data_type: list of str
-                         either ['data0D', 'data1D', 'data2D', 'dataND']
-        title: str, optional
-               a title for this node, will be saved as metadata
-        settings_as_xml: str, optional
-                         XML string created from a Parameter object to be saved as metadata
-        metadata: dict, optional
-                  will be saved as a new metadata attribute with name: key and value: dict value
-
-        Returns
-        -------
-        group: group node
-
-        See Also
-        --------
-        :py:meth:`àdd_group`
-        """
-        if group_data_type not in group_data_types:
-            raise InvalidGroupDataType('Invalid data group type')
-        metadata.update(settings=settings_as_xml)
-        group = self.add_group(group_data_type, '', where, title, metadata)
-        return group
-
-    def add_navigation_axis(self, data, parent_group, axis='x_axis', enlargeable=False, title='', metadata=dict([])):
-        """
-        Create carray or earray for navigation axis within a scan
-        Parameters
-        ----------
-        data: (ndarray) of dimension 1
-        parent_group: (str or node) parent node where to save new data
-        axis: (str) either x_axis, y_axis, z_axis or time_axis. 'x_axis', 'y_axis', 'z_axis', 'time_axis' are axes containing scalar values (floats or ints). 'time_axis' can be interpreted as the posix timestamp corresponding to a datetime object, see datetime.timestamp()
-        enlargeable: (bool) if True the created array is a earray type if False the created array is a carray type
-        """
-
-        if axis not in ['x_axis', 'y_axis', 'z_axis', 'time_axis']:
-            if 'axis' not in axis:  # this take care of the case of sequential scans where axes are labelled with indexes
-                raise NameError('Invalid navigation axis name')
-
-        array = self.add_array(parent_group, f"{self.settings.child(('save_type')).value()}_{axis}", 'navigation_axis',
-                               data_shape=data.shape,
-                               data_dimension='1D', array_to_save=data, enlargeable=enlargeable, title=title,
-                               metadata=metadata)
-        return array
-
-    def add_data_live_scan(self, channel_group, data_dict, scan_type='scan1D', title='', scan_subtype=''):
-        isadaptive = scan_subtype == 'Adaptive'
-        if not isadaptive:
-            shape, dimension, size = utils.get_data_dimension(data_dict['data'], scan_type=scan_type,
-                                                              remove_scan_dimension=True)
-        else:
-            shape, dimension, size = data_dict['data'].shape, '0D', 1
-        data_array = self.add_array(channel_group, 'Data', 'data', array_type=np.float,
-                                    title=title,
-                                    data_shape=shape,
-                                    data_dimension=dimension, scan_type=scan_type,
-                                    scan_subtype=scan_subtype,
-                                    array_to_save=data_dict['data'])
-        if 'x_axis' in data_dict:
-            if not isinstance(data_dict['x_axis'], dict):
-                array_to_save = data_dict['x_axis']
-                tmp_dict = dict(label='', units='')
-            else:
-                tmp_dict = copy.deepcopy(data_dict['x_axis'])
-                array_to_save = tmp_dict.pop('data')
-            self.add_array(channel_group, 'x_axis', 'axis',
-                           array_type=np.float, array_to_save=array_to_save,
-                           enlargeable=False, data_dimension='1D', metadata=tmp_dict)
-        if 'y_axis' in data_dict:
-            if not isinstance(data_dict['y_axis'], dict):
-                array_to_save = data_dict['y_axis']
-                tmp_dict = dict(label='', units='')
-            else:
-                tmp_dict = copy.deepcopy(data_dict['y_axis'])
-                array_to_save = tmp_dict.pop('data')
-            self.add_array(channel_group, 'y_axis', 'axis',
-                           array_type=np.float, array_to_save=array_to_save,
-                           enlargeable=False, data_dimension='1D', metadata=tmp_dict)
-        return data_array
-
-    def add_data(self, channel_group, data_dict, scan_type='scan1D', scan_subtype='',
-                 scan_shape=[], title='', enlargeable=False,
-                 init=False, add_scan_dim=False, metadata=dict([])):
-        """save data within the hdf5 file together with axes data (if any) and metadata, node name will be 'Data'
-
-        Parameters
-        ----------
-        channel_group: (hdf5 node) node where to save the array, in general within a channel type group
-        data_dict: (dict) dictionnary containing the data to save and all the axis and metadata mandatory key: 'data':
-         (ndarray) data to save other keys: 'xxx_axis' (for instance x_axis, y_axis, 'nav_x_axis'....) or background
-        scan_type: (str) either '', 'scan1D' or 'scan2D' or Tabular or sequential
-        scan_subtype: (str) see scanner module
-        scan_shape: (iterable) the shape of the scan dimensions
-        title: (str) the title attribute of the array node
-        enlargeable: (bool) if False, data are save as a CARRAY, otherwise as a EARRAY (for ragged data, see add_sting_array)
-        init: (bool) if True, the array saved in the h5 file is initialized with the correct type but all element equal
-                     to zero. Else, the 'data' key of data_dict is saved as is
-        add_scan_dim: (bool) if True, the scan axes dimension (scan_shape iterable) is prepended to the array shape on the hdf5
-                      In that case, the array is usually initialized as zero and further populated
-        metadata: (dict) dictionnary whose keys will be saved as the array attributes
-
-
-        Returns
-        -------
-        array (CARRAY or EARRAY)
-
-        See Also
-        --------
-        add_array, add_string_array
-        """
-
-        shape, dimension, size = utils.get_data_dimension(data_dict['data'])
-        tmp_data_dict = copy.deepcopy(data_dict)
-        array_type = getattr(np, self.settings.child('dynamic').value())
-        # save axis
-        # this loop covers all type of axis : x_axis, y_axis... nav_x_axis, ...
-        axis_keys = [k for k in tmp_data_dict.keys() if 'axis' in k]
-        for key in axis_keys:
-            if not isinstance(tmp_data_dict[key], dict):
-                array_to_save = tmp_data_dict[key]
-                tmp_dict = dict(label='', units='')
-            else:
-                tmp_dict = copy.deepcopy(tmp_data_dict[key])
-                array_to_save = tmp_dict.pop('data')
-                tmp_data_dict.pop(key)
-
-            self.add_array(channel_group, key, 'axis', array_type=None, array_to_save=array_to_save,
-                           enlargeable=False, data_dimension='1D', metadata=tmp_dict)
-
-        array_to_save = tmp_data_dict.pop('data')
-        if 'type' in tmp_data_dict:
-            tmp_data_dict.pop('type')  # otherwise this metadata would overide mandatory attribute 'type' for a h5 node
-
-        if 'bkg' in tmp_data_dict:
-            bkg = tmp_data_dict.pop('bkg')
-            self.add_array(channel_group, 'Bkg', 'bkg', array_type=array_type, array_to_save=bkg,
-                           data_dimension=dimension)
-        tmp_data_dict.update(metadata)
-        array_to_save = array_to_save.astype(array_type)
-        data_array = self.add_array(channel_group, 'Data', 'data', array_type=array_type,
-                                    title=title, data_shape=shape, enlargeable=enlargeable, data_dimension=dimension,
-                                    scan_type=scan_type, scan_subtype=scan_subtype, scan_shape=scan_shape,
-                                    array_to_save=array_to_save,
-                                    init=init, add_scan_dim=add_scan_dim, metadata=tmp_data_dict)
-
-        self.flush()
-        return data_array
-
-    def add_array(self, where, name, data_type, data_shape=None, data_dimension=None, scan_type='', scan_subtype='',
-                  scan_shape=[],
-                  title='', array_to_save=None, array_type=None, enlargeable=False, metadata=dict([]),
-                  init=False, add_scan_dim=False):
-        """save data arrays on the hdf5 file together with metadata
-        Parameters
-        ----------
-        where: (hdf5 node) node where to save the array
-        name: (str) name of the array in the hdf5 file
-        data_type: (str) one of ['data', 'axis', 'live_scan', 'navigation_axis', 'external_h5', 'strings', 'bkg'], mandatory
-            so that the h5Browsr interpret correctly the array (see add_data)
-        data_shape: (iterable) the shape of the array to save, mandatory if array_to_save is None
-        data_dimension: (str) one of ['0D', '1D', '2D', 'ND']
-        scan_type: (str) either '', 'scan1D' or 'scan2D'
-        scan_shape: (iterable): the shape of the scan dimensions
-        title: (str) the title attribute of the array node
-        array_to_save: (ndarray or None) data to be saved in the array. If None, array_type and data_shape
-                        should be specified
-        array_type: (np.dtype or numpy types), eg np.float, np.int32 ...
-        enlargeable: (bool) if False, data are save as a CARRAY, otherwise as a EARRAY (for ragged data, see add_sting_array)
-        metadata: (dict) dictionnary whose keys will be saved as the array attributes
-        init: (bool) if True, the array saved in the h5 file is initialized with the correct type but all element equal
-                     to zero. Else, the 'data' key of data_dict is saved as is
-        add_scan_dim: if True, the scan axes dimension (scan_shape iterable) is prepended to the array shape on the hdf5
-                      In that case, the array is usually initialized as zero and further populated
-
-        Returns
-        -------
-        array (CARRAY or EARRAY)
-
-        See Also
-        --------
-        add_data, add_string_array
-        """
-        if array_type is None:
-            if array_to_save is None:
-                array_type = getattr(np, self.settings.child('dynamic').value())
-            else:
-                array_type = array_to_save.dtype
-
-        if data_dimension not in data_dimensions:
-            raise InvalidDataDimension('Invalid data dimension')
-        if data_type not in data_types:
-            raise InvalidDataType('Invalid data type')
-        if scan_type != '':
-            scan_type = utils.uncapitalize(scan_type)
-        if scan_type.lower() not in [s.lower() for s in scan_types]:
-            raise InvalidScanType('Invalid scan type')
-        if enlargeable:
-            if data_shape == (1,):
-                data_shape = None
-            array = self.create_earray(where, utils.capitalize(name), dtype=np.dtype(array_type),
-                                       data_shape=data_shape, title=title)
-        else:
-            if add_scan_dim:  # means it is an array initialization to zero
-                shape = list(scan_shape[:])
-                shape.extend(data_shape)
-                if init or array_to_save is None:
-                    array_to_save = np.zeros(shape, dtype=np.dtype(array_type))
-
-            array = self.create_carray(where, utils.capitalize(name), obj=array_to_save, title=title)
-        self.set_attr(array, 'type', data_type)
-        self.set_attr(array, 'data_dimension', data_dimension)
-        self.set_attr(array, 'scan_type', scan_type)
-        self.set_attr(array, 'scan_subtype', scan_subtype)
-
-        for metadat in metadata:
-            self.set_attr(array, metadat, metadata[metadat])
-        return array
-
-    def add_string_array(self, where, name, title='', metadata=dict([])):
-        array = self.create_vlarray(where, name, dtype='string', title=title)
-        array.attrs['shape'] = (0,)
-        array.attrs['data_dimension'] = '0D'
-        array.attrs['scan_type'] = 'scan1D'
-
-        for metadat in metadata:
-            array.attrs[metadat] = metadata[metadat]
-        return array
-
-    def get_set_group(self, where, name, title=''):
-        self.current_group = super().get_set_group(where, name, title)
-        return self.current_group
-
-    def add_incremental_group(self, group_type, where, title='', settings_as_xml='', metadata=dict([])):
-        """
-        Add a node in the h5 file tree of the group type with an increment in the given name
-        Parameters
-        ----------
-        group_type: (str) one of the possible values of **group_types**
-        where: (str or node) parent node where to create the new group
-        title: (str) node title
-        settings_as_xml: (str) XML string containing Parameters representation (see custom_Tree)
-        metadata: (dict) extra metadata to be saved with this new group node
-
-        Returns
-        -------
-        (node): newly created group node
-        """
-        if group_type not in group_types:
-            raise InvalidGroupType('Invalid group type')
-        nodes = [name for name in self.get_children(self.get_node(where))]
-        nodes_tmp = []
-        for node in nodes:
-            if utils.capitalize(group_type) in node:
-                nodes_tmp.append(node)
-        nodes_tmp.sort()
-        if len(nodes_tmp) == 0:
-            ind_group = -1
-        else:
-            ind_group = int(nodes_tmp[-1][-3:])
-        group = self.get_set_group(where, utils.capitalize(group_type) + '{:03d}'.format(ind_group + 1), title)
-        self.set_attr(group, 'settings', settings_as_xml)
-        if group_type.lower() != 'ch':
-            self.set_attr(group, 'type', group_type.lower())
-        else:
-            self.set_attr(group, 'type', '')
-        for metadat in metadata:
-            self.set_attr(group, metadat, metadata[metadat])
-        return group
-
-    def add_det_group(self, where, title='', settings_as_xml='', metadata=dict([])):
-        """
-        Add a new group of type detector
-        See Also
-        -------
-        add_incremental_group
-        """
-        group = self.add_incremental_group('detector', where, title, settings_as_xml, metadata)
-        return group
-
-    def add_CH_group(self, where, title='', settings_as_xml='', metadata=dict([])):
-        """
-        Add a new group of type channel
-        See Also
-        -------
-        add_incremental_group
-        """
-        group = self.add_incremental_group('ch', where, title, settings_as_xml, metadata)
-        return group
-
-    def add_live_scan_group(self, where, dimensionality, title='', settings_as_xml='', metadata=dict([])):
-        """
-        Add a new group of type live scan
-        See Also
-        -------
-        add_incremental_group
-        """
-        metadata.update(settings=settings_as_xml)
-        group = self.add_group(utils.capitalize('Live_scan_{:s}'.format(dimensionality)), '', where, title=title,
-                               metadata=metadata)
-        return group
-
-    def add_move_group(self, where, title='', settings_as_xml='', metadata=dict([])):
-        """
-        Add a new group of type move
-        See Also
-        -------
-        add_incremental_group
-        """
-        group = self.add_incremental_group('move', where, title, settings_as_xml, metadata)
-        return group
-
-    def parameter_tree_changed(self, param, changes):
-        for param, change, data in changes:
-            path = self.settings.childPath(param)
-
-            if change == 'childAdded':
-                pass
-
-            elif change == 'value':
-                if param.name() == 'show_file':
-                    param.setValue(False)
-                    self.show_file_content()
-
-                elif param.name() == 'base_path':
-                    try:
-                        if not os.path.isdir(param.value()):
-                            os.mkdir(param.value())
-                    except Exception as e:
-                        logger.warning(f"The base path couldn't be set, please check your options: {str(e)}")
-                        self.update_status("The base path couldn't be set, please check your options")
-
-                elif param.name() in putils.iter_children(self.settings.child('compression_options'), []):
-                    compression = self.settings.child('compression_options', 'h5comp_library').value()
-                    compression_opts = self.settings.child('compression_options', 'h5comp_level').value()
-                    self.define_compression(compression, compression_opts)
-
-            elif change == 'parent':
-                pass
-
-    def update_status(self, status):
-        # self.status_sig.emit(utils.ThreadCommand("Update_Status", [status, 'log']))
-        # logger.info(status)
-        pass
-
-    def show_file_content(self):
-        form = QtWidgets.QWidget()
-        if not self.isopen():
-            if self.h5_file_path is not None:
-                if self.h5_file_path.exists():
-                    self.analysis_prog = H5Browser(form, h5file_path=self.h5_file_path)
-                else:
-                    logger.warning('The h5 file path has not been defined yet')
-            else:
-                logger.warning('The h5 file path has not been defined yet')
-        else:
-            self.flush()
-            self.analysis_prog = H5Browser(form, h5file=self.h5file)
-        form.show()
-
-
-class H5Saver(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
-    """
-
-    status_sig = Signal(utils.ThreadCommand)
-    new_file_sig = Signal(bool)
-
-    def __init__(self, *args, **kwargs):
-        QObject.__init__(self)
-        H5SaverBase.__init__(self, *args, **kwargs)
-
-        self.settings_tree = ParameterTree()
-        self.settings_tree.setMinimumHeight(310)
-        self.settings_tree.setParameters(self.settings, showTop=False)
-        self.settings.child(('new_file')).sigActivated.connect(lambda: self.emit_new_file(True))
-
-    def close(self):
-        # to display the correct interface to other parts of the library
-        # TODO create the related interface/abstract class
-
-        self.close_file()
-
-    def emit_new_file(self, 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
-        """
-        self.new_file_sig.emit(status)
-
-
-class H5Logger(AbstractLogger):
-    def __init__(self, *args, **kwargs):
-        self.h5saver = H5Saver(*args, save_type='logger', **kwargs)
-
-    def close(self):
-        self.h5saver.close_file()
-
-    @property
-    def settings_tree(self):
-        return self.h5saver.settings_tree
-
-    @property
-    def settings(self):
-        return self.h5saver.settings
-
-    def init_logger(self, settings):
-        self.h5saver.init_file(update_h5=True, metadata=dict(settings=settings))
-        self.h5saver.flush()
-        return True
-
-    def get_handler(self):
-        return H5LogHandler(self.h5saver)
-
-    def add_detector(self, det_name, settings):
-        if det_name not in self.h5saver.raw_group.children_name():
-            det_group = self.h5saver.add_det_group(self.h5saver.raw_group, det_name, settings)
-            self.h5saver.add_navigation_axis(np.array([0.0, ]),
-                                             det_group, 'time_axis', enlargeable=True,
-                                             title='Time axis',
-                                             metadata=dict(label='Time axis', units='s', nav_index=0))
-
-    def add_datas(self, datas):
-        det_name = datas['name']
-        det_group = self.h5saver.get_group_by_title(self.h5saver.raw_group, det_name)
-        time_array = self.h5saver.get_node(det_group, 'Logger_time_axis')
-        time_array.append(np.array([datas['acq_time_s']]))
-
-        data_types = ['data0D', 'data1D']
-        if self.settings.child(('save_2D')).value():
-            data_types.extend(['data2D', 'dataND'])
-
-        for data_type in data_types:
-            if data_type in datas.keys() and len(datas[data_type]) != 0:
-                if not self.h5saver.is_node_in_group(det_group, data_type):
-                    data_group = self.h5saver.add_data_group(det_group, data_type, metadata=dict(type='scan'))
-                else:
-                    data_group = self.h5saver.get_node(det_group, utils.capitalize(data_type))
-                for ind_channel, channel in enumerate(datas[data_type]):
-                    channel_group = self.h5saver.get_group_by_title(data_group, channel)
-                    if channel_group is None:
-                        channel_group = self.h5saver.add_CH_group(data_group, title=channel)
-                        data_array = self.h5saver.add_data(channel_group, datas[data_type][channel],
-                                                           scan_type='scan1D', enlargeable=True)
-                    else:
-                        data_array = self.h5saver.get_node(channel_group, 'Data')
-                    if data_type == 'data0D':
-                        data_array.append(np.array([datas[data_type][channel]['data']]))
-                    else:
-                        data_array.append(datas[data_type][channel]['data'])
-        self.h5saver.flush()
-        self.settings.child(('N_saved')).setValue(
-            self.settings.child(('N_saved')).value() + 1)
-
-    def stop_logger(self):
-        self.h5saver.flush()
-
-
-def find_scan_node(scan_node):
-    """
-    utility function to find the parent node of "scan" type, meaning some of its children (DAQ_scan case)
-    or co-nodes (daq_logger case) are navigation axes
-    Parameters
-    ----------
-    scan_node: (pytables node)
-        data node from where this function look for its navigation axes if any
-    Returns
-    -------
-    node: the parent node of 'scan' type
-    list: the data nodes of type 'navigation_axis' corresponding to the initial data node
-
-
-    """
-    try:
-        while True:
-            if scan_node.attrs['type'] == 'scan':
-                break
-            else:
-                scan_node = scan_node.parent_node
-        children = list(scan_node.children().values())  # for data saved using daq_scan
-        children.extend([scan_node.parent_node.children()[child] for child in
-                         scan_node.parent_node.children_name()])  # for data saved using the daq_logger
-        nav_children = []
-        for child in children:
-            if 'type' in child.attrs.attrs_name:
-                if child.attrs['type'] == 'navigation_axis':
-                    nav_children.append(child)
-        return scan_node, nav_children
-    except Exception:
-        return None, []
-
-
-class H5BrowserUtil(H5Backend):
-    """Class to handle manipulation and export of h5 nodes"""
-
-    def __init__(self, backend='tables'):
-        super().__init__(backend=backend)
-
-    def export_data(self, node_path='/', filesavename: str = 'datafile.h5'):
-        """Initialize the correct exporter and export the node"""
-
-        # Format the node and file type
-        filepath = Path(filesavename)
-        node = self.get_node(node_path)
-        # Separate dot from extension
-        extension = filepath.suffix[1:]
-        # Obtain the suitable exporter object
-        exporter = ExporterFactory.create_exporter(extension)
-        # Export the data
-        exporter._export_data(node, filepath)
-
-    def get_h5file_scans(self, where='/'):
-        # TODO add a test for this method
-        scan_list = []
-        where = self.get_node(where)
-        for node in self.walk_nodes(where):
-            if 'pixmap2D' in node.attrs.attrs_name:
-                scan_list.append(
-                    dict(scan_name='{:s}_{:s}'.format(node.parent_node.name, node.name), path=node.path,
-                         data=node.attrs['pixmap2D']))
-
-        return scan_list
-
-    def get_h5_attributes(self, node_path):
-        """
-
-        """
-
-        node = self.get_node(node_path)
-        attrs_names = node.attrs.attrs_name
-        attr_dict = OrderedDict([])
-        for attr in attrs_names:
-            # if attr!='settings':
-            attr_dict[attr] = node.attrs[attr]
-
-        settings = None
-        scan_settings = None
-        if 'settings' in attrs_names:
-            if node.attrs['settings'] != '':
-                settings = node.attrs['settings']
-
-        if 'scan_settings' in attrs_names:
-            if node.attrs['scan_settings'] != '':
-                scan_settings = node.attrs['scan_settings']
-        pixmaps = []
-        for attr in attrs_names:
-            if 'pixmap' in attr:
-                pixmaps.append(node.attrs[attr])
-
-        return attr_dict, settings, scan_settings, pixmaps
-
-
-class H5Browser(QObject):
-    """UI used to explore h5 files, plot and export subdatas"""
-    data_node_signal = Signal(
-        str)  # the path of a node where data should be monitored, displayed...whatever use from the caller
-    status_signal = Signal(str)
-
-    def __init__(self, parent, h5file=None, h5file_path=None, backend='tables'):
-        """
-
-        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) eitre 'tables, 'h5py' or 'h5pyd'
-
-        See Also
-        --------
-        H5Backend, H5Backend
-        """
-
-        super(H5Browser, self).__init__()
-        if not (isinstance(parent, QtWidgets.QWidget) or isinstance(parent, QtWidgets.QMainWindow)):
-            raise Exception('no valid parent container, expected a QWidget or a QMainWindow')
-
-        if isinstance(parent, QtWidgets.QMainWindow):
-            self.main_window = parent
-            self.parent = QtWidgets.QWidget()
-            self.main_window.setCentralWidget(self.parent)
-        else:
-            self.main_window = None
-            self.parent = parent
-
-        self.backend = backend
-        self.current_node_path = None
-
-        # construct the UI interface
-        self.ui = QObject()  # the user interface
-        self.set_GUI()
-
-        # construct the h5 interface and load the file (or open a select file message)
-        self.h5utils = H5BrowserUtil(backend=self.backend)
-        if h5file is None:
-            if h5file_path is None:
-                h5file_path = select_file(save=False, ext=['h5', 'hdf5'])
-            if h5file_path != '':
-                self.h5utils.open_file(h5file_path, 'r+')
-            else:
-                return
-        else:
-            self.h5utils.h5file = h5file
-
-        self.check_version()
-        self.populate_tree()
-        self.ui.h5file_tree.ui.Open_Tree.click()
-
-    def check_version(self):
-        if 'pymodaq_version' in self.h5utils.root().attrs.attrs_name:
-            if version_mod.parse(self.h5utils.root().attrs['pymodaq_version']) < version_mod.parse('2.0'):
-                msgBox = QtWidgets.QMessageBox(parent=None)
-                msgBox.setWindowTitle("Invalid version")
-                msgBox.setText(f"Your file has been saved using PyMoDAQ "
-                               f"version {self.h5utils.root().attrs['pymodaq_version']} "
-                               f"while you're using version: {utils.get_version()}\n"
-                               f"Please create and use an adapted environment to use this version (up to 1.6.4):\n"
-                               f"pip install pymodaq==1.6.4")
-                ret = msgBox.exec()
-                self.quit_fun()
-                if self.main_window is not None:
-                    self.main_window.close()
-                else:
-                    self.parent.close()
-
-    def add_comments(self, status, comment=''):
-        try:
-            self.current_node_path = self.get_tree_node_path()
-            node = self.h5utils.get_node(self.current_node_path)
-            if 'comments' in node.attrs.attrs_name:
-                tmp = node.attrs['comments']
-            else:
-                tmp = ''
-            if comment == '':
-                text, res = QtWidgets.QInputDialog.getMultiLineText(None, 'Enter comments', 'Enter comments here:', tmp)
-                if res and text != '':
-                    comment = text
-                node.attrs['comments'] = comment
-            else:
-                node.attrs['comments'] = tmp + comment
-
-            self.h5utils.flush()
-
-        except Exception as e:
-            logger.exception(str(e))
-
-    def get_tree_node_path(self):
-        return self.ui.h5file_tree.ui.Tree.currentItem().text(2)
-
-    def export_data(self):
-        try:
-            # get file filters automatically
-            file_filter = ExporterFactory.get_file_filters()
-            file = select_file(save=True, filter=file_filter)
-            self.current_node_path = self.get_tree_node_path()
-            # Here select and initialize exporter from extension
-            if file != '':
-                self.h5utils.export_data(self.current_node_path, str(file))
-
-        except Exception as e:
-            logger.exception(str(e))
-
-    def save_file(self, filename=None):
-        if filename is None:
-            filename = select_file(save=True, ext='txt')
-        if filename != '':
-            self.h5utils.save_file(filename)
-
-    def quit_fun(self):
-        """
-        """
-        try:
-            self.h5utils.close_file()
-            if self.main_window is None:
-                self.parent.close()
-            else:
-                self.main_window.close()
-        except Exception as e:
-            logger.exception(str(e))
-
-    def create_menu(self):
-        """
-
-        """
-        self.menubar = self.main_window.menuBar()
-
-        # %% create Settings menu
-        self.file_menu = self.menubar.addMenu('File')
-        load_action = self.file_menu.addAction('Load file')
-        load_action.triggered.connect(lambda: self.load_file(None))
-        save_action = self.file_menu.addAction('Save file')
-        save_action.triggered.connect(self.save_file)
-        self.file_menu.addSeparator()
-        quit_action = self.file_menu.addAction('Quit')
-        quit_action.triggered.connect(self.quit_fun)
-
-        # help menu
-        help_menu = self.menubar.addMenu('?')
-        action_about = help_menu.addAction('About')
-        action_about.triggered.connect(self.show_about)
-        action_help = help_menu.addAction('Help')
-        action_help.triggered.connect(self.show_help)
-        action_help.setShortcut(QtCore.Qt.Key_F1)
-        log_action = help_menu.addAction('Show log')
-        log_action.triggered.connect(self.show_log)
-
-    def show_about(self):
-        splash_path = os.path.join(os.path.split(os.path.split(__file__)[0])[0], 'splash.png')
-        splash = QtGui.QPixmap(splash_path)
-        self.splash_sc = QtWidgets.QSplashScreen(splash, QtCore.Qt.WindowStaysOnTopHint)
-        self.splash_sc.setVisible(True)
-        self.splash_sc.showMessage(f"PyMoDAQ version {utils.get_version()}\n"
-                                   f"Modular Acquisition with Python\nWritten by Sébastien Weber",
-                                   QtCore.Qt.AlignRight, QtCore.Qt.white)
-
-    def show_log(self):
-        import webbrowser
-        webbrowser.open(logger.handlers[0].baseFilename)
-
-    def show_help(self):
-        QtGui.QDesktopServices.openUrl(QtCore.QUrl("http://pymodaq.cnrs.fr"))
-
-    def set_GUI(self):
-
-        if self.main_window is not None:
-            self.create_menu()
-
-        layout = QtWidgets.QGridLayout()
-
-        V_splitter = QtWidgets.QSplitter(Qt.Vertical)
-        V_splitter2 = QtWidgets.QSplitter(Qt.Vertical)
-        H_splitter = QtWidgets.QSplitter(Qt.Horizontal)
-
-        Form = QtWidgets.QWidget()
-        # self.ui.h5file_tree = Tree_layout(Form,col_counts=2,labels=["Node",'Pixmap'])
-        self.ui.h5file_tree = Tree_layout(Form, col_counts=1, labels=["Node"])
-        self.ui.h5file_tree.ui.Tree.setMinimumWidth(300)
-        self.ui.h5file_tree.ui.Tree.itemClicked.connect(self.show_h5_attributes)
-        self.ui.h5file_tree.ui.Tree.itemDoubleClicked.connect(self.show_h5_data)
-
-        self.export_action = QtWidgets.QAction("Export data", None)
-        self.export_action.triggered.connect(self.export_data)
-
-        self.add_comments_action = QtWidgets.QAction("Add comments to this node", None)
-        self.add_comments_action.triggered.connect(self.add_comments)
-        self.ui.h5file_tree.ui.Tree.addAction(self.export_action)
-        self.ui.h5file_tree.ui.Tree.addAction(self.add_comments_action)
-
-        V_splitter.addWidget(Form)
-        self.ui.attributes_tree = ParameterTree()
-        self.ui.attributes_tree.setMinimumWidth(300)
-        V_splitter.addWidget(self.ui.attributes_tree)
-
-        self.settings_raw = Parameter.create(name='Param_raw', type='group')
-        self.ui.attributes_tree.setParameters(self.settings_raw, showTop=False)
-
-        H_splitter.addWidget(V_splitter)
-        self.pixmap_widget = QtWidgets.QWidget()
-        self.pixmap_widget.setMaximumHeight(100)
-        V_splitter2.addWidget(self.pixmap_widget)
-        self.ui.settings_tree = ParameterTree()
-        self.ui.settings_tree.setMinimumWidth(300)
-        V_splitter2.addWidget(self.ui.settings_tree)
-        self.ui.text_list = QtWidgets.QListWidget()
-
-        V_splitter2.addWidget(self.ui.text_list)
-
-        H_splitter.addWidget(V_splitter2)
-
-        form_viewer = QtWidgets.QWidget()
-        self.viewer_area = DockArea()
-        self.hyperviewer = ViewerND(self.viewer_area)
-        H_splitter.addWidget(self.viewer_area)
-
-        layout.addWidget(H_splitter)
-        self.parent.setLayout(layout)
-
-        self.settings = Parameter.create(name='Param', type='group')
-        self.ui.settings_tree.setParameters(self.settings, showTop=False)
-
-        self.status_signal.connect(self.add_log)
-
-    def add_log(self, txt):
-        logger.info(txt)
-
-    def show_h5_attributes(self, item):
-        """
-
-        """
-        try:
-            self.current_node_path = self.get_tree_node_path()
-
-            attr_dict, settings, scan_settings, pixmaps = self.h5utils.get_h5_attributes(self.current_node_path)
-
-            for child in self.settings_raw.children():
-                child.remove()
-            params = []
-            for attr in attr_dict:
-                params.append({'title': attr, 'name': attr, 'type': 'str', 'value': attr_dict[attr], 'readonly': True})
-            self.settings_raw.addChildren(params)
-
-            if settings is not None:
-                for child in self.settings.children():
-                    child.remove()
-                QtWidgets.QApplication.processEvents()  # so that the tree associated with settings updates
-                params = pymodaq.daq_utils.parameter.ioxml.XML_string_to_parameter(settings)
-                self.settings.addChildren(params)
-
-            if scan_settings is not None:
-                params = pymodaq.daq_utils.parameter.ioxml.XML_string_to_parameter(scan_settings)
-                self.settings.addChildren(params)
-
-            if pixmaps == []:
-                self.pixmap_widget.setVisible(False)
-            else:
-                self.pixmap_widget.setVisible(True)
-                self.show_pixmaps(pixmaps)
-
-        except Exception as e:
-            logger.exception(str(e))
-
-    def show_pixmaps(self, pixmaps=[]):
-        if self.pixmap_widget.layout() is None:
-            layout = QtWidgets.QHBoxLayout()
-            self.pixmap_widget.setLayout(layout)
-        while 1:
-            child = self.pixmap_widget.layout().takeAt(0)
-            if not child:
-                break
-            child.widget().deleteLater()
-            QtWidgets.QApplication.processEvents()
-        labs = []
-        for pix in pixmaps:
-            labs.append(pngbinary2Qlabel(pix))
-            self.pixmap_widget.layout().addWidget(labs[-1])
-
-    def show_h5_data(self, item):
-        """
-        """
-        try:
-            self.current_node_path = item.text(2)
-            self.show_h5_attributes(item)
-            node = self.h5utils.get_node(self.current_node_path)
-            self.data_node_signal.emit(self.current_node_path)
-            if 'ARRAY' in node.attrs['CLASS']:
-                data, axes, nav_axes, is_spread = get_h5_data_from_node(node)
-                # data, axes, nav_axes, is_spread = self.h5utils.get_h5_data(self.current_node_path)
-                if isinstance(data, np.ndarray):
-                    if 'scan_type' in node.attrs.attrs_name:
-                        scan_type = node.attrs['scan_type']
-                    else:
-                        scan_type = ''
-                    self.hyperviewer.show_data(copy.deepcopy(data), nav_axes=nav_axes, is_spread=is_spread,
-                                               scan_type=scan_type, **copy.deepcopy(axes))
-                    self.hyperviewer.init_ROI()
-                elif isinstance(data, list):
-                    if not (not data):
-                        if isinstance(data[0], str):
-                            self.ui.text_list.clear()
-                            for txt in data:
-                                self.ui.text_list.addItem(txt)
-        except Exception as e:
-            logger.exception(str(e))
-
-    def populate_tree(self):
-        """
-            | Init the ui-tree and store data into calling the h5_tree_to_Qtree convertor method
-
-            See Also
-            --------
-            h5tree_to_QTree, update_status
-        """
-        try:
-            if self.h5utils.h5file is not None:
-                self.ui.h5file_tree.ui.Tree.clear()
-                base_node = self.h5utils.root()
-                base_tree_item, pixmap_items = h5tree_to_QTree(base_node)
-                self.ui.h5file_tree.ui.Tree.addTopLevelItem(base_tree_item)
-                self.add_widget_totree(pixmap_items)
-
-        except Exception as e:
-            logger.exception(str(e))
-
-    def add_widget_totree(self, pixmap_items):
-
-        for item in pixmap_items:
-            widget = QtWidgets.QWidget()
-
-            vLayout = QtWidgets.QVBoxLayout()
-            label1D = QtWidgets.QLabel()
-            bytes = QByteArray(item['node'].attrs['pixmap1D'])
-            im1 = QtGui.QImage.fromData(bytes)
-            a = QtGui.QPixmap.fromImage(im1)
-            label1D.setPixmap(a)
-
-            label2D = QtWidgets.QLabel()
-            bytes = QByteArray(item['node'].attrs['pixmap2D'])
-            im2 = QtGui.QImage.fromData(bytes)
-            b = QtGui.QPixmap.fromImage(im2)
-            label2D.setPixmap(b)
-
-            vLayout.addWidget(label1D)
-            vLayout.addwidget(label2D)
-            widget.setLayout(vLayout)
-            self.ui.h5file_tree.ui.Tree.setItemWidget(item['item'], 1, widget)
-
-
-def browse_data(fname=None, ret_all=False, message=None):
-    """
-        | Browse data present in any h5 file, when user has selected the one,
-    """
-    if fname is None:
-        fname = str(select_file(start_path=config('data_saving', 'h5file', 'save_path'), save=False, ext='h5'))
-
-    if type(fname) != str:
-        try:
-            fname = str(fname)
-        except Exception:
-            raise Exception('filename in browse data is not valid')
-    if fname != '':
-        (root, ext) = os.path.splitext(fname)
-        if not ('h5' in ext or 'hdf5' in ext):
-            warnings.warn('This is not a PyMODAQ h5 file, there could be issues', Warning)
-
-        form = QtWidgets.QWidget()
-        browser = H5Browser(form, h5file_path=fname)
-
-        dialog = QtWidgets.QDialog()
-        vlayout = QtWidgets.QVBoxLayout()
-
-        vlayout.addWidget(form)
-        dialog.setLayout(vlayout)
-        buttonBox = QtWidgets.QDialogButtonBox(parent=dialog)
-
-        buttonBox.addButton('OK', buttonBox.AcceptRole)
-        buttonBox.accepted.connect(dialog.accept)
-        buttonBox.addButton('Cancel', buttonBox.RejectRole)
-        buttonBox.rejected.connect(dialog.reject)
-        vlayout.addWidget(buttonBox)
-
-        dialog.setWindowTitle('Select a data node in the tree')
-        if message is None or not isinstance(message, str):
-            dialog.setWindowTitle('Select a data node in the tree')
-        else:
-            dialog.setWindowTitle(message)
-        res = dialog.exec()
-
-        if res == dialog.Accepted:
-            node_path = browser.current_node_path
-            data = browser.h5utils.get_node(node_path).read()
-        else:
-            data = None
-            node_path = None
-
-        browser.h5utils.close_file()
-
-        if ret_all:
-            return data, fname, node_path
-        else:
-            return data
-    return None, '', ''
-
-
-### Additional imports. This is needed to register additional formats in the Exporterfactory
-
-# This Exporter depends on the availability of the hyperspy package.
-# In the future, adding an optional dependency
-found = importlib.util.find_spec("hyperspy")
-if not found:
-    logger.warning('Hyperspy module not found. To save data in the .hspy format, install hyperspy 1.7 or more recent.')
-else:
-    import pymodaq.daq_utils.h5exporter_hyperspy
-
-if __name__ == '__main__':
-    app = QtWidgets.QApplication(sys.argv)
-    win = QtWidgets.QMainWindow()
-    area = DockArea()
-    win.setCentralWidget(area)
-    win.resize(1000, 500)
-    win.setWindowTitle('PyMoDAQ H5Browser')
-    prog = H5Browser(win)
-    win.show()
-    QtWidgets.QApplication.processEvents()
-    sys.exit(app.exec_())