pymodaq_data 5.1.7__tar.gz → 5.2.0a1__tar.gz

{pymodaq_data-5.1.7 → pymodaq_data-5.2.0a1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymodaq_data
-Version: 5.1.7
+Version: 5.2.0a1
 Summary: Modular Data Acquisition with Python
 Project-URL: Homepage, http://pymodaq.cnrs.fr
 Project-URL: Source, https://github.com/PyMoDAQ/PyMoDAQ
@@ -45,8 +45,7 @@ Classifier: Topic :: Software Development :: User Interfaces
 Requires-Python: >=3.8
 Requires-Dist: pymodaq-utils>=0.0.8
 Requires-Dist: scipy
-Requires-Dist: tables<3.9; python_version < '3.10'
-Requires-Dist: tables>=3.10; python_version >= '3.10'
+Requires-Dist: tables>=3.10
 Provides-Extra: dev
 Requires-Dist: flake8; extra == 'dev'
 Requires-Dist: h5py; extra == 'dev'
@@ -69,52 +68,52 @@ PyMoDAQ Data
    :target: https://pypi.org/project/pymodaq_data/
    :alt: Latest Version
 
-.. image:: https://readthedocs.org/projects/pymodaq/badge/?version=latest
-   :target: https://pymodaq.readthedocs.io/en/stable/?badge=latest
+.. image:: https://readthedocs.org/projects/pymodaq/badge/?version=malik-irain-patch-2
+   :target: https://pymodaq.readthedocs.io/en/stable/?badge=malik-irain-patch-2
    :alt: Documentation Status
 
-.. image:: https://codecov.io/gh/PyMoDAQ/pymodaq_data/branch/5.0.x_dev/graph/badge.svg?token=H32JflMEYR 
- :target: https://codecov.io/gh/PyMoDAQ/pymodaq_data
+.. image:: https://codecov.io/gh/PyMoDAQ/PyMoDAQ/branch/malik-irain-patch-2/graph/badge.svg?token=IQNJRCQDM2 
+ :target: https://codecov.io/gh/PyMoDAQ/PyMoDAQ
 
 +-------------+-------------+---------------+
 |             | Linux       | Windows       |
 +=============+=============+===============+
-| Python 3.9  | |39-linux|  | |39-windows|  |
-+-------------+-------------+---------------+
 | Python 3.10 | |310-linux| | |310-windows| |
 +-------------+-------------+---------------+
 | Python 3.11 | |311-linux| | |311-windows| |
 +-------------+-------------+---------------+
 | Python 3.12 | |312-linux| | |312-windows| |
 +-------------+-------------+---------------+
+| Python 3.13 | |313-linux| | |313-windows| |
++-------------+-------------+---------------+
 
 
 
 
-.. |39-linux| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/5.1.x/tests_Linux_3.9.svg
-    :target: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/tests-data.yml
 
-.. |310-linux| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/5.1.x/tests_Linux_3.10.svg
-    :target: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/tests-data.yml
+.. |310-linux| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/malik-irain-patch-2/tests_Linux_3.10.svg
+    :target: https://github.com/PyMoDAQ/PyMoDAQ/actions/workflows/tests-data.yml
 
-.. |311-linux| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/5.1.x/tests_Linux_3.11.svg
-    :target: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/tests-data.yml
+.. |311-linux| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/malik-irain-patch-2/tests_Linux_3.11.svg
+    :target: https://github.com/PyMoDAQ/PyMoDAQ/actions/workflows/tests-data.yml
 
-.. |312-linux| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/5.1.x/tests_Linux_3.12.svg
-    :target: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/tests-data.yml
+.. |312-linux| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/malik-irain-patch-2/tests_Linux_3.12.svg
+    :target: https://github.com/PyMoDAQ/PyMoDAQ/actions/workflows/tests-data.yml
 
-.. |39-windows| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/5.1.x/tests_Windows_3.9.svg
-    :target: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/tests-data.yml
+.. |313-linux| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/malik-irain-patch-2/tests_Linux_3.13.svg
+    :target: https://github.com/PyMoDAQ/PyMoDAQ/actions/workflows/tests-data.yml
 
-.. |310-windows| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/5.1.x/tests_Windows_3.10.svg
-    :target: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/tests-data.yml
+.. |310-windows| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/malik-irain-patch-2/tests_Windows_3.10.svg
+    :target: https://github.com/PyMoDAQ/PyMoDAQ/actions/workflows/tests-data.yml
 
-.. |311-windows| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/5.1.x/tests_Windows_3.11.svg
-    :target: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/tests-data.yml
+.. |311-windows| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/malik-irain-patch-2/tests_Windows_3.11.svg
+    :target: https://github.com/PyMoDAQ/PyMoDAQ/actions/workflows/tests-data.yml
 
-.. |312-windows| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/5.1.x/tests_Windows_3.12.svg
-    :target: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/tests-data.yml
+.. |312-windows| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/malik-irain-patch-2/tests_Windows_3.12.svg
+    :target: https://github.com/PyMoDAQ/PyMoDAQ/actions/workflows/tests-data.yml
 
+.. |313-windows| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/malik-irain-patch-2/tests_Windows_3.13.svg
+    :target: https://github.com/PyMoDAQ/PyMoDAQ/actions/workflows/tests-data.yml
 
 
 

{pymodaq_data-5.1.7 → pymodaq_data-5.2.0a1}/README.rst

@@ -11,52 +11,52 @@ PyMoDAQ Data
    :target: https://pypi.org/project/pymodaq_data/
    :alt: Latest Version
 
-.. image:: https://readthedocs.org/projects/pymodaq/badge/?version=latest
-   :target: https://pymodaq.readthedocs.io/en/stable/?badge=latest
+.. image:: https://readthedocs.org/projects/pymodaq/badge/?version=malik-irain-patch-2
+   :target: https://pymodaq.readthedocs.io/en/stable/?badge=malik-irain-patch-2
    :alt: Documentation Status
 
-.. image:: https://codecov.io/gh/PyMoDAQ/pymodaq_data/branch/5.0.x_dev/graph/badge.svg?token=H32JflMEYR 
- :target: https://codecov.io/gh/PyMoDAQ/pymodaq_data
+.. image:: https://codecov.io/gh/PyMoDAQ/PyMoDAQ/branch/malik-irain-patch-2/graph/badge.svg?token=IQNJRCQDM2 
+ :target: https://codecov.io/gh/PyMoDAQ/PyMoDAQ
 
 +-------------+-------------+---------------+
 |             | Linux       | Windows       |
 +=============+=============+===============+
-| Python 3.9  | |39-linux|  | |39-windows|  |
-+-------------+-------------+---------------+
 | Python 3.10 | |310-linux| | |310-windows| |
 +-------------+-------------+---------------+
 | Python 3.11 | |311-linux| | |311-windows| |
 +-------------+-------------+---------------+
 | Python 3.12 | |312-linux| | |312-windows| |
 +-------------+-------------+---------------+
+| Python 3.13 | |313-linux| | |313-windows| |
++-------------+-------------+---------------+
 
 
 
 
-.. |39-linux| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/5.1.x/tests_Linux_3.9.svg
-    :target: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/tests-data.yml
 
-.. |310-linux| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/5.1.x/tests_Linux_3.10.svg
-    :target: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/tests-data.yml
+.. |310-linux| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/malik-irain-patch-2/tests_Linux_3.10.svg
+    :target: https://github.com/PyMoDAQ/PyMoDAQ/actions/workflows/tests-data.yml
 
-.. |311-linux| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/5.1.x/tests_Linux_3.11.svg
-    :target: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/tests-data.yml
+.. |311-linux| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/malik-irain-patch-2/tests_Linux_3.11.svg
+    :target: https://github.com/PyMoDAQ/PyMoDAQ/actions/workflows/tests-data.yml
 
-.. |312-linux| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/5.1.x/tests_Linux_3.12.svg
-    :target: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/tests-data.yml
+.. |312-linux| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/malik-irain-patch-2/tests_Linux_3.12.svg
+    :target: https://github.com/PyMoDAQ/PyMoDAQ/actions/workflows/tests-data.yml
 
-.. |39-windows| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/5.1.x/tests_Windows_3.9.svg
-    :target: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/tests-data.yml
+.. |313-linux| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/malik-irain-patch-2/tests_Linux_3.13.svg
+    :target: https://github.com/PyMoDAQ/PyMoDAQ/actions/workflows/tests-data.yml
 
-.. |310-windows| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/5.1.x/tests_Windows_3.10.svg
-    :target: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/tests-data.yml
+.. |310-windows| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/malik-irain-patch-2/tests_Windows_3.10.svg
+    :target: https://github.com/PyMoDAQ/PyMoDAQ/actions/workflows/tests-data.yml
 
-.. |311-windows| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/5.1.x/tests_Windows_3.11.svg
-    :target: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/tests-data.yml
+.. |311-windows| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/malik-irain-patch-2/tests_Windows_3.11.svg
+    :target: https://github.com/PyMoDAQ/PyMoDAQ/actions/workflows/tests-data.yml
 
-.. |312-windows| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/5.1.x/tests_Windows_3.12.svg
-    :target: https://github.com/PyMoDAQ/pymodaq_data/actions/workflows/tests-data.yml
+.. |312-windows| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/malik-irain-patch-2/tests_Windows_3.12.svg
+    :target: https://github.com/PyMoDAQ/PyMoDAQ/actions/workflows/tests-data.yml
 
+.. |313-windows| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/malik-irain-patch-2/tests_Windows_3.13.svg
+    :target: https://github.com/PyMoDAQ/PyMoDAQ/actions/workflows/tests-data.yml
 
 
 

{pymodaq_data-5.1.7 → pymodaq_data-5.2.0a1}/pyproject.toml

@@ -33,8 +33,7 @@ classifiers = [
 dependencies = [
     "pymodaq_utils>=0.0.8",
     "scipy",
-    "tables>=3.10; python_version>=\"3.10\"",  # issue with some version of required package blosc2>=2.2.8
-    "tables<3.9; python_version<\"3.10\"",  # issue with some version of required package blosc2>=2.2.8
+    "tables>=3.10",
 ]
 
 [project.optional-dependencies]

{pymodaq_data-5.1.7 → pymodaq_data-5.2.0a1}/src/pymodaq_data/__init__.py

@@ -15,11 +15,12 @@ try:
     except Exception:
         print("Couldn't create the local folder to store logs , presets...")
 
+    import pymodaq_data.config
     logger.info('************************')
     logger.info('Initializing the pint unit register')
     logger.info('************************')
     ureg = UnitRegistry()
-    ureg.default_format = '~'
+    ureg.formatter.default_format = '~'
     Q_ = ureg.Quantity
     Unit = ureg.Unit
     logger.info('')
@@ -45,7 +46,8 @@ try:
 
 
     from pymodaq_data.data import (DataRaw, DataWithAxes, DataToExport, Axis,
-                                   DataCalculated, DataDim, DataDistribution, DataSource, DataBase)
+                                   DataCalculated, DataDim, DataDistribution, DataSource, DataBase,
+                                   )
 
 except Exception as e:
     try:

pymodaq_data-5.2.0a1/src/pymodaq_data/config.py

@@ -0,0 +1,11 @@
+from pathlib import Path
+
+from pymodaq_utils.config import (GlobalConfig, BaseConfig)
+
+
+@GlobalConfig.register()
+class Config(BaseConfig):
+    """Main class to deal with configuration values for this plugin"""
+    config_template_path = Path(__file__).parent.joinpath('resources/config_template.toml')
+    config_name = f"data"
+

{pymodaq_data-5.1.7 → pymodaq_data-5.2.0a1}/src/pymodaq_data/data.py

@@ -6,13 +6,13 @@ Created the 28/10/2022
 """
 from __future__ import annotations
 
-from abc import ABCMeta, abstractmethod, abstractproperty
+from abc import ABCMeta, abstractmethod
 import numbers
 from copy import deepcopy
 
 import numpy as np
 from numpy.lib.mixins import NDArrayOperatorsMixin
-from typing import List, Tuple, Union, Any, Callable
+from typing import List, Tuple, Union, Any, Callable, Type
 from typing import Iterable as IterableType
 from collections.abc import Iterable
 from collections import OrderedDict
@@ -26,25 +26,41 @@ from pint.compat import upcast_type_map
 
 from multipledispatch import dispatch
 
+
 from pymodaq_utils.enums import BaseEnum, enum_checker
 from pymodaq_utils.warnings import deprecation_msg
 from pymodaq_utils.utils import find_objects_in_list_from_attr_name_val
 from pymodaq_utils.logger import set_logger, get_module_name
 
 from pymodaq_utils import math_utils as mutils
-from pymodaq_utils.config import Config
+from pymodaq_utils.config import GlobalConfig as Config
 
 from pymodaq_data.plotting.plotter.plotter import PlotterFactory
 from pymodaq_data.numpy_func import HANDLED_FUNCTIONS, HANDLED_UFUNCS, process_arguments_for_ufuncs
 from pymodaq_data import Q_, ureg, Unit
 from pymodaq_data.slicing import SpecialSlicersData
-from pymodaq_utils.serialize.factory import SerializableFactory, SerializableBase
+from serializall import SerializableFactory, SerializableBase
 
 config = Config()
 plotter_factory = PlotterFactory()
 ser_factory = SerializableFactory()
 logger = set_logger(get_module_name(__file__))
 
+def dimensionless_aware_reduce_units(q: Type[Q_]) -> Type[Q_]:
+    """
+    Take a quantity q and converts it to its reduced units.
+    For dimensionless units it compact them
+
+    Parameters
+    ----------
+    q: The quantity to be reduced
+
+    Returns
+    -------
+    The reduced quantity
+    """
+
+    return q.to_compact() if q.dimensionless else q.to_reduced_units()
 
 def check_units(units: str):
     try:
@@ -364,7 +380,7 @@ class Axis(SerializableBase):
                             data=self.get_quantity().to(units))
 
     def to_reduced_units(self, inplace=False):
-        quantity = self.get_quantity().to_reduced_units()
+        quantity = dimensionless_aware_reduce_units(self.get_quantity())
         if inplace:
             self.data = quantity.magnitude
             self.force_units(str(quantity.units))
@@ -898,6 +914,17 @@ class DataBase(DataLowLevel, NDArrayOperatorsMixin):
         """Convenience method to wrap the DataWithAxes object into a DataToExport"""
         return DataToExport(name, data=[self])
 
+    def split_as_dte(self, name: str = 'mydte') -> DataToExport:
+        """ Convenience method to split each ndarray into a DataWithAxes object """
+        return DataToExport(name, data=[type(self)(self.labels[ind],
+                                                   source=self.source,
+                                                   dim = self.dim,
+                                                   data=[array],
+                                                   labels = [self.labels[ind]],
+                                                   axes = deepcopy(self.axes),
+                                                   units = self.units,
+                                                   ) for ind, array in enumerate(self)])
+
     def add_extra_attribute(self, **kwargs):
         for key in kwargs:
             if key not in self.extra_attributes:
@@ -961,7 +988,7 @@ class DataBase(DataLowLevel, NDArrayOperatorsMixin):
             units = dwa.units
             ufunc_results = [ufunc(*zipped, **kwargs) for zipped in list(zip(*elts))]
             if isinstance(ufunc_results[0], Q_):
-                ufunc_results = [ufunc_result.to_reduced_units() for ufunc_result in ufunc_results]
+                ufunc_results = [dimensionless_aware_reduce_units(ufunc_result) for ufunc_result in ufunc_results]
                 units = str(ufunc_results[0].units)
                 ufunc_results = [ufunc_result.magnitude for ufunc_result in ufunc_results]
             dwa.data = ufunc_results
@@ -2089,7 +2116,7 @@ class DataWithAxes(DataBase, SerializableBase):
         else:
             raise ValueError(f'Cannot create a dwa from a None, should be a list of ndarray')
 
-    def plot(self, plotter_backend: str = config('plotting', 'backend'), *args, viewer=None,
+    def plot(self, plotter_backend: str = config('data', 'plotting', 'backend')[0], *args, viewer=None,
              **kwargs):
         """ Call a plotter factory and its plot method over the actual data"""
         return plotter_factory.get(plotter_backend).plot(self, *args, viewer=viewer, **kwargs)
@@ -3024,7 +3051,7 @@ class DataToExport(DataLowLevel, SerializableBase):
 
         return dte, remaining_bytes
 
-    def plot(self, plotter_backend: str = config('plotting', 'backend'), *args, **kwargs):
+    def plot(self, plotter_backend: str = config('data', 'plotting', 'backend')[0], *args, **kwargs):
         """ Call a plotter factory and its plot method over the actual data"""
         return plotter_factory.get(plotter_backend).plot(self, *args, **kwargs)
 

{pymodaq_data-5.1.7 → pymodaq_data-5.2.0a1}/src/pymodaq_data/h5modules/backends.py

@@ -13,7 +13,7 @@ import pickle
 from typing import Dict
 
 from pymodaq_utils.logger import set_logger, get_module_name
-from pymodaq_utils.config import Config
+from pymodaq_utils.config import GlobalConfig as Config
 from pymodaq_utils.utils import capitalize, JsonConverter
 from pymodaq_utils import utils
 from pymodaq_utils.enums import BaseEnum, enum_checker
@@ -1011,7 +1011,7 @@ class H5Backend:
         array.attrs['backend'] = self.backend
         return array
 
-    def add_group(self, group_name, group_type: Union[GroupType, str], where, title='', metadata=dict([])) -> GROUP:
+    def add_group(self, group_name, group_type: Union[GroupType, str], where, title='', metadata=None) -> GROUP:
         """
         Add a node in the h5 file tree of the group type
         Parameters
@@ -1026,6 +1026,8 @@ class H5Backend:
         -------
         (node): newly created group node
         """
+        if metadata is None:
+            metadata = {}
         if isinstance(where, Node):
             where = where.node
 

{pymodaq_data-5.1.7 → pymodaq_data-5.2.0a1}/src/pymodaq_data/h5modules/browsing.py

@@ -16,7 +16,7 @@ from pathlib import Path
 from packaging import version as version_mod
 
 from pymodaq_utils.logger import set_logger, get_module_name
-from pymodaq_utils.config import Config
+from pymodaq_utils.config import GlobalConfig as Config
 from .backends import H5Backend
 from .exporter import ExporterFactory
 

{pymodaq_data-5.1.7 → pymodaq_data-5.2.0a1}/src/pymodaq_data/h5modules/data_saving.py

@@ -15,7 +15,7 @@ from pymodaq_utils.enums import enum_checker
 from pymodaq_data.data import (Axis, DataDim, DataWithAxes, DataToExport, DataDistribution,
                                DataDimError, squeeze)
 from .saving import DataType, H5SaverLowLevel
-from .backends import GROUP, CARRAY, Node, EARRAY, NodeError
+from .backends import GROUP, CARRAY, Node, EARRAY, NodeError, GroupType # noqa: F401
 from pymodaq_utils.utils import capitalize
 from pymodaq_data.h5modules.saving import SaveType
 
@@ -52,6 +52,14 @@ class DataManagement(metaclass=ABCMeta):
         """
         return f'{capitalize(cls.data_type.value)}{ind:02d}'
 
+    def __getattr__(self, item):
+        """ Allows to call attributes of the underlying H5Saver object"""
+
+        if hasattr(self._h5saver, item):
+            return getattr(self._h5saver, item)
+        else:
+            raise AttributeError(item)
+
     def __enter__(self):
         return self
 
@@ -283,18 +291,21 @@ class DataSaverLoader(DataManagement):
     """
     data_type = DataType['data']
 
-    def __init__(self, h5saver: Union[H5SaverLowLevel, Path]):
+    def __init__(self, h5saver: Union[H5SaverLowLevel, Path],
+                 new_file: bool = False, metadata: dict = None, save_type=SaveType.custom):
         self.data_type = enum_checker(DataType, self.data_type)
 
         if isinstance(h5saver, Path) or isinstance(h5saver, str):
-            h5saver_tmp = H5SaverLowLevel()
-            h5saver_tmp.init_file(file_name=Path(h5saver))
+            h5saver_tmp = H5SaverLowLevel(save_type)
+            h5saver_tmp.init_file(file_name=Path(h5saver),
+                                  new_file=new_file,
+                                  metadata=metadata)
             h5saver = h5saver_tmp
 
         self._h5saver = h5saver
-        self._axis_saver = AxisSaverLoader(h5saver)
+        self._axis_saver = AxisSaverLoader(self._h5saver)
         if not isinstance(self, ErrorSaverLoader):
-            self._error_saver = ErrorSaverLoader(h5saver)
+            self._error_saver = ErrorSaverLoader(self._h5saver)
 
     def isopen(self) -> bool:
         """ Get the opened status of the underlying hdf5 file"""
@@ -754,15 +765,27 @@ class DataToExportSaver:
     h5saver: H5SaverLowLevel
 
     """
-    def __init__(self, h5saver: Union[H5SaverLowLevel, Path, str], save_type=SaveType.scan):
+    def __init__(self, h5saver: Union[H5SaverLowLevel, Path, str], save_type=SaveType.custom,
+                 new_file: bool = False, metadata: dict = None):
+
         if isinstance(h5saver, Path) or isinstance(h5saver, str):
-            h5saver_tmp = H5SaverLowLevel(save_type=save_type)
-            h5saver_tmp.init_file(file_name=Path(h5saver))
+            h5saver_tmp = H5SaverLowLevel(save_type)
+            h5saver_tmp.init_file(file_name=Path(h5saver),
+                                  new_file=new_file,
+                                  metadata=metadata)
             h5saver = h5saver_tmp
 
         self._h5saver = h5saver
-        self._data_saver = DataSaverLoader(h5saver)
-        self._bkg_saver = BkgSaver(h5saver)
+        self._data_saver = DataSaverLoader(self._h5saver)
+        self._bkg_saver = BkgSaver(self._h5saver)
+
+    def __getattr__(self, item):
+        """ Allows to call attributes of the underlying H5Saver object"""
+
+        if hasattr(self._h5saver, item):
+            return getattr(self._h5saver, item)
+        else:
+            raise AttributeError(item)
 
     def _get_node(self, where: Union[Node, str]) -> Node:
         return self._h5saver.get_node(where)
@@ -805,6 +828,8 @@ class DataToExportSaver:
         """
 
         dims = data.get_dim_presents()
+        if settings_as_xml != '' and 'settings' not in kwargs:
+            kwargs['settings]'] = settings_as_xml
         for dim in dims:
             dim_group = self._h5saver.get_set_group(where, dim)
             for ind, dwa in enumerate(data.get_data_from_dim(dim)):
@@ -812,6 +837,7 @@ class DataToExportSaver:
                 dwa_group = self._h5saver.get_set_group(dim_group, self.channel_formatter(ind),
                                                         dwa.name, origin=dwa.origin)
                 # dwa_group = self._h5saver.add_ch_group(dim_group, dwa.name)
+
                 self._data_saver.add_data(dwa_group, dwa, **kwargs)
 
     def add_bkg(self, where: Union[Node, str], data: DataToExport):
@@ -856,7 +882,7 @@ class DataToExportEnlargeableSaver(DataToExportSaver):
     axis_units: str, deprecated use enl_axis_units
         the units of the enlarged axis array
     """
-    def __init__(self, h5saver: H5SaverLowLevel,
+    def __init__(self, h5saver: Union[Path, H5SaverLowLevel],
                  enl_axis_names: Iterable[str] = None,
                  enl_axis_units: Iterable[str] = None,
                  axis_name: str = 'nav axis', axis_units: str = ''):
@@ -874,8 +900,8 @@ class DataToExportEnlargeableSaver(DataToExportSaver):
         self._enl_axis_units = enl_axis_units
         self._n_enl = len(enl_axis_names)
 
-        self._data_saver = DataEnlargeableSaver(h5saver)
-        self._nav_axis_saver = AxisSaverLoader(h5saver)
+        self._data_saver = DataEnlargeableSaver(self._h5saver)
+        self._nav_axis_saver = AxisSaverLoader(self._h5saver)
 
     def add_data(self, where: Union[Node, str], data: DataToExport,
                  axis_values: List[Union[float, np.ndarray]] = None,
@@ -954,8 +980,8 @@ class DataToExportExtendedSaver(DataToExportSaver):
 
     def __init__(self, h5saver: H5SaverLowLevel, extended_shape: Tuple[int]):
         super().__init__(h5saver)
-        self._data_saver = DataExtendedSaver(h5saver, extended_shape)
-        self._nav_axis_saver = AxisSaverLoader(h5saver)
+        self._data_saver = DataExtendedSaver(self._h5saver, extended_shape)
+        self._nav_axis_saver = AxisSaverLoader(self._h5saver)
 
     def add_nav_axes(self, where: Union[Node, str], axes: List[Axis]):
         """Used to add navigation axes related to the extended array
@@ -971,7 +997,7 @@ class DataToExportExtendedSaver(DataToExportSaver):
                 self._nav_axis_saver.add_axis(nav_group, axis)
 
     def add_data(self, where: Union[Node, str], data: DataToExport, indexes: Iterable[int],
-                 distribution=DataDistribution['uniform'],
+                 distribution=DataDistribution.uniform,
                  settings_as_xml='', **kwargs):
 
         """

{pymodaq_data-5.1.7 → pymodaq_data-5.2.0a1}/src/pymodaq_data/h5modules/saving.py

@@ -20,7 +20,7 @@ import numpy as np
 from pymodaq_utils.logger import set_logger, get_module_name
 
 from pymodaq_utils import utils
-from pymodaq_utils.config import Config
+from pymodaq_utils.config import GlobalConfig as Config
 from pymodaq_data.data import DataDim, DataToExport, Axis, DataWithAxes
 from pymodaq_utils.enums import BaseEnum, enum_checker
 from pymodaq_utils.warnings import deprecation_msg
@@ -227,7 +227,7 @@ class H5SaverLowLevel(H5Backend):
         """
         if array_type is None:
             if array_to_save is None:
-                array_type = config('data_saving', 'data_type', 'dynamics')[0]
+                array_type = config('data', 'data_saving', 'data_type', 'dynamic')[0]
             else:
                 array_type = array_to_save.dtype
 
@@ -292,20 +292,24 @@ class H5SaverLowLevel(H5Backend):
         """Get a Node starting from a given node (Group) matching the given title"""
         return self.get_node_from_attribute_match(where, 'TITLE', title)
 
-    def add_data_group(self, where, data_dim: DataDim, title='', settings_as_xml='', metadata=None):
+    def add_data_group(self, where, data_dim: DataDim, title='', settings_as_xml='', metadata=None,
+                       group_name: str = None):
         """Creates a group node at given location in the tree
 
         Parameters
         ----------
         where: group node
                where to create data group
-        group_data_type: DataDim
+        data_dim: DataDim
+            the dimensionality of the data group
         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
+        group_name: str, optional
+            the name of the group to create if None, the name of the DataDim enum is used (default)
 
         Returns
         -------
@@ -315,11 +319,14 @@ class H5SaverLowLevel(H5Backend):
         --------
         :py:meth:`add_group`
         """
+        data_dim = enum_checker(DataDim, data_dim)
+        if group_name is None:
+            group_name = data_dim.name
         if metadata is None:
             metadata = {}
-        data_dim = enum_checker(DataDim, data_dim)
+
         metadata.update(settings=settings_as_xml)
-        group = self.add_group(data_dim.name, 'data_dim', where, title, metadata)
+        group = self.add_group(group_name, GroupType.data, where, title, metadata)
         return group
 
     def add_incremental_group(self, group_type: Union[str, GroupType, enum.Enum], where, title='', settings_as_xml='', metadata=None):

{pymodaq_data-5.1.7 → pymodaq_data-5.2.0a1}/src/pymodaq_data/plotting/plotter/plotters/matplotlib_plotters.py

@@ -16,7 +16,7 @@ if TYPE_CHECKING:
     pass
 
 logger = set_logger(get_module_name(__file__))
-config = configmod.Config()
+config = configmod.GlobalConfig()
 
 PLOT_COLORS = utils.plot_colors.copy()
 PLOT_COLORS.remove((255, 255, 255))  # remove white color as plotted on white background

pymodaq_data-5.2.0a1/src/pymodaq_data/plotting/utils.py

@@ -0,0 +1,52 @@
+import copy
+from typing import Iterable as IterableType, Iterable
+
+from pymodaq_utils.utils import config
+
+
+class PlotColors:
+
+    def __init__(self, colors=config('data', 'plotting', 'plot_colors')[:]):
+
+        self._internal_counter = -1
+
+        self.check_colors(colors)
+        self._plot_colors = [tuple(color) for color in colors]
+
+    def copy(self):
+        return copy.copy(self)
+
+    def remove(self, item):
+        self._plot_colors.remove(item)
+
+    def __getitem__(self, item: int):
+        if not isinstance(item, int):
+            raise TypeError('getter should be an integer')
+        return tuple(self._plot_colors[item % len(self._plot_colors)])
+
+    def __len__(self):
+        return len(self._plot_colors)
+
+    def __iter__(self):
+        self._internal_counter = -1
+        return self
+
+    def __next__(self):
+        if self._internal_counter >= len(self) - 1:
+            raise StopIteration
+        self._internal_counter += 1
+        return self[self._internal_counter]
+
+    def check_colors(self, colors: IterableType):
+        if not isinstance(colors, Iterable):
+            raise TypeError('Colors should be a list of 3-tuple 8 bits integer (0-255)')
+        for color in colors:
+            self.check_color(color)
+
+    @staticmethod
+    def check_color(color: IterableType):
+        if not isinstance(color, Iterable) and len(color) != 3:
+            raise TypeError('Colors should be a list of 3-tuple 8 bits integer (0-255)')
+        for col_val in color:
+            if not (isinstance(col_val, int) and 0 <= col_val <= 255):
+                raise TypeError('Colors should be a list of 3-tuple 8 bits integer (0-255)')

pymodaq_data-5.2.0a1/src/pymodaq_data/resources/config_template.toml

@@ -0,0 +1,26 @@
+#this is the configuration file of the pymodaq_data package
+
+[data_saving]
+    [data_saving.h5file]
+    save_path = "C:\\Data"  #base path where data are automatically saved
+    compression_level = 5  # for hdf5 files between 0(min) and 9 (max)
+
+    [data_saving.hsds] #hsds connection option (https://www.hdfgroup.org/solutions/highly-scalable-data-service-hsds/)
+    #to save data in pymodaq using hpyd backend towards distant server or cloud (mimicking hdf5 files)
+    root_url = "http://hsds.sebastienweber.fr"
+    username = "pymodaq_user"
+    pwd = "pymodaq"
+
+    [data_saving.data_type]
+    # choose from below. This will force the datatype to be saved to
+    dynamic =  [ 'float64', 'uint8', 'int8', 'uint16', 'int16', 'uint32', 'int32', 'uint64', 'int64',]
+
+
+[general]
+hdf5_backend = 'tables'  # could be among ['tables', 'h5py', 'h5pyd'], mostly tested with tables
+
+[plotting]
+backend = ['matplotlib']  # either 'matplotlib' or 'qt' or any other custom backend
+plot_colors = [[255, 255, 255], [255, 0, 0], [0, 255, 0], [0, 0, 255], [14, 207, 189], [207, 14, 166], [207, 204, 14]]
+process_roi = true  # if True subdata is extracted from the ROI in the data viewers
+