pymodaq_data 5.2.12__tar.gz → 5.3.0__tar.gz

{pymodaq_data-5.2.12 → pymodaq_data-5.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: pymodaq_data
-Version: 5.2.12
+Version: 5.3.0
 Summary: Modular Data Acquisition with Python
 Project-URL: Homepage, http://pymodaq.cnrs.fr
 Project-URL: Source, https://github.com/PyMoDAQ/PyMoDAQ
@@ -71,11 +71,11 @@ PyMoDAQ Data
    :target: https://pypi.org/project/pymodaq_data/
    :alt: Latest Version
 
-.. image:: https://readthedocs.org/projects/pymodaq/badge/?version=dev
-   :target: https://pymodaq.readthedocs.io/en/stable/?badge=dev
+.. image:: https://readthedocs.org/projects/pymodaq/badge/?version=patch-3
+   :target: https://pymodaq.readthedocs.io/en/stable/?badge=patch-3
    :alt: Documentation Status
 
-.. image:: https://codecov.io/gh/PyMoDAQ/PyMoDAQ/branch/dev/graph/badge.svg?token=IQNJRCQDM2 
+.. image:: https://codecov.io/gh/PyMoDAQ/PyMoDAQ/branch/patch-3/graph/badge.svg?token=IQNJRCQDM2 
  :target: https://codecov.io/gh/PyMoDAQ/PyMoDAQ
 
 +-------------+-------------+---------------+
@@ -94,28 +94,28 @@ PyMoDAQ Data
 
 
 
-.. |310-linux| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/dev/tests_Linux_3.10.svg
+.. |310-linux| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/patch-3/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/dev/tests_Linux_3.11.svg
+.. |311-linux| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/patch-3/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/dev/tests_Linux_3.12.svg
+.. |312-linux| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/patch-3/tests_Linux_3.12.svg
     :target: https://github.com/PyMoDAQ/PyMoDAQ/actions/workflows/tests-data.yml
 
-.. |313-linux| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/dev/tests_Linux_3.13.svg
+.. |313-linux| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/patch-3/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/dev/tests_Windows_3.10.svg
+.. |310-windows| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/patch-3/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/dev/tests_Windows_3.11.svg
+.. |311-windows| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/patch-3/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/dev/tests_Windows_3.12.svg
+.. |312-windows| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/patch-3/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/dev/tests_Windows_3.13.svg
+.. |313-windows| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/patch-3/tests_Windows_3.13.svg
     :target: https://github.com/PyMoDAQ/PyMoDAQ/actions/workflows/tests-data.yml
 
 

{pymodaq_data-5.2.12 → pymodaq_data-5.3.0}/README.rst

@@ -11,11 +11,11 @@ PyMoDAQ Data
    :target: https://pypi.org/project/pymodaq_data/
    :alt: Latest Version
 
-.. image:: https://readthedocs.org/projects/pymodaq/badge/?version=dev
-   :target: https://pymodaq.readthedocs.io/en/stable/?badge=dev
+.. image:: https://readthedocs.org/projects/pymodaq/badge/?version=patch-3
+   :target: https://pymodaq.readthedocs.io/en/stable/?badge=patch-3
    :alt: Documentation Status
 
-.. image:: https://codecov.io/gh/PyMoDAQ/PyMoDAQ/branch/dev/graph/badge.svg?token=IQNJRCQDM2 
+.. image:: https://codecov.io/gh/PyMoDAQ/PyMoDAQ/branch/patch-3/graph/badge.svg?token=IQNJRCQDM2 
  :target: https://codecov.io/gh/PyMoDAQ/PyMoDAQ
 
 +-------------+-------------+---------------+
@@ -34,28 +34,28 @@ PyMoDAQ Data
 
 
 
-.. |310-linux| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/dev/tests_Linux_3.10.svg
+.. |310-linux| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/patch-3/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/dev/tests_Linux_3.11.svg
+.. |311-linux| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/patch-3/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/dev/tests_Linux_3.12.svg
+.. |312-linux| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/patch-3/tests_Linux_3.12.svg
     :target: https://github.com/PyMoDAQ/PyMoDAQ/actions/workflows/tests-data.yml
 
-.. |313-linux| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/dev/tests_Linux_3.13.svg
+.. |313-linux| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/patch-3/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/dev/tests_Windows_3.10.svg
+.. |310-windows| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/patch-3/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/dev/tests_Windows_3.11.svg
+.. |311-windows| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/patch-3/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/dev/tests_Windows_3.12.svg
+.. |312-windows| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/patch-3/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/dev/tests_Windows_3.13.svg
+.. |313-windows| image:: https://raw.githubusercontent.com/PyMoDAQ/PyMoDAQ/badges/pymodaq_data/patch-3/tests_Windows_3.13.svg
     :target: https://github.com/PyMoDAQ/PyMoDAQ/actions/workflows/tests-data.yml
 
 

{pymodaq_data-5.2.12 → pymodaq_data-5.3.0}/src/pymodaq_data/data.py

@@ -86,7 +86,9 @@ def dimensionless_aware_reduce_units(q: Type[Q_]) -> Type[Q_]:
     -------
     The reduced quantity
     """
-
+    # this may fire a pint.errors.UndefinedBehavior warning when the magnitude is a numpy array
+    # but pint https://github.com/hgrecco/pint/issues/2274 fixed this in July 2026
+    # at the moment, it just returns the same quantity layout
     return q.to_compact() if q.dimensionless else q.to_reduced_units()
 
 def check_units(units: str):
@@ -529,6 +531,16 @@ class Axis(SerializableBase):
         if self._data is None:
             self._size = _size
 
+    @property
+    def axis_width(self) -> Q_:
+        """get the width of the axis in axis unit
+
+        That is the difference between the max value and the min value of the axis
+        """
+        if self.scaling is not None:
+            return Q_(self.size * self.scaling, self.units)
+        else:
+            return Q_(self.get_data().max() - self.get_data().min(), self.units)
     @staticmethod
     def _check_index_valid(index: int):
         if not isinstance(index, int):
@@ -653,10 +665,10 @@ class Axis(SerializableBase):
         """find the index of the threshold value within the axis"""
         if isinstance(threshold, Q_):
             threshold = threshold.m_as(self.units)
-        if threshold < self.min():
+        if threshold <= self.min():
             return 0
-        elif threshold > self.max():
-            return len(self) - 1
+        elif threshold >= self.max():
+            return len(self)
         elif self._data is not None:
             return mutils.find_index(self._data, threshold)[0][0]
         else:
@@ -702,7 +714,7 @@ class DataLowLevel:
 
     @name.setter
     def name(self, other_name: str):
-        self._name = other_name
+        self._name = str(other_name)
 
     @property
     def timestamp(self):
@@ -2141,6 +2153,10 @@ class DataWithAxes(DataBase, SerializableBase):
         dwa.timestamp = timestamp
         return dwa, remaining_bytes
 
+    def get_axes_sizes(self) -> Iterable[Q_]:
+        self.create_missing_axes()
+        return [self.get_axis_from_index(index)[0].axis_width for index in range(len(self.axes))]
+
     def check_axes_linear(self, axes: List[Axis] = None) -> bool:
         """ Check if any axis may be non linear
 
@@ -3390,19 +3406,67 @@ class DataToExport(DataLowLevel, SerializableBase):
             if dat.origin is None or dat.origin == '':
                 dat.origin = self.name
 
+    def _combine(self, other: object, op: Callable, reflected: bool = False) -> 'DataToExport':
+        """Combine self and other elementwise, applying ``op`` to every element.
+
+        *other* may be:
+
+        - a plain number: broadcast to every element. Whether this is
+          actually valid is decided by DataWithAxes/pint arithmetic itself,
+          not pre-judged here — e.g. adding a bare number only makes sense
+          for dimensionless data (pint raises otherwise), while multiplying
+          by one is always valid regardless of units.
+        - another DataToExport of the same length: paired by list position
+          (index i of self with index i of other), not by name.
+          DataToExport is used to combine structurally-parallel containers
+          (e.g. successive snapshots from the same DAQ_Scan/ModulesManager
+          run, always iterated in the same order), and existing callers rely
+          on being able to combine elements whose *names* legitimately
+          differ between the two operands (e.g. a signal container and a
+          differently-named background container). Only the count and,
+          per-pair, the array shapes/units need to match — the latter
+          enforced by DataWithAxes arithmetic itself.
+
+        Parameters
+        ----------
+        other: DataToExport or numbers.Number
+        op: Callable
+            Binary operation applied to each pair, e.g. ``np.subtract``. Its
+            ``__name__`` is used in error messages.
+        reflected: bool
+            If True, apply ``op(other_i, self_i)`` instead of
+            ``op(self_i, other_i)``, for the non-commutative ``__r*__`` methods.
+        """
+        if isinstance(other, numbers.Number):
+            others = [other] * len(self)
+        elif not isinstance(other, DataToExport):
+            raise TypeError(f'Could not {op.__name__} a {self.__class__.__name__} and a '
+                            f'{other.__class__.__name__}: only a number or another '
+                            f'{self.__class__.__name__} is supported')
+        elif len(other) != len(self):
+            raise TypeError(f'Could not {op.__name__} a {other.__class__.__name__} with a '
+                            f'{self.__class__.__name__} of a different length')
+        else:
+            others = other
+        new_data = copy.deepcopy(self)
+        for ind_dfp, (dwa, other_dwa) in enumerate(zip(self, others)):
+            new_data[ind_dfp] = op(other_dwa, dwa) if reflected else op(dwa, other_dwa)
+        return new_data
+
     def __sub__(self, other: object):
-        if isinstance(other, DataToExport) and len(other) == len(self):
-            new_data = copy.deepcopy(self)
-            for ind_dfp in range(len(self)):
-                new_data[ind_dfp] = self[ind_dfp] - other[ind_dfp]
-            return new_data
-        else:
-            raise TypeError(f'Could not substract a {other.__class__.__name__} or a {self.__class__.__name__} '
-                            f'of a different length')
+        return self._combine(other, np.subtract)
+
+    def __rsub__(self, other: object):
+        return self._combine(other, np.subtract, reflected=True)
 
     def __eq__(self, other):
         if not isinstance(other, DataToExport):
             return False
+        if len(self) != len(other):
+            # zip() below would otherwise silently truncate to the shorter of
+            # the two, letting a DataToExport compare equal to a strict
+            # superset of itself.
+            return False
 
         for dwa, other_dwa in zip(self, other):
             if dwa != other_dwa:
@@ -3417,31 +3481,20 @@ class DataToExport(DataLowLevel, SerializableBase):
 
 
     def __add__(self, other: object):
-        if isinstance(other, DataToExport) and len(other) == len(self):
-            new_data = copy.deepcopy(self)
-            for ind_dfp in range(len(self)):
-                new_data[ind_dfp] = self[ind_dfp] + other[ind_dfp]
-            return new_data
-        else:
-            raise TypeError(f'Could not add a {other.__class__.__name__} or a {self.__class__.__name__} '
-                            f'of a different length')
+        return self._combine(other, np.add)
+
+    __radd__ = __add__  # addition is commutative
 
     def __mul__(self, other: object):
-        if isinstance(other, numbers.Number):
-            new_data = copy.deepcopy(self)
-            for ind_dfp in range(len(self)):
-                new_data[ind_dfp] = self[ind_dfp] * other
-            return new_data
-        else:
-            raise TypeError(f'Could not multiply a {other.__class__.__name__} with a {self.__class__.__name__} '
-                            f'of a different length')
+        return self._combine(other, np.multiply)
+
+    __rmul__ = __mul__  # multiplication is commutative
 
     def __truediv__(self, other: object):
-        if isinstance(other, numbers.Number):
-            return self * (1 / other)
-        else:
-            raise TypeError(f'Could not divide a {other.__class__.__name__} with a {self.__class__.__name__} '
-                            f'of a different length')
+        return self._combine(other, np.true_divide)
+
+    def __rtruediv__(self, other: object):
+        return self._combine(other, np.true_divide, reflected=True)
 
     def average(self, other: DataToExport, weight: int) -> DataToExport:
         """ Compute the weighted average between self and other DataToExport and attributes it to self
@@ -3453,14 +3506,10 @@ class DataToExport(DataLowLevel, SerializableBase):
             The weight the 'other_data' holds with respect to self
 
         """
-        if isinstance(other, DataToExport) and len(other) == len(self):
-            new_data = copy.copy(self)
-            for ind_dfp in range(len(self)):
-                new_data[ind_dfp] = self[ind_dfp].average(other[ind_dfp], weight)
-            return new_data
-        else:
-            raise TypeError(f'Could not average a {other.__class__.__name__} with a {self.__class__.__name__} '
-                            f'of a different length')
+        def average(dwa: DataWithAxes, other_dwa: DataWithAxes) -> DataWithAxes:
+            return dwa.average(other_dwa, weight)
+
+        return self._combine(other, average)
 
     def merge_as_dwa(self, dim: Union[str, DataDim], name: str = None) -> DataRaw:
         """ attempt to merge filtered dwa into one
@@ -3747,9 +3796,16 @@ class DataToExport(DataLowLevel, SerializableBase):
         data, _ = find_objects_in_list_from_attr_name_val(self.data, 'name', name, return_first=True)
         return data
 
-    def get_data_from_names(self, names: List[str]) -> DataToExport:
+    def get_data_from_names(self, names: List[str] | str) -> DataToExport:
+        if isinstance(names, str):
+            names = [names]
         return DataToExport(self.name, data=[dwa for dwa in self if dwa.name in names])
 
+    def get_data_from_origins(self, origins: list[str] | str) -> DataToExport:
+        if isinstance(origins, str):
+            origins = [origins]
+        return DataToExport(self.name, data=[dwa for dwa in self if dwa.origin in origins])
+
     def get_data_from_name_origin(self, name: str, origin: str = '') -> DataWithAxes:
         """Get the data matching the given name and the given origin"""
         if origin == '':
@@ -3771,9 +3827,8 @@ class DataToExport(DataLowLevel, SerializableBase):
                 return ind
         raise ValueError
 
-    def index_from_name_origin(self, name: str, origin: str = '') -> List[DataWithAxes]:
+    def index_from_name_origin(self, name: str, origin: str = '') -> int:
         """Get the index of a given DataWithAxes within the list of data"""
-        """Get the data matching the given name and the given origin"""
         if origin == '':
             _, index = find_objects_in_list_from_attr_name_val(self.data, 'name', name, return_first=True)
         else:

{pymodaq_data-5.2.12 → pymodaq_data-5.3.0}/src/pymodaq_data/h5modules/backends.py

@@ -242,15 +242,13 @@ class Node(object):
         return self.attrs['TITLE']
 
     @property
-    def path(self):
+    def path(self) -> str:
         """return node path
-        Parameters
-        ----------
-        node (str or node instance), see h5py and pytables documentation on nodes
 
         Returns
         -------
-        str : full path of the node
+        str
+            full path of the node
         """
         if self.backend == 'tables':
             return self._node._v_pathname
@@ -288,7 +286,8 @@ class GROUP(Node):
 
         Returns
         -------
-        dict: keys are children node names, values are the children nodes
+        dict
+            keys are children node names, values are the children nodes
 
         See Also
         --------
@@ -387,8 +386,8 @@ class EARRAY(CARRAY):
         The data to append could be:
 
         * a single element (without the enlargeable shape index that is always the first
-        index, that is of shape length n). In that case the first index of the enlargeable array
-        is increased by one.
+          index, that is of shape length n). In that case the first index of the enlargeable array
+          is increased by one.
         * an ensemble of elements (a ndarray) of shape length of (n+1).
 
         Parameters
@@ -575,6 +574,11 @@ class H5Backend:
         self._swmr_enabled = False
         self.set_backend(backend)
 
+    @property
+    def swmr_mode(self) -> bool:
+        return self._swmr_mode
+
+
     def set_backend(self, backend: str):
         """Switch the active backend, closing any open file first.
 
@@ -658,7 +662,7 @@ class H5Backend:
             return self._h5file
         else:
             if swmr_mode and self.backend == 'h5py':
-                if mode == 'w':
+                if mode in ('w', 'a'):
                     kwargs['libver'] = 'latest'
                 elif mode == 'r':
                     kwargs['swmr'] = True
@@ -804,22 +808,24 @@ class H5Backend:
 
     def get_set_group(self, where, name, title='', **kwargs):
         """Retrieve or create (if absent) a node group
+
         Get attributed to the class attribute ``current_group``
 
         Parameters
         ----------
-        where: str or node
-               path or parent node instance
+        where: str or Node
+            path or parent node instance
         name: str
-              group node name
+            group node name
         title: str
-               node title
-
-        Keyword Arguments:
+            node title
+        kwargs: dict
             any other metadata related to this node (for example: origin)
+
         Returns
         -------
-        group: group node
+        GROUP
+            the group node
         """
 
         if isinstance(where, Node):
@@ -858,12 +864,13 @@ class H5Backend:
     def is_node_in_group(self, where, name):
         """
         Check if a given node with name is in the group defined by where (comparison on lower case strings)
+
         Parameters
         ----------
-        where: (str or node)
-                path or parent node instance
-        name: (str)
-              group node name
+        where: str or Node
+            path or parent node instance
+        name: str
+            group node name
 
         Returns
         -------
@@ -940,13 +947,16 @@ class H5Backend:
 
     def get_node_name(self, node):
         """return node name
+
         Parameters
         ----------
-        node (str or node instance), see h5py and pytables documentation on nodes
+        node: str or Node
+            see h5py and pytables documentation on nodes
 
         Returns
         -------
-        str: name of the node
+        str
+            name of the node
         """
         if isinstance(node, Node):
             node = node.node
@@ -954,13 +964,16 @@ class H5Backend:
 
     def get_node_path(self, node):
         """return node path
+
         Parameters
         ----------
-        node (str or node instance), see h5py and pytables documentation on nodes
+        node: str or Node
+            see h5py and pytables documentation on nodes
 
         Returns
         -------
-        str : full path of the node
+        str
+            full path of the node
         """
         if isinstance(node, Node):
             node = node.node
@@ -977,18 +990,19 @@ class H5Backend:
         else:
             return self.get_node(node.parent)
 
-    def get_children(self, where):
+    def get_children(self, where) -> dict[str, Node]:
         """Get a dict containing all children node hanging from where with their name as keys and types among Node,
         CARRAY, EARRAY, VLARRAY or StringARRAY
 
         Parameters
         ----------
-        where (str or node instance)
+        where: str or Node
             see h5py and pytables documentation on nodes, and Node objects of this module
 
         Returns
         -------
-        dict: keys are children node names, values are the children nodes
+        dict
+            keys are children node names, values are the children nodes
 
         See Also
         --------
@@ -1023,12 +1037,45 @@ class H5Backend:
                 children[child_name] = _cls(child, self.backend)
         return children
 
-    def walk_nodes(self, where):
+    def walk_nodes(self, where: str| Node, depth: int = None, only_groups=False):
+        """ Node Generator recursively iterating in the tree starting from where down to the specified depth
+        (counted from where).
+
+
+        Parameters
+        ----------
+        where: str | Node
+            The starting node of the iteration
+        depth: int
+            The depth of the iteration in the h5 tree
+        only_groups: bool
+            if False (default) return all nodes otherwise retruns only GROUP instances
+
+        Yields
+        ------
+        Node
+        """
         where = self.get_node(where)  # return a node object in case where is a string
-        yield where
-        for gr in self.walk_groups(where):
-            for child in self.get_children(gr).values():
-                yield child
+        if only_groups and where.attrs['CLASS'] != 'GROUP':
+            pass
+        else:
+            yield where
+
+        if depth == 0:
+            return
+        else:
+            for gr in self.walk_groups(where):
+                for child in self.get_children(gr).values():
+                    node_path = child.path[len(where.path):]
+                    if node_path[0] == '/':
+                        node_path = node_path[1:]
+                    if depth is not None and node_path.count('/') == depth:
+                        return
+                    else:
+                        if only_groups and child.attrs['CLASS'] != 'GROUP':
+                            pass
+                        else:
+                            yield child
 
     def walk_groups(self, where):
         where = self.get_node(where)  # return a node object in case where is a string
@@ -1126,14 +1173,18 @@ class H5Backend:
 
         Parameters
         ----------
-        where: (str) group location in the file where to create the array node
-        name: (str) name of the array
-        dtype: (dtype) numpy dtype style, for particular case of strings, use dtype='string'
-        title: (str) node title attribute (written in capitals)
+        where: str
+            group location in the file where to create the array node
+        name: str
+            name of the array
+        dtype: dtype
+            numpy dtype style, for particular case of strings, use dtype='string'
+        title: str
+            node title attribute (written in capitals)
 
         Returns
         -------
-        array
+        VLARRAY
 
         """
         if isinstance(where, Node):
@@ -1189,15 +1240,19 @@ class H5Backend:
         Add a node in the h5 file tree of the group type
         Parameters
         ----------
-        group_name: (str) a custom name for this group
+        group_name: str
+            a custom name for this group
         group_type: str or GroupType enum
             one of the possible values of GroupType, should be enforced by higher level modules not here
-        where: (str or node) parent node where to create the new group
-        metadata: (dict) extra metadata to be saved with this new group node
+        where: str or Node
+            parent node where to create the new group
+        metadata: dict
+            extra metadata to be saved with this new group node
 
         Returns
         -------
-        (node): newly created group node
+        GROUP
+            newly created group node
         """
         if metadata is None:
             metadata = {}

{pymodaq_data-5.2.12 → pymodaq_data-5.3.0}/src/pymodaq_data/h5modules/data_saving.py

@@ -4,6 +4,10 @@ Created the 21/11/2022
 
 @author: Sebastien Weber
 """
+from __future__ import annotations
+
+from dataclasses import dataclass, field
+
 from time import time
 from typing import Union, List, Tuple, Iterable
 from pathlib import Path
@@ -18,7 +22,7 @@ from .saving import DataType, H5SaverLowLevel
 from .backends import GROUP, CARRAY, Node, EARRAY, NodeError, GroupType  # noqa: F401
 from pymodaq_utils.utils import capitalize
 from pymodaq_data.h5modules.saving import SaveType
-
+from .. import DataToExport, DataDistribution
 
 SPECIAL_GROUP_NAMES = dict(nav_axes='NavAxes')
 
@@ -27,6 +31,21 @@ class AxisError(Exception):
     pass
 
 
+@dataclass
+class DataBundle:
+    """Convenience class to hold data to be saved or plotted"""
+    dte: DataToExport
+    node: str = None
+    settings: str = ''
+    indexes: list[int] = None  # indexes within an eventual Extended array (see DAQ_Scan)
+    axis_values: list[float | np.ndarray] = None  # axis values within an eventual Enlargeable array (see Optimizers)
+    distribution: DataDistribution = field(
+        default_factory=lambda: DataDistribution.uniform
+    )  # type of data to be saved
+    save_index: int = 0  # an index to know what step in the saving process we're in (see DAQ_Scan)
+
+
+
 class DataManagement(metaclass=ABCMeta):
     """Base abstract class to be used for all specialized object saving and loading data to/from a h5file
 
@@ -297,12 +316,17 @@ class DataSaverLoader(DataManagement):
     data_type = DataType['data']
 
     def __init__(self, h5saver: Union[H5SaverLowLevel, Path],
-                 new_file: bool = False, metadata: dict = None, save_type=SaveType.custom):
+                 new_file: bool = False,
+                 metadata: dict = None,
+                 save_type=SaveType.custom,
+                 swmr_mode=False):
         self.data_type = enum_checker(DataType, self.data_type)
 
         if isinstance(h5saver, (Path, str)):
             h5saver = H5SaverLowLevel.from_file(h5saver, save_type,
-                                                new_file=new_file, metadata=metadata)
+                                                new_file=new_file,
+                                                metadata=metadata,
+                                                swmr_mode=swmr_mode)
 
         self._h5saver = h5saver
         self._axis_saver = AxisSaverLoader(self._h5saver)
@@ -708,7 +732,7 @@ class DataExtendedSaver(DataSaverLoader):
     Parameters
     ----------
     h5saver: H5SaverLowLevel
-    extended_shape: Tuple[int]
+    extended_shape: Iterable[int]
         the extra shape compared to the data the h5array will have
 
     Attributes
@@ -718,7 +742,9 @@ class DataExtendedSaver(DataSaverLoader):
     """
     data_type = DataType['data']
 
-    def __init__(self, h5saver: H5SaverLowLevel, extended_shape: Tuple[int], fill_value=None):
+    def __init__(self, h5saver: H5SaverLowLevel,
+                 extended_shape: Iterable[int],
+                 fill_value=None):
         super().__init__(h5saver)
         self.extended_shape = extended_shape
         self.fill_value = fill_value
@@ -784,7 +810,9 @@ class DataExtendedSaver(DataSaverLoader):
                     # because there will be len(self.extended_shape) extra navigation axes
                     self._axis_saver.add_axis(where, axis)
 
-    def add_data(self, where: Union[Node, str], data: DataWithAxes, indexes: List[int],
+    def add_data(self, where: Union[Node, str],
+                 data: DataWithAxes,
+                 indexes: Iterable[int],
                  distribution=DataDistribution['uniform']):
         """Adds given DataWithAxes at a location within the initialized h5 array
 
@@ -835,6 +863,14 @@ class DataToExportSaver:
         self._data_saver = DataSaverLoader(self._h5saver)
         self._bkg_saver = BkgSaver(self._h5saver)
 
+    @property
+    def h5saver(self) -> H5SaverLowLevel:
+        return self._h5saver
+
+    @h5saver.setter
+    def h5saver(self, h5saver: H5SaverLowLevel):
+        self._h5saver = h5saver
+
     def __getattr__(self, item):
         """ Allows to call attributes of the underlying H5Saver object"""
 
@@ -868,6 +904,9 @@ class DataToExportSaver:
         and formatted as below"""
         return f'CH{ind:02d}'
 
+    def add_data_bundle(self, data: DataBundle):
+        self.add_data(data.node, data.dte, data.settings)
+
     def add_data(self, where: Union[Node, str], data: DataToExport, settings_as_xml='', **kwargs):
         """
 
@@ -959,6 +998,9 @@ class DataToExportEnlargeableSaver(DataToExportSaver):
         self._data_saver = DataEnlargeableSaver(self._h5saver)
         self._nav_axis_saver = AxisSaverLoader(self._h5saver)
 
+    def add_data_bundle(self, data: DataBundle):
+        self.add_data(data.node, data.dte, axis_values=data.axis_values, settings_as_xml=data.settings)
+
     def add_data(self, where: Union[Node, str], data: DataToExport,
                  axis_values: List[Union[float, np.ndarray]] = None,
                  axis_value: Union[float, np.ndarray] = None,
@@ -1022,6 +1064,9 @@ class DataToExportTimedSaver(DataToExportEnlargeableSaver):
     def add_data(self, where: Union[Node, str], data: DataToExport, settings_as_xml='', **kwargs):
         super().add_data(where, data, axis_values=[data.timestamp], settings_as_xml=settings_as_xml, **kwargs)
 
+    def add_data_bundle(self, data: DataBundle):
+        self.add_data(data.node, data.dte, settings_as_xml=data.settings)
+
 
 class DataToExportExtendedSaver(DataToExportSaver):
     """Object to save DataToExport at given indexes within arrays including extended shape
@@ -1035,7 +1080,10 @@ class DataToExportExtendedSaver(DataToExportSaver):
         the extra shape compared to the data the h5array will have
     """
 
-    def __init__(self, h5saver: H5SaverLowLevel, extended_shape: Tuple[int], fill_value=None):
+    def __init__(self,
+                 h5saver: H5SaverLowLevel,
+                 extended_shape: Iterable[int],
+                 fill_value=None):
         super().__init__(h5saver)
         self._data_saver = DataExtendedSaver(h5saver, extended_shape, fill_value=fill_value)
         self._nav_axis_saver = AxisSaverLoader(h5saver)
@@ -1054,7 +1102,12 @@ class DataToExportExtendedSaver(DataToExportSaver):
             for axis in axes:
                 self._nav_axis_saver.add_axis(nav_group, axis)
 
-    def add_data(self, where: Union[Node, str], data: DataToExport, indexes: Iterable[int],
+    def add_data_bundle(self, data: DataBundle):
+        self.add_data(data.node, data.dte, data.indexes, data.distribution, data.settings)
+
+    def add_data(self, where: Union[Node, str],
+                 data: DataToExport,
+                 indexes: Iterable[int],
                  distribution=DataDistribution.uniform,
                  settings_as_xml='', **kwargs):
 
@@ -1095,7 +1148,7 @@ class DataToExportExtendedSaver(DataToExportSaver):
 
 
 class DataLoader:
-    """Specialized Object to load DataWithAxes object from a h5file
+    """Specialized Object to load DataWithAxes / DataToExport objects from a h5file
 
     On the contrary to DataSaverLoader, does include navigation axes stored elsewhere in the h5file
     (for instance if saved from the DAQ_Scan)
@@ -1105,12 +1158,15 @@ class DataLoader:
     h5saver: H5SaverLowLevel or Path
     """
 
-    def __init__(self, h5saver: Union[H5SaverLowLevel, Path]):
+    def __init__(self, h5saver: Union[H5SaverLowLevel, Path],
+                 swmr_mode = False):
         self._axis_loader: AxisSaverLoader = None
         self._data_loader: DataSaverLoader = None
 
         if isinstance(h5saver, (Path, str)):
-            h5saver = H5SaverLowLevel.from_file(h5saver)
+            h5saver = H5SaverLowLevel.from_file(h5saver,
+                                                swmr_mode=swmr_mode,
+                                                mode='r')
 
         self.h5saver = h5saver
 
@@ -1129,8 +1185,8 @@ class DataLoader:
 
     def __exit__(self, exc_type, exc_val, exc_tb):
         self.close_file()
-    @property
 
+    @property
     def raw_group(self) -> Node:
         """ Get the base RawGroup where raw data should be saved
 
@@ -1141,9 +1197,11 @@ class DataLoader:
     def close_file(self):
         self._h5saver.close_file()
 
-    def walk_nodes(self, where: Union[str, Node] = '/'):
+    def walk_nodes(self, where: Union[str, Node] = '/', depth: int = None,
+                   only_groups=False) -> Iterable[Node]:
         """Return a Node generator iterating over the h5file content"""
-        return self.h5saver.walk_nodes(where)
+        return self.h5saver.walk_nodes(where, depth=depth,
+                                       only_groups=only_groups)
 
     def get_node(self, where: Union[Node, str], name: str = None) -> Node:
         """ Convenience method to get node"""
@@ -1159,8 +1217,8 @@ class DataLoader:
 
         Returns
         -------
-        GROUP: returns the group named SPECIAL_GROUP_NAMES['nav_axes'] holding all NavAxis for
-        those data
+        GROUP
+            the group named ``SPECIAL_GROUP_NAMES['nav_axes']`` holding all NavAxis for those data
 
         See Also
         --------
@@ -1198,17 +1256,25 @@ class DataLoader:
             if nav_group is not None:
                 nav_axes = self._axis_loader.get_axes(nav_group)
                 axes = data.axes[:]
+                # in swmr mode, if at the time where the axis is read, a writer added stuff
+                # then the axis and the data may not be consistent. Below is an attempt to correct this
+                for ind_nav, nav_axe in enumerate(nav_axes):
+                    if nav_axe.size > data.shape[data.nav_indexes[nav_axe.index]]:
+                        nav_axe.data = nav_axe.get_data()[:data.shape[data.nav_indexes[nav_axe.index]]]
                 axes.extend(nav_axes)
                 data.axes = axes
                 data.get_dim_from_data_axes()
         data.create_missing_axes()
         return data
 
-    def load_all(self, where: GROUP, data: DataToExport = None, with_bkg=False) -> DataToExport:
+    def load_all(self, where: GROUP | str, data: DataToExport = None, with_bkg=False) -> DataToExport:
         if data is None:
             data = DataToExport('Loaded data')
         where = self._h5saver.get_node(where)
-        children_dict = where.children()
+        try:
+            children_dict = where.children()
+        except AttributeError:
+            children_dict = {where.name: where}
         data_list = []
         for child in children_dict:
             if isinstance(children_dict[child], GROUP):
@@ -1263,4 +1329,6 @@ class DataLoader:
         # if not returned so far raise a NameError
         raise NameError(f'No dwa matching this name: {name} and '
                         f'origin: {origin} hanging from '
-                        f'{where}')
+                        f'{where}')
+
+

{pymodaq_data-5.2.12 → pymodaq_data-5.3.0}/src/pymodaq_data/h5modules/saving.py

@@ -92,11 +92,14 @@ class H5SaverLowLevel(H5Backend):
 
     @classmethod
     def from_file(cls, path: Union[Path, str], save_type: SaveType = 'scan',
-                  new_file: bool = False, metadata: dict = None) -> 'H5SaverLowLevel':
+                  new_file: bool = False, metadata: dict = None,
+                  swmr_mode: bool = False,
+                  mode='a') -> 'H5SaverLowLevel':
         """Create and initialise an H5SaverLowLevel from a file path.
 
         Convenience factory that combines the constructor and :meth:`init_file`
         call into a single expression.
+
         Parameters
         ----------
         path: Path or str
@@ -108,6 +111,11 @@ class H5SaverLowLevel(H5Backend):
             opened for appending.
         metadata: dict or None
             Extra attributes written to the raw-data group on creation.
+        swmr_mode: bool
+            If True, prepare the file for SWMR (h5py backend only)
+        mode: str
+            valid if new_file is False. Then could be 'r' for readonly or 'a' to append data
+
 
         Returns
         -------
@@ -115,7 +123,11 @@ class H5SaverLowLevel(H5Backend):
             A fully initialised instance ready for reading/writing.
         """
         h5saver = cls(save_type)
-        h5saver.init_file(file_name=Path(path), new_file=new_file, metadata=metadata)
+        h5saver.init_file(file_name=Path(path),
+                          new_file=new_file,
+                          metadata=metadata,
+                          swmr_mode=swmr_mode,
+                          mode=mode)
         return h5saver
 
     def set_swmr_flush_interval(self, interval: int):
@@ -149,8 +161,11 @@ class H5SaverLowLevel(H5Backend):
     def h5_file(self):
         return self._h5file
 
-    def init_file(self, file_name: Path, raw_group_name='RawData', new_file=False,
-                  metadata: dict = None, swmr_mode: bool = False):
+    def init_file(self, file_name: Path, raw_group_name='RawData',
+                  new_file=False,
+                  metadata: dict = None,
+                  swmr_mode: bool = False,
+                  mode: str = 'a'):
         """Initializes a new h5 file,
 
         Should have an extension with h5 in it.
@@ -167,6 +182,8 @@ class H5SaverLowLevel(H5Backend):
             A dictionary to be saved as attributes
         swmr_mode: bool
             If True, prepare the file for SWMR (h5py backend only)
+        mode: str
+            valid if new_file is False. Then could be 'r' for readonly or 'a' to append data
 
         Returns
         -------
@@ -200,7 +217,7 @@ class H5SaverLowLevel(H5Backend):
             return
 
         self.close_file()
-        self.open_file(self.h5_file_path.joinpath(self.h5_file_name), 'w' if new_file else 'a',
+        self.open_file(self.h5_file_path.joinpath(self.h5_file_name), 'w' if new_file else mode,
                        title='PyMoDAQ file', swmr_mode=swmr_mode)
 
         self._raw_group = self.get_set_group(self.root(), raw_group_name, title='Data from PyMoDAQ modules')
@@ -267,6 +284,7 @@ class H5SaverLowLevel(H5Backend):
                   title: str = '', metadata=dict([])):
 
         """save data arrays on the hdf5 file together with metadata
+
         Parameters
         ----------
         where: GROUP
@@ -278,7 +296,7 @@ class H5SaverLowLevel(H5Backend):
         data_shape: Iterable
             the shape of the array to save, mandatory if array_to_save is None
         data_dimension: DataDim
-         The data's dimension
+            The data's dimension
         scan_shape: Iterable
             the shape of the scan dimensions
         title: str
@@ -294,12 +312,13 @@ class H5SaverLowLevel(H5Backend):
             if False, data are saved as a CARRAY, otherwise as a EARRAY (for ragged data, see add_string_array)
         metadata: dict
             dictionnary whose keys will be saved as the array attributes
-        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
+        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
 
         Returns
         -------
-        array (CARRAY or EARRAY)
+        CARRAY or EARRAY
 
         See Also
         --------

{pymodaq_data-5.2.12 → pymodaq_data-5.3.0}/src/pymodaq_data/plotting/plotter/plotters/matplotlib_plotters.py

@@ -20,7 +20,10 @@ logger = set_logger(get_module_name(__file__))
 config = configmod.GlobalConfig()
 
 PLOT_COLORS = PlotColors()
-PLOT_COLORS.remove((255, 255, 255))  # remove white color as plotted on white background
+try:
+    PLOT_COLORS.remove((255, 255, 255))# remove white color as plotted on white background
+except ValueError:
+    pass  # this color is not in PLOT_COLORS (maybe because light style is used)
 PLOT_COLORS = PlotColors([(np.array(color) / 255).tolist() for color in PLOT_COLORS])  # translation to matplotlib
 
 
@@ -38,18 +41,26 @@ class Plotter(PlotterBase):
     def plot(self, data: Union[DataWithAxes, DataToExport], *args, viewer=None,
              **kwargs) -> plt.Figure:
         fig = plt.figure()
+        if 'linewidth' in kwargs:
+            linewidth = kwargs['linewidth']
+        else:
+            linewidth = self.linewidth
 
         if isinstance(data, DataWithAxes):
             self.n_columns = len(data) if data.dim.name == 'Data2D' else 1
-            self.plot_dwa(data, *args, **kwargs)
+            self.plot_dwa(data, *args, linewidth=linewidth, **kwargs)
         elif isinstance(data, DataToExport):
             self.n_columns = max([len(dwa) if dwa.dim.name == 'Data2D' else 1 for dwa in data])
             self.n_lines = len(data)
-            self.plot_dte(data, *args, **kwargs)
+            self.plot_dte(data, *args, linewidth=linewidth, **kwargs)
         plt.tight_layout()
         fig.suptitle(f'{data.name} taken the {datetime.datetime.fromtimestamp(data.timestamp)}')
         return fig
 
+    @property
+    def linewidth(self) -> int:
+        return config('data', 'plotting', 'linewidth')
+
     def plot_dwa(self, dwa: DataWithAxes, *args, **kwargs):
         if dwa.dim.name == 'Data1D':
             if len(dwa.axes) == 0:

{pymodaq_data-5.2.12 → pymodaq_data-5.3.0}/src/pymodaq_data/plotting/utils.py

@@ -1,7 +1,8 @@
 import copy
 from typing import Iterable as IterableType, Iterable
 
-from pymodaq_utils.utils import config
+from pymodaq_utils.config import GlobalConfig
+config = GlobalConfig()
 
 
 class PlotColors:

{pymodaq_data-5.2.12 → pymodaq_data-5.3.0}/src/pymodaq_data/resources/config_template.toml

@@ -26,3 +26,4 @@ backend = ['h5py', 'tables', 'h5pyd']  # first element is the default, mostly te
 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
+linewidth = 1  # default linewidth of the plots