pymodaq_data 5.0.20__tar.gz → 5.0.22__tar.gz

{pymodaq_data-5.0.20 → pymodaq_data-5.0.22}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymodaq_data
-Version: 5.0.20
+Version: 5.0.22
 Summary: Modular Data Acquisition with Python
 Project-URL: Homepage, http://pymodaq.cnrs.fr
 Project-URL: Source, https://github.com/PyMoDAQ/pymodaq_data

{pymodaq_data-5.0.20 → pymodaq_data-5.0.22}/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '5.0.20'
-__version_tuple__ = version_tuple = (5, 0, 20)
+__version__ = version = '5.0.22'
+__version_tuple__ = version_tuple = (5, 0, 22)

{pymodaq_data-5.0.20 → pymodaq_data-5.0.22}/src/pymodaq_data/data.py

@@ -443,6 +443,7 @@ class Axis(SerializableBase):
                 self._scaling = np.mean(np.diff(data))
             self._offset = data[0]
             self._data = None
+            self._size = len(data)
 
     def is_axis_linear(self, data=None):
         if data is None:
@@ -523,16 +524,11 @@ class Axis(SerializableBase):
         elif _slice is Ellipsis:
             return ax
         elif isinstance(_slice, slice):
-            if ax._data is not None:
-                ax.data = ax._data.__getitem__(_slice)
-                return ax
+            if ax.is_axis_linear():
+                ax.get_scale_offset_from_data(ax.get_data().__getitem__(_slice))
             else:
-                start = _slice.start if _slice.start is not None else 0
-                stop = _slice.stop if _slice.stop is not None else self.size
-
-                ax._offset = ax.offset + start * ax.scaling
-                ax._size = stop - start
-                return ax
+                ax.data = ax.get_data().__getitem__(_slice)
+            return ax
 
     def __getitem__(self, item):
         if hasattr(self, item):
@@ -2094,12 +2090,12 @@ class DataWithAxes(DataBase, SerializableBase):
         return plotter_factory.get(plotter_backend).plot(self, *args, viewer=viewer, **kwargs)
 
     def set_axes_manager(self, data_shape, axes, nav_indexes, **kwargs):
-        if self.distribution.name == DataDistribution.uniform.name or len(nav_indexes) == 0:
+        if self.distribution == DataDistribution.uniform or len(nav_indexes) == 0:
             self._distribution = DataDistribution.uniform
             self.axes_manager = AxesManagerUniform(data_shape=data_shape, axes=axes,
                                                    nav_indexes=nav_indexes,
                                                    **kwargs)
-        elif self.distribution.name == DataDistribution.spread.name:
+        elif self.distribution == DataDistribution.spread:
             self.axes_manager = AxesManagerSpread(data_shape=data_shape, axes=axes,
                                                   nav_indexes=nav_indexes,
                                                   **kwargs)

{pymodaq_data-5.0.20 → pymodaq_data-5.0.22}/src/pymodaq_data/h5modules/backends.py

@@ -4,6 +4,8 @@ Created the 15/11/2022
 
 @author: Sebastien Weber
 """
+from typing import Union
+from enum import Enum
 import numpy as np
 import importlib
 from importlib import metadata
@@ -63,6 +65,7 @@ class SaveType(BaseEnum):
     logger = 2
     custom = 3
     actuator = 4
+    optimizer = 5
 
 
 class GroupType(BaseEnum):
@@ -1008,14 +1011,14 @@ class H5Backend:
         array.attrs['backend'] = self.backend
         return array
 
-    def add_group(self, group_name, group_type: GroupType, where, title='', metadata=dict([])) -> GROUP:
+    def add_group(self, group_name, group_type: Union[GroupType, str], where, title='', metadata=dict([])) -> GROUP:
         """
         Add a node in the h5 file tree of the group type
         Parameters
         ----------
         group_name: (str) a custom name for this group
         group_type: str or GroupType enum
-            one of the possible values of GroupType
+            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
 
@@ -1026,14 +1029,15 @@ class H5Backend:
         if isinstance(where, Node):
             where = where.node
 
-        group_type = enum_checker(GroupType, group_type)
+        if isinstance(group_type, Enum):
+            group_type = group_type.name
 
         if group_name in self.get_children(self.get_node(where)):
             node = self.get_node(where, group_name)
 
         else:
             node = self.get_set_group(where, utils.capitalize(group_name), title)
-            node.attrs['type'] = group_type.name.lower()
+            node.attrs['type'] = group_type.lower()
             for metadat in metadata:
                 node.attrs[metadat] = metadata[metadat]
         node.attrs['backend'] = self.backend

{pymodaq_data-5.0.20 → pymodaq_data-5.0.22}/src/pymodaq_data/h5modules/saving.py

@@ -6,6 +6,8 @@ Created the 15/11/2022
 """
 import copy
 import datetime
+import enum
+
 from dateutil import parser
 from numbers import Number
 import os
@@ -262,16 +264,18 @@ class H5SaverLowLevel(H5Backend):
         self._current_group = super().get_set_group(where, name, title, **kwargs)
         return self._current_group
 
-    def get_groups(self, where: Union[str, GROUP], group_type: GroupType):
+    def get_groups(self, where: Union[str, GROUP], group_type: Union[str, GroupType, BaseEnum]):
         """Get all groups hanging from a Group and of a certain type"""
         groups = []
+        if isinstance(group_type, enum.Enum):
+            group_type = group_type.name
         for node_name in list(self.get_children(where)):
             group = self.get_node(where, node_name)
-            if 'type' in group.attrs and group.attrs['type'] == group_type.name:
+            if 'type' in group.attrs and group.attrs['type'].lower() == group_type.lower():
                 groups.append(group)
         return groups
 
-    def get_last_group(self, where: GROUP, group_type: GroupType):
+    def get_last_group(self, where: GROUP, group_type: Union[str, GroupType, enum.Enum]):
         groups = self.get_groups(where, group_type)
         if len(groups) != 0:
             return groups[-1]
@@ -288,7 +292,7 @@ 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=dict([])):
+    def add_data_group(self, where, data_dim: DataDim, title='', settings_as_xml='', metadata=None):
         """Creates a group node at given location in the tree
 
         Parameters
@@ -311,12 +315,14 @@ class H5SaverLowLevel(H5Backend):
         --------
         :py:meth:`add_group`
         """
+        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)
         return group
 
-    def add_incremental_group(self, group_type, where, title='', settings_as_xml='', metadata=dict([])):
+    def add_incremental_group(self, group_type: Union[str, GroupType, enum.Enum], where, title='', settings_as_xml='', metadata=None):
         """
         Add a node in the h5 file tree of the group type with an increment in the given name
         Parameters
@@ -336,50 +342,58 @@ class H5SaverLowLevel(H5Backend):
         -------
         node: newly created group node
         """
-        group_type = enum_checker(GroupType, group_type)
+        if metadata is None:
+            metadata = {}
+        if isinstance(group_type, enum.Enum):
+            group_type = group_type.name
 
         nodes = [name for name in self.get_children(self.get_node(where))]
         nodes_tmp = []
         for node in nodes:
-            if utils.capitalize(group_type.name) in node:
+            if utils.capitalize(group_type.lower()) 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, f'{utils.capitalize(group_type.name)}{ind_group + 1:03d}', title)
+        group = self.get_set_group(where, f'{utils.capitalize(group_type.lower())}{ind_group + 1:03d}', title)
         self.set_attr(group, 'settings', settings_as_xml)
-        if group_type.name.lower() != 'ch':
-            self.set_attr(group, 'type', group_type.name.lower())
+        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_act_group(self, where, title='', settings_as_xml='', metadata=dict([])):
+    def add_act_group(self, where, title='', settings_as_xml='', metadata=None):
         """
         Add a new group of type detector
         See Also
         -------
         add_incremental_group
         """
+        if metadata is None:
+            metadata = {}
         group = self.add_incremental_group('actuator', where, title, settings_as_xml, metadata)
         return group
 
-    def add_det_group(self, where, title='', settings_as_xml='', metadata=dict([])):
+    def add_det_group(self, where, title='', settings_as_xml='', metadata=None):
         """
         Add a new group of type detector
         See Also
         -------
         add_incremental_group
         """
+        if metadata is None:
+            metadata = {}
         group = self.add_incremental_group('detector', where, title, settings_as_xml, metadata)
         return group
 
-    def add_scan_group(self, where='/RawData', title='', settings_as_xml='', metadata=dict([])):
-        """Add a new group of type scan
+    def add_generic_group(self, where='/RawData', title='', settings_as_xml='', metadata=None,
+                          group_type=GroupType.scan):
+        """Add a new group of type given by the input argument group_type
 
         At creation adds the attributes description and scan_done to be used elsewhere
 
@@ -387,28 +401,45 @@ class H5SaverLowLevel(H5Backend):
         -------
         add_incremental_group
         """
+        if metadata is None:
+            metadata = {}
+        metadata.update(dict(description='', scan_done=False))
+        group = self.add_incremental_group(group_type, where, title, settings_as_xml, metadata)
+        return group
+
+    def add_scan_group(self, where='/RawData', title='', settings_as_xml='', metadata=None,):
+        """Add a new group of type scan
+
+        deprecated, use add_generic_group with a group type as GroupType.scan
+        """
+        if metadata is None:
+            metadata = {}
         metadata.update(dict(description='', scan_done=False))
-        group = self.add_incremental_group(GroupType['scan'], where, title, settings_as_xml, metadata)
+        group = self.add_generic_group(where, title, settings_as_xml, metadata, group_type=GroupType.scan)
         return group
 
-    def add_ch_group(self, where, title='', settings_as_xml='', metadata=dict([])):
+    def add_ch_group(self, where, title='', settings_as_xml='', metadata=None):
         """
         Add a new group of type channel
         See Also
         -------
         add_incremental_group
         """
+        if metadata is None:
+            metadata = {}
         group = self.add_incremental_group('ch', where, title, settings_as_xml, metadata)
         return group
 
 
-    def add_move_group(self, where, title='', settings_as_xml='', metadata=dict([])):
+    def add_move_group(self, where, title='', settings_as_xml='', metadata=None):
         """
         Add a new group of type actuator
         See Also
         -------
         add_incremental_group
         """
+        if metadata is None:
+            metadata = {}
         group = self.add_incremental_group('actuator', where, title, settings_as_xml, metadata)
         return group