pymodaq 4.4.7__tar.gz → 4.4.11__tar.gz

pymodaq-4.4.11/AUTHORS.md

@@ -0,0 +1,46 @@
+Here is a list of the main contributors:
+
+## Main modules
+***************
+
+Functionalities
+---------------
+
+* Sébastien Weber, Research Engineer at CEMES/CNRS
+* David Bresteau, Research Engineer at Attolab facility, CEA Saclay
+* Nicolas Tappy, Engineer at Attolight (https://attolight.com/)
+
+Cleaning
+--------
+
+* Sébastien Weber, Research Engineer at CEMES/CNRS
+* David Trémouilles, Researcher at LAAS/CNRS
+* Loïc GUILMARD, Engineer at CETHIL/CNRS
+
+## Plugins
+**********
+
+* Sébastien Weber, Research Engineer at CEMES/CNRS
+* Sophie Meuret, Researcher at CEMES/CNRS
+* David Bresteau, Research Engineer at Attolab facility, CEA Saclay
+* and many others...
+
+## Extensions
+*************
+
+* Sébastien Weber, Research Engineer at CEMES/CNRS
+* Romain Geneaux, Researcher at CEA Saclay contributed to the PyMoDAQ-Femto extension
+
+## Documentation
+****************
+
+* Sébastien Weber, Research Engineer at CEMES/CNRS
+* Matthieu Cabos helped with this documentation
+* David Bresteau wrote the documentation of the PID extension and the tutorial: :ref:`plugin_development`
+* Loïc GUILMARD, Engineer at CETHIL/CNRS
+
+## Testing
+**********
+
+* Sébastien Weber, Research Engineer at CEMES/CNRS
+* Pierre Jannot wrote tests with a total of 5000 lines of code tested during his internship at CEMES in 2021

{pymodaq-4.4.7 → pymodaq-4.4.11}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: pymodaq
-Version: 4.4.7
+Version: 4.4.11
 Summary: Modular Data Acquisition with Python
 Project-URL: Homepage, http://pymodaq.cnrs.fr
 Project-URL: Source, https://github.com/PyMoDAQ/PyMoDAQ
@@ -27,6 +27,8 @@ License: The MIT License (MIT)
         LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
         OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
         THE SOFTWARE.
+License-File: AUTHORS.md
+License-File: LICENSE
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Other Environment
 Classifier: Intended Audience :: Science/Research
@@ -61,7 +63,8 @@ Requires-Dist: qtpy
 Requires-Dist: scipy
 Requires-Dist: setuptools>=60
 Requires-Dist: simple-pid
-Requires-Dist: tables<3.9
+Requires-Dist: tables<3.9; python_version < '3.10'
+Requires-Dist: tables>=3.10; python_version >= '3.10'
 Requires-Dist: toml
 Description-Content-Type: text/x-rst
 

{pymodaq-4.4.7 → pymodaq-4.4.11}/pyproject.toml

@@ -50,7 +50,8 @@ dependencies = [
     "simple_pid",
     "toml",
     "qtconsole",
-    "tables<3.9",  # issue with some version of required package blosc2>=2.2.8
+    "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
     "pyleco>0.3; python_version>=\"3.8\"",
     "bayesian-optimization<2.0.0",
 ]

{pymodaq-4.4.7 → pymodaq-4.4.11}/src/pymodaq/control_modules/daq_move.py

@@ -616,10 +616,12 @@ class DAQ_Move(ParameterControlModule):
         if ('°' in unit or 'degree' in unit) and not '°C' in unit:
             # special cas as pint base unit for angles are radians
             return '°'
-        elif 'W' in unit or 'watt' in unit:
+        elif 'W' in unit or 'watt' in unit.lower():
             return 'W'
         elif '°C' in unit or 'Celsius' in unit:
             return '°C'
+        elif 'V' in unit or 'volt' in unit.lower():
+            return 'V'
         else:
             return str(Q_(1, unit).to_base_units().units)
 
@@ -711,7 +713,8 @@ class DAQ_Move_Hardware(QObject):
             Uninitialize the stage closing the hardware.
 
         """
-        self.hardware.close()
+        if self.hardware is not None:
+            self.hardware.close()
 
         return "Stage uninitialized"
 
@@ -786,7 +789,7 @@ class DAQ_Move_Hardware(QObject):
         self.hardware.move_is_done = False
         self.hardware.ispolling = polling
         if self.hardware.data_actuator_type.name == 'float':
-            self.hardware.move_abs(position.value())
+            self.hardware.move_abs(position.units_as(self.hardware.axis_unit).value()) # convert to plugin controller current axis units
         else:
             position.units = self.hardware.axis_unit  # convert to plugin controller current axis units
             self.hardware.move_abs(position)

{pymodaq-4.4.7 → pymodaq-4.4.11}/src/pymodaq/control_modules/daq_move_ui.py

@@ -15,7 +15,7 @@ from qtpy.QtWidgets import QHBoxLayout, QVBoxLayout, QGridLayout, QWidget, QTool
 
 from pymodaq.utils.daq_utils import ThreadCommand
 from pymodaq.utils.gui_utils.custom_app import CustomApp
-from pymodaq.utils.gui_utils.widgets import PushButtonIcon, LabelWithFont, SpinBox, QSpinBox_ro, QLED
+from pymodaq.utils.gui_utils.widgets import PushButtonIcon, LabelWithFont, SpinBox, QSpinBox_ro, QLED, QSpinBoxWithShortcut
 from pymodaq.control_modules.utils import ControlModuleUI
 from pymodaq.utils.gui_utils import DockArea
 from pymodaq.utils.plotting.data_viewers.viewer import ViewerDispatcher
@@ -199,9 +199,9 @@ class DAQ_Move_UI(ControlModuleUI):
         self.main_ui.layout().addWidget(self.toolbar, 0, 0, 1, 2)
         self.main_ui.layout().addWidget(self.move_toolbar, 1, 0, 1, 2)
 
-        self.abs_value_sb = SpinBox(step=0.1, dec=True, siPrefix=config('actuator', 'siprefix'))
+        self.abs_value_sb = QSpinBoxWithShortcut(step=0.1, dec=True, siPrefix=config('actuator', 'siprefix'))
         self.abs_value_sb.setStyleSheet("background-color : lightgreen; color: black")
-        self.abs_value_sb_2 = SpinBox(step=0.1, dec=True, siPrefix=config('actuator', 'siprefix'))
+        self.abs_value_sb_2 = QSpinBoxWithShortcut(step=0.1, dec=True, siPrefix=config('actuator', 'siprefix'))
         self.abs_value_sb_2.setStyleSheet("background-color : lightcoral; color: black")
         self.move_toolbar.addWidget(self.abs_value_sb)
         self.move_toolbar.addWidget(self.abs_value_sb_2)
@@ -227,7 +227,7 @@ class DAQ_Move_UI(ControlModuleUI):
         self.control_ui.layout().addWidget(LabelWithFont('Abs. Value'), 0, 0)
         self.find_home_pb = PushButtonIcon('home2', 'Find Home')
         self.control_ui.layout().addWidget(self.find_home_pb, 0, 1)
-        self.abs_value_sb_bis = SpinBox(step=0.1, dec=True, siPrefix=config('actuator', 'siprefix'))
+        self.abs_value_sb_bis = QSpinBoxWithShortcut(step=0.1, dec=True, siPrefix=config('actuator', 'siprefix'))
         self.control_ui.layout().addWidget(self.abs_value_sb_bis, 1, 0)
         self.move_abs_pb = PushButtonIcon('Move', 'Set Abs.',
                                           tip='Set the value of the actuator to the set absolute value')
@@ -236,7 +236,7 @@ class DAQ_Move_UI(ControlModuleUI):
         self.move_rel_plus_pb = PushButtonIcon('MoveUp', 'Set Rel. (+)')
         self.control_ui.layout().addWidget(self.move_rel_plus_pb, 2, 1)
 
-        self.rel_value_sb = SpinBox(step=0.1, dec=True, siPrefix=config('actuator', 'siprefix'))
+        self.rel_value_sb = QSpinBoxWithShortcut(step=0.1, dec=True, siPrefix=config('actuator', 'siprefix'), key_sequences=("Ctrl+Enter","Ctrl+Shift+Enter"),)
         self.control_ui.layout().addWidget(self.rel_value_sb, 3, 0)
         self.move_rel_minus_pb = PushButtonIcon('MoveDown', 'Set Rel. (-)')
         self.control_ui.layout().addWidget(self.move_rel_minus_pb, 3, 1)
@@ -302,9 +302,16 @@ class DAQ_Move_UI(ControlModuleUI):
         self.connect_action('show_config', lambda: self.command_sig.emit(ThreadCommand('show_config', )))
 
         self.move_abs_pb.clicked.connect(lambda: self.emit_move_abs(self.abs_value_sb_bis))
+        self.abs_value_sb.shortcut["Ctrl+Enter"].activated.connect(lambda: self.emit_move_abs(self.abs_value_sb))
+        self.abs_value_sb_2.shortcut["Ctrl+Enter"].activated.connect(lambda: self.emit_move_abs(self.abs_value_sb_2))
+        self.abs_value_sb_bis.shortcut["Ctrl+Enter"].activated.connect(lambda: self.emit_move_abs(self.abs_value_sb_bis))
 
         self.rel_value_sb.valueChanged.connect(lambda: self.command_sig.emit(
             ThreadCommand('rel_value', self.rel_value_sb.value())))
+        
+        self.rel_value_sb.shortcut["Ctrl+Enter"].activated.connect(lambda: self.emit_move_rel('+'))
+        self.rel_value_sb.shortcut["Ctrl+Shift+Enter"].activated.connect(lambda: self.emit_move_rel('-'))
+
         self.move_rel_plus_pb.clicked.connect(lambda: self.emit_move_rel('+'))
         self.move_rel_minus_pb.clicked.connect(lambda: self.emit_move_rel('-'))
 

{pymodaq-4.4.7 → pymodaq-4.4.11}/src/pymodaq/control_modules/move_utility_classes.py

@@ -67,11 +67,11 @@ class DataActuatorType(BaseEnum):
 def comon_parameters(epsilon=config('actuator', 'epsilon_default'),
                      epsilons=None):
     if epsilons is not None:
-        epsilon=epsilons
+        epsilon = epsilons
     if isinstance(epsilon, list):
-        epsilon=epsilon[0]
+        epsilon = epsilon[0]
     elif isinstance(epsilon, dict):
-        epsilon=epsilon[list[epsilon.keys()][0]]
+        epsilon = epsilon[list[epsilon.keys()][0]]
 
     return [{'title': 'Units:', 'name': 'units', 'type': 'str', 'value': '', 'readonly': True},
             {'title': 'Epsilon:', 'name': 'epsilon', 'type': 'float',
@@ -124,7 +124,7 @@ def comon_parameters_fun(is_multiaxes=False, axes_names=None,
 
     Parameters
     ----------
-    is_multiaxes: bool  # deprecated not need anymore
+    is_multiaxes: bool
         If True, display the particular settings to define which axis the controller is driving
     axes_names: deprecated, use axis_names
     axis_names: list of str or dictionnary of string as key and integer as value
@@ -140,7 +140,7 @@ def comon_parameters_fun(is_multiaxes=False, axes_names=None,
             axes_names = ['']
         axis_names = axes_names
 
-    is_multiaxes = len(axis_names) > 1
+    is_multiaxes = len(axis_names) > 1 or is_multiaxes
     if isinstance(axis_names, list):
         if len(axis_names) > 0:
             axis_name = axis_names[0]
@@ -617,6 +617,10 @@ class DAQ_Move_base(QObject):
         else:
             raise NotImplementedError
 
+
+    def close(self):
+        raise NotImplementedError
+
     def move_abs(self, value: Union[float, DataActuator]):
         if hasattr(self, 'move_Abs'):
             deprecation_msg('move_Abs method in plugins is deprecated, use move_abs', 3)

{pymodaq-4.4.7 → pymodaq-4.4.11}/src/pymodaq/control_modules/utils.py

@@ -358,7 +358,6 @@ class ParameterControlModule(ParameterManager, ControlModule):
     listener_class: Type[ActorListener] = ActorListener
 
     def __init__(self, **kwargs):
-        QObject.__init__(self)
         ParameterManager.__init__(self, action_list=('save', 'update'))
         ControlModule.__init__(self)
 

{pymodaq-4.4.7 → pymodaq-4.4.11}/src/pymodaq/extensions/daq_scan.py

@@ -82,7 +82,12 @@ class DAQScan(QObject, ParameterManager):
             {'title': 'Timeout (ms)', 'name': 'timeout', 'type': 'int', 'value': 10000},
         ]},
         {'title': 'Scan options', 'name': 'scan_options', 'type': 'group', 'children': [
-            {'title': 'Naverage:', 'name': 'scan_average', 'type': 'int', 'value': 1, 'min': 1},
+            {'title': 'Naverage:', 'name': 'scan_average', 'type': 'int',
+             'value': config('scan', 'Naverage'), 'min': 1},
+            {'title': 'Plot on top:', 'name': 'average_on_top', 'type': 'bool',
+             'value': config('scan', 'average_on_top'),
+             'tip': 'At the second iteration will plot the averaged scan on top (True) of the current one'
+                    'or in a second panel (False)'},
         ]},
 
         {'title': 'Plotting options', 'name': 'plot_options', 'type': 'group', 'children': [
@@ -629,6 +634,10 @@ class DAQScan(QObject, ParameterManager):
             viewers_enum.extend([ViewersEnum('Data1D').increase_dim(self.scanner.n_axes)
                                  for _ in range(len(self.settings['plot_options', 'plot_1d']['selected']))])
             data_names.extend(self.settings['plot_options', 'plot_1d']['selected'][:])
+        if not self.settings['scan_options', 'average_on_top']:
+
+            viewers_enum = viewers_enum + viewers_enum
+            data_names = data_names + [f'{data_name}_averaged' for data_name in data_names]
         self.live_plotter.prepare_viewers(viewers_enum, viewers_name=data_names)
 
     def update_status(self, txt: str, wait_time=0):
@@ -668,6 +677,7 @@ class DAQScan(QObject, ParameterManager):
             self.ui.set_scan_step_average(status.attribute[1] + 1)
 
         elif status.command == "Scan_done":
+
             self.modules_manager.reset_signals()
             self.live_timer.stop()
             self.ui.set_scan_done()
@@ -732,6 +742,7 @@ class DAQScan(QObject, ParameterManager):
             self.live_plotter.load_plot_data(group_0D=self.settings['plot_options', 'group0D'],
                                              average_axis=average_axis,
                                              average_index=self.ind_average,
+                                             separate_average= not self.settings['scan_options', 'average_on_top'],
                                              target_at=self.scanner.positions[self.ind_scan],
                                              last_step=(self.ind_scan ==
                                                         self.scanner.positions.size - 1 and
@@ -765,6 +776,8 @@ class DAQScan(QObject, ParameterManager):
                 messagebox(text="There are not enough or too much selected move modules for this scan")
                 return False
 
+            ## TODO the stuff about adaptive scans have to be moved into a dedicated extension. M
+            ## Most similat to the Bayesian one!
             if self.scanner.scan_sub_type == 'Adaptive':
                 #todo include this in scanners objects for the adaptive scanners
                 if len(self.modules_manager.get_selected_probed_data('0D')) == 0:
@@ -852,9 +865,15 @@ class DAQScan(QObject, ParameterManager):
             self.save_metadata(scan_node, 'scan_info')
 
             self._init_live()
+            Naverage = self.settings['scan_options', 'scan_average']
+            if Naverage > 1:
+                scan_shape = [Naverage]
+                scan_shape.extend(self.scanner.get_scan_shape())
+            else:
+                scan_shape = self.scanner.get_scan_shape()
             for det in self.modules_manager.detectors:
                 det.module_and_data_saver = (
-                    module_saving.DetectorExtendedSaver(det, self.scanner.get_scan_shape()))
+                    module_saving.DetectorExtendedSaver(det, scan_shape))
             self.module_and_data_saver.h5saver = self.h5saver  # force the update as the h5saver ill also be set on each detectors
 
             # mandatory to deal with multithreads
@@ -1034,7 +1053,7 @@ class DAQScanAcquisition(QObject):
 
     def start_acquisition(self):
         try:
-            #todo hoaw to apply newlayout to adaptive mode?
+            #todo hoaw to apply newlayout to adaptive mode? => cannot has to be a new extension
 
             self.modules_manager.connect_actuators()
             self.modules_manager.connect_detectors()
@@ -1106,6 +1125,7 @@ class DAQScanAcquisition(QObject):
                     # daq_scan wait time
                     QThread.msleep(self.scan_settings.child('time_flow', 'wait_time').value())
 
+            self.modules_manager.timeout_signal.disconnect()
             self.modules_manager.connect_actuators(False)
             self.modules_manager.connect_detectors(False)
 
@@ -1113,6 +1133,7 @@ class DAQScanAcquisition(QObject):
                                                      attribute="Acquisition has finished"))
             self.status_sig.emit(utils.ThreadCommand("Scan_done"))
 
+
         except Exception as e:
             logger.exception(str(e))
 
@@ -1148,7 +1169,8 @@ class DAQScanAcquisition(QObject):
             full_names: list = self.scan_settings['plot_options', 'plot_0d']['selected'][:]
             full_names.extend(self.scan_settings['plot_options', 'plot_1d']['selected'][:])
             data_temp = det_done_datas.get_data_from_full_names(full_names, deepcopy=False)
-            data_temp = data_temp.get_data_with_naxes_lower_than(2-len(indexes))  # maximum Data2D included nav indexes
+            n_nav_axis_selection = 2-len(indexes) + 1 if self.Naverage > 1 else 2-len(indexes)
+            data_temp = data_temp.get_data_with_naxes_lower_than(n_nav_axis_selection)  # maximum Data2D included nav indexes
 
             self.scan_data_tmp.emit(ScanDataTemp(self.ind_scan, indexes, data_temp))
 

{pymodaq-4.4.7 → pymodaq-4.4.11}/src/pymodaq/extensions/daq_scan_ui.py

@@ -114,7 +114,7 @@ class DAQScanUI(CustomApp, ViewerDispatcher):
 
         settings_widget = QtWidgets.QWidget()
         settings_widget.setLayout(QtWidgets.QVBoxLayout())
-        settings_widget.setMinimumWidth(220)
+        #settings_widget.setMinimumWidth(220)
 
         splitter_v_widget.addWidget(self.module_widget)
         splitter_v_widget.addWidget(self.plotting_widget)

{pymodaq-4.4.7 → pymodaq-4.4.11}/src/pymodaq/extensions/pid/daq_move_PID.py

@@ -1,4 +1,4 @@
-from pymodaq_utils.utils import ThreadCommand
+from pymodaq.utils.daq_utils import ThreadCommand
 
 from pymodaq.control_modules.move_utility_classes import (DAQ_Move_base, comon_parameters_fun,
                                                           DataActuatorType, DataActuator)

{pymodaq-4.4.7 → pymodaq-4.4.11}/src/pymodaq/post_treatment/load_and_plot.py

@@ -67,7 +67,7 @@ class LoaderPlotter:
     def load_data(self, filter_dims: List[Union[DataDim, str]] = None,
                   filter_full_names: List[str] = None, remove_navigation: bool = True,
                   group_0D=False, average_axis: int=None, average_index: int = 0,
-                  last_step=False):
+                  last_step=False, separate_average=False):
         """Load Data from the h5 node of the dataloader and apply some filtering/manipulation before
         plotting
 
@@ -89,6 +89,8 @@ class LoaderPlotter:
             which step in the averaging process are we in.
         last_step: bool
             tells if this is the very last step of the (averaged) scan
+        separate_average: bool
+            Tells if the averaged data are to be plotted on the same data viewer panel or another one
 
         Returns
         -------
@@ -99,7 +101,8 @@ class LoaderPlotter:
         self.dataloader.load_all('/', self._data)
 
         if average_axis is not None:
-            self.average_axis(average_axis, average_index, last_step=last_step)
+            self.average_axis(average_axis, average_index, last_step=last_step,
+                              separate_average=separate_average)
 
         if filter_dims is not None:
             filter_dims[:] = [enum_checker(DataDim, dim) for dim in filter_dims]
@@ -110,14 +113,15 @@ class LoaderPlotter:
                                   filter_full_names]
 
         if group_0D:  # 0D initial data
-            self.group_0D_data()
+            self.group_0D_data(separate_average=separate_average)
 
         if remove_navigation:
             self.remove_navigation_axes()
 
         return self._data
 
-    def average_axis(self, average_axis, average_index, last_step=False) -> None:
+    def average_axis(self, average_axis, average_index, last_step=False,
+                     separate_average=False) -> None:
         """ Average the data along their average axis
 
         Parameters
@@ -129,7 +133,12 @@ class LoaderPlotter:
             which step in the averaging process are we in.
         last_step: bool
             tells if this is the very last step of the (averaged) scan
+        separate_average: bool
+            Tells if the averaged data are to be plotted on the same data viewer panel or another one
+
         """
+        if separate_average and average_index > 0:
+            averaged_data = DataToExport('Averaged')
         for ind, data in enumerate(self._data):
             current_data = data.inav[average_index, ...]
             if average_index > 0:
@@ -140,10 +149,16 @@ class LoaderPlotter:
                         data_to_append = data.inav[0, ...]
                     else:
                         data_to_append = data.inav[0:average_index, ...].mean(axis=average_axis)
-
+                data_to_append.name = f'{data_to_append.name}_averaged'
                 data_to_append.labels = [f'{label}_averaged' for label in data_to_append.labels]
-                current_data.append(data_to_append)
+                if not (separate_average and average_index > 0):
+                    current_data.append(data_to_append)
+                else:
+                    averaged_data.append(data_to_append)
             self._data[ind] = current_data
+        if separate_average and average_index > 0:
+            self._data.append(averaged_data.data)
+
 
     def remove_navigation_axes(self):
         """Make the navigation axes as signal axes
@@ -156,18 +171,27 @@ class LoaderPlotter:
             data.transpose()  # because usual ND data should be plotted here as 2D with the nav axes as the minor
             # (horizontal)
 
-    def group_0D_data(self):
+    def group_0D_data(self, separate_average=False):
         """Group in a single DataFromPlugins all data that are initialy Data0D
 
         """
         data = self._data.get_data_from_sig_axes(0)
         if len(data) > 0:
             data0D_arrays = []
+            data0D_arrays_averaged = []
             labels = []
+            labels_averaged = []
             for dwa in data:
-                data0D_arrays.extend(dwa.data)
-                labels.extend([f'{dwa.get_full_name()}/{label}' for label in dwa.labels])
-                self._data.remove(dwa)
+                if 'averaged' in dwa.name and separate_average:
+                    data0D_arrays_averaged.extend(dwa.data)
+                    labels_averaged.extend([f'{dwa.get_full_name()}/{label}' for label in dwa.labels])
+                    self._data.remove(dwa)
+
+
+                else:
+                    data0D_arrays.extend(dwa.data)
+                    labels.extend([f'{dwa.get_full_name()}/{label}' for label in dwa.labels])
+                    self._data.remove(dwa)
 
             data0D = DataFromPlugins(self.grouped_data0D_fullname.split('/')[1],
                                      data=data0D_arrays, labels=labels,
@@ -176,6 +200,15 @@ class LoaderPlotter:
                                      axes=dwa.axes, nav_indexes=dwa.nav_indexes,
                                      )
             self._data.append(data0D)
+            if 'averaged' in dwa.name and separate_average:
+                data0D_averaged = DataFromPlugins(
+                    f"{self.grouped_data0D_fullname.split('/')[1]}_averaged",
+                    data=data0D_arrays_averaged, labels=labels_averaged,
+                    dim='DataND',
+                    origin=self.grouped_data0D_fullname.split('/')[0],
+                    axes=dwa.axes, nav_indexes=dwa.nav_indexes,
+                )
+                self._data.append(data0D_averaged)
 
     def load_plot_data(self, **kwargs):
         """Load and plot all data from the current H5Saver

{pymodaq-4.4.7 → pymodaq-4.4.11}/src/pymodaq/resources/QtDesigner_Ressources/QtDesigner_ressources_rc.py

@@ -6,7 +6,7 @@
 #
 # WARNING! All changes made in this file will be lost!
 
-from PyQt5 import QtCore
+from qtpy import QtCore
 
 qt_resource_data = b"\
 \x00\x00\x07\xbc\

pymodaq-4.4.11/src/pymodaq/resources/VERSION

@@ -0,0 +1,2 @@
+version = '4.4.11'
+

{pymodaq-4.4.7 → pymodaq-4.4.11}/src/pymodaq/resources/config_template.toml

@@ -86,6 +86,7 @@ scan_in_thread = true
 show_popups = true
 default = "Scan2D"
 Naverage = 1  # minimum is 1
+average_on_top = true
 steps_limit = 1000  # the limit of the number of steps you can set in a given scan
 sort1D = true
 

{pymodaq-4.4.7 → pymodaq-4.4.11}/src/pymodaq/utils/data.py

@@ -20,7 +20,6 @@ from time import time
 import copy
 import pint
 from multipledispatch import dispatch
-import pymodaq
 from pymodaq.utils.enums import BaseEnum, enum_checker
 from pymodaq.utils.messenger import deprecation_msg
 from pymodaq.utils.daq_utils import find_objects_in_list_from_attr_name_val
@@ -157,6 +156,24 @@ class DataDistribution(BaseEnum):
     spread = 1
 
 
+def _compute_slices_from_axis(axis: Axis, _slice, *ignored, is_index=True, **ignored_also):
+    if not is_index:
+        if isinstance(_slice, numbers.Number):
+            if not is_index:
+                _slice = axis.find_index(_slice)
+        elif _slice is Ellipsis:
+            return _slice
+        elif isinstance(_slice, slice):
+            if not (_slice.start is None and
+                    _slice.stop is None and _slice.step is None):
+                start = axis.find_index(
+                    _slice.start if _slice.start is not None else axis.get_data()[0])
+                stop = axis.find_index(
+                    _slice.stop if _slice.stop is not None else axis.get_data()[-1])
+                _slice = slice(start, stop)
+    return _slice
+
+
 class Axis:
     """Object holding info and data about physical axis of some data
 
@@ -367,8 +384,9 @@ class Axis:
     def __len__(self):
         return self.size
 
-    def _compute_slices(self, slices, *ignored, **ignored_also):
-        return slices
+    def _compute_slices(self, _slice, *ignored, is_index=True, **ignored_also):
+        _slice = _compute_slices_from_axis(self, _slice, is_index=is_index)
+        return _slice, _slice
 
     def _slicer(self, _slice, *ignored, **ignored_also):
         ax: Axis = copy.deepcopy(self)
@@ -2188,11 +2206,22 @@ class DataWithAxes(DataBase):
                         axes.append(ax)
         self.axes = axes
 
-    def _compute_slices(self, slices, is_navigation=True):
+    def _compute_slices(self, slices, is_navigation=True, is_index=True):
         """Compute the total slice to apply to the data
 
         Filling in Ellipsis when no slicing should be done
+        Parameters
+        ----------
+        slices: List of slice
+        is_navigation: bool
+        is_index: bool
+            if False, the slice are on the values of the underlying axes
+        Returns
+        -------
+        list(slice): the computed slices as index (eventually for all axes)
+        list(slice): a version as index of the input argument
         """
+        _slices_as_index = []
         if isinstance(slices, numbers.Number) or isinstance(slices, slice):
             slices = [slices]
         if is_navigation:
@@ -2203,13 +2232,29 @@ class DataWithAxes(DataBase):
         slices = list(slices)
         for ind in range(len(self.shape)):
             if ind in indexes:
-                total_slices.append(slices.pop(0))
+                _slice = slices.pop(0)
+                if not is_index:
+                    axis = self.get_axis_from_index(ind)[0]
+                    _slice = _compute_slices_from_axis(axis, _slice, is_index=is_index)
+                _slices_as_index.append(_slice)
+                total_slices.append(_slice)
             elif len(total_slices) == 0:
                 total_slices.append(Ellipsis)
             elif not (Ellipsis in total_slices and total_slices[-1] is Ellipsis):
                 total_slices.append(slice(None))
+            if len(slices) == 0 and self.distribution == DataDistribution.uniform and is_navigation:
+                if total_slices[-1] is Ellipsis:
+                    for ind in range(len(total_slices), len(indexes)):
+                        _slices_as_index.append(slice(None))
+                else:
+                    for ind in range(len(total_slices), len(indexes)):
+                        _slices_as_index.insert(0, Ellipsis)
+                    for ind in range(len(indexes), len(self.shape)):
+                        total_slices.append(slice(None))
+
+                break
         total_slices = tuple(total_slices)
-        return total_slices
+        return total_slices, _slices_as_index
 
     def check_squeeze(self, total_slices: List[slice], is_navigation: bool):
 
@@ -2221,7 +2266,7 @@ class DataWithAxes(DataBase):
                 do_squeeze = False
         return do_squeeze
 
-    def _slicer(self, slices, is_navigation=True):
+    def _slicer(self, slices, is_navigation=True, is_index=True):
         """Apply a given slice to the data either navigation or signal dimension
 
         Parameters
@@ -2230,6 +2275,8 @@ class DataWithAxes(DataBase):
             the slices to apply to the data
         is_navigation: bool
             if True apply the slices to the navigation dimension else to the signal ones
+        is_index: bool
+            if True the slices are indexes otherwise the slices are axes values to be indexed first
 
         Returns
         -------
@@ -2237,10 +2284,10 @@ class DataWithAxes(DataBase):
             Object of the same type as the initial data, derived from DataWithAxes. But with lower
             data size due to the slicing and with eventually less axes.
         """
-
         if isinstance(slices, numbers.Number) or isinstance(slices, slice):
             slices = [slices]
-        total_slices = self._compute_slices(slices, is_navigation)
+
+        total_slices, slices = self._compute_slices(slices, is_navigation, is_index=is_index)
 
         do_squeeze = self.check_squeeze(total_slices, is_navigation)
         new_arrays_data = [squeeze(dat[total_slices], do_squeeze) for dat in self.data]
@@ -2290,11 +2337,11 @@ class DataWithAxes(DataBase):
         if len(nav_indexes) != 0:
             distribution = self.distribution
         else:
-            distribution = DataDistribution['uniform']
+            distribution = DataDistribution.uniform
 
         data = DataWithAxes(self.name, data=new_arrays_data, nav_indexes=tuple(nav_indexes),
                             axes=axes,
-                            source='calculated', origin=self.origin,
+                            source=DataSource.calculated, origin=self.origin,
                             labels=self.labels[:],
                             distribution=distribution)
         return data

{pymodaq-4.4.7 → pymodaq-4.4.11}/src/pymodaq/utils/gui_utils/widgets/__init__.py

@@ -1,5 +1,5 @@
 from .qled import QLED
 from .push import PushButtonIcon, EditPush, EditPushRel
-from .spinbox import QSpinBox_ro, SpinBox
+from .spinbox import QSpinBox_ro, SpinBox, QSpinBoxWithShortcut
 from .table import TableView, TableModel
 from .label import LabelWithFont