Added option to change the coloring for NaN values

.reuse/dep5

@@ -19,6 +19,7 @@ Files:
     pydidas/resources/*.png
     resources/*.png
     resources/*.svg
+    resources/*.ico
     resources/graphics_for_gui/*
     resources/documentation/dev_guide/*
 Copyright: 2023 - 2024, Helmholtz-Zentrum Hereon

CHANGELOG.rst

@@ -2,13 +2,33 @@
 .. SPDX-License-Identifier: CC0-1.0
 
 
-v24.03.25
+v24.xx.yy
 =========
 
-
 Improvements
 ------------
+- Improved the naming and tooltips of scan parameters with respect to the 
+  file numbers and indices.
+- Added the ParameterCollection creation the the ParameterCollectionMixin
+  class initialization.
+
+
+Bugfixes
+--------
+- Fixed a display issue in the title of the logging dockable widget.
+- Fixed an issue in the pyFAI calibration frame where the supported file 
+  formats where not correctly available in the file dialog.
+- Fixed an issue with settings the X-ray energy / wavelength in the 
+  DiffractionExperimentContext on the command line with wrong data types.
+- Fixed an issue with convenience type conversions in the Parameter class.
+- Fixed an issue with possibly joining queues twice on exit of WorkerController.
 
+
+v24.03.25
+=========
+
+Improvements
+------------
 - Changed a number of filenames and paths (mainly in the documentation) to 
   reduce the total length of the file names.
 - Updated files to new black 2024 style.

formatter.py

@@ -149,7 +149,7 @@ def check_version_tags(directory: Optional[Path] = None):
     with open(_directory.joinpath("pydidas", "version.py"), "r") as f:
         _line = [_line for _line in f.readlines() if _line.startswith("__version__")]
     _version = _line[0].split("=")[1].strip().strip('"')
-    _timed_print(f"Starting version tag check.", new_lines=1)
+    _timed_print("Starting version tag check.", new_lines=1)
     with open(_directory.joinpath("CHANGELOG.rst"), "r") as f:
         _changelog_lines = f.readlines()
     _changelog_okay = f"v{_version}" in [_line.strip() for _line in _changelog_lines]

pydidas/apps/directory_spy_app.py

@@ -1,6 +1,6 @@
 # This file is part of pydidas.
 #
-# Copyright 2023, Helmholtz-Zentrum Hereon
+# Copyright 2023 - 2024, Helmholtz-Zentrum Hereon
 # SPDX-License-Identifier: GPL-3.0-only
 #
 # pydidas is free software: you can redistribute it and/or modify
@@ -21,7 +21,7 @@
 """
 
 __author__ = "Malte Storm"
-__copyright__ = "Copyright 2023, Helmholtz-Zentrum Hereon"
+__copyright__ = "Copyright 2023 - 2024, Helmholtz-Zentrum Hereon"
 __license__ = "GPL-3.0-only"
 __maintainer__ = "Malte Storm"
 __status__ = "Production"

pydidas/contexts/diff_exp/diff_exp.py

@@ -104,10 +104,10 @@ def set_param_value(self, param_key: str, value: object):
         """
         self._check_key(param_key)
         if param_key == "xray_energy":
-            self.params["xray_energy"].value = value
+            self.params.set_value("xray_energy", value)
             self.params["xray_wavelength"].value = LAMBDA_IN_A_TO_E / value
         elif param_key == "xray_wavelength":
-            self.params["xray_wavelength"].value = value
+            self.params.set_value("xray_wavelength", value)
             self.params["xray_energy"].value = LAMBDA_IN_A_TO_E / value
         else:
             self.params.set_value(param_key, value)

pydidas/core/generic_params/generic_params_scan.py

@@ -86,26 +86,30 @@
         "scan_start_index": {
             "type": int,
             "default": 0,
-            "name": "Starting index",
+            "name": "First filename number",
             "choices": None,
             "unit": "",
             "allow_None": False,
             "tooltip": (
-                "The starting index offset for the index used to identify data "
-                "points in the scan."
+                "The number of the first file to be used in processing. This number "
+                "will be applied as offset in the scan naming pattern to identify "
+                "the respective filename for scan points."
             ),
         },
         "scan_index_stepping": {
             "type": int,
             "default": 1,
-            "name": "Index stepping",
+            "name": "Frame index stepping",
             "choices": None,
             "unit": "",
             "allow_None": False,
             "tooltip": (
-                "The stepping of the index. A value of n corresponds to only using "
-                "every n-th index. For example, an index stepping of 3 with an offset "
-                "of 5 would process the frames 5, 8, 11, 14 etc."
+                "The stepping of the index in frames. A value of n corresponds to only "
+                "using every n-th index. For example, an index stepping of 3 with an "
+                "offset of 5 would process the frames 5, 8, 11, 14 etc. \n"
+                "Please note that the index stepping refers to the frames, not the "
+                "filenames. In the case of container files (e.g. hdf5), the index "
+                "stepping will skip process every n-th frame, not every n-th file."
             ),
         },
         "scan_multi_image_handling": {

pydidas/core/object_with_parameter_collection.py

@@ -1,6 +1,6 @@
 # This file is part of pydidas.
 #
-# Copyright 2023, Helmholtz-Zentrum Hereon
+# Copyright 2023 - 2024, Helmholtz-Zentrum Hereon
 # SPDX-License-Identifier: GPL-3.0-only
 #
 # pydidas is free software: you can redistribute it and/or modify
@@ -22,7 +22,7 @@
 """
 
 __author__ = "Malte Storm"
-__copyright__ = "Copyright 2023, Helmholtz-Zentrum Hereon"
+__copyright__ = "Copyright 2023 - 2024, Helmholtz-Zentrum Hereon"
 __license__ = "GPL-3.0-only"
 __maintainer__ = "Malte Storm"
 __status__ = "Production"
@@ -35,7 +35,6 @@
 
 from qtpy import QtCore
 
-from .parameter_collection import ParameterCollection
 from .parameter_collection_mixin import ParameterCollectionMixIn
 from .pydidas_q_settings_mixin import PydidasQsettingsMixin
 
@@ -54,7 +53,7 @@ class ObjectWithParameterCollection(
     def __init__(self):
         QtCore.QObject.__init__(self)
         PydidasQsettingsMixin.__init__(self)
-        self.params = ParameterCollection()
+        ParameterCollectionMixIn.__init__(self)
         self._config = {}
 
     def __copy__(self) -> Self:

pydidas/core/parameter.py

@@ -1,6 +1,6 @@
 # This file is part of pydidas.
 #
-# Copyright 2023, Helmholtz-Zentrum Hereon
+# Copyright 2023 - 2024, Helmholtz-Zentrum Hereon
 # SPDX-License-Identifier: GPL-3.0-only
 #
 # pydidas is free software: you can redistribute it and/or modify
@@ -21,23 +21,23 @@
 """
 
 __author__ = "Malte Storm"
-__copyright__ = "Copyright 2023, Helmholtz-Zentrum Hereon"
+__copyright__ = "Copyright 2023 - 2024, Helmholtz-Zentrum Hereon"
 __license__ = "GPL-3.0-only"
 __maintainer__ = "Malte Storm"
 __status__ = "Production"
 __all__ = ["Parameter"]
 
 
-import numbers
 import warnings
 from collections.abc import Iterable
+from numbers import Integral, Real
 from pathlib import Path
-from typing import Dict, List, Self, Set, Tuple, Type, Union
+from typing import Any, Dict, List, Self, Set, Tuple, Type, Union
 
 from .hdf5_key import Hdf5key
 
 
-def _get_base_class(cls) -> type:
+def _get_base_class(cls: Any) -> Union[type, Real, Integral, None]:
     """
     Filter numerical classes and return the corresponding abstract base class.
 
@@ -53,14 +53,14 @@ def _get_base_class(cls) -> type:
     Returns
     -------
     object
-        The base class of the input class if the inpu.
+        The base class of the input class if the input.
     """
     if cls is None:
         return None
-    if numbers.Integral.__subclasscheck__(cls):
-        return numbers.Integral
-    if numbers.Real.__subclasscheck__(cls):
-        return numbers.Real
+    if issubclass(cls, Integral):
+        return Integral
+    if issubclass(cls, Real):
+        return Real
     return cls
 
 
@@ -70,7 +70,7 @@ class Parameter:
 
     The Parameter has the following properties which can be accessed.
     Only the value and choices properties can be edited at runtime, all other
-    properties are fixed at instanciation.
+    properties are fixed at instantiation.
 
     +------------+-----------+-------------------------------------------+
     | property   | editable  | description                               |
@@ -104,7 +104,7 @@ class Parameter:
     +------------+-----------+-------------------------------------------+
 
     Parameters can be passed either as a complete meta_dict or as individual
-    keyword arguments. The meta_dict will take precendence.
+    keyword arguments. The meta_dict will take precedence.
 
     Parameters
     ----------
@@ -120,7 +120,7 @@ class Parameter:
         The default value. The data type must be of the same type as
         param_type. None is only accepted if param_type is None as well.
     meta : Union[dict, None], optional
-        A dictionary with meta data. Any keys specified as meta will
+        A dictionary with metadata. Any keys specified as meta will
         overwrite the kwargs dictionary. This is added merely as
         convenience to facility copying Parameter instances. If None,
         this entry will be ignored. The default is None.
@@ -171,13 +171,13 @@ def __init__(
         self.__process_choices_input(kwargs)
         self.value = kwargs.get("value", self.__meta["default"])
 
-    def __process_default_input(self, default: Type):
+    def __process_default_input(self, default: object):
         """
         Process the default value.
 
         Parameters
         ----------
-        default : Type
+        default : object
             The default attribute passed to init.
 
         Raises
@@ -206,7 +206,7 @@ def __process_choices_input(self, kwargs: Dict):
         TypeError
             If choices is not of an accepted type (None, list, tuple)
         ValueError
-            If the default has been set and it is not in choices.
+            If the default has been set, and it is not in choices.
         """
         _choices = kwargs.get("choices", None)
         if not (isinstance(_choices, (list, tuple, set)) or _choices is None):
@@ -224,7 +224,7 @@ def __process_choices_input(self, kwargs: Dict):
 
     def __typecheck(self, val: object) -> bool:
         """
-        Check the type of a new input.
+        Check the type of new input.
 
         Parameters
         ----------
@@ -268,19 +268,22 @@ def __convenience_type_conversion(self, value: object) -> object:
         Returns
         -------
         value : any
-            The value with the above mentioned type conversions applied.
+            The value with the above-mentioned type conversions applied.
         """
         if isinstance(value, str):
             if self.__type == Path:
                 value = Path(value)
             elif self.__type == Hdf5key:
                 value = Hdf5key(value)
-        if self.__type == numbers.Real and not self.__meta["allow_None"]:
-            return float(value)
-        if isinstance(value, list) and self.__type == tuple:
-            return tuple(value)
-        if isinstance(value, tuple) and self.__type == list:
-            return list(value)
+        if self.__type in [Real, Integral] and not self.__meta["allow_None"]:
+            try:
+                value = float(value) if self.__type == Real else int(value)
+            except ValueError:
+                pass
+            finally:
+                return value
+        if isinstance(value, Iterable) and self.__type in [list, set, tuple]:
+            return self.__type(value)
         return value
 
     @property
@@ -310,7 +313,7 @@ def allow_None(self) -> bool:
     @property
     def refkey(self) -> str:
         """
-        Return the paramter reference key.
+        Return the parameter reference key.
 
         Returns
         -------
@@ -356,9 +359,9 @@ def tooltip(self) -> str:
         _t = self.__meta["tooltip"]
         if self.unit:
             _t += f" (unit: {self.unit})"
-        if self.dtype == numbers.Integral:
+        if self.dtype == Integral:
             _t += " (type: integer)"
-        elif self.dtype == numbers.Real:
+        elif self.dtype == Real:
             _t += " (type: float)"
         elif self.dtype == str:
             _t += " (type: str)"
@@ -375,13 +378,6 @@ def choices(self) -> Union[None, List]:
         """
         Get or set the allowed choices for the Parameter value.
 
-        Parameters
-        ----------
-        choices : Union[list, tuple, set]
-            A list or tuple of allowed choices. A check will be performed that
-            all entries correspond to the defined data type and that the
-            curent parameter value is one of the allowed choices.
-
         Returns
         -------
         Union[list, None]
@@ -394,11 +390,18 @@ def choices(self, choices: Union[None, List, Tuple, Set]):
         """
         Update the allowed choices of a Parameter.
 
+        Parameters
+        ----------
+        choices : Union[list, tuple, set]
+            A list or tuple of allowed choices. A check will be performed that
+            all entries correspond to the defined data type and that the
+            current parameter value is one of the allowed choices.
+
         Raises
         ------
         TypeError
             If the supplied choices are not of datatype list or tuple.
-        ValueErrror
+        ValueError
             If any choice in choices does not pass the datatype check.
         ValueError
             If the current Parameter value is not included in the list of
@@ -505,9 +508,9 @@ def value_for_export(self) -> object:
             return None
         if self.__type in (str, Hdf5key, Path):
             return str(self.value)
-        if self.__type == numbers.Integral:
+        if self.__type == Integral:
             return int(self.value)
-        if self.__type == numbers.Real:
+        if self.__type == Real:
             return float(self.value)
         if self.__type in (list, tuple, dict):
             return self.value
@@ -542,7 +545,7 @@ def restore_default(self):
 
     def copy(self) -> Self:
         """
-        A method to get the a copy of the Parameter object.
+        A method to get a copy of the Parameter object.
 
         Returns
         -------
@@ -575,7 +578,7 @@ def dump(self) -> Tuple:
         _default = self.__meta["default"]
         if self.choices is not None and self.__meta["default"] not in self.choices:
             _default = self.value
-        return (self.__refkey, self.__type, _default, _meta)
+        return self.__refkey, self.__type, _default, _meta
 
     def export_refkey_and_value(self) -> Tuple:
         """
@@ -587,7 +590,7 @@ def export_refkey_and_value(self) -> Tuple:
         tuple
             The tuple of (refkey, value as pickleable format)
         """
-        return (self.__refkey, self.value_for_export)
+        return self.__refkey, self.value_for_export
 
     def __str__(self) -> str:
         """