Adapt the Converter GUI to the nee code structure

MDANSE/Src/Framework/Converters/ASE.py

@@ -321,6 +321,8 @@ class ASEInteractiveConverter(InteractiveConverter):
     Converts any trajectory to a HDF trajectory using the ASE io module.
     """
 
+    category = ("InteractiveConverter",)
+
     label = "ASE"
 
     input_files = collections.OrderedDict()

MDANSE/Src/Framework/Converters/Converter.py

@@ -22,6 +22,8 @@
 
 
 class InteractiveConverter(IJob):
+    category = ("InteractiveConverter",)
+
     _converter_registry = {}
     _next_number = 1
 

MDANSE/Src/Framework/Converters/DL_POLY.py

@@ -379,7 +379,10 @@ class DL_POLY(Converter):
             "label": "Input HISTORY file",
         },
     )
-    settings["atom_aliases"] = ("python_object", {"default": {}})
+    settings["atom_aliases"] = (
+        "PythonObjectConfigurator",
+        {"default": {}, "label": "Atom aliases (Python dictionary)"},
+    )
     settings["fold"] = (
         "BooleanConfigurator",
         {"default": False, "label": "Fold coordinates into box"},

MDANSE/Src/Framework/Converters/XPLOR.py

@@ -17,7 +17,7 @@
 from MDANSE.Framework.Converters.DCD import DCD
 
 
-class XPLORConverter(DCD):
+class XPLOR(DCD):
     """
     Converts an Xplor trajectory to a HDF trajectory.
     """

MDANSE/Src/Framework/Jobs/DistanceHistogram.py

@@ -31,6 +31,11 @@ class DistanceHistogram(IJob):
 
     type = None
 
+    category = (
+        "Analysis",
+        "Structure",
+    )
+
     settings = collections.OrderedDict()
     settings["trajectory"] = ("HDFTrajectoryConfigurator", {})
     settings["frames"] = (

MDANSE_GUI/Src/PyQtGUI/BackEnd.py

@@ -129,8 +129,8 @@ def checkConverters(self):
         self._reverse_converters = {}
         for key, conv in Converter.indirect_subclass_dictionary().items():
             ic(f"key:{key}, val:{conv}")
-            self._converters.append(conv)
-            self._reverse_converters[str(conv)] = Converter.create(str(key))
+            self._converters.append(key)
+            self._reverse_converters[str(key)] = Converter.create(str(key))
         self.lock.unlock()
 
     def getConverters(self):

MDANSE_GUI/Src/PyQtGUI/InputWidgets/AtomSelectionWidget.py

@@ -32,7 +32,7 @@ class SelectionDialog(QDialog):
 class AtomSelectionWidget(WidgetBase):
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
-        default_value = "atom_symbol *"
+        default_value = "all"
         self._value = default_value
         self.field = QLineEdit(default_value, self._base)
         browse_button = QPushButton("Atom selection creator", self._base)

MDANSE_GUI/Src/PyQtGUI/InputWidgets/AtomTransmutationWidget.py

@@ -39,7 +39,7 @@ def add_line(self):
         line_base = QWidget(self._base)
         line_layout = QHBoxLayout(line_base)
         line_base.setLayout(line_layout)
-        default_value = "atom_symbol *"
+        default_value = "all"
         starter = QLabel("Transmute ", line_base)
         leftfield = QLineEdit(default_value, self._base)
         spacer = QLabel(" to ", line_base)

MDANSE_GUI/Src/PyQtGUI/InputWidgets/RangeWidget.py

@@ -0,0 +1,79 @@
+# **************************************************************************
+#
+# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
+#
+# @file      Src/PyQtGUI/InputWidgets/FramesWidget.py
+# @brief     Implements module/class/test FramesWidget
+#
+# @homepage  https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
+# @license   GNU General Public License v3 or higher (see LICENSE)
+# @copyright Institut Laue Langevin 2013-now
+# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now
+# @authors   Scientific Computing Group at ILL (see AUTHORS)
+#
+# **************************************************************************
+
+from qtpy.QtWidgets import QLineEdit, QSpinBox, QLabel
+from qtpy.QtCore import Slot, Signal
+from qtpy.QtGui import QDoubleValidator, QIntValidator
+
+from MDANSE_GUI.PyQtGUI.InputWidgets.WidgetBase import WidgetBase
+
+
+class RangeWidget(WidgetBase):
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, layout_type="QGridLayout", **kwargs)
+        source_object = kwargs.get("source_object", None)
+        num_type = kwargs.get("valueType", int)
+        if num_type is int:
+            step_val = 1
+        else:
+            step_val = 0.1
+        labels = [
+            QLabel("From", self._base),
+            QLabel("to", self._base),
+            QLabel("in steps of", self._base),
+        ]
+        fields = [
+            QLineEdit(str(num_type(0)), self._base),
+            QLineEdit(str(num_type(5)), self._base),
+            QLineEdit(str(num_type(step_val)), self._base),
+        ]
+        if num_type is int:
+            validators = [QIntValidator(parent_field) for parent_field in fields]
+        else:
+            validators = [QDoubleValidator(parent_field) for parent_field in fields]
+        for field_num in range(3):
+            self._layout.addWidget(labels[field_num], 0, 2 * field_num)
+            self._layout.addWidget(fields[field_num], 0, 2 * field_num + 1)
+            fields[field_num].setValidator(validators[field_num])
+            fields[field_num].textChanged.connect(self.updateValue)
+        self._fields = fields
+        self._validators = validators
+        self._num_type = num_type
+        self.default_labels()
+        self.update_labels()
+
+    def default_labels(self):
+        """Each Widget should have a default tooltip and label,
+        which will be set in this method, unless specific
+        values are provided in the settings of the job that
+        is being configured."""
+        if self._label_text == "":
+            self._label_text = "RangeWidget"
+        if self._tooltip == "":
+            self._tooltip = "Values to be used, given as (First, Last, StepSize)"
+
+    def value_from_configurator(self):
+        if self._configurator.check_dependencies():
+            minval, maxval = self._configurator._mini, self._configurator._maxi
+            print(f"Configurator min/max: {minval}, {maxval}")
+            if maxval is None:
+                return
+            for val in self._validators:
+                val.setBottom(-abs(maxval))
+                val.setTop(abs(maxval))
+
+    def get_widget_value(self):
+        val = [self._num_type(field.text()) for field in self._fields]
+        return val

MDANSE_GUI/Src/PyQtGUI/InputWidgets/__init__.py

@@ -34,6 +34,7 @@
     "FloatWidget",
     "StringWidget",
     "FramesWidget",
+    "RangeWidget",
     "HDFTrajectoryWidget",
     "DummyWidget",
     "InterpolationOrderWidget",

MDANSE_GUI/Src/PyQtGUI/MolecularViewer/AtomProperties.py

@@ -140,16 +140,14 @@ def initialise_from_database(
         index_list = []
         for nat, atom in enumerate(atoms):
             row = []
-            rgb = [int(x) for x in element_database["atoms"][atom]["color"].split(";")]
+            rgb = [int(x) for x in element_database[atom]["color"].split(";")]
             index_list.append(self.add_colour(rgb))
             row.append(QStandardItem(str(nat + 1)))  # atom number
             row.append(
-                QStandardItem(str(element_database["atoms"][atom]["symbol"]))
+                QStandardItem(str(element_database[atom]["symbol"]))
             )  # chemical element name
             row.append(
-                QStandardItem(
-                    str(round(element_database["atoms"][atom]["atomic_radius"], 2))
-                )
+                QStandardItem(str(round(element_database[atom]["atomic_radius"], 2)))
             )
             row.append(
                 QStandardItem(

MDANSE_GUI/Src/PyQtGUI/MolecularViewer/MolecularViewer.py

@@ -25,8 +25,9 @@
 from vtkmodules.qt.QVTKRenderWindowInteractor import QVTKRenderWindowInteractor
 
 from MDANSE.Framework.InputData.HDFTrajectoryInputData import HDFTrajectoryInputData
+from MDANSE.Chemistry import ATOMS_DATABASE as CHEMICAL_ELEMENTS
 
-from MDANSE_GUI.PyQtGUI.MolecularViewer.database import CHEMICAL_ELEMENTS
+# from MDANSE_GUI.PyQtGUI.MolecularViewer.database import CHEMICAL_ELEMENTS
 from MDANSE_GUI.PyQtGUI.MolecularViewer.readers import hdf5wrapper
 from MDANSE_GUI.PyQtGUI.MolecularViewer.Dummy import PyConnectivity
 from MDANSE_GUI.PyQtGUI.MolecularViewer.Contents import TrajectoryAtomData
@@ -544,8 +545,7 @@ def set_coordinates(self, frame: int):
         self._polydata.SetPoints(atoms)
 
         covalent_radii = [
-            CHEMICAL_ELEMENTS["atoms"][at]["covalent_radius"]
-            for at in self._reader.atom_types
+            CHEMICAL_ELEMENTS[at]["covalent_radius"] for at in self._reader.atom_types
         ]
         self.set_connectivity_builder(coords, covalent_radii)
         chemical_bonds = self._fixed_bonds
@@ -599,7 +599,7 @@ def set_reader(self, reader, frame=0):
         # this returs a list of indices, mapping colours to atoms
 
         self._atom_scales = np.array(
-            [CHEMICAL_ELEMENTS["atoms"][at]["vdw_radius"] for at in self._atoms]
+            [CHEMICAL_ELEMENTS[at]["vdw_radius"] for at in self._atoms]
         ).astype(np.float32)
 
         scalars = ndarray_to_vtkarray(

MDANSE_GUI/Src/PyQtGUI/SubclassViewer.py

@@ -128,6 +128,7 @@ def parentsFromCategories(self, category_tuple):
                 self._categories[cat_string] = current_node
             else:
                 current_node = self._categories[cat_string]
+                parent = current_node
         return current_node
 
 

MDANSE_GUI/Src/PyQtGUI/Widgets/ActionDialog.py

@@ -59,6 +59,7 @@
     "StringConfigurator": StringWidget,
     "IntegerConfigurator": IntegerWidget,
     "FramesConfigurator": FramesWidget,
+    "RangeConfigurator": RangeWidget,
     "HDFTrajectoryConfigurator": HDFTrajectoryWidget,
     "InterpolationOrderConfigurator": InterpolationOrderWidget,
     "OutputFilesConfigurator": OutputFilesWidget,

MDANSE_GUI/Src/PyQtGUI/Widgets/ConvertDialog.py

@@ -84,7 +84,7 @@ def __init__(self, *args, converter: IJob = "Dummy", **kwargs):
                 ]
             )
         else:
-            converter_instance = converter()
+            converter_instance = converter
             converter_instance.build_configuration()
             settings = converter_instance.settings
             self.converter_instance = converter_instance

MDANSE_GUI/Src/PyQtGUI/Widgets/GeneralWidgets.py

@@ -277,25 +277,25 @@ def createInputField(*args, **kwargs):
         Returns:
             [QWidget, GeneralInput] pair
         """
-        kind = kwargs.get("kind", "str")
+        kind = kwargs.get("kind", "String")
 
-        if kind == "str":
+        if kind == "StringConfigurator":
             result = InputFactory.createSingle(*args, **kwargs)
-        elif kind == "int" or kind == "integer":
+        elif kind == "PythonObjectConfigurator":
             result = InputFactory.createSingle(*args, **kwargs)
-        elif kind == "range" or kind == "intrange":
-            result = InputFactory.createMultiple(*args, **kwargs)
-        elif kind == "arange" or kind == "floatrange":
+        elif kind == "IntegerConfigurator":
+            result = InputFactory.createSingle(*args, **kwargs)
+        elif kind == "RangeConfigurator":
             result = InputFactory.createMultiple(*args, **kwargs)
-        elif kind == "float":
+        elif kind == "FloatConfigurator":
             result = InputFactory.createSingle(*args, **kwargs)
-        elif kind == "single_choice":
+        elif kind == "SingleChoiceConfigurator":
             result = InputFactory.createCombo(*args, **kwargs)
-        elif kind == "bool" or kind == "boolean":
+        elif kind == "BooleanConfigurator":
             result = InputFactory.createBool(*args, **kwargs)
-        elif kind == "input_file":
+        elif kind == "InputFileConfigurator":
             result = InputFactory.createFile(*args, direction="in", **kwargs)
-        elif kind == "single_output_file":
+        elif kind == "SingleOutputFileConfigurator":
             result = InputFactory.createFile(*args, direction="out", **kwargs)
         else:
             result = InputFactory.createBlank(*args, **kwargs)
@@ -326,7 +326,7 @@ def createBlank(*args, **kwargs):
         the users that the requested input field could not
         be constructed.
         """
-        kind = kwargs.get("kind", "str")
+        kind = kwargs.get("kind", "String")
         base, layout = InputFactory.createBase(
             label=f"<b>MISSING TYPE</b>:{kind}",
             tooltip="This is not handled by the MDANSE GUI correctly! Please report the problem to the authors.",
@@ -341,7 +341,7 @@ def createFile(*args, direction="in", **kwargs):
             direction -- if 'in', create a FileDialog for an exisitng file,
               if 'out', a FileDialog for creating a new file.
         """
-        kind = kwargs.get("kind", "str")
+        kind = kwargs.get("kind", "String")
         default_value = kwargs.get("default", "")
         tooltip_text = kwargs.get("tooltip", "Specify a path to an existing file.")
         file_association = kwargs.get("wildcard", "")
@@ -373,7 +373,7 @@ def createBool(*args, **kwargs):
         """Creates an input field for a logical variable,
         which is currently implemented as a check box.
         """
-        kind = kwargs.get("kind", "bool")
+        kind = kwargs.get("kind", "Boolean")
         default_value = kwargs.get("default", False)
         tooltip_text = kwargs.get("tooltip", None)
         ic(kind)
@@ -406,13 +406,13 @@ def createSingle(*args, **kwargs):
         ic(kwargs)
         base, layout = InputFactory.createBase(*args, **kwargs)
         field = QLineEdit(base)
-        if kind == "int" or kind == "integer":
+        if "Integer" in kind:
             data_handler = GeneralInput(data_type=int, **kwargs)
             validator = QIntValidator(field)
-        elif kind == "float":
+        elif "Float" in kind:
             data_handler = GeneralInput(data_type=float, **kwargs)
             validator = QDoubleValidator(field)
-        elif kind == "str":
+        else:
             data_handler = GeneralInput(data_type=str, **kwargs)
             validator = None
         if validator is not None:
@@ -432,7 +432,7 @@ def createMultiple(*args, **kwargs):
         For numerical values, it adds a QValidator instance
         to filter out invalid inputs.
         """
-        kind = kwargs.get("kind", "str")
+        kind = kwargs.get("kind", "String")
         default_value = kwargs.get("default", None)
         tooltip_text = kwargs.get("tooltip", None)
         minval = kwargs.get("mini", None)
@@ -447,13 +447,13 @@ def createMultiple(*args, **kwargs):
         main_handler = InputGroup(base)
         for nfield in range(number_of_fields):
             field = QLineEdit(base)
-            if kind == "int" or kind == "integer":
+            if "Integer" in kind:
                 data_handler = GeneralInput(data_type=int, **kwargs)
                 validator = QIntValidator(field)
-            elif kind == "float":
+            elif "Float" in kind:
                 data_handler = GeneralInput(data_type=float, **kwargs)
                 validator = QDoubleValidator(field)
-            elif kind == "str":
+            else:
                 data_handler = GeneralInput(data_type=str, **kwargs)
                 validator = None
             if validator is not None:
@@ -470,7 +470,7 @@ def createMultiple(*args, **kwargs):
     def createCombo(*args, **kwargs):
         """For the variable where one option has to be picked from
         a list of possible values, we create a ComboBox"""
-        kind = kwargs.get("kind", "str")
+        kind = kwargs.get("kind", "String")
         default_value = kwargs.get("default", False)
         tooltip_text = kwargs.get("tooltip", None)
         option_list = kwargs.get("choices", [])