Fix the output trajectory dialog for converters

MDANSE/Src/MDANSE/Framework/Configurators/OutputTrajectoryConfigurator.py

@@ -38,7 +38,7 @@ class OutputTrajectoryConfigurator(IConfigurator):
     conversion, you must inherit from the MDANSE.Framework.Formats.IFormat.IFormat interface.
     """
 
-    _default = ("OUTPUT_TRAJECTORY", "MDTFormat")
+    _default = ("OUTPUT_TRAJECTORY", 64, "none")
 
     def __init__(self, name, format=None, **kwargs):
         """
@@ -52,7 +52,7 @@ def __init__(self, name, format=None, **kwargs):
 
         IConfigurator.__init__(self, name, **kwargs)
 
-        self._format = OutputTrajectoryConfigurator._default[-1]
+        self._format = "MDTFormat"
         self._dtype = np.float64
         self._compression = "none"
 

MDANSE/Src/MDANSE/Framework/Jobs/CenterOfMassesTrajectory.py

@@ -85,7 +85,7 @@ def initialize(self):
 
         # The output trajectory is opened for writing.
         self._output_trajectory = TrajectoryWriter(
-            self.configuration["output_file"]["files"][0],
+            self.configuration["output_file"]["file"],
             chemical_system,
             self.numberOfSteps,
             positions_dtype=self.configuration["output_file"]["dtype"],

MDANSE/Src/MDANSE/Framework/Jobs/CroppedTrajectory.py

@@ -72,7 +72,7 @@ def initialize(self):
 
         # The output trajectory is opened for writing.
         self._output_trajectory = TrajectoryWriter(
-            self.configuration["output_file"]["files"][0],
+            self.configuration["output_file"]["file"],
             self.configuration["trajectory"]["instance"].chemical_system,
             self.numberOfSteps,
             self._selectedAtoms,

MDANSE/Src/MDANSE/Framework/Jobs/GlobalMotionFilteredTrajectory.py

@@ -99,7 +99,7 @@ def initialize(self):
         self._reference_atoms = AtomGroup(self._reference_atoms)
 
         self._output_trajectory = TrajectoryWriter(
-            self.configuration["output_file"]["files"][0],
+            self.configuration["output_file"]["file"],
             self.configuration["trajectory"]["instance"].chemical_system,
             self.numberOfSteps,
             self._selected_atoms.atom_list,

MDANSE/Src/MDANSE/Framework/Jobs/MoleculeFinder.py

@@ -51,7 +51,7 @@ class MoleculeFinder(IJob):
         "FramesConfigurator",
         {"dependencies": {"trajectory": "trajectory"}, "default": (0, -1, 1)},
     )
-    settings["output_files"] = (
+    settings["output_file"] = (
         "OutputTrajectoryConfigurator",
         {"format": "MDTFormat"},
     )
@@ -77,7 +77,7 @@ def initialize(self):
 
         # The output trajectory is opened for writing.
         self._output_trajectory = TrajectoryWriter(
-            self.configuration["output_files"]["files"][0],
+            self.configuration["output_file"]["file"],
             chemical_system,
             self.numberOfSteps,
             positions_dtype=self.configuration["output_file"]["dtype"],

MDANSE/Src/MDANSE/Framework/Jobs/RigidBodyTrajectory.py

@@ -66,7 +66,7 @@ class RigidBodyTrajectory(IJob):
     )
     settings["reference"] = ("IntegerConfigurator", {"mini": 0})
     settings["remove_translation"] = ("BooleanConfigurator", {"default": False})
-    settings["output_files"] = ("OutputTrajectoryConfigurator", {"format": "MDTFormat"})
+    settings["output_file"] = ("OutputTrajectoryConfigurator", {"format": "MDTFormat"})
 
     def initialize(self):
         """ """
@@ -135,7 +135,7 @@ def initialize(self):
 
         # Create trajectory
         self._output_trajectory = TrajectoryWriter(
-            self.configuration["output_files"]["files"][0],
+            self.configuration["output_file"]["file"],
             trajectory.chemical_system,
             self.configuration["frames"]["number"],
             selectedAtoms,
@@ -226,7 +226,7 @@ def finalize(self):
                 time, units={"time": "ps", "unit_cell": "nm", "coordinates": "nm"}
             )
 
-        outputFile = h5py.File(self.configuration["output_files"]["files"][0], "r+")
+        outputFile = h5py.File(self.configuration["output_file"]["file"], "r+")
 
         n_groups = self.configuration["atom_selection"]["selection_length"]
         n_frames = self.configuration["frames"]["number"]

MDANSE/Src/MDANSE/MolecularDynamics/Connectivity.py

@@ -20,17 +20,17 @@
 
 from MDANSE.Chemistry import ATOMS_DATABASE
 from MDANSE.Chemistry.ChemicalEntity import ChemicalSystem
-from MDANSE.Framework.InputData.HDFTrajectoryInputData import HDFTrajectoryInputData
+from MDANSE.MolecularDynamics.Trajectory import Trajectory
 
 
 class Connectivity:
     """This class calculates the distances between atoms in a trajectory,
     and identifies potential molecules based on distances alone.
     """
 
-    def __init__(self, *args, trajectory: HDFTrajectoryInputData = None, **kwargs):
+    def __init__(self, *args, trajectory: Trajectory = None, **kwargs):
         self._chemical_system = trajectory.chemical_system
-        self._frames = trajectory.trajectory
+        self._frames = trajectory
         self._unit_cell = self._chemical_system.configuration
         self._periodic = self._chemical_system.configuration.is_periodic
         self.check_composition(self._chemical_system)

MDANSE/Tests/UnitTests/molecules/test_connectivity.py

@@ -3,6 +3,7 @@
 import numpy as np
 from MDANSE.MolecularDynamics.Connectivity import Connectivity
 from MDANSE.Framework.InputData.HDFTrajectoryInputData import HDFTrajectoryInputData
+from MDANSE.MolecularDynamics.Trajectory import Trajectory
 from MDANSE.Chemistry.Structrures import MoleculeTester
 
 
@@ -12,30 +13,30 @@
 
 
 @pytest.fixture(scope="module")
-def trajectory() -> HDFTrajectoryInputData:
+def trajectory() -> Trajectory:
     trajectory = HDFTrajectoryInputData(short_traj)
-    yield trajectory
+    yield trajectory.trajectory
 
 
-def test_create_connectivity(trajectory: HDFTrajectoryInputData):
+def test_create_connectivity(trajectory: Trajectory):
     conn = Connectivity(trajectory=trajectory)
     print(conn._unique_elements)
     assert len(conn._unique_elements) == 2
 
 
-def test_find_bonds(trajectory: HDFTrajectoryInputData):
+def test_find_bonds(trajectory: Trajectory):
     conn = Connectivity(trajectory=trajectory)
     conn.find_bonds()
     assert len(conn._unique_bonds) == 40
 
 
-def test_find_molecules(trajectory: HDFTrajectoryInputData):
+def test_find_molecules(trajectory: Trajectory):
     conn = Connectivity(trajectory=trajectory)
     conn.find_molecules()
     assert len(conn._molecules) == 20
 
 
-def test_rebuild_molecules(trajectory: HDFTrajectoryInputData):
+def test_rebuild_molecules(trajectory: Trajectory):
     print(trajectory.chemical_system.atom_list)
     conn = Connectivity(trajectory=trajectory)
     conn.find_molecules()
@@ -47,7 +48,7 @@ def test_rebuild_molecules(trajectory: HDFTrajectoryInputData):
     assert atoms_before == atoms_after
 
 
-def test_unwrap_molecules(trajectory: HDFTrajectoryInputData):
+def test_unwrap_molecules(trajectory: Trajectory):
     conn = Connectivity(trajectory=trajectory)
     conn.find_molecules()
     chemical_system = trajectory.chemical_system
@@ -61,7 +62,7 @@ def test_unwrap_molecules(trajectory: HDFTrajectoryInputData):
     assert not np.allclose(original_coords, contiguous_config.coordinates)
 
 
-def test_identify_molecules(trajectory: HDFTrajectoryInputData):
+def test_identify_molecules(trajectory: Trajectory):
     conn = Connectivity(trajectory=trajectory)
     conn.find_molecules()
     chemical_system = trajectory.chemical_system

MDANSE_GUI/Src/MDANSE_GUI/PyQtGUI/InputWidgets/FloatWidget.py

@@ -76,9 +76,6 @@ def newFloat(self, num: float):
         self._value = num
         self.updateValue()
 
-    @Slot()
-    def updateValue(self):
-        self._configurator.configure(self._value)
-
-    def get_value(self):
-        return self._configurator["value"]
+    def get_widget_value(self):
+        """Collect the results from the input widgets and return the value."""
+        return float(self._field.text())

MDANSE_GUI/Src/MDANSE_GUI/PyQtGUI/InputWidgets/IntegerWidget.py

@@ -73,9 +73,6 @@ def newInt(self, num: int):
         self._value = num
         self.updateValue()
 
-    @Slot()
-    def updateValue(self):
-        self._configurator.configure(self._value)
-
-    def get_value(self):
-        return self._configurator["value"]
+    def get_widget_value(self):
+        """Collect the results from the input widgets and return the value."""
+        return int(self._field.text())

MDANSE_GUI/Src/MDANSE_GUI/PyQtGUI/InputWidgets/OutputTrajectoryWidget.py

@@ -18,9 +18,8 @@
 import os
 import os.path
 
-from qtpy.QtWidgets import QComboBox, QLabel, QLineEdit, QPushButton, QFileDialog
+from qtpy.QtWidgets import QComboBox, QLineEdit, QPushButton, QFileDialog
 from qtpy.QtCore import Qt, Slot
-from qtpy.QtGui import QStandardItemModel, QStandardItem
 
 from MDANSE.MolecularDynamics.Trajectory import TrajectoryWriter
 from MDANSE_GUI.PyQtGUI.InputWidgets.WidgetBase import WidgetBase
@@ -47,10 +46,10 @@ def __init__(self, *args, **kwargs):
         self.field = QLineEdit(default_value[0], self._base)
         self.dtype_box = QComboBox(self._base)
         self.dtype_box.addItems(["float16", "float32", "float64", "float128"])
-        self.dtype_box.set_default("float64")
+        self.dtype_box.setCurrentText("float64")
         self.compression_box = QComboBox(self._base)
         self.compression_box.addItems(["none"] + TrajectoryWriter.allowed_compression)
-        self.compression_box.set_default("lza")
+        self.compression_box.setCurrentText("lzf")
         # self.type_box.setCurrentText(default_value[1])
         browse_button = QPushButton("Browse", self._base)
         browse_button.clicked.connect(self.file_dialog)

MDANSE_GUI/Src/MDANSE_GUI/PyQtGUI/InputWidgets/StringWidget.py

@@ -42,9 +42,6 @@ def default_labels(self):
         if self._tooltip == "":
             self._tooltip = "A text string variable. Do you know what to type in?"
 
-    @Slot()
-    def updateValue(self):
-        self._configurator.configure(self._field.text())
-
-    def get_value(self):
-        return self._configurator["value"]
+    def get_widget_value(self):
+        """Collect the results from the input widgets and return the value."""
+        return self._field.text()

MDANSE_GUI/Src/MDANSE_GUI/PyQtGUI/Widgets/GeneralWidgets.py

@@ -161,8 +161,6 @@ def returnValue(self):
         if self.file_dialog is not None:
             ic(f"File Field Return Value: {self.current_value}")
         self.final_value.emit(self.current_value)
-        if self.file_direction == "out":
-            return (self.current_value, "MDTFormat")
         return self.current_value
 
     @Slot()
@@ -229,6 +227,12 @@ def register_value(self, field: GeneralInput):
         self.fields.append(field)
         field.value_changed.connect(self.valueChanged)
 
+    def returnValue(self):
+        result = []
+        for field in self.fields:
+            result.append(field.returnValue())
+        return result
+
 
 def translate_file_associations(input_str: str):
     """Takes the string describing valid file formats, as specified for
@@ -297,6 +301,8 @@ def createInputField(*args, **kwargs):
             result = InputFactory.createFile(*args, direction="in", **kwargs)
         elif kind == "SingleOutputFileConfigurator":
             result = InputFactory.createFile(*args, direction="out", **kwargs)
+        elif kind == "OutputTrajectoryConfigurator":
+            result = InputFactory.createTrajectory(*args, direction="out", **kwargs)
         else:
             result = InputFactory.createBlank(*args, **kwargs)
 
@@ -369,6 +375,59 @@ def createFile(*args, direction="in", **kwargs):
         layout.addWidget(button)
         return [base, data_handler]
 
+    def createTrajectory(*args, direction="out", **kwargs):
+        """Creates an input field with an additional button which
+        creates a FileDialog, to allow the user to browse the file system.
+
+        Keyword Arguments:
+            direction -- if 'in', create a FileDialog for an exisitng file,
+              if 'out', a FileDialog for creating a new file.
+        """
+        kind = kwargs.get("kind", "String")
+        default_value = kwargs.get("default", "")
+        tooltip_text = kwargs.get(
+            "tooltip", "Specify the name of the output trajectory."
+        )
+        file_association = kwargs.get("wildcard", "")
+        qt_file_association = translate_file_associations(file_association)
+        base, layout = InputFactory.createBase(*args, **kwargs)
+        field = QLineEdit(base)
+        main_handler = InputGroup(base)
+        data_handler1 = GeneralInput(
+            data_type=str,
+            file_association=qt_file_association,
+            file_direction=direction,
+            **kwargs,
+        )
+        data_handler2 = GeneralInput(
+            data_type=int,
+        )
+        data_handler3 = GeneralInput(
+            data_type=str,
+        )
+        main_handler.register_value(data_handler1)
+        main_handler.register_value(data_handler2)
+        main_handler.register_value(data_handler3)
+        data_handler1.string_value.connect(field.setText)
+        field.textChanged.connect(data_handler1.updateValue)
+        field.setText(str(default_value))
+        field.setToolTip(tooltip_text)
+        layout.addWidget(field)
+        cbox1 = QComboBox(base)
+        cbox1.addItems(["16", "32", "64", "128"])
+        cbox1.setCurrentText("64")
+        layout.addWidget(cbox1)
+        cbox2 = QComboBox(base)
+        cbox2.addItems(["no compression", "gzip"])
+        cbox2.setCurrentText("gzip")
+        layout.addWidget(cbox2)
+        cbox1.currentTextChanged.connect(data_handler2.updateValue)
+        cbox2.currentTextChanged.connect(data_handler3.updateValue)
+        button = QPushButton("Browse", base)
+        button.clicked.connect(data_handler1.valueFromDialog)
+        layout.addWidget(button)
+        return [base, main_handler]
+
     def createBool(*args, **kwargs):
         """Creates an input field for a logical variable,
         which is currently implemented as a check box.