Merge remote-tracking branch 'origin/master' into 661_byte_strings_no…

…t_displayed_correctly

# Conflicts:
#	nexus_constructor/component/component.py
#	nexus_constructor/transformations.py

nexus_constructor/component/component.py

@@ -8,7 +8,11 @@
 from nexus_constructor.component.pixel_shape import PixelShape
 from nexus_constructor.component.transformations_list import TransformationsList
 from nexus_constructor.nexus import nexus_wrapper as nx
-from nexus_constructor.nexus.nexus_wrapper import get_nx_class, to_string
+
+from nexus_constructor.nexus.nexus_wrapper import (
+    get_nx_class,
+    get_name_of_node,
+)
 from nexus_constructor.field_utils import get_fields_with_update_functions
 from nexus_constructor.pixel_data import PixelMapping, PixelGrid, PixelData
 from nexus_constructor.pixel_data_to_nexus_utils import (
@@ -170,9 +174,11 @@ def _get_transform(
             if (
                 transforms
                 and depends_on
-                == to_string(transforms[-1].dataset.attrs[CommonAttrs.DEPENDS_ON])
+                == self.file.get_attribute_value(
+                    transforms[-1].dataset, CommonAttrs.DEPENDS_ON
+                )
                 and depends_on
-                in [x.split("/")[-1] for x in transforms[-1].dataset.parent.keys()]
+                in [get_name_of_node(x) for x in transforms[-1].dataset.parent.values()]
             ):
                 # depends_on is recursive, ie one transformation in this group depends on another transformation in the group, and it is also relative
                 transform_dataset = self.file.nexus_file[
@@ -193,7 +199,10 @@ def _get_transform(
             new_transform = create_transformation(self.file, transform_dataset)
             new_transform.parent = transforms
             transforms.append(new_transform)
-            if CommonAttrs.DEPENDS_ON in transform_dataset.attrs.keys():
+            if (
+                self.file.get_attribute_value(transform_dataset, CommonAttrs.DEPENDS_ON)
+                is not None
+            ):
                 self._get_transform(
                     self.file.get_attribute_value(
                         transform_dataset, CommonAttrs.DEPENDS_ON
@@ -235,27 +244,15 @@ def add_translation(
         :param name: name of the translation group (Optional)
         :param depends_on: existing transformation which the new one depends on (otherwise relative to origin)
         """
-        transforms_group = self.file.create_transformations_group_if_does_not_exist(
-            self.group
-        )
-        if name is None:
-            name = _generate_incremental_name(
-                TransformationType.TRANSLATION, transforms_group
-            )
         unit_vector, magnitude = _normalise(vector)
-        field = self.file.set_field_value(transforms_group, name, magnitude, float)
-        self.file.set_attribute_value(field, CommonAttrs.UNITS, "m")
-        self.file.set_attribute_value(
-            field, CommonAttrs.VECTOR, qvector3d_to_numpy_array(unit_vector)
+        return self._create_transform(
+            name,
+            TransformationType.TRANSLATION,
+            magnitude,
+            "m",
+            unit_vector,
+            depends_on,
         )
-        self.file.set_attribute_value(
-            field, CommonAttrs.TRANSFORMATION_TYPE, TransformationType.TRANSLATION
-        )
-
-        translation_transform = create_transformation(self.file, field)
-        translation_transform.ui_value = magnitude
-        translation_transform.depends_on = depends_on
-        return translation_transform
 
     def add_rotation(
         self,
@@ -271,25 +268,39 @@ def add_rotation(
         :param name: Name of the rotation group (Optional)
         :param depends_on: existing transformation which the new one depends on (otherwise relative to origin)
         """
+        return self._create_transform(
+            name, TransformationType.ROTATION, angle, "degrees", axis, depends_on
+        )
+
+    def _create_transform(
+        self,
+        name: str,
+        transformation_type: TransformationType,
+        angle_or_magnitude: float,
+        units: str,
+        vector: QVector3D,
+        depends_on: Transformation,
+    ):
         transforms_group = self.file.create_transformations_group_if_does_not_exist(
             self.group
         )
         if name is None:
-            name = _generate_incremental_name(
-                TransformationType.ROTATION, transforms_group
-            )
-        field = self.file.set_field_value(transforms_group, name, angle, float)
-        self.file.set_attribute_value(field, CommonAttrs.UNITS, "degrees")
+            name = _generate_incremental_name(transformation_type, transforms_group)
+
+        field = self.file.set_field_value(
+            transforms_group, name, angle_or_magnitude, float
+        )
+        self.file.set_attribute_value(field, CommonAttrs.UNITS, units)
         self.file.set_attribute_value(
-            field, CommonAttrs.VECTOR, qvector3d_to_numpy_array(axis)
+            field, CommonAttrs.VECTOR, qvector3d_to_numpy_array(vector)
         )
         self.file.set_attribute_value(
-            field, CommonAttrs.TRANSFORMATION_TYPE, TransformationType.ROTATION
+            field, CommonAttrs.TRANSFORMATION_TYPE, transformation_type
         )
-        rotation_transform = create_transformation(self.file, field)
-        rotation_transform.depends_on = depends_on
-        rotation_transform.ui_value = angle
-        return rotation_transform
+        transform = create_transformation(self.file, field)
+        transform.ui_value = angle_or_magnitude
+        transform.depends_on = depends_on
+        return transform
 
     def _transform_is_in_this_component(self, transform: Transformation) -> bool:
         return transform._dataset.parent.parent.name == self.absolute_path
@@ -299,24 +310,23 @@ def remove_transformation(self, transform: Transformation):
             raise PermissionError(
                 "Transform is not in this component, do not have permission to delete"
             )
-
-        dependents = transform.get_dependents()
+        dependents = transform.dependents
         if dependents:
             raise DependencyError(
                 f"Cannot delete transformation, it is a dependency of {dependents}"
             )
 
         # Remove whole transformations group if this is the only transformation in it
-        if len(transform._dataset.parent.keys()) == 1:
-            self.file.delete_node(transform._dataset.parent)
+        if len(transform.dataset.parent.keys()) == 1:
+            self.file.delete_node(transform.dataset.parent)
         # Otherwise just remove the transformation from the group
         else:
-            self.file.delete_node(transform._dataset)
+            self.file.delete_node(transform.dataset)
 
     @property
     def depends_on(self) -> Optional[Transformation]:
         depends_on_path = self.file.get_field_value(self.group, CommonAttrs.DEPENDS_ON)
-        if depends_on_path is None:
+        if depends_on_path in [None, "."]:
             return None
         return create_transformation(self.file, self.file.nexus_file[depends_on_path])
 

nexus_constructor/component/component_factory.py

@@ -1,30 +1,23 @@
-from nexus_constructor.common_attrs import CommonAttrs
 from nexus_constructor.component.component import Component
 from nexus_constructor.component.chopper_shape import ChopperShape
 from nexus_constructor.component.pixel_shape import PixelShape
 from nexus_constructor.component.component_type import (
     CHOPPER_CLASS_NAME,
     PIXEL_COMPONENT_TYPES,
 )
-from nexus_constructor.nexus.nexus_wrapper import NexusWrapper
+from nexus_constructor.nexus.nexus_wrapper import NexusWrapper, get_nx_class
 import h5py
 
 
 def create_component(
     nexus_wrapper: NexusWrapper, component_group: h5py.Group
 ) -> Component:
-    if (
-        nexus_wrapper.get_attribute_value(component_group, CommonAttrs.NX_CLASS)
-        == CHOPPER_CLASS_NAME
-    ):
+    nx_class = get_nx_class(component_group)
+    if nx_class == CHOPPER_CLASS_NAME:
         return Component(
             nexus_wrapper, component_group, ChopperShape(nexus_wrapper, component_group)
         )
-    if (
-        nexus_wrapper.get_attribute_value(component_group, CommonAttrs.NX_CLASS)
-        in PIXEL_COMPONENT_TYPES
-        and "pixel_shape" in component_group
-    ):
+    if nx_class in PIXEL_COMPONENT_TYPES and "pixel_shape" in component_group:
         return Component(
             nexus_wrapper, component_group, PixelShape(nexus_wrapper, component_group)
         )

nexus_constructor/component_tree_model.py

@@ -129,7 +129,7 @@ def _remove_transformation(self, index: QModelIndex):
     def _remove_component(self, index: QModelIndex):
         component = index.internalPointer()
         transforms = component.transforms
-        if transforms and transforms[0].get_dependents():
+        if transforms and transforms[0].dependents():
             reply = QMessageBox.question(
                 None,
                 "Delete component?",

nexus_constructor/field_utils.py

@@ -7,7 +7,10 @@
 from nexus_constructor.common_attrs import CommonAttrs
 from nexus_constructor.field_widget import FieldWidget
 from nexus_constructor.invalid_field_names import INVALID_FIELD_NAMES
-from nexus_constructor.nexus.nexus_wrapper import get_name_of_node
+from nexus_constructor.nexus.nexus_wrapper import (
+    get_name_of_node,
+    get_nx_class,
+)
 from nexus_constructor.validators import FieldType
 from nexus_constructor.nexus.nexus_wrapper import h5Node
 
@@ -87,10 +90,7 @@ def find_field_type(item: h5Node) -> Callable:
     elif isinstance(item, h5py.Group):
         if isinstance(item.parent.get(item.name, getlink=True), h5py.SoftLink):
             return update_existing_link_field
-        elif (
-            CommonAttrs.NX_CLASS in item.attrs.keys()
-            and item.attrs[CommonAttrs.NX_CLASS] == CommonAttrs.NC_STREAM
-        ):
+        elif get_nx_class(item) == CommonAttrs.NC_STREAM:
             return update_existing_stream_field
     logging.debug(
         f"Object {get_name_of_node(item)} not handled as field - could be used for other parts of UI instead"

nexus_constructor/file_writer_ctrl_window.py

@@ -7,8 +7,8 @@
 from nexus_constructor.validators import BrokerAndTopicValidator
 from ui.led import Led
 from ui.filewriter_ctrl_frame import Ui_FilewriterCtrl
-from PySide2.QtWidgets import QMainWindow, QLineEdit
-from PySide2.QtCore import QTimer, QAbstractItemModel
+from PySide2.QtWidgets import QMainWindow, QLineEdit, QApplication
+from PySide2.QtCore import QTimer, QAbstractItemModel, QSettings
 from PySide2.QtGui import QStandardItemModel, QCloseEvent
 from PySide2 import QtCore
 from nexus_constructor.instrument import Instrument
@@ -39,16 +39,86 @@ class File:
     last_time = attr.ib(default=0)
 
 
+class FileWriterSettings:
+    STATUS_BROKER_ADDR = "status_broker_addr"
+    COMMAND_BROKER_ADDR = "command_broker_addr"
+    FILE_BROKER_ADDR = "file_broker_addr"
+    USE_START_TIME = "use_start_time"
+    USE_STOP_TIME = "use_stop_time"
+    FILE_NAME = "file_name"
+
+
+def extract_bool_from_qsettings(setting: Union[str, bool]):
+    if type(setting) == str:
+        setting = setting == "True"
+    return setting
+
+
 class FileWriterCtrl(Ui_FilewriterCtrl, QMainWindow):
-    def __init__(self, instrument: Instrument):
+    def __init__(self, instrument: Instrument, settings: QSettings):
         super().__init__()
+        self.settings = settings
         self.instrument = instrument
         self.setupUi()
         self.known_writers = {}
         self.known_files = {}
         self.status_consumer = None
         self.command_producer = None
 
+    def _restore_settings(self):
+        """
+        Restore persistent broker config settings from file.
+        """
+        self.status_broker_edit.setText(
+            self.settings.value(FileWriterSettings.STATUS_BROKER_ADDR)
+        )
+        self.command_broker_edit.setText(
+            self.settings.value(FileWriterSettings.COMMAND_BROKER_ADDR)
+        )
+        self.command_widget.broker_line_edit.setText(
+            self.settings.value(FileWriterSettings.FILE_BROKER_ADDR)
+        )
+        self.command_widget.start_time_enabled.setChecked(
+            extract_bool_from_qsettings(
+                self.settings.value(FileWriterSettings.USE_START_TIME, False)
+            )
+        )
+        self.command_widget.stop_time_enabled.setChecked(
+            extract_bool_from_qsettings(
+                self.settings.value(FileWriterSettings.USE_STOP_TIME, False)
+            )
+        )
+        self.command_widget.nexus_file_name_edit.setText(
+            self.settings.value(FileWriterSettings.FILE_NAME)
+        )
+
+    def _store_settings(self):
+        """
+        Store persistent broker config settings to file.
+        """
+        self.settings.setValue(
+            FileWriterSettings.STATUS_BROKER_ADDR, self.status_broker_edit.text()
+        )
+        self.settings.setValue(
+            FileWriterSettings.COMMAND_BROKER_ADDR, self.command_broker_edit.text()
+        )
+        self.settings.setValue(
+            FileWriterSettings.FILE_BROKER_ADDR,
+            self.command_widget.broker_line_edit.text(),
+        )
+        self.settings.setValue(
+            FileWriterSettings.USE_START_TIME,
+            self.command_widget.start_time_enabled.isChecked(),
+        )
+        self.settings.setValue(
+            FileWriterSettings.USE_STOP_TIME,
+            self.command_widget.stop_time_enabled.isChecked(),
+        )
+        self.settings.setValue(
+            FileWriterSettings.FILE_NAME,
+            self.command_widget.nexus_file_name_edit.text(),
+        )
+
     def setupUi(self):
         super().setupUi(self)
 
@@ -96,6 +166,8 @@ def setupUi(self):
         self.file_list_model.setHeaderData(1, QtCore.Qt.Horizontal, "Last seen")
         self.file_list_model.setHeaderData(2, QtCore.Qt.Horizontal, "File writer")
         self.files_list.setModel(self.file_list_model)
+        self._restore_settings()
+        QApplication.instance().aboutToQuit.connect(self._store_settings)
 
     @staticmethod
     def _set_up_broker_fields(
@@ -215,7 +287,6 @@ def send_command(self):
                 stop_time,
                 service_id,
                 abort_on_uninitialised_stream,
-                use_swmr,
             ) = self.command_widget.get_arguments()
             self.command_producer.send_command(
                 bytes(

nexus_constructor/filewriter_command_widget.py

@@ -35,8 +35,6 @@ def __init__(self, parent=None):
         self.nexus_file_name_edit = QLineEdit()
 
         self.ok_button = QPushButton("Ok")
-        if parent is not None:
-            self.ok_button.clicked.connect(parent.close)
 
         self.broker_line_edit = QLineEdit()
         self.broker_line_edit.setPlaceholderText("broker:port")
@@ -84,8 +82,6 @@ def __init__(self, parent=None):
         self.service_id_lineedit = QLineEdit()
         self.service_id_lineedit.setPlaceholderText("(Optional)")
         self.abort_on_uninitialised_stream_checkbox = QCheckBox()
-        self.use_swmr_checkbox = QCheckBox()
-        self.use_swmr_checkbox.setChecked(True)
 
         self.layout().addRow("nexus_file_name", self.nexus_file_name_edit)
         self.layout().addRow("broker", self.broker_line_edit)
@@ -97,7 +93,6 @@ def __init__(self, parent=None):
         self.layout().addRow(
             "abort_on_uninitialised_stream", self.abort_on_uninitialised_stream_checkbox
         )
-        self.layout().addRow("use_hdf_swmr", self.use_swmr_checkbox)
         self.layout().addRow(self.ok_button)
 
     def state_changed(self, is_start_time: bool, state: Qt.CheckState):
@@ -112,7 +107,7 @@ def state_changed(self, is_start_time: bool, state: Qt.CheckState):
 
     def get_arguments(
         self,
-    ) -> Tuple[str, str, Union[str, None], Union[str, None], str, bool, bool]:
+    ) -> Tuple[str, str, Union[str, None], Union[str, None], str, bool]:
         """
         gets the arguments of required and optional fields for the filewriter command.
         :return: Tuple containing all of the fields.
@@ -129,5 +124,4 @@ def get_arguments(
             self.service_id_lineedit.text(),
             self.abort_on_uninitialised_stream_checkbox.checkState()
             == Qt.CheckState.Checked,
-            self.use_swmr_checkbox.checkState() == Qt.CheckState.Checked,
         )

nexus_constructor/geometry/cylindrical_geometry.py

@@ -150,7 +150,7 @@ def axis_direction(self) -> QVector3D:
         return QVector3D(0, 0, 1)
 
     @property
-    def off_geometry(self, steps: int = 20) -> OFFGeometry:
+    def off_geometry(self, steps: int = 10) -> OFFGeometry:
         unit_conversion_factor = calculate_unit_conversion_factor(self.units, METRES)
 
         # A list of vertices describing the circle at the bottom of the cylinder