Multiprobe (#54)

- Add support for working with multiple probes
- Fix probe energy units in cxi reader
- Update detector view to present diffraction dataset as a tree; selecting root displays sum of child diffraction patterns
- Add probe initializer for disk and test patterns
- Reparameterize supergaussian probe initializer using FWHM
- Probe/object controllers live update views while editing parameters
- Autoselect new scan/probe/object after reconstruction
- Add NPZ scan plugin

ptychodus/api/settings.py

@@ -2,7 +2,7 @@
 from collections.abc import Iterator
 from decimal import Decimal
 from pathlib import Path
-from typing import Any, Callable, Final, Generic, TypeVar, Union
+from typing import Any, Callable, Final, Generic, TypeVar
 from uuid import UUID
 import configparser
 import logging
@@ -79,8 +79,7 @@ def createIntegerEntry(self, name: str, defaultValue: int) -> SettingsEntry[int]
                                             lambda valueString: int(valueString))
         return self._registerEntryIfNonexistent(candidateEntry)
 
-    def createRealEntry(self, name: str, defaultValue: Union[str,
-                                                             Decimal]) -> SettingsEntry[Decimal]:
+    def createRealEntry(self, name: str, defaultValue: str | Decimal) -> SettingsEntry[Decimal]:
         defaultDecimal = Decimal(defaultValue) if isinstance(defaultValue, str) else defaultValue
         candidateEntry = SettingsEntry[Decimal](name, defaultDecimal,
                                                 lambda valueString: Decimal(valueString))

ptychodus/api/tree.py

@@ -1,18 +1,19 @@
 from __future__ import annotations
+from collections.abc import Sequence
 
 
 class SimpleTreeNode:
 
-    def __init__(self, parentItem: SimpleTreeNode | None, itemData: list[str]) -> None:
+    def __init__(self, parentItem: SimpleTreeNode | None, itemData: Sequence[str]) -> None:
         self.parentItem = parentItem
         self.itemData = itemData
         self.childItems: list[SimpleTreeNode] = list()
 
     @classmethod
-    def createRoot(cls, itemData: list[str]) -> SimpleTreeNode:
+    def createRoot(cls, itemData: Sequence[str]) -> SimpleTreeNode:
         return cls(None, itemData)
 
-    def createChild(self, itemData: list[str]) -> SimpleTreeNode:
+    def createChild(self, itemData: Sequence[str]) -> SimpleTreeNode:
         childItem = SimpleTreeNode(self, itemData)
         self.childItems.append(childItem)
         return childItem

ptychodus/controller/automation.py

@@ -1,15 +1,14 @@
 from __future__ import annotations
 from pathlib import Path
-from typing import Optional
 
 from PyQt5.QtCore import Qt, QAbstractListModel, QModelIndex, QObject, QTimer, QVariant
 from PyQt5.QtGui import QFont
 
 from ..api.observer import Observable, Observer
 from ..model.automation import (AutomationCore, AutomationDatasetState, AutomationPresenter,
                                 AutomationProcessingPresenter)
-from ..view import (AutomationView, AutomationParametersView, AutomationProcessingView,
-                    AutomationWatchdogView)
+from ..view.automation import (AutomationView, AutomationParametersView, AutomationProcessingView,
+                               AutomationWatchdogView)
 from .data import FileDialogFactory
 
 
@@ -119,7 +118,7 @@ class AutomationProcessingListModel(QAbstractListModel):
 
     def __init__(self,
                  presenter: AutomationProcessingPresenter,
-                 parent: Optional[QObject] = None) -> None:
+                 parent: QObject | None = None) -> None:
         super().__init__(parent)
         self._presenter = presenter
 

ptychodus/controller/core.py

@@ -7,7 +7,7 @@
 from ..view import ViewCore
 from .automation import AutomationController
 from .data import DataParametersController, FileDialogFactory
-from .detector import (DatasetImageController, DatasetParametersController, DetectorController)
+from .detector import DetectorController
 from .object import ObjectImageController, ObjectController
 from .probe import ProbeImageController, ProbeController
 from .ptychonn import PtychoNNViewControllerFactory
@@ -38,27 +38,20 @@ def __init__(self, model: ModelCore, view: ViewCore) -> None:
                                                                      view.settingsEntryView,
                                                                      self._fileDialogFactory)
         self._detectorController = DetectorController.createInstance(
-            model.detectorPresenter, model.apparatusPresenter,
-            view.detectorParametersView.detectorView)
-        self._datasetParametersController = DatasetParametersController.createInstance(
-            model.diffractionDatasetPresenter, model.activeDiffractionPatternPresenter,
-            view.detectorParametersView.patternView)
-        self._datasetImageController = DatasetImageController.createInstance(
-            model.activeDiffractionPatternPresenter, model.detectorImagePresenter,
-            view.detectorImageView, self._fileDialogFactory)
-        self._probeController = ProbeController.createInstance(model.probePresenter,
-                                                               view.probeView,
-                                                               model.probeImagePresenter,
-                                                               view.probeImageView,
-                                                               self._fileDialogFactory)
+            model.detectorPresenter, model.apparatusPresenter, model.diffractionDatasetPresenter,
+            model.detectorImagePresenter, view.detectorView, view.detectorImageView,
+            self._fileDialogFactory)
         self._scanController = ScanController.createInstance(model.scanRepositoryPresenter,
                                                              view.scanView, view.scanPlotView,
                                                              self._fileDialogFactory)
-        self._objectController = ObjectController.createInstance(model.objectRepositoryPresenter,
-                                                                 model.objectImagePresenter,
-                                                                 view.objectView,
-                                                                 view.objectImageView,
-                                                                 self._fileDialogFactory)
+        self._probeController = ProbeController.createInstance(model.apparatusPresenter,
+                                                               model.probeRepositoryPresenter,
+                                                               model.probeImagePresenter,
+                                                               view.probeView, view.probeImageView,
+                                                               self._fileDialogFactory)
+        self._objectController = ObjectController.createInstance(
+            model.apparatusPresenter, model.objectRepositoryPresenter, model.objectImagePresenter,
+            view.objectView, view.objectImageView, self._fileDialogFactory)
         self._dataParametersController = DataParametersController.createInstance(
             model.settingsRegistry, model.diffractionDatasetInputOutputPresenter,
             model.diffractionDatasetPresenter, model.metadataPresenter, model.patternPresenter,

ptychodus/controller/data/dataset.py

@@ -2,7 +2,7 @@
 
 from ...api.observer import Observable, Observer
 from ...model.data import DiffractionDatasetInputOutputPresenter, DiffractionDatasetPresenter
-from ...view import DataNavigationPage, DatasetView
+from ...view.data import DataNavigationPage, DatasetView
 from .dialogFactory import FileDialogFactory
 
 

ptychodus/controller/data/file.py

@@ -8,7 +8,7 @@
 
 from ...api.observer import Observable, Observer
 from ...model.data import DiffractionDatasetInputOutputPresenter
-from ...view import DataNavigationPage, DatasetFileView
+from ...view.data import DataNavigationPage, DatasetFileView
 from .dialogFactory import FileDialogFactory
 
 logger = logging.getLogger(__name__)

ptychodus/controller/data/metadata.py

@@ -2,7 +2,7 @@
 
 from ...api.observer import Observable, Observer
 from ...model import MetadataPresenter
-from ...view import DataNavigationPage, MetadataView
+from ...view.data import DataNavigationPage, MetadataView
 
 
 class MetadataController(Observer):

ptychodus/controller/data/parameters.py

@@ -8,7 +8,7 @@
 from ...model import MetadataPresenter
 from ...model.data import (DiffractionDatasetInputOutputPresenter, DiffractionDatasetPresenter,
                            DiffractionPatternPresenter)
-from ...view import DataParametersView
+from ...view.data import DataParametersView
 from ..tree import SimpleTreeModel
 from .dataset import DatasetController
 from .dialogFactory import FileDialogFactory

ptychodus/controller/data/patterns.py

@@ -4,8 +4,8 @@
 from ...api.observer import Observable, Observer
 from ...model.data import (DiffractionDatasetInputOutputPresenter, DiffractionDatasetPresenter,
                            DiffractionPatternPresenter)
-from ...view import (DataNavigationPage, PatternCropView, PatternLoadView, PatternMemoryMapView,
-                     PatternTransformView, PatternsView)
+from ...view.data import (DataNavigationPage, PatternCropView, PatternLoadView,
+                          PatternMemoryMapView, PatternTransformView, PatternsView)
 from ..data import FileDialogFactory
 
 

ptychodus/controller/detector/__init__.py

@@ -0,0 +1,5 @@
+from .controller import DetectorController
+
+__all__ = [
+    'DetectorController',
+]