Ptycho+XRF Demo (#101)

- Working implementation of Ptycho-enhanced XRF VSPI algorithm with GUI
- Implemented requested GUI changes: start on diffraction patterns view; rename HDF5 file reader; prompt user to choose data format

ptychodus/api/fluorescence.py

@@ -24,6 +24,12 @@ class FluorescenceDataset:
     # scan_indexes: IntegerArray
 
 
+class FluorescenceEnhancingAlgorithm(ABC):
+    @abstractmethod
+    def enhance(self, dataset: FluorescenceDataset, product: Product) -> FluorescenceDataset:
+        pass
+
+
 class FluorescenceFileReader(ABC):
     @abstractmethod
     def read(self, filePath: Path) -> FluorescenceDataset:

ptychodus/controller/core.py

@@ -136,9 +136,12 @@ def __init__(self, model: ModelCore, view: ViewCore) -> None:
         self._refreshDataTimer.timeout.connect(model.refreshActiveDataset)
         self._refreshDataTimer.start(1000)  # TODO make configurable
 
-        view.navigationActionGroup.triggered.connect(lambda action: self.swapCentralWidgets(action))
         view.workflowAction.setVisible(model.areWorkflowsSupported)
 
+        self.swapCentralWidgets(view.patternsAction)
+        view.patternsAction.setChecked(True)
+        view.navigationActionGroup.triggered.connect(lambda action: self.swapCentralWidgets(action))
+
     def showMainWindow(self, windowTitle: str) -> None:
         self.view.setWindowTitle(windowTitle)
         self.view.show()

ptychodus/controller/probe/core.py

@@ -8,10 +8,10 @@
 
 from ...model.analysis import (
     ExposureAnalyzer,
-    FluorescenceEnhancer,
     ProbePropagator,
     STXMSimulator,
 )
+from ...model.fluorescence import FluorescenceEnhancer
 from ...model.product import ProbeAPI, ProbeRepository
 from ...model.product.probe import ProbeRepositoryItem
 from ...model.visualization import VisualizationEngine

ptychodus/controller/probe/fluorescence.py

@@ -1,13 +1,23 @@
-from typing import Any
+from decimal import Decimal
+from typing import Any, Final
 import logging
 
 from PyQt5.QtCore import Qt, QAbstractListModel, QModelIndex, QObject, QStringListModel
+from PyQt5.QtWidgets import QWidget
 
 from ptychodus.api.observer import Observable, Observer
 
-from ...model.analysis import FluorescenceEnhancer
+from ...model.fluorescence import (
+    FluorescenceEnhancer,
+    TwoStepFluorescenceEnhancingAlgorithm,
+    VSPIFluorescenceEnhancingAlgorithm,
+)
 from ...model.visualization import VisualizationEngine
-from ...view.probe import FluorescenceDialog
+from ...view.probe import (
+    FluorescenceDialog,
+    FluorescenceTwoStepParametersView,
+    FluorescenceVSPIParametersView,
+)
 from ...view.widgets import ExceptionDialog
 from ..data import FileDialogFactory
 from ..visualization import (
@@ -33,6 +43,71 @@ def rowCount(self, parent: QModelIndex = QModelIndex()) -> int:
         return self._enhancer.getNumberOfChannels()
 
 
+class FluorescenceTwoStepViewController(Observer):
+    def __init__(self, algorithm: TwoStepFluorescenceEnhancingAlgorithm) -> None:
+        super().__init__()
+        self._algorithm = algorithm
+        self._view = FluorescenceTwoStepParametersView()
+
+        self._upscalingModel = QStringListModel()
+        self._upscalingModel.setStringList(self._algorithm.getUpscalingStrategyList())
+        self._view.upscalingStrategyComboBox.setModel(self._upscalingModel)
+        self._view.upscalingStrategyComboBox.textActivated.connect(algorithm.setUpscalingStrategy)
+
+        self._deconvolutionModel = QStringListModel()
+        self._deconvolutionModel.setStringList(self._algorithm.getDeconvolutionStrategyList())
+        self._view.deconvolutionStrategyComboBox.setModel(self._deconvolutionModel)
+        self._view.deconvolutionStrategyComboBox.textActivated.connect(
+            algorithm.setDeconvolutionStrategy
+        )
+
+        self._syncModelToView()
+        algorithm.addObserver(self)
+
+    def getWidget(self) -> QWidget:
+        return self._view
+
+    def _syncModelToView(self) -> None:
+        self._view.upscalingStrategyComboBox.setCurrentText(self._algorithm.getUpscalingStrategy())
+        self._view.deconvolutionStrategyComboBox.setCurrentText(
+            self._algorithm.getDeconvolutionStrategy()
+        )
+
+    def update(self, observable: Observable) -> None:
+        if observable is self._algorithm:
+            self._syncModelToView()
+
+
+class FluorescenceVSPIViewController(Observer):
+    MAX_INT: Final[int] = 0x7FFFFFFF
+
+    def __init__(self, algorithm: VSPIFluorescenceEnhancingAlgorithm) -> None:
+        super().__init__()
+        self._algorithm = algorithm
+        self._view = FluorescenceVSPIParametersView()
+
+        self._view.dampingFactorLineEdit.valueChanged.connect(self._syncDampingFactorToModel)
+        self._view.maxIterationsSpinBox.setRange(1, self.MAX_INT)
+        self._view.maxIterationsSpinBox.valueChanged.connect(algorithm.setMaxIterations)
+
+        algorithm.addObserver(self)
+        self._syncModelToView()
+
+    def getWidget(self) -> QWidget:
+        return self._view
+
+    def _syncDampingFactorToModel(self, value: Decimal) -> None:
+        self._algorithm.setDampingFactor(float(value))
+
+    def _syncModelToView(self) -> None:
+        self._view.dampingFactorLineEdit.setValue(Decimal(repr(self._algorithm.getDampingFactor())))
+        self._view.maxIterationsSpinBox.setValue(self._algorithm.getMaxIterations())
+
+    def update(self, observable: Observable) -> None:
+        if observable is self._algorithm:
+            self._syncModelToView()
+
+
 class FluorescenceViewController(Observer):
     def __init__(
         self,
@@ -46,41 +121,42 @@ def __init__(
         self._fileDialogFactory = fileDialogFactory
         self._dialog = FluorescenceDialog()
         self._enhancementModel = QStringListModel()
-        self._enhancementModel.setStringList(self._enhancer.getEnhancementStrategyList())
-        self._upscalingModel = QStringListModel()
-        self._upscalingModel.setStringList(self._enhancer.getUpscalingStrategyList())
-        self._deconvolutionModel = QStringListModel()
-        self._deconvolutionModel.setStringList(self._enhancer.getDeconvolutionStrategyList())
+        self._enhancementModel.setStringList(self._enhancer.getAlgorithmList())
         self._channelListModel = FluorescenceChannelListModel(enhancer)
 
         self._dialog.fluorescenceParametersView.openButton.clicked.connect(
             self._openMeasuredDataset
         )
 
-        self._dialog.fluorescenceParametersView.enhancementStrategyComboBox.setModel(
-            self._enhancementModel
+        twoStepViewController = FluorescenceTwoStepViewController(
+            enhancer.twoStepEnhancingAlgorithm
+        )
+        self._dialog.fluorescenceParametersView.algorithmComboBox.addItem(
+            TwoStepFluorescenceEnhancingAlgorithm.DISPLAY_NAME,
+            self._dialog.fluorescenceParametersView.algorithmComboBox.count(),
         )
-        self._dialog.fluorescenceParametersView.enhancementStrategyComboBox.textActivated.connect(
-            enhancer.setEnhancementStrategy
+        self._dialog.fluorescenceParametersView.stackedWidget.addWidget(
+            twoStepViewController.getWidget()
         )
 
-        self._dialog.fluorescenceParametersView.upscalingStrategyComboBox.setModel(
-            self._upscalingModel
+        vspiViewController = FluorescenceVSPIViewController(enhancer.vspiEnhancingAlgorithm)
+        self._dialog.fluorescenceParametersView.algorithmComboBox.addItem(
+            VSPIFluorescenceEnhancingAlgorithm.DISPLAY_NAME,
+            self._dialog.fluorescenceParametersView.algorithmComboBox.count(),
         )
-        self._dialog.fluorescenceParametersView.upscalingStrategyComboBox.textActivated.connect(
-            enhancer.setUpscalingStrategy
+        self._dialog.fluorescenceParametersView.stackedWidget.addWidget(
+            vspiViewController.getWidget()
         )
 
-        self._dialog.fluorescenceParametersView.deconvolutionStrategyComboBox.setModel(
-            self._deconvolutionModel
+        self._dialog.fluorescenceParametersView.algorithmComboBox.textActivated.connect(
+            enhancer.setAlgorithm
         )
-        self._dialog.fluorescenceParametersView.deconvolutionStrategyComboBox.textActivated.connect(
-            enhancer.setDeconvolutionStrategy
+        self._dialog.fluorescenceParametersView.algorithmComboBox.currentIndexChanged.connect(
+            self._dialog.fluorescenceParametersView.stackedWidget.setCurrentIndex
         )
-
-        self._dialog.fluorescenceChannelListView.setModel(self._channelListModel)
-        self._dialog.fluorescenceChannelListView.selectionModel().currentChanged.connect(
-            self._updateView
+        self._dialog.fluorescenceParametersView.algorithmComboBox.setModel(self._enhancementModel)
+        self._dialog.fluorescenceParametersView.algorithmComboBox.textActivated.connect(
+            enhancer.setAlgorithm
         )
 
         self._dialog.fluorescenceParametersView.enhanceButton.clicked.connect(
@@ -90,6 +166,11 @@ def __init__(
             self._saveEnhancedDataset
         )
 
+        self._dialog.fluorescenceChannelListView.setModel(self._channelListModel)
+        self._dialog.fluorescenceChannelListView.selectionModel().currentChanged.connect(
+            self._updateView
+        )
+
         self._measuredWidgetController = VisualizationWidgetController(
             engine,
             self._dialog.measuredWidget,
@@ -160,16 +241,9 @@ def _saveEnhancedDataset(self) -> None:
                 ExceptionDialog.showException(title, err)
 
     def _syncModelToView(self) -> None:
-        self._dialog.fluorescenceParametersView.enhancementStrategyComboBox.setCurrentText(
-            self._enhancer.getEnhancementStrategy()
-        )
-        self._dialog.fluorescenceParametersView.upscalingStrategyComboBox.setCurrentText(
-            self._enhancer.getUpscalingStrategy()
+        self._dialog.fluorescenceParametersView.algorithmComboBox.setCurrentText(
+            self._enhancer.getAlgorithm()
         )
-        self._dialog.fluorescenceParametersView.deconvolutionStrategyComboBox.setCurrentText(
-            self._enhancer.getDeconvolutionStrategy()
-        )
-
         self._channelListModel.beginResetModel()
         self._channelListModel.endResetModel()
 

ptychodus/model/analysis/__init__.py

@@ -1,6 +1,5 @@
 from .core import AnalysisCore
 from .exposure import ExposureAnalyzer, ExposureMap
-from .fluorescence import FluorescenceEnhancer
 from .frc import FourierRingCorrelator
 from .objectInterpolator import ObjectLinearInterpolator
 from .objectStitcher import ObjectStitcher
@@ -12,7 +11,6 @@
     'AnalysisCore',
     'ExposureAnalyzer',
     'ExposureMap',
-    'FluorescenceEnhancer',
     'FourierRingCorrelator',
     'ObjectLinearInterpolator',
     'ObjectStitcher',

ptychodus/model/analysis/core.py

@@ -1,23 +1,14 @@
-from pathlib import Path
 import logging
 
-from ptychodus.api.fluorescence import (
-    DeconvolutionStrategy,
-    FluorescenceFileReader,
-    FluorescenceFileWriter,
-    UpscalingStrategy,
-)
-from ptychodus.api.plugins import PluginChooser
 from ptychodus.api.settings import SettingsRegistry
 
 from ..product import ObjectRepository, ProductRepository
 from ..reconstructor import DiffractionPatternPositionMatcher
 from ..visualization import VisualizationEngine
 from .exposure import ExposureAnalyzer
-from .fluorescence import FluorescenceEnhancer
 from .frc import FourierRingCorrelator
 from .propagator import ProbePropagator
-from .settings import FluorescenceSettings, ProbePropagationSettings
+from .settings import ProbePropagationSettings
 from .stxm import STXMSimulator
 from .xmcd import XMCDAnalyzer
 
@@ -31,10 +22,6 @@ def __init__(
         dataMatcher: DiffractionPatternPositionMatcher,
         productRepository: ProductRepository,
         objectRepository: ObjectRepository,
-        upscalingStrategyChooser: PluginChooser[UpscalingStrategy],
-        deconvolutionStrategyChooser: PluginChooser[DeconvolutionStrategy],
-        fluorescenceFileReaderChooser: PluginChooser[FluorescenceFileReader],
-        fluorescenceFileWriterChooser: PluginChooser[FluorescenceFileWriter],
     ) -> None:
         self.stxmSimulator = STXMSimulator(dataMatcher)
         self.stxmVisualizationEngine = VisualizationEngine(isComplex=False)
@@ -46,32 +33,5 @@ def __init__(
         self.exposureVisualizationEngine = VisualizationEngine(isComplex=False)
         self.fourierRingCorrelator = FourierRingCorrelator(objectRepository)
 
-        self._fluorescenceSettings = FluorescenceSettings(settingsRegistry)
-        self.fluorescenceEnhancer = FluorescenceEnhancer(
-            self._fluorescenceSettings,
-            productRepository,
-            upscalingStrategyChooser,
-            deconvolutionStrategyChooser,
-            fluorescenceFileReaderChooser,
-            fluorescenceFileWriterChooser,
-            settingsRegistry,
-        )
-        self.fluorescenceVisualizationEngine = VisualizationEngine(isComplex=False)
         self.xmcdAnalyzer = XMCDAnalyzer(objectRepository)
         self.xmcdVisualizationEngine = VisualizationEngine(isComplex=False)
-
-    def enhanceFluorescence(
-        self, productIndex: int, inputFilePath: Path, outputFilePath: Path
-    ) -> int:
-        fileType = 'XRF-Maps'
-
-        try:
-            self.fluorescenceEnhancer.setProduct(productIndex)
-            self.fluorescenceEnhancer.openMeasuredDataset(inputFilePath, fileType)
-            self.fluorescenceEnhancer.enhanceFluorescence()
-            self.fluorescenceEnhancer.saveEnhancedDataset(outputFilePath, fileType)
-        except Exception as exc:
-            logger.exception(exc)
-            return -1
-
-        return 0