Refactor Settings (#98)

- Add BDP hooks for ptycho-enhanced XRF
- Implement numpy 2.0 fix
- Workflow to autoload product files as they appear
- Extract reconstructor API
- Clean up timers
- Fix crash when selecting zero-sized region with rectangle tool
- Refactor settings classes to use parametric classes
- Add tooltip support to parametric view builder
- Refactor Tike GUI to use parametric view controllers
- Reformat repository using ruff format
- Enable syncing product/scan/probe/object parameters to settings
- Make default product name configurable and validate renaming

ptychodus/__main__.py

@@ -34,6 +34,18 @@ def main() -> int:
         action='store_true',
         help=argparse.SUPPRESS,
     )
+    parser.add_argument(
+        '--fluorescence-input',
+        metavar='FLUORESCENCE_INPUT_FILE',
+        type=argparse.FileType('r'),
+        help=argparse.SUPPRESS,
+    )
+    parser.add_argument(
+        '--fluorescence-output',
+        metavar='FLUORESCENCE_OUTPUT_FILE',
+        type=argparse.FileType('w'),
+        help=argparse.SUPPRESS,
+    )
     parser.add_argument(
         '-i',
         '--input',
@@ -88,7 +100,22 @@ def main() -> int:
             action = parsedArgs.batch
             inputFilePath = Path(parsedArgs.input.name)
             outputFilePath = Path(parsedArgs.output.name)
-            return model.batchModeExecute(action, inputFilePath, outputFilePath)
+            fluorescenceInputFilePath: Path | None = None
+            fluorescenceOutputFilePath: Path | None = None
+
+            if parsedArgs.flourescence_input is not None:
+                fluorescenceInputFilePath = Path(parsedArgs.fluorescence_input.name)
+
+            if parsedArgs.flourescence_output is not None:
+                fluorescenceOutputFilePath = Path(parsedArgs.fluorescence_output.name)
+
+            return model.batchModeExecute(
+                action,
+                inputFilePath,
+                outputFilePath,
+                fluorescenceInputFilePath=fluorescenceInputFilePath,
+                fluorescenceOutputFilePath=fluorescenceOutputFilePath,
+            )
 
         try:
             from PyQt5.QtWidgets import QApplication
@@ -100,9 +127,11 @@ def main() -> int:
         verifyAllArgumentsParsed(parser, app.arguments()[1:])
 
         from ptychodus.view import ViewCore
+
         view = ViewCore.createInstance(parsedArgs.dev)
 
         from ptychodus.controller import ControllerCore
+
         controller = ControllerCore(model, view)
         controller.showMainWindow(versionString())
 

ptychodus/api/fluorescence.py

@@ -21,37 +21,35 @@ class FluorescenceDataset:
 
     # TODO need to communicate association between element map pixels and scan order.
     #      integer-valued, same shape as counts_per_second
-    #scan_indexes: IntegerArray
+    # scan_indexes: IntegerArray
 
 
 class FluorescenceFileReader(ABC):
-
     @abstractmethod
     def read(self, filePath: Path) -> FluorescenceDataset:
-        '''reads a fluorescence dataset from file'''
+        """reads a fluorescence dataset from file"""
         pass
 
 
 class FluorescenceFileWriter(ABC):
-
     @abstractmethod
     def write(self, filePath: Path, dataset: FluorescenceDataset) -> None:
-        '''writes a fluorescence dataset to file'''
+        """writes a fluorescence dataset to file"""
         pass
 
 
 class UpscalingStrategy(ABC):
-    '''Uses ptychography-corrected scan positions to remap element
-    concentrations from the regular scan grid to the upscaled grid'''
+    """Uses ptychography-corrected scan positions to remap element
+    concentrations from the regular scan grid to the upscaled grid"""
 
     @abstractmethod
     def __call__(self, emap: ElementMap, product: Product) -> ElementMap:
         pass
 
 
 class DeconvolutionStrategy(ABC):
-    '''Deconvolves the kernel from the accumulated array to obtain the
-    resolution-enhanced element map'''
+    """Deconvolves the kernel from the accumulated array to obtain the
+    resolution-enhanced element map"""
 
     @abstractmethod
     def __call__(self, emap: ElementMap, product: Product) -> ElementMap:

ptychodus/api/geometry.py

@@ -22,17 +22,17 @@ class ImageExtent:
 
     @property
     def size(self) -> int:
-        '''returns the number of pixels in the image'''
+        """returns the number of pixels in the image"""
         return self.widthInPixels * self.heightInPixels
 
     @property
     def shape(self) -> tuple[int, int]:
-        '''returns the image shape (heightInPixels, widthInPixels) tuple'''
+        """returns the image shape (heightInPixels, widthInPixels) tuple"""
         return self.heightInPixels, self.widthInPixels
 
     def __eq__(self, other: object) -> bool:
         if isinstance(other, ImageExtent):
-            return (self.shape == other.shape)
+            return self.shape == other.shape
 
         return False
 
@@ -92,7 +92,6 @@ def __repr__(self) -> str:
 
 
 class Interval(Generic[T]):
-
     def __init__(self, lower: T, upper: T) -> None:
         self.lower: T = lower
         self.upper: T = upper
@@ -130,7 +129,7 @@ def copy(self) -> Interval[T]:
         return Interval[T](self.lower, self.upper)
 
     def __contains__(self, item: T) -> bool:
-        return (self.lower <= item and item < self.upper)
+        return self.lower <= item and item < self.upper
 
     def __repr__(self) -> str:
         return f'{type(self).__name__}({self.lower}, {self.upper})'

ptychodus/api/object.py

@@ -40,11 +40,11 @@ def heightInMeters(self) -> float:
 
     @property
     def minimumXInMeters(self) -> float:
-        return self.centerXInMeters - self.widthInMeters / 2.
+        return self.centerXInMeters - self.widthInMeters / 2.0
 
     @property
     def minimumYInMeters(self) -> float:
-        return self.centerYInMeters - self.heightInMeters / 2.
+        return self.centerYInMeters - self.heightInMeters / 2.0
 
     def getPixelGeometry(self) -> PixelGeometry:
         return PixelGeometry(
@@ -79,26 +79,26 @@ def contains(self, geometry: ObjectGeometry) -> bool:
         dy = self.centerYInMeters - geometry.centerYInMeters
         dw = self.widthInMeters - geometry.widthInMeters
         dh = self.heightInMeters - geometry.heightInMeters
-        return (abs(dx) <= dw and abs(dy) <= dh)
+        return abs(dx) <= dw and abs(dy) <= dh
 
 
 class ObjectGeometryProvider(ABC):
-
     @abstractmethod
     def getObjectGeometry(self) -> ObjectGeometry:
         pass
 
 
 class Object:
-
-    def __init__(self,
-                 array: ObjectArrayType | None = None,
-                 layerDistanceInMeters: Sequence[float] | None = None,
-                 *,
-                 pixelWidthInMeters: float = 0.,
-                 pixelHeightInMeters: float = 0.,
-                 centerXInMeters: float = 0.,
-                 centerYInMeters: float = 0.) -> None:
+    def __init__(
+        self,
+        array: ObjectArrayType | None = None,
+        layerDistanceInMeters: Sequence[float] | None = None,
+        *,
+        pixelWidthInMeters: float = 0.0,
+        pixelHeightInMeters: float = 0.0,
+        centerXInMeters: float = 0.0,
+        centerYInMeters: float = 0.0,
+    ) -> None:
         if array is None:
             self._array = numpy.zeros((1, 0, 0), dtype=complex)
         else:
@@ -212,32 +212,28 @@ def getTotalLayerDistanceInMeters(self) -> float:
 
 
 class ObjectInterpolator(ABC):
-
     @abstractmethod
     def getPatch(self, patchCenter: ScanPoint, patchExtent: ImageExtent) -> Object:
-        '''returns an interpolated patch from the object array'''
+        """returns an interpolated patch from the object array"""
         pass
 
 
 class ObjectPhaseCenteringStrategy(ABC):
-
     @abstractmethod
     def __call__(self, array: ObjectArrayType) -> ObjectArrayType:
-        '''returns the phase-centered array'''
+        """returns the phase-centered array"""
         pass
 
 
 class ObjectFileReader(ABC):
-
     @abstractmethod
     def read(self, filePath: Path) -> Object:
-        '''reads an object from file'''
+        """reads an object from file"""
         pass
 
 
 class ObjectFileWriter(ABC):
-
     @abstractmethod
     def write(self, filePath: Path, object_: Object) -> None:
-        '''writes an object to file'''
+        """writes an object to file"""
         pass

ptychodus/api/observer.py

@@ -14,14 +14,12 @@
 
 
 class Observer(ABC):
-
     @abstractmethod
     def update(self, observable: Observable) -> None:
         pass
 
 
 class Observable:
-
     def __init__(self) -> None:
         self._observerList: list[Observer] = list()
 
@@ -41,7 +39,6 @@ def notifyObservers(self) -> None:
 
 
 class SequenceObserver(Generic[T], ABC):
-
     @abstractmethod
     def handleItemInserted(self, index: int, item: T) -> None:
         pass
@@ -56,7 +53,6 @@ def handleItemRemoved(self, index: int, item: T) -> None:
 
 
 class ObservableSequence(Sequence[T]):
-
     def __init__(self) -> None:
         self._observerList: list[SequenceObserver[T]] = list()