fix propagation distance option

Author: stevehenke

src/ptychodus/model/patterns/dataset.py

@@ -140,6 +140,8 @@ def _load_arrays(self) -> None:
                 processed_array = processor(task.array)
             except FileNotFoundError:
                 logger.warning(f'File not found for array index={task.index}.')
+            except OSError:
+                logger.error(f'OS error while reading array index={task.index}.')
             except Exception:
                 logger.exception(f'Error while loading array index={task.index}!')
             else:
@@ -273,7 +275,7 @@ def get_assembled_indexes(self) -> PatternIndexesType:
     def get_assembled_patterns(self) -> PatternDataType:
         return self._data[self._indexes >= 0]
 
-    def get_maximum_pattern_counts(self) -> int:  # FIXME use
+    def get_maximum_pattern_counts(self) -> int:
         patterns = self.get_assembled_patterns()
         good_pixels = numpy.logical_not(self.get_processed_bad_pixels())
         total_counts = numpy.sum(patterns[:, good_pixels], axis=-1)

src/ptychodus/model/product/item.py

@@ -76,11 +76,11 @@ def assignItem(self, item: ProductRepositoryItem, *, notify: bool = True) -> Non
         if notify:
             self._parent.handleCostsChanged(self)
 
-    def assign(self, product: Product) -> None:
+    def assign(self, product: Product, *, mutable: bool = True) -> None:
         self._metadata.assign(product.metadata)
-        self._scan.assign(product.scan)
-        self._probe.assign(product.probe)
-        self._object.assign(product.object_)
+        self._scan.assign(product.scan, mutable=mutable)
+        self._probe.assign(product.probe, mutable=mutable)
+        self._object.assign(product.object_, mutable=mutable)
         self._costs = list(product.costs)
         self._parent.handleCostsChanged(self)
 

src/ptychodus/model/product/object/item.py

@@ -36,9 +36,9 @@ def assignItem(self, item: ObjectRepositoryItem) -> None:
         self.setBuilder(item.getBuilder().copy())
         self._rebuild()
 
-    def assign(self, object_: Object) -> None:
+    def assign(self, object_: Object, *, mutable: bool = True) -> None:
         builder = FromMemoryObjectBuilder(self._settings, object_)
-        self.setBuilder(builder)
+        self.setBuilder(builder, mutable=mutable)
 
     def syncToSettings(self) -> None:
         for parameter in self.parameters().values():
@@ -73,15 +73,15 @@ def getObject(self) -> Object:
     def getBuilder(self) -> ObjectBuilder:
         return self._builder
 
-    def setBuilder(self, builder: ObjectBuilder) -> None:
+    def setBuilder(self, builder: ObjectBuilder, *, mutable: bool = True) -> None:
         self._removeGroup('builder')
         self._builder.removeObserver(self)
         self._builder = builder
         self._builder.addObserver(self)
         self._addGroup('builder', self._builder, observe=True)
-        self._rebuild()
+        self._rebuild(mutable=mutable)
 
-    def _rebuild(self) -> None:
+    def _rebuild(self, *, mutable: bool = True) -> None:
         try:
             object_ = self._builder.build(
                 self._geometryProvider, self.layerDistanceInMeters.getValue()
@@ -90,6 +90,7 @@ def _rebuild(self) -> None:
             logger.error(''.join(exc.args))
             return
 
+        # TODO mutable is unused
         self._object = object_
         self.layerDistanceInMeters.setValue(object_.layerDistanceInMeters)
         self.notifyObservers()

src/ptychodus/model/product/probe/item.py

@@ -42,9 +42,9 @@ def assignItem(self, item: ProbeRepositoryItem) -> None:
         self.setBuilder(item.getBuilder().copy())
         self._rebuild()
 
-    def assign(self, probe: Probe) -> None:
+    def assign(self, probe: Probe, *, mutable: bool = True) -> None:
         builder = FromMemoryProbeBuilder(self._settings, probe)
-        self.setBuilder(builder)
+        self.setBuilder(builder, mutable=mutable)
 
     def syncToSettings(self) -> None:
         for parameter in self.parameters().values():
@@ -59,22 +59,24 @@ def getProbe(self) -> Probe:
     def getBuilder(self) -> ProbeBuilder:
         return self._builder
 
-    def setBuilder(self, builder: ProbeBuilder) -> None:
+    def setBuilder(self, builder: ProbeBuilder, *, mutable: bool = True) -> None:
         self._removeGroup('builder')
         self._builder.removeObserver(self)
         self._builder = builder
         self._builder.addObserver(self)
         self._addGroup('builder', self._builder, observe=True)
-        self._rebuild()
+        self._rebuild(mutable=mutable)
 
-    def _rebuild(self) -> None:
+    def _rebuild(self, *, mutable: bool = True) -> None:
         try:
             probe = self._builder.build(self._geometryProvider)
         except Exception as exc:
             logger.error(''.join(exc.args))
             return
 
-        self._probe = self._additionalModesBuilder.build(probe, self._geometryProvider)
+        self._probe = (
+            self._additionalModesBuilder.build(probe, self._geometryProvider) if mutable else probe
+        )
         self.notifyObservers()
 
     def getAdditionalModesBuilder(self) -> MultimodalProbeBuilder:

src/ptychodus/model/product/probe/multimodal.py

@@ -105,12 +105,6 @@ def _adjust_power(self, probe: WavefieldArrayType, power: float) -> WavefieldArr
         return array
 
     def build(self, probe: Probe, geometryProvider: ProbeGeometryProvider) -> Probe:
-        num_requested_modes = self.numberOfIncoherentModes.getValue()
-        num_existing_modes = probe.numberOfIncoherentModes
-
-        if num_requested_modes <= num_existing_modes:
-            return probe
-
         array = self._init_modes(probe.getArray())
 
         if self.orthogonalizeIncoherentModes.getValue():

src/ptychodus/model/product/scan/item.py

@@ -70,9 +70,9 @@ def assignItem(self, item: ScanRepositoryItem) -> None:
 
         self.setBuilder(item.getBuilder().copy())
 
-    def assign(self, scan: Scan) -> None:
+    def assign(self, scan: Scan, *, mutable: bool = True) -> None:
         builder = FromMemoryScanBuilder(self._settings, scan)
-        self.setBuilder(builder)
+        self.setBuilder(builder, mutable=mutable)
 
     def syncToSettings(self) -> None:
         for parameter in self.parameters().values():
@@ -87,13 +87,13 @@ def getScan(self) -> Scan:
     def getBuilder(self) -> ScanBuilder:
         return self._builder
 
-    def setBuilder(self, builder: ScanBuilder) -> None:
+    def setBuilder(self, builder: ScanBuilder, *, mutable: bool = True) -> None:
         self._removeGroup('builder')
         self._builder.removeObserver(self)
         self._builder = builder
         self._builder.addObserver(self)
         self._addGroup('builder', self._builder)
-        self._rebuild()
+        self._rebuild(mutable=mutable)
 
     def getBoundingBox(self) -> ScanBoundingBox | None:
         bbox = self._boundingBoxBuilder.getBoundingBox()
@@ -132,14 +132,14 @@ def _transformScan(self) -> None:
         self._lengthInMeters = lengthInMeters
         self.notifyObservers()
 
-    def _rebuild(self) -> None:
+    def _rebuild(self, *, mutable: bool = True) -> None:
         try:
             scan = self._builder.build()
         except Exception as exc:
             logger.error(''.join(exc.args))
         else:
             self._untransformedScan = scan
-            self._transformScan()
+            self._transformScan()  # FIXME mutable
 
     def getTransform(self) -> ScanPointTransform:
         return self._transform

src/ptychodus/model/ptychi/helper.py

@@ -562,9 +562,14 @@ def __init__(
     def create_data_options(self, parameters: ReconstructInput) -> PtychographyDataOptions:
         metadata = parameters.product.metadata
         pixel_geometry = self._pattern_sizer.get_processed_pixel_geometry()
+        free_space_propagation_distance_m = (
+            numpy.inf
+            if self._reconstructor_settings.useFarFieldPropagation
+            else metadata.detectorDistanceInMeters
+        )
         return PtychographyDataOptions(
             data=parameters.patterns,
-            free_space_propagation_distance_m=metadata.detectorDistanceInMeters,
+            free_space_propagation_distance_m=free_space_propagation_distance_m,
             wavelength_m=metadata.probeWavelengthInMeters,
             fft_shift=self._reconstructor_settings.fftShiftDiffractionPatterns.getValue(),
             detector_pixel_size_m=pixel_geometry.widthInMeters,

src/ptychodus/model/ptychi/settings.py

@@ -22,6 +22,10 @@ def __init__(self, registry: SettingsRegistry) -> None:
             'UseLowMemoryMode', False
         )
         self.padForShift = self._settingsGroup.createIntegerParameter('PadForShift', 0, minimum=0)
+
+        self.useFarFieldPropagation = self._settingsGroup.createBooleanParameter(
+            'UseFarFieldPropagation', True
+        )
         self.fftShiftDiffractionPatterns = self._settingsGroup.createBooleanParameter(
             'FFTShiftDiffractionPatterns', True
         )

src/ptychodus/model/reconstructor/queue.py

@@ -27,7 +27,7 @@ def __init__(self, result: ReconstructOutput, product: ProductRepositoryItem) ->
 
     def execute(self) -> None:
         name = self._product.getName()
-        self._product.assign(self._result.product)
+        self._product.assign(self._result.product, mutable=False)
         self._product.setName(name)