Stage Reconstruction Inputs (#86)

- stage reconstruction inputs to directory - add exposure time metadata - prototype analysis dialogs
AdvancedPhotonSource · May 23, 2024 · c43c5a9 · c43c5a9
1 parent 37e0e3e
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diff --git a/README.rst b/README.rst
@@ -36,7 +36,7 @@ Standard Installation
        $ conda activate ptychodus
        $ ptychodus -h
 
-       usage: ptychodus [-h] [-b {reconstruct,train}] [-f FILE_PREFIX] [-i INPUT_FILE] [-o OUTPUT_FILE] [-p PATTERNS_FILE] [-s SETTINGS] [-v]
+       usage: ptychodus [-h] [-b {reconstruct,train}] [-f FILE_PREFIX] [-s SETTINGS_FILE] [-v] [-w OUTPUT_DIR]
 
        ptychodus is a ptychography analysis application
 
@@ -46,15 +46,11 @@ Standard Installation
                                run action non-interactively
          -f FILE_PREFIX, --file-prefix FILE_PREFIX
                                replace file path prefix in settings
-         -i INPUT_FILE, --input INPUT_FILE
-                               input data product file (batch mode)
-         -o OUTPUT_FILE, --output OUTPUT_FILE
-                               output data product file (batch mode)
-         -p PATTERNS_FILE, --patterns PATTERNS_FILE
-                               use diffraction patterns from file
-         -s SETTINGS, --settings SETTINGS
+         -s SETTINGS_FILE, --settings SETTINGS_FILE
                                use settings from file
          -v, --version         show program's version number and exit
+         -w OUTPUT_DIR, --write OUTPUT_DIR
+                               stage reconstruction inputs to directory
 
        $ ptychodus
 

diff --git a/ptychodus/__main__.py b/ptychodus/__main__.py
@@ -17,6 +17,17 @@ def verifyAllArgumentsParsed(parser: argparse.ArgumentParser, argv: list[str]) -
         parser.error('unrecognized arguments: %s' % ' '.join(argv))
 
 
+class DirectoryType:
+
+    def __call__(self, string: str) -> Path:
+        path = Path(string)
+
+        if not path.is_dir():
+            raise argparse.ArgumentTypeError(f'\"{string}\" is not a directory!')
+
+        return path
+
+
 def main() -> int:
     parser = argparse.ArgumentParser(
         prog=ptychodus.__name__.lower(),
@@ -40,29 +51,33 @@ def main() -> int:
         help='replace file path prefix in settings',
     )
     parser.add_argument(
+        # input data product file (batch mode)
         '-i',
         '--input',
         metavar='INPUT_FILE',
-        help='input data product file (batch mode)',
         type=argparse.FileType('r'),
+        help=argparse.SUPPRESS,
     )
     parser.add_argument(
+        # output data product file (batch mode)
         '-o',
         '--output',
         metavar='OUTPUT_FILE',
-        help='output data product file (batch mode)',
         type=argparse.FileType('w'),
+        help=argparse.SUPPRESS,
     )
     parser.add_argument(
+        # preprocessed diffraction patterns file (batch mode)
         '-p',
         '--patterns',
         metavar='PATTERNS_FILE',
-        help='use diffraction patterns from file',
         type=argparse.FileType('r'),
+        help=argparse.SUPPRESS,
     )
     parser.add_argument(
         '-s',
         '--settings',
+        metavar='SETTINGS_FILE',
         help='use settings from file',
         type=argparse.FileType('r'),
     )
@@ -72,6 +87,14 @@ def main() -> int:
         action='version',
         version=versionString(),
     )
+    parser.add_argument(
+        '-w',
+        '--write',
+        metavar='OUTPUT_DIR',
+        type=DirectoryType(),
+        help='stage reconstruction inputs to directory',
+    )
+
     parsedArgs, unparsedArgs = parser.parse_known_args()
 
     modelArgs = ModelArgs(
@@ -81,6 +104,9 @@ def main() -> int:
     )
 
     with ModelCore(modelArgs, isDeveloperModeEnabled=parsedArgs.dev) as model:
+        if parsedArgs.write is not None:
+            return model.stageReconstructionInputs(parsedArgs.write)
+
         if parsedArgs.batch is not None:
             verifyAllArgumentsParsed(parser, unparsedArgs)
 

diff --git a/ptychodus/api/fluorescence.py b/ptychodus/api/fluorescence.py
@@ -0,0 +1,58 @@
+from abc import ABC, abstractmethod
+from collections.abc import Sequence
+from dataclasses import dataclass
+from pathlib import Path
+
+from .product import Product
+from .typing import RealArrayType
+
+
+@dataclass(frozen=True)
+class ElementMap:
+    name: str
+    counts_per_second: RealArrayType
+
+
+@dataclass(frozen=True)
+class FluorescenceDataset:
+    element_maps: Sequence[ElementMap]
+    counts_per_second_path: str
+    channel_names_path: str
+
+    # TODO need to communicate association between element map pixels and scan order.
+    #      integer-valued, same shape as counts_per_second
+    #scan_indexes: IntegerArray
+
+
+class FluorescenceFileReader(ABC):
+
+    @abstractmethod
+    def read(self, filePath: Path) -> FluorescenceDataset:
+        '''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'''
+        pass
+
+
+class UpscalingStrategy(ABC):
+    '''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'''
+
+    @abstractmethod
+    def __call__(self, emap: ElementMap, product: Product) -> ElementMap:
+        pass
diff --git a/ptychodus/api/plugins.py b/ptychodus/api/plugins.py
@@ -9,6 +9,8 @@
 import re
 
 from .automation import FileBasedWorkflow
+from .fluorescence import (DeconvolutionStrategy, FluorescenceFileReader, FluorescenceFileWriter,
+                           UpscalingStrategy)
 from .object import ObjectPhaseCenteringStrategy, ObjectFileReader, ObjectFileWriter
 from .observer import Observable
 from .patterns import DiffractionFileReader, DiffractionFileWriter
@@ -111,6 +113,10 @@ def __init__(self) -> None:
         self.productFileReaders = PluginChooser[ProductFileReader]()
         self.productFileWriters = PluginChooser[ProductFileWriter]()
         self.fileBasedWorkflows = PluginChooser[FileBasedWorkflow]()
+        self.fluorescenceFileReaders = PluginChooser[FluorescenceFileReader]()
+        self.fluorescenceFileWriters = PluginChooser[FluorescenceFileWriter]()
+        self.upscalingStrategies = PluginChooser[UpscalingStrategy]()
+        self.deconvolutionStrategies = PluginChooser[DeconvolutionStrategy]()
 
     @classmethod
     def loadPlugins(cls) -> PluginRegistry:

diff --git a/ptychodus/api/probe.py b/ptychodus/api/probe.py
@@ -3,14 +3,14 @@
 from collections.abc import Sequence
 from dataclasses import dataclass
 from pathlib import Path
-from typing import Any, TypeAlias
+from typing import TypeAlias
 
 import numpy
-import numpy.typing
 
 from .geometry import ImageExtent, PixelGeometry
+from .typing import ComplexArrayType, RealArrayType
 
-WavefieldArrayType: TypeAlias = numpy.typing.NDArray[numpy.complexfloating[Any, Any]]
+WavefieldArrayType: TypeAlias = ComplexArrayType
 
 
 @dataclass(frozen=True)
@@ -180,6 +180,9 @@ def getModeRelativePower(self, number: int) -> float:
     def getCoherence(self) -> float:
         return numpy.sqrt(numpy.sum(numpy.square(self._modeRelativePower)))
 
+    def getIntensity(self) -> RealArrayType:
+        return numpy.absolute(self._array).sum(axis=-3)
+
 
 class ProbeFileReader(ABC):
 

diff --git a/ptychodus/api/product.py b/ptychodus/api/product.py
@@ -16,6 +16,7 @@ class ProductMetadata:
     detectorDistanceInMeters: float
     probeEnergyInElectronVolts: float
     probePhotonsPerSecond: float
+    exposureTimeInSeconds: float
 
     @property
     def sizeInBytes(self) -> int:
@@ -24,6 +25,7 @@ def sizeInBytes(self) -> int:
         sz += getsizeof(self.detectorDistanceInMeters)
         sz += getsizeof(self.probeEnergyInElectronVolts)
         sz += getsizeof(self.probePhotonsPerSecond)
+        sz += getsizeof(self.exposureTimeInSeconds)
         return sz
 
 

diff --git a/ptychodus/api/typing.py b/ptychodus/api/typing.py
@@ -0,0 +1,12 @@
+from typing import Any, TypeAlias
+
+import numpy
+import numpy.typing
+
+IntegerArrayType: TypeAlias = numpy.typing.NDArray[numpy.integer[Any]]
+Float32ArrayType: TypeAlias = numpy.typing.NDArray[numpy.float32]
+RealArrayType: TypeAlias = numpy.typing.NDArray[numpy.floating[Any]]
+ComplexArrayType: TypeAlias = numpy.typing.NDArray[numpy.complexfloating[Any, Any]]
+
+NumberTypes: TypeAlias = numpy.integer[Any] | numpy.floating[Any] | numpy.complexfloating[Any, Any]
+NumberArrayType: TypeAlias = numpy.typing.NDArray[NumberTypes]
diff --git a/ptychodus/api/visualization.py b/ptychodus/api/visualization.py
@@ -1,17 +1,13 @@
 from __future__ import annotations
 from collections.abc import Iterator, Sequence
 from dataclasses import dataclass
-from typing import Any, Final, TypeAlias
+from typing import Final
 
 from scipy.stats import gaussian_kde
 import numpy
-import numpy.typing
 
 from .geometry import Box2D, Interval, Line2D, PixelGeometry
-
-RealArrayType: TypeAlias = numpy.typing.NDArray[numpy.floating[Any]]
-NumberTypes: TypeAlias = numpy.integer[Any] | numpy.floating[Any] | numpy.complexfloating[Any, Any]
-NumberArrayType: TypeAlias = numpy.typing.NDArray[NumberTypes]
+from .typing import NumberArrayType, RealArrayType
 
 
 @dataclass(frozen=True)

diff --git a/ptychodus/controller/automation.py b/ptychodus/controller/automation.py
@@ -5,7 +5,8 @@
 from PyQt5.QtCore import Qt, QAbstractListModel, QModelIndex, QObject, QTimer
 from PyQt5.QtGui import QFont
 
-from ..api.observer import Observable, Observer
+from ptychodus.api.observer import Observable, Observer
+
 from ..model.automation import (AutomationCore, AutomationDatasetState, AutomationPresenter,
                                 AutomationProcessingPresenter)
 from ..view.automation import AutomationView, AutomationProcessingView, AutomationWatchdogView

diff --git a/ptychodus/controller/core.py b/ptychodus/controller/core.py
@@ -58,14 +58,16 @@ def __init__(self, model: ModelCore, view: ViewCore) -> None:
         self._probeController = ProbeController.createInstance(
             model.probeRepository, model.probeAPI, self._probeImageController,
             model.probePropagator, model.probePropagatorVisualizationEngine, view.probeView,
-            view.statusBar(), self._fileDialogFactory)
+            self._fileDialogFactory)
         self._objectImageController = ImageController.createInstance(
             model.objectVisualizationEngine, view.objectImageView, view.statusBar(),
             self._fileDialogFactory)
         self._objectController = ObjectController.createInstance(
             model.objectRepository, model.objectAPI, self._objectImageController,
-            model.fourierRingCorrelator, model.dichroicAnalyzer, model.dichroicVisualizationEngine,
-            view.objectView, view.statusBar(), self._fileDialogFactory)
+            model.fourierRingCorrelator, model.stxmAnalyzer, model.stxmVisualizationEngine,
+            model.exposureAnalyzer, model.exposureVisualizationEngine, model.fluorescenceEnhancer,
+            model.fluorescenceVisualizationEngine, model.xmcdAnalyzer,
+            model.xmcdVisualizationEngine, view.objectView, self._fileDialogFactory)
         self._reconstructorParametersController = ReconstructorController.createInstance(
             model.reconstructorPresenter,
             model.productRepository,