misc requested fixes

src/ptychodus/controller/ptychi/reconstructor.py

@@ -127,12 +127,13 @@ def __init__(
         layout.addRow('Batch Size:', self._batchSizeViewController.getWidget())
         layout.addRow('Batch Mode:', self._batchingModeViewController.getWidget())
         layout.addRow('Batch Stride:', self._batchStride.getWidget())
-        layout.addRow('Precision:', self._precisionViewController.getWidget())
-        layout.addRow(self._useLowMemoryViewController.getWidget())
 
         if repository:
             layout.addRow(self._deviceViewController.getWidget())
 
+        layout.addRow('Precision:', self._precisionViewController.getWidget())
+        layout.addRow(self._useLowMemoryViewController.getWidget())
+
         self._widget.setLayout(layout)
 
     def getWidget(self) -> QWidget:

src/ptychodus/model/ptychi/device.py

@@ -1,4 +1,5 @@
 from collections.abc import Sequence
+from importlib.metadata import version
 from typing import overload
 import logging
 
@@ -15,6 +16,9 @@ def __init__(self, *, isDeveloperModeEnabled: bool) -> None:
             if isDeveloperModeEnabled:
                 self._devices.extend(f'gpu:{n}' for n in range(4))
         else:
+            ptychiVersion = version('ptychi')
+            logger.info(f'\tPty-Chi {ptychiVersion}')
+
             for device in ptychi.list_available_devices():
                 logger.info(device)
                 self._devices.append(f'{device.name} ({device.torch_device})')

src/ptychodus/plugins/csaxsDiffractionFile.py

@@ -0,0 +1,88 @@
+from pathlib import Path
+from typing import Final
+import logging
+
+import h5py
+
+from ptychodus.api.geometry import ImageExtent, PixelGeometry
+from ptychodus.api.patterns import (
+    DiffractionDataset,
+    DiffractionFileReader,
+    DiffractionMetadata,
+    SimpleDiffractionDataset,
+)
+from ptychodus.api.plugins import PluginRegistry
+
+from .h5DiffractionFile import H5DiffractionPatternArray, H5DiffractionFileTreeBuilder
+
+logger = logging.getLogger(__name__)
+
+
+class CSAXSDiffractionFileReader(DiffractionFileReader):
+    SIMPLE_NAME: Final[str] = 'SLS_cSAXS'
+    DISPLAY_NAME: Final[str] = 'SLS cSAXS Diffraction Files (*.h5 *.hdf5)'
+    ONE_MICRON_M: Final[float] = 1e-6
+    ONE_MILLIMETER_M: Final[float] = 1e-3
+
+    def __init__(self) -> None:
+        self._dataPath = '/entry/data/data'
+        self._treeBuilder = H5DiffractionFileTreeBuilder()
+
+    def read(self, filePath: Path) -> DiffractionDataset:
+        dataset = SimpleDiffractionDataset.createNullInstance(filePath)
+
+        try:
+            with h5py.File(filePath, 'r') as h5File:
+                contentsTree = self._treeBuilder.build(h5File)
+
+                try:
+                    data = h5File[self._dataPath]
+                    x_pixel_size_um = h5File['/entry/instrument/eiger_4/x_pixel_size']
+                    y_pixel_size_um = h5File['/entry/instrument/eiger_4/y_pixel_size']
+                    distance_mm = h5File['/entry/instrument/monochromator/distance']
+                    energy_keV = h5File['/entry/instrument/monochromator/energy']
+                except KeyError:
+                    logger.warning('Unable to load data.')
+                else:
+                    numberOfPatterns, detectorHeight, detectorWidth = data.shape
+                    detectorDistanceInMeters = float(distance_mm[()]) * self.ONE_MILLIMETER_M
+                    detectorPixelGeometry = PixelGeometry(
+                        widthInMeters=float(x_pixel_size_um[()]) * self.ONE_MICRON_M,
+                        heightInMeters=float(y_pixel_size_um[()]) * self.ONE_MICRON_M,
+                    )
+                    probeEnergyInElectronVolts = 1000 * float(energy_keV[()])
+
+                    metadata = DiffractionMetadata(
+                        numberOfPatternsPerArray=numberOfPatterns,
+                        numberOfPatternsTotal=numberOfPatterns,
+                        patternDataType=data.dtype,
+                        detectorDistanceInMeters=abs(detectorDistanceInMeters),
+                        detectorExtent=ImageExtent(detectorWidth, detectorHeight),
+                        detectorPixelGeometry=detectorPixelGeometry,
+                        probeEnergyInElectronVolts=probeEnergyInElectronVolts,
+                        filePath=filePath,
+                    )
+
+                    print(metadata.detectorDistanceInMeters)  # FIXME
+                    print(repr(metadata))  # FIXME
+
+                    array = H5DiffractionPatternArray(
+                        label=filePath.stem,
+                        index=0,
+                        filePath=filePath,
+                        dataPath=self._dataPath,
+                    )
+
+                    dataset = SimpleDiffractionDataset(metadata, contentsTree, [array])
+        except OSError:
+            logger.warning(f'Unable to read file "{filePath}".')
+
+        return dataset
+
+
+def registerPlugins(registry: PluginRegistry) -> None:
+    registry.diffractionFileReaders.registerPlugin(
+        CSAXSDiffractionFileReader(),
+        simpleName=CSAXSDiffractionFileReader.SIMPLE_NAME,
+        displayName=CSAXSDiffractionFileReader.DISPLAY_NAME,
+    )

src/ptychodus/plugins/h5DiffractionFile.py

@@ -201,11 +201,6 @@ def registerPlugins(registry: PluginRegistry) -> None:
         simpleName='APS_HXN',
         displayName='CNM/APS HXN Diffraction Files (*.h5 *.hdf5)',
     )
-    registry.diffractionFileReaders.registerPlugin(
-        H5DiffractionFileReader(dataPath='/entry/data/data'),
-        simpleName='SLS_cSAXS',
-        displayName='SLS cSAXS Diffraction Files (*.h5 *.hdf5)',
-    )
     registry.diffractionFileReaders.registerPlugin(
         H5DiffractionFileReader(dataPath='/entry/measurement/Eiger/data'),
         simpleName='MAX_IV_NanoMax',

src/ptychodus/plugins/h5ProductFile.py

@@ -50,12 +50,19 @@ def read(self, filePath: Path) -> Product:
         scanPointList: list[ScanPoint] = list()
 
         with h5py.File(filePath, 'r') as h5File:
+            probePhotonCount = 0.0
+
+            try:
+                probePhotonCount = float(h5File.attrs[self.PROBE_PHOTON_COUNT])
+            except KeyError:
+                logger.debug('Probe photon count not found.')
+
             metadata = ProductMetadata(
                 name=str(h5File.attrs[self.NAME]),
                 comments=str(h5File.attrs[self.COMMENTS]),
                 detectorDistanceInMeters=float(h5File.attrs[self.DETECTOR_OBJECT_DISTANCE]),
                 probeEnergyInElectronVolts=float(h5File.attrs[self.PROBE_ENERGY]),
-                probePhotonCount=float(h5File.attrs[self.PROBE_PHOTON_COUNT]),
+                probePhotonCount=probePhotonCount,
                 exposureTimeInSeconds=float(h5File.attrs[self.EXPOSURE_TIME]),
             )
 

src/ptychodus/plugins/npzProductFile.py

@@ -1,5 +1,6 @@
 from pathlib import Path
 from typing import Any, Final
+import logging
 
 import numpy
 
@@ -15,6 +16,8 @@
 )
 from ptychodus.api.scan import Scan, ScanFileReader, ScanPoint
 
+logger = logging.getLogger(__name__)
+
 
 class NPZProductFileIO(ProductFileReader, ProductFileWriter):
     SIMPLE_NAME: Final[str] = 'NPZ'
@@ -45,12 +48,19 @@ class NPZProductFileIO(ProductFileReader, ProductFileWriter):
 
     def read(self, filePath: Path) -> Product:
         with numpy.load(filePath) as npzFile:
+            probePhotonCount = 0.0
+
+            try:
+                probePhotonCount = float(npzFile[self.PROBE_PHOTON_COUNT])
+            except KeyError:
+                logger.debug('Probe photon count not found.')
+
             metadata = ProductMetadata(
                 name=str(npzFile[self.NAME]),
                 comments=str(npzFile[self.COMMENTS]),
                 detectorDistanceInMeters=float(npzFile[self.DETECTOR_OBJECT_DISTANCE]),
                 probeEnergyInElectronVolts=float(npzFile[self.PROBE_ENERGY]),
-                probePhotonCount=float(npzFile[self.PROBE_PHOTON_COUNT]),
+                probePhotonCount=probePhotonCount,
                 exposureTimeInSeconds=float(npzFile[self.EXPOSURE_TIME]),
             )