improve ptychoshelves product reader; add cSAXS diffraction reader

pyproject.toml

@@ -9,7 +9,7 @@ readme = "README.rst"
 requires-python = ">=3.10"
 license = {file = "LICENSE.txt"}
 dependencies = [
-    "h5py",
+    "h5py>=3",
     "hdf5plugin",
     "matplotlib",
     "numpy",

requirements-dev.txt

@@ -1,4 +1,4 @@
-h5py
+h5py>=3
 hdf5plugin
 matplotlib
 mypy

src/ptychodus/model/patterns/detector.py

@@ -10,25 +10,19 @@ def __init__(self, registry: SettingsRegistry) -> None:
         self._settingsGroup.addObserver(self)
 
         self.widthInPixels = self._settingsGroup.createIntegerParameter(
-            'WidthInPixels', 1024, minimum=0
+            'WidthInPixels', 1024, minimum=1
         )
         self.pixelWidthInMeters = self._settingsGroup.createRealParameter(
             'PixelWidthInMeters', 75e-6, minimum=0.0
         )
         self.heightInPixels = self._settingsGroup.createIntegerParameter(
-            'HeightInPixels', 1024, minimum=0
+            'HeightInPixels', 1024, minimum=1
         )
         self.pixelHeightInMeters = self._settingsGroup.createRealParameter(
             'PixelHeightInMeters', 75e-6, minimum=0.0
         )
         self.bitDepth = self._settingsGroup.createIntegerParameter('BitDepth', 8, minimum=1)
 
-    def getImageExtent(self) -> ImageExtent:
-        return ImageExtent(
-            widthInPixels=self.widthInPixels.getValue(),
-            heightInPixels=self.heightInPixels.getValue(),
-        )
-
     def setImageExtent(self, imageExtent: ImageExtent) -> None:
         self.widthInPixels.setValue(imageExtent.widthInPixels)
         self.heightInPixels.setValue(imageExtent.heightInPixels)

src/ptychodus/model/patterns/sizer.py

@@ -27,18 +27,17 @@ def setCropEnabled(self, value: bool) -> None:
         self._settings.cropEnabled.setValue(value)
 
     def getWidthLimitsInPixels(self) -> Interval[int]:
-        return Interval[int](1, self._detector.getImageExtent().widthInPixels)
+        return Interval[int](1, self._detector.widthInPixels.getValue())
 
     def getWidthInPixels(self) -> int:
-        limitsInPixels = self.getWidthLimitsInPixels()
-        return (
-            limitsInPixels.clamp(self._settings.cropWidthInPixels.getValue())
-            if self.isCropEnabled()
-            else limitsInPixels.upper
-        )
+        if self.isCropEnabled():
+            limits = self.getWidthLimitsInPixels()
+            return limits.clamp(self._settings.cropWidthInPixels.getValue())
+
+        return self._detector.widthInPixels.getValue()
 
     def getCenterXLimitsInPixels(self) -> Interval[int]:
-        return Interval[int](0, self._detector.getImageExtent().widthInPixels)
+        return Interval[int](0, self._detector.widthInPixels.getValue())
 
     def getCenterXInPixels(self) -> int:
         limitsInPixels = self.getCenterXLimitsInPixels()
@@ -50,7 +49,7 @@ def getCenterXInPixels(self) -> int:
 
     def _getSafeCenterXInPixels(self) -> int:
         lower = self.getWidthInPixels() // 2
-        upper = self._detector.getImageExtent().widthInPixels - 1 - lower
+        upper = self._detector.widthInPixels.getValue() - 1 - lower
         limits = Interval[int](lower, upper)
         return limits.clamp(self.getCenterXInPixels())
 
@@ -61,18 +60,17 @@ def getWidthInMeters(self) -> float:
         return self.getWidthInPixels() * self.getPixelWidthInMeters()
 
     def getHeightLimitsInPixels(self) -> Interval[int]:
-        return Interval[int](1, self._detector.getImageExtent().heightInPixels)
+        return Interval[int](1, self._detector.heightInPixels.getValue())
 
     def getHeightInPixels(self) -> int:
-        limitsInPixels = self.getHeightLimitsInPixels()
-        return (
-            limitsInPixels.clamp(self._settings.cropHeightInPixels.getValue())
-            if self.isCropEnabled()
-            else limitsInPixels.upper
-        )
+        if self.isCropEnabled():
+            limits = self.getHeightLimitsInPixels()
+            return limits.clamp(self._settings.cropHeightInPixels.getValue())
+
+        return self._detector.heightInPixels.getValue()
 
     def getCenterYLimitsInPixels(self) -> Interval[int]:
-        return Interval[int](0, self._detector.getImageExtent().heightInPixels)
+        return Interval[int](0, self._detector.heightInPixels.getValue())
 
     def getCenterYInPixels(self) -> int:
         limitsInPixels = self.getCenterYLimitsInPixels()
@@ -84,7 +82,7 @@ def getCenterYInPixels(self) -> int:
 
     def _getSafeCenterYInPixels(self) -> int:
         lower = self.getHeightInPixels() // 2
-        upper = self._detector.getImageExtent().heightInPixels - 1 - lower
+        upper = self._detector.heightInPixels.getValue() - 1 - lower
         limits = Interval[int](lower, upper)
         return limits.clamp(self.getCenterYInPixels())
 

src/ptychodus/plugins/h5DiffractionFile.py

@@ -67,13 +67,15 @@ def _addAttributes(
                 itemDetails = f'STRING = "{value}"'
             elif isinstance(value, h5py.Empty):
                 logger.debug(f'Skipping empty attribute {name}.')
+            elif isinstance(value, numpy.ndarray):
+                itemDetails = f'ARRAY = {value}'
             else:
                 stringInfo = h5py.check_string_dtype(value.dtype)
-                itemDetails = (
-                    f'STRING = "{value.decode(stringInfo.encoding)}"'
-                    if stringInfo
-                    else f'SCALAR {value.dtype} = {value}'
-                )
+
+                if stringInfo:
+                    itemDetails = f'STRING = "{value.decode(stringInfo.encoding)}"'
+                else:
+                    itemDetails = f'SCALAR {value.dtype} = {value}'
 
             treeNode.createChild([str(name), 'Attribute', itemDetails])
 
@@ -112,13 +114,18 @@ def build(self, h5File: h5py.File) -> SimpleTreeNode:
 
                             if isinstance(value, bytes):
                                 itemDetails = value.decode()
+                            elif isinstance(value, numpy.ndarray):
+                                itemDetails = f'STRING = {h5Item.asstr()}'
                             else:
                                 stringInfo = h5py.check_string_dtype(value.dtype)
-                                itemDetails = (
-                                    f'STRING = "{value.decode(stringInfo.encoding)}"'
-                                    if stringInfo
-                                    else f'SCALAR {value.dtype} = {value}'
-                                )
+
+                                if stringInfo:
+                                    itemDetails = f'STRING = "{value.decode(stringInfo.encoding)}"'
+                                else:
+                                    itemDetails = f'SCALAR {value.dtype} = {value}'
+                        elif h5Item.size == 1:
+                            value = h5Item[()]
+                            itemDetails = f'DATASET {value.dtype} = {value}'
                         else:
                             itemDetails = f'{h5Item.shape} {h5Item.dtype}'
                 elif isinstance(h5Item, h5py.SoftLink):
@@ -194,10 +201,15 @@ 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='NanoMax',
-        displayName='NanoMax Diffraction Files (*.h5 *.hdf5)',
+        simpleName='MAX_IV_NanoMax',
+        displayName='MAX IV NanoMax Diffraction Files (*.h5 *.hdf5)',
     )
     registry.diffractionFileReaders.registerPlugin(
         H5DiffractionFileReader(dataPath='/dp'),

src/ptychodus/plugins/lynxDiffractionFile.py

@@ -63,6 +63,6 @@ def read(self, filePath: Path) -> DiffractionDataset:
 def registerPlugins(registry: PluginRegistry) -> None:
     registry.diffractionFileReaders.registerPlugin(
         LYNXDiffractionFileReader(),
-        simpleName='LYNX',
-        displayName='LYNX Diffraction Files (*.h5 *.hdf5)',
+        simpleName='APS_LYNX',
+        displayName='APS LYNX Diffraction Files (*.h5 *.hdf5)',
     )

src/ptychodus/plugins/ptychoShelvesProductFile.py

@@ -5,9 +5,9 @@
 import scipy.io
 
 from ptychodus.api.geometry import PixelGeometry
-from ptychodus.api.object import Object, ObjectFileReader, ObjectFileWriter
+from ptychodus.api.object import Object
 from ptychodus.api.plugins import PluginRegistry
-from ptychodus.api.probe import Probe, ProbeFileReader, ProbeFileWriter
+from ptychodus.api.probe import Probe
 from ptychodus.api.product import (
     ELECTRON_VOLT_J,
     LIGHT_SPEED_M_PER_S,
@@ -19,7 +19,7 @@
 from ptychodus.api.scan import Scan, ScanPoint
 
 
-class PtychoShelvesProductFileIO(ProductFileReader):
+class PtychoShelvesProductFileReader(ProductFileReader):
     SIMPLE_NAME: Final[str] = 'PtychoShelves'
     DISPLAY_NAME: Final[str] = 'PtychoShelves Files (*.mat)'
 
@@ -56,13 +56,23 @@ def read(self, filePath: Path) -> Product:
             )
             scanPointList.append(point)
 
-        probe = Probe(
-            # probeMatrix[width, height, num_shared_modes, num_varying_modes]
-            matDict['probe'].transpose(),
-            pixel_geometry,
-        )
+        probe_array = matDict['probe']
+
+        if probe_array.ndim == 3:
+            # probe_array[height, width, num_shared_modes]
+            probe_array = probe_array.transpose(2, 0, 1)
+        elif probe_array.ndim == 4:
+            # probe_array[height, width, num_shared_modes, num_varying_modes]
+            probe_array = probe_array.transpose(3, 2, 0, 1)
+
+        probe = Probe(array=probe_array, pixelGeometry=pixel_geometry)
+
+        object_array = matDict['object']
+
+        if object_array.ndim == 3:
+            # object_array[height, width, num_layers]
+            object_array = object_array.transpose(2, 0, 1)
 
-        object_array = matDict['object'].transpose()
         layer_distance_m: Sequence[float] = list()
 
         try:
@@ -75,7 +85,6 @@ def read(self, filePath: Path) -> Product:
             layer_distance_m = numpy.squeeze(z_distance)[:num_spaces]
 
         object_ = Object(
-            # object[width, height, num_layers]
             array=object_array,
             pixelGeometry=pixel_geometry,
             center=None,
@@ -92,91 +101,9 @@ def read(self, filePath: Path) -> Product:
         )
 
 
-class PtychoShelvesProbeFileReader(ProbeFileReader):
-    def read(self, filePath: Path) -> Probe:
-        matDict = scipy.io.loadmat(filePath)
-
-        # array[width, height, num_shared_modes, num_varying_modes]
-        array = matDict['probe']
-        p_struct = matDict['p']
-        dx_spec = p_struct['dx_spec']
-        pixel_width_m = dx_spec[0]
-        pixel_height_m = dx_spec[1]
-        pixel_geometry = PixelGeometry(widthInMeters=pixel_width_m, heightInMeters=pixel_height_m)
-
-        return Probe(array=array.transpose(), pixelGeometry=pixel_geometry)
-
-
-class PtychoShelvesProbeFileWriter(ProbeFileWriter):
-    def write(self, filePath: Path, probe: Probe) -> None:
-        array = probe.getArray()
-        matDict = {'probe': array.transpose()}
-        scipy.io.savemat(filePath, matDict)
-
-
-class PtychoShelvesObjectFileReader(ObjectFileReader):
-    def read(self, filePath: Path) -> Object:
-        matDict = scipy.io.loadmat(filePath)
-
-        # array[width, height, num_layers]
-        p_struct = matDict['p']
-        dx_spec = p_struct['dx_spec']
-        pixel_width_m = dx_spec[0]
-        pixel_height_m = dx_spec[1]
-        pixel_geometry = PixelGeometry(widthInMeters=pixel_width_m, heightInMeters=pixel_height_m)
-
-        object_array = matDict['object'].transpose()
-        layer_distance_m: Sequence[float] = list()
-
-        try:
-            multi_slice_param = p_struct['multi_slice_param']
-            z_distance = multi_slice_param['z_distance']
-        except KeyError:
-            pass
-        else:
-            num_spaces = object_array.shape[-3] - 1
-            layer_distance_m = numpy.squeeze(z_distance)[:num_spaces]
-
-        return Object(
-            # object[width, height, num_layers]
-            array=object_array,
-            pixelGeometry=pixel_geometry,
-            center=None,
-            layerDistanceInMeters=layer_distance_m,
-        )
-
-
-class PtychoShelvesObjectFileWriter(ObjectFileWriter):
-    def write(self, filePath: Path, object_: Object) -> None:
-        array = object_.getArray()
-        matDict = {'object': array.transpose()}
-        # TODO layer distance to p.z_distance
-        scipy.io.savemat(filePath, matDict)
-
-
 def registerPlugins(registry: PluginRegistry) -> None:
     registry.productFileReaders.registerPlugin(
-        PtychoShelvesProductFileIO(),
-        simpleName=PtychoShelvesProductFileIO.SIMPLE_NAME,
-        displayName=PtychoShelvesProductFileIO.DISPLAY_NAME,
-    )
-    registry.probeFileReaders.registerPlugin(
-        PtychoShelvesProbeFileReader(),
-        simpleName=PtychoShelvesProductFileIO.SIMPLE_NAME,
-        displayName=PtychoShelvesProductFileIO.DISPLAY_NAME,
-    )
-    registry.probeFileWriters.registerPlugin(
-        PtychoShelvesProbeFileWriter(),
-        simpleName=PtychoShelvesProductFileIO.SIMPLE_NAME,
-        displayName=PtychoShelvesProductFileIO.DISPLAY_NAME,
-    )
-    registry.objectFileReaders.registerPlugin(
-        PtychoShelvesObjectFileReader(),
-        simpleName=PtychoShelvesProductFileIO.SIMPLE_NAME,
-        displayName=PtychoShelvesProductFileIO.DISPLAY_NAME,
-    )
-    registry.objectFileWriters.registerPlugin(
-        PtychoShelvesObjectFileWriter(),
-        simpleName=PtychoShelvesProductFileIO.SIMPLE_NAME,
-        displayName=PtychoShelvesProductFileIO.DISPLAY_NAME,
+        PtychoShelvesProductFileReader(),
+        simpleName=PtychoShelvesProductFileReader.SIMPLE_NAME,
+        displayName=PtychoShelvesProductFileReader.DISPLAY_NAME,
     )