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Update computations for new parameter passing compatibility (always data source). #82

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Merged
cmeyer merged 1 commit into from
Mar 10, 2025
Merged

Update computations for new parameter passing compatibility (always data source). #82

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12 changes: 9 additions & 3 deletions nionswift_plugin/nion_eels_analysis/ElementalMappingController.py
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Original file line number Diff line number Diff line change
Expand Up @@ -39,8 +39,11 @@ class EELSBackgroundSubtraction:
def __init__(self, computation: Facade.Computation, **kwargs: typing.Any) -> None:
self.computation = computation

def execute(self, eels_xdata: DataAndMetadata.DataAndMetadata, region: Facade.Graphic, fit_interval: DataArrayType, signal_interval: DataArrayType, **kwargs: typing.Any) -> None:
eels_spectrum_xdata = xd.sum_region(eels_xdata, region.mask_xdata_with_shape(eels_xdata.data_shape[0:2]))
def execute(self, eels_xdata: Facade.DataSource, region: Facade.Graphic, fit_interval: DataArrayType, signal_interval: DataArrayType, **kwargs: typing.Any) -> None:
# note: 'eels_xdata' is actually a 'data source' and not a 'data item'. leaving name as is for now for backward compatibility.
eels_xdata_xdata = eels_xdata.xdata
assert eels_xdata_xdata
eels_spectrum_xdata = xd.sum_region(eels_xdata_xdata, region.mask_xdata_with_shape(eels_xdata_xdata.data_shape[0:2]))
signal = eels_analysis.make_signal_like(eels_analysis.extract_original_signal(eels_spectrum_xdata, [fit_interval], signal_interval), eels_spectrum_xdata)
background_xdata = eels_analysis.make_signal_like(eels_analysis.calculate_background_signal(eels_spectrum_xdata, [fit_interval], signal_interval), eels_spectrum_xdata)
assert signal
Expand Down Expand Up @@ -211,7 +214,8 @@ def __init__(self, computation: Facade.Computation, **kwargs: typing.Any) -> Non
self.computation = computation

def execute(self, **kwargs: typing.Any) -> None:
spectrum_image_xdata = kwargs["spectrum_image_xdata"]
# note: 'spectrum_image_xdata' is actually a 'data source' and not a 'data item'. leaving name as is for now for backward compatibility.
spectrum_image = typing.cast(Facade.DataSource, kwargs["spectrum_image_xdata"])
fit_interval = kwargs["fit_interval"]
signal_interval = kwargs["signal_interval"]
atomic_number = kwargs.get("atomic_number")
Expand All @@ -220,6 +224,8 @@ def execute(self, **kwargs: typing.Any) -> None:
electron_shell = None
if atomic_number is not None and shell_number is not None and subshell_index is not None:
electron_shell = PeriodicTable.ElectronShell(atomic_number, shell_number, subshell_index)
spectrum_image_xdata = spectrum_image.xdata
assert spectrum_image_xdata
self.__mapped_xdata = eels_analysis.map_background_subtracted_signal(spectrum_image_xdata, electron_shell, [fit_interval], signal_interval)

def commit(self) -> None:
Expand Down