# SPDX-License-Identifier: BSD-3-Clause
# Copyright (c) 2024 Scipp contributors (https://github.com/scipp)
import sciline as sl
import scipp as sc
from .io import (
DEFAULT_FILE_LOCK,
FileLock,
MaxDim1,
MaxDim2,
MinDim1,
MinDim2,
apply_logs_as_coords,
load_nexus_histogram_mode_detector,
load_nexus_rotation_logs,
retrieve_dark_current_images,
retrieve_open_beam_images,
retrieve_sample_images,
separate_detector_images,
separate_image_by_keys,
separate_image_key_logs,
)
from .normalize import (
BackgroundPixelThreshold,
SamplePixelThreshold,
apply_threshold_to_background_image,
apply_threshold_to_sample_images,
average_background_pixel_counts,
average_dark_current_images,
average_open_beam_images,
average_sample_pixel_counts,
calculate_scale_factor,
cleanse_open_beam_image,
cleanse_sample_images,
normalize_sample_images,
)
from .types import (
DEFAULT_HISTOGRAM_PATH,
HistogramModeDetectorsPath,
ImageDetectorName,
RotationMotionSensorName,
)
_IO_PROVIDERS = (
apply_logs_as_coords,
load_nexus_histogram_mode_detector,
load_nexus_rotation_logs,
retrieve_dark_current_images,
retrieve_open_beam_images,
retrieve_sample_images,
separate_detector_images,
separate_image_by_keys,
separate_image_key_logs,
)
_NORMALIZATION_PROVIDERS = (
apply_threshold_to_background_image,
apply_threshold_to_sample_images,
average_background_pixel_counts,
average_dark_current_images,
average_open_beam_images,
average_sample_pixel_counts,
calculate_scale_factor,
cleanse_open_beam_image,
cleanse_sample_images,
normalize_sample_images,
)
_DEFAULT_BACKGROUND_THRESHOLD = BackgroundPixelThreshold(sc.scalar(1.0, unit="counts"))
_DEFAULT_SAMPLE_THRESHOLD = SamplePixelThreshold(sc.scalar(0.0, unit="counts"))
[docs]
def YmirImageNormalizationWorkflow() -> sl.Pipeline:
"""
Ymir histogram mode imaging normalization workflow.
Default Normalization Formula
-----------------------------
.. math::
NormalizedSample_{i} = SampleImageStacks_{i} / BackgroundImage * ScaleFactor
.. math::
ScaleFactor = AverageBackgroundPixelCounts / AverageSamplePixelCounts
.. math::
SampleImageStacks_{i} = Sample_{i} - mean(DarkCurrent, dim=\\text{'time'})
\\text{where } i \\text{ is an index of an image.}
\\text{Pixel values less than sample_threshold}
\\text{ are replaced with sample_threshold}.
.. math::
BackgroundImage = mean(OpenBeam, dim=\\text{'time'})
- mean(DarkCurrent, dim=\\text{'time'})
\\text{Pixel values less than } \\text{background_threshold}
\\text{ are replaced with } \\text{background_threshold}.
"""
return sl.Pipeline(
(*_IO_PROVIDERS, *_NORMALIZATION_PROVIDERS),
params={
MinDim1: MinDim1(None),
MaxDim1: MaxDim1(None),
MinDim2: MinDim2(None),
MaxDim2: MaxDim2(None),
HistogramModeDetectorsPath: DEFAULT_HISTOGRAM_PATH,
ImageDetectorName: ImageDetectorName('orca'),
RotationMotionSensorName: RotationMotionSensorName('motion_cabinet_2'),
BackgroundPixelThreshold: _DEFAULT_BACKGROUND_THRESHOLD,
SamplePixelThreshold: _DEFAULT_SAMPLE_THRESHOLD,
FileLock: DEFAULT_FILE_LOCK,
},
)
