"""Public header schema for MeasureOrientationZones (category ``OrientZones``).
Existing absolute-orientation headers use
``OrientZones_<Metric>-<Variant>-<Zone>``. Radial-relative headers use the
detected-structure selector explicitly:
``OrientZones_<Metric>-Mask-<Region>``. Region is usually one of
{Overall, Dense, Sparse}; longer-range rotation also includes the paired
DenseToSparse transition.
Canonical geometry excludes CoreZone from every orientation estimate:
Overall is ``CoreZoneEndRadius .. OuterRadius``, Dense is
``CoreZoneEndRadius .. DenseRadius``, and Sparse is
``DenseRadius .. OuterRadius``. Descriptions below use those domains.
``legacy_mode=True`` retains the historical selectors.
"""
from __future__ import annotations
from ._measurement_info import Entry
from ._tiers import DescriptiveTrait, QualityInfo
[docs]
class ORIENTATION_ZONE_PRIMARY(DescriptiveTrait):
"""Primary outward-rotation traits over resolved branch zones."""
[docs]
@classmethod
def category(cls) -> str:
return "OrientZones"
OUTWARD_ROTATION_SUSTAINED_PEAK_OVERALL = Entry(
"OutwardRotationSustainedPeak-Mask-Overall",
"Largest rolling-median absolute cumulative rotation across consecutive "
"supported literal skeleton-ring crossings from the CoreZone "
"boundary through the configured SparseZone outer boundary. Reported in degrees, "
"nonnegative with no fixed upper bound. The default three-ring window "
"rejects a one-ring spike; NaN means no complete supported window.",
)
OUTWARD_ROTATION_SUSTAINED_PEAK_DENSE = Entry(
"OutwardRotationSustainedPeak-Mask-Dense",
"Largest rolling-median absolute cumulative rotation across consecutive "
"supported literal skeleton-ring crossings from the CoreZone "
"boundary to dense_end. Reported in degrees, nonnegative with no fixed "
"upper bound. The default three-ring window rejects a one-ring spike; "
"NaN means no complete supported window.",
)
OUTWARD_ROTATION_SUSTAINED_PEAK_SPARSE = Entry(
"OutwardRotationSustainedPeak-Mask-Sparse",
"Largest rolling-median absolute cumulative rotation across consecutive "
"supported literal skeleton-ring crossings from dense_end through the "
"configured SparseZone outer boundary. Reported in degrees, nonnegative with no "
"fixed upper bound. The default three-ring window rejects a one-ring "
"spike; NaN means no complete supported window. Cumulative rotation is "
"not rebased at dense_end, so this Sparse magnitude may include rotation "
"accumulated while the profile was in Dense.",
)
OUTWARD_ROTATION_NET_OVERALL = Entry(
"OutwardRotationNet-Mask-Overall",
"Outer endpoint median minus inner endpoint median of cumulative literal "
"skeleton-ring rotation along the longest supported run from the inferred "
"inoculum boundary through the configured SparseZone outer boundary. Reported in "
"signed degrees with no fixed bounds; positive is clockwise and negative "
"is counterclockwise while moving outward in image coordinates. NaN means "
"the run is shorter than the configured minimum.",
)
OUTWARD_ROTATION_NET_DENSE = Entry(
"OutwardRotationNet-Mask-Dense",
"Outer endpoint median minus inner endpoint median of cumulative literal "
"skeleton-ring rotation along the longest supported run from the inferred "
"inoculum boundary to dense_end. Reported in signed degrees with no fixed "
"bounds; positive is clockwise and negative is counterclockwise while "
"moving outward in image coordinates. NaN means the run is shorter than "
"the configured minimum.",
)
OUTWARD_ROTATION_NET_SPARSE = Entry(
"OutwardRotationNet-Mask-Sparse",
"Outer endpoint median minus inner endpoint median of cumulative literal "
"skeleton-ring rotation along the longest supported run from dense_end "
"through the configured SparseZone outer boundary. Reported in signed degrees with "
"no fixed bounds; positive is clockwise and negative is counterclockwise "
"while moving outward in image coordinates. NaN means the run is shorter "
"than the configured minimum. Because this is a difference, cumulative "
"rotation carried into Sparse cancels from the result.",
)
OUTWARD_ROTATION_RATE_OVERALL = Entry(
"OutwardRotationRate-Mask-Overall",
"Median of all pairwise cumulative-rotation slopes along the longest "
"supported literal skeleton-ring run from the CoreZone boundary "
"through the configured SparseZone outer boundary. Reported in signed degrees per "
"pixel; positive is clockwise and negative is counterclockwise while "
"moving outward in image coordinates. NaN means the run is shorter than "
"the configured minimum.",
)
OUTWARD_ROTATION_RATE_DENSE = Entry(
"OutwardRotationRate-Mask-Dense",
"Median of all pairwise cumulative-rotation slopes along the longest "
"supported literal skeleton-ring run from the CoreZone boundary "
"to dense_end. Reported in signed degrees per pixel; positive is clockwise "
"and negative is counterclockwise while moving outward in image "
"coordinates. NaN means the run is shorter than the configured minimum.",
)
OUTWARD_ROTATION_RATE_SPARSE = Entry(
"OutwardRotationRate-Mask-Sparse",
"Median of all pairwise cumulative-rotation slopes along the longest "
"supported literal skeleton-ring run from dense_end through the full "
"detected outer boundary. Reported in signed degrees per pixel; positive "
"is clockwise and negative is counterclockwise while moving outward in "
"image coordinates. NaN means the run is shorter than the configured "
"minimum. The slope is unchanged by cumulative rotation carried into "
"Sparse.",
)
OUTWARD_ROTATION_CONSISTENCY_OVERALL = Entry(
"OutwardRotationConsistency-Mask-Overall",
"Absolute Kendall tau-b association between radius and cumulative literal "
"skeleton-ring rotation along the longest supported run from the inferred "
"inoculum boundary through the configured SparseZone outer boundary. Dimensionless "
"in [0, 1]; 1 is fully monotonic and values near 0 indicate reversals, "
"plateaus, or no ordered trend. Direction is carried by the rotation "
"rate. NaN means the run is shorter than the configured minimum.",
)
OUTWARD_ROTATION_CONSISTENCY_DENSE = Entry(
"OutwardRotationConsistency-Mask-Dense",
"Absolute Kendall tau-b association between radius and cumulative literal "
"skeleton-ring rotation along the longest supported run from the inferred "
"inoculum boundary to dense_end. Dimensionless in [0, 1]; 1 is fully "
"monotonic and values near 0 indicate reversals, plateaus, or no ordered "
"trend. Direction is carried by the rotation rate. NaN means the run is "
"shorter than the configured minimum.",
)
OUTWARD_ROTATION_CONSISTENCY_SPARSE = Entry(
"OutwardRotationConsistency-Mask-Sparse",
"Absolute Kendall tau-b association between radius and cumulative literal "
"skeleton-ring rotation along the longest supported run from dense_end "
"through the configured SparseZone outer boundary. Dimensionless in [0, 1]; 1 is "
"fully monotonic and values near 0 indicate reversals, plateaus, or no "
"ordered trend. Direction is carried by the rotation rate, and the rank "
"association is unchanged by rotation carried into Sparse. NaN means the "
"run is shorter than the configured minimum.",
)
[docs]
class ORIENTATION_ZONE_DIAGNOSTIC(QualityInfo):
"""Opt-in validation, comparator, and legacy orientation-zone columns.
Canonical diagnostics use the shared CoreZone / DenseZone / SparseZone
geometry. ``Radial`` variants use all tile pixels in the corresponding
annulus; ``Mask`` variants use target-object pixels. Explicit legacy mode
retains the historical symmetric-radius selectors. See
:class:`MeasureOrientationZones` for parameters and method.
"""
[docs]
@classmethod
def category(cls) -> str:
return "OrientZones"
OUTWARD_ROTATION_RAW_PEAK_OVERALL = Entry(
"OutwardRotationRawPeak-Mask-Overall",
"Largest absolute cumulative literal skeleton-ring rotation from the "
"CoreZone boundary through the configured SparseZone outer boundary. "
"Reported in degrees, nonnegative with no fixed upper bound. This raw "
"maximum is outlier-sensitive and should be compared with the primary "
"sustained peak.",
)
OUTWARD_ROTATION_RAW_PEAK_DENSE = Entry(
"OutwardRotationRawPeak-Mask-Dense",
"Largest absolute cumulative literal skeleton-ring rotation from the "
"CoreZone boundary to dense_end. Reported in degrees, "
"nonnegative with no fixed upper bound. This raw maximum is "
"outlier-sensitive and should be compared with the primary sustained "
"peak.",
)
OUTWARD_ROTATION_RAW_PEAK_SPARSE = Entry(
"OutwardRotationRawPeak-Mask-Sparse",
"Largest absolute cumulative literal skeleton-ring rotation from "
"dense_end through the configured SparseZone outer boundary. Reported in degrees, "
"nonnegative with no fixed upper bound. This raw maximum is "
"outlier-sensitive. Cumulative rotation is not rebased at dense_end, so "
"this Sparse magnitude may include rotation accumulated while the profile "
"was in Dense.",
)
OUTWARD_ROTATION_P90_OVERALL = Entry(
"OutwardRotationP90-Mask-Overall",
"90th percentile of absolute cumulative literal skeleton-ring rotation "
"over supported rings from the CoreZone boundary through the "
"configured SparseZone outer boundary. Reported in degrees, nonnegative with no "
"fixed upper bound. This validation comparator ignores radial order.",
)
OUTWARD_ROTATION_P90_DENSE = Entry(
"OutwardRotationP90-Mask-Dense",
"90th percentile of absolute cumulative literal skeleton-ring rotation "
"over supported rings from the CoreZone boundary to dense_end. "
"Reported in degrees, nonnegative with no fixed upper bound. This "
"validation comparator ignores radial order.",
)
OUTWARD_ROTATION_P90_SPARSE = Entry(
"OutwardRotationP90-Mask-Sparse",
"90th percentile of absolute cumulative literal skeleton-ring rotation "
"over supported rings from dense_end through the configured SparseZone "
"outer boundary. Reported in degrees, nonnegative with no fixed upper bound. This "
"comparator ignores radial order. Cumulative rotation is not rebased at "
"dense_end, so this Sparse magnitude may include rotation accumulated "
"while the profile was in Dense.",
)
OUTWARD_ROTATION_P95_OVERALL = Entry(
"OutwardRotationP95-Mask-Overall",
"95th percentile of absolute cumulative literal skeleton-ring rotation "
"over supported rings from the CoreZone boundary through the "
"configured SparseZone outer boundary. Reported in degrees, nonnegative with no "
"fixed upper bound. With few supported rings it remains close to the raw "
"maximum and is not the primary robust metric.",
)
OUTWARD_ROTATION_P95_DENSE = Entry(
"OutwardRotationP95-Mask-Dense",
"95th percentile of absolute cumulative literal skeleton-ring rotation "
"over supported rings from the CoreZone boundary to dense_end. "
"Reported in degrees, nonnegative with no fixed upper bound. With few "
"supported rings it remains close to the raw maximum.",
)
OUTWARD_ROTATION_P95_SPARSE = Entry(
"OutwardRotationP95-Mask-Sparse",
"95th percentile of absolute cumulative literal skeleton-ring rotation "
"over supported rings from dense_end through the configured SparseZone "
"outer boundary. Reported in degrees, nonnegative with no fixed upper bound. "
"Cumulative rotation is not rebased at dense_end, so this Sparse "
"magnitude may include rotation accumulated while the profile was in "
"Dense.",
)
OUTWARD_ROTATION_MEDIAN_MAGNITUDE_OVERALL = Entry(
"OutwardRotationMedianMagnitude-Mask-Overall",
"Median absolute cumulative literal skeleton-ring rotation over supported "
"rings from the CoreZone boundary through the configured SparseZone outer "
"outer boundary. Reported in degrees, nonnegative with no fixed upper "
"bound. This validation comparator describes typical magnitude but "
"ignores radial order and localized outer turns.",
)
OUTWARD_ROTATION_MEDIAN_MAGNITUDE_DENSE = Entry(
"OutwardRotationMedianMagnitude-Mask-Dense",
"Median absolute cumulative literal skeleton-ring rotation over supported "
"rings from the CoreZone boundary to dense_end. Reported in "
"degrees, nonnegative with no fixed upper bound. This validation "
"comparator describes typical magnitude but ignores radial order.",
)
OUTWARD_ROTATION_MEDIAN_MAGNITUDE_SPARSE = Entry(
"OutwardRotationMedianMagnitude-Mask-Sparse",
"Median absolute cumulative literal skeleton-ring rotation over supported "
"rings from dense_end through the configured SparseZone outer boundary. Reported "
"in degrees, nonnegative with no fixed upper bound. Cumulative rotation "
"is not rebased at dense_end, so this Sparse magnitude may include "
"rotation accumulated while the profile was in Dense.",
)
OUTWARD_ROTATION_ABSOLUTE_AREA_OVERALL = Entry(
"OutwardRotationAbsoluteArea-Mask-Overall",
"Trapezoidal area under absolute cumulative rotation within supported "
"runs from the CoreZone boundary through the configured SparseZone outer "
"outer boundary, divided by their total supported radial span. Reported "
"in degrees, nonnegative with no fixed upper bound. It describes "
"radially persistent rotation but can remain high after one early step.",
)
OUTWARD_ROTATION_ABSOLUTE_AREA_DENSE = Entry(
"OutwardRotationAbsoluteArea-Mask-Dense",
"Trapezoidal area under absolute cumulative rotation within supported "
"runs from the CoreZone boundary to dense_end, divided by their "
"total supported radial span. Reported in degrees, nonnegative with no "
"fixed upper bound. It describes radially persistent rotation but can "
"remain high after one early step.",
)
OUTWARD_ROTATION_ABSOLUTE_AREA_SPARSE = Entry(
"OutwardRotationAbsoluteArea-Mask-Sparse",
"Trapezoidal area under absolute cumulative rotation within supported "
"runs from dense_end through the configured SparseZone outer boundary, divided by "
"their total supported radial span. Reported in degrees, nonnegative with "
"no fixed upper bound. Cumulative rotation is not rebased at dense_end, "
"so this Sparse magnitude may include rotation accumulated while the "
"profile was in Dense.",
)
OUTWARD_ROTATION_TOTAL_VARIATION_OVERALL = Entry(
"OutwardRotationTotalVariation-Mask-Overall",
"Sum of absolute adjacent cumulative-rotation changes within supported "
"runs from the CoreZone boundary through the configured SparseZone outer "
"outer boundary, without bridging gaps. Reported in degrees, nonnegative "
"with no fixed upper bound. It is sensitive to oscillation, profile "
"length, and noise and is diagnostic only.",
)
OUTWARD_ROTATION_TOTAL_VARIATION_DENSE = Entry(
"OutwardRotationTotalVariation-Mask-Dense",
"Sum of absolute adjacent cumulative-rotation changes within supported "
"runs from the CoreZone boundary to dense_end, without bridging "
"gaps. Reported in degrees, nonnegative with no fixed upper bound. It is "
"sensitive to oscillation, profile length, and noise and is diagnostic "
"only.",
)
OUTWARD_ROTATION_TOTAL_VARIATION_SPARSE = Entry(
"OutwardRotationTotalVariation-Mask-Sparse",
"Sum of absolute adjacent cumulative-rotation changes within supported "
"runs from dense_end through the configured SparseZone outer boundary, without "
"bridging gaps. Reported in degrees, nonnegative with no fixed upper "
"bound. It is sensitive to oscillation, profile length, and noise and is "
"diagnostic only.",
)
OUTWARD_ROTATION_RATE_GRADIENT_OVERALL = Entry(
"OutwardRotationRateGradient-Mask-Overall",
"Outer-half robust rotation rate minus inner-half robust rotation rate, "
"divided by the separation of their median radii, along the longest "
"supported run from the CoreZone boundary through the full "
"detected outer boundary. Reported in signed degrees per pixel squared. "
"This is a spatial rate gradient, not temporal acceleration, and is NaN "
"unless the run meets both the configured minimum and eight rings.",
)
OUTWARD_ROTATION_RATE_GRADIENT_DENSE = Entry(
"OutwardRotationRateGradient-Mask-Dense",
"Outer-half robust rotation rate minus inner-half robust rotation rate, "
"divided by the separation of their median radii, along the longest "
"supported run from the CoreZone boundary to dense_end. Reported "
"in signed degrees per pixel squared. This is a spatial rate gradient, "
"not temporal acceleration, and is NaN unless the run meets both the "
"configured minimum and eight rings.",
)
OUTWARD_ROTATION_RATE_GRADIENT_SPARSE = Entry(
"OutwardRotationRateGradient-Mask-Sparse",
"Outer-half robust rotation rate minus inner-half robust rotation rate, "
"divided by the separation of their median radii, along the longest "
"supported run from dense_end through the configured SparseZone outer boundary. "
"Reported in signed degrees per pixel squared. This is a spatial rate "
"gradient, not temporal acceleration, and is NaN for runs shorter than "
"the larger of eight rings and the configured minimum.",
)
OUTWARD_ROTATION_RING_SUPPORT_OVERALL = Entry(
"OutwardRotationRingSupport-Mask-Overall",
"Fraction of candidate literal sampling rings from the CoreZone "
"boundary through the configured SparseZone outer boundary with a finite "
"cumulative-rotation state. Dimensionless in [0, 1]. This is a "
"density-sensitive quality diagnostic, not an orientation phenotype.",
)
OUTWARD_ROTATION_RING_SUPPORT_DENSE = Entry(
"OutwardRotationRingSupport-Mask-Dense",
"Fraction of candidate literal sampling rings from the CoreZone "
"boundary to dense_end with a finite cumulative-rotation state. "
"Dimensionless in [0, 1]. This is a density-sensitive quality diagnostic, "
"not an orientation phenotype.",
)
OUTWARD_ROTATION_RING_SUPPORT_SPARSE = Entry(
"OutwardRotationRingSupport-Mask-Sparse",
"Fraction of candidate literal sampling rings from dense_end through the "
"configured SparseZone outer boundary with a finite cumulative-rotation state. "
"Dimensionless in [0, 1]. This is a density-sensitive quality diagnostic, "
"not an orientation phenotype.",
)
OUTWARD_ROTATION_RUN_SPAN_SUPPORT_OVERALL = Entry(
"OutwardRotationRunSpanSupport-Mask-Overall",
"Radial span of the longest contiguous supported literal-crossing run "
"divided by the full candidate span from the CoreZone boundary "
"through the configured SparseZone outer boundary. Dimensionless in [0, 1]. This "
"reports continuity of usable evidence, not orientation.",
)
OUTWARD_ROTATION_RUN_SPAN_SUPPORT_DENSE = Entry(
"OutwardRotationRunSpanSupport-Mask-Dense",
"Radial span of the longest contiguous supported literal-crossing run "
"divided by the full candidate span from the CoreZone boundary "
"to dense_end. Dimensionless in [0, 1]. This reports continuity of usable "
"evidence, not orientation.",
)
OUTWARD_ROTATION_RUN_SPAN_SUPPORT_SPARSE = Entry(
"OutwardRotationRunSpanSupport-Mask-Sparse",
"Radial span of the longest contiguous supported literal-crossing run "
"divided by the full candidate span from dense_end through the full "
"detected outer boundary. Dimensionless in [0, 1]. This reports continuity "
"of usable evidence, not orientation.",
)
OUTWARD_ROTATION_MEDIAN_RESULTANT_OVERALL = Entry(
"OutwardRotationMedianResultant-Mask-Overall",
"Median doubled-angle resultant of crossing orientations among eligible "
"literal rings from the CoreZone boundary through the full "
"detected outer boundary. Dimensionless in [0, 1]; larger values mean "
"stronger within-ring axial agreement. This is an orientation-reliability "
"diagnostic, not a rotation phenotype.",
)
OUTWARD_ROTATION_MEDIAN_RESULTANT_DENSE = Entry(
"OutwardRotationMedianResultant-Mask-Dense",
"Median doubled-angle resultant of crossing orientations among eligible "
"literal rings from the CoreZone boundary to dense_end. "
"Dimensionless in [0, 1]; larger values mean stronger within-ring axial "
"agreement. This is an orientation-reliability diagnostic, not a rotation "
"phenotype.",
)
OUTWARD_ROTATION_MEDIAN_RESULTANT_SPARSE = Entry(
"OutwardRotationMedianResultant-Mask-Sparse",
"Median doubled-angle resultant of crossing orientations among eligible "
"literal rings from dense_end through the configured SparseZone outer boundary. "
"Dimensionless in [0, 1]; larger values mean stronger within-ring axial "
"agreement. This is an orientation-reliability diagnostic, not a rotation "
"phenotype.",
)
CONCENTRATION_RADIAL_OVERALL = Entry(
"Concentration-Radial-Overall",
"Coherence-weighted resultant length R of the doubled-angle orientation field "
"over all tile pixels in the canonical Overall annulus (core_end .. sparse_end) "
"region. Dimensionless in [0, 1]; 1 = perfectly aligned hyphae, 0 = "
"isotropic. NaN when the summed coherence over the selector is ~0 or the zone "
"has zero width.",
)
CONCENTRATION_RADIAL_DENSE = Entry(
"Concentration-Radial-Dense",
"Coherence-weighted resultant length R of the doubled-angle orientation field "
"over all tile pixels in the dense ring (core_end .. dense_end radii) region. "
"Dimensionless in [0, 1]; 1 = perfectly aligned hyphae, 0 = isotropic. NaN "
"when the summed coherence over the selector is ~0 or the zone has zero "
"width.",
)
CONCENTRATION_RADIAL_SPARSE = Entry(
"Concentration-Radial-Sparse",
"Coherence-weighted resultant length R of the doubled-angle orientation field "
"over all tile pixels in the sparse ring (dense_end .. sparse_end radii) "
"region. Dimensionless in [0, 1]; 1 = perfectly aligned hyphae, 0 = "
"isotropic. NaN when the summed coherence over the selector is ~0 or the zone "
"has zero width.",
)
CONCENTRATION_MASK_OVERALL = Entry(
"Concentration-Mask-Overall",
"Coherence-weighted resultant length R of the doubled-angle orientation field "
"over detected-object pixels in the canonical Overall annulus (core_end .. "
"sparse_end) region. Dimensionless in [0, 1]; 1 = perfectly aligned "
"hyphae, 0 = isotropic. NaN when the summed coherence over the selector is ~0 "
"or the zone has zero width.",
)
CONCENTRATION_MASK_DENSE = Entry(
"Concentration-Mask-Dense",
"Coherence-weighted resultant length R of the doubled-angle orientation field "
"over detected-object pixels in the dense ring (core_end .. dense_end radii) "
"region. Dimensionless in [0, 1]; 1 = perfectly aligned hyphae, 0 = "
"isotropic. NaN when the summed coherence over the selector is ~0 or the zone "
"has zero width.",
)
CONCENTRATION_MASK_SPARSE = Entry(
"Concentration-Mask-Sparse",
"Coherence-weighted resultant length R of the doubled-angle orientation field "
"over detected-object pixels in the sparse ring (dense_end .. sparse_end "
"radii) region. Dimensionless in [0, 1]; 1 = perfectly aligned hyphae, 0 = "
"isotropic. NaN when the summed coherence over the selector is ~0 or the zone "
"has zero width.",
)
TURNING_RADIAL_OVERALL = Entry(
"Turning-Radial-Overall",
"Coherence-weighted mean orientation-gradient magnitude <|grad phi|> over all "
"tile pixels in the canonical Overall annulus (core_end .. sparse_end), in "
"degrees per pixel. Higher values indicate curving/fanning hyphae; ~0 "
"indicates straight parallel growth.",
)
TURNING_RADIAL_DENSE = Entry(
"Turning-Radial-Dense",
"Coherence-weighted mean orientation-gradient magnitude <|grad phi|> over all "
"tile pixels in the dense ring (core_end .. dense_end radii) region, in "
"degrees per pixel. Higher values indicate curving/fanning hyphae; ~0 "
"indicates straight parallel growth.",
)
TURNING_RADIAL_SPARSE = Entry(
"Turning-Radial-Sparse",
"Coherence-weighted mean orientation-gradient magnitude <|grad phi|> over all "
"tile pixels in the sparse ring (dense_end .. sparse_end radii) region, in "
"degrees per pixel. Higher values indicate curving/fanning hyphae; ~0 "
"indicates straight parallel growth.",
)
TURNING_MASK_OVERALL = Entry(
"Turning-Mask-Overall",
"Coherence-weighted mean orientation-gradient magnitude <|grad phi|> over "
"detected-object pixels in the canonical Overall annulus (core_end .. sparse_end) "
"region, in degrees per pixel. Higher values indicate curving/fanning hyphae; "
"~0 indicates straight parallel growth.",
)
TURNING_MASK_DENSE = Entry(
"Turning-Mask-Dense",
"Coherence-weighted mean orientation-gradient magnitude <|grad phi|> over "
"detected-object pixels in the dense ring (core_end .. dense_end radii) "
"region, in degrees per pixel. Higher values indicate curving/fanning hyphae; "
"~0 indicates straight parallel growth.",
)
TURNING_MASK_SPARSE = Entry(
"Turning-Mask-Sparse",
"Coherence-weighted mean orientation-gradient magnitude <|grad phi|> over "
"detected-object pixels in the sparse ring (dense_end .. sparse_end radii) "
"region, in degrees per pixel. Higher values indicate curving/fanning hyphae; "
"~0 indicates straight parallel growth.",
)
COHERENCE_RADIAL_OVERALL = Entry(
"Coherence-Radial-Overall",
"Mean structure-tensor coherence C over all tile pixels in the canonical Overall "
"annulus (core_end .. sparse_end). Dimensionless in [0, 1]; a "
"confidence/QC readout for how well orientation is defined there (low where "
"texture is isotropic).",
)
COHERENCE_RADIAL_DENSE = Entry(
"Coherence-Radial-Dense",
"Mean structure-tensor coherence C over all tile pixels in the dense ring "
"(core_end .. dense_end radii) region. Dimensionless in [0, 1]; a "
"confidence/QC readout for how well orientation is defined there (low where "
"texture is isotropic).",
)
COHERENCE_RADIAL_SPARSE = Entry(
"Coherence-Radial-Sparse",
"Mean structure-tensor coherence C over all tile pixels in the sparse ring "
"(dense_end .. sparse_end radii) region. Dimensionless in [0, 1]; a "
"confidence/QC readout for how well orientation is defined there (low where "
"texture is isotropic).",
)
COHERENCE_MASK_OVERALL = Entry(
"Coherence-Mask-Overall",
"Mean structure-tensor coherence C over detected-object pixels in the canonical "
"Overall annulus (core_end .. sparse_end). Dimensionless in [0, 1]; a "
"confidence/QC readout for how well orientation is defined there (low where "
"texture is isotropic).",
)
COHERENCE_MASK_DENSE = Entry(
"Coherence-Mask-Dense",
"Mean structure-tensor coherence C over detected-object pixels in the dense "
"ring (core_end .. dense_end radii) region. Dimensionless in [0, 1]; a "
"confidence/QC readout for how well orientation is defined there (low where "
"texture is isotropic).",
)
COHERENCE_MASK_SPARSE = Entry(
"Coherence-Mask-Sparse",
"Mean structure-tensor coherence C over detected-object pixels in the sparse "
"ring (dense_end .. sparse_end radii) region. Dimensionless in [0, 1]; a "
"confidence/QC readout for how well orientation is defined there (low where "
"texture is isotropic).",
)
RADIAL_TILT_MASK_OVERALL = Entry(
"RadialTilt-Mask-Overall",
"Equal-angular-sector mean of the coherence-weighted absolute axial "
"difference between the local fiber axis and the outward radial spoke at the "
"same pixel, over detected-object pixels in the canonical Overall annulus "
"(core_end .. sparse_end). Reported in degrees in [0, 90]; 0 = locally radial "
"and 90 = locally tangential. Each occupied 10-degree angular sector "
"contributes equally. For a fixed set of reliable sectors, multiplying branch "
"evidence without changing within-sector tilt distributions leaves the result "
"unchanged. A support-threshold crossing can add a newly reliable sector and "
"change the estimate; mixed orientations within one sector remain "
"pixel-weighted.",
)
RADIAL_TILT_MASK_DENSE = Entry(
"RadialTilt-Mask-Dense",
"Equal-angular-sector mean of the coherence-weighted absolute axial "
"difference between the local fiber axis and the outward radial spoke at the "
"same pixel, over detected-object pixels in the dense ring (core_end .. "
"dense_end radii) region. Reported in degrees in [0, 90]; 0 = locally radial "
"and 90 = locally tangential. Each occupied 10-degree angular sector "
"contributes equally. For a fixed set of reliable sectors, multiplying branch "
"evidence without changing within-sector tilt distributions leaves the result "
"unchanged. A support-threshold crossing can add a newly reliable sector and "
"change the estimate; mixed orientations within one sector remain "
"pixel-weighted.",
)
RADIAL_TILT_MASK_SPARSE = Entry(
"RadialTilt-Mask-Sparse",
"Equal-angular-sector mean of the coherence-weighted absolute axial "
"difference between the local fiber axis and the outward radial spoke at the "
"same pixel, over detected-object pixels in the sparse ring (dense_end .. "
"sparse_end radii) region. Reported in degrees in [0, 90]; 0 = locally radial "
"and 90 = locally tangential. Each occupied 10-degree angular sector "
"contributes equally. For a fixed set of reliable sectors, multiplying branch "
"evidence without changing within-sector tilt distributions leaves the result "
"unchanged. A support-threshold crossing can add a newly reliable sector and "
"change the estimate; mixed orientations within one sector remain "
"pixel-weighted.",
)
OUTWARD_TURNING_MASK_OVERALL = Entry(
"OutwardTurning-Mask-Overall",
"Equal-angular-sector mean radial derivative magnitude of the radial-relative "
"fiber tilt, over detected-object pixels in the canonical Overall annulus "
"(core_end .. sparse_end). Reported in degrees per pixel. 0 means the tilt "
"stays constant while moving outward; larger values mean the local fiber "
"field rotates relative to its radial spoke. The aggregation gives each "
"occupied 10-degree angular sector equal weight. This is a field-level "
"curvature measure, not parent-to-daughter branch tracking.",
)
OUTWARD_TURNING_MASK_DENSE = Entry(
"OutwardTurning-Mask-Dense",
"Equal-angular-sector mean radial derivative magnitude of the radial-relative "
"fiber tilt, over detected-object pixels in the dense ring (core_end .. "
"dense_end radii) region. Reported in degrees per pixel. 0 means the tilt "
"stays constant while moving outward; larger values mean the local fiber "
"field rotates relative to its radial spoke. The aggregation gives each "
"occupied 10-degree angular sector equal weight. This is a field-level "
"curvature measure, not parent-to-daughter branch tracking.",
)
OUTWARD_TURNING_MASK_SPARSE = Entry(
"OutwardTurning-Mask-Sparse",
"Equal-angular-sector mean radial derivative magnitude of the radial-relative "
"fiber tilt, over detected-object pixels in the sparse ring (dense_end .. "
"sparse_end radii) region. Reported in degrees per pixel. 0 means the tilt "
"stays constant while moving outward; larger values mean the local fiber "
"field rotates relative to its radial spoke. The aggregation gives each "
"occupied 10-degree angular sector equal weight. This is a field-level "
"curvature measure, not parent-to-daughter branch tracking.",
)
RADIAL_SECTOR_SUPPORT_MASK_OVERALL = Entry(
"RadialSectorSupport-Mask-Overall",
"Fraction of the 36 fixed 10-degree sectors in the canonical Overall annulus "
"(core_end .. sparse_end) that contain at least three detected-structure "
"pixels with structure-tensor coherence C >= 0.15. Dimensionless in [0, 1]. "
"This is a density-sensitive quality diagnostic for interpreting radial tilt "
"and outward turning, not an orientation phenotype.",
)
RADIAL_SECTOR_SUPPORT_MASK_DENSE = Entry(
"RadialSectorSupport-Mask-Dense",
"Fraction of the 36 fixed 10-degree sectors in the dense ring (core_end .. "
"dense_end radii) region that contain at least three detected-structure "
"pixels with structure-tensor coherence C >= 0.15. Dimensionless in [0, 1]. "
"This is a density-sensitive quality diagnostic for interpreting radial tilt "
"and outward turning, not an orientation phenotype.",
)
RADIAL_SECTOR_SUPPORT_MASK_SPARSE = Entry(
"RadialSectorSupport-Mask-Sparse",
"Fraction of the 36 fixed 10-degree sectors in the sparse ring (dense_end .. "
"sparse_end radii) region that contain at least three detected-structure "
"pixels with structure-tensor coherence C >= 0.15. Dimensionless in [0, 1]. "
"This is a density-sensitive quality diagnostic for interpreting radial tilt "
"and outward turning, not an orientation phenotype.",
)
LONG_RANGE_ROTATION_MASK_OVERALL = Entry(
"LongRangeRotation-Mask-Overall",
"Equal-cell mean absolute seam-safe axial change between matching 10-degree "
"sectors in configured-width Sholl-style annular bands (8 pixels by default) "
"whose centres are separated by the configured long-range lag (16 pixels by "
"default). Ring pairs are assigned to the canonical Overall annulus "
"(core_end .. sparse_end) region by their midpoint. "
"Reported in degrees in [0, 90]. Annular bands begin outside the operational "
"CoreZone. Each reliable ring-sector comparison contributes equally, so "
"multiplying same-orientation branch evidence within an already reliable cell "
"does not change its contribution.",
)
LONG_RANGE_ROTATION_MASK_DENSE = Entry(
"LongRangeRotation-Mask-Dense",
"Equal-cell mean absolute seam-safe axial change between matching 10-degree "
"sectors in configured-width Sholl-style annular bands (8 pixels by default) "
"whose centres are separated by the configured long-range lag (16 pixels by "
"default). Ring pairs are assigned to the dense ring (core_end .. dense_end "
"radii) region by their midpoint. Reported in degrees in [0, 90]. Annular "
"bands begin outside the operational CoreZone. Each reliable ring-sector "
"comparison contributes equally, so multiplying same-orientation branch "
"evidence within an already reliable cell does not change its contribution.",
)
LONG_RANGE_ROTATION_MASK_SPARSE = Entry(
"LongRangeRotation-Mask-Sparse",
"Equal-cell mean absolute seam-safe axial change between matching 10-degree "
"sectors in configured-width Sholl-style annular bands (8 pixels by default) "
"whose centres are separated by the configured long-range lag (16 pixels by "
"default). Ring pairs are assigned to the sparse ring (dense_end .. "
"sparse_end radii) region by their midpoint. Reported in degrees in [0, 90]. "
"Annular bands begin outside the operational CoreZone. Each reliable "
"ring-sector comparison contributes equally, so multiplying same-orientation "
"branch evidence within an already reliable cell does not change its "
"contribution.",
)
SIGNED_LONG_RANGE_ROTATION_MASK_OVERALL = Entry(
"SignedLongRangeRotation-Mask-Overall",
"Signed counterpart of LongRangeRotation over the canonical Overall "
"annulus (core_end .. sparse_end), in degrees in "
"[-90, 90]. Positive means the radial-relative fiber axis rotates clockwise "
"and negative means counterclockwise while moving outward in image "
"coordinates. Opposing reliable ring-sector changes cancel in this "
"directional summary; inspect the absolute metric and support alongside it.",
)
SIGNED_LONG_RANGE_ROTATION_MASK_DENSE = Entry(
"SignedLongRangeRotation-Mask-Dense",
"Signed counterpart of LongRangeRotation over the dense ring (core_end .. "
"dense_end radii) region, in degrees in [-90, 90]. Positive means the "
"radial-relative fiber axis rotates clockwise and negative means "
"counterclockwise while moving outward in image coordinates. Opposing "
"reliable ring-sector changes cancel in this directional summary; inspect the "
"absolute metric and support alongside it.",
)
SIGNED_LONG_RANGE_ROTATION_MASK_SPARSE = Entry(
"SignedLongRangeRotation-Mask-Sparse",
"Signed counterpart of LongRangeRotation over the sparse ring (dense_end .. "
"sparse_end radii) region, in degrees in [-90, 90]. Positive means the "
"radial-relative fiber axis rotates clockwise and negative means "
"counterclockwise while moving outward in image coordinates. Opposing "
"reliable ring-sector changes cancel in this directional summary; inspect the "
"absolute metric and support alongside it.",
)
LONG_RANGE_ROTATION_SUPPORT_MASK_OVERALL = Entry(
"LongRangeRotationSupport-Mask-Overall",
"Fraction of fixed-lag ring-sector comparison cells assigned to the "
"canonical Overall annulus (core_end .. sparse_end) that has reliable "
"orientation estimates at both "
"radii. Dimensionless in [0, 1]. This is a density-sensitive quality "
"diagnostic, not an orientation phenotype.",
)
LONG_RANGE_ROTATION_SUPPORT_MASK_DENSE = Entry(
"LongRangeRotationSupport-Mask-Dense",
"Fraction of fixed-lag ring-sector comparison cells assigned to the dense "
"ring (core_end .. dense_end radii) region that have reliable orientation "
"estimates at both radii. Dimensionless in [0, 1]. This is a "
"density-sensitive quality diagnostic, not an orientation phenotype.",
)
LONG_RANGE_ROTATION_SUPPORT_MASK_SPARSE = Entry(
"LongRangeRotationSupport-Mask-Sparse",
"Fraction of fixed-lag ring-sector comparison cells assigned to the sparse "
"ring (dense_end .. sparse_end radii) region that have reliable orientation "
"estimates at both radii. Dimensionless in [0, 1]. This is a "
"density-sensitive quality diagnostic, not an orientation phenotype.",
)
LONG_RANGE_ROTATION_MASK_DENSE_TO_SPARSE = Entry(
"LongRangeRotation-Mask-DenseToSparse",
"Equal-sector mean absolute seam-safe axial difference between the broad "
"Dense-zone and Sparse-zone radial-relative fiber means. Reported in degrees "
"in [0, 90]. Only 10-degree sectors reliable in both zones contribute, and "
"each paired sector receives equal weight. This measures accumulated "
"zone-to-zone rotation without detecting individual branches.",
)
SIGNED_LONG_RANGE_ROTATION_MASK_DENSE_TO_SPARSE = Entry(
"SignedLongRangeRotation-Mask-DenseToSparse",
"Signed mean Dense-to-Sparse axial change over paired reliable 10-degree "
"sectors, in degrees in [-90, 90]. Positive means clockwise and negative "
"means counterclockwise radial-relative rotation while moving outward in "
"image coordinates. Opposing sector rotations cancel.",
)
LONG_RANGE_ROTATION_SUPPORT_MASK_DENSE_TO_SPARSE = Entry(
"LongRangeRotationSupport-Mask-DenseToSparse",
"Fraction of the 36 fixed 10-degree sectors with reliable radial-relative "
"orientation estimates in both the Dense and Sparse zones. Dimensionless in "
"[0, 1]. This is a density-sensitive quality diagnostic, not an orientation "
"phenotype.",
)
ZONE_SEGMENTATION_METHOD_CODE = Entry(
"ZoneSegmentationMethodCode",
"Zone resolver provenance: 0 is legacy colony-ness, 1 is exact "
"two-change Method B, 2 is collapsed one-change Method B, and 4 is "
"canonical failure with missing zone measurements. This is a "
"dimensionless categorical code.",
)
CORE_ZONE_END_RADIUS = Entry(
"CoreZoneEndRadius",
"Outer radius in pixels of the operational CoreZone, which includes "
"the inoculum and any inner region without resolvable branch orientation.",
)
DENSE_RADIUS = Entry(
"DenseRadius",
"Outer radius in pixels of the Method B DenseZone. It equals "
"CoreZoneEndRadius for a collapsed one-change solution.",
)
OUTER_RADIUS = Entry(
"OuterRadius",
"Exact outer measurement radius in pixels selected by "
"outer_zone_percentile.",
)
FULL_EXTENT_RADIUS = Entry(
"FullExtentRadius",
"Maximum target-mask radius in pixels before percentile clipping.",
)
OUTER_ZONE_PERCENTILE = Entry(
"OuterZonePercentile",
"Configured target-mask radial percentile used as the canonical outer "
"measurement boundary. This is a dimensionless percentage.",
)
OUTER_ZONE_RETAINED_MASK_FRACTION = Entry(
"OuterZoneRetainedMaskFraction",
"Fraction of target-mask pixels at or inside the configured outer "
"measurement boundary. This is a dimensionless fraction in [0, 1].",
)
ZONE_SUPPORTED_RING_FRACTION = Entry(
"ZoneSupportedRingFraction",
"Fraction of center-origin rings satisfying the bridged Method B "
"crossing, resultant, and coherence support gate.",
)
ZONE_CHANGE_POINT_OBJECTIVE = Entry(
"ZoneChangePointObjective",
"Within-segment sum of squared error for the selected exact or "
"collapsed Method B partition in dimensionless standardized-feature "
"units.",
)
ZONE_CHANGE_POINT_RING_COUNT = Entry(
"ZoneChangePointRingCount",
"Number of center-origin Sholl-style rings fitted by Method B.",
)
ZONE_CHANGE_POINT_MINIMUM_SEGMENT = Entry(
"ZoneChangePointMinimumSegment",
"Configured minimum number of rings in each Method B segment.",
)
# Preserve member-level access for callers that imported the former legacy enum.
# The diagnostic class contains every former member plus the new opt-in fields.
# New code should use the explicit primary/diagnostic names above.
ORIENTATION_ZONES = ORIENTATION_ZONE_DIAGNOSTIC
