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Set background_median and background_std to None when no background ROI's present #355

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merged 2 commits into from
Mar 31, 2021
Merged

Set background_median and background_std to None when no background ROI's present #355

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f069364
Set background_median and background_std to None when no background R…
randlet Mar 31, 2021
41b72a7
change background_median to background_mean
randlet Mar 31, 2021
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18 changes: 12 additions & 6 deletions pylinac/ct.py
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Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,7 @@ class HUDiskROI(DiskROI):
def __init__(self, array: np.ndarray, angle: float, roi_radius: float, dist_from_center: float,
phantom_center: Union[tuple, Point], nominal_value: Optional[int] = None,
tolerance: Optional[int] = None,
background_median: Optional[float]=None, background_std: Optional[float]=None):
background_mean: Optional[float]=None, background_std: Optional[float]=None):
"""
Parameters
----------
Expand All @@ -70,13 +70,15 @@ def __init__(self, array: np.ndarray, angle: float, roi_radius: float, dist_from
super().__init__(array, angle, roi_radius, dist_from_center, phantom_center)
self.nominal_val = nominal_value
self.tolerance = tolerance
self.background_median = background_median
self.background_mean = background_mean
self.background_std = background_std

@property
def cnr(self) -> float:
"""The contrast-to-noise value of the HU disk"""
return 2*abs(self.pixel_value - self.background_median) / (self.std + self.background_std)
if self.background_mean is None or self.background_std is None:
return None
return 2*abs(self.pixel_value - self.background_mean) / (self.std + self.background_std)

@property
def value_diff(self) -> float:
Expand Down Expand Up @@ -248,14 +250,18 @@ def _setup_rois(self) -> None:
for name, setting in self.background_roi_settings.items():
self.background_rois[name] = HUDiskROI(self.image, setting['angle_corrected'], setting['radius_pixels'], setting['distance_pixels'],
self.phan_center)
background_median = np.mean([roi.pixel_value for roi in self.background_rois.values()])
background_std = np.std([roi.pixel_value for roi in self.background_rois.values()])
if self.background_rois:
background_mean = np.mean([roi.pixel_value for roi in self.background_rois.values()])
background_std = np.std([roi.pixel_value for roi in self.background_rois.values()])
else:
background_mean = None
background_std = None

for name, setting in self.roi_settings.items():
nominal_value = setting.get('value', 0)
self.rois[name] = HUDiskROI(self.image, setting['angle_corrected'], setting['radius_pixels'], setting['distance_pixels'],
self.phan_center, nominal_value, self.tolerance,
background_median=background_median, background_std=background_std)
background_mean=background_mean, background_std=background_std)

# TODO: better define threshold
def plot_rois(self, axis: plt.Axes, threshold=None) -> None:
Expand Down