def getArrayRegion(self, arr, img=None, axes=(0, 1), **kwds):
"""
Return the result of ROI.getArrayRegion() masked by the elliptical shape
of the ROI. Regions outside the ellipse are set to 0.
"""
# Note: we could use the same method as used by PolyLineROI, but this
# implementation produces a nicer mask.
if kwds["returnMappedCoords"]:
arr, coords = pgROI.getArrayRegion(self, arr, img, axes, **kwds)
else:
arr = pgROI.getArrayRegion(self, arr, img, axes, **kwds)
if arr is None or arr.shape[axes[0]] == 0 or arr.shape[axes[1]] == 0:
return arr
w = arr.shape[axes[0]]
h = arr.shape[axes[1]]
## generate an ellipsoidal mask
mask = np.fromfunction(
lambda x, y: (((x + 0.5) / (w / 2.) - 1)**2 +
((y + 0.5) / (h / 2.) - 1)**2)**0.5 < 1, (w, h))
# reshape to match array axes
if axes[0] > axes[1]:
mask = mask.T
shape = [(n if i in axes else 1) for i, n in enumerate(arr.shape)]
mask = mask.reshape(shape)
if kwds["returnMappedCoords"]:
return arr * mask, coords
else:
return arr * mask
def getArrayRegion(self, data, img, axes=(0, 1), **kwds):
"""
Return the result of ROI.getArrayRegion(), masked by the shape of the
ROI. Values outside the ROI shape are set to 0.
"""
br = self.boundingRect()
if br.width() > 1000:
raise Exception()
sliced = ROI.getArrayRegion(self,
data,
img,
axes=axes,
fromBoundingRect=True,
**kwds)
if kwds.get("returnMappedCoords"):
sliced, mapped = sliced
if img.axisOrder == "col-major":
mask = self.renderShapeMask(sliced.shape[axes[0]],
sliced.shape[axes[1]])
else:
mask = self.renderShapeMask(sliced.shape[axes[1]],
sliced.shape[axes[0]])
mask = mask.T
# reshape mask to ensure it is applied to the correct data axes
shape = [1] * data.ndim
shape[axes[0]] = sliced.shape[axes[0]]
shape[axes[1]] = sliced.shape[axes[1]]
mask = mask.reshape(shape)
if kwds.get("returnMappedCoords"):
return sliced * mask, mapped
else:
return sliced * mask
