def _getPolarProjection(self, pos):
"""
Return the polar projection of the image at the given position.
pos (tuple of 2 floats): position (must be part of the ._sempos
returns DataArray: the polar projection
"""
if pos in self._polar:
polard = self._polar[pos]
else:
# Compute the polar representation
data = self._sempos[pos]
try:
if numpy.prod(data.shape) > (1280 * 1080):
# AR conversion fails one very large images due to too much
# memory consumed (> 2Gb). So, rescale + use a "degraded" type that
# uses less memory. As the display size is small (compared
# to the size of the input image, it shouldn't actually
# affect much the output.
logging.info(
"AR image is very large %s, will convert to "
"azymuthal projection in reduced precision.",
data.shape)
y, x = data.shape
if y > x:
small_shape = 1024, int(round(1024 * x / y))
else:
small_shape = int(round(1024 * y / x)), 1024
# resize
data = img.rescale_hq(data, small_shape)
dtype = numpy.float16
else:
dtype = None # just let the function use the best one
size = min(min(data.shape) * 2, 1134)
# TODO: First compute quickly a low resolution and then
# compute a high resolution version.
# TODO: could use the size of the canvas that will display
# the image to save some computation time.
bg_data = self.background.value
if bg_data is None:
# Simple version: remove the background value
data0 = polar.ARBackgroundSubtract(data)
else:
data0 = img.Subtract(data, bg_data) # metadata from data
# 2 x size of original image (on smallest axis) and at most
# the size of a full-screen canvas
polard = polar.AngleResolved2Polar(data0,
size,
hole=False,
dtype=dtype)
self._polar[pos] = polard
except Exception:
logging.exception("Failed to convert to azymuthal projection")
return data # display it raw as fallback
return polard
def test_background_substraction_precomputed(self):
"""
Test clean up before polar conversion
"""
data = self.data
C, T, Z, Y, X = data[0].shape
data[0].shape = Y, X
clean_data = polar.ARBackgroundSubtract(data[0])
result = polar.AngleResolved2Polar(clean_data, 201)
desired_output = hdf5.read_data("substracted_background_image.h5")
C, T, Z, Y, X = desired_output[0].shape
desired_output[0].shape = Y, X
numpy.testing.assert_allclose(result, desired_output[0], rtol=1e-04)
def test_background_substraction_float_input(self):
"""
Tests for input of DataArray with float ndarray.
"""
data = self.data
data[0] = data[0].astype(numpy.float)
C, T, Z, Y, X = data[0].shape
data[0].shape = Y, X
clean_data = polar.ARBackgroundSubtract(data[0])
result = polar.AngleResolved2Polar(clean_data, 201)
desired_output = hdf5.read_data("substracted_background_image.h5")
C, T, Z, Y, X = desired_output[0].shape
desired_output[0].shape = Y, X
numpy.testing.assert_allclose(result, desired_output[0], rtol=1e-04)
def test_background_substraction_int8_input(self):
"""
Tests for input of DataArray with int8 ndarray.
"""
data = self.data
# scipy.misc.bytescale(data)
data[0] = data[0].astype(numpy.int64)
data[0] = numpy.right_shift(data[0], 8)
data[0] = data[0].astype(numpy.int8)
C, T, Z, Y, X = data[0].shape
data[0].shape = Y, X
clean_data = polar.ARBackgroundSubtract(data[0])
result = polar.AngleResolved2Polar(clean_data, 201)
desired_output = polar.AngleResolved2Polar(data[0].astype(float), 201)
numpy.testing.assert_allclose(result, desired_output, rtol=1)