def _compute_object_count(self, raw):
data = raw.data()[:, :, 0]
data = skimage.exposure.equalize_adapthist(data)
lm = skimage.feature.peak_local_max(data,
threshold_abs=np.percentile(
data, 95),
min_distance=10)
return len(lm)
def _compute_shape(self, raw):
x, y = np.mgrid[:raw.data().shape[0], :raw.data().shape[1]]
initial = astropy.modeling.models.Gaussian2D(x_stddev=1, y_stddev=1)
fitter = astropy.modeling.fitting.LevMarLSQFitter()
fit = fitter(initial, x, y, raw.data()[:, :, 0])
return fit.x_stddev / fit.y_stddev
def _compute_percentile_95(self, raw):
return np.percentile(raw.data(), 95)
def _compute_mean(self, raw):
return raw.data().mean()
def _compute_shape(self, raw):
x, y = np.mgrid[:raw.data().shape[0], :raw.data().shape[1]]
initial = astropy.modeling.models.Gaussian2D(x_stddev=1, y_stddev=1)
fitter = astropy.modeling.fitting.LevMarLSQFitter()
fit = fitter(initial, x, y, raw.data()[:, :, 0])
return fit.x_stddev / fit.y_stddev
def _compute_percentile_95(self, raw):
return np.percentile(raw.data(), 95)
def _compute_object_count(self, raw):
data = raw.data()[:, :, 0]
data = skimage.exposure.equalize_adapthist(data)
lm = skimage.feature.peak_local_max(data, threshold_abs=np.percentile(data, 95), min_distance=10)
return len(lm)
def _compute_mean(self, raw):
return raw.data().mean()