def lmlabel(self, threshold=0):
""" Label pixels using the localmax assigment code
Fills in:
self.nlabels = number of peaks per frame
self.labels = peak labels (should be unique)
self.total_labels = total number of peaks
"""
self.nlabels = np.zeros(len(self.nnz), np.int32)
self.labels = np.zeros(len(self.row), "i")
# temporary workspaces
npxmax = self.nnz.max()
vmx = np.zeros(npxmax, np.float32)
imx = np.zeros(npxmax, 'i')
nl = 0
# TODO: run this in parallel with threads?
for i, npx in enumerate(self.nnz):
s = self.ipt[i]
e = self.ipt[i + 1]
if npx > 0:
self.nlabels[i] = cImageD11.sparse_localmaxlabel(
self.intensity[s:e], self.row[s:e], self.col[s:e],
vmx[:npx], imx[:npx], self.labels[s:e])
assert (self.labels[s:e] > 0).all()
self.labels[s:e] += nl
else:
self.nlabels[i] = 0
nl += self.nlabels[i]
self.total_labels = nl
def sparse_localmax(frame, label_name="localmax", data_name="intensity"):
labels = np.zeros(frame.nnz, "i")
vmx = np.zeros(frame.nnz, np.float32)
imx = np.zeros(frame.nnz, 'i')
nlabel = cImageD11.sparse_localmaxlabel(frame.pixels[data_name], frame.row,
frame.col, vmx, imx, labels)
frame.set_pixels(label_name, labels, {"nlabel": nlabel})
return nlabel
def test1(self):
import h5py
nnz = self.row.shape[0]
labels = np.zeros(nnz, "i")
vmx = np.zeros(nnz, np.float32)
imx = np.zeros(nnz, 'i')
nlabel = cImageD11.sparse_localmaxlabel(self.vals, self.row, self.col,
vmx, imx, labels)
self.assertTrue(nlabel > 0)
def sparse_localmax(frame, label_name="localmax", data_name="intensity"):
labels = np.zeros(frame.nnz, "i")
vmx = np.zeros(frame.nnz, np.float32)
imx = np.zeros(frame.nnz, 'i')
nlabel = cImageD11.sparse_localmaxlabel(frame.pixels[data_name].data,
frame.row, frame.col, vmx, imx,
labels)
px = Container(labels, **{"data_name": data_name, "nlabel": nlabel})
frame.set_pixels(label_name, px)
def __init__(self, frame, name='data'):
"""
adds an array names mxlabels
"""
sparse_labelling.__init__(self, frame, name=name)
vmx = np.zeros(self.frame.nnz, np.float32)
imx = np.zeros(self.frame.nnz, 'i')
self.nlabel = cImageD11.sparse_localmaxlabel(
self.frame.pixels[self.name], self.frame.row, self.frame.col, vmx,
imx, self.labels)