def diagnose_center(args):
"""
Diagnostic tools to find rotation center.
Helps finding the rotation center manually by
visual inspection of the selected reconstructions
with different centers. The outputs for different
centers are put into ``data/diagnose`` directory
and the corresponding center positions are printed
so that one can skim through the images and
select the best.
Parameters
----------
data : ndarray
Input data.
slice_no : scalar, optional
The index of the slice to be used for diagnostics.
center_start, center_end, center_step : scalar, optional
Values of the start, end and step of the center values to
be used for diagnostics.
"""
data, theta, dir_path, slice_no, center_start, center_end, center_step = args
num_projections = data.shape[0]
num_slices = data.shape[1]
num_pixels = data.shape[2]
# Define diagnose region.
if slice_no is None:
slice_no = num_slices / 2
if center_start is None:
center_start = (num_pixels / 2) - 20
if center_end is None:
center_end = (num_pixels / 2) + 20
if center_step is None:
center_step = 1
center_step /= 2.
# Make preperations for the slices and corresponding centers.
slice_data = data[:, slice_no, :]
center = np.arange(center_start, center_end, center_step)
num_center = center.size
stacked_slices = np.zeros((num_projections, num_center, num_pixels))
for m in range(num_center):
stacked_slices[:, m, :] = slice_data
# Reconstruct the same slice with different centers.
recon = Gridrec(stacked_slices)
recon.run(stacked_slices, center=center, theta=theta)
# Save it to a temporary directory for manual inspection.
for m in range(center.size):
if m % 2 == 0: # 2 slices same bec of gridrec
img = misc.toimage(recon.data_recon[m, :, :])
file_name = dir_path + str(np.squeeze(center[m])) + ".tif"
img.save(file_name)
def gridrec_wrapper(TomoObj, *args, **kwargs):
if not TomoObj.FLAG_DATA:
logger.warning("optimize rotation center (data missing) [bypassed]")
return
if not TomoObj.FLAG_THETA:
logger.warning("optimize rotation center (angles missing) [bypassed]")
return
# Find center if center is absent.
if not hasattr(TomoObj, 'center'):
TomoObj.center = optimize_center(TomoObj.data, TomoObj.theta)
recon = Gridrec(TomoObj.data, *args, **kwargs)
recon.run(TomoObj.data, center=TomoObj.center, theta=TomoObj.theta)
TomoObj.data_recon = recon.data_recon
TomoObj.gridrec_pars = recon.params
TomoObj.FLAG_DATA_RECON = True
TomoObj.provenance['gridrec'] = (args, kwargs)
logger.info("gridrec reconstruction [ok]")
