def test_create_header_string_has_newline(self):
header_names = [
'_rlnCoordinateX', '_rlnCoordinateY', '_rlnHelicalTubeID',
'_rlnHelicalTrackLength'
]
header_string = write_star.create_header_string(header_names)
assert (header_string[-1] == '\n')
def test_create_header_string_is_string(self):
header_names = [
'_rlnCoordinateX', '_rlnCoordinateY', '_rlnHelicalTubeID',
'_rlnHelicalTrackLength'
]
header_string = write_star.create_header_string(header_names)
assert (isinstance(header_string, basestring))
def test_create_header_string_check_content_number(self):
header_names = [
'_rlnCoordinateX', '_rlnCoordinateY', '_rlnHelicalTubeID',
'_rlnHelicalTrackLength'
]
header_string = write_star.create_header_string(header_names)
for idx, entry in enumerate(header_names):
assert (str(idx + 1) in header_string)
def main(file_name,
tolerance_psi,
tolerance_theta,
tolerance_filament,
window_size,
plot=False,
typ='sphire',
params=None,
index=None,
output_dir=None):
"""Start calculation"""
if output_dir is None:
output_dir = '.'
# Check angle range, import arrays
if typ == 'sphire':
angle_max = 360
angle_min = 0
original_stack = read_sphire.get_sphire_stack(file_name)
parameter = read_sphire.get_sphire_file('params', params)
indices = read_sphire.get_sphire_file('index', index)
substack = create_substack(original_stack, indices)
array = combine_arrays(substack, parameter)
id_name = 'filament'
particle_name = 'data_n'
micrograph_name = 'ptcl_source_image'
angle_name = ['psi', 'theta']
angle_name_new = ['psi_prior', 'theta_prior']
output_names = list(parameter.dtype.names)
elif typ == 'relion':
angle_max = 180
angle_min = -180
array, header, path = read_star.import_star_file(file_name)
id_name = '_rlnHelicalTubeID'
micrograph_name = '_rlnMicrographName'
particle_name = '_rlnImageName'
angle_name = ['_rlnAnglePsi', '_rlnAngleTilt']
angle_name_new = ['_rlnAnglePsiPrior', '_rlnAngleTiltPrior']
output_names = list(array.dtype.names) + angle_name_new
else:
print('Unreachable code!')
return 'Unreachable code!'
# Add the particle number to the array
array_order = 'particle_order'
order_numbers = np.arange(len(array))
array = add_column(array, order_numbers, array_order)
# Sort the array
array = np.sort(array, order=[micrograph_name, id_name, particle_name])
for angle in angle_name:
# Add rotated data column to the array
data_rotated_name = 'data_rotated_{0}'.format(angle)
array = add_column(array, array[angle], data_rotated_name)
print(np.shape(array))
filament_array = calculations.get_filaments(array, id_name)
array_modified = None
if plot:
do_plot = True
else:
do_plot = False
for angle, angle_new, tolerance in zip(angle_name, angle_name_new,
[tolerance_psi, tolerance_theta]):
print(angle)
data_rotated_name = 'data_rotated_{0}'.format(angle)
for idx, filament in enumerate(filament_array):
if do_plot:
if idx % 10000 == 0:
plot = True
else:
plot = False
if idx % 10000 == 0:
print('{0}%'.format(idx * 100 / len(filament_array)),
len(filament_array))
plot = True
else:
plot = False
if plot:
calculations.plot_polar('raw_data',
filament[data_rotated_name],
0,
angle_max,
0,
output=output_dir)
filament[
data_rotated_name] = calculations.subtract_and_adjust_angles(
filament[data_rotated_name], 0, 180, -180)
filament[
data_rotated_name], rotate_angle = calculations.rotate_angles(
filament[data_rotated_name], plot, output=output_dir)
is_outlier, filament[
data_rotated_name], rotate_angle, inside_tol_idx, outside_tol_idx = calculations.get_filament_outliers(
data_rotated=filament[data_rotated_name],
rotate_angle=rotate_angle,
tolerance=tolerance,
tolerance_filament=tolerance_filament,
plot=plot,
output=output_dir)
mean_array = calculations.calculate_mean_prior(
input_array=filament[data_rotated_name],
window_size=window_size,
inside_tolerance_idx=inside_tol_idx,
outside_tolerance_idx=outside_tol_idx,
plot=plot,
output=output_dir)
if plot:
calculations.plot_polar('mean_array',
mean_array,
rotate_angle,
180,
-180,
output=output_dir)
mean_array = calculations.subtract_and_adjust_angles(
mean_array, -rotate_angle, angle_max, angle_min)
if plot:
calculations.plot_polar('mean_array',
mean_array,
0,
angle_max,
angle_min,
output=output_dir)
filament = add_column(filament, mean_array, angle_new)
if idx == 0:
new_array = filament
else:
new_array = np.append(new_array, filament)
array = add_column(array, new_array[angle_new], angle_new)
if typ == 'sphire':
array = swap_columns(array, angle, angle_new)
else:
pass
# Sort the array back to the original order
array = np.sort(array, order=array_order)
if not os.path.exists(output_dir):
os.mkdir(output_dir)
if typ == 'relion':
header_string = write_star.create_header_string(output_names)
write_star.write_star_file(array[output_names], header_string,
'{0}/TEST.star'.format(output_dir))
elif typ == 'sphire':
write_sphire.write_params_file(
array, output_names, '{0}/{1}.txt'.format(output_dir, params))
else:
pass
def main(file_name, tolerance_psi, tolerance_theta, tolerance_filament, window_size, plot=False, typ='sphire', params=None, index=None, output_dir=None):
"""Start calculation"""
if output_dir is None:
output_dir = '.'
# Check angle range, import arrays
if typ == 'sphire':
angle_max = 360
angle_min = 0
original_stack = read_sphire.get_sphire_stack(file_name)
parameter = read_sphire.get_sphire_file('params', params)
indices = read_sphire.get_sphire_file('index', index)
substack = create_substack(original_stack, indices)
array = combine_arrays(substack, parameter)
id_name = 'filament'
particle_name = 'data_n'
micrograph_name = 'ptcl_source_image'
angle_name = ['theta', 'psi']
angle_name_new = [['theta_prior', 'theta_std'], ['psi_prior', 'psi_std']]
output_names = list(parameter.dtype.names)
for entry in angle_name_new:
output_names += entry
elif typ == 'relion':
angle_max = 180
angle_min = -180
array, header, path = read_star.import_star_file(file_name)
id_name = '_rlnHelicalTubeID'
micrograph_name = '_rlnMicrographName'
particle_name = '_rlnImageName'
angle_name = ['_rlnAngleTilt', '_rlnAnglePsi']
angle_name_new = [['_rlnAngleTiltPrior', '_rlnAngleTiltStd'], ['_rlnAnglePsiPrior', '_rlnAnglePsiStd']]
output_names = list(array.dtype.names)
for entry in angle_name_new:
output_names.append(entry[0])
else:
print('Unreachable code!')
return 'Unreachable code!'
# Add the particle number to the array and sort it by filament and particle
order_idx = 'particle_order'
ordered_numbers = np.arange(len(array))
array = add_column(array, ordered_numbers, order_idx)
array = np.sort(array, order=[micrograph_name, id_name, particle_name])
filament_array = calculations.get_filaments(array, id_name)
if plot:
do_plot = True
else:
do_plot = False
for angle, angle_new, tolerance in zip(angle_name, angle_name_new, [tolerance_psi, tolerance_theta]):
for idx, filament in enumerate(filament_array):
if do_plot:
if idx % 1000 == 0:
plot = True
else:
plot = False
mean_list, std_list = wrapped_distribution(filament[angle])
for name, entry in zip(angle_new, [mean_list, std_list]):
filament = add_column(filament, entry, name)
if idx == 0:
new_array = filament
else:
new_array = np.append(new_array, filament)
if plot:
calculations.plot_polar('raw_data', filament[angle], 0, angle_max, 0, output=output_dir)
calculations.plot_polar('mean', filament[angle], 0, angle_max, 0, mean=np.degrees(mean_list[0]), output=output_dir)
calculations.plot_polar('sigma1', filament[angle], 0, angle_max, 0, mean=np.degrees(mean_list[0]), output=output_dir, tol=np.degrees(std_list[0]))
calculations.plot_polar('sigma2', filament[angle], 0, angle_max, 0, mean=np.degrees(mean_list[0]), output=output_dir, tol=2*np.degrees(std_list[0]))
for idx, name in enumerate(angle_new):
array = add_column(array, new_array[name], name)
# Sort the array back to the original order
array = np.sort(array, order=order_idx)
if not os.path.exists(output_dir):
os.mkdir(output_dir)
if typ == 'relion':
header_string = write_star.create_header_string(output_names)
write_star.write_star_file(array[output_names], header_string, '{0}/TEST.star'.format(output_dir))
elif typ == 'sphire':
write_sphire.write_params_file(array, output_names, '{0}/TEST.txt'.format(output_dir))
else:
pass
def main(file_name,
data,
tolerance_psi,
tolerance_theta,
tolerance_filament,
window_size,
plot=False,
typ='sphire',
output_dir=None,
params=None):
"""Start calculation"""
# Extract data
array, stack_id, mic_name, filament_name, particle_id, angle_name, output_names, angle_max, angle_min = data
if output_dir is None:
output_dir = '.'
if plot:
do_plot = True
else:
do_plot = False
# Add new angle names to the output dtype
IDX_OLD = 0
IDX_NEW = 1
IDX_ROT = 2
dtype_temp = array.dtype.descr
for angle in angle_name:
dtype_temp.append((angle[IDX_NEW], '<f8'))
dtype_temp.append((angle[IDX_ROT], '<f8'))
output_names.append(angle[IDX_NEW])
# Create a new combined array
array_temp = np.empty(len(array), dtype=dtype_temp)
for name in array.dtype.names:
array_temp[name] = array[name]
for angle in angle_name:
array_temp[angle[IDX_ROT]] = np.copy(array[angle[IDX_OLD]])
# Sort the array and remove array_temp from scope
array = np.sort(array_temp, order=[mic_name, filament_name, particle_id])
del array_temp
# Split the array into filaments
filament_array = calculations.get_filaments(array=array,
filament_name=filament_name)
# Loop over both angles and their tolerance
for angle, tolerance in zip(angle_name, [tolerance_psi, tolerance_theta]):
# Array names
angle_old = angle[IDX_OLD]
angle_prior = angle[IDX_NEW]
angle_rot = angle[IDX_ROT]
print(angle_old)
# Loop over all filaments
for idx, filament in enumerate(filament_array):
# Do plot if necessary
if do_plot:
if idx % 1000 == 0:
plot = True
else:
plot = False
if plot:
calculations.plot_polar('raw_data',
filament[angle_rot],
0,
angle_max,
0,
output=output_dir)
# Shift the angle range from 180 to -180
calculations.subtract_and_adjust_angles(filament[angle_rot], 0,
180, -180)
# Rotate the angle range, so that the median is the new center
rotate_angle = calculations.rotate_angles(filament[angle_rot],
plot,
output=output_dir)
# Calculate the indices of outliers
is_outlier, rotate_angle, inside_tol_idx, outside_tol_idx = calculations.get_filament_outliers(
data_rotated=filament[angle_rot],
rotate_angle=rotate_angle,
tolerance=tolerance,
tolerance_filament=tolerance_filament,
plot=plot,
output=output_dir)
# Calculate the new prior values
calculations.calculate_mean_prior(
input_array=filament[angle_rot],
mean_array=filament[angle_prior],
window_size=window_size,
inside_tolerance_idx=inside_tol_idx,
outside_tolerance_idx=outside_tol_idx,
plot=plot,
output=output_dir)
if plot:
calculations.plot_polar('mean_array',
filament[angle_prior],
rotate_angle,
180,
-180,
output=output_dir)
# Adjust the angles to match the aimed angle range
calculations.subtract_and_adjust_angles(filament[angle_prior],
-rotate_angle, angle_max,
angle_min)
if plot:
calculations.plot_polar('mean_array',
filament[angle_prior],
0,
angle_max,
angle_min,
output=output_dir)
# Combine the filaments to one array
array_out = np.empty(len(array), dtype=array.dtype.descr)
index = 0
for entry in filament_array:
for row in entry:
array_out[index] = row
index += 1
# Sort the array back to the original order
array_out = np.sort(array_out, order=stack_id)
# Write output
if not os.path.exists(output_dir):
os.mkdir(output_dir)
if typ == 'relion':
header_string = write_star.create_header_string(output_names)
write_star.write_star_file(
array_out[output_names], header_string,
'{0}_prior.star'.format(file_name.split('.star')[0]))
elif typ == 'sphire':
write_sphire.write_params_file(
array_out, output_names,
'{0}_prior.txt'.format(params.split('.txt')[0]))
else:
assert (False)