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calculate spectrum whitening filter only in the search region #81

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merged 3 commits into from
Jan 26, 2024
Merged

calculate spectrum whitening filter only in the search region #81

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86a2d02
calculate the whitening filter only in the user specified region of i…
McHaillet Jan 24, 2024
62e8ec1
always calculate a new whitening filter, since version 0.3.3 its fast…
McHaillet Jan 26, 2024
c3f77db
test the size of whitening filter upon reducing search box
McHaillet Jan 26, 2024
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12 changes: 10 additions & 2 deletions src/pytom_tm/tmjob.py
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Original file line number Diff line number Diff line change
Expand Up @@ -177,9 +177,17 @@ def __init__(
self.ctf_data = ctf_data
self.whiten_spectrum = whiten_spectrum
self.whitening_filter = self.output_dir.joinpath(f'{self.tomo_id}_whitening_filter.npy')
if self.whiten_spectrum and not self.whitening_filter.exists():
if self.whiten_spectrum:
logging.info('Estimating whitening filter...')
weights = 1 / np.sqrt(power_spectrum_profile(read_mrc(self.tomogram)))
weights = 1 / np.sqrt(
power_spectrum_profile(
read_mrc(self.tomogram)[
self.search_origin[0]: self.search_origin[0] + self.search_size[0],
self.search_origin[1]: self.search_origin[1] + self.search_size[1],
self.search_origin[2]: self.search_origin[2] + self.search_size[2]
]
)
)
weights /= weights.max() # scale to 1
np.save(self.whitening_filter, weights)

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12 changes: 12 additions & 0 deletions tests/test_tmjob.py
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Original file line number Diff line number Diff line change
Expand Up @@ -182,6 +182,18 @@ def test_tm_job_weighting_options(self):
score, angle = job.start_job(0, return_volumes=True)
self.assertEqual(score.shape, job.tomo_shape, msg='TMJob with only whitening filter failed')

# load the whitening filter from previous job to compare against
whitening_filter = np.load(TEST_WHITENING_FILTER)
job = TMJob('0', 10, TEST_TOMOGRAM, TEST_TEMPLATE, TEST_MASK, TEST_DATA_DIR,
angle_increment='90.00', voxel_size=1., whiten_spectrum=True, search_y=[10, 90])
new_whitening_filter = np.load(TEST_WHITENING_FILTER)
self.assertNotEqual(whitening_filter.shape, new_whitening_filter.shape,
msg='After reducing the search region along the largest dimension the whitening filter '
'should have less sampling points')
self.assertEqual(new_whitening_filter.shape, (max(job.search_size) // 2 + 1, ),
msg='The whitening filter does not have the expected size, it should be equal (x // 2) + 1, '
'where x is the largest dimension of the search box.')

# TMJob with none of these weighting options is tested in all other runs in this file.

def test_custom_angular_search(self):
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