def create_CRANE_denoised_file(tof, param_set1, param_set2):
ms1_denoiser = initialise_denoiser_crane(param_set1)
ms2_denoiser = initialise_denoiser_crane(param_set2)
tof_path = tof_dir + tof
if ms1_denoiser.levels > 7:
split_size = ms1_denoiser.levels ** 2
else:
split_size = 128
if len(tof_path) > 0:
denoiser = App(
tof_fname=tof_path,
srl_paths=[srl_path, irt_srl_path],
denoiser=ms2_denoiser,
mass_range_calculator=MassRangeCalculatorNonOverlappingPPMFullWidth(
ppm_full_width=100,
split_size=split_size,
),
ms1_denoiser=ms1_denoiser, # None = same as MS2
denoised_fname=tof_path.replace(
'.tof',
'.crane_MS1_{}_MS2_{}_64var.tof'.format(param_set1, param_set2)
),
window_name=None,
include_ms1=True,
)
if not os.path.isfile(denoiser.denoised_fname):
print('Denoising:', denoiser.denoised_fname)
denoiser.run()
return denoiser.denoised_fname + ' created successfully'
else:
return denoiser.denoised_fname + ' already exists'
def create_BEADS_denoised_file(tof):
ms1_denoiser = BEADS()
ms2_denoiser = BEADS()
tof_path = tof_dir + tof
split_size = 128
if len(tof_path) > 0:
denoiser = App(
tof_fname=tof_path,
srl_paths=[srl_path, irt_srl_path],
denoiser=ms2_denoiser,
mass_range_calculator=MassRangeCalculatorNonOverlappingPPMFullWidth(
ppm_full_width=100,
split_size=split_size,
),
ms1_denoiser=ms1_denoiser, # None = same as MS2
denoised_fname=tof_path.replace('.tof', '.BEADS_64fix.tof'),
window_name=None,
include_ms1=True,
)
if not os.path.isfile(denoiser.denoised_fname):
print('Denoising:', denoiser.denoised_fname)
denoiser.run()
return denoiser.denoised_fname + ' created successfully'
else:
return denoiser.denoised_fname + ' already exists'