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WIP: Bval error check #1133

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WIP: Bval error check #1133

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89f6f8e
Adds initial bval error checking
teresamg May 2, 2024
370f32a
Reverts other changes
teresamg May 2, 2024
16fecec
Reverts other changes
teresamg May 2, 2024
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55 changes: 55 additions & 0 deletions AFQ/api/participant.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,9 @@
from AFQ.utils.path import apply_cmd_to_afq_derivs
from AFQ.viz.utils import BEST_BUNDLE_ORIENTATIONS, trim, get_eye

from AFQ.definitions.image import ScalarImage
import dipy.core.gradients as dpg


__all__ = ["ParticipantAFQ"]

Expand Down Expand Up @@ -98,6 +101,58 @@ def __init__(self,
self.logger = logging.getLogger('AFQ')
self.output_dir = output_dir

"""
bmag : int
From dipy.core.gradients:
The order of magnitude that the bvalues have to differ to be
considered an unique b-value. B-values are also rounded up to
this order of magnitude. Default: derive this value from the
maximal b-value provided: $bmag=log_{10}(max(bvals)) - 1$.
"""

if "bmag" not in kwargs:
kwargs.bmag = None

gtab = dpg.gradient_table(bval_file, bvec_file)
unique_bvals = dpg.unique_bvals_magnitude(gtab.bvals, kwargs.bmag)

if len(unique_bvals) < 3:
if "scalars" in kwargs:
for ii, scalar in enumerate(kwargs["scalars"]):
if scalar == "dki_fa":
# kwargs["scalars"][ii] = "dti_fa"
# self.logger.info("Not enough bvals, dki -> dti")
raise ValueError("Not enough bvals for dki_fa")
if scalar == "dki_md":
# kwargs["scalars"][ii] = "dti_md"
# self.logger.info("Not enough bvals, dki -> dti")
raise ValueError("Not enough bvals for dki_md")
if "tracking_params" in kwargs:
if "seed_mask" in kwargs["tracking_params"]:
seed_mask = kwargs["tracking_params"]["seed_mask"]
if seed_mask == ScalarImage("dki_fa"):
# kwargs["tracking_params"]["seed_mask"] = \
# ScalarImage("dti_fa")
# self.logger.info("Not enough bvals, dki -> dti")
raise ValueError("Not enough bvals for dki_fa")
if seed_mask == ScalarImage("dki_md"):
# kwargs["tracking_params"]["seed_mask"] = \
# ScalarImage("dti_md")
# self.logger.info("Not enough bvals, dki -> dti")
raise ValueError("Not enough bvals for dki_md")
if "stop_mask" in kwargs["tracking_params"]:
stop_mask = kwargs["tracking_params"]["stop_mask"]
if stop_mask == ScalarImage("dki_fa"):
# kwargs["tracking_params"]["stop_mask"] = \
# ScalarImage("dti_fa")
# self.logger.info("Not enough bvals, dki -> dti")
raise ValueError("Not enough bvals for dki_fa")
if stop_mask == ScalarImage("dki_md"):
# kwargs["tracking_params"]["stop_mask"] = \
# ScalarImage("dti_md")
# self.logger.info("Not enough bvals, dki -> dti")
raise ValueError("Not enough bvals for dki_md")

self.kwargs = dict(
dwi_path=dwi_data_file,
bval=bval_file,
Expand Down