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Matrix reader for affine and slice timings in fmr.py using numpy.fromstring method #48

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Matrix reader for affine and slice timings in fmr.py using numpy.fromstring method #48

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ddc7228
update method for reading affine and slice timing arrays
ChengranAA Dec 10, 2023
ab51891
minor fix method for reading affine array
ChengranAA Dec 10, 2023
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30 changes: 3 additions & 27 deletions bvbabel/fmr.py
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Original file line number Diff line number Diff line change
Expand Up @@ -196,24 +196,8 @@ def read_fmr(filename, rearrange_data_axes=True):
info_tra[content[0]] = content[1]
elif content[0] == "NrOfTransformationValues":
info_tra[content[0]] = content[1]

# NOTE(Faruk): I dont like this matrix reader but I don't see a
# more elegant way for now.
nr_values = int(content[1])
affine = []
v = 0 # Counter for values
n = 1 # Counter for lines
while v < nr_values:
line = lines[j + n]
content = line.strip()
content = content.split()
for val in content:
affine.append(float(val))
v += len(content) # Count values
n += 1 # Iterate line
affine = np.reshape(np.asarray(affine), (4, 4))
info_tra["Transformation matrix"] = affine

affine_matrix = np.fromstring(' '.join(lines[j + 1 : j + 1 + (int(content[1]) + 3) // 4 ]), sep=' ').reshape(4, 4)
info_tra["Transformation matrix"] = affine_matrix
# -----------------------------------------------------------------
# This part only contains a single information
elif content[0] == "LeftRightConvention":
Expand All @@ -229,15 +213,7 @@ def read_fmr(filename, rearrange_data_axes=True):
info_multiband[content[0]] = content[1]
elif content[0] == "SliceTimingTableSize":
info_multiband[content[0]] = int(content[1])

# NOTE(Faruk): I dont like this matrix reader but I don't see a
# more elegant way for now.
nr_values = int(content[1])
slice_timings = []
for n in range(1, nr_values+1):
line = lines[j + n]
content = line.strip()
slice_timings.append(float(content))
slice_timings = np.ndarray.tolist(np.fromstring(''.join(lines[j + 1 : j + 1 + int(content[1])]), sep='\n'))
info_multiband["Slice timings"] = slice_timings

elif content[0] == "AcqusitionTime":
Expand Down