"""Siemens specific rawdat reader, wrapper over pymapVBVD."""
from __future__ import annotations
import numpy as np
[docs]
def read_siemens_rawdat(
filename: str,
removeOS: bool = False,
doAverage: bool = True,
squeeze: bool = True,
return_twix: bool = True,
slice_num: int | None = None,
contrast_num: int | None = None,
): # pragma: no cover
"""Read raw data from a Siemens MRI file.
Parameters
----------
filename : str
The path to the Siemens MRI file.
removeOS : bool, optional
Whether to remove the oversampling, by default False.
doAverage : bool, option
Whether to average the data acquired along NAve dimension.
squeeze : bool, optional
Whether to squeeze the dimensions of the data, by default True.
data_type : str, optional
The type of data to read, by default 'ARBGRAD_VE11C'.
return_twix : bool, optional
Whether to return the twix object, by default True.
slice_num : int, optional
The slice to read, by default None. This applies for 2D data.
contrast_num: int, optional
The contrast to read, by default None.
Returns
-------
data: ndarray
Imported data formatted as n_coils X n_samples X n_slices X n_contrasts
hdr: dict
Extra information about the data parsed from the twix file
Raises
------
ImportError
If the mapVBVD module is not available.
Notes
-----
This function requires the mapVBVD module to be installed.
You can install it using the following command:
`pip install pymapVBVD`
"""
try:
from mapvbvd import mapVBVD
except ImportError as err:
raise ImportError(
"The mapVBVD module is not available. Please install "
"it along with the [extra] dependencies "
"or using `pip install pymapVBVD`."
) from err
twixObj = mapVBVD(filename)
if isinstance(twixObj, list):
twixObj = twixObj[-1]
twixObj.image.flagRemoveOS = removeOS
twixObj.image.flagDoAverage = doAverage
hdr = {
"n_coils": int(twixObj.image.NCha),
"n_shots": int(twixObj.image.NLin) * int(twixObj.image.NPar),
"n_contrasts": int(twixObj.image.NSet),
"n_adc_samples": int(twixObj.image.NCol),
"n_slices": int(twixObj.image.NSli),
"n_average": int(twixObj.image.NAve),
}
if slice_num is not None and hdr["n_slices"] < slice_num:
raise ValueError("The slice number is out of bounds.")
if contrast_num is not None and hdr["n_contrasts"] < contrast_num:
raise ValueError("The contrast number is out of bounds.")
# Shape : NCol X NCha X NLin X NAve X NSli X NPar X ..., NSet
if slice_num is not None and contrast_num is not None:
raw_kspace = twixObj.image[
(slice(None),) * 4 + (slice_num,) + (slice(None),) * 4 + (contrast_num,)
]
elif slice_num is not None:
raw_kspace = twixObj.image[(slice(None),) * 4 + (slice_num,)]
elif contrast_num is not None:
raw_kspace = twixObj.image[(slice(None),) * 9 + (contrast_num,)]
else:
raw_kspace = twixObj.image[""]
if squeeze:
raw_kspace = np.squeeze(raw_kspace)
data = np.moveaxis(raw_kspace, 0, 2)
data = data.reshape(
hdr["n_coils"],
hdr["n_shots"] * hdr["n_adc_samples"],
hdr["n_slices"] if slice_num is None else 1,
hdr["n_contrasts"] if contrast_num is None else 1,
hdr["n_average"] if hdr["n_average"] > 1 and not doAverage else 1,
)
if return_twix:
return data, hdr, twixObj
return data, hdr
