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Add average and fix bug for cartesian data #166

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merged 3 commits into from
Jul 19, 2024
Merged

Add average and fix bug for cartesian data #166

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6b62e35
Add average and fix bug for cartesian data
chaithyagr Jul 19, 2024
a9e26cf
Added codes
chaithyagr Jul 19, 2024
f9aaa04
Fix style
chaithyagr Jul 19, 2024
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4 changes: 4 additions & 0 deletions src/mrinufft/io/nsp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -404,6 +404,7 @@ def read_trajectory(
def read_arbgrad_rawdat(
filename: str,
removeOS: bool = False,
doAverage: bool = True,
squeeze: bool = True,
slice_num: int | None = None,
contrast_num: int | None = None,
Expand All @@ -417,6 +418,8 @@ def read_arbgrad_rawdat(
The path to the Siemens MRI file.
removeOS : bool, optional
Whether to remove the oversampling, by default False.
doAverage : bool, optional
Whether to average the data acquired along NAve dimension, by default True.
squeeze : bool, optional
Whether to squeeze the dimensions of the data, by default True.
slice_num : int, optional
Expand Down Expand Up @@ -447,6 +450,7 @@ def read_arbgrad_rawdat(
data, hdr, twixObj = read_siemens_rawdat(
filename=filename,
removeOS=removeOS,
doAverage=doAverage,
squeeze=squeeze,
slice_num=slice_num,
contrast_num=contrast_num,
Expand Down
8 changes: 7 additions & 1 deletion src/mrinufft/io/siemens.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@
def read_siemens_rawdat(
filename: str,
removeOS: bool = False,
doAverage: bool = True,
squeeze: bool = True,
return_twix: bool = True,
slice_num: int | None = None,
Expand All @@ -21,6 +22,8 @@ def read_siemens_rawdat(
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
Expand Down Expand Up @@ -61,12 +64,14 @@ def read_siemens_rawdat(
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),
"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.")
Expand All @@ -92,6 +97,7 @@ def read_siemens_rawdat(
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
Expand Down
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