Add some extra features to Siemens reader.

src/mrinufft/io/nsp.py

@@ -484,7 +484,7 @@ def read_arbgrad_rawdat(
     if "ARBGRAD_VE11C" in data_type:
         hdr["type"] = "ARBGRAD_GRE"
         hdr["shifts"] = ()
-        for s in [7, 6, 8]:
+        for s in [6, 7, 8]:
             shift = twixObj.search_header_for_val(
                 "Phoenix", ("sWiPMemBlock", "adFree", str(s))
             )

src/mrinufft/io/siemens.py

@@ -42,6 +42,7 @@ def read_siemens_rawdat(
         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
+        This header also contains the ACS data as "acs" if it was found in raw data.
 
     Raises
     ------
@@ -75,7 +76,12 @@ def read_siemens_rawdat(
         "n_slices": int(twixObj.image.NSli),
         "n_average": int(twixObj.image.NAve),
         "orientation": siemens_quat_to_rot_mat(twixObj.image.slicePos[0][-4:]),
+        "acs": None,
     }
+    if "refscan" in twixObj.keys():
+        twixObj.refscan.squeeze = True
+        acs = twixObj.refscan[""].astype(np.complex64)
+        hdr["acs"] = acs.swapaxes(0, 1)
     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:
@@ -97,7 +103,8 @@ def read_siemens_rawdat(
 
     data = data.reshape(
         hdr["n_coils"],
-        hdr["n_shots"] * hdr["n_adc_samples"],
+        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,

src/mrinufft/io/utils.py

@@ -60,3 +60,30 @@ def siemens_quat_to_rot_mat(quat):
         R[2] = -R[2]
     R[-1, -1] = 1
     return R
+
+
+def remove_extra_kspace_samples(kspace_data, num_samples_per_shot):
+    """Remove extra samples from k-space data.
+
+    This function is useful when the k-space data has extra samples
+    mainly as ADC samples at only at specific number of samples.
+    This sometimes leads to a situation where we will have more ADC samples
+    than what is expected.
+
+    Parameters
+    ----------
+    kspace_data : np.ndarray
+        The k-space data ordered as NCha X NShot X NSamples.
+    num_samples_per_shot : int
+        The number of samples per shot in trajectory
+
+    Returns
+    -------
+    np.ndarray
+        The k-space data with extra samples removed.
+    """
+    n_samples = kspace_data.shape[-1]
+    n_extra_samples = n_samples - num_samples_per_shot
+    if n_extra_samples > 0:
+        kspace_data = kspace_data[..., :-n_extra_samples]
+    return kspace_data