Merge branch 'spectro' into 'master'

Spectro

See merge request reconframe/precon!12

examples/spectro_sv_recon.py

@@ -0,0 +1,60 @@
+# ----------------------------------------------------------------------------------------
+# spectro_recon
+# ----------------------------------------------------------------------------------------
+# A simple reconstruction for single-voxel spectroscopy data
+#
+# Args:
+#        rawfile (required)    : The path to the Philips rawfile to be reconstructed
+#        output_path (optional): The output path where the results are stored
+
+import argparse
+from pathlib import Path
+
+from scipy.io import savemat
+
+import precon as pr
+
+parser = argparse.ArgumentParser(description="normal recon")
+parser.add_argument("rawfile", help="path to the raw or lab file")
+parser.add_argument(
+    "--output-path", default="./", help="path where the output is saved"
+)
+args = parser.parse_args()
+
+# read parameter
+pars = pr.Parameter(Path(args.rawfile))
+
+# define what to read
+parameter2read = pr.Parameter2Read(pars.labels)
+
+# enable performance logging (reconstruction times)
+pars.performance_logging = True
+
+# dictionary for matlab export
+mdic = dict()
+
+# reconstruct the first mix and stack
+parameter2read.stack = 0
+parameter2read.mix = 0
+
+# read data
+with open(pars.rawfile, "rb") as raw:
+    data, labels = pr.read(raw, parameter2read, pars.labels, pars.coil_info, oversampling_removal=False)
+
+data, labels = pr.sort(data, labels, immediate_averaging=True, zeropad=(False, False, False))
+
+# determine the oversampling factor and remove oversampling
+cur_recon_resolution = pars.get_recon_resolution()
+xovs = pr.get_data_size(data)[pr.Enums.X_DIM] / cur_recon_resolution[pr.Enums.X_DIM]
+data = pr.spectro_downsample(data, xovs)
+
+# combine coils with a svd combination
+data = pr.spectro_combine_coils(data)
+
+# FFT
+data = pr.k2i(data, axis=(0, 1, 2))
+
+# save data in .mat format
+mdic[f"data"] = data
+
+savemat(Path(args.output_path) / "data.mat", mdic)