Added --save-phase and --suffix parameters to entrypoint

README.md

@@ -182,8 +182,8 @@ if __name__ == "__main__":
     tissue_params = qsm_forward.TissueParams(root_dir="~/data", chi="ChiModelMIX.nii.gz")
 
     recon_params_all = [
-        qsm_forward.ReconParams(voxel_size=voxel_size, session=session, TEs=TEs, TR=TR, flip_angle=flip_angle, suffix=suffix, export_phase=export_phase)
-        for (voxel_size, session, TEs, TR, flip_angle, suffix, export_phase) in [
+        qsm_forward.ReconParams(voxel_size=voxel_size, session=session, TEs=TEs, TR=TR, flip_angle=flip_angle, suffix=suffix, save_phase=save_phase)
+        for (voxel_size, session, TEs, TR, flip_angle, suffix, save_phase) in [
             (np.array([0.64, 0.64, 0.64]), "0p64", np.array([3.5e-3]), 7.5e-3, 40, "T1w", False),
             (np.array([0.64, 0.64, 0.64]), "0p64", np.array([0.004, 0.012, 0.02, 0.028]), 0.05, 15, "T2starw", True),
         ]

qsm_forward/examples/head_phantom_maps.py

@@ -20,8 +20,8 @@
     tissue_params = qsm_forward.TissueParams(root_dir="~/data")
 
     recon_params_all = [
-        qsm_forward.ReconParams(voxel_size=voxel_size, TEs=TEs, TR=TR, flip_angle=flip_angle, suffix=suffix, export_phase=export_phase)
-        for (voxel_size, TEs, TR, flip_angle, suffix, export_phase) in [
+        qsm_forward.ReconParams(voxel_size=voxel_size, TEs=TEs, TR=TR, flip_angle=flip_angle, suffix=suffix, save_phase=save_phase)
+        for (voxel_size, TEs, TR, flip_angle, suffix, save_phase) in [
             (np.array([1.0, 1.0, 1.0]), np.array([0.004, 0.012, 0.02, 0.028]), 0.05, 15, "T2starw", True),
             (np.array([1.0, 1.0, 1.0]), np.array([0.0035]), 0.0075, 40, "T1w", False)
         ]

qsm_forward/main.py

@@ -35,14 +35,16 @@ def argparse_bool(user_in):
         sub_parser.add_argument('--run', default=None),
         sub_parser.add_argument('--TR', default=50e-3, type=float),
         sub_parser.add_argument('--TEs', default=[ 4e-3, 12e-3, 20e-3, 28e-3 ], type=float, nargs='+')
-        sub_parser.add_argument('--flip_angle', default=15)
+        sub_parser.add_argument('--flip_angle', default=15, type=float)
         sub_parser.add_argument('--B0', default=7, type=float)
         sub_parser.add_argument('--B0-dir', default=[0., 0., 1.], type=float, nargs=3)
+        sub_parser.add_argument('--suffix', default='MEGRE')
         sub_parser.add_argument('--generate-phase-offset', nargs='?', type=argparse_bool, const=True, default=True)
         sub_parser.add_argument('--generate-shim-field', nargs='?', type=argparse_bool, const=True, default=True)
         sub_parser.add_argument('--voxel-size', default=[1., 1., 1.], type=float, nargs=3)
         sub_parser.add_argument('--peak-snr', default=np.inf, type=float)
         sub_parser.add_argument('--random-seed', default=None, type=int)
+        sub_parser.add_argument('--save-phase', nargs='?', type=argparse_bool, const=True, default=None)
         sub_parser.add_argument('--save-chi', nargs='?', type=argparse_bool, const=True, default=True)
         sub_parser.add_argument('--save-mask', nargs='?', type=argparse_bool, const=True, default=True)
         sub_parser.add_argument('--save-segmentation', nargs='?', type=argparse_bool, const=True, default=True)
@@ -93,7 +95,9 @@ def argparse_bool(user_in):
         generate_shim_field=True,
         voxel_size=np.array(args.voxel_size),
         peak_snr=args.peak_snr,
-        random_seed=args.random_seed
+        random_seed=args.random_seed,
+        save_phase=args.save_phase,
+        suffix=args.suffix
     )
 
     qsm_forward.generate_bids(

qsm_forward/qsm_forward.py

@@ -144,8 +144,8 @@ class ReconParams:
         Random seed to use for noise.
     suffix : string
         The BIDS-compliant suffix that defines the weighting of the images (e.g. T1w, T2starw, PD).
-    export_phase : bool
-        Boolean to control whether phase images are exported.
+    save_phase : bool
+        Boolean to control whether phase images are saved.
     """
 
     def __init__(
@@ -166,7 +166,7 @@ def __init__(
             peak_snr=np.inf,
             random_seed=None,
             suffix="T2starw",
-            export_phase=True
+            save_phase=True
         ):
         self.subject = subject
         self.session = session
@@ -184,7 +184,7 @@ def __init__(
         self.peak_snr = peak_snr
         self.random_seed = random_seed
         self.suffix = suffix
-        self.export_phase = export_phase
+        self.save_phase = save_phase
 
 def rotation_matrix_from_vectors(vec1, vec2):
     """ Compute the rotation matrix that aligns vec1 to vec2 """
@@ -328,10 +328,10 @@ def generate_bids(tissue_params: TissueParams, recon_params: ReconParams, bids_d
         del sigHR_cropped
 
         # save nifti images
-        mag_filename = f"{recon_name_i}" + ("_part-mag" if recon_params.export_phase else "") + f"_{recon_params.suffix}"
-        phs_filename = f"{recon_name_i}" + ("_part-phase" if recon_params.export_phase else "") + f"_{recon_params.suffix}"
+        mag_filename = f"{recon_name_i}" + ("_part-mag" if recon_params.save_phase else "") + f"_{recon_params.suffix}"
+        phs_filename = f"{recon_name_i}" + ("_part-phase" if recon_params.save_phase else "") + f"_{recon_params.suffix}"
         nib.save(nib.Nifti1Image(dataobj=np.abs(sigHR_cropped_noisy), affine=chi_downsampled_nii.affine, header=chi_downsampled_nii.header), filename=os.path.join(subject_dir, "anat", f"{mag_filename}.nii"))
-        if recon_params.export_phase: nib.save(nib.Nifti1Image(dataobj=np.angle(sigHR_cropped_noisy), affine=chi_downsampled_nii.affine, header=chi_downsampled_nii.header), filename=os.path.join(subject_dir, "anat", f"{phs_filename}.nii"))
+        if recon_params.save_phase: nib.save(nib.Nifti1Image(dataobj=np.angle(sigHR_cropped_noisy), affine=chi_downsampled_nii.affine, header=chi_downsampled_nii.header), filename=os.path.join(subject_dir, "anat", f"{phs_filename}.nii"))
 
         # json header
         print(f"Creating JSON headers...")
@@ -357,7 +357,7 @@ def generate_bids(tissue_params: TissueParams, recon_params: ReconParams, bids_d
 
         with open(os.path.join(subject_dir, "anat", f"{mag_filename}.json"), 'w') as mag_json_file:
             json.dump(json_dict_mag, mag_json_file)
-        if recon_params.export_phase:
+        if recon_params.save_phase:
             with open(os.path.join(subject_dir, "anat", f"{phs_filename}.json"), 'w') as phs_json_file:
                 json.dump(json_dict_phs, phs_json_file)
 

setup.py

@@ -2,7 +2,7 @@
 
 setup(
     name='qsm-forward',
-    version='0.19',
+    version='0.20',
     packages=find_packages(),
     url='https://github.com/astewartau/qsm-forward',
     author='Ashley Stewart',