Update to use full 'data' dir from head phantom

.gitignore

@@ -1,5 +1,5 @@
 dist/
-head-phantom-maps/
+data/
 qsm_forward.egg-info/
 *.nii*
 *__pycache__*

README.md

@@ -75,14 +75,14 @@ Some repesentative images including the mask, first and last-echo phase image, a
 
 ## Example using head phantom data
 
-In this example, we generate a BIDS-compliant dataset based on head phantom maps. You must provide these maps yourself by gaining access to the QSM Challenge 2.0 head phantom data or generating your own realistic maps:
+In this example, we generate a BIDS-compliant dataset based on the [realistic in-silico head phantom](https://doi.org/10.34973/m20r-jt17). If you have access to the head phantom, you need to retain the `data` directory which provides relevant tissue parameters:
 
 ```python
 import qsm_forward
 import numpy as np
 
 if __name__ == "__main__":
-    tissue_params = qsm_forward.TissueParams("../head-phantom-maps")
+    tissue_params = qsm_forward.TissueParams(root_dir="~/data")
 
     recon_params_all = [
         qsm_forward.ReconParams(voxel_size=voxel_size, peak_snr=100, session=session)
@@ -179,7 +179,7 @@ import qsm_forward
 import numpy as np
 
 if __name__ == "__main__":
-    tissue_params = qsm_forward.TissueParams("../head-phantom-maps", chi="ChiModelMIX.nii.gz")
+    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)

qsm_forward/examples/head_phantom_maps.py

@@ -7,7 +7,8 @@
 The simulations are carried out with various reconstruction parameters 
 (which include different voxel sizes), and the results are saved in the "bids" directory.
 
-The tissue parameters are loaded from the directory "../head-phantom-maps".
+The tissue parameters are loaded from the directory "../data". The data directory can
+be downloaded from https://doi.org/10.34973/m20r-jt17.
 
 Author: Ashley Stewart ([email protected])
 """
@@ -16,7 +17,7 @@
 import numpy as np
 
 if __name__ == "__main__":
-    tissue_params = qsm_forward.TissueParams("~/head-phantom-maps", chi="ChiModelMIX.nii.gz")
+    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)

qsm_forward/main.py

@@ -12,7 +12,7 @@ def main():
 
     # Create subcommands
     subparsers = parser.add_subparsers(dest='mode')
-    headphantom_parser = subparsers.add_parser('head', help='Use head phantom maps for simulation')
+    headphantom_parser = subparsers.add_parser('head', help='Use realistic in-silico head phantom for simulation')
     simplephantom_parser = subparsers.add_parser('simple', help='Generate simple susceptibility sources for simulation')
 
     def argparse_bool(user_in):
@@ -23,7 +23,7 @@ def argparse_bool(user_in):
         if user_in in ['off', 'false', 'no']: return False
         raise ValueError(f"Invalid boolean value {user_in}; use on/yes/true or off/false/no")# Arguments specific to phantom simulation
 
-    headphantom_parser.add_argument('maps', help='Head phantom maps directory')
+    headphantom_parser.add_argument('data', help='Head phantom data directory (download from https://doi.org/10.34973/m20r-jt17)')
 
     # Arguments common to both subcommands
     for sub_parser in [headphantom_parser, simplephantom_parser]:
@@ -60,7 +60,7 @@ def argparse_bool(user_in):
     args = parser.parse_args()
 
     if args.mode == 'head':
-        tissue_params = qsm_forward.TissueParams(args.maps)
+        tissue_params = qsm_forward.TissueParams(args.data)
 
     elif args.mode == 'simple':
         tissue_params = qsm_forward.TissueParams(

qsm_forward/qsm_forward.py

@@ -17,6 +17,8 @@ class TissueParams:
 
     Attributes
     ----------
+    root_dir : str or None
+        The path to the root directory containing the tissue parameter files.
     chi_path : str or ndarray
         The path to the Chi file or a 3D numpy array containing Chi values.
     M0_path : str or ndarray
@@ -34,12 +36,12 @@ class TissueParams:
     def __init__(
             self,
             root_dir = "",
-            chi = "ChiModelMIX_noCalc.nii.gz",
-            M0 = "M0.nii.gz",
-            R1 = "R1.nii.gz",
-            R2star = "R2star.nii.gz",
-            mask = "BrainMask.nii.gz",
-            seg = "SegmentedModel.nii.gz",
+            chi = "chimodel/ChiModelMIX.nii",
+            M0 = "maps/M0.nii.gz",
+            R1 = "maps/R1.nii.gz",
+            R2star = "maps/R2star.nii.gz",
+            mask = "masks/BrainMask.nii.gz",
+            seg = "masks/SegmentedModel.nii.gz",
             apply_mask = False
     ):
         if isinstance(chi, str) and not os.path.exists(os.path.join(root_dir, chi)):

setup.py

@@ -2,7 +2,7 @@
 
 setup(
     name='qsm-forward',
-    version='0.18',
+    version='0.19',
     packages=find_packages(),
     url='https://github.com/astewartau/qsm-forward',
     author='Ashley Stewart',