Merge pull request #335 from arnaudbore/update_NODDI_and_freewater

Update NODDI and freewater

scilpy/io/utils.py

@@ -353,8 +353,8 @@ def check(path):
             if not args.overwrite:
                 parser.error(
                     'Output directory {} isn\'t empty and some files could be '
-                    'overwritten. Use -f option if you want to continue.'
-                    .format(path))
+                    'overwritten or even deleted. Use -f option if you want '
+                    'to continue.'.format(path))
             else:
                 for the_file in os.listdir(path):
                     file_path = os.path.join(path, the_file)

scripts/scil_compute_NODDI.py

@@ -11,8 +11,8 @@
 import io
 import logging
 import os
-import tempfile
 import sys
+import tempfile
 
 import amico
 from dipy.io.gradients import read_bvals_bvecs
@@ -47,7 +47,7 @@ def _build_arg_parser():
     p.add_argument('in_bvec',
                    help='b-vectors filename, in FSL format (.bvec).')
 
-    p.add_argument('--in_mask',
+    p.add_argument('--mask',
                    help='Brain mask filename.')
     p.add_argument('--out_dir', default="results",
                    help='Output directory for the NODDI results. '
@@ -95,9 +95,10 @@ def main():
     args = parser.parse_args()
 
     assert_inputs_exist(parser, [args.in_dwi, args.in_bval, args.in_bvec],
-                        args.in_mask)
+                        args.mask)
+
     assert_output_dirs_exist_and_empty(parser, args,
-                                       os.path.join(args.out_dir, 'NODDI'),
+                                       args.out_dir,
                                        optional=args.save_kernels)
 
     # COMMIT has some c-level stdout and non-logging print that cannot
@@ -130,7 +131,7 @@ def main():
         ae = amico.Evaluation('.', '.')
         ae.load_data(args.in_dwi,
                      tmp_scheme_filename,
-                     mask_filename=args.in_mask)
+                     mask_filename=args.mask)
         # Compute the response functions
         ae.set_model("NODDI")
 
@@ -156,8 +157,7 @@ def main():
             regenerate_kernels = True
 
         ae.set_config('ATOMS_path', kernels_dir)
-        out_model_dir = os.path.join(args.out_dir, ae.model.id)
-        ae.set_config('OUTPUT_path', out_model_dir)
+        ae.set_config('OUTPUT_path', args.out_dir)
         ae.generate_kernels(regenerate=regenerate_kernels)
         ae.load_kernels()
 

scripts/scil_compute_freewater.py

@@ -11,8 +11,8 @@
 import io
 import logging
 import os
-import tempfile
 import sys
+import tempfile
 
 import amico
 from dipy.io.gradients import read_bvals_bvecs
@@ -47,11 +47,11 @@ def _build_arg_parser():
     p.add_argument('in_bvec',
                    help='b-vectors filename, in FSL format (.bvec).')
 
-    p.add_argument('--in_mask',
+    p.add_argument('--mask',
                    help='Brain mask filename.')
     p.add_argument('--out_dir', default="results",
                    help='Output directory for the Free Water results. '
-                        '[current_directory]')
+                        '[%(default)s]')
     p.add_argument('--b_thr', type=int, default=40,
                    help='Limit value to consider that a b-value is on an '
                         'existing shell. Above this limit, the b-value is '
@@ -102,9 +102,11 @@ def main():
     parser = _build_arg_parser()
     args = parser.parse_args()
 
-    assert_inputs_exist(parser, args.in_dwi, args.in_mask)
+    assert_inputs_exist(parser, [args.in_dwi, args.in_bval, args.in_bvec],
+                        args.mask)
+
     assert_output_dirs_exist_and_empty(parser, args,
-                                       os.path.join(args.out_dir, 'FreeWater'),
+                                       args.out_dir,
                                        optional=args.save_kernels)
 
     # COMMIT has some c-level stdout and non-logging print that cannot
@@ -139,7 +141,7 @@ def main():
         # Load the data
         ae.load_data(args.in_dwi,
                      scheme_filename=tmp_scheme_filename,
-                     mask_filename=args.in_mask)
+                     mask_filename=args.mask)
 
         # Compute the response functions
         ae.set_model("FreeWater")
@@ -169,8 +171,7 @@ def main():
             regenerate_kernels = True
 
         ae.set_config('ATOMS_path', kernels_dir)
-        out_model_dir = os.path.join(args.out_dir, ae.model.id)
-        ae.set_config('OUTPUT_path', out_model_dir)
+        ae.set_config('OUTPUT_path', args.out_dir)
         ae.generate_kernels(regenerate=regenerate_kernels)
         ae.load_kernels()
 

scripts/tests/test_compute_NODDI.py

@@ -24,11 +24,11 @@ def test_execution_commit_amico(script_runner):
                            'dwi.bval')
     in_bvec = os.path.join(get_home(), 'commit_amico',
                            'dwi.bvec')
-    in_mask = os.path.join(get_home(), 'commit_amico',
-                           'mask.nii.gz')
+    mask = os.path.join(get_home(), 'commit_amico',
+                        'mask.nii.gz')
     ret = script_runner.run('scil_compute_NODDI.py', in_dwi,
-                            in_bval, in_bvec, '--in_mask', in_mask,
-                            '--out_dir', 'noddi/', '--b_thr', '30',
+                            in_bval, in_bvec, '--mask', mask,
+                            '--out_dir', 'noddi', '--b_thr', '30',
                             '--para_diff', '0.0017', '--iso_diff', '0.003',
                             '--lambda1', '0.5', '--lambda2', '0.001',
                             '--processes', '1')

scripts/tests/test_compute_freewater.py

@@ -24,11 +24,11 @@ def test_execution_commit_amico(script_runner):
                            'dwi.bval')
     in_bvec = os.path.join(get_home(), 'commit_amico',
                            'dwi.bvec')
-    in_mask = os.path.join(get_home(), 'commit_amico',
-                           'mask.nii.gz')
+    mask = os.path.join(get_home(), 'commit_amico',
+                        'mask.nii.gz')
     ret = script_runner.run('scil_compute_freewater.py', in_dwi,
-                            in_bval, in_bvec, '--in_mask', in_mask,
-                            '--out_dir', 'freewater/', '--b_thr', '30',
+                            in_bval, in_bvec, '--mask', mask,
+                            '--out_dir', 'freewater', '--b_thr', '30',
                             '--para_diff', '0.0015',
                             '--perp_diff_min', '0.0001',
                             '--perp_diff_max', '0.0007',