Small fixes

scilpy/stats/stats.py

@@ -20,14 +20,16 @@ def estimate_piesno_sigma(data, number_coils=0):
     ----------
     data: np.ndarray
         The 4D volume.
+    number_coils: int
+        The number of coils in the scanner.
     """
     assert len(data.shape) == 4
 
     sigma = np.zeros(data.shape[:3], dtype=np.float32)
     mask_noise = np.zeros(data.shape[:3], dtype=np.int16)
 
     for idx in range(data.shape[-2]):
-        logging.info('Now processing slice {} / {}}'
+        logging.info('Now processing slice {} / {}'
                      .format(idx + 1, data.shape[-2]))
         sigma[..., idx], mask_noise[..., idx] = \
             piesno(data[..., idx, :], N=number_coils, return_mask=True)

scripts/scil_denoising_nlmeans.py

@@ -152,8 +152,8 @@ def main():
                      "and piesno options.")
 
     if args.piesno or args.sigma:
-        if args.noise_from_all_voxels:
-            parser.error("You selected --noise_from_all_voxels, but this is "
+        if args.sigma_from_all_voxels:
+            parser.error("You selected --sigma_from_all_voxels, but this is "
                          "only available for the --basic_sigma method.")
         if args.mask_sigma:
             parser.error("You selected --mask_sigma, but this is "
@@ -163,7 +163,8 @@ def main():
         parser.error("Option --save_piesno_mask cannot be used when --pieno "
                      "is not selected.")
 
-    assert_inputs_exist(parser, args.in_image, args.mask)
+    assert_inputs_exist(parser, args.in_image,
+                        [args.mask_denoise, args.mask_sigma])
     assert_outputs_exist(parser, args, args.out_image,
                          [args.logfile, args.save_piesno_mask])
     assert_headers_compatible(parser, args.in_image,
@@ -173,7 +174,7 @@ def main():
     vol = nib.load(args.in_image)
     vol_data = vol.get_fdata(dtype=np.float32)
 
-    if len(vol_data.shape) != 4 or vol_data.shape[3] == 1:
+    if args.piesno and (len(vol_data.shape) != 4 or vol_data.shape[3] == 1):
         parser.error("The piesno method requires 4D data.")
 
     # Denoising mask
@@ -224,7 +225,7 @@ def main():
     with warnings.catch_warnings():
         warnings.simplefilter("ignore", category=DeprecationWarning)
         data_denoised = nlmeans(
-            vol_data, sigma, mask=mask_denoise, rician=args.rician,
+            vol_data, sigma, mask=mask_denoise, rician=not args.gaussian,
             num_threads=args.nbr_processes)
 
     # Saving

scripts/tests/test_denoising_nlmeans.py

@@ -22,7 +22,8 @@ def test_execution_basic(script_runner, monkeypatch):
     in_img = os.path.join(SCILPY_HOME, 'others', 't1_resample.nii.gz')
     ret = script_runner.run('scil_denoising_nlmeans.py', in_img,
                             't1_denoised.nii.gz', '--processes', '1',
-                            '--basic_sigma')
+                            '--basic_sigma', '--number_coils', 0,
+                            '--gaussian')
     assert ret.success
 
 
@@ -31,6 +32,6 @@ def test_execution_piesno(script_runner, monkeypatch):
     in_img = os.path.join(SCILPY_HOME, 'processing', 'dwi.nii.gz')
     ret = script_runner.run('scil_denoising_nlmeans.py', in_img,
                             'dwi_denoised.nii.gz', '--processes', '1',
-                            '--piesno')
+                            '--piesno', '--number_coils', '4')
     assert ret.success