Merge pull request #24 from smoia/fix/dmat

Fix denoise_matrix input from CLI that was causing it to be a list of lists
smoia · Oct 30, 2021 · e1d502f · e1d502f
2 parents 1bcbebd + 830e597
commit e1d502f
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/phys2cvr/cli/run.py b/phys2cvr/cli/run.py
@@ -193,10 +193,9 @@ def _get_parser():
                           default=0)
     opt_regr.add_argument('-dmat', '--denoise-matrix',
                           dest='denoise_matrix',
-                          action='append',
                           nargs='*',
                           type=str,
-                          help=('Complete path (absolute or relative) and name '
+                          help=('Complete path (absolute or relative) and filename '
                                 'of denoising matrices to add to the regression model. '
                                 'This option can be specified multiple times to '
                                 'add multiple denoising matrices, but multiple '

diff --git a/phys2cvr/phys2cvr.py b/phys2cvr/phys2cvr.py
@@ -127,7 +127,7 @@ def phys2cvr(fname_func, fname_co2=None, fname_pidx=None, fname_mask=None,
         phys2cvr will add all polynomials up to the specified order 
         (e.g. if user specifies 3, orders 0, 1, 2, and 3 will be added). 
         Default is 0, which will model only the mean of the timeseries.
-    denoise_matrix : list of np.array(s), optional
+    denoise_matrix : list of str(s) or path(s), optional
         Add one or multiple denoising matrices to the regression model.
         Ignored if not performing the regression step.
     scale_factor : str, int, or float, optional
@@ -359,6 +359,7 @@ def phys2cvr(fname_func, fname_co2=None, fname_pidx=None, fname_mask=None,
 
         # Read in eventual denoising factors
         if denoise_matrix:
+            denoise_matrix = io.if_declared_force_type(denoise_matrix, 'list', 'denoise_matrix')
             for matrix in denoise_matrix:
                 LGR.info(f'Read confounding factor from {matrix}')
                 conf = np.genfromtxt(matrix)