Merge pull request #40 from LOAMRI/copilot/fix-22

Add default options to cbf, te_asl and dw_asl scripts

Author: acsenrafilho

asltk/scripts/cbf.py

@@ -43,19 +43,21 @@
     default=os.path.expanduser('~'),
     help='The output folder that is the reference to save all the output images in the script. The images selected to be saved are given as tags in the script caller, e.g. the options --cbf_map and --att_map. By default, the TblGM map is placed in the output folder with the name tblgm_map.nii.gz',
 )
-required.add_argument(
+optional.add_argument(
     '--pld',
     type=str,
     nargs='+',
-    required=True,
-    help='Posts Labeling Delay (PLD) trend, arranged in a sequence of float numbers',
+    required=False,
+    default=[170.0, 270.0, 370.0, 520.0, 670.0, 1070.0, 1870.0],
+    help='Posts Labeling Delay (PLD) trend, arranged in a sequence of float numbers. If not passed, the default values will be used.',
 )
-required.add_argument(
+optional.add_argument(
     '--ld',
     type=str,
     nargs='+',
-    required=True,
-    help='Labeling Duration trend (LD), arranged in a sequence of float numbers.',
+    required=False,
+    default=[100.0, 100.0, 150.0, 150.0, 400.0, 800.0, 1800.0],
+    help='Labeling Duration trend (LD), arranged in a sequence of float numbers. If not passed, the default values will be used.',
 )
 optional.add_argument(
     '--verbose',

asltk/scripts/dw_asl.py

@@ -57,26 +57,29 @@
     required=False,
     help='The ATT map that is provided to skip this step in the MultiTE-ASL calculation. If ATT is not provided, than a ATT map is calculated at the runtime.',
 )
-required.add_argument(
+optional.add_argument(
     '--pld',
     type=str,
     nargs='+',
-    required=True,
-    help='Posts Labeling Delay (PLD) trend, arranged in a sequence of float numbers',
+    required=False,
+    default=[170.0, 270.0, 370.0, 520.0, 670.0, 1070.0, 1870.0],
+    help='Posts Labeling Delay (PLD) trend, arranged in a sequence of float numbers. If not passed, the default values will be used.',
 )
-required.add_argument(
+optional.add_argument(
     '--ld',
     type=str,
     nargs='+',
-    required=True,
-    help='Labeling Duration trend (LD), arranged in a sequence of float numbers.',
+    required=False,
+    default=[100.0, 100.0, 150.0, 150.0, 400.0, 800.0, 1800.0],
+    help='Labeling Duration trend (LD), arranged in a sequence of float numbers. If not passed, the default values will be used.',
 )
-required.add_argument(
+optional.add_argument(
     '--dw',
     type=str,
     nargs='+',
-    required=True,
-    help='Diffusion b-values arranged in a sequence of float numbers.',
+    required=False,
+    default=[0, 50, 100, 250],
+    help='Diffusion b-values arranged in a sequence of float numbers. If not passed, the default values will be used.',
 )
 optional.add_argument(
     '--verbose',

asltk/scripts/te_asl.py

@@ -54,26 +54,29 @@
     required=False,
     help='The ATT map that is provided to skip this step in the MultiTE-ASL calculation. If ATT is not provided, than a ATT map is calculated at the runtime.',
 )
-required.add_argument(
+optional.add_argument(
     '--pld',
     type=str,
     nargs='+',
-    required=True,
-    help='Posts Labeling Delay (PLD) trend, arranged in a sequence of float numbers',
+    required=False,
+    default=[170.0, 270.0, 370.0, 520.0, 670.0, 1070.0, 1870.0],
+    help='Posts Labeling Delay (PLD) trend, arranged in a sequence of float numbers. If not passed, the default values will be used.',
 )
-required.add_argument(
+optional.add_argument(
     '--ld',
     type=str,
     nargs='+',
-    required=True,
-    help='Labeling Duration trend (LD), arranged in a sequence of float numbers.',
+    required=False,
+    default=[100.0, 100.0, 150.0, 150.0, 400.0, 800.0, 1800.0],
+    help='Labeling Duration trend (LD), arranged in a sequence of float numbers. If not passed, the default values will be used.',
 )
-required.add_argument(
+optional.add_argument(
     '--te',
     type=str,
     nargs='+',
-    required=True,
-    help='Time of Echos (TE), arranged in a sequence of float numbers.',
+    required=False,
+    default=[13.56, 67.82, 122.08, 176.33, 230.59, 284.84, 339.1, 393.36],
+    help='Time of Echos (TE), arranged in a sequence of float numbers. If not passed, the default values will be used.',
 )
 optional.add_argument(
     '--verbose',