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FIX/BREAK/TEST preprocess interface failed
FIX - * FAST doc test BREAK - * fNIRT - assertion error with output file * SUSAN - run time error; possibly fixable with more suitable test data
1 parent df4bc0d commit 0746d11

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11 files changed

+202
-202
lines changed

11 files changed

+202
-202
lines changed

‎pydra/tasks/fsl/preprocess/applywarp.py

Lines changed: 13 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -7,8 +7,8 @@
77
"in_file",
88
specs.File,
99
{
10-
"argstr": "--in={in_file}",
1110
"help_string": "image to be warped",
11+
"argstr": "--in={in_file}",
1212
"mandatory": True,
1313
"position": 0,
1414
},
@@ -17,8 +17,8 @@
1717
"out_file",
1818
str,
1919
{
20-
"argstr": "--out={out_file}",
2120
"help_string": "output filename",
21+
"argstr": "--out={out_file}",
2222
"position": 2,
2323
"output_file_template": "{in_file}_warp",
2424
},
@@ -27,32 +27,32 @@
2727
"ref_file",
2828
specs.File,
2929
{
30-
"argstr": "--ref={ref_file}",
3130
"help_string": "reference image",
31+
"argstr": "--ref={ref_file}",
3232
"mandatory": True,
3333
"position": 1,
3434
},
3535
),
3636
(
3737
"field_file",
3838
specs.File,
39-
{"argstr": "--warp={field_file}", "help_string": "file containing warp field"},
39+
{"help_string": "file containing warp field", "argstr": "--warp={field_file}"},
4040
),
4141
(
4242
"abswarp",
4343
bool,
4444
{
45-
"argstr": "--abs",
4645
"help_string": "treat warp field as absolute: x' = w(x)",
46+
"argstr": "--abs",
4747
"xor": ["relwarp"],
4848
},
4949
),
5050
(
5151
"relwarp",
5252
bool,
5353
{
54-
"argstr": "--rel",
5554
"help_string": "treat warp field as relative: x' = x + w(x)",
55+
"argstr": "--rel",
5656
"position": -1,
5757
"xor": ["abswarp"],
5858
},
@@ -61,56 +61,56 @@
6161
"datatype",
6262
ty.Any,
6363
{
64-
"argstr": "--datatype={datatype}",
6564
"help_string": "Force output data type [char short int float double].",
65+
"argstr": "--datatype={datatype}",
6666
},
6767
),
6868
(
6969
"supersample",
7070
bool,
7171
{
72-
"argstr": "--super",
7372
"help_string": "intermediary supersampling of output, default is off",
73+
"argstr": "--super",
7474
},
7575
),
7676
(
7777
"superlevel",
7878
ty.Any,
7979
{
80-
"argstr": "--superlevel={superlevel}",
8180
"help_string": "level of intermediary supersampling, a for 'automatic' or integer level. Default = 2",
81+
"argstr": "--superlevel={superlevel}",
8282
},
8383
),
8484
(
8585
"premat",
8686
specs.File,
8787
{
88-
"argstr": "--premat={premat}",
8988
"help_string": "filename for pre-transform (affine matrix)",
89+
"argstr": "--premat={premat}",
9090
},
9191
),
9292
(
9393
"postmat",
9494
specs.File,
9595
{
96-
"argstr": "--postmat={postmat}",
9796
"help_string": "filename for post-transform (affine matrix)",
97+
"argstr": "--postmat={postmat}",
9898
},
9999
),
100100
(
101101
"mask_file",
102102
specs.File,
103103
{
104-
"argstr": "--mask={mask_file}",
105104
"help_string": "filename for mask image (in reference space)",
105+
"argstr": "--mask={mask_file}",
106106
},
107107
),
108108
(
109109
"interp",
110110
ty.Any,
111111
{
112-
"argstr": "--interp={interp}",
113112
"help_string": "interpolation method",
113+
"argstr": "--interp={interp}",
114114
"position": -2,
115115
},
116116
),

‎pydra/tasks/fsl/preprocess/bet.py

Lines changed: 19 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -7,8 +7,8 @@
77
"in_file",
88
specs.File,
99
{
10-
"argstr": "{in_file}",
1110
"help_string": "input file to skull strip",
11+
"argstr": "{in_file}",
1212
"mandatory": True,
1313
"position": 0,
1414
},
@@ -17,58 +17,58 @@
1717
"out_file",
1818
str,
1919
{
20-
"argstr": "{out_file}",
2120
"help_string": "name of output skull stripped image",
21+
"argstr": "{out_file}",
2222
"position": 1,
2323
"output_file_template": "{in_file}_brain",
2424
},
2525
),
26-
("outline", bool, {"argstr": "-o", "help_string": "create surface outline image"}),
27-
("mask", bool, {"argstr": "-m", "help_string": "create binary mask image"}),
28-
("skull", bool, {"argstr": "-s", "help_string": "create skull image"}),
26+
("outline", bool, {"help_string": "create surface outline image", "argstr": "-o"}),
27+
("mask", bool, {"help_string": "create binary mask image", "argstr": "-m"}),
28+
("skull", bool, {"help_string": "create skull image", "argstr": "-s"}),
2929
(
3030
"no_output",
3131
bool,
32-
{"argstr": "-n", "help_string": "Don't generate segmented output"},
32+
{"help_string": "Don't generate segmented output", "argstr": "-n"},
3333
),
3434
(
3535
"frac",
3636
float,
37-
{"argstr": "-f {frac:.2f}", "help_string": "fractional intensity threshold"},
37+
{"help_string": "fractional intensity threshold", "argstr": "-f {frac:.2f}"},
3838
),
3939
(
4040
"vertical_gradient",
4141
float,
4242
{
43-
"argstr": "-g {vertical_gradient:.2f}",
4443
"help_string": "vertical gradient in fractional intensity threshold (-1, 1)",
44+
"argstr": "-g {vertical_gradient:.2f}",
4545
},
4646
),
47-
("radius", int, {"argstr": "-r {radius}", "help_string": "head radius"}),
47+
("radius", int, {"help_string": "head radius", "argstr": "-r {radius}"}),
4848
(
4949
"center",
5050
list,
51-
{"argstr": "-c {center}", "help_string": "center of gravity in voxels"},
51+
{"help_string": "center of gravity in voxels", "argstr": "-c {center}"},
5252
),
5353
(
5454
"threshold",
5555
bool,
5656
{
57-
"argstr": "-t",
5857
"help_string": "apply thresholding to segmented brain image and mask",
58+
"argstr": "-t",
5959
},
6060
),
6161
(
6262
"mesh",
6363
bool,
64-
{"argstr": "-e", "help_string": "generate a vtk mesh brain surface"},
64+
{"help_string": "generate a vtk mesh brain surface", "argstr": "-e"},
6565
),
6666
(
6767
"robust",
6868
bool,
6969
{
70-
"argstr": "-R",
7170
"help_string": "robust brain centre estimation (iterates BET several times)",
71+
"argstr": "-R",
7272
"xor": (
7373
"functional",
7474
"reduce_bias",
@@ -84,8 +84,8 @@
8484
"padding",
8585
bool,
8686
{
87-
"argstr": "-Z",
8887
"help_string": "improve BET if FOV is very small in Z (by temporarily padding end slices)",
88+
"argstr": "-Z",
8989
"xor": (
9090
"functional",
9191
"reduce_bias",
@@ -101,8 +101,8 @@
101101
"remove_eyes",
102102
bool,
103103
{
104-
"argstr": "-S",
105104
"help_string": "eye & optic nerve cleanup (can be useful in SIENA)",
105+
"argstr": "-S",
106106
"xor": (
107107
"functional",
108108
"reduce_bias",
@@ -118,8 +118,8 @@
118118
"surfaces",
119119
bool,
120120
{
121-
"argstr": "-A",
122121
"help_string": "run bet2 and then betsurf to get additional skull and scalp surfaces (includes registrations)",
122+
"argstr": "-A",
123123
"xor": (
124124
"functional",
125125
"reduce_bias",
@@ -135,8 +135,8 @@
135135
"t2_guided",
136136
str,
137137
{
138-
"argstr": "-A2 {t2_guided}",
139138
"help_string": "as with creating surfaces, when also feeding in non-brain-extracted T2 (includes registrations)",
139+
"argstr": "-A2 {t2_guided}",
140140
"xor": (
141141
"functional",
142142
"reduce_bias",
@@ -152,8 +152,8 @@
152152
"functional",
153153
bool,
154154
{
155-
"argstr": "-F",
156155
"help_string": "apply to 4D fMRI data",
156+
"argstr": "-F",
157157
"xor": (
158158
"functional",
159159
"reduce_bias",
@@ -169,8 +169,8 @@
169169
"reduce_bias",
170170
bool,
171171
{
172-
"argstr": "-B",
173172
"help_string": "bias field and neck cleanup",
173+
"argstr": "-B",
174174
"xor": (
175175
"functional",
176176
"reduce_bias",

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