Merge pull request #4 from djarecka/fix_pos

removing fix_position method

Author: djarecka

pydra/tasks/fsl/preprocess/applywarp.py

@@ -10,7 +10,7 @@
             "argstr": "--in={in_file}",
             "help_string": "image to be warped",
             "mandatory": True,
-            "position": 2,
+            "position": 0,
         },
     ),
     (
@@ -19,7 +19,7 @@
         {
             "argstr": "--out={out_file}",
             "help_string": "output filename",
-            "position": 4,
+            "position": 2,
             "output_file_template": "{in_file}_warp",
         },
     ),
@@ -30,7 +30,7 @@
             "argstr": "--ref={ref_file}",
             "help_string": "reference image",
             "mandatory": True,
-            "position": 3,
+            "position": 1,
         },
     ),
     (
@@ -53,7 +53,7 @@
         {
             "argstr": "--rel",
             "help_string": "treat warp field as relative: x' = x + w(x)",
-            "position": 1,
+            "position": -1,
             "xor": ["abswarp"],
         },
     ),
@@ -111,7 +111,7 @@
         {
             "argstr": "--interp={interp}",
             "help_string": "interpolation method",
-            "position": 5,
+            "position": -2,
         },
     ),
 ]

pydra/tasks/fsl/preprocess/bet.py

@@ -10,7 +10,7 @@
             "argstr": "{in_file}",
             "help_string": "input file to skull strip",
             "mandatory": True,
-            "position": 1,
+            "position": 0,
         },
     ),
     (
@@ -19,7 +19,7 @@
         {
             "argstr": "{out_file}",
             "help_string": "name of output skull stripped image",
-            "position": 2,
+            "position": 1,
             "output_file_template": "{in_file}_brain",
         },
     ),

pydra/tasks/fsl/preprocess/fast.py

@@ -97,7 +97,7 @@ def FAST_output_nclass(field, in_files, nclasses, out_basename):
             "copyfile": False,
             "help_string": "image, or multi-channel set of images, to be segmented",
             "mandatory": True,
-            "position": 1,
+            "position": -1,
         },
     ),
     (

pydra/tasks/fsl/preprocess/first.py

@@ -11,7 +11,7 @@
             "copyfile": False,
             "help_string": "input data file",
             "mandatory": True,
-            "position": 9,
+            "position": -2,
         },
     ),
     (
@@ -21,21 +21,21 @@
             "argstr": "-o {out_file}",
             "help_string": "output data file",
             "mandatory": True,
-            "position": 1,
+            "position": -1,
         },
     ),
     (
         "verbose",
         bool,
-        {"argstr": "-v", "help_string": "Use verbose logging.", "position": 2},
+        {"argstr": "-v", "help_string": "Use verbose logging.", "position": 1},
     ),
     (
         "brain_extracted",
         bool,
         {
             "argstr": "-b",
             "help_string": "Input structural image is already brain-extracted",
-            "position": 3,
+            "position": 2,
         },
     ),
     (
@@ -44,7 +44,7 @@
         {
             "argstr": "-d",
             "help_string": "Input structural image is already brain-extracted",
-            "position": 4,
+            "position": 3,
         },
     ),
     (
@@ -54,7 +54,7 @@
         {
             "argstr": "-m {method}",
             "help_string": "Method must be one of auto, fast, none, or it can be entered using the 'method_as_numerical_threshold' input",
-            "position": 6,
+            "position": 4,
             "xor": ["method_as_numerical_threshold"],
         },
     ),
@@ -64,7 +64,7 @@
         {
             "argstr": "-m {method_as_numerical_threshold:.4f}",
             "help_string": "Specify a numerical threshold value or use the 'method' input to choose auto, fast, or none",
-            "position": 6,
+            "position": 4,
         },
     ),
     (
@@ -73,7 +73,7 @@
         {
             "argstr": "-s {list_of_specific_structures}",
             "help_string": "Runs only on the specified structures (e.g. L_Hipp, R_HippL_Accu, R_Accu, L_Amyg, R_AmygL_Caud, R_Caud, L_Pall, R_PallL_Puta, R_Puta, L_Thal, R_Thal, BrStem",
-            "position": 7,
+            "position": 5,
             "sep": ",",
         },
     ),
@@ -83,7 +83,7 @@
         {
             "argstr": "-a {affine_file}",
             "help_string": "Affine matrix to use (e.g. img2std.mat) (does not re-run registration)",
-            "position": 8,
+            "position": 6,
         },
     ),
 ]

pydra/tasks/fsl/preprocess/flirt.py

@@ -10,7 +10,7 @@
             "argstr": "-in {in_file}",
             "help_string": "input file",
             "mandatory": True,
-            "position": 1,
+            "position": 0,
         },
     ),
     (
@@ -20,7 +20,7 @@
             "argstr": "-ref {reference}",
             "help_string": "reference file",
             "mandatory": True,
-            "position": 2,
+            "position": 1,
         },
     ),
     (
@@ -29,7 +29,7 @@
         {
             "argstr": "-out {out_file}",
             "help_string": "registered output file",
-            "position": 3,
+            "position": 2,
             "output_file_template": "{in_file}_flirt",
         },
     ),
@@ -39,7 +39,7 @@
         {
             "argstr": "-omat {out_matrix_file}",
             "help_string": "output affine matrix in 4x4 asciii format",
-            "position": 4,
+            "position": 3,
             "output_file_template": "{in_file}_flirt.mat",
         },
     ),

pydra/tasks/fsl/preprocess/mcflirt.py

@@ -10,7 +10,7 @@
             "argstr": "-in {in_file}",
             "help_string": "timeseries to motion-correct",
             "mandatory": True,
-            "position": 1,
+            "position": 0,
         },
     ),
     (

pydra/tasks/fsl/preprocess/slicetimer.py

@@ -10,7 +10,7 @@
             "argstr": "--in={in_file}",
             "help_string": "filename of input timeseries",
             "mandatory": True,
-            "position": 1,
+            "position": 0,
         },
     ),
     (

pydra/tasks/fsl/preprocess/susan.py

@@ -69,7 +69,7 @@
         {
             "argstr": "{out_file}",
             "help_string": "output file name",
-            "position": 7,
+            "position": -1,
             "output_file_template": "{in_file}_smooth",
         },
     ),

tools/converter.py

@@ -236,9 +236,6 @@ def convert_input_fields(self):
             if pos is not None:
                 position_dict[name] = pos
 
-        if position_dict:
-            fields_pdr_dict = self.fix_position(fields_pdr_dict, position_dict)
-
         fields_pdr_l = list(fields_pdr_dict.values())
         return fields_pdr_l, has_template
 
@@ -400,28 +397,6 @@ def pydra_type_converter(self, field, spec_type, name):
         return tp_pdr
 
 
-    def fix_position(self, fields_dict, positions):
-        """ fixing positions all of the fields"""
-        positions_list = list(positions.values())
-        positions_list.sort()
-    #    if positions_list[0] < -1:
-    #        raise Exception("position in nipype interface < -1")
-        if positions_list[0] <= -1:
-            positions_list.append(positions_list.pop(0))
-
-        positions_map = {}
-        for ii, el in enumerate(positions_list):
-            if el != ii + 1:
-                positions_map[el] = ii + 1
-
-        for nm, pos in positions.items():
-            if pos in positions_map:
-                # dictionary with metadata should be the last element
-                fields_dict[nm][-1]["position"] = positions_map[pos]
-
-        return fields_dict
-
-
     def string_formats(self, argstr, name):
         import re
         if "%s" in argstr: