FIX: Use equal-separated option value pairs in eddy (#67)

Author: NicolasGensollen

src/pydra/tasks/fsl/eddy/eddy.py

@@ -17,8 +17,8 @@
 ...     fieldmap_image="fieldmap.nii",
 ... )
 >>> task.cmdline    # doctest: +ELLIPSIS
-'eddy --imain input.nii --mask brain.nii --acqp params.txt --index index.txt \
---bvecs input.bvec --bvals input.bval --field fieldmap.nii --out eddy ...'
+'eddy --imain=input.nii --mask=brain.nii --acqp=params.txt --index=index.txt \
+--bvecs=input.bvec --bvals=input.bval --field=fieldmap.nii --out=eddy ...'
 """
 
 __all__ = ["Eddy"]
@@ -37,41 +37,59 @@ class EddySpec(ShellSpec):
 
     # Parameters that specify input files.
     input_image: PathLike = field(
-        metadata={"help_string": "input image as a 4D volume", "mandatory": True, "argstr": "--imain"}
+        metadata={
+            "help_string": "input image as a 4D volume",
+            "mandatory": True,
+            "argstr": "--imain={input_image}",
+        }
     )
 
     brain_mask: PathLike = field(
-        metadata={"help_string": "brain mask as a single volume image", "mandatory": True, "argstr": "--mask"}
+        metadata={
+            "help_string": "brain mask as a single volume image",
+            "mandatory": True,
+            "argstr": "--mask={brain_mask}",
+        }
     )
 
     encoding_file: PathLike = field(
         metadata={
             "help_string": "acquisition parameters for the diffusion protocol",
             "mandatory": True,
-            "argstr": "--acqp",
+            "argstr": "--acqp={encoding_file}",
         }
     )
 
     index_file: PathLike = field(
         metadata={
             "help_string": "mapping from volume index to encoding parameters",
             "mandatory": True,
-            "argstr": "--index",
+            "argstr": "--index={index_file}",
         }
     )
 
     bvec_file: PathLike = field(
-        metadata={"help_string": "diffusion directions", "mandatory": True, "argstr": "--bvecs"}
+        metadata={
+            "help_string": "diffusion directions",
+            "mandatory": True,
+            "argstr": "--bvecs={bvec_file}",
+        }
     )
 
-    bval_file: PathLike = field(metadata={"help_string": "diffusion weighting", "mandatory": True, "argstr": "--bvals"})
+    bval_file: PathLike = field(
+        metadata={
+            "help_string": "diffusion weighting",
+            "mandatory": True,
+            "argstr": "--bvals={bval_file}",
+        }
+    )
 
-    fieldmap_image: PathLike = field(metadata={"help_string": "fieldmap image", "argstr": "--field"})
+    fieldmap_image: PathLike = field(metadata={"help_string": "fieldmap image", "argstr": "--field={fieldmap_image}"})
 
     fieldmap_matrix: PathLike = field(
         metadata={
             "help_string": "rigid-body transformation matrix from fieldmap to first input volume",
-            "argstr": "--field_mat",
+            "argstr": "--field_mat={fieldmap_matrix}",
             "requires": {"fieldmap_image"},
         }
     )
@@ -82,15 +100,19 @@ class EddySpec(ShellSpec):
 
     # Parameters specifying names of output-files.
     output_basename: str = field(
-        default="eddy", metadata={"help_string": "basename for output files", "argstr": "--out"}
+        default="eddy",
+        metadata={
+            "help_string": "basename for output files",
+            "argstr": "--out={output_basename}",
+        },
     )
 
     # Parameters specifying how eddy should be run.
     first_level_model: str = field(
         default="quadratic",
         metadata={
             "help_string": "model for the magnetic field generated by Eddy currents",
-            "argstr": "--flm",
+            "argstr": "--flm={first_level_model}",
             "allowed_values": {"movement", "linear", "quadratic", "cubic"},
         },
     )
@@ -99,7 +121,7 @@ class EddySpec(ShellSpec):
         default="none",
         metadata={
             "help_string": "model for how diffusion gradients generate Eddy currents",
-            "argstr": "--slm",
+            "argstr": "--slm={second_level_model}",
             "allowed_values": {"none", "linear", "quadratic"},
         },
     )
@@ -108,12 +130,16 @@ class EddySpec(ShellSpec):
         default=0,
         metadata={
             "help_string": "filter width used for pre-conditioning data prior to estimating distortions",
-            "argstr": "--fwhm",
+            "argstr": "--fwhm={fwhm}",
         },
     )
 
     num_iterations: int = field(
-        default=5, metadata={"help_string": "number of iterations for eddy", "argstr": "--niter"}
+        default=5,
+        metadata={
+            "help_string": "number of iterations for eddy",
+            "argstr": "--niter={num_iterations}",
+        },
     )
 
     fill_empty_planes: bool = field(metadata={"help_string": "detect and fill empty planes", "argstr": "--fep"})
@@ -122,23 +148,34 @@ class EddySpec(ShellSpec):
         default="spline",
         metadata={
             "help_string": "interpolation method for the estimation phase",
-            "argstr": "--interp",
+            "argstr": "--interp={interpolation}",
             "allowed_values": {"spline", "trilinear"},
         },
     )
 
     resampling: str = field(
         default="jac",
-        metadata={"help_string": "final resampling strategy", "argstr": "--resamp", "allowed_values": {"jac", "lsr"}},
+        metadata={
+            "help_string": "final resampling strategy",
+            "argstr": "--resamp={resampling}",
+            "allowed_values": {"jac", "lsr"},
+        },
     )
 
     num_voxels: int = field(
         default=1000,
-        metadata={"help_string": "number of voxels to use for GP hyperparameter estimation", "argstr": "--nvoxhp"},
+        metadata={
+            "help_string": "number of voxels to use for GP hyperparameter estimation",
+            "argstr": "--nvoxhp={num_voxels}",
+        },
     )
 
     fudge_factor: int = field(
-        default=10, metadata={"help_string": "fudge factor for Q-space smoothing during estimation", "argstr": "--ff"}
+        default=10,
+        metadata={
+            "help_string": "fudge factor for Q-space smoothing during estimation",
+            "argstr": "--ff={fudge_factor}",
+        },
     )
 
     # Parameters for outlier replacement (ol)
@@ -147,67 +184,81 @@ class EddySpec(ShellSpec):
     outlier_num_stdevs: int = field(
         metadata={
             "help_string": "number of times off the standard deviation to qualify as outlier",
-            "argstr": "--ol_nstd",
+            "argstr": "--ol_nstd={outlier_num_stdevs}",
             "requires": {"replace_outliers"},
         }
     )
 
     outlier_num_voxels: int = field(
         metadata={
             "help_string": "minimum number of voxels in a slice to qualify for outlier detection",
-            "argstr": "--ol_nvox",
+            "argstr": "--ol_nvox={outlier_num_voxels}",
             "requires": {"replace_outliers"},
         }
     )
 
     outlier_type: str = field(
         metadata={
             "help_string": "type of outliers detected",
-            "argstr": "--ol_type",
+            "argstr": "--ol_type={outlier_type}",
             "allowed_values": {"both", "gw", "sw"},
             "requires": {"replace_outliers"},
         }
     )
 
-    multiband_factor: int = field(metadata={"help_string": "multiband factor", "argstr": "--mb"})
+    multiband_factor: int = field(metadata={"help_string": "multiband factor", "argstr": "--mb={multiband_factor}"})
 
     multiband_offset: int = field(
-        metadata={"help_string": "multiband slice offset", "argstr": "--mb_offs", "requires": {"multiband_factor"}}
+        metadata={
+            "help_string": "multiband slice offset",
+            "argstr": "--mb_offs={multiband_offset}",
+            "requires": {"multiband_factor"},
+        }
     )
 
     # Parameters for intra-volume movement correction (s2v)
     movement_prediction_order: int = field(
-        default=0, metadata={"help_string": "order of movement prediction model", "argstr": "--mporder"}
+        default=0,
+        metadata={
+            "help_string": "order of movement prediction model",
+            "argstr": "--mporder={movement_prediction_order}",
+        },
     )
 
     s2v_num_iterations: int = field(
-        metadata={"help_string": "number of iterations for s2v movement estimation", "argstr": "--s2v_niter"}
+        metadata={
+            "help_string": "number of iterations for s2v movement estimation",
+            "argstr": "--s2v_niter={s2v_num_iterations}",
+        }
     )
 
     s2v_lambda: float = field(
-        metadata={"help_string": "weighting of regularization for s2v movement estimation", "argstr": "--s2v_lambda"}
+        metadata={
+            "help_string": "weighting of regularization for s2v movement estimation",
+            "argstr": "--s2v_lambda={s2v_lambda}",
+        }
     )
 
     s2v_interpolation: str = field(
         metadata={
             "help_string": "interpolation method for s2v movement estimation.",
-            "argstr": "--s2v_interp",
+            "argstr": "--s2v_interp={s2v_interpolation}",
             "allowed_values": {"spline", "trilinear"},
         }
     )
 
     slice_grouping_file: PathLike = field(
         metadata={
             "help_string": "file containing slice grouping information",
-            "argstr": "--slspec",
+            "argstr": "--slspec={slice_grouping_file}",
             "xor": {"slice_timing_file"},
         }
     )
 
     slice_timing_file: PathLike = field(
         metadata={
             "help_string": "file containing slice timing information",
-            "argstr": "--json",
+            "argstr": "--json={slice_timing_file}",
             "xor": {"slice_grouping_file"},
         }
     )
@@ -223,23 +274,23 @@ class EddySpec(ShellSpec):
     mbs_num_iterations: int = field(
         metadata={
             "help_string": "number of iterations for MBS field estimation",
-            "argstr": "--mbs_niter",
+            "argstr": "--mbs_niter={mbs_num_iterations}",
             "requires": {"estimate_move_by_susceptibility"},
         }
     )
 
     mbs_lambda: int = field(
         metadata={
             "help_string": "weighting of regularization for MBS field estimation",
-            "argstr": "--mbs_lambda",
+            "argstr": "--mbs_lambda={mbs_lambda}",
             "requires": {"estimate_move_by_susceptibility"},
         }
     )
 
     mbs_knot_spacing: int = field(
         metadata={
             "help_string": "knot-spacing for MBS field estimation",
-            "argstr": "--mbs_ksp",
+            "argstr": "--mbs_ksp={mbs_knot_spacing}",
             "requires": {"estimate_move_by_susceptibility"},
         }
     )
@@ -249,7 +300,9 @@ class EddySpec(ShellSpec):
         metadata={"help_string": "bypass checks for data shelling", "argstr": "--data_is_shelled"}
     )
 
-    random_seed: int = field(metadata={"help_string": "random seed for voxel selection", "argstr": "--initrand"})
+    random_seed: int = field(
+        metadata={"help_string": "random seed for voxel selection", "argstr": "--initrand={random_seed}"}
+    )
 
     save_cnr_maps: bool = field(metadata={"help_string": "save shell-wise CNR maps", "argstr": "--cnr_maps"})