niwrap-freesurfer 0.6.2__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/make_folding_atlas.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MAKE_FOLDING_ATLAS_METADATA = Metadata(
-    id="5c53218428de33badf3c43ee3c12c11136a54df8.boutiques",
+    id="153fb163dd26597740f452df478d4ac29c867616.boutiques",
     name="make_folding_atlas",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,30 @@ MAKE_FOLDING_ATLAS_METADATA = Metadata(
 
 
 MakeFoldingAtlasParameters = typing.TypedDict('MakeFoldingAtlasParameters', {
-    "__STYXTYPE__": typing.Literal["make_folding_atlas"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/make_folding_atlas"]],
+    "subjlistfile": typing.NotRequired[InputPathType | None],
+    "fsgdfile": typing.NotRequired[InputPathType | None],
+    "subjects": typing.NotRequired[list[str] | None],
+    "output_base": typing.NotRequired[str | None],
+    "max_iterations": typing.NotRequired[float | None],
+    "xhemi": bool,
+    "init_surf_reg": typing.NotRequired[str | None],
+    "init_subject": typing.NotRequired[str | None],
+    "no_annot_template": bool,
+    "left_hemisphere": bool,
+    "right_hemisphere": bool,
+    "lhrh": bool,
+    "ico_order": typing.NotRequired[float | None],
+    "no_vol_on_last": bool,
+    "vol": bool,
+    "init": bool,
+    "short_sleep": bool,
+    "no_template_only": bool,
+    "threads": typing.NotRequired[float | None],
+    "slurm_account": typing.NotRequired[str | None],
+})
+MakeFoldingAtlasParametersTagged = typing.TypedDict('MakeFoldingAtlasParametersTagged', {
+    "@type": typing.Literal["freesurfer/make_folding_atlas"],
     "subjlistfile": typing.NotRequired[InputPathType | None],
     "fsgdfile": typing.NotRequired[InputPathType | None],
     "subjects": typing.NotRequired[list[str] | None],
@@ -36,49 +59,14 @@ MakeFoldingAtlasParameters = typing.TypedDict('MakeFoldingAtlasParameters', {
     "threads": typing.NotRequired[float | None],
     "slurm_account": typing.NotRequired[str | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "make_folding_atlas": make_folding_atlas_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-        "make_folding_atlas": make_folding_atlas_outputs,
-    }.get(t)
 
 
 class MakeFoldingAtlasOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `make_folding_atlas(...)`.
+    Output object returned when calling `MakeFoldingAtlasParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    average_subject_folder: OutputPathType | None
-    """Average subject folder that contains the atlas files for each
-    iteration."""
 
 
 def make_folding_atlas_params(
@@ -102,7 +90,7 @@ def make_folding_atlas_params(
     no_template_only: bool = False,
     threads: float | None = None,
     slurm_account: str | None = None,
-) -> MakeFoldingAtlasParameters:
+) -> MakeFoldingAtlasParametersTagged:
     """
     Build parameters.
     
@@ -136,7 +124,7 @@ def make_folding_atlas_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "make_folding_atlas",
+        "@type": "freesurfer/make_folding_atlas",
         "xhemi": xhemi,
         "no_annot_template": no_annot_template,
         "left_hemisphere": left_hemisphere,
@@ -186,75 +174,75 @@ def make_folding_atlas_cargs(
     """
     cargs = []
     cargs.append("make_folding_atlas")
-    if params.get("subjlistfile") is not None:
+    if params.get("subjlistfile", None) is not None:
         cargs.extend([
             "--f",
-            execution.input_file(params.get("subjlistfile"))
+            execution.input_file(params.get("subjlistfile", None))
         ])
-    if params.get("fsgdfile") is not None:
+    if params.get("fsgdfile", None) is not None:
         cargs.extend([
             "--fsgd",
-            execution.input_file(params.get("fsgdfile"))
+            execution.input_file(params.get("fsgdfile", None))
         ])
-    if params.get("subjects") is not None:
+    if params.get("subjects", None) is not None:
         cargs.extend([
             "--s",
-            *params.get("subjects")
+            *params.get("subjects", None)
         ])
-    if params.get("output_base") is not None:
+    if params.get("output_base", None) is not None:
         cargs.extend([
             "--b",
-            params.get("output_base")
+            params.get("output_base", None)
         ])
-    if params.get("max_iterations") is not None:
+    if params.get("max_iterations", None) is not None:
         cargs.extend([
             "--nmax",
-            str(params.get("max_iterations"))
+            str(params.get("max_iterations", None))
         ])
-    if params.get("xhemi"):
+    if params.get("xhemi", False):
         cargs.append("--xhemi")
-    if params.get("init_surf_reg") is not None:
+    if params.get("init_surf_reg", None) is not None:
         cargs.extend([
             "--init-surf-reg",
-            params.get("init_surf_reg")
+            params.get("init_surf_reg", None)
         ])
-    if params.get("init_subject") is not None:
+    if params.get("init_subject", None) is not None:
         cargs.extend([
             "--init-subject",
-            params.get("init_subject")
+            params.get("init_subject", None)
         ])
-    if params.get("no_annot_template"):
+    if params.get("no_annot_template", False):
         cargs.append("--no-annot-template")
-    if params.get("left_hemisphere"):
+    if params.get("left_hemisphere", False):
         cargs.append("--lh")
-    if params.get("right_hemisphere"):
+    if params.get("right_hemisphere", False):
         cargs.append("--rh")
-    if params.get("lhrh"):
+    if params.get("lhrh", False):
         cargs.append("--lhrh")
-    if params.get("ico_order") is not None:
+    if params.get("ico_order", None) is not None:
         cargs.extend([
             "--ico",
-            str(params.get("ico_order"))
+            str(params.get("ico_order", None))
         ])
-    if params.get("no_vol_on_last"):
+    if params.get("no_vol_on_last", False):
         cargs.append("--no-vol-on-last")
-    if params.get("vol"):
+    if params.get("vol", False):
         cargs.append("--vol")
-    if params.get("init"):
+    if params.get("init", False):
         cargs.append("--init")
-    if params.get("short_sleep"):
+    if params.get("short_sleep", False):
         cargs.append("--short-sleep")
-    if params.get("no_template_only"):
+    if params.get("no_template_only", False):
         cargs.append("--no-template-only")
-    if params.get("threads") is not None:
+    if params.get("threads", None) is not None:
         cargs.extend([
             "--threads",
-            str(params.get("threads"))
+            str(params.get("threads", None))
         ])
-    if params.get("slurm_account") is not None:
+    if params.get("slurm_account", None) is not None:
         cargs.extend([
             "--account",
-            params.get("slurm_account")
+            params.get("slurm_account", None)
         ])
     return cargs
 
@@ -274,16 +262,17 @@ def make_folding_atlas_outputs(
     """
     ret = MakeFoldingAtlasOutputs(
         root=execution.output_file("."),
-        average_subject_folder=execution.output_file(params.get("output_base") + ".i*") if (params.get("output_base") is not None) else None,
     )
     return ret
 
 
 def make_folding_atlas_execute(
     params: MakeFoldingAtlasParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MakeFoldingAtlasOutputs:
     """
+    make_folding_atlas
+    
     Script to iteratively create a cortical folding atlas.
     
     Author: FreeSurfer Developers
@@ -292,10 +281,12 @@ def make_folding_atlas_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MakeFoldingAtlasOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MAKE_FOLDING_ATLAS_METADATA)
     params = execution.params(params)
     cargs = make_folding_atlas_cargs(params, execution)
     ret = make_folding_atlas_outputs(params, execution)
@@ -327,6 +318,8 @@ def make_folding_atlas(
     runner: Runner | None = None,
 ) -> MakeFoldingAtlasOutputs:
     """
+    make_folding_atlas
+    
     Script to iteratively create a cortical folding atlas.
     
     Author: FreeSurfer Developers
@@ -363,8 +356,6 @@ def make_folding_atlas(
     Returns:
         NamedTuple of outputs (described in `MakeFoldingAtlasOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MAKE_FOLDING_ATLAS_METADATA)
     params = make_folding_atlas_params(
         subjlistfile=subjlistfile,
         fsgdfile=fsgdfile,
@@ -387,13 +378,13 @@ def make_folding_atlas(
         threads=threads,
         slurm_account=slurm_account,
     )
-    return make_folding_atlas_execute(params, execution)
+    return make_folding_atlas_execute(params, runner)
 
 
 __all__ = [
     "MAKE_FOLDING_ATLAS_METADATA",
     "MakeFoldingAtlasOutputs",
-    "MakeFoldingAtlasParameters",
     "make_folding_atlas",
+    "make_folding_atlas_execute",
     "make_folding_atlas_params",
 ]

niwrap_freesurfer/freesurfer/make_hemi_mask.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MAKE_HEMI_MASK_METADATA = Metadata(
-    id="b15d79958c2f6378c79d67869d258254bc5455d0.boutiques",
+    id="4b94a6ae8c0d8d637191b874a8b7d772a046b018.boutiques",
     name="make_hemi_mask",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ MAKE_HEMI_MASK_METADATA = Metadata(
 
 
 MakeHemiMaskParameters = typing.TypedDict('MakeHemiMaskParameters', {
-    "__STYXTYPE__": typing.Literal["make_hemi_mask"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/make_hemi_mask"]],
+    "hemi": str,
+    "input_file": InputPathType,
+    "output_file": str,
+})
+MakeHemiMaskParametersTagged = typing.TypedDict('MakeHemiMaskParametersTagged', {
+    "@type": typing.Literal["freesurfer/make_hemi_mask"],
     "hemi": str,
     "input_file": InputPathType,
     "output_file": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "make_hemi_mask": make_hemi_mask_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-        "make_hemi_mask": make_hemi_mask_outputs,
-    }.get(t)
 
 
 class MakeHemiMaskOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `make_hemi_mask(...)`.
+    Output object returned when calling `MakeHemiMaskParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def make_hemi_mask_params(
     hemi: str,
     input_file: InputPathType,
     output_file: str,
-) -> MakeHemiMaskParameters:
+) -> MakeHemiMaskParametersTagged:
     """
     Build parameters.
     
@@ -80,7 +54,7 @@ def make_hemi_mask_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "make_hemi_mask",
+        "@type": "freesurfer/make_hemi_mask",
         "hemi": hemi,
         "input_file": input_file,
         "output_file": output_file,
@@ -103,9 +77,9 @@ def make_hemi_mask_cargs(
     """
     cargs = []
     cargs.append("make_hemi_mask")
-    cargs.append(params.get("hemi"))
-    cargs.append(execution.input_file(params.get("input_file")))
-    cargs.append(params.get("output_file"))
+    cargs.append(params.get("hemi", None))
+    cargs.append(execution.input_file(params.get("input_file", None)))
+    cargs.append(params.get("output_file", None))
     return cargs
 
 
@@ -124,16 +98,18 @@ def make_hemi_mask_outputs(
     """
     ret = MakeHemiMaskOutputs(
         root=execution.output_file("."),
-        outfile=execution.output_file(params.get("output_file")),
+        outfile=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def make_hemi_mask_execute(
     params: MakeHemiMaskParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MakeHemiMaskOutputs:
     """
+    make_hemi_mask
+    
     Generates a hemisphere mask by registering input to the left/right reversed
     version using mri_robust_register, then keeps only the selected hemisphere.
     
@@ -143,10 +119,12 @@ def make_hemi_mask_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MakeHemiMaskOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MAKE_HEMI_MASK_METADATA)
     params = execution.params(params)
     cargs = make_hemi_mask_cargs(params, execution)
     ret = make_hemi_mask_outputs(params, execution)
@@ -161,6 +139,8 @@ def make_hemi_mask(
     runner: Runner | None = None,
 ) -> MakeHemiMaskOutputs:
     """
+    make_hemi_mask
+    
     Generates a hemisphere mask by registering input to the left/right reversed
     version using mri_robust_register, then keeps only the selected hemisphere.
     
@@ -177,20 +157,18 @@ def make_hemi_mask(
     Returns:
         NamedTuple of outputs (described in `MakeHemiMaskOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MAKE_HEMI_MASK_METADATA)
     params = make_hemi_mask_params(
         hemi=hemi,
         input_file=input_file,
         output_file=output_file,
     )
-    return make_hemi_mask_execute(params, execution)
+    return make_hemi_mask_execute(params, runner)
 
 
 __all__ = [
     "MAKE_HEMI_MASK_METADATA",
     "MakeHemiMaskOutputs",
-    "MakeHemiMaskParameters",
     "make_hemi_mask",
+    "make_hemi_mask_execute",
     "make_hemi_mask_params",
 ]

niwrap_freesurfer/freesurfer/make_segvol_table.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MAKE_SEGVOL_TABLE_METADATA = Metadata(
-    id="b482a517b89a3c5621f48031455d531957274674.boutiques",
+    id="2dee9099ff0b7fdeae8bb8b1fdb070731c25ef0f.boutiques",
     name="make-segvol-table",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,20 @@ MAKE_SEGVOL_TABLE_METADATA = Metadata(
 
 
 MakeSegvolTableParameters = typing.TypedDict('MakeSegvolTableParameters', {
-    "__STYXTYPE__": typing.Literal["make-segvol-table"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/make-segvol-table"]],
+    "subjects": list[str],
+    "subject_file": InputPathType,
+    "outfile": str,
+    "idmap": typing.NotRequired[InputPathType | None],
+    "structure_ids": typing.NotRequired[list[str] | None],
+    "segdir": typing.NotRequired[str | None],
+    "subjects_dir": typing.NotRequired[str | None],
+    "umask": typing.NotRequired[str | None],
+    "version": bool,
+    "help": bool,
+})
+MakeSegvolTableParametersTagged = typing.TypedDict('MakeSegvolTableParametersTagged', {
+    "@type": typing.Literal["freesurfer/make-segvol-table"],
     "subjects": list[str],
     "subject_file": InputPathType,
     "outfile": str,
@@ -26,43 +39,11 @@ MakeSegvolTableParameters = typing.TypedDict('MakeSegvolTableParameters', {
     "version": bool,
     "help": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "make-segvol-table": make_segvol_table_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-        "make-segvol-table": make_segvol_table_outputs,
-    }.get(t)
 
 
 class MakeSegvolTableOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `make_segvol_table(...)`.
+    Output object returned when calling `MakeSegvolTableParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -82,7 +63,7 @@ def make_segvol_table_params(
     umask: str | None = None,
     version: bool = False,
     help_: bool = False,
-) -> MakeSegvolTableParameters:
+) -> MakeSegvolTableParametersTagged:
     """
     Build parameters.
     
@@ -105,7 +86,7 @@ def make_segvol_table_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "make-segvol-table",
+        "@type": "freesurfer/make-segvol-table",
         "subjects": subjects,
         "subject_file": subject_file,
         "outfile": outfile,
@@ -142,44 +123,44 @@ def make_segvol_table_cargs(
     cargs.append("make-segvol-table")
     cargs.extend([
         "-s",
-        *params.get("subjects")
+        *params.get("subjects", None)
     ])
     cargs.extend([
         "-sf",
-        execution.input_file(params.get("subject_file"))
+        execution.input_file(params.get("subject_file", None))
     ])
     cargs.extend([
         "-o",
-        params.get("outfile")
+        params.get("outfile", None)
     ])
-    if params.get("idmap") is not None:
+    if params.get("idmap", None) is not None:
         cargs.extend([
             "-idmap",
-            execution.input_file(params.get("idmap"))
+            execution.input_file(params.get("idmap", None))
         ])
-    if params.get("structure_ids") is not None:
+    if params.get("structure_ids", None) is not None:
         cargs.extend([
             "-id",
-            *params.get("structure_ids")
+            *params.get("structure_ids", None)
         ])
-    if params.get("segdir") is not None:
+    if params.get("segdir", None) is not None:
         cargs.extend([
             "-segdir",
-            params.get("segdir")
+            params.get("segdir", None)
         ])
-    if params.get("subjects_dir") is not None:
+    if params.get("subjects_dir", None) is not None:
         cargs.extend([
             "-sd",
-            params.get("subjects_dir")
+            params.get("subjects_dir", None)
         ])
-    if params.get("umask") is not None:
+    if params.get("umask", None) is not None:
         cargs.extend([
             "-umask",
-            params.get("umask")
+            params.get("umask", None)
         ])
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("-version")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
     return cargs
 
@@ -199,16 +180,18 @@ def make_segvol_table_outputs(
     """
     ret = MakeSegvolTableOutputs(
         root=execution.output_file("."),
-        output_table=execution.output_file(params.get("outfile")),
+        output_table=execution.output_file(params.get("outfile", None)),
     )
     return ret
 
 
 def make_segvol_table_execute(
     params: MakeSegvolTableParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MakeSegvolTableOutputs:
     """
+    make-segvol-table
+    
     Creates a table of volumes of subcortical structures for a given list of
     subjects using FreeSurfer.
     
@@ -218,10 +201,12 @@ def make_segvol_table_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MakeSegvolTableOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MAKE_SEGVOL_TABLE_METADATA)
     params = execution.params(params)
     cargs = make_segvol_table_cargs(params, execution)
     ret = make_segvol_table_outputs(params, execution)
@@ -243,6 +228,8 @@ def make_segvol_table(
     runner: Runner | None = None,
 ) -> MakeSegvolTableOutputs:
     """
+    make-segvol-table
+    
     Creates a table of volumes of subcortical structures for a given list of
     subjects using FreeSurfer.
     
@@ -269,8 +256,6 @@ def make_segvol_table(
     Returns:
         NamedTuple of outputs (described in `MakeSegvolTableOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MAKE_SEGVOL_TABLE_METADATA)
     params = make_segvol_table_params(
         subjects=subjects,
         subject_file=subject_file,
@@ -283,13 +268,13 @@ def make_segvol_table(
         version=version,
         help_=help_,
     )
-    return make_segvol_table_execute(params, execution)
+    return make_segvol_table_execute(params, runner)
 
 
 __all__ = [
     "MAKE_SEGVOL_TABLE_METADATA",
     "MakeSegvolTableOutputs",
-    "MakeSegvolTableParameters",
     "make_segvol_table",
+    "make_segvol_table_execute",
     "make_segvol_table_params",
 ]