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

niwrap_freesurfer/freesurfer/mri_fslmat_to_lta.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_FSLMAT_TO_LTA_METADATA = Metadata(
-    id="43d6ea5a8918dcf72ca72861a59575adb4671e75.boutiques",
+    id="652c7278bbf588b572170b8876e93b2e9013d33f.boutiques",
     name="mri_fslmat_to_lta",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ MRI_FSLMAT_TO_LTA_METADATA = Metadata(
 
 
 MriFslmatToLtaParameters = typing.TypedDict('MriFslmatToLtaParameters', {
-    "__STYXTYPE__": typing.Literal["mri_fslmat_to_lta"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_fslmat_to_lta"]],
+    "src_vol": InputPathType,
+    "target_vol": InputPathType,
+    "fslmat_file": InputPathType,
+    "lta_file": str,
+})
+MriFslmatToLtaParametersTagged = typing.TypedDict('MriFslmatToLtaParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_fslmat_to_lta"],
     "src_vol": InputPathType,
     "target_vol": InputPathType,
     "fslmat_file": InputPathType,
     "lta_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 {
-        "mri_fslmat_to_lta": mri_fslmat_to_lta_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 {
-        "mri_fslmat_to_lta": mri_fslmat_to_lta_outputs,
-    }.get(t)
 
 
 class MriFslmatToLtaOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_fslmat_to_lta(...)`.
+    Output object returned when calling `MriFslmatToLtaParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -70,7 +45,7 @@ def mri_fslmat_to_lta_params(
     target_vol: InputPathType,
     fslmat_file: InputPathType,
     lta_file: str,
-) -> MriFslmatToLtaParameters:
+) -> MriFslmatToLtaParametersTagged:
     """
     Build parameters.
     
@@ -83,7 +58,7 @@ def mri_fslmat_to_lta_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_fslmat_to_lta",
+        "@type": "freesurfer/mri_fslmat_to_lta",
         "src_vol": src_vol,
         "target_vol": target_vol,
         "fslmat_file": fslmat_file,
@@ -107,10 +82,10 @@ def mri_fslmat_to_lta_cargs(
     """
     cargs = []
     cargs.append("mri_fslmat_to_lta")
-    cargs.append(execution.input_file(params.get("src_vol")))
-    cargs.append(execution.input_file(params.get("target_vol")))
-    cargs.append(execution.input_file(params.get("fslmat_file")))
-    cargs.append(params.get("lta_file"))
+    cargs.append(execution.input_file(params.get("src_vol", None)))
+    cargs.append(execution.input_file(params.get("target_vol", None)))
+    cargs.append(execution.input_file(params.get("fslmat_file", None)))
+    cargs.append(params.get("lta_file", None))
     return cargs
 
 
@@ -129,18 +104,20 @@ def mri_fslmat_to_lta_outputs(
     """
     ret = MriFslmatToLtaOutputs(
         root=execution.output_file("."),
-        output_lta_file=execution.output_file(params.get("lta_file")),
+        output_lta_file=execution.output_file(params.get("lta_file", None)),
     )
     return ret
 
 
 def mri_fslmat_to_lta_execute(
     params: MriFslmatToLtaParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriFslmatToLtaOutputs:
     """
-    This program creates the LTA transformation file using information from the src
-    and target volumes and an FSL matrix file.
+    mri_fslmat_to_lta
+    
+    This program creates the LTA transformation file using information from the
+    src and target volumes and an FSL matrix file.
     
     Author: FreeSurfer Developers
     
@@ -148,10 +125,12 @@ def mri_fslmat_to_lta_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriFslmatToLtaOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_FSLMAT_TO_LTA_METADATA)
     params = execution.params(params)
     cargs = mri_fslmat_to_lta_cargs(params, execution)
     ret = mri_fslmat_to_lta_outputs(params, execution)
@@ -167,8 +146,10 @@ def mri_fslmat_to_lta(
     runner: Runner | None = None,
 ) -> MriFslmatToLtaOutputs:
     """
-    This program creates the LTA transformation file using information from the src
-    and target volumes and an FSL matrix file.
+    mri_fslmat_to_lta
+    
+    This program creates the LTA transformation file using information from the
+    src and target volumes and an FSL matrix file.
     
     Author: FreeSurfer Developers
     
@@ -183,21 +164,19 @@ def mri_fslmat_to_lta(
     Returns:
         NamedTuple of outputs (described in `MriFslmatToLtaOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_FSLMAT_TO_LTA_METADATA)
     params = mri_fslmat_to_lta_params(
         src_vol=src_vol,
         target_vol=target_vol,
         fslmat_file=fslmat_file,
         lta_file=lta_file,
     )
-    return mri_fslmat_to_lta_execute(params, execution)
+    return mri_fslmat_to_lta_execute(params, runner)
 
 
 __all__ = [
     "MRI_FSLMAT_TO_LTA_METADATA",
     "MriFslmatToLtaOutputs",
-    "MriFslmatToLtaParameters",
     "mri_fslmat_to_lta",
+    "mri_fslmat_to_lta_execute",
     "mri_fslmat_to_lta_params",
 ]

niwrap_freesurfer/freesurfer/mri_func2sph.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_FUNC2SPH_METADATA = Metadata(
-    id="07527586a882465863cf7ef1f979d3d044731e6d.boutiques",
+    id="513183fc43583bba0e42d4b2f95a3e588f6e1b58.boutiques",
     name="mri-func2sph",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,18 @@ MRI_FUNC2SPH_METADATA = Metadata(
 
 
 MriFunc2sphParameters = typing.TypedDict('MriFunc2sphParameters', {
-    "__STYXTYPE__": typing.Literal["mri-func2sph"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri-func2sph"]],
+    "instem": str,
+    "outstem": str,
+    "hemisphere": typing.Literal["lh", "rh"],
+    "fvitdir": str,
+    "hole_filling_iters": typing.NotRequired[float | None],
+    "icosahedron_size": typing.NotRequired[float | None],
+    "input_type": typing.NotRequired[str | None],
+    "umask": typing.NotRequired[str | None],
+})
+MriFunc2sphParametersTagged = typing.TypedDict('MriFunc2sphParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri-func2sph"],
     "instem": str,
     "outstem": str,
     "hemisphere": typing.Literal["lh", "rh"],
@@ -24,42 +35,11 @@ MriFunc2sphParameters = typing.TypedDict('MriFunc2sphParameters', {
     "input_type": typing.NotRequired[str | None],
     "umask": 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 {
-        "mri-func2sph": mri_func2sph_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 {
-    }.get(t)
 
 
 class MriFunc2sphOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_func2sph(...)`.
+    Output object returned when calling `MriFunc2sphParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -70,11 +50,11 @@ def mri_func2sph_params(
     outstem: str,
     hemisphere: typing.Literal["lh", "rh"],
     fvitdir: str,
-    hole_filling_iters: float | None = 100,
-    icosahedron_size: float | None = 10242,
+    hole_filling_iters: float | None = None,
+    icosahedron_size: float | None = None,
     input_type: str | None = None,
     umask: str | None = None,
-) -> MriFunc2sphParameters:
+) -> MriFunc2sphParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +71,7 @@ def mri_func2sph_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri-func2sph",
+        "@type": "freesurfer/mri-func2sph",
         "instem": instem,
         "outstem": outstem,
         "hemisphere": hemisphere,
@@ -125,39 +105,39 @@ def mri_func2sph_cargs(
     cargs.append("mri-func2sph")
     cargs.extend([
         "-i",
-        params.get("instem")
+        params.get("instem", None)
     ])
     cargs.extend([
         "-o",
-        params.get("outstem")
+        params.get("outstem", None)
     ])
     cargs.extend([
         "-hemi",
-        params.get("hemisphere")
+        params.get("hemisphere", None)
     ])
     cargs.extend([
         "-fvitdir",
-        params.get("fvitdir")
+        params.get("fvitdir", None)
     ])
-    if params.get("hole_filling_iters") is not None:
+    if params.get("hole_filling_iters", None) is not None:
         cargs.extend([
             "-niters",
-            str(params.get("hole_filling_iters"))
+            str(params.get("hole_filling_iters", None))
         ])
-    if params.get("icosahedron_size") is not None:
+    if params.get("icosahedron_size", None) is not None:
         cargs.extend([
             "-icosize",
-            str(params.get("icosahedron_size"))
+            str(params.get("icosahedron_size", None))
         ])
-    if params.get("input_type") is not None:
+    if params.get("input_type", None) is not None:
         cargs.extend([
             "-intype",
-            params.get("input_type")
+            params.get("input_type", 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)
         ])
     return cargs
 
@@ -183,9 +163,11 @@ def mri_func2sph_outputs(
 
 def mri_func2sph_execute(
     params: MriFunc2sphParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriFunc2sphOutputs:
     """
+    mri-func2sph
+    
     Maps functional data from volume space to spherical surface space.
     
     Author: FreeSurfer Developers
@@ -194,10 +176,12 @@ def mri_func2sph_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriFunc2sphOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_FUNC2SPH_METADATA)
     params = execution.params(params)
     cargs = mri_func2sph_cargs(params, execution)
     ret = mri_func2sph_outputs(params, execution)
@@ -210,13 +194,15 @@ def mri_func2sph(
     outstem: str,
     hemisphere: typing.Literal["lh", "rh"],
     fvitdir: str,
-    hole_filling_iters: float | None = 100,
-    icosahedron_size: float | None = 10242,
+    hole_filling_iters: float | None = None,
+    icosahedron_size: float | None = None,
     input_type: str | None = None,
     umask: str | None = None,
     runner: Runner | None = None,
 ) -> MriFunc2sphOutputs:
     """
+    mri-func2sph
+    
     Maps functional data from volume space to spherical surface space.
     
     Author: FreeSurfer Developers
@@ -236,8 +222,6 @@ def mri_func2sph(
     Returns:
         NamedTuple of outputs (described in `MriFunc2sphOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_FUNC2SPH_METADATA)
     params = mri_func2sph_params(
         instem=instem,
         outstem=outstem,
@@ -248,13 +232,13 @@ def mri_func2sph(
         input_type=input_type,
         umask=umask,
     )
-    return mri_func2sph_execute(params, execution)
+    return mri_func2sph_execute(params, runner)
 
 
 __all__ = [
     "MRI_FUNC2SPH_METADATA",
     "MriFunc2sphOutputs",
-    "MriFunc2sphParameters",
     "mri_func2sph",
+    "mri_func2sph_execute",
     "mri_func2sph_params",
 ]

niwrap_freesurfer/freesurfer/mri_funcvits.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_FUNCVITS_METADATA = Metadata(
-    id="c31b3fea785150e0e49672d8b3bcc550b5d3bfdb.boutiques",
+    id="1540b967af27194342e796045e007f5e105616e5.boutiques",
     name="mri-funcvits",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,22 @@ MRI_FUNCVITS_METADATA = Metadata(
 
 
 MriFuncvitsParameters = typing.TypedDict('MriFuncvitsParameters', {
-    "__STYXTYPE__": typing.Literal["mri-funcvits"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri-funcvits"]],
+    "stem": str,
+    "outdir": str,
+    "reg": typing.NotRequired[str | None],
+    "paintsurf": typing.NotRequired[str | None],
+    "sphere": typing.NotRequired[str | None],
+    "icosize": typing.NotRequired[int | None],
+    "hemi": typing.NotRequired[list[str] | None],
+    "svitdir": typing.NotRequired[str | None],
+    "icodir": typing.NotRequired[str | None],
+    "umask": typing.NotRequired[str | None],
+    "mail": typing.NotRequired[str | None],
+    "noforce": bool,
+})
+MriFuncvitsParametersTagged = typing.TypedDict('MriFuncvitsParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri-funcvits"],
     "stem": str,
     "outdir": str,
     "reg": typing.NotRequired[str | None],
@@ -28,42 +43,11 @@ MriFuncvitsParameters = typing.TypedDict('MriFuncvitsParameters', {
     "mail": typing.NotRequired[str | None],
     "noforce": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mri-funcvits": mri_funcvits_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 {
-    }.get(t)
 
 
 class MriFuncvitsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_funcvits(...)`.
+    Output object returned when calling `MriFuncvitsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,16 +57,16 @@ def mri_funcvits_params(
     stem: str,
     outdir: str,
     reg: str | None = None,
-    paintsurf: str | None = "white",
-    sphere: str | None = "sphere",
-    icosize: int | None = 10242,
+    paintsurf: str | None = None,
+    sphere: str | None = None,
+    icosize: int | None = None,
     hemi: list[str] | None = None,
     svitdir: str | None = None,
-    icodir: str | None = "/usr/local/freesurfer/lib/bem",
+    icodir: str | None = None,
     umask: str | None = None,
     mail: str | None = None,
     noforce: bool = False,
-) -> MriFuncvitsParameters:
+) -> MriFuncvitsParametersTagged:
     """
     Build parameters.
     
@@ -103,7 +87,7 @@ def mri_funcvits_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri-funcvits",
+        "@type": "freesurfer/mri-funcvits",
         "stem": stem,
         "outdir": outdir,
         "noforce": noforce,
@@ -146,58 +130,58 @@ def mri_funcvits_cargs(
     cargs.append("mri-funcvits")
     cargs.extend([
         "--stem",
-        params.get("stem")
+        params.get("stem", None)
     ])
     cargs.extend([
         "--outdir",
-        params.get("outdir")
+        params.get("outdir", None)
     ])
-    if params.get("reg") is not None:
+    if params.get("reg", None) is not None:
         cargs.extend([
             "--reg",
-            params.get("reg")
+            params.get("reg", None)
         ])
-    if params.get("paintsurf") is not None:
+    if params.get("paintsurf", None) is not None:
         cargs.extend([
             "--paintsurf",
-            params.get("paintsurf")
+            params.get("paintsurf", None)
         ])
-    if params.get("sphere") is not None:
+    if params.get("sphere", None) is not None:
         cargs.extend([
             "--sphere",
-            params.get("sphere")
+            params.get("sphere", None)
         ])
-    if params.get("icosize") is not None:
+    if params.get("icosize", None) is not None:
         cargs.extend([
             "--icosize",
-            str(params.get("icosize"))
+            str(params.get("icosize", None))
         ])
-    if params.get("hemi") is not None:
+    if params.get("hemi", None) is not None:
         cargs.extend([
             "--hemi",
-            *params.get("hemi")
+            *params.get("hemi", None)
         ])
-    if params.get("svitdir") is not None:
+    if params.get("svitdir", None) is not None:
         cargs.extend([
             "--svitdir",
-            params.get("svitdir")
+            params.get("svitdir", None)
         ])
-    if params.get("icodir") is not None:
+    if params.get("icodir", None) is not None:
         cargs.extend([
             "--icodir",
-            params.get("icodir")
+            params.get("icodir", 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("mail") is not None:
+    if params.get("mail", None) is not None:
         cargs.extend([
             "--mail",
-            params.get("mail")
+            params.get("mail", None)
         ])
-    if params.get("noforce"):
+    if params.get("noforce", False):
         cargs.append("--noforce")
     return cargs
 
@@ -223,9 +207,11 @@ def mri_funcvits_outputs(
 
 def mri_funcvits_execute(
     params: MriFuncvitsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriFuncvitsOutputs:
     """
+    mri-funcvits
+    
     Tool for functional volume to surface conversion in neuroimaging analysis.
     
     Author: FreeSurfer Developers
@@ -234,10 +220,12 @@ def mri_funcvits_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriFuncvitsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_FUNCVITS_METADATA)
     params = execution.params(params)
     cargs = mri_funcvits_cargs(params, execution)
     ret = mri_funcvits_outputs(params, execution)
@@ -249,18 +237,20 @@ def mri_funcvits(
     stem: str,
     outdir: str,
     reg: str | None = None,
-    paintsurf: str | None = "white",
-    sphere: str | None = "sphere",
-    icosize: int | None = 10242,
+    paintsurf: str | None = None,
+    sphere: str | None = None,
+    icosize: int | None = None,
     hemi: list[str] | None = None,
     svitdir: str | None = None,
-    icodir: str | None = "/usr/local/freesurfer/lib/bem",
+    icodir: str | None = None,
     umask: str | None = None,
     mail: str | None = None,
     noforce: bool = False,
     runner: Runner | None = None,
 ) -> MriFuncvitsOutputs:
     """
+    mri-funcvits
+    
     Tool for functional volume to surface conversion in neuroimaging analysis.
     
     Author: FreeSurfer Developers
@@ -284,8 +274,6 @@ def mri_funcvits(
     Returns:
         NamedTuple of outputs (described in `MriFuncvitsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_FUNCVITS_METADATA)
     params = mri_funcvits_params(
         stem=stem,
         outdir=outdir,
@@ -300,13 +288,13 @@ def mri_funcvits(
         mail=mail,
         noforce=noforce,
     )
-    return mri_funcvits_execute(params, execution)
+    return mri_funcvits_execute(params, runner)
 
 
 __all__ = [
     "MRI_FUNCVITS_METADATA",
     "MriFuncvitsOutputs",
-    "MriFuncvitsParameters",
     "mri_funcvits",
+    "mri_funcvits_execute",
     "mri_funcvits_params",
 ]