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

niwrap_freesurfer/freesurfer/biasfield.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 BIASFIELD_METADATA = Metadata(
-    id="5981ee8ca338526bd3e95eb71c3b7956f4c7d239.boutiques",
+    id="791c68624f21165063a1669d3c6117e3219b6789.boutiques",
     name="biasfield",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ BIASFIELD_METADATA = Metadata(
 
 
 BiasfieldParameters = typing.TypedDict('BiasfieldParameters', {
-    "__STYXTYPE__": typing.Literal["biasfield"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/biasfield"]],
+    "subject": str,
+    "tmpdir": typing.NotRequired[str | None],
+    "no_cleanup": bool,
+    "help": bool,
+    "debug": bool,
+    "version": bool,
+})
+BiasfieldParametersTagged = typing.TypedDict('BiasfieldParametersTagged', {
+    "@type": typing.Literal["freesurfer/biasfield"],
     "subject": str,
     "tmpdir": typing.NotRequired[str | None],
     "no_cleanup": bool,
@@ -22,43 +31,11 @@ BiasfieldParameters = typing.TypedDict('BiasfieldParameters', {
     "debug": bool,
     "version": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "biasfield": biasfield_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 {
-        "biasfield": biasfield_outputs,
-    }.get(t)
 
 
 class BiasfieldOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `biasfield(...)`.
+    Output object returned when calling `BiasfieldParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +52,7 @@ def biasfield_params(
     help_: bool = False,
     debug: bool = False,
     version: bool = False,
-) -> BiasfieldParameters:
+) -> BiasfieldParametersTagged:
     """
     Build parameters.
     
@@ -90,7 +67,7 @@ def biasfield_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "biasfield",
+        "@type": "freesurfer/biasfield",
         "subject": subject,
         "no_cleanup": no_cleanup,
         "help": help_,
@@ -119,20 +96,20 @@ def biasfield_cargs(
     cargs.append("biasfield")
     cargs.extend([
         "--s",
-        params.get("subject")
+        params.get("subject", None)
     ])
-    if params.get("tmpdir") is not None:
+    if params.get("tmpdir", None) is not None:
         cargs.extend([
             "--tmp",
-            params.get("tmpdir")
+            params.get("tmpdir", None)
         ])
-    if params.get("no_cleanup"):
+    if params.get("no_cleanup", False):
         cargs.append("--nocleanup")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("--help")
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("--version")
     return cargs
 
@@ -160,10 +137,13 @@ def biasfield_outputs(
 
 def biasfield_execute(
     params: BiasfieldParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> BiasfieldOutputs:
     """
-    Computes the bias field by dividing the (unconformed) orig.mgz by the norm.mgz.
+    biasfield
+    
+    Computes the bias field by dividing the (unconformed) orig.mgz by the
+    norm.mgz.
     
     Author: FreeSurfer Developers
     
@@ -171,10 +151,12 @@ def biasfield_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `BiasfieldOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(BIASFIELD_METADATA)
     params = execution.params(params)
     cargs = biasfield_cargs(params, execution)
     ret = biasfield_outputs(params, execution)
@@ -192,7 +174,10 @@ def biasfield(
     runner: Runner | None = None,
 ) -> BiasfieldOutputs:
     """
-    Computes the bias field by dividing the (unconformed) orig.mgz by the norm.mgz.
+    biasfield
+    
+    Computes the bias field by dividing the (unconformed) orig.mgz by the
+    norm.mgz.
     
     Author: FreeSurfer Developers
     
@@ -209,8 +194,6 @@ def biasfield(
     Returns:
         NamedTuple of outputs (described in `BiasfieldOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(BIASFIELD_METADATA)
     params = biasfield_params(
         subject=subject,
         tmpdir=tmpdir,
@@ -219,13 +202,13 @@ def biasfield(
         debug=debug,
         version=version,
     )
-    return biasfield_execute(params, execution)
+    return biasfield_execute(params, runner)
 
 
 __all__ = [
     "BIASFIELD_METADATA",
     "BiasfieldOutputs",
-    "BiasfieldParameters",
     "biasfield",
+    "biasfield_execute",
     "biasfield_params",
 ]

niwrap_freesurfer/freesurfer/bmedits2surf.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 BMEDITS2SURF_METADATA = Metadata(
-    id="c1daef85bf5d51503b439d0cfd018ad263aba494.boutiques",
+    id="c47e55f7cd9d1ed03e771450953c43ca7b2b70e4.boutiques",
     name="bmedits2surf",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,20 @@ BMEDITS2SURF_METADATA = Metadata(
 
 
 Bmedits2surfParameters = typing.TypedDict('Bmedits2surfParameters', {
-    "__STYXTYPE__": typing.Literal["bmedits2surf"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/bmedits2surf"]],
+    "subject": str,
+    "self": bool,
+    "overwrite": bool,
+    "tmp_dir": typing.NotRequired[str | None],
+    "cleanup": bool,
+    "no_cleanup": bool,
+    "debug": bool,
+    "left_hemisphere": bool,
+    "right_hemisphere": bool,
+    "no_surfs": bool,
+})
+Bmedits2surfParametersTagged = typing.TypedDict('Bmedits2surfParametersTagged', {
+    "@type": typing.Literal["freesurfer/bmedits2surf"],
     "subject": str,
     "self": bool,
     "overwrite": bool,
@@ -26,43 +39,11 @@ Bmedits2surfParameters = typing.TypedDict('Bmedits2surfParameters', {
     "right_hemisphere": bool,
     "no_surfs": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "bmedits2surf": bmedits2surf_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 {
-        "bmedits2surf": bmedits2surf_outputs,
-    }.get(t)
 
 
 class Bmedits2surfOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `bmedits2surf(...)`.
+    Output object returned when calling `Bmedits2surfParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -95,7 +76,7 @@ def bmedits2surf_params(
     left_hemisphere: bool = False,
     right_hemisphere: bool = False,
     no_surfs: bool = False,
-) -> Bmedits2surfParameters:
+) -> Bmedits2surfParametersTagged:
     """
     Build parameters.
     
@@ -113,7 +94,7 @@ def bmedits2surf_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "bmedits2surf",
+        "@type": "freesurfer/bmedits2surf",
         "subject": subject,
         "self": self,
         "overwrite": overwrite,
@@ -146,28 +127,28 @@ def bmedits2surf_cargs(
     cargs.append("bmedits2surf")
     cargs.extend([
         "-s",
-        params.get("subject")
+        params.get("subject", None)
     ])
-    if params.get("self"):
+    if params.get("self", False):
         cargs.append("--self")
-    if params.get("overwrite"):
+    if params.get("overwrite", False):
         cargs.append("--overwrite")
-    if params.get("tmp_dir") is not None:
+    if params.get("tmp_dir", None) is not None:
         cargs.extend([
             "--tmp",
-            params.get("tmp_dir")
+            params.get("tmp_dir", None)
         ])
-    if params.get("cleanup"):
+    if params.get("cleanup", False):
         cargs.append("--cleanup")
-    if params.get("no_cleanup"):
+    if params.get("no_cleanup", False):
         cargs.append("--no-cleanup")
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
-    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("no_surfs"):
+    if params.get("no_surfs", False):
         cargs.append("--no-surfs")
     return cargs
 
@@ -187,21 +168,23 @@ def bmedits2surf_outputs(
     """
     ret = Bmedits2surfOutputs(
         root=execution.output_file("."),
-        lh_bmerase=execution.output_file(params.get("subject") + "/surf/lh.bmerase.fsa.mgh"),
-        rh_bmerase=execution.output_file(params.get("subject") + "/surf/rh.bmerase.fsa.mgh"),
-        lh_bmclone=execution.output_file(params.get("subject") + "/surf/lh.bmclone.fsa.mgh"),
-        rh_bmclone=execution.output_file(params.get("subject") + "/surf/rh.bmclone.fsa.mgh"),
-        bmclone_stats=execution.output_file(params.get("subject") + "/stats/bmclone.dat"),
-        bmerase_stats=execution.output_file(params.get("subject") + "/stats/bmerase.dat"),
+        lh_bmerase=execution.output_file(params.get("subject", None) + "/surf/lh.bmerase.fsa.mgh"),
+        rh_bmerase=execution.output_file(params.get("subject", None) + "/surf/rh.bmerase.fsa.mgh"),
+        lh_bmclone=execution.output_file(params.get("subject", None) + "/surf/lh.bmclone.fsa.mgh"),
+        rh_bmclone=execution.output_file(params.get("subject", None) + "/surf/rh.bmclone.fsa.mgh"),
+        bmclone_stats=execution.output_file(params.get("subject", None) + "/stats/bmclone.dat"),
+        bmerase_stats=execution.output_file(params.get("subject", None) + "/stats/bmerase.dat"),
     )
     return ret
 
 
 def bmedits2surf_execute(
     params: Bmedits2surfParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Bmedits2surfOutputs:
     """
+    bmedits2surf
+    
     Computes a binary map of surface locations where the brainmask.mgz has been
     edited.
     
@@ -211,10 +194,12 @@ def bmedits2surf_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Bmedits2surfOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(BMEDITS2SURF_METADATA)
     params = execution.params(params)
     cargs = bmedits2surf_cargs(params, execution)
     ret = bmedits2surf_outputs(params, execution)
@@ -236,6 +221,8 @@ def bmedits2surf(
     runner: Runner | None = None,
 ) -> Bmedits2surfOutputs:
     """
+    bmedits2surf
+    
     Computes a binary map of surface locations where the brainmask.mgz has been
     edited.
     
@@ -257,8 +244,6 @@ def bmedits2surf(
     Returns:
         NamedTuple of outputs (described in `Bmedits2surfOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(BMEDITS2SURF_METADATA)
     params = bmedits2surf_params(
         subject=subject,
         self=self,
@@ -271,13 +256,13 @@ def bmedits2surf(
         right_hemisphere=right_hemisphere,
         no_surfs=no_surfs,
     )
-    return bmedits2surf_execute(params, execution)
+    return bmedits2surf_execute(params, runner)
 
 
 __all__ = [
     "BMEDITS2SURF_METADATA",
     "Bmedits2surfOutputs",
-    "Bmedits2surfParameters",
     "bmedits2surf",
+    "bmedits2surf_execute",
     "bmedits2surf_params",
 ]

niwrap_freesurfer/freesurfer/brec.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 BREC_METADATA = Metadata(
-    id="b85a2d15360507de8faa909c425df2fb82e4ca9d.boutiques",
+    id="ce9f9f5bb497c6bb574e5731aafa611a10debdc6.boutiques",
     name="brec",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,20 @@ BREC_METADATA = Metadata(
 
 
 BrecParameters = typing.TypedDict('BrecParameters', {
-    "__STYXTYPE__": typing.Literal["brec"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/brec"]],
+    "my_file": str,
+    "depth_limit": bool,
+})
+BrecParametersTagged = typing.TypedDict('BrecParametersTagged', {
+    "@type": typing.Literal["freesurfer/brec"],
     "my_file": str,
     "depth_limit": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "brec": brec_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 BrecOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `brec(...)`.
+    Output object returned when calling `BrecParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -62,7 +36,7 @@ class BrecOutputs(typing.NamedTuple):
 def brec_params(
     my_file: str,
     depth_limit: bool = False,
-) -> BrecParameters:
+) -> BrecParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +47,7 @@ def brec_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "brec",
+        "@type": "freesurfer/brec",
         "my_file": my_file,
         "depth_limit": depth_limit,
     }
@@ -95,8 +69,8 @@ def brec_cargs(
     """
     cargs = []
     cargs.append("brec")
-    cargs.append(params.get("my_file"))
-    if params.get("depth_limit"):
+    cargs.append(params.get("my_file", None))
+    if params.get("depth_limit", False):
         cargs.append("-depth_limit")
     return cargs
 
@@ -122,9 +96,11 @@ def brec_outputs(
 
 def brec_execute(
     params: BrecParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> BrecOutputs:
     """
+    brec
+    
     A description for brec tool could not be retrieved.
     
     Author: FreeSurfer Developers
@@ -133,10 +109,12 @@ def brec_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `BrecOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(BREC_METADATA)
     params = execution.params(params)
     cargs = brec_cargs(params, execution)
     ret = brec_outputs(params, execution)
@@ -150,6 +128,8 @@ def brec(
     runner: Runner | None = None,
 ) -> BrecOutputs:
     """
+    brec
+    
     A description for brec tool could not be retrieved.
     
     Author: FreeSurfer Developers
@@ -163,19 +143,17 @@ def brec(
     Returns:
         NamedTuple of outputs (described in `BrecOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(BREC_METADATA)
     params = brec_params(
         my_file=my_file,
         depth_limit=depth_limit,
     )
-    return brec_execute(params, execution)
+    return brec_execute(params, runner)
 
 
 __all__ = [
     "BREC_METADATA",
     "BrecOutputs",
-    "BrecParameters",
     "brec",
+    "brec_execute",
     "brec_params",
 ]

niwrap_freesurfer/freesurfer/browse_minc_header_tcl.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 BROWSE_MINC_HEADER_TCL_METADATA = Metadata(
-    id="22e391d58621f276bcf2d734a8c66b008bb55ba4.boutiques",
+    id="bdcd4ebf4d35174bac49f3caff6d3c3854ff552f.boutiques",
     name="browse-minc-header.tcl",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ BROWSE_MINC_HEADER_TCL_METADATA = Metadata(
 
 
 BrowseMincHeaderTclParameters = typing.TypedDict('BrowseMincHeaderTclParameters', {
-    "__STYXTYPE__": typing.Literal["browse-minc-header.tcl"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/browse-minc-header.tcl"]],
+    "infile": InputPathType,
+})
+BrowseMincHeaderTclParametersTagged = typing.TypedDict('BrowseMincHeaderTclParametersTagged', {
+    "@type": typing.Literal["freesurfer/browse-minc-header.tcl"],
     "infile": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "browse-minc-header.tcl": browse_minc_header_tcl_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 BrowseMincHeaderTclOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `browse_minc_header_tcl(...)`.
+    Output object returned when calling `BrowseMincHeaderTclParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class BrowseMincHeaderTclOutputs(typing.NamedTuple):
 
 def browse_minc_header_tcl_params(
     infile: InputPathType,
-) -> BrowseMincHeaderTclParameters:
+) -> BrowseMincHeaderTclParametersTagged:
     """
     Build parameters.
     
@@ -70,7 +43,7 @@ def browse_minc_header_tcl_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "browse-minc-header.tcl",
+        "@type": "freesurfer/browse-minc-header.tcl",
         "infile": infile,
     }
     return params
@@ -91,7 +64,7 @@ def browse_minc_header_tcl_cargs(
     """
     cargs = []
     cargs.append("browse-minc-header.tcl")
-    cargs.append(execution.input_file(params.get("infile")))
+    cargs.append(execution.input_file(params.get("infile", None)))
     return cargs
 
 
@@ -116,10 +89,13 @@ def browse_minc_header_tcl_outputs(
 
 def browse_minc_header_tcl_execute(
     params: BrowseMincHeaderTclParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> BrowseMincHeaderTclOutputs:
     """
-    A tool for browsing MINC file headers, likely part of the FreeSurfer package.
+    browse-minc-header.tcl
+    
+    A tool for browsing MINC file headers, likely part of the FreeSurfer
+    package.
     
     Author: FreeSurfer Developers
     
@@ -127,10 +103,12 @@ def browse_minc_header_tcl_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `BrowseMincHeaderTclOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(BROWSE_MINC_HEADER_TCL_METADATA)
     params = execution.params(params)
     cargs = browse_minc_header_tcl_cargs(params, execution)
     ret = browse_minc_header_tcl_outputs(params, execution)
@@ -143,7 +121,10 @@ def browse_minc_header_tcl(
     runner: Runner | None = None,
 ) -> BrowseMincHeaderTclOutputs:
     """
-    A tool for browsing MINC file headers, likely part of the FreeSurfer package.
+    browse-minc-header.tcl
+    
+    A tool for browsing MINC file headers, likely part of the FreeSurfer
+    package.
     
     Author: FreeSurfer Developers
     
@@ -155,18 +136,16 @@ def browse_minc_header_tcl(
     Returns:
         NamedTuple of outputs (described in `BrowseMincHeaderTclOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(BROWSE_MINC_HEADER_TCL_METADATA)
     params = browse_minc_header_tcl_params(
         infile=infile,
     )
-    return browse_minc_header_tcl_execute(params, execution)
+    return browse_minc_header_tcl_execute(params, runner)
 
 
 __all__ = [
     "BROWSE_MINC_HEADER_TCL_METADATA",
     "BrowseMincHeaderTclOutputs",
-    "BrowseMincHeaderTclParameters",
     "browse_minc_header_tcl",
+    "browse_minc_header_tcl_execute",
     "browse_minc_header_tcl_params",
 ]