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

niwrap_freesurfer/freesurfer/vol2symsurf.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 VOL2SYMSURF_METADATA = Metadata(
-    id="f7fafa95d03d4b203414d428de80f8e3b613706f.boutiques",
+    id="f9b74e075d1b520305f8a58ca53902f3545b9e66.boutiques",
     name="vol2symsurf",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,18 @@ VOL2SYMSURF_METADATA = Metadata(
 
 
 Vol2symsurfParameters = typing.TypedDict('Vol2symsurfParameters', {
-    "__STYXTYPE__": typing.Literal["vol2symsurf"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/vol2symsurf"]],
+    "registration_file": InputPathType,
+    "input_volume": InputPathType,
+    "fwhm": float,
+    "output_stem": typing.NotRequired[str | None],
+    "regheader": typing.NotRequired[str | None],
+    "projection_fraction": typing.NotRequired[float | None],
+    "no_diff": bool,
+    "laterality_index": bool,
+})
+Vol2symsurfParametersTagged = typing.TypedDict('Vol2symsurfParametersTagged', {
+    "@type": typing.Literal["freesurfer/vol2symsurf"],
     "registration_file": InputPathType,
     "input_volume": InputPathType,
     "fwhm": float,
@@ -24,43 +35,11 @@ Vol2symsurfParameters = typing.TypedDict('Vol2symsurfParameters', {
     "no_diff": bool,
     "laterality_index": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "vol2symsurf": vol2symsurf_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 {
-        "vol2symsurf": vol2symsurf_outputs,
-    }.get(t)
 
 
 class Vol2symsurfOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `vol2symsurf(...)`.
+    Output object returned when calling `Vol2symsurfParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -78,12 +57,12 @@ def vol2symsurf_params(
     registration_file: InputPathType,
     input_volume: InputPathType,
     fwhm: float,
-    output_stem: str | None = "instem.fsaverage_sym.smFWHM.lh.hemi",
+    output_stem: str | None = None,
     regheader: str | None = None,
-    projection_fraction: float | None = 0.5,
+    projection_fraction: float | None = None,
     no_diff: bool = False,
     laterality_index: bool = False,
-) -> Vol2symsurfParameters:
+) -> Vol2symsurfParametersTagged:
     """
     Build parameters.
     
@@ -100,7 +79,7 @@ def vol2symsurf_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "vol2symsurf",
+        "@type": "freesurfer/vol2symsurf",
         "registration_file": registration_file,
         "input_volume": input_volume,
         "fwhm": fwhm,
@@ -133,34 +112,34 @@ def vol2symsurf_cargs(
     cargs.append("vol2symsurf")
     cargs.extend([
         "--reg",
-        execution.input_file(params.get("registration_file"))
+        execution.input_file(params.get("registration_file", None))
     ])
     cargs.extend([
         "--i",
-        execution.input_file(params.get("input_volume"))
+        execution.input_file(params.get("input_volume", None))
     ])
     cargs.extend([
         "--fwhm",
-        str(params.get("fwhm"))
+        str(params.get("fwhm", None))
     ])
-    if params.get("output_stem") is not None:
+    if params.get("output_stem", None) is not None:
         cargs.extend([
             "--o",
-            params.get("output_stem")
+            params.get("output_stem", None)
         ])
-    if params.get("regheader") is not None:
+    if params.get("regheader", None) is not None:
         cargs.extend([
             "--regheader",
-            params.get("regheader")
+            params.get("regheader", None)
         ])
-    if params.get("projection_fraction") is not None:
+    if params.get("projection_fraction", None) is not None:
         cargs.extend([
             "--projfrac",
-            str(params.get("projection_fraction"))
+            str(params.get("projection_fraction", None))
         ])
-    if params.get("no_diff"):
+    if params.get("no_diff", False):
         cargs.append("--no-diff")
-    if params.get("laterality_index"):
+    if params.get("laterality_index", False):
         cargs.append("--li")
     return cargs
 
@@ -180,19 +159,21 @@ def vol2symsurf_outputs(
     """
     ret = Vol2symsurfOutputs(
         root=execution.output_file("."),
-        output_lh=execution.output_file(params.get("output_stem") + ".lh.nii") if (params.get("output_stem") is not None) else None,
-        output_rh=execution.output_file(params.get("output_stem") + ".rh.nii") if (params.get("output_stem") is not None) else None,
-        output_lh_rh_difference=execution.output_file(params.get("output_stem") + ".lh-rh.nii") if (params.get("output_stem") is not None) else None,
-        output_li_difference=execution.output_file(params.get("output_stem") + ".li.lh-rh.nii") if (params.get("output_stem") is not None) else None,
+        output_lh=execution.output_file(params.get("output_stem", None) + ".lh.nii") if (params.get("output_stem") is not None) else None,
+        output_rh=execution.output_file(params.get("output_stem", None) + ".rh.nii") if (params.get("output_stem") is not None) else None,
+        output_lh_rh_difference=execution.output_file(params.get("output_stem", None) + ".lh-rh.nii") if (params.get("output_stem") is not None) else None,
+        output_li_difference=execution.output_file(params.get("output_stem", None) + ".li.lh-rh.nii") if (params.get("output_stem") is not None) else None,
     )
     return ret
 
 
 def vol2symsurf_execute(
     params: Vol2symsurfParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Vol2symsurfOutputs:
     """
+    vol2symsurf
+    
     A tool that samples a volume onto the surface of the left-right symmetric
     subject (fsaverage_sym).
     
@@ -202,10 +183,12 @@ def vol2symsurf_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Vol2symsurfOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(VOL2SYMSURF_METADATA)
     params = execution.params(params)
     cargs = vol2symsurf_cargs(params, execution)
     ret = vol2symsurf_outputs(params, execution)
@@ -217,14 +200,16 @@ def vol2symsurf(
     registration_file: InputPathType,
     input_volume: InputPathType,
     fwhm: float,
-    output_stem: str | None = "instem.fsaverage_sym.smFWHM.lh.hemi",
+    output_stem: str | None = None,
     regheader: str | None = None,
-    projection_fraction: float | None = 0.5,
+    projection_fraction: float | None = None,
     no_diff: bool = False,
     laterality_index: bool = False,
     runner: Runner | None = None,
 ) -> Vol2symsurfOutputs:
     """
+    vol2symsurf
+    
     A tool that samples a volume onto the surface of the left-right symmetric
     subject (fsaverage_sym).
     
@@ -245,8 +230,6 @@ def vol2symsurf(
     Returns:
         NamedTuple of outputs (described in `Vol2symsurfOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(VOL2SYMSURF_METADATA)
     params = vol2symsurf_params(
         registration_file=registration_file,
         input_volume=input_volume,
@@ -257,13 +240,13 @@ def vol2symsurf(
         no_diff=no_diff,
         laterality_index=laterality_index,
     )
-    return vol2symsurf_execute(params, execution)
+    return vol2symsurf_execute(params, runner)
 
 
 __all__ = [
     "VOL2SYMSURF_METADATA",
     "Vol2symsurfOutputs",
-    "Vol2symsurfParameters",
     "vol2symsurf",
+    "vol2symsurf_execute",
     "vol2symsurf_params",
 ]

niwrap_freesurfer/freesurfer/vsm_smooth.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 VSM_SMOOTH_METADATA = Metadata(
-    id="620a6bccb466424ba83ef7108c99f0114a863d88.boutiques",
+    id="e12550ca003ab947235b329f588749bc271132bd.boutiques",
     name="vsm-smooth",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ VSM_SMOOTH_METADATA = Metadata(
 
 
 VsmSmoothParameters = typing.TypedDict('VsmSmoothParameters', {
-    "__STYXTYPE__": typing.Literal["vsm-smooth"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/vsm-smooth"]],
+    "input_file": InputPathType,
+    "output_file": str,
+    "fwhm_value": float,
+    "temp_dir": str,
+})
+VsmSmoothParametersTagged = typing.TypedDict('VsmSmoothParametersTagged', {
+    "@type": typing.Literal["freesurfer/vsm-smooth"],
     "input_file": InputPathType,
     "output_file": str,
     "fwhm_value": float,
     "temp_dir": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "vsm-smooth": vsm_smooth_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 {
-        "vsm-smooth": vsm_smooth_outputs,
-    }.get(t)
 
 
 class VsmSmoothOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `vsm_smooth(...)`.
+    Output object returned when calling `VsmSmoothParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def vsm_smooth_params(
     output_file: str,
     fwhm_value: float,
     temp_dir: str,
-) -> VsmSmoothParameters:
+) -> VsmSmoothParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +57,7 @@ def vsm_smooth_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "vsm-smooth",
+        "@type": "freesurfer/vsm-smooth",
         "input_file": input_file,
         "output_file": output_file,
         "fwhm_value": fwhm_value,
@@ -108,19 +83,19 @@ def vsm_smooth_cargs(
     cargs.append("vsm-smooth")
     cargs.extend([
         "--i",
-        execution.input_file(params.get("input_file"))
+        execution.input_file(params.get("input_file", None))
     ])
     cargs.extend([
         "--o",
-        params.get("output_file")
+        params.get("output_file", None)
     ])
     cargs.extend([
         "--fwhm",
-        str(params.get("fwhm_value"))
+        str(params.get("fwhm_value", None))
     ])
     cargs.extend([
         "--tmpdir",
-        params.get("temp_dir")
+        params.get("temp_dir", None)
     ])
     return cargs
 
@@ -140,23 +115,25 @@ def vsm_smooth_outputs(
     """
     ret = VsmSmoothOutputs(
         root=execution.output_file("."),
-        output_vsm=execution.output_file(params.get("output_file")),
+        output_vsm=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def vsm_smooth_execute(
     params: VsmSmoothParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VsmSmoothOutputs:
     """
-    Implements a masked smoothing in which the input (vsm) is unchanged in voxels
-    that have a non-zero value. In voxels with a zero value, the value is replaced
-    with vsm smoothed by the given amount. This will likely only change the voxels
-    that are near the edge of the non-zero voxels. This is a simple way to
-    extrapolate the non-zero voxels beyond their range. This works well for a B0
-    distortion correction voxel shift map (vsm), but it can be applied to other
-    maps.
+    vsm-smooth
+    
+    Implements a masked smoothing in which the input (vsm) is unchanged in
+    voxels that have a non-zero value. In voxels with a zero value, the value is
+    replaced with vsm smoothed by the given amount. This will likely only change
+    the voxels that are near the edge of the non-zero voxels. This is a simple
+    way to extrapolate the non-zero voxels beyond their range. This works well
+    for a B0 distortion correction voxel shift map (vsm), but it can be applied
+    to other maps.
     
     Author: FreeSurfer Developers
     
@@ -164,10 +141,12 @@ def vsm_smooth_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VsmSmoothOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(VSM_SMOOTH_METADATA)
     params = execution.params(params)
     cargs = vsm_smooth_cargs(params, execution)
     ret = vsm_smooth_outputs(params, execution)
@@ -183,13 +162,15 @@ def vsm_smooth(
     runner: Runner | None = None,
 ) -> VsmSmoothOutputs:
     """
-    Implements a masked smoothing in which the input (vsm) is unchanged in voxels
-    that have a non-zero value. In voxels with a zero value, the value is replaced
-    with vsm smoothed by the given amount. This will likely only change the voxels
-    that are near the edge of the non-zero voxels. This is a simple way to
-    extrapolate the non-zero voxels beyond their range. This works well for a B0
-    distortion correction voxel shift map (vsm), but it can be applied to other
-    maps.
+    vsm-smooth
+    
+    Implements a masked smoothing in which the input (vsm) is unchanged in
+    voxels that have a non-zero value. In voxels with a zero value, the value is
+    replaced with vsm smoothed by the given amount. This will likely only change
+    the voxels that are near the edge of the non-zero voxels. This is a simple
+    way to extrapolate the non-zero voxels beyond their range. This works well
+    for a B0 distortion correction voxel shift map (vsm), but it can be applied
+    to other maps.
     
     Author: FreeSurfer Developers
     
@@ -204,21 +185,19 @@ def vsm_smooth(
     Returns:
         NamedTuple of outputs (described in `VsmSmoothOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(VSM_SMOOTH_METADATA)
     params = vsm_smooth_params(
         input_file=input_file,
         output_file=output_file,
         fwhm_value=fwhm_value,
         temp_dir=temp_dir,
     )
-    return vsm_smooth_execute(params, execution)
+    return vsm_smooth_execute(params, runner)
 
 
 __all__ = [
     "VSM_SMOOTH_METADATA",
     "VsmSmoothOutputs",
-    "VsmSmoothParameters",
     "vsm_smooth",
+    "vsm_smooth_execute",
     "vsm_smooth_params",
 ]

niwrap_freesurfer/freesurfer/wfilemask.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 WFILEMASK_METADATA = Metadata(
-    id="d9499795a211ad7cff6445d0424d21c8e2190d0f.boutiques",
+    id="fc866e920f78fa34baf268cd3a0920066c7272ec.boutiques",
     name="wfilemask",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ WFILEMASK_METADATA = Metadata(
 
 
 WfilemaskParameters = typing.TypedDict('WfilemaskParameters', {
-    "__STYXTYPE__": typing.Literal["wfilemask"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/wfilemask"]],
+    "w_file": InputPathType,
+    "label_file": InputPathType,
+    "output_file": str,
+    "permission_mask": typing.NotRequired[str | None],
+    "help_flag": bool,
+    "version_flag": bool,
+})
+WfilemaskParametersTagged = typing.TypedDict('WfilemaskParametersTagged', {
+    "@type": typing.Literal["freesurfer/wfilemask"],
     "w_file": InputPathType,
     "label_file": InputPathType,
     "output_file": str,
@@ -22,43 +31,11 @@ WfilemaskParameters = typing.TypedDict('WfilemaskParameters', {
     "help_flag": bool,
     "version_flag": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "wfilemask": wfilemask_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 {
-        "wfilemask": wfilemask_outputs,
-    }.get(t)
 
 
 class WfilemaskOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `wfilemask(...)`.
+    Output object returned when calling `WfilemaskParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +50,7 @@ def wfilemask_params(
     permission_mask: str | None = None,
     help_flag: bool = False,
     version_flag: bool = False,
-) -> WfilemaskParameters:
+) -> WfilemaskParametersTagged:
     """
     Build parameters.
     
@@ -88,7 +65,7 @@ def wfilemask_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "wfilemask",
+        "@type": "freesurfer/wfilemask",
         "w_file": w_file,
         "label_file": label_file,
         "output_file": output_file,
@@ -117,24 +94,24 @@ def wfilemask_cargs(
     cargs.append("wfilemask")
     cargs.extend([
         "-w",
-        execution.input_file(params.get("w_file"))
+        execution.input_file(params.get("w_file", None))
     ])
     cargs.extend([
         "-l",
-        execution.input_file(params.get("label_file"))
+        execution.input_file(params.get("label_file", None))
     ])
     cargs.extend([
         "-o",
-        params.get("output_file")
+        params.get("output_file", None)
     ])
-    if params.get("permission_mask") is not None:
+    if params.get("permission_mask", None) is not None:
         cargs.extend([
             "-umask",
-            params.get("permission_mask")
+            params.get("permission_mask", None)
         ])
-    if params.get("help_flag"):
+    if params.get("help_flag", False):
         cargs.append("-help")
-    if params.get("version_flag"):
+    if params.get("version_flag", False):
         cargs.append("-version")
     return cargs
 
@@ -154,16 +131,18 @@ def wfilemask_outputs(
     """
     ret = WfilemaskOutputs(
         root=execution.output_file("."),
-        output_w_file=execution.output_file(params.get("output_file")),
+        output_w_file=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def wfilemask_execute(
     params: WfilemaskParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> WfilemaskOutputs:
     """
+    wfilemask
+    
     Zero-out regions of a surface value file (.w file) using a label.
     
     Author: FreeSurfer Developers
@@ -172,10 +151,12 @@ def wfilemask_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `WfilemaskOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(WFILEMASK_METADATA)
     params = execution.params(params)
     cargs = wfilemask_cargs(params, execution)
     ret = wfilemask_outputs(params, execution)
@@ -193,6 +174,8 @@ def wfilemask(
     runner: Runner | None = None,
 ) -> WfilemaskOutputs:
     """
+    wfilemask
+    
     Zero-out regions of a surface value file (.w file) using a label.
     
     Author: FreeSurfer Developers
@@ -210,8 +193,6 @@ def wfilemask(
     Returns:
         NamedTuple of outputs (described in `WfilemaskOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(WFILEMASK_METADATA)
     params = wfilemask_params(
         w_file=w_file,
         label_file=label_file,
@@ -220,13 +201,13 @@ def wfilemask(
         help_flag=help_flag,
         version_flag=version_flag,
     )
-    return wfilemask_execute(params, execution)
+    return wfilemask_execute(params, runner)
 
 
 __all__ = [
     "WFILEMASK_METADATA",
     "WfilemaskOutputs",
-    "WfilemaskParameters",
     "wfilemask",
+    "wfilemask_execute",
     "wfilemask_params",
 ]