niwrap-freesurfer 0.6.3__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mris_multiscale_stats.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_MULTISCALE_STATS_METADATA = Metadata(
-    id="70485123c5f0182ca6af11b7463e3a674edf9419.boutiques",
+    id="10e7d73f783449c7aa286eab95584fefc27b016a.boutiques",
     name="mris_multiscale_stats",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ MRIS_MULTISCALE_STATS_METADATA = Metadata(
 
 
 MrisMultiscaleStatsParameters = typing.TypedDict('MrisMultiscaleStatsParameters', {
-    "__STYXTYPE__": typing.Literal["mris_multiscale_stats"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_multiscale_stats"]],
+    "output_subject": str,
+    "hemi": str,
+    "surf": InputPathType,
+    "curv": InputPathType,
+    "class1_subjects": list[str],
+    "class2_subjects": list[str],
+})
+MrisMultiscaleStatsParametersTagged = typing.TypedDict('MrisMultiscaleStatsParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_multiscale_stats"],
     "output_subject": str,
     "hemi": str,
     "surf": InputPathType,
@@ -22,42 +31,11 @@ MrisMultiscaleStatsParameters = typing.TypedDict('MrisMultiscaleStatsParameters'
     "class1_subjects": list[str],
     "class2_subjects": list[str],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_multiscale_stats": mris_multiscale_stats_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 MrisMultiscaleStatsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_multiscale_stats(...)`.
+    Output object returned when calling `MrisMultiscaleStatsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -70,7 +48,7 @@ def mris_multiscale_stats_params(
     curv: InputPathType,
     class1_subjects: list[str],
     class2_subjects: list[str],
-) -> MrisMultiscaleStatsParameters:
+) -> MrisMultiscaleStatsParametersTagged:
     """
     Build parameters.
     
@@ -85,7 +63,7 @@ def mris_multiscale_stats_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_multiscale_stats",
+        "@type": "freesurfer/mris_multiscale_stats",
         "output_subject": output_subject,
         "hemi": hemi,
         "surf": surf,
@@ -113,13 +91,13 @@ def mris_multiscale_stats_cargs(
     cargs.append("mris_multiscale_stats")
     cargs.extend([
         "-o",
-        params.get("output_subject")
+        params.get("output_subject", None)
     ])
-    cargs.append(params.get("hemi"))
-    cargs.append(execution.input_file(params.get("surf")))
-    cargs.append(execution.input_file(params.get("curv")))
-    cargs.extend(params.get("class1_subjects"))
-    cargs.extend(params.get("class2_subjects"))
+    cargs.append(params.get("hemi", None))
+    cargs.append(execution.input_file(params.get("surf", None)))
+    cargs.append(execution.input_file(params.get("curv", None)))
+    cargs.extend(params.get("class1_subjects", None))
+    cargs.extend(params.get("class2_subjects", None))
     return cargs
 
 
@@ -144,9 +122,11 @@ def mris_multiscale_stats_outputs(
 
 def mris_multiscale_stats_execute(
     params: MrisMultiscaleStatsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisMultiscaleStatsOutputs:
     """
+    mris_multiscale_stats
+    
     Compute the autocorrelation function of a curvature file using multiscale
     statistical techniques.
     
@@ -156,10 +136,12 @@ def mris_multiscale_stats_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisMultiscaleStatsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_MULTISCALE_STATS_METADATA)
     params = execution.params(params)
     cargs = mris_multiscale_stats_cargs(params, execution)
     ret = mris_multiscale_stats_outputs(params, execution)
@@ -177,6 +159,8 @@ def mris_multiscale_stats(
     runner: Runner | None = None,
 ) -> MrisMultiscaleStatsOutputs:
     """
+    mris_multiscale_stats
+    
     Compute the autocorrelation function of a curvature file using multiscale
     statistical techniques.
     
@@ -195,8 +179,6 @@ def mris_multiscale_stats(
     Returns:
         NamedTuple of outputs (described in `MrisMultiscaleStatsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_MULTISCALE_STATS_METADATA)
     params = mris_multiscale_stats_params(
         output_subject=output_subject,
         hemi=hemi,
@@ -205,13 +187,13 @@ def mris_multiscale_stats(
         class1_subjects=class1_subjects,
         class2_subjects=class2_subjects,
     )
-    return mris_multiscale_stats_execute(params, execution)
+    return mris_multiscale_stats_execute(params, runner)
 
 
 __all__ = [
     "MRIS_MULTISCALE_STATS_METADATA",
     "MrisMultiscaleStatsOutputs",
-    "MrisMultiscaleStatsParameters",
     "mris_multiscale_stats",
+    "mris_multiscale_stats_execute",
     "mris_multiscale_stats_params",
 ]

niwrap_freesurfer/freesurfer/mris_niters2fwhm.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_NITERS2FWHM_METADATA = Metadata(
-    id="2e0641d671ca38217303524c22a35b4ae4f19dd4.boutiques",
+    id="67f812d1bc5f61d8d34293d691cff3d0d282b1aa.boutiques",
     name="mris_niters2fwhm",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,19 @@ MRIS_NITERS2FWHM_METADATA = Metadata(
 
 
 MrisNiters2fwhmParameters = typing.TypedDict('MrisNiters2fwhmParameters', {
-    "__STYXTYPE__": typing.Literal["mris_niters2fwhm"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_niters2fwhm"]],
+    "subject": str,
+    "hemi": str,
+    "surf": str,
+    "dof": float,
+    "niters": float,
+    "debug": bool,
+    "checkopts": bool,
+    "help": bool,
+    "version": bool,
+})
+MrisNiters2fwhmParametersTagged = typing.TypedDict('MrisNiters2fwhmParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_niters2fwhm"],
     "subject": str,
     "hemi": str,
     "surf": str,
@@ -25,42 +37,11 @@ MrisNiters2fwhmParameters = typing.TypedDict('MrisNiters2fwhmParameters', {
     "help": 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 {
-        "mris_niters2fwhm": mris_niters2fwhm_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 MrisNiters2fwhmOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_niters2fwhm(...)`.
+    Output object returned when calling `MrisNiters2fwhmParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -76,7 +57,7 @@ def mris_niters2fwhm_params(
     checkopts: bool = False,
     help_: bool = False,
     version: bool = False,
-) -> MrisNiters2fwhmParameters:
+) -> MrisNiters2fwhmParametersTagged:
     """
     Build parameters.
     
@@ -94,7 +75,7 @@ def mris_niters2fwhm_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_niters2fwhm",
+        "@type": "freesurfer/mris_niters2fwhm",
         "subject": subject,
         "hemi": hemi,
         "surf": surf,
@@ -125,31 +106,31 @@ def mris_niters2fwhm_cargs(
     cargs.append("mris_niters2fwhm")
     cargs.extend([
         "--s",
-        params.get("subject")
+        params.get("subject", None)
     ])
     cargs.extend([
         "--h",
-        params.get("hemi")
+        params.get("hemi", None)
     ])
     cargs.extend([
         "--surf",
-        params.get("surf")
+        params.get("surf", None)
     ])
     cargs.extend([
         "--dof",
-        str(params.get("dof"))
+        str(params.get("dof", None))
     ])
     cargs.extend([
         "--niters",
-        str(params.get("niters"))
+        str(params.get("niters", None))
     ])
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
-    if params.get("checkopts"):
+    if params.get("checkopts", False):
         cargs.append("--checkopts")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("--help")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("--version")
     return cargs
 
@@ -175,10 +156,13 @@ def mris_niters2fwhm_outputs(
 
 def mris_niters2fwhm_execute(
     params: MrisNiters2fwhmParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisNiters2fwhmOutputs:
     """
-    Convert number of iterations to full width at half maximum (FWHM) for surface.
+    mris_niters2fwhm
+    
+    Convert number of iterations to full width at half maximum (FWHM) for
+    surface.
     
     Author: FreeSurfer Developers
     
@@ -186,10 +170,12 @@ def mris_niters2fwhm_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisNiters2fwhmOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_NITERS2FWHM_METADATA)
     params = execution.params(params)
     cargs = mris_niters2fwhm_cargs(params, execution)
     ret = mris_niters2fwhm_outputs(params, execution)
@@ -210,7 +196,10 @@ def mris_niters2fwhm(
     runner: Runner | None = None,
 ) -> MrisNiters2fwhmOutputs:
     """
-    Convert number of iterations to full width at half maximum (FWHM) for surface.
+    mris_niters2fwhm
+    
+    Convert number of iterations to full width at half maximum (FWHM) for
+    surface.
     
     Author: FreeSurfer Developers
     
@@ -230,8 +219,6 @@ def mris_niters2fwhm(
     Returns:
         NamedTuple of outputs (described in `MrisNiters2fwhmOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_NITERS2FWHM_METADATA)
     params = mris_niters2fwhm_params(
         subject=subject,
         hemi=hemi,
@@ -243,13 +230,13 @@ def mris_niters2fwhm(
         help_=help_,
         version=version,
     )
-    return mris_niters2fwhm_execute(params, execution)
+    return mris_niters2fwhm_execute(params, runner)
 
 
 __all__ = [
     "MRIS_NITERS2FWHM_METADATA",
     "MrisNiters2fwhmOutputs",
-    "MrisNiters2fwhmParameters",
     "mris_niters2fwhm",
+    "mris_niters2fwhm_execute",
     "mris_niters2fwhm_params",
 ]

niwrap_freesurfer/freesurfer/mris_nudge.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_NUDGE_METADATA = Metadata(
-    id="5f454aae29ceb9c63bd2c4fefab5025548bdb2e0.boutiques",
+    id="248273cfa5785567fee638e109250d6fc7e73335.boutiques",
     name="mris_nudge",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,50 +14,26 @@ MRIS_NUDGE_METADATA = Metadata(
 
 
 MrisNudgeParameters = typing.TypedDict('MrisNudgeParameters', {
-    "__STYXTYPE__": typing.Literal["mris_nudge"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_nudge"]],
+    "input_surface": InputPathType,
+    "input_volume": InputPathType,
+    "vertex": int,
+    "target_val": float,
+    "nbhd": int,
+})
+MrisNudgeParametersTagged = typing.TypedDict('MrisNudgeParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_nudge"],
     "input_surface": InputPathType,
     "input_volume": InputPathType,
     "vertex": int,
     "target_val": float,
     "nbhd": int,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_nudge": mris_nudge_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 {
-        "mris_nudge": mris_nudge_outputs,
-    }.get(t)
 
 
 class MrisNudgeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_nudge(...)`.
+    Output object returned when calling `MrisNudgeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +47,7 @@ def mris_nudge_params(
     vertex: int,
     target_val: float,
     nbhd: int,
-) -> MrisNudgeParameters:
+) -> MrisNudgeParametersTagged:
     """
     Build parameters.
     
@@ -85,7 +61,7 @@ def mris_nudge_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_nudge",
+        "@type": "freesurfer/mris_nudge",
         "input_surface": input_surface,
         "input_volume": input_volume,
         "vertex": vertex,
@@ -110,11 +86,11 @@ def mris_nudge_cargs(
     """
     cargs = []
     cargs.append("mris_nudge")
-    cargs.append(execution.input_file(params.get("input_surface")))
-    cargs.append(execution.input_file(params.get("input_volume")))
-    cargs.append(str(params.get("vertex")))
-    cargs.append(str(params.get("target_val")))
-    cargs.append(str(params.get("nbhd")))
+    cargs.append(execution.input_file(params.get("input_surface", None)))
+    cargs.append(execution.input_file(params.get("input_volume", None)))
+    cargs.append(str(params.get("vertex", None)))
+    cargs.append(str(params.get("target_val", None)))
+    cargs.append(str(params.get("nbhd", None)))
     return cargs
 
 
@@ -140,9 +116,11 @@ def mris_nudge_outputs(
 
 def mris_nudge_execute(
     params: MrisNudgeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisNudgeOutputs:
     """
+    mris_nudge
+    
     A tool to nudge vertex positions on a surface using a volume.
     
     Author: FreeSurfer Developers
@@ -151,10 +129,12 @@ def mris_nudge_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisNudgeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_NUDGE_METADATA)
     params = execution.params(params)
     cargs = mris_nudge_cargs(params, execution)
     ret = mris_nudge_outputs(params, execution)
@@ -171,6 +151,8 @@ def mris_nudge(
     runner: Runner | None = None,
 ) -> MrisNudgeOutputs:
     """
+    mris_nudge
+    
     A tool to nudge vertex positions on a surface using a volume.
     
     Author: FreeSurfer Developers
@@ -187,8 +169,6 @@ def mris_nudge(
     Returns:
         NamedTuple of outputs (described in `MrisNudgeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_NUDGE_METADATA)
     params = mris_nudge_params(
         input_surface=input_surface,
         input_volume=input_volume,
@@ -196,13 +176,13 @@ def mris_nudge(
         target_val=target_val,
         nbhd=nbhd,
     )
-    return mris_nudge_execute(params, execution)
+    return mris_nudge_execute(params, runner)
 
 
 __all__ = [
     "MRIS_NUDGE_METADATA",
     "MrisNudgeOutputs",
-    "MrisNudgeParameters",
     "mris_nudge",
+    "mris_nudge_execute",
     "mris_nudge_params",
 ]

niwrap_freesurfer/freesurfer/mris_parcellate_connectivity.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_PARCELLATE_CONNECTIVITY_METADATA = Metadata(
-    id="6e249aa368d9ee8a5a4ff1ad332d424e79a14920.boutiques",
+    id="f2f884c57ec77a0bdb1506da6e55dc8de6e1e233.boutiques",
     name="mris_parcellate_connectivity",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ MRIS_PARCELLATE_CONNECTIVITY_METADATA = Metadata(
 
 
 MrisParcellateConnectivityParameters = typing.TypedDict('MrisParcellateConnectivityParameters', {
-    "__STYXTYPE__": typing.Literal["mris_parcellate_connectivity"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_parcellate_connectivity"]],
+    "smooth_iterations": typing.NotRequired[float | None],
+    "input_surface": InputPathType,
+    "input_correlations": InputPathType,
+    "output_parcellation": str,
+})
+MrisParcellateConnectivityParametersTagged = typing.TypedDict('MrisParcellateConnectivityParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_parcellate_connectivity"],
     "smooth_iterations": typing.NotRequired[float | None],
     "input_surface": InputPathType,
     "input_correlations": InputPathType,
     "output_parcellation": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_parcellate_connectivity": mris_parcellate_connectivity_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 {
-        "mris_parcellate_connectivity": mris_parcellate_connectivity_outputs,
-    }.get(t)
 
 
 class MrisParcellateConnectivityOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_parcellate_connectivity(...)`.
+    Output object returned when calling `MrisParcellateConnectivityParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def mris_parcellate_connectivity_params(
     input_correlations: InputPathType,
     output_parcellation: str,
     smooth_iterations: float | None = None,
-) -> MrisParcellateConnectivityParameters:
+) -> MrisParcellateConnectivityParametersTagged:
     """
     Build parameters.
     
@@ -83,7 +58,7 @@ def mris_parcellate_connectivity_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_parcellate_connectivity",
+        "@type": "freesurfer/mris_parcellate_connectivity",
         "input_surface": input_surface,
         "input_correlations": input_correlations,
         "output_parcellation": output_parcellation,
@@ -108,14 +83,14 @@ def mris_parcellate_connectivity_cargs(
     """
     cargs = []
     cargs.append("mris_parcellate_connectivity")
-    if params.get("smooth_iterations") is not None:
+    if params.get("smooth_iterations", None) is not None:
         cargs.extend([
             "-n",
-            str(params.get("smooth_iterations"))
+            str(params.get("smooth_iterations", None))
         ])
-    cargs.append(execution.input_file(params.get("input_surface")))
-    cargs.append(execution.input_file(params.get("input_correlations")))
-    cargs.append(params.get("output_parcellation"))
+    cargs.append(execution.input_file(params.get("input_surface", None)))
+    cargs.append(execution.input_file(params.get("input_correlations", None)))
+    cargs.append(params.get("output_parcellation", None))
     return cargs
 
 
@@ -134,16 +109,18 @@ def mris_parcellate_connectivity_outputs(
     """
     ret = MrisParcellateConnectivityOutputs(
         root=execution.output_file("."),
-        parcellation_output=execution.output_file(params.get("output_parcellation")),
+        parcellation_output=execution.output_file(params.get("output_parcellation", None)),
     )
     return ret
 
 
 def mris_parcellate_connectivity_execute(
     params: MrisParcellateConnectivityParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisParcellateConnectivityOutputs:
     """
+    mris_parcellate_connectivity
+    
     A tool to parcellate brain connectivity using surface and correlation data.
     
     Author: FreeSurfer Developers
@@ -152,10 +129,12 @@ def mris_parcellate_connectivity_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisParcellateConnectivityOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_PARCELLATE_CONNECTIVITY_METADATA)
     params = execution.params(params)
     cargs = mris_parcellate_connectivity_cargs(params, execution)
     ret = mris_parcellate_connectivity_outputs(params, execution)
@@ -171,6 +150,8 @@ def mris_parcellate_connectivity(
     runner: Runner | None = None,
 ) -> MrisParcellateConnectivityOutputs:
     """
+    mris_parcellate_connectivity
+    
     A tool to parcellate brain connectivity using surface and correlation data.
     
     Author: FreeSurfer Developers
@@ -187,21 +168,19 @@ def mris_parcellate_connectivity(
     Returns:
         NamedTuple of outputs (described in `MrisParcellateConnectivityOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_PARCELLATE_CONNECTIVITY_METADATA)
     params = mris_parcellate_connectivity_params(
         smooth_iterations=smooth_iterations,
         input_surface=input_surface,
         input_correlations=input_correlations,
         output_parcellation=output_parcellation,
     )
-    return mris_parcellate_connectivity_execute(params, execution)
+    return mris_parcellate_connectivity_execute(params, runner)
 
 
 __all__ = [
     "MRIS_PARCELLATE_CONNECTIVITY_METADATA",
     "MrisParcellateConnectivityOutputs",
-    "MrisParcellateConnectivityParameters",
     "mris_parcellate_connectivity",
+    "mris_parcellate_connectivity_execute",
     "mris_parcellate_connectivity_params",
 ]