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

niwrap_freesurfer/freesurfer/aparcstatsdiff.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 APARCSTATSDIFF_METADATA = Metadata(
-    id="4a3d5285bb31b350d627388c14efaeed5f882361.boutiques",
+    id="cfdd4096c5662aa4f9a9611baf465343bb043a77.boutiques",
     name="aparcstatsdiff",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ APARCSTATSDIFF_METADATA = Metadata(
 
 
 AparcstatsdiffParameters = typing.TypedDict('AparcstatsdiffParameters', {
-    "__STYXTYPE__": typing.Literal["aparcstatsdiff"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/aparcstatsdiff"]],
+    "subj1": str,
+    "subj2": str,
+    "hemi": str,
+    "parc": str,
+    "meas": str,
+    "outdir": typing.NotRequired[str | None],
+})
+AparcstatsdiffParametersTagged = typing.TypedDict('AparcstatsdiffParametersTagged', {
+    "@type": typing.Literal["freesurfer/aparcstatsdiff"],
     "subj1": str,
     "subj2": str,
     "hemi": str,
@@ -22,43 +31,11 @@ AparcstatsdiffParameters = typing.TypedDict('AparcstatsdiffParameters', {
     "meas": str,
     "outdir": 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 {
-        "aparcstatsdiff": aparcstatsdiff_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 {
-        "aparcstatsdiff": aparcstatsdiff_outputs,
-    }.get(t)
 
 
 class AparcstatsdiffOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `aparcstatsdiff(...)`.
+    Output object returned when calling `AparcstatsdiffParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +50,7 @@ def aparcstatsdiff_params(
     parc: str,
     meas: str,
     outdir: str | None = None,
-) -> AparcstatsdiffParameters:
+) -> AparcstatsdiffParametersTagged:
     """
     Build parameters.
     
@@ -88,7 +65,7 @@ def aparcstatsdiff_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "aparcstatsdiff",
+        "@type": "freesurfer/aparcstatsdiff",
         "subj1": subj1,
         "subj2": subj2,
         "hemi": hemi,
@@ -115,13 +92,13 @@ def aparcstatsdiff_cargs(
     """
     cargs = []
     cargs.append("aparcstatsdiff")
-    cargs.append(params.get("subj1"))
-    cargs.append(params.get("subj2"))
-    cargs.append(params.get("hemi"))
-    cargs.append(params.get("parc"))
-    cargs.append(params.get("meas"))
-    if params.get("outdir") is not None:
-        cargs.append(params.get("outdir"))
+    cargs.append(params.get("subj1", None))
+    cargs.append(params.get("subj2", None))
+    cargs.append(params.get("hemi", None))
+    cargs.append(params.get("parc", None))
+    cargs.append(params.get("meas", None))
+    if params.get("outdir", None) is not None:
+        cargs.append(params.get("outdir", None))
     return cargs
 
 
@@ -140,18 +117,20 @@ def aparcstatsdiff_outputs(
     """
     ret = AparcstatsdiffOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file("aparcstats-" + params.get("hemi") + "." + params.get("parc") + "." + params.get("meas") + ".txt"),
+        output_file=execution.output_file("aparcstats-" + params.get("hemi", None) + "." + params.get("parc", None) + "." + params.get("meas", None) + ".txt"),
     )
     return ret
 
 
 def aparcstatsdiff_execute(
     params: AparcstatsdiffParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> AparcstatsdiffOutputs:
     """
-    Utility to calculate percentage differences in aparc morphometry data between
-    two subjects.
+    aparcstatsdiff
+    
+    Utility to calculate percentage differences in aparc morphometry data
+    between two subjects.
     
     Author: FreeSurfer Developers
     
@@ -159,10 +138,12 @@ def aparcstatsdiff_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `AparcstatsdiffOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(APARCSTATSDIFF_METADATA)
     params = execution.params(params)
     cargs = aparcstatsdiff_cargs(params, execution)
     ret = aparcstatsdiff_outputs(params, execution)
@@ -180,8 +161,10 @@ def aparcstatsdiff(
     runner: Runner | None = None,
 ) -> AparcstatsdiffOutputs:
     """
-    Utility to calculate percentage differences in aparc morphometry data between
-    two subjects.
+    aparcstatsdiff
+    
+    Utility to calculate percentage differences in aparc morphometry data
+    between two subjects.
     
     Author: FreeSurfer Developers
     
@@ -198,8 +181,6 @@ def aparcstatsdiff(
     Returns:
         NamedTuple of outputs (described in `AparcstatsdiffOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(APARCSTATSDIFF_METADATA)
     params = aparcstatsdiff_params(
         subj1=subj1,
         subj2=subj2,
@@ -208,13 +189,13 @@ def aparcstatsdiff(
         meas=meas,
         outdir=outdir,
     )
-    return aparcstatsdiff_execute(params, execution)
+    return aparcstatsdiff_execute(params, runner)
 
 
 __all__ = [
     "APARCSTATSDIFF_METADATA",
     "AparcstatsdiffOutputs",
-    "AparcstatsdiffParameters",
     "aparcstatsdiff",
+    "aparcstatsdiff_execute",
     "aparcstatsdiff_params",
 ]

niwrap_freesurfer/freesurfer/apas2aseg.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 APAS2ASEG_METADATA = Metadata(
-    id="eda1865146654f4bd355ad2e45b11e2c26036db4.boutiques",
+    id="627d5b27298b79e63428388e1d9b98b7af3b2395.boutiques",
     name="apas2aseg",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ APAS2ASEG_METADATA = Metadata(
 
 
 Apas2asegParameters = typing.TypedDict('Apas2asegParameters', {
-    "__STYXTYPE__": typing.Literal["apas2aseg"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/apas2aseg"]],
+    "subject": typing.NotRequired[str | None],
+    "input_aparc_aseg": typing.NotRequired[InputPathType | None],
+    "output_seg": typing.NotRequired[str | None],
+})
+Apas2asegParametersTagged = typing.TypedDict('Apas2asegParametersTagged', {
+    "@type": typing.Literal["freesurfer/apas2aseg"],
     "subject": typing.NotRequired[str | None],
     "input_aparc_aseg": typing.NotRequired[InputPathType | None],
     "output_seg": 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 {
-        "apas2aseg": apas2aseg_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 {
-        "apas2aseg": apas2aseg_outputs,
-    }.get(t)
 
 
 class Apas2asegOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `apas2aseg(...)`.
+    Output object returned when calling `Apas2asegParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -66,8 +40,8 @@ class Apas2asegOutputs(typing.NamedTuple):
 def apas2aseg_params(
     subject: str | None = None,
     input_aparc_aseg: InputPathType | None = None,
-    output_seg: str | None = "apas-aseg.mgz",
-) -> Apas2asegParameters:
+    output_seg: str | None = None,
+) -> Apas2asegParametersTagged:
     """
     Build parameters.
     
@@ -80,7 +54,7 @@ def apas2aseg_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "apas2aseg",
+        "@type": "freesurfer/apas2aseg",
     }
     if subject is not None:
         params["subject"] = subject
@@ -106,20 +80,20 @@ def apas2aseg_cargs(
     """
     cargs = []
     cargs.append("apas2aseg")
-    if params.get("subject") is not None:
+    if params.get("subject", None) is not None:
         cargs.extend([
             "--s",
-            params.get("subject")
+            params.get("subject", None)
         ])
-    if params.get("input_aparc_aseg") is not None:
+    if params.get("input_aparc_aseg", None) is not None:
         cargs.extend([
             "--i",
-            execution.input_file(params.get("input_aparc_aseg"))
+            execution.input_file(params.get("input_aparc_aseg", None))
         ])
-    if params.get("output_seg") is not None:
+    if params.get("output_seg", None) is not None:
         cargs.extend([
             "--o",
-            params.get("output_seg")
+            params.get("output_seg", None)
         ])
     return cargs
 
@@ -139,18 +113,20 @@ def apas2aseg_outputs(
     """
     ret = Apas2asegOutputs(
         root=execution.output_file("."),
-        output_seg_file=execution.output_file(params.get("output_seg")) if (params.get("output_seg") is not None) else None,
+        output_seg_file=execution.output_file(params.get("output_seg", None)) if (params.get("output_seg") is not None) else None,
     )
     return ret
 
 
 def apas2aseg_execute(
     params: Apas2asegParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Apas2asegOutputs:
     """
-    Converts aparc+aseg.mgz into aseg.mgz-like format by replacing specific cortical
-    segmentations.
+    apas2aseg
+    
+    Converts aparc+aseg.mgz into aseg.mgz-like format by replacing specific
+    cortical segmentations.
     
     Author: FreeSurfer Developers
     
@@ -158,10 +134,12 @@ def apas2aseg_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Apas2asegOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(APAS2ASEG_METADATA)
     params = execution.params(params)
     cargs = apas2aseg_cargs(params, execution)
     ret = apas2aseg_outputs(params, execution)
@@ -172,12 +150,14 @@ def apas2aseg_execute(
 def apas2aseg(
     subject: str | None = None,
     input_aparc_aseg: InputPathType | None = None,
-    output_seg: str | None = "apas-aseg.mgz",
+    output_seg: str | None = None,
     runner: Runner | None = None,
 ) -> Apas2asegOutputs:
     """
-    Converts aparc+aseg.mgz into aseg.mgz-like format by replacing specific cortical
-    segmentations.
+    apas2aseg
+    
+    Converts aparc+aseg.mgz into aseg.mgz-like format by replacing specific
+    cortical segmentations.
     
     Author: FreeSurfer Developers
     
@@ -192,20 +172,18 @@ def apas2aseg(
     Returns:
         NamedTuple of outputs (described in `Apas2asegOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(APAS2ASEG_METADATA)
     params = apas2aseg_params(
         subject=subject,
         input_aparc_aseg=input_aparc_aseg,
         output_seg=output_seg,
     )
-    return apas2aseg_execute(params, execution)
+    return apas2aseg_execute(params, runner)
 
 
 __all__ = [
     "APAS2ASEG_METADATA",
     "Apas2asegOutputs",
-    "Apas2asegParameters",
     "apas2aseg",
+    "apas2aseg_execute",
     "apas2aseg_params",
 ]

niwrap_freesurfer/freesurfer/apply_morph.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 APPLY_MORPH_METADATA = Metadata(
-    id="a7cb7e420a1c51fbb13f7cd6c2a1a9581804bf02.boutiques",
+    id="132df3f4036c201bd32bea9d1d867e1167f7130a.boutiques",
     name="applyMorph",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,26 @@ APPLY_MORPH_METADATA = Metadata(
 
 
 ApplyMorphParameters = typing.TypedDict('ApplyMorphParameters', {
-    "__STYXTYPE__": typing.Literal["applyMorph"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/applyMorph"]],
+    "inputs": list[InputPathType],
+    "template": InputPathType,
+    "transform": InputPathType,
+    "zlib_buffer": typing.NotRequired[float | None],
+    "dbg_coords": typing.NotRequired[list[float] | None],
+})
+ApplyMorphParametersTagged = typing.TypedDict('ApplyMorphParametersTagged', {
+    "@type": typing.Literal["freesurfer/applyMorph"],
     "inputs": list[InputPathType],
     "template": InputPathType,
     "transform": InputPathType,
     "zlib_buffer": typing.NotRequired[float | None],
     "dbg_coords": typing.NotRequired[list[float] | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "applyMorph": apply_morph_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 ApplyMorphOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `apply_morph(...)`.
+    Output object returned when calling `ApplyMorphParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -68,7 +45,7 @@ def apply_morph_params(
     transform: InputPathType,
     zlib_buffer: float | None = None,
     dbg_coords: list[float] | None = None,
-) -> ApplyMorphParameters:
+) -> ApplyMorphParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +59,7 @@ def apply_morph_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "applyMorph",
+        "@type": "freesurfer/applyMorph",
         "inputs": inputs,
         "template": template,
         "transform": transform,
@@ -109,24 +86,24 @@ def apply_morph_cargs(
     """
     cargs = []
     cargs.append("applyMorph")
-    cargs.extend([execution.input_file(f) for f in params.get("inputs")])
+    cargs.extend([execution.input_file(f) for f in params.get("inputs", None)])
     cargs.extend([
         "--template",
-        execution.input_file(params.get("template"))
+        execution.input_file(params.get("template", None))
     ])
     cargs.extend([
         "--transform",
-        execution.input_file(params.get("transform"))
+        execution.input_file(params.get("transform", None))
     ])
-    if params.get("zlib_buffer") is not None:
+    if params.get("zlib_buffer", None) is not None:
         cargs.extend([
             "--zlib_buffer",
-            str(params.get("zlib_buffer"))
+            str(params.get("zlib_buffer", None))
         ])
-    if params.get("dbg_coords") is not None:
+    if params.get("dbg_coords", None) is not None:
         cargs.extend([
             "--dbg_coords",
-            *map(str, params.get("dbg_coords"))
+            *map(str, params.get("dbg_coords", None))
         ])
     return cargs
 
@@ -152,9 +129,11 @@ def apply_morph_outputs(
 
 def apply_morph_execute(
     params: ApplyMorphParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ApplyMorphOutputs:
     """
+    applyMorph
+    
     A tool for applying a morph to a volume using a template and a transform.
     
     Author: FreeSurfer Developers
@@ -163,10 +142,12 @@ def apply_morph_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ApplyMorphOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(APPLY_MORPH_METADATA)
     params = execution.params(params)
     cargs = apply_morph_cargs(params, execution)
     ret = apply_morph_outputs(params, execution)
@@ -183,6 +164,8 @@ def apply_morph(
     runner: Runner | None = None,
 ) -> ApplyMorphOutputs:
     """
+    applyMorph
+    
     A tool for applying a morph to a volume using a template and a transform.
     
     Author: FreeSurfer Developers
@@ -199,8 +182,6 @@ def apply_morph(
     Returns:
         NamedTuple of outputs (described in `ApplyMorphOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(APPLY_MORPH_METADATA)
     params = apply_morph_params(
         inputs=inputs,
         template=template,
@@ -208,13 +189,13 @@ def apply_morph(
         zlib_buffer=zlib_buffer,
         dbg_coords=dbg_coords,
     )
-    return apply_morph_execute(params, execution)
+    return apply_morph_execute(params, runner)
 
 
 __all__ = [
     "APPLY_MORPH_METADATA",
     "ApplyMorphOutputs",
-    "ApplyMorphParameters",
     "apply_morph",
+    "apply_morph_execute",
     "apply_morph_params",
 ]