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

niwrap_freesurfer/freesurfer/mris_sample_label.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_SAMPLE_LABEL_METADATA = Metadata(
-    id="74b041ea42284364577c7763d289942c9947372b.boutiques",
+    id="f029196caebf35562f18760628d53363794be05f.boutiques",
     name="mris_sample_label",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ MRIS_SAMPLE_LABEL_METADATA = Metadata(
 
 
 MrisSampleLabelParameters = typing.TypedDict('MrisSampleLabelParameters', {
-    "__STYXTYPE__": typing.Literal["mris_sample_label"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_sample_label"]],
+    "input_label_file": InputPathType,
+    "input_surface_file": InputPathType,
+    "output_label_file": str,
+})
+MrisSampleLabelParametersTagged = typing.TypedDict('MrisSampleLabelParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_sample_label"],
     "input_label_file": InputPathType,
     "input_surface_file": InputPathType,
     "output_label_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 {
-        "mris_sample_label": mris_sample_label_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_sample_label": mris_sample_label_outputs,
-    }.get(t)
 
 
 class MrisSampleLabelOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_sample_label(...)`.
+    Output object returned when calling `MrisSampleLabelParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def mris_sample_label_params(
     input_label_file: InputPathType,
     input_surface_file: InputPathType,
     output_label_file: str,
-) -> MrisSampleLabelParameters:
+) -> MrisSampleLabelParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +53,7 @@ def mris_sample_label_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_sample_label",
+        "@type": "freesurfer/mris_sample_label",
         "input_label_file": input_label_file,
         "input_surface_file": input_surface_file,
         "output_label_file": output_label_file,
@@ -102,9 +76,9 @@ def mris_sample_label_cargs(
     """
     cargs = []
     cargs.append("mris_sample_label")
-    cargs.append(execution.input_file(params.get("input_label_file")))
-    cargs.append(execution.input_file(params.get("input_surface_file")))
-    cargs.append(params.get("output_label_file"))
+    cargs.append(execution.input_file(params.get("input_label_file", None)))
+    cargs.append(execution.input_file(params.get("input_surface_file", None)))
+    cargs.append(params.get("output_label_file", None))
     return cargs
 
 
@@ -123,16 +97,18 @@ def mris_sample_label_outputs(
     """
     ret = MrisSampleLabelOutputs(
         root=execution.output_file("."),
-        output_label_file=execution.output_file(params.get("output_label_file")),
+        output_label_file=execution.output_file(params.get("output_label_file", None)),
     )
     return ret
 
 
 def mris_sample_label_execute(
     params: MrisSampleLabelParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisSampleLabelOutputs:
     """
+    mris_sample_label
+    
     This tool samples a label onto a surface model.
     
     Author: FreeSurfer Developers
@@ -141,10 +117,12 @@ def mris_sample_label_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisSampleLabelOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_SAMPLE_LABEL_METADATA)
     params = execution.params(params)
     cargs = mris_sample_label_cargs(params, execution)
     ret = mris_sample_label_outputs(params, execution)
@@ -159,6 +137,8 @@ def mris_sample_label(
     runner: Runner | None = None,
 ) -> MrisSampleLabelOutputs:
     """
+    mris_sample_label
+    
     This tool samples a label onto a surface model.
     
     Author: FreeSurfer Developers
@@ -173,20 +153,18 @@ def mris_sample_label(
     Returns:
         NamedTuple of outputs (described in `MrisSampleLabelOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_SAMPLE_LABEL_METADATA)
     params = mris_sample_label_params(
         input_label_file=input_label_file,
         input_surface_file=input_surface_file,
         output_label_file=output_label_file,
     )
-    return mris_sample_label_execute(params, execution)
+    return mris_sample_label_execute(params, runner)
 
 
 __all__ = [
     "MRIS_SAMPLE_LABEL_METADATA",
     "MrisSampleLabelOutputs",
-    "MrisSampleLabelParameters",
     "mris_sample_label",
+    "mris_sample_label_execute",
     "mris_sample_label_params",
 ]

niwrap_freesurfer/freesurfer/mris_sample_parc.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_SAMPLE_PARC_METADATA = Metadata(
-    id="630f4107826cbf1f372159b4ffd743acb835e4cc.boutiques",
+    id="6830ad64ede3b858ce0b3aac5cc09d3f3a91b2e6.boutiques",
     name="mris_sample_parc",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,33 @@ MRIS_SAMPLE_PARC_METADATA = Metadata(
 
 
 MrisSampleParcParameters = typing.TypedDict('MrisSampleParcParameters', {
-    "__STYXTYPE__": typing.Literal["mris_sample_parc"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_sample_parc"]],
+    "subject_name": str,
+    "hemisphere": str,
+    "parc_name": str,
+    "output_annot": str,
+    "sdir": typing.NotRequired[str | None],
+    "surf": typing.NotRequired[str | None],
+    "fix": typing.NotRequired[float | None],
+    "replace": typing.NotRequired[float | None],
+    "trans": typing.NotRequired[list[float] | None],
+    "cortex": typing.NotRequired[str | None],
+    "projmm": typing.NotRequired[float | None],
+    "proj": typing.NotRequired[float | None],
+    "projfrac": typing.NotRequired[float | None],
+    "file": typing.NotRequired[str | None],
+    "ct": typing.NotRequired[str | None],
+    "v_level": typing.NotRequired[float | None],
+    "filter": typing.NotRequired[float | None],
+    "smooth": typing.NotRequired[float | None],
+    "w_size": typing.NotRequired[float | None],
+    "thickness": typing.NotRequired[str | None],
+    "change_unknown": typing.NotRequired[float | None],
+    "help": bool,
+    "version": bool,
+})
+MrisSampleParcParametersTagged = typing.TypedDict('MrisSampleParcParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_sample_parc"],
     "subject_name": str,
     "hemisphere": str,
     "parc_name": str,
@@ -39,43 +65,11 @@ MrisSampleParcParameters = typing.TypedDict('MrisSampleParcParameters', {
     "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_sample_parc": mris_sample_parc_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_sample_parc": mris_sample_parc_outputs,
-    }.get(t)
 
 
 class MrisSampleParcOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_sample_parc(...)`.
+    Output object returned when calling `MrisSampleParcParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -107,7 +101,7 @@ def mris_sample_parc_params(
     change_unknown: float | None = None,
     help_: bool = False,
     version: bool = False,
-) -> MrisSampleParcParameters:
+) -> MrisSampleParcParametersTagged:
     """
     Build parameters.
     
@@ -144,7 +138,7 @@ def mris_sample_parc_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_sample_parc",
+        "@type": "freesurfer/mris_sample_parc",
         "subject_name": subject_name,
         "hemisphere": hemisphere,
         "parc_name": parc_name,
@@ -204,98 +198,98 @@ def mris_sample_parc_cargs(
     """
     cargs = []
     cargs.append("mris_sample_parc")
-    cargs.append(params.get("subject_name"))
-    cargs.append(params.get("hemisphere"))
-    cargs.append(params.get("parc_name"))
-    cargs.append(params.get("output_annot"))
-    if params.get("sdir") is not None:
+    cargs.append(params.get("subject_name", None))
+    cargs.append(params.get("hemisphere", None))
+    cargs.append(params.get("parc_name", None))
+    cargs.append(params.get("output_annot", None))
+    if params.get("sdir", None) is not None:
         cargs.extend([
             "-sdir",
-            params.get("sdir")
+            params.get("sdir", None)
         ])
-    if params.get("surf") is not None:
+    if params.get("surf", None) is not None:
         cargs.extend([
             "-surf",
-            params.get("surf")
+            params.get("surf", None)
         ])
-    if params.get("fix") is not None:
+    if params.get("fix", None) is not None:
         cargs.extend([
             "-fix",
-            str(params.get("fix"))
+            str(params.get("fix", None))
         ])
-    if params.get("replace") is not None:
+    if params.get("replace", None) is not None:
         cargs.extend([
             "-replace",
-            str(params.get("replace"))
+            str(params.get("replace", None))
         ])
-    if params.get("trans") is not None:
+    if params.get("trans", None) is not None:
         cargs.extend([
             "-trans",
-            *map(str, params.get("trans"))
+            *map(str, params.get("trans", None))
         ])
-    if params.get("cortex") is not None:
+    if params.get("cortex", None) is not None:
         cargs.extend([
             "-cortex",
-            params.get("cortex")
+            params.get("cortex", None)
         ])
-    if params.get("projmm") is not None:
+    if params.get("projmm", None) is not None:
         cargs.extend([
             "-projmm",
-            str(params.get("projmm"))
+            str(params.get("projmm", None))
         ])
-    if params.get("proj") is not None:
+    if params.get("proj", None) is not None:
         cargs.extend([
             "-proj",
-            str(params.get("proj"))
+            str(params.get("proj", None))
         ])
-    if params.get("projfrac") is not None:
+    if params.get("projfrac", None) is not None:
         cargs.extend([
             "-projfrac",
-            str(params.get("projfrac"))
+            str(params.get("projfrac", None))
         ])
-    if params.get("file") is not None:
+    if params.get("file", None) is not None:
         cargs.extend([
             "-file",
-            params.get("file")
+            params.get("file", None)
         ])
-    if params.get("ct") is not None:
+    if params.get("ct", None) is not None:
         cargs.extend([
             "-ct",
-            params.get("ct")
+            params.get("ct", None)
         ])
-    if params.get("v_level") is not None:
+    if params.get("v_level", None) is not None:
         cargs.extend([
             "-v",
-            str(params.get("v_level"))
+            str(params.get("v_level", None))
         ])
-    if params.get("filter") is not None:
+    if params.get("filter", None) is not None:
         cargs.extend([
             "-f",
-            str(params.get("filter"))
+            str(params.get("filter", None))
         ])
-    if params.get("smooth") is not None:
+    if params.get("smooth", None) is not None:
         cargs.extend([
             "-a",
-            str(params.get("smooth"))
+            str(params.get("smooth", None))
         ])
-    if params.get("w_size") is not None:
+    if params.get("w_size", None) is not None:
         cargs.extend([
             "-w",
-            str(params.get("w_size"))
+            str(params.get("w_size", None))
         ])
-    if params.get("thickness") is not None:
+    if params.get("thickness", None) is not None:
         cargs.extend([
             "-t",
-            params.get("thickness")
+            params.get("thickness", None)
         ])
-    if params.get("change_unknown") is not None:
+    if params.get("change_unknown", None) is not None:
         cargs.extend([
             "-u",
-            str(params.get("change_unknown"))
+            str(params.get("change_unknown", None))
         ])
-    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
 
@@ -315,16 +309,18 @@ def mris_sample_parc_outputs(
     """
     ret = MrisSampleParcOutputs(
         root=execution.output_file("."),
-        outfile=execution.output_file(params.get("output_annot")),
+        outfile=execution.output_file(params.get("output_annot", None)),
     )
     return ret
 
 
 def mris_sample_parc_execute(
     params: MrisSampleParcParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisSampleParcOutputs:
     """
+    mris_sample_parc
+    
     This program samples a volumetric parcellation onto a surface.
     
     Author: FreeSurfer Developers
@@ -333,10 +329,12 @@ def mris_sample_parc_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisSampleParcOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_SAMPLE_PARC_METADATA)
     params = execution.params(params)
     cargs = mris_sample_parc_cargs(params, execution)
     ret = mris_sample_parc_outputs(params, execution)
@@ -371,6 +369,8 @@ def mris_sample_parc(
     runner: Runner | None = None,
 ) -> MrisSampleParcOutputs:
     """
+    mris_sample_parc
+    
     This program samples a volumetric parcellation onto a surface.
     
     Author: FreeSurfer Developers
@@ -410,8 +410,6 @@ def mris_sample_parc(
     Returns:
         NamedTuple of outputs (described in `MrisSampleParcOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_SAMPLE_PARC_METADATA)
     params = mris_sample_parc_params(
         subject_name=subject_name,
         hemisphere=hemisphere,
@@ -437,13 +435,13 @@ def mris_sample_parc(
         help_=help_,
         version=version,
     )
-    return mris_sample_parc_execute(params, execution)
+    return mris_sample_parc_execute(params, runner)
 
 
 __all__ = [
     "MRIS_SAMPLE_PARC_METADATA",
     "MrisSampleParcOutputs",
-    "MrisSampleParcParameters",
     "mris_sample_parc",
+    "mris_sample_parc_execute",
     "mris_sample_parc_params",
 ]

niwrap_freesurfer/freesurfer/mris_seg2annot.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_SEG2ANNOT_METADATA = Metadata(
-    id="55808890fcb2dab6adced966808ff3a154a41714.boutiques",
+    id="2908e47d0e8ec511e03b3869cd0b2a8e89e97657.boutiques",
     name="mris_seg2annot",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,21 @@ MRIS_SEG2ANNOT_METADATA = Metadata(
 
 
 MrisSeg2annotParameters = typing.TypedDict('MrisSeg2annotParameters', {
-    "__STYXTYPE__": typing.Literal["mris_seg2annot"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_seg2annot"]],
+    "surfseg": InputPathType,
+    "colortable": typing.NotRequired[InputPathType | None],
+    "auto_ctab": typing.NotRequired[str | None],
+    "subject": str,
+    "hemi": str,
+    "output_annotation": str,
+    "surf": typing.NotRequired[str | None],
+    "debug": bool,
+    "debug_vertex": typing.NotRequired[float | None],
+    "checkopts": bool,
+    "version": bool,
+})
+MrisSeg2annotParametersTagged = typing.TypedDict('MrisSeg2annotParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_seg2annot"],
     "surfseg": InputPathType,
     "colortable": typing.NotRequired[InputPathType | None],
     "auto_ctab": typing.NotRequired[str | None],
@@ -27,43 +41,11 @@ MrisSeg2annotParameters = typing.TypedDict('MrisSeg2annotParameters', {
     "checkopts": 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_seg2annot": mris_seg2annot_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_seg2annot": mris_seg2annot_outputs,
-    }.get(t)
 
 
 class MrisSeg2annotOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_seg2annot(...)`.
+    Output object returned when calling `MrisSeg2annotParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -83,7 +65,7 @@ def mris_seg2annot_params(
     debug_vertex: float | None = None,
     checkopts: bool = False,
     version: bool = False,
-) -> MrisSeg2annotParameters:
+) -> MrisSeg2annotParametersTagged:
     """
     Build parameters.
     
@@ -105,7 +87,7 @@ def mris_seg2annot_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_seg2annot",
+        "@type": "freesurfer/mris_seg2annot",
         "surfseg": surfseg,
         "subject": subject,
         "hemi": hemi,
@@ -142,45 +124,45 @@ def mris_seg2annot_cargs(
     cargs.append("mris_seg2annot")
     cargs.extend([
         "--seg",
-        execution.input_file(params.get("surfseg"))
+        execution.input_file(params.get("surfseg", None))
     ])
-    if params.get("colortable") is not None:
+    if params.get("colortable", None) is not None:
         cargs.extend([
             "--ctab",
-            execution.input_file(params.get("colortable"))
+            execution.input_file(params.get("colortable", None))
         ])
-    if params.get("auto_ctab") is not None:
+    if params.get("auto_ctab", None) is not None:
         cargs.extend([
             "--ctab-auto",
-            params.get("auto_ctab")
+            params.get("auto_ctab", None)
         ])
     cargs.extend([
         "--s",
-        params.get("subject")
+        params.get("subject", None)
     ])
     cargs.extend([
         "--h",
-        params.get("hemi")
+        params.get("hemi", None)
     ])
     cargs.extend([
         "--o",
-        params.get("output_annotation")
+        params.get("output_annotation", None)
     ])
-    if params.get("surf") is not None:
+    if params.get("surf", None) is not None:
         cargs.extend([
             "--surf",
-            params.get("surf")
+            params.get("surf", None)
         ])
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
-    if params.get("debug_vertex") is not None:
+    if params.get("debug_vertex", None) is not None:
         cargs.extend([
             "--debug-vertex",
-            str(params.get("debug_vertex"))
+            str(params.get("debug_vertex", None))
         ])
-    if params.get("checkopts"):
+    if params.get("checkopts", False):
         cargs.append("--checkopts")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("--version")
     return cargs
 
@@ -200,16 +182,18 @@ def mris_seg2annot_outputs(
     """
     ret = MrisSeg2annotOutputs(
         root=execution.output_file("."),
-        annotation_file=execution.output_file(params.get("output_annotation")),
+        annotation_file=execution.output_file(params.get("output_annotation", None)),
     )
     return ret
 
 
 def mris_seg2annot_execute(
     params: MrisSeg2annotParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisSeg2annotOutputs:
     """
+    mris_seg2annot
+    
     Converts a surface-based segmentation into a custom annotation file.
     
     Author: FreeSurfer Developers
@@ -218,10 +202,12 @@ def mris_seg2annot_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisSeg2annotOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_SEG2ANNOT_METADATA)
     params = execution.params(params)
     cargs = mris_seg2annot_cargs(params, execution)
     ret = mris_seg2annot_outputs(params, execution)
@@ -244,6 +230,8 @@ def mris_seg2annot(
     runner: Runner | None = None,
 ) -> MrisSeg2annotOutputs:
     """
+    mris_seg2annot
+    
     Converts a surface-based segmentation into a custom annotation file.
     
     Author: FreeSurfer Developers
@@ -268,8 +256,6 @@ def mris_seg2annot(
     Returns:
         NamedTuple of outputs (described in `MrisSeg2annotOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_SEG2ANNOT_METADATA)
     params = mris_seg2annot_params(
         surfseg=surfseg,
         colortable=colortable,
@@ -283,13 +269,13 @@ def mris_seg2annot(
         checkopts=checkopts,
         version=version,
     )
-    return mris_seg2annot_execute(params, execution)
+    return mris_seg2annot_execute(params, runner)
 
 
 __all__ = [
     "MRIS_SEG2ANNOT_METADATA",
     "MrisSeg2annotOutputs",
-    "MrisSeg2annotParameters",
     "mris_seg2annot",
+    "mris_seg2annot_execute",
     "mris_seg2annot_params",
 ]