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

niwrap_freesurfer/freesurfer/mris_convert.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_CONVERT_METADATA = Metadata(
-    id="1d19416b8d60b6d508587fe18bc53b66a00c61d5.boutiques",
+    id="1fa8ea61b6014f81465c2838041c431e0d412b45.boutiques",
     name="mris_convert",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,48 @@ MRIS_CONVERT_METADATA = Metadata(
 
 
 MrisConvertParameters = typing.TypedDict('MrisConvertParameters', {
-    "__STYXTYPE__": typing.Literal["mris_convert"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_convert"]],
+    "input_file": InputPathType,
+    "second_input_file": typing.NotRequired[InputPathType | None],
+    "output_file": str,
+    "patch": bool,
+    "curv_overlay_files": typing.NotRequired[list[str] | None],
+    "functional_data_file": typing.NotRequired[InputPathType | None],
+    "orig_positions": typing.NotRequired[str | None],
+    "scale": typing.NotRequired[float | None],
+    "rescale": bool,
+    "talairach_xfm": typing.NotRequired[str | None],
+    "normals": bool,
+    "neighbors": bool,
+    "xyz": bool,
+    "annotation_file": typing.NotRequired[InputPathType | None],
+    "parcstats_file": typing.NotRequired[InputPathType | None],
+    "gifti_dataarray_num": typing.NotRequired[float | None],
+    "label_file": typing.NotRequired[InputPathType | None],
+    "label_stats_file": typing.NotRequired[str | None],
+    "combine_surfs": bool,
+    "merge_gifti": bool,
+    "split_gifti": bool,
+    "gifti_outdir": typing.NotRequired[str | None],
+    "delete_cmds": bool,
+    "center": bool,
+    "vol_geom": typing.NotRequired[str | None],
+    "remove_vol_geom": bool,
+    "to_surf": typing.NotRequired[str | None],
+    "to_scanner": bool,
+    "to_tkr": bool,
+    "userealras": bool,
+    "usesurfras": bool,
+    "upsample": typing.NotRequired[str | None],
+    "volume": typing.NotRequired[str | None],
+    "area": typing.NotRequired[str | None],
+    "angle": typing.NotRequired[str | None],
+    "label_to_mask": typing.NotRequired[str | None],
+    "cras_add": bool,
+    "cras_subtract": bool,
+})
+MrisConvertParametersTagged = typing.TypedDict('MrisConvertParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_convert"],
     "input_file": InputPathType,
     "second_input_file": typing.NotRequired[InputPathType | None],
     "output_file": str,
@@ -54,43 +95,11 @@ MrisConvertParameters = typing.TypedDict('MrisConvertParameters', {
     "cras_add": bool,
     "cras_subtract": 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_convert": mris_convert_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_convert": mris_convert_outputs,
-    }.get(t)
 
 
 class MrisConvertOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_convert(...)`.
+    Output object returned when calling `MrisConvertParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -137,7 +146,7 @@ def mris_convert_params(
     label_to_mask: str | None = None,
     cras_add: bool = False,
     cras_subtract: bool = False,
-) -> MrisConvertParameters:
+) -> MrisConvertParametersTagged:
     """
     Build parameters.
     
@@ -192,7 +201,7 @@ def mris_convert_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_convert",
+        "@type": "freesurfer/mris_convert",
         "input_file": input_file,
         "output_file": output_file,
         "patch": patch,
@@ -269,133 +278,133 @@ def mris_convert_cargs(
     """
     cargs = []
     cargs.append("mris_convert")
-    cargs.append(execution.input_file(params.get("input_file")))
-    if params.get("second_input_file") is not None:
-        cargs.append(execution.input_file(params.get("second_input_file")))
-    cargs.append(params.get("output_file"))
-    if params.get("patch"):
+    cargs.append(execution.input_file(params.get("input_file", None)))
+    if params.get("second_input_file", None) is not None:
+        cargs.append(execution.input_file(params.get("second_input_file", None)))
+    cargs.append(params.get("output_file", None))
+    if params.get("patch", False):
         cargs.append("-p")
-    if params.get("curv_overlay_files") is not None:
+    if params.get("curv_overlay_files", None) is not None:
         cargs.extend([
             "-c",
-            *params.get("curv_overlay_files")
+            *params.get("curv_overlay_files", None)
         ])
-    if params.get("functional_data_file") is not None:
+    if params.get("functional_data_file", None) is not None:
         cargs.extend([
             "-f",
-            execution.input_file(params.get("functional_data_file"))
+            execution.input_file(params.get("functional_data_file", None))
         ])
-    if params.get("orig_positions") is not None:
+    if params.get("orig_positions", None) is not None:
         cargs.extend([
             "-o",
-            params.get("orig_positions")
+            params.get("orig_positions", None)
         ])
-    if params.get("scale") is not None:
+    if params.get("scale", None) is not None:
         cargs.extend([
             "-s",
-            str(params.get("scale"))
+            str(params.get("scale", None))
         ])
-    if params.get("rescale"):
+    if params.get("rescale", False):
         cargs.append("-r")
-    if params.get("talairach_xfm") is not None:
+    if params.get("talairach_xfm", None) is not None:
         cargs.extend([
             "-t",
-            params.get("talairach_xfm")
+            params.get("talairach_xfm", None)
         ])
-    if params.get("normals"):
+    if params.get("normals", False):
         cargs.append("-n")
-    if params.get("neighbors"):
+    if params.get("neighbors", False):
         cargs.append("-v")
-    if params.get("xyz"):
+    if params.get("xyz", False):
         cargs.append("-a")
-    if params.get("annotation_file") is not None:
+    if params.get("annotation_file", None) is not None:
         cargs.extend([
             "--annot",
-            execution.input_file(params.get("annotation_file"))
+            execution.input_file(params.get("annotation_file", None))
         ])
-    if params.get("parcstats_file") is not None:
+    if params.get("parcstats_file", None) is not None:
         cargs.extend([
             "--parcstats",
-            execution.input_file(params.get("parcstats_file"))
+            execution.input_file(params.get("parcstats_file", None))
         ])
-    if params.get("gifti_dataarray_num") is not None:
+    if params.get("gifti_dataarray_num", None) is not None:
         cargs.extend([
             "--da_num",
-            str(params.get("gifti_dataarray_num"))
+            str(params.get("gifti_dataarray_num", None))
         ])
-    if params.get("label_file") is not None:
+    if params.get("label_file", None) is not None:
         cargs.extend([
             "--label",
-            execution.input_file(params.get("label_file"))
+            execution.input_file(params.get("label_file", None))
         ])
-    if params.get("label_stats_file") is not None:
+    if params.get("label_stats_file", None) is not None:
         cargs.extend([
             "--labelstats",
-            params.get("label_stats_file")
+            params.get("label_stats_file", None)
         ])
-    if params.get("combine_surfs"):
+    if params.get("combine_surfs", False):
         cargs.append("--combinesurfs")
-    if params.get("merge_gifti"):
+    if params.get("merge_gifti", False):
         cargs.append("--mergegifti")
-    if params.get("split_gifti"):
+    if params.get("split_gifti", False):
         cargs.append("--splitgifti")
-    if params.get("gifti_outdir") is not None:
+    if params.get("gifti_outdir", None) is not None:
         cargs.extend([
             "--giftioutdir",
-            params.get("gifti_outdir")
+            params.get("gifti_outdir", None)
         ])
-    if params.get("delete_cmds"):
+    if params.get("delete_cmds", False):
         cargs.append("--delete-cmds")
-    if params.get("center"):
+    if params.get("center", False):
         cargs.append("--center")
-    if params.get("vol_geom") is not None:
+    if params.get("vol_geom", None) is not None:
         cargs.extend([
             "--vol-geom",
-            params.get("vol_geom")
+            params.get("vol_geom", None)
         ])
-    if params.get("remove_vol_geom"):
+    if params.get("remove_vol_geom", False):
         cargs.append("--remove-vol-geom")
-    if params.get("to_surf") is not None:
+    if params.get("to_surf", None) is not None:
         cargs.extend([
             "--to-surf",
-            params.get("to_surf")
+            params.get("to_surf", None)
         ])
-    if params.get("to_scanner"):
+    if params.get("to_scanner", False):
         cargs.append("--to-scanner")
-    if params.get("to_tkr"):
+    if params.get("to_tkr", False):
         cargs.append("--to-tkr")
-    if params.get("userealras"):
+    if params.get("userealras", False):
         cargs.append("--userealras")
-    if params.get("usesurfras"):
+    if params.get("usesurfras", False):
         cargs.append("--usesurfras")
-    if params.get("upsample") is not None:
+    if params.get("upsample", None) is not None:
         cargs.extend([
             "--upsample",
-            params.get("upsample")
+            params.get("upsample", None)
         ])
-    if params.get("volume") is not None:
+    if params.get("volume", None) is not None:
         cargs.extend([
             "--volume",
-            params.get("volume")
+            params.get("volume", None)
         ])
-    if params.get("area") is not None:
+    if params.get("area", None) is not None:
         cargs.extend([
             "--area",
-            params.get("area")
+            params.get("area", None)
         ])
-    if params.get("angle") is not None:
+    if params.get("angle", None) is not None:
         cargs.extend([
             "--angle",
-            params.get("angle")
+            params.get("angle", None)
         ])
-    if params.get("label_to_mask") is not None:
+    if params.get("label_to_mask", None) is not None:
         cargs.extend([
             "--label2mask",
-            params.get("label_to_mask")
+            params.get("label_to_mask", None)
         ])
-    if params.get("cras_add"):
+    if params.get("cras_add", False):
         cargs.append("--cras_add")
-    if params.get("cras_subtract"):
+    if params.get("cras_subtract", False):
         cargs.append("--cras_subtract")
     return cargs
 
@@ -415,16 +424,18 @@ def mris_convert_outputs(
     """
     ret = MrisConvertOutputs(
         root=execution.output_file("."),
-        converted_surface=execution.output_file(params.get("output_file")),
+        converted_surface=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def mris_convert_execute(
     params: MrisConvertParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisConvertOutputs:
     """
+    mris_convert
+    
     This program will convert MRI-surface data formats.
     
     Author: FreeSurfer Developers
@@ -433,10 +444,12 @@ def mris_convert_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisConvertOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_CONVERT_METADATA)
     params = execution.params(params)
     cargs = mris_convert_cargs(params, execution)
     ret = mris_convert_outputs(params, execution)
@@ -486,6 +499,8 @@ def mris_convert(
     runner: Runner | None = None,
 ) -> MrisConvertOutputs:
     """
+    mris_convert
+    
     This program will convert MRI-surface data formats.
     
     Author: FreeSurfer Developers
@@ -543,8 +558,6 @@ def mris_convert(
     Returns:
         NamedTuple of outputs (described in `MrisConvertOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_CONVERT_METADATA)
     params = mris_convert_params(
         input_file=input_file,
         second_input_file=second_input_file,
@@ -585,13 +598,13 @@ def mris_convert(
         cras_add=cras_add,
         cras_subtract=cras_subtract,
     )
-    return mris_convert_execute(params, execution)
+    return mris_convert_execute(params, runner)
 
 
 __all__ = [
     "MRIS_CONVERT_METADATA",
     "MrisConvertOutputs",
-    "MrisConvertParameters",
     "mris_convert",
+    "mris_convert_execute",
     "mris_convert_params",
 ]

niwrap_freesurfer/freesurfer/mris_copy_header.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_COPY_HEADER_METADATA = Metadata(
-    id="50f2639b90417e8c54457d6126e715ee07fb0d8e.boutiques",
+    id="f168cb910e38c60cae89203ba6900d503e421706.boutiques",
     name="mris_copy_header",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ MRIS_COPY_HEADER_METADATA = Metadata(
 
 
 MrisCopyHeaderParameters = typing.TypedDict('MrisCopyHeaderParameters', {
-    "__STYXTYPE__": typing.Literal["mris_copy_header"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_copy_header"]],
+    "input_surface": InputPathType,
+    "template_surface": InputPathType,
+    "output_surface": str,
+})
+MrisCopyHeaderParametersTagged = typing.TypedDict('MrisCopyHeaderParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_copy_header"],
     "input_surface": InputPathType,
     "template_surface": InputPathType,
     "output_surface": 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_copy_header": mris_copy_header_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_copy_header": mris_copy_header_outputs,
-    }.get(t)
 
 
 class MrisCopyHeaderOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_copy_header(...)`.
+    Output object returned when calling `MrisCopyHeaderParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def mris_copy_header_params(
     input_surface: InputPathType,
     template_surface: InputPathType,
     output_surface: str,
-) -> MrisCopyHeaderParameters:
+) -> MrisCopyHeaderParametersTagged:
     """
     Build parameters.
     
@@ -80,7 +54,7 @@ def mris_copy_header_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_copy_header",
+        "@type": "freesurfer/mris_copy_header",
         "input_surface": input_surface,
         "template_surface": template_surface,
         "output_surface": output_surface,
@@ -103,9 +77,9 @@ def mris_copy_header_cargs(
     """
     cargs = []
     cargs.append("mris_copy_header")
-    cargs.append(execution.input_file(params.get("input_surface")))
-    cargs.append(execution.input_file(params.get("template_surface")))
-    cargs.append(params.get("output_surface"))
+    cargs.append(execution.input_file(params.get("input_surface", None)))
+    cargs.append(execution.input_file(params.get("template_surface", None)))
+    cargs.append(params.get("output_surface", None))
     return cargs
 
 
@@ -124,18 +98,20 @@ def mris_copy_header_outputs(
     """
     ret = MrisCopyHeaderOutputs(
         root=execution.output_file("."),
-        out_surface=execution.output_file(params.get("output_surface")),
+        out_surface=execution.output_file(params.get("output_surface", None)),
     )
     return ret
 
 
 def mris_copy_header_execute(
     params: MrisCopyHeaderParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisCopyHeaderOutputs:
     """
-    Tool to copy the header from a template surface to an input surface and save as
-    the output surface.
+    mris_copy_header
+    
+    Tool to copy the header from a template surface to an input surface and save
+    as the output surface.
     
     Author: FreeSurfer Developers
     
@@ -143,10 +119,12 @@ def mris_copy_header_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisCopyHeaderOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_COPY_HEADER_METADATA)
     params = execution.params(params)
     cargs = mris_copy_header_cargs(params, execution)
     ret = mris_copy_header_outputs(params, execution)
@@ -161,8 +139,10 @@ def mris_copy_header(
     runner: Runner | None = None,
 ) -> MrisCopyHeaderOutputs:
     """
-    Tool to copy the header from a template surface to an input surface and save as
-    the output surface.
+    mris_copy_header
+    
+    Tool to copy the header from a template surface to an input surface and save
+    as the output surface.
     
     Author: FreeSurfer Developers
     
@@ -177,20 +157,18 @@ def mris_copy_header(
     Returns:
         NamedTuple of outputs (described in `MrisCopyHeaderOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_COPY_HEADER_METADATA)
     params = mris_copy_header_params(
         input_surface=input_surface,
         template_surface=template_surface,
         output_surface=output_surface,
     )
-    return mris_copy_header_execute(params, execution)
+    return mris_copy_header_execute(params, runner)
 
 
 __all__ = [
     "MRIS_COPY_HEADER_METADATA",
     "MrisCopyHeaderOutputs",
-    "MrisCopyHeaderParameters",
     "mris_copy_header",
+    "mris_copy_header_execute",
     "mris_copy_header_params",
 ]