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

niwrap_freesurfer/freesurfer/mri_mc.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_MC_METADATA = Metadata(
-    id="9e6e0910561ae66cef8a0a6a59788fbf92c19e5f.boutiques",
+    id="49179ab79374b3c5b08a2b72c8d599c9afb7eb18.boutiques",
     name="mri_mc",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ MRI_MC_METADATA = Metadata(
 
 
 MriMcParameters = typing.TypedDict('MriMcParameters', {
-    "__STYXTYPE__": typing.Literal["mri_mc"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_mc"]],
+    "input_volume": InputPathType,
+    "label_value": float,
+    "output_surface": str,
+    "connectivity": typing.NotRequired[float | None],
+})
+MriMcParametersTagged = typing.TypedDict('MriMcParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_mc"],
     "input_volume": InputPathType,
     "label_value": float,
     "output_surface": str,
     "connectivity": typing.NotRequired[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 {
-        "mri_mc": mri_mc_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 {
-        "mri_mc": mri_mc_outputs,
-    }.get(t)
 
 
 class MriMcOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_mc(...)`.
+    Output object returned when calling `MriMcParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -68,8 +43,8 @@ def mri_mc_params(
     input_volume: InputPathType,
     label_value: float,
     output_surface: str,
-    connectivity: float | None = 1,
-) -> MriMcParameters:
+    connectivity: float | None = None,
+) -> MriMcParametersTagged:
     """
     Build parameters.
     
@@ -84,7 +59,7 @@ def mri_mc_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_mc",
+        "@type": "freesurfer/mri_mc",
         "input_volume": input_volume,
         "label_value": label_value,
         "output_surface": output_surface,
@@ -109,10 +84,10 @@ def mri_mc_cargs(
     """
     cargs = []
     cargs.append("mri_mc")
-    cargs.append(execution.input_file(params.get("input_volume")))
-    cargs.append(str(params.get("label_value")))
-    if params.get("connectivity") is not None:
-        cargs.append(params.get("output_surface") + str(params.get("connectivity")))
+    cargs.append(execution.input_file(params.get("input_volume", None)))
+    cargs.append(str(params.get("label_value", None)))
+    if params.get("connectivity", None) is not None:
+        cargs.append(params.get("output_surface", None) + str(params.get("connectivity", None)))
     return cargs
 
 
@@ -131,16 +106,18 @@ def mri_mc_outputs(
     """
     ret = MriMcOutputs(
         root=execution.output_file("."),
-        extracted_surface=execution.output_file(params.get("output_surface")),
+        extracted_surface=execution.output_file(params.get("output_surface", None)),
     )
     return ret
 
 
 def mri_mc_execute(
     params: MriMcParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriMcOutputs:
     """
+    mri_mc
+    
     Extract a surface from a label volume using Marching Cubes algorithm.
     
     Author: FreeSurfer Developers
@@ -149,10 +126,12 @@ def mri_mc_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriMcOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_MC_METADATA)
     params = execution.params(params)
     cargs = mri_mc_cargs(params, execution)
     ret = mri_mc_outputs(params, execution)
@@ -164,10 +143,12 @@ def mri_mc(
     input_volume: InputPathType,
     label_value: float,
     output_surface: str,
-    connectivity: float | None = 1,
+    connectivity: float | None = None,
     runner: Runner | None = None,
 ) -> MriMcOutputs:
     """
+    mri_mc
+    
     Extract a surface from a label volume using Marching Cubes algorithm.
     
     Author: FreeSurfer Developers
@@ -185,21 +166,19 @@ def mri_mc(
     Returns:
         NamedTuple of outputs (described in `MriMcOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_MC_METADATA)
     params = mri_mc_params(
         input_volume=input_volume,
         label_value=label_value,
         output_surface=output_surface,
         connectivity=connectivity,
     )
-    return mri_mc_execute(params, execution)
+    return mri_mc_execute(params, runner)
 
 
 __all__ = [
     "MRI_MC_METADATA",
     "MriMcOutputs",
-    "MriMcParameters",
     "mri_mc",
+    "mri_mc_execute",
     "mri_mc_params",
 ]

niwrap_freesurfer/freesurfer/mri_mcsim.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_MCSIM_METADATA = Metadata(
-    id="02637c2ef96d96491e552044c44e51e417c89838.boutiques",
+    id="49b8e9f48f3fddd28e2a3ac19856a9138f514966.boutiques",
     name="mri_mcsim",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,33 @@ MRI_MCSIM_METADATA = Metadata(
 
 
 MriMcsimParameters = typing.TypedDict('MriMcsimParameters', {
-    "__STYXTYPE__": typing.Literal["mri_mcsim"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_mcsim"]],
+    "top_output_dir": str,
+    "base_name": str,
+    "surface": list[str],
+    "num_repetitions": float,
+    "fwhm_values": typing.NotRequired[list[float] | None],
+    "fwhm_max": typing.NotRequired[float | None],
+    "avg_vertex_area": bool,
+    "random_seed": typing.NotRequired[float | None],
+    "label_file": typing.NotRequired[InputPathType | None],
+    "mask_file": typing.NotRequired[InputPathType | None],
+    "no_label": bool,
+    "no_save_mask": bool,
+    "surface_name": typing.NotRequired[str | None],
+    "log_file": typing.NotRequired[str | None],
+    "done_file": typing.NotRequired[str | None],
+    "stop_file": typing.NotRequired[str | None],
+    "save_file": typing.NotRequired[str | None],
+    "save_iter": bool,
+    "subjects_dir": typing.NotRequired[str | None],
+    "debug": bool,
+    "check_opts": bool,
+    "help": bool,
+    "version": bool,
+})
+MriMcsimParametersTagged = typing.TypedDict('MriMcsimParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_mcsim"],
     "top_output_dir": str,
     "base_name": str,
     "surface": list[str],
@@ -39,43 +65,11 @@ MriMcsimParameters = typing.TypedDict('MriMcsimParameters', {
     "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 {
-        "mri_mcsim": mri_mcsim_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 {
-        "mri_mcsim": mri_mcsim_outputs,
-    }.get(t)
 
 
 class MriMcsimOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_mcsim(...)`.
+    Output object returned when calling `MriMcsimParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -113,7 +107,7 @@ def mri_mcsim_params(
     check_opts: bool = False,
     help_: bool = False,
     version: bool = False,
-) -> MriMcsimParameters:
+) -> MriMcsimParametersTagged:
     """
     Build parameters.
     
@@ -146,7 +140,7 @@ def mri_mcsim_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_mcsim",
+        "@type": "freesurfer/mri_mcsim",
         "top_output_dir": top_output_dir,
         "base_name": base_name,
         "surface": surface,
@@ -202,90 +196,90 @@ def mri_mcsim_cargs(
     cargs.append("mri_mcsim")
     cargs.extend([
         "--o",
-        params.get("top_output_dir")
+        params.get("top_output_dir", None)
     ])
     cargs.extend([
         "--base",
-        params.get("base_name")
+        params.get("base_name", None)
     ])
     cargs.extend([
         "--surface",
-        *params.get("surface")
+        *params.get("surface", None)
     ])
     cargs.extend([
         "--nreps",
-        str(params.get("num_repetitions"))
+        str(params.get("num_repetitions", None))
     ])
-    if params.get("fwhm_values") is not None:
+    if params.get("fwhm_values", None) is not None:
         cargs.extend([
             "--fwhm",
-            *map(str, params.get("fwhm_values"))
+            *map(str, params.get("fwhm_values", None))
         ])
-    if params.get("fwhm_max") is not None:
+    if params.get("fwhm_max", None) is not None:
         cargs.extend([
             "--fwhm-max",
-            str(params.get("fwhm_max"))
+            str(params.get("fwhm_max", None))
         ])
-    if params.get("avg_vertex_area"):
+    if params.get("avg_vertex_area", False):
         cargs.append("--avgvtxarea")
-    if params.get("random_seed") is not None:
+    if params.get("random_seed", None) is not None:
         cargs.extend([
             "--seed",
-            str(params.get("random_seed"))
+            str(params.get("random_seed", 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("mask_file") is not None:
+    if params.get("mask_file", None) is not None:
         cargs.extend([
             "--mask",
-            execution.input_file(params.get("mask_file"))
+            execution.input_file(params.get("mask_file", None))
         ])
-    if params.get("no_label"):
+    if params.get("no_label", False):
         cargs.append("--no-label")
-    if params.get("no_save_mask"):
+    if params.get("no_save_mask", False):
         cargs.append("--no-save-mask")
-    if params.get("surface_name") is not None:
+    if params.get("surface_name", None) is not None:
         cargs.extend([
             "--surfname",
-            params.get("surface_name")
+            params.get("surface_name", None)
         ])
-    if params.get("log_file") is not None:
+    if params.get("log_file", None) is not None:
         cargs.extend([
             "--log",
-            params.get("log_file")
+            params.get("log_file", None)
         ])
-    if params.get("done_file") is not None:
+    if params.get("done_file", None) is not None:
         cargs.extend([
             "--done",
-            params.get("done_file")
+            params.get("done_file", None)
         ])
-    if params.get("stop_file") is not None:
+    if params.get("stop_file", None) is not None:
         cargs.extend([
             "--stop",
-            params.get("stop_file")
+            params.get("stop_file", None)
         ])
-    if params.get("save_file") is not None:
+    if params.get("save_file", None) is not None:
         cargs.extend([
             "--save",
-            params.get("save_file")
+            params.get("save_file", None)
         ])
-    if params.get("save_iter"):
+    if params.get("save_iter", False):
         cargs.append("--save-iter")
-    if params.get("subjects_dir") is not None:
+    if params.get("subjects_dir", None) is not None:
         cargs.extend([
             "--sd",
-            params.get("subjects_dir")
+            params.get("subjects_dir", None)
         ])
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
-    if params.get("check_opts"):
+    if params.get("check_opts", 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
 
@@ -305,19 +299,21 @@ def mri_mcsim_outputs(
     """
     ret = MriMcsimOutputs(
         root=execution.output_file("."),
-        csd_output=execution.output_file(params.get("top_output_dir") + "/" + params.get("base_name") + ".csd"),
-        done_output=execution.output_file(params.get("top_output_dir") + "/done/" + params.get("done_file")) if (params.get("done_file") is not None) else None,
-        iteration_save=execution.output_file(params.get("top_output_dir") + "/" + params.get("save_file")) if (params.get("save_file") is not None) else None,
-        log_output=execution.output_file(params.get("top_output_dir") + "/log/" + params.get("log_file")) if (params.get("log_file") is not None) else None,
+        csd_output=execution.output_file(params.get("top_output_dir", None) + "/" + params.get("base_name", None) + ".csd"),
+        done_output=execution.output_file(params.get("top_output_dir", None) + "/done/" + params.get("done_file", None)) if (params.get("done_file") is not None) else None,
+        iteration_save=execution.output_file(params.get("top_output_dir", None) + "/" + params.get("save_file", None)) if (params.get("save_file") is not None) else None,
+        log_output=execution.output_file(params.get("top_output_dir", None) + "/log/" + params.get("log_file", None)) if (params.get("log_file") is not None) else None,
     )
     return ret
 
 
 def mri_mcsim_execute(
     params: MriMcsimParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriMcsimOutputs:
     """
+    mri_mcsim
+    
     Monte Carlo simulation tool for surface-based multiple comparisons.
     
     Author: FreeSurfer Developers
@@ -326,10 +322,12 @@ def mri_mcsim_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriMcsimOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_MCSIM_METADATA)
     params = execution.params(params)
     cargs = mri_mcsim_cargs(params, execution)
     ret = mri_mcsim_outputs(params, execution)
@@ -364,6 +362,8 @@ def mri_mcsim(
     runner: Runner | None = None,
 ) -> MriMcsimOutputs:
     """
+    mri_mcsim
+    
     Monte Carlo simulation tool for surface-based multiple comparisons.
     
     Author: FreeSurfer Developers
@@ -399,8 +399,6 @@ def mri_mcsim(
     Returns:
         NamedTuple of outputs (described in `MriMcsimOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_MCSIM_METADATA)
     params = mri_mcsim_params(
         top_output_dir=top_output_dir,
         base_name=base_name,
@@ -426,13 +424,13 @@ def mri_mcsim(
         help_=help_,
         version=version,
     )
-    return mri_mcsim_execute(params, execution)
+    return mri_mcsim_execute(params, runner)
 
 
 __all__ = [
     "MRI_MCSIM_METADATA",
     "MriMcsimOutputs",
-    "MriMcsimParameters",
     "mri_mcsim",
+    "mri_mcsim_execute",
     "mri_mcsim_params",
 ]

niwrap_freesurfer/freesurfer/mri_mergelabels.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_MERGELABELS_METADATA = Metadata(
-    id="6bb9780e2621eb708a1827e5de3a8163f55a21b4.boutiques",
+    id="92b8ea866e024868c9418a4954dce0cbbc1b29c6.boutiques",
     name="mri_mergelabels",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ MRI_MERGELABELS_METADATA = Metadata(
 
 
 MriMergelabelsParameters = typing.TypedDict('MriMergelabelsParameters', {
-    "__STYXTYPE__": typing.Literal["mri_mergelabels"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_mergelabels"]],
+    "input_labels": list[InputPathType],
+    "output_label": str,
+    "input_directory": typing.NotRequired[str | None],
+})
+MriMergelabelsParametersTagged = typing.TypedDict('MriMergelabelsParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_mergelabels"],
     "input_labels": list[InputPathType],
     "output_label": str,
     "input_directory": 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 {
-        "mri_mergelabels": mri_mergelabels_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 {
-        "mri_mergelabels": mri_mergelabels_outputs,
-    }.get(t)
 
 
 class MriMergelabelsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_mergelabels(...)`.
+    Output object returned when calling `MriMergelabelsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def mri_mergelabels_params(
     input_labels: list[InputPathType],
     output_label: str,
     input_directory: str | None = None,
-) -> MriMergelabelsParameters:
+) -> MriMergelabelsParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +53,7 @@ def mri_mergelabels_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_mergelabels",
+        "@type": "freesurfer/mri_mergelabels",
         "input_labels": input_labels,
         "output_label": output_label,
     }
@@ -105,16 +79,16 @@ def mri_mergelabels_cargs(
     cargs.append("mri_mergelabels")
     cargs.extend([
         "-i",
-        *[execution.input_file(f) for f in params.get("input_labels")]
+        *[execution.input_file(f) for f in params.get("input_labels", None)]
     ])
     cargs.extend([
         "-o",
-        params.get("output_label")
+        params.get("output_label", None)
     ])
-    if params.get("input_directory") is not None:
+    if params.get("input_directory", None) is not None:
         cargs.extend([
             "-d",
-            params.get("input_directory")
+            params.get("input_directory", None)
         ])
     return cargs
 
@@ -134,16 +108,18 @@ def mri_mergelabels_outputs(
     """
     ret = MriMergelabelsOutputs(
         root=execution.output_file("."),
-        merged_label_file=execution.output_file(params.get("output_label")),
+        merged_label_file=execution.output_file(params.get("output_label", None)),
     )
     return ret
 
 
 def mri_mergelabels_execute(
     params: MriMergelabelsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriMergelabelsOutputs:
     """
+    mri_mergelabels
+    
     A tool to merge two or more label files by concatenating them together.
     
     Author: FreeSurfer Developers
@@ -152,10 +128,12 @@ def mri_mergelabels_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriMergelabelsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_MERGELABELS_METADATA)
     params = execution.params(params)
     cargs = mri_mergelabels_cargs(params, execution)
     ret = mri_mergelabels_outputs(params, execution)
@@ -170,6 +148,8 @@ def mri_mergelabels(
     runner: Runner | None = None,
 ) -> MriMergelabelsOutputs:
     """
+    mri_mergelabels
+    
     A tool to merge two or more label files by concatenating them together.
     
     Author: FreeSurfer Developers
@@ -184,20 +164,18 @@ def mri_mergelabels(
     Returns:
         NamedTuple of outputs (described in `MriMergelabelsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_MERGELABELS_METADATA)
     params = mri_mergelabels_params(
         input_labels=input_labels,
         output_label=output_label,
         input_directory=input_directory,
     )
-    return mri_mergelabels_execute(params, execution)
+    return mri_mergelabels_execute(params, runner)
 
 
 __all__ = [
     "MRI_MERGELABELS_METADATA",
     "MriMergelabelsOutputs",
-    "MriMergelabelsParameters",
     "mri_mergelabels",
+    "mri_mergelabels_execute",
     "mri_mergelabels_params",
 ]