niwrap-freesurfer 0.6.2__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/compute_label_volumes_csh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 COMPUTE_LABEL_VOLUMES_CSH_METADATA = Metadata(
-    id="868d89d16779dfaa8674d3cf6361c520a6cdcca9.boutiques",
+    id="52410a05119da4136f893a14e5b1520221bccbbf.boutiques",
     name="compute_label_volumes.csh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,59 +14,39 @@ COMPUTE_LABEL_VOLUMES_CSH_METADATA = Metadata(
 
 
 ComputeLabelVolumesCshLabelLParameters = typing.TypedDict('ComputeLabelVolumesCshLabelLParameters', {
-    "__STYXTYPE__": typing.Literal["label_L"],
+    "@type": typing.NotRequired[typing.Literal["label_L"]],
+    "upper_L": typing.NotRequired[str | None],
+    "lower_L": typing.NotRequired[str | None],
+})
+ComputeLabelVolumesCshLabelLParametersTagged = typing.TypedDict('ComputeLabelVolumesCshLabelLParametersTagged', {
+    "@type": typing.Literal["label_L"],
     "upper_L": typing.NotRequired[str | None],
     "lower_L": typing.NotRequired[str | None],
 })
 
 
 ComputeLabelVolumesCshParameters = typing.TypedDict('ComputeLabelVolumesCshParameters', {
-    "__STYXTYPE__": typing.Literal["compute_label_volumes.csh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/compute_label_volumes.csh"]],
+    "label_vol": InputPathType,
+    "output_file": str,
+    "label_L": typing.NotRequired[ComputeLabelVolumesCshLabelLParameters | None],
+    "version": bool,
+    "help": bool,
+})
+ComputeLabelVolumesCshParametersTagged = typing.TypedDict('ComputeLabelVolumesCshParametersTagged', {
+    "@type": typing.Literal["freesurfer/compute_label_volumes.csh"],
     "label_vol": InputPathType,
     "output_file": str,
     "label_L": typing.NotRequired[ComputeLabelVolumesCshLabelLParameters | None],
     "version": bool,
     "help": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "compute_label_volumes.csh": compute_label_volumes_csh_cargs,
-        "label_L": compute_label_volumes_csh_label_l_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 {
-        "compute_label_volumes.csh": compute_label_volumes_csh_outputs,
-    }.get(t)
 
 
 def compute_label_volumes_csh_label_l_params(
     upper_l: str | None = None,
     lower_l: str | None = None,
-) -> ComputeLabelVolumesCshLabelLParameters:
+) -> ComputeLabelVolumesCshLabelLParametersTagged:
     """
     Build parameters.
     
@@ -77,7 +57,7 @@ def compute_label_volumes_csh_label_l_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "label_L",
+        "@type": "label_L",
     }
     if upper_l is not None:
         params["upper_L"] = upper_l
@@ -100,22 +80,22 @@ def compute_label_volumes_csh_label_l_cargs(
         Command-line arguments.
     """
     cargs = []
-    if params.get("upper_L") is not None:
+    if params.get("upper_L", None) is not None:
         cargs.extend([
             "--L",
-            params.get("upper_L")
+            params.get("upper_L", None)
         ])
-    if params.get("lower_L") is not None:
+    if params.get("lower_L", None) is not None:
         cargs.extend([
             "--l",
-            params.get("lower_L")
+            params.get("lower_L", None)
         ])
     return cargs
 
 
 class ComputeLabelVolumesCshOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `compute_label_volumes_csh(...)`.
+    Output object returned when calling `ComputeLabelVolumesCshParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -129,7 +109,7 @@ def compute_label_volumes_csh_params(
     label_l: ComputeLabelVolumesCshLabelLParameters | None = None,
     version: bool = False,
     help_: bool = False,
-) -> ComputeLabelVolumesCshParameters:
+) -> ComputeLabelVolumesCshParametersTagged:
     """
     Build parameters.
     
@@ -143,7 +123,7 @@ def compute_label_volumes_csh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "compute_label_volumes.csh",
+        "@type": "freesurfer/compute_label_volumes.csh",
         "label_vol": label_vol,
         "output_file": output_file,
         "version": version,
@@ -171,17 +151,17 @@ def compute_label_volumes_csh_cargs(
     cargs.append("compute_label_volumes.csh")
     cargs.extend([
         "--vol",
-        execution.input_file(params.get("label_vol"))
+        execution.input_file(params.get("label_vol", None))
     ])
     cargs.extend([
         "--out",
-        params.get("output_file")
+        params.get("output_file", None)
     ])
-    if params.get("label_L") is not None:
-        cargs.extend(dyn_cargs(params.get("label_L")["__STYXTYPE__"])(params.get("label_L"), execution))
-    if params.get("version"):
+    if params.get("label_L", None) is not None:
+        cargs.extend(compute_label_volumes_csh_label_l_cargs(params.get("label_L", None), execution))
+    if params.get("version", False):
         cargs.append("--version")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("--help")
     return cargs
 
@@ -201,16 +181,18 @@ def compute_label_volumes_csh_outputs(
     """
     ret = ComputeLabelVolumesCshOutputs(
         root=execution.output_file("."),
-        result_file=execution.output_file(params.get("output_file")),
+        result_file=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def compute_label_volumes_csh_execute(
     params: ComputeLabelVolumesCshParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ComputeLabelVolumesCshOutputs:
     """
+    compute_label_volumes.csh
+    
     Computes the number of voxels and the volumes of either all or a particular
     label in the input label volume.
     
@@ -220,10 +202,12 @@ def compute_label_volumes_csh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ComputeLabelVolumesCshOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(COMPUTE_LABEL_VOLUMES_CSH_METADATA)
     params = execution.params(params)
     cargs = compute_label_volumes_csh_cargs(params, execution)
     ret = compute_label_volumes_csh_outputs(params, execution)
@@ -240,6 +224,8 @@ def compute_label_volumes_csh(
     runner: Runner | None = None,
 ) -> ComputeLabelVolumesCshOutputs:
     """
+    compute_label_volumes.csh
+    
     Computes the number of voxels and the volumes of either all or a particular
     label in the input label volume.
     
@@ -257,8 +243,6 @@ def compute_label_volumes_csh(
     Returns:
         NamedTuple of outputs (described in `ComputeLabelVolumesCshOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(COMPUTE_LABEL_VOLUMES_CSH_METADATA)
     params = compute_label_volumes_csh_params(
         label_vol=label_vol,
         output_file=output_file,
@@ -266,15 +250,14 @@ def compute_label_volumes_csh(
         version=version,
         help_=help_,
     )
-    return compute_label_volumes_csh_execute(params, execution)
+    return compute_label_volumes_csh_execute(params, runner)
 
 
 __all__ = [
     "COMPUTE_LABEL_VOLUMES_CSH_METADATA",
-    "ComputeLabelVolumesCshLabelLParameters",
     "ComputeLabelVolumesCshOutputs",
-    "ComputeLabelVolumesCshParameters",
     "compute_label_volumes_csh",
+    "compute_label_volumes_csh_execute",
     "compute_label_volumes_csh_label_l_params",
     "compute_label_volumes_csh_params",
 ]

niwrap_freesurfer/freesurfer/compute_vox2vox.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 COMPUTE_VOX2VOX_METADATA = Metadata(
-    id="9a7bf87929e316ff71cbf7100a4c060f4d38576b.boutiques",
+    id="73b2097f0e34a9af6523d118eff4b6ab65435900.boutiques",
     name="compute_vox2vox",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,60 +14,32 @@ COMPUTE_VOX2VOX_METADATA = Metadata(
 
 
 ComputeVox2voxParameters = typing.TypedDict('ComputeVox2voxParameters', {
-    "__STYXTYPE__": typing.Literal["compute_vox2vox"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/compute_vox2vox"]],
+    "source": InputPathType,
+    "t4file": InputPathType,
+    "target": InputPathType,
+})
+ComputeVox2voxParametersTagged = typing.TypedDict('ComputeVox2voxParametersTagged', {
+    "@type": typing.Literal["freesurfer/compute_vox2vox"],
     "source": InputPathType,
     "t4file": InputPathType,
     "target": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "compute_vox2vox": compute_vox2vox_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 {
-        "compute_vox2vox": compute_vox2vox_outputs,
-    }.get(t)
 
 
 class ComputeVox2voxOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `compute_vox2vox(...)`.
+    Output object returned when calling `ComputeVox2voxParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    output: OutputPathType
-    """The resulting transformed voxel-to-voxel 4dfp output file."""
 
 
 def compute_vox2vox_params(
     source: InputPathType,
     t4file: InputPathType,
     target: InputPathType,
-) -> ComputeVox2voxParameters:
+) -> ComputeVox2voxParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +51,7 @@ def compute_vox2vox_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "compute_vox2vox",
+        "@type": "freesurfer/compute_vox2vox",
         "source": source,
         "t4file": t4file,
         "target": target,
@@ -102,9 +74,9 @@ def compute_vox2vox_cargs(
     """
     cargs = []
     cargs.append("compute_vox2vox")
-    cargs.append(execution.input_file(params.get("source")))
-    cargs.append(execution.input_file(params.get("t4file")))
-    cargs.append(execution.input_file(params.get("target")))
+    cargs.append(execution.input_file(params.get("source", None)))
+    cargs.append(execution.input_file(params.get("t4file", None)))
+    cargs.append(execution.input_file(params.get("target", None)))
     return cargs
 
 
@@ -123,16 +95,17 @@ def compute_vox2vox_outputs(
     """
     ret = ComputeVox2voxOutputs(
         root=execution.output_file("."),
-        output=execution.output_file("<replace_with_output_path_pattern>"),
     )
     return ret
 
 
 def compute_vox2vox_execute(
     params: ComputeVox2voxParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ComputeVox2voxOutputs:
     """
+    compute_vox2vox
+    
     Tool for computing voxel-to-voxel transformations.
     
     Author: FreeSurfer Developers
@@ -141,10 +114,12 @@ def compute_vox2vox_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ComputeVox2voxOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(COMPUTE_VOX2VOX_METADATA)
     params = execution.params(params)
     cargs = compute_vox2vox_cargs(params, execution)
     ret = compute_vox2vox_outputs(params, execution)
@@ -159,6 +134,8 @@ def compute_vox2vox(
     runner: Runner | None = None,
 ) -> ComputeVox2voxOutputs:
     """
+    compute_vox2vox
+    
     Tool for computing voxel-to-voxel transformations.
     
     Author: FreeSurfer Developers
@@ -173,20 +150,18 @@ def compute_vox2vox(
     Returns:
         NamedTuple of outputs (described in `ComputeVox2voxOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(COMPUTE_VOX2VOX_METADATA)
     params = compute_vox2vox_params(
         source=source,
         t4file=t4file,
         target=target,
     )
-    return compute_vox2vox_execute(params, execution)
+    return compute_vox2vox_execute(params, runner)
 
 
 __all__ = [
     "COMPUTE_VOX2VOX_METADATA",
     "ComputeVox2voxOutputs",
-    "ComputeVox2voxParameters",
     "compute_vox2vox",
+    "compute_vox2vox_execute",
     "compute_vox2vox_params",
 ]

niwrap_freesurfer/freesurfer/conf2hires.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 CONF2HIRES_METADATA = Metadata(
-    id="539c4acfba831cfb4f99ac6d61aa594dba2bc3f2.boutiques",
+    id="c326b081c5f5603acadc449e53ae6ec356eea705.boutiques",
     name="conf2hires",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,31 @@ CONF2HIRES_METADATA = Metadata(
 
 
 Conf2hiresParameters = typing.TypedDict('Conf2hiresParameters', {
-    "__STYXTYPE__": typing.Literal["conf2hires"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/conf2hires"]],
+    "subject": str,
+    "t2": bool,
+    "no_t2": bool,
+    "mm_norm_sigma": typing.NotRequired[float | None],
+    "flair": bool,
+    "no_flair": bool,
+    "threads": typing.NotRequired[float | None],
+    "copy_bias_from_conf": bool,
+    "norm_opts_rca": bool,
+    "cubic": bool,
+    "trilin": bool,
+    "dev": bool,
+    "no_dev": bool,
+    "bbr_con": typing.NotRequired[str | None],
+    "bbr_t1": bool,
+    "bbr_t2": bool,
+    "first_peak_d1": bool,
+    "first_peak_d2": bool,
+    "stopmask": typing.NotRequired[str | None],
+    "expert": typing.NotRequired[str | None],
+    "force_update": bool,
+})
+Conf2hiresParametersTagged = typing.TypedDict('Conf2hiresParametersTagged', {
+    "@type": typing.Literal["freesurfer/conf2hires"],
     "subject": str,
     "t2": bool,
     "no_t2": bool,
@@ -37,42 +61,11 @@ Conf2hiresParameters = typing.TypedDict('Conf2hiresParameters', {
     "expert": typing.NotRequired[str | None],
     "force_update": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "conf2hires": conf2hires_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 Conf2hiresOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `conf2hires(...)`.
+    Output object returned when calling `Conf2hiresParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -82,7 +75,7 @@ def conf2hires_params(
     subject: str,
     t2: bool = False,
     no_t2: bool = False,
-    mm_norm_sigma: float | None = 8,
+    mm_norm_sigma: float | None = None,
     flair: bool = False,
     no_flair: bool = False,
     threads: float | None = None,
@@ -100,7 +93,7 @@ def conf2hires_params(
     stopmask: str | None = None,
     expert: str | None = None,
     force_update: bool = False,
-) -> Conf2hiresParameters:
+) -> Conf2hiresParametersTagged:
     """
     Build parameters.
     
@@ -135,7 +128,7 @@ def conf2hires_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "conf2hires",
+        "@type": "freesurfer/conf2hires",
         "subject": subject,
         "t2": t2,
         "no_t2": no_t2,
@@ -183,62 +176,62 @@ def conf2hires_cargs(
     cargs.append("conf2hires")
     cargs.extend([
         "--s",
-        params.get("subject")
+        params.get("subject", None)
     ])
-    if params.get("t2"):
+    if params.get("t2", False):
         cargs.append("--t2")
-    if params.get("no_t2"):
+    if params.get("no_t2", False):
         cargs.append("--no-t2")
-    if params.get("mm_norm_sigma") is not None:
+    if params.get("mm_norm_sigma", None) is not None:
         cargs.extend([
             "--mm-norm-sigma",
-            str(params.get("mm_norm_sigma"))
+            str(params.get("mm_norm_sigma", None))
         ])
-    if params.get("flair"):
+    if params.get("flair", False):
         cargs.append("--flair")
-    if params.get("no_flair"):
+    if params.get("no_flair", False):
         cargs.append("--no-flair")
-    if params.get("threads") is not None:
+    if params.get("threads", None) is not None:
         cargs.extend([
             "--threads",
-            str(params.get("threads"))
+            str(params.get("threads", None))
         ])
-    if params.get("copy_bias_from_conf"):
+    if params.get("copy_bias_from_conf", False):
         cargs.append("--copy-bias-from-conf")
-    if params.get("norm_opts_rca"):
+    if params.get("norm_opts_rca", False):
         cargs.append("--norm-opts-rca")
-    if params.get("cubic"):
+    if params.get("cubic", False):
         cargs.append("--cubic")
-    if params.get("trilin"):
+    if params.get("trilin", False):
         cargs.append("--trilin")
-    if params.get("dev"):
+    if params.get("dev", False):
         cargs.append("--dev")
-    if params.get("no_dev"):
+    if params.get("no_dev", False):
         cargs.append("--no-dev")
-    if params.get("bbr_con") is not None:
+    if params.get("bbr_con", None) is not None:
         cargs.extend([
             "--bbr-con",
-            params.get("bbr_con")
+            params.get("bbr_con", None)
         ])
-    if params.get("bbr_t1"):
+    if params.get("bbr_t1", False):
         cargs.append("--bbr-t1")
-    if params.get("bbr_t2"):
+    if params.get("bbr_t2", False):
         cargs.append("--bbr-t2")
-    if params.get("first_peak_d1"):
+    if params.get("first_peak_d1", False):
         cargs.append("--first-peak-d1")
-    if params.get("first_peak_d2"):
+    if params.get("first_peak_d2", False):
         cargs.append("--first-peak-d2")
-    if params.get("stopmask") is not None:
+    if params.get("stopmask", None) is not None:
         cargs.extend([
             "--stopmask",
-            params.get("stopmask")
+            params.get("stopmask", None)
         ])
-    if params.get("expert") is not None:
+    if params.get("expert", None) is not None:
         cargs.extend([
             "--expert",
-            params.get("expert")
+            params.get("expert", None)
         ])
-    if params.get("force_update"):
+    if params.get("force_update", False):
         cargs.append("--force-update")
     return cargs
 
@@ -264,9 +257,11 @@ def conf2hires_outputs(
 
 def conf2hires_execute(
     params: Conf2hiresParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Conf2hiresOutputs:
     """
+    conf2hires
+    
     Places the surfaces on high resolution T1 (and maybe T2) volumes based on an
     initial placement on a conformed volume.
     
@@ -276,10 +271,12 @@ def conf2hires_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Conf2hiresOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(CONF2HIRES_METADATA)
     params = execution.params(params)
     cargs = conf2hires_cargs(params, execution)
     ret = conf2hires_outputs(params, execution)
@@ -291,7 +288,7 @@ def conf2hires(
     subject: str,
     t2: bool = False,
     no_t2: bool = False,
-    mm_norm_sigma: float | None = 8,
+    mm_norm_sigma: float | None = None,
     flair: bool = False,
     no_flair: bool = False,
     threads: float | None = None,
@@ -312,6 +309,8 @@ def conf2hires(
     runner: Runner | None = None,
 ) -> Conf2hiresOutputs:
     """
+    conf2hires
+    
     Places the surfaces on high resolution T1 (and maybe T2) volumes based on an
     initial placement on a conformed volume.
     
@@ -350,8 +349,6 @@ def conf2hires(
     Returns:
         NamedTuple of outputs (described in `Conf2hiresOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(CONF2HIRES_METADATA)
     params = conf2hires_params(
         subject=subject,
         t2=t2,
@@ -375,13 +372,13 @@ def conf2hires(
         expert=expert,
         force_update=force_update,
     )
-    return conf2hires_execute(params, execution)
+    return conf2hires_execute(params, runner)
 
 
 __all__ = [
     "CONF2HIRES_METADATA",
     "Conf2hiresOutputs",
-    "Conf2hiresParameters",
     "conf2hires",
+    "conf2hires_execute",
     "conf2hires_params",
 ]