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

niwrap_freesurfer/freesurfer/mri_cnr.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_CNR_METADATA = Metadata(
-    id="34e4848716ab0ea4fe90a1336b47fb8b0d5d00d0.boutiques",
+    id="249a13827f999466eba8e033ff312a9ead206a4c.boutiques",
     name="mri_cnr",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,18 @@ MRI_CNR_METADATA = Metadata(
 
 
 MriCnrParameters = typing.TypedDict('MriCnrParameters', {
-    "__STYXTYPE__": typing.Literal["mri_cnr"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_cnr"]],
+    "surf_dir": str,
+    "volume_files": list[InputPathType],
+    "slope": typing.NotRequired[list[str] | None],
+    "logfile": typing.NotRequired[str | None],
+    "labels": typing.NotRequired[list[str] | None],
+    "print_total_cnr": bool,
+    "version_flag": bool,
+    "help_flag": bool,
+})
+MriCnrParametersTagged = typing.TypedDict('MriCnrParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_cnr"],
     "surf_dir": str,
     "volume_files": list[InputPathType],
     "slope": typing.NotRequired[list[str] | None],
@@ -24,42 +35,11 @@ MriCnrParameters = typing.TypedDict('MriCnrParameters', {
     "version_flag": bool,
     "help_flag": 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_cnr": mri_cnr_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 MriCnrOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_cnr(...)`.
+    Output object returned when calling `MriCnrParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -74,7 +54,7 @@ def mri_cnr_params(
     print_total_cnr: bool = False,
     version_flag: bool = False,
     help_flag: bool = False,
-) -> MriCnrParameters:
+) -> MriCnrParametersTagged:
     """
     Build parameters.
     
@@ -96,7 +76,7 @@ def mri_cnr_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_cnr",
+        "@type": "freesurfer/mri_cnr",
         "surf_dir": surf_dir,
         "volume_files": volume_files,
         "print_total_cnr": print_total_cnr,
@@ -127,28 +107,28 @@ def mri_cnr_cargs(
     """
     cargs = []
     cargs.append("mri_cnr")
-    cargs.append(params.get("surf_dir"))
-    cargs.extend([execution.input_file(f) for f in params.get("volume_files")])
-    if params.get("slope") is not None:
+    cargs.append(params.get("surf_dir", None))
+    cargs.extend([execution.input_file(f) for f in params.get("volume_files", None)])
+    if params.get("slope", None) is not None:
         cargs.extend([
             "-s",
-            *params.get("slope")
+            *params.get("slope", None)
         ])
-    if params.get("logfile") is not None:
+    if params.get("logfile", None) is not None:
         cargs.extend([
             "-l",
-            params.get("logfile")
+            params.get("logfile", None)
         ])
-    if params.get("labels") is not None:
+    if params.get("labels", None) is not None:
         cargs.extend([
             "label",
-            *params.get("labels")
+            *params.get("labels", None)
         ])
-    if params.get("print_total_cnr"):
+    if params.get("print_total_cnr", False):
         cargs.append("-t")
-    if params.get("version_flag"):
+    if params.get("version_flag", False):
         cargs.append("-version")
-    if params.get("help_flag"):
+    if params.get("help_flag", False):
         cargs.append("-help")
     return cargs
 
@@ -174,10 +154,13 @@ def mri_cnr_outputs(
 
 def mri_cnr_execute(
     params: MriCnrParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriCnrOutputs:
     """
-    Compute the gray/white/csf contrast-to-noise ratio for volumes using FreeSurfer.
+    mri_cnr
+    
+    Compute the gray/white/csf contrast-to-noise ratio for volumes using
+    FreeSurfer.
     
     Author: FreeSurfer Developers
     
@@ -185,10 +168,12 @@ def mri_cnr_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriCnrOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_CNR_METADATA)
     params = execution.params(params)
     cargs = mri_cnr_cargs(params, execution)
     ret = mri_cnr_outputs(params, execution)
@@ -208,7 +193,10 @@ def mri_cnr(
     runner: Runner | None = None,
 ) -> MriCnrOutputs:
     """
-    Compute the gray/white/csf contrast-to-noise ratio for volumes using FreeSurfer.
+    mri_cnr
+    
+    Compute the gray/white/csf contrast-to-noise ratio for volumes using
+    FreeSurfer.
     
     Author: FreeSurfer Developers
     
@@ -232,8 +220,6 @@ def mri_cnr(
     Returns:
         NamedTuple of outputs (described in `MriCnrOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_CNR_METADATA)
     params = mri_cnr_params(
         surf_dir=surf_dir,
         volume_files=volume_files,
@@ -244,13 +230,13 @@ def mri_cnr(
         version_flag=version_flag,
         help_flag=help_flag,
     )
-    return mri_cnr_execute(params, execution)
+    return mri_cnr_execute(params, runner)
 
 
 __all__ = [
     "MRI_CNR_METADATA",
     "MriCnrOutputs",
-    "MriCnrParameters",
     "mri_cnr",
+    "mri_cnr_execute",
     "mri_cnr_params",
 ]

niwrap_freesurfer/freesurfer/mri_compile_edits.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_COMPILE_EDITS_METADATA = Metadata(
-    id="b746923a3f58164c4779c06642364dcd1adf6e9f.boutiques",
+    id="1c123bf77d93b82ac6fe9748c62009b32815e8a7.boutiques",
     name="mri_compile_edits",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ MRI_COMPILE_EDITS_METADATA = Metadata(
 
 
 MriCompileEditsParameters = typing.TypedDict('MriCompileEditsParameters', {
-    "__STYXTYPE__": typing.Literal["mri_compile_edits"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_compile_edits"]],
+    "subject_name": str,
+    "output_volume": str,
+})
+MriCompileEditsParametersTagged = typing.TypedDict('MriCompileEditsParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_compile_edits"],
     "subject_name": str,
     "output_volume": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mri_compile_edits": mri_compile_edits_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_compile_edits": mri_compile_edits_outputs,
-    }.get(t)
 
 
 class MriCompileEditsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_compile_edits(...)`.
+    Output object returned when calling `MriCompileEditsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class MriCompileEditsOutputs(typing.NamedTuple):
 def mri_compile_edits_params(
     subject_name: str,
     output_volume: str,
-) -> MriCompileEditsParameters:
+) -> MriCompileEditsParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def mri_compile_edits_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_compile_edits",
+        "@type": "freesurfer/mri_compile_edits",
         "subject_name": subject_name,
         "output_volume": output_volume,
     }
@@ -98,8 +71,8 @@ def mri_compile_edits_cargs(
     """
     cargs = []
     cargs.append("mri_compile_edits")
-    cargs.append(params.get("subject_name"))
-    cargs.append(params.get("output_volume"))
+    cargs.append(params.get("subject_name", None))
+    cargs.append(params.get("output_volume", None))
     return cargs
 
 
@@ -118,16 +91,18 @@ def mri_compile_edits_outputs(
     """
     ret = MriCompileEditsOutputs(
         root=execution.output_file("."),
-        compiled_edit_volume=execution.output_file(params.get("output_volume")),
+        compiled_edit_volume=execution.output_file(params.get("output_volume", None)),
     )
     return ret
 
 
 def mri_compile_edits_execute(
     params: MriCompileEditsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriCompileEditsOutputs:
     """
+    mri_compile_edits
+    
     Program to create a single volume showing all the volumetric edits made to a
     subject.
     
@@ -137,10 +112,12 @@ def mri_compile_edits_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriCompileEditsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_COMPILE_EDITS_METADATA)
     params = execution.params(params)
     cargs = mri_compile_edits_cargs(params, execution)
     ret = mri_compile_edits_outputs(params, execution)
@@ -154,6 +131,8 @@ def mri_compile_edits(
     runner: Runner | None = None,
 ) -> MriCompileEditsOutputs:
     """
+    mri_compile_edits
+    
     Program to create a single volume showing all the volumetric edits made to a
     subject.
     
@@ -168,19 +147,17 @@ def mri_compile_edits(
     Returns:
         NamedTuple of outputs (described in `MriCompileEditsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_COMPILE_EDITS_METADATA)
     params = mri_compile_edits_params(
         subject_name=subject_name,
         output_volume=output_volume,
     )
-    return mri_compile_edits_execute(params, execution)
+    return mri_compile_edits_execute(params, runner)
 
 
 __all__ = [
     "MRI_COMPILE_EDITS_METADATA",
     "MriCompileEditsOutputs",
-    "MriCompileEditsParameters",
     "mri_compile_edits",
+    "mri_compile_edits_execute",
     "mri_compile_edits_params",
 ]

niwrap_freesurfer/freesurfer/mri_compute_bias.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_COMPUTE_BIAS_METADATA = Metadata(
-    id="fd8e507da48077556003e985db0ee8f6c8bbbc9b.boutiques",
+    id="6db834c786647e9384d2bb5c471bfe16ceddd6dd.boutiques",
     name="mri_compute_bias",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ MRI_COMPUTE_BIAS_METADATA = Metadata(
 
 
 MriComputeBiasParameters = typing.TypedDict('MriComputeBiasParameters', {
-    "__STYXTYPE__": typing.Literal["mri_compute_bias"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_compute_bias"]],
+    "subjects": list[str],
+    "output_volume": str,
+})
+MriComputeBiasParametersTagged = typing.TypedDict('MriComputeBiasParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_compute_bias"],
     "subjects": list[str],
     "output_volume": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mri_compute_bias": mri_compute_bias_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_compute_bias": mri_compute_bias_outputs,
-    }.get(t)
 
 
 class MriComputeBiasOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_compute_bias(...)`.
+    Output object returned when calling `MriComputeBiasParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class MriComputeBiasOutputs(typing.NamedTuple):
 def mri_compute_bias_params(
     subjects: list[str],
     output_volume: str,
-) -> MriComputeBiasParameters:
+) -> MriComputeBiasParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def mri_compute_bias_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_compute_bias",
+        "@type": "freesurfer/mri_compute_bias",
         "subjects": subjects,
         "output_volume": output_volume,
     }
@@ -98,8 +71,8 @@ def mri_compute_bias_cargs(
     """
     cargs = []
     cargs.append("mri_compute_bias")
-    cargs.extend(params.get("subjects"))
-    cargs.append(params.get("output_volume"))
+    cargs.extend(params.get("subjects", None))
+    cargs.append(params.get("output_volume", None))
     return cargs
 
 
@@ -118,18 +91,20 @@ def mri_compute_bias_outputs(
     """
     ret = MriComputeBiasOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("output_volume")),
+        output_file=execution.output_file(params.get("output_volume", None)),
     )
     return ret
 
 
 def mri_compute_bias_execute(
     params: MriComputeBiasParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriComputeBiasOutputs:
     """
-    Compute bias correction volumes for the given subjects and outputs the result to
-    a specified volume.
+    mri_compute_bias
+    
+    Compute bias correction volumes for the given subjects and outputs the
+    result to a specified volume.
     
     Author: FreeSurfer Developers
     
@@ -137,10 +112,12 @@ def mri_compute_bias_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriComputeBiasOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_COMPUTE_BIAS_METADATA)
     params = execution.params(params)
     cargs = mri_compute_bias_cargs(params, execution)
     ret = mri_compute_bias_outputs(params, execution)
@@ -154,8 +131,10 @@ def mri_compute_bias(
     runner: Runner | None = None,
 ) -> MriComputeBiasOutputs:
     """
-    Compute bias correction volumes for the given subjects and outputs the result to
-    a specified volume.
+    mri_compute_bias
+    
+    Compute bias correction volumes for the given subjects and outputs the
+    result to a specified volume.
     
     Author: FreeSurfer Developers
     
@@ -168,19 +147,17 @@ def mri_compute_bias(
     Returns:
         NamedTuple of outputs (described in `MriComputeBiasOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_COMPUTE_BIAS_METADATA)
     params = mri_compute_bias_params(
         subjects=subjects,
         output_volume=output_volume,
     )
-    return mri_compute_bias_execute(params, execution)
+    return mri_compute_bias_execute(params, runner)
 
 
 __all__ = [
     "MRI_COMPUTE_BIAS_METADATA",
     "MriComputeBiasOutputs",
-    "MriComputeBiasParameters",
     "mri_compute_bias",
+    "mri_compute_bias_execute",
     "mri_compute_bias_params",
 ]

niwrap_freesurfer/freesurfer/mri_compute_change_map.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_COMPUTE_CHANGE_MAP_METADATA = Metadata(
-    id="c07e8edeac78e2a82c376fc8f8459476863b4c9d.boutiques",
+    id="00ec20a20d9fe3c6c5a8821183ceec75976b7daf.boutiques",
     name="mri_compute_change_map",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ MRI_COMPUTE_CHANGE_MAP_METADATA = Metadata(
 
 
 MriComputeChangeMapParameters = typing.TypedDict('MriComputeChangeMapParameters', {
-    "__STYXTYPE__": typing.Literal["mri_compute_change_map"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_compute_change_map"]],
+    "mean_filter": bool,
+    "gaussian_sigma": typing.NotRequired[float | None],
+    "volume1": InputPathType,
+    "volume2": InputPathType,
+    "transform": InputPathType,
+    "outvolume": str,
+})
+MriComputeChangeMapParametersTagged = typing.TypedDict('MriComputeChangeMapParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_compute_change_map"],
     "mean_filter": bool,
     "gaussian_sigma": typing.NotRequired[float | None],
     "volume1": InputPathType,
@@ -22,43 +31,11 @@ MriComputeChangeMapParameters = typing.TypedDict('MriComputeChangeMapParameters'
     "transform": InputPathType,
     "outvolume": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mri_compute_change_map": mri_compute_change_map_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_compute_change_map": mri_compute_change_map_outputs,
-    }.get(t)
 
 
 class MriComputeChangeMapOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_compute_change_map(...)`.
+    Output object returned when calling `MriComputeChangeMapParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +50,7 @@ def mri_compute_change_map_params(
     outvolume: str,
     mean_filter: bool = False,
     gaussian_sigma: float | None = None,
-) -> MriComputeChangeMapParameters:
+) -> MriComputeChangeMapParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +68,7 @@ def mri_compute_change_map_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_compute_change_map",
+        "@type": "freesurfer/mri_compute_change_map",
         "mean_filter": mean_filter,
         "volume1": volume1,
         "volume2": volume2,
@@ -118,17 +95,17 @@ def mri_compute_change_map_cargs(
     """
     cargs = []
     cargs.append("mri_compute_change_map")
-    if params.get("mean_filter"):
+    if params.get("mean_filter", False):
         cargs.append("-m")
-    if params.get("gaussian_sigma") is not None:
+    if params.get("gaussian_sigma", None) is not None:
         cargs.extend([
             "-s",
-            str(params.get("gaussian_sigma"))
+            str(params.get("gaussian_sigma", None))
         ])
-    cargs.append(execution.input_file(params.get("volume1")))
-    cargs.append(execution.input_file(params.get("volume2")))
-    cargs.append(execution.input_file(params.get("transform")))
-    cargs.append(params.get("outvolume"))
+    cargs.append(execution.input_file(params.get("volume1", None)))
+    cargs.append(execution.input_file(params.get("volume2", None)))
+    cargs.append(execution.input_file(params.get("transform", None)))
+    cargs.append(params.get("outvolume", None))
     return cargs
 
 
@@ -147,16 +124,18 @@ def mri_compute_change_map_outputs(
     """
     ret = MriComputeChangeMapOutputs(
         root=execution.output_file("."),
-        out_change_map=execution.output_file(params.get("outvolume")),
+        out_change_map=execution.output_file(params.get("outvolume", None)),
     )
     return ret
 
 
 def mri_compute_change_map_execute(
     params: MriComputeChangeMapParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriComputeChangeMapOutputs:
     """
+    mri_compute_change_map
+    
     Compute the change map between two MRI volumes.
     
     Author: FreeSurfer Developers
@@ -165,10 +144,12 @@ def mri_compute_change_map_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriComputeChangeMapOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_COMPUTE_CHANGE_MAP_METADATA)
     params = execution.params(params)
     cargs = mri_compute_change_map_cargs(params, execution)
     ret = mri_compute_change_map_outputs(params, execution)
@@ -186,6 +167,8 @@ def mri_compute_change_map(
     runner: Runner | None = None,
 ) -> MriComputeChangeMapOutputs:
     """
+    mri_compute_change_map
+    
     Compute the change map between two MRI volumes.
     
     Author: FreeSurfer Developers
@@ -206,8 +189,6 @@ def mri_compute_change_map(
     Returns:
         NamedTuple of outputs (described in `MriComputeChangeMapOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_COMPUTE_CHANGE_MAP_METADATA)
     params = mri_compute_change_map_params(
         mean_filter=mean_filter,
         gaussian_sigma=gaussian_sigma,
@@ -216,13 +197,13 @@ def mri_compute_change_map(
         transform=transform,
         outvolume=outvolume,
     )
-    return mri_compute_change_map_execute(params, execution)
+    return mri_compute_change_map_execute(params, runner)
 
 
 __all__ = [
     "MRI_COMPUTE_CHANGE_MAP_METADATA",
     "MriComputeChangeMapOutputs",
-    "MriComputeChangeMapParameters",
     "mri_compute_change_map",
+    "mri_compute_change_map_execute",
     "mri_compute_change_map_params",
 ]