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

niwrap_freesurfer/freesurfer/ants_denoise_image_fs.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 ANTS_DENOISE_IMAGE_FS_METADATA = Metadata(
-    id="ceaab64d93fccf1f1155efcaaae5de0e2ed14132.boutiques",
+    id="f9289acabc02e5068ccac6d203b039dabfab1bc0.boutiques",
     name="AntsDenoiseImageFs",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ ANTS_DENOISE_IMAGE_FS_METADATA = Metadata(
 
 
 AntsDenoiseImageFsParameters = typing.TypedDict('AntsDenoiseImageFsParameters', {
-    "__STYXTYPE__": typing.Literal["AntsDenoiseImageFs"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/AntsDenoiseImageFs"]],
+    "input_image": InputPathType,
+    "output_image": str,
+    "rician_flag": bool,
+})
+AntsDenoiseImageFsParametersTagged = typing.TypedDict('AntsDenoiseImageFsParametersTagged', {
+    "@type": typing.Literal["freesurfer/AntsDenoiseImageFs"],
     "input_image": InputPathType,
     "output_image": str,
     "rician_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 {
-        "AntsDenoiseImageFs": ants_denoise_image_fs_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 {
-        "AntsDenoiseImageFs": ants_denoise_image_fs_outputs,
-    }.get(t)
 
 
 class AntsDenoiseImageFsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `ants_denoise_image_fs(...)`.
+    Output object returned when calling `AntsDenoiseImageFsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def ants_denoise_image_fs_params(
     input_image: InputPathType,
     output_image: str = "output.nii",
     rician_flag: bool = False,
-) -> AntsDenoiseImageFsParameters:
+) -> AntsDenoiseImageFsParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +53,7 @@ def ants_denoise_image_fs_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "AntsDenoiseImageFs",
+        "@type": "freesurfer/AntsDenoiseImageFs",
         "input_image": input_image,
         "output_image": output_image,
         "rician_flag": rician_flag,
@@ -104,13 +78,13 @@ def ants_denoise_image_fs_cargs(
     cargs.append("AntsDenoiseImageFs")
     cargs.extend([
         "-i",
-        execution.input_file(params.get("input_image"))
+        execution.input_file(params.get("input_image", None))
     ])
     cargs.extend([
         "-o",
-        params.get("output_image")
+        params.get("output_image", "output.nii")
     ])
-    if params.get("rician_flag"):
+    if params.get("rician_flag", False):
         cargs.append("--rician")
     return cargs
 
@@ -130,16 +104,18 @@ def ants_denoise_image_fs_outputs(
     """
     ret = AntsDenoiseImageFsOutputs(
         root=execution.output_file("."),
-        denoised_output=execution.output_file(params.get("output_image")),
+        denoised_output=execution.output_file(params.get("output_image", "output.nii")),
     )
     return ret
 
 
 def ants_denoise_image_fs_execute(
     params: AntsDenoiseImageFsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> AntsDenoiseImageFsOutputs:
     """
+    AntsDenoiseImageFs
+    
     Denoises an image with a spatially adaptive filter. This program wraps the
     AntsDenoiseImage utility available in the ANTs package.
     
@@ -149,10 +125,12 @@ def ants_denoise_image_fs_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `AntsDenoiseImageFsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ANTS_DENOISE_IMAGE_FS_METADATA)
     params = execution.params(params)
     cargs = ants_denoise_image_fs_cargs(params, execution)
     ret = ants_denoise_image_fs_outputs(params, execution)
@@ -167,6 +145,8 @@ def ants_denoise_image_fs(
     runner: Runner | None = None,
 ) -> AntsDenoiseImageFsOutputs:
     """
+    AntsDenoiseImageFs
+    
     Denoises an image with a spatially adaptive filter. This program wraps the
     AntsDenoiseImage utility available in the ANTs package.
     
@@ -182,20 +162,18 @@ def ants_denoise_image_fs(
     Returns:
         NamedTuple of outputs (described in `AntsDenoiseImageFsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(ANTS_DENOISE_IMAGE_FS_METADATA)
     params = ants_denoise_image_fs_params(
         input_image=input_image,
         output_image=output_image,
         rician_flag=rician_flag,
     )
-    return ants_denoise_image_fs_execute(params, execution)
+    return ants_denoise_image_fs_execute(params, runner)
 
 
 __all__ = [
     "ANTS_DENOISE_IMAGE_FS_METADATA",
     "AntsDenoiseImageFsOutputs",
-    "AntsDenoiseImageFsParameters",
     "ants_denoise_image_fs",
+    "ants_denoise_image_fs_execute",
     "ants_denoise_image_fs_params",
 ]

niwrap_freesurfer/freesurfer/ants_n4_bias_field_correction_fs.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 ANTS_N4_BIAS_FIELD_CORRECTION_FS_METADATA = Metadata(
-    id="fa3c503d811c832b99fa1f69e112206d024886d1.boutiques",
+    id="f7c05eb76747f2bed1da5f76ca71a39e0e609b4c.boutiques",
     name="AntsN4BiasFieldCorrectionFs",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,17 @@ ANTS_N4_BIAS_FIELD_CORRECTION_FS_METADATA = Metadata(
 
 
 AntsN4BiasFieldCorrectionFsParameters = typing.TypedDict('AntsN4BiasFieldCorrectionFsParameters', {
-    "__STYXTYPE__": typing.Literal["AntsN4BiasFieldCorrectionFs"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/AntsN4BiasFieldCorrectionFs"]],
+    "input_file": InputPathType,
+    "output_file": str,
+    "mask_file": typing.NotRequired[InputPathType | None],
+    "shrink_factor": typing.NotRequired[int | None],
+    "iterations": typing.NotRequired[list[float] | None],
+    "output_dtype": typing.NotRequired[str | None],
+    "replace_zeros": typing.NotRequired[str | None],
+})
+AntsN4BiasFieldCorrectionFsParametersTagged = typing.TypedDict('AntsN4BiasFieldCorrectionFsParametersTagged', {
+    "@type": typing.Literal["freesurfer/AntsN4BiasFieldCorrectionFs"],
     "input_file": InputPathType,
     "output_file": str,
     "mask_file": typing.NotRequired[InputPathType | None],
@@ -23,43 +33,11 @@ AntsN4BiasFieldCorrectionFsParameters = typing.TypedDict('AntsN4BiasFieldCorrect
     "output_dtype": typing.NotRequired[str | None],
     "replace_zeros": 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 {
-        "AntsN4BiasFieldCorrectionFs": ants_n4_bias_field_correction_fs_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 {
-        "AntsN4BiasFieldCorrectionFs": ants_n4_bias_field_correction_fs_outputs,
-    }.get(t)
 
 
 class AntsN4BiasFieldCorrectionFsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `ants_n4_bias_field_correction_fs(...)`.
+    Output object returned when calling `AntsN4BiasFieldCorrectionFsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,11 +49,11 @@ def ants_n4_bias_field_correction_fs_params(
     input_file: InputPathType,
     output_file: str,
     mask_file: InputPathType | None = None,
-    shrink_factor: int | None = 4,
+    shrink_factor: int | None = None,
     iterations: list[float] | None = None,
-    output_dtype: str | None = "float",
+    output_dtype: str | None = None,
     replace_zeros: str | None = None,
-) -> AntsN4BiasFieldCorrectionFsParameters:
+) -> AntsN4BiasFieldCorrectionFsParametersTagged:
     """
     Build parameters.
     
@@ -96,7 +74,7 @@ def ants_n4_bias_field_correction_fs_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "AntsN4BiasFieldCorrectionFs",
+        "@type": "freesurfer/AntsN4BiasFieldCorrectionFs",
         "input_file": input_file,
         "output_file": output_file,
     }
@@ -130,36 +108,36 @@ def ants_n4_bias_field_correction_fs_cargs(
     cargs.append("AntsN4BiasFieldCorrectionFs")
     cargs.extend([
         "-i",
-        execution.input_file(params.get("input_file"))
+        execution.input_file(params.get("input_file", None))
     ])
     cargs.extend([
         "-o",
-        params.get("output_file")
+        params.get("output_file", None)
     ])
-    if params.get("mask_file") is not None:
+    if params.get("mask_file", None) is not None:
         cargs.extend([
             "-m",
-            execution.input_file(params.get("mask_file"))
+            execution.input_file(params.get("mask_file", None))
         ])
-    if params.get("shrink_factor") is not None:
+    if params.get("shrink_factor", None) is not None:
         cargs.extend([
             "-s",
-            str(params.get("shrink_factor"))
+            str(params.get("shrink_factor", None))
         ])
-    if params.get("iterations") is not None:
+    if params.get("iterations", None) is not None:
         cargs.extend([
             "-t",
-            *map(str, params.get("iterations"))
+            *map(str, params.get("iterations", None))
         ])
-    if params.get("output_dtype") is not None:
+    if params.get("output_dtype", None) is not None:
         cargs.extend([
             "-d",
-            params.get("output_dtype")
+            params.get("output_dtype", None)
         ])
-    if params.get("replace_zeros") is not None:
+    if params.get("replace_zeros", None) is not None:
         cargs.extend([
             "-r",
-            params.get("replace_zeros")
+            params.get("replace_zeros", None)
         ])
     return cargs
 
@@ -179,19 +157,21 @@ def ants_n4_bias_field_correction_fs_outputs(
     """
     ret = AntsN4BiasFieldCorrectionFsOutputs(
         root=execution.output_file("."),
-        corrected_output_file=execution.output_file(params.get("output_file")),
+        corrected_output_file=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def ants_n4_bias_field_correction_fs_execute(
     params: AntsN4BiasFieldCorrectionFsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> AntsN4BiasFieldCorrectionFsOutputs:
     """
-    Runs N4 (nonparameteric, nonuniform normalization) retrospective bias correction
-    on an image. This program wraps the AntsN4BiasFieldCorrection utility available
-    in the ANTs package.
+    AntsN4BiasFieldCorrectionFs
+    
+    Runs N4 (nonparameteric, nonuniform normalization) retrospective bias
+    correction on an image. This program wraps the AntsN4BiasFieldCorrection
+    utility available in the ANTs package.
     
     Author: FreeSurfer Developers
     
@@ -199,10 +179,12 @@ def ants_n4_bias_field_correction_fs_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `AntsN4BiasFieldCorrectionFsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ANTS_N4_BIAS_FIELD_CORRECTION_FS_METADATA)
     params = execution.params(params)
     cargs = ants_n4_bias_field_correction_fs_cargs(params, execution)
     ret = ants_n4_bias_field_correction_fs_outputs(params, execution)
@@ -214,16 +196,18 @@ def ants_n4_bias_field_correction_fs(
     input_file: InputPathType,
     output_file: str,
     mask_file: InputPathType | None = None,
-    shrink_factor: int | None = 4,
+    shrink_factor: int | None = None,
     iterations: list[float] | None = None,
-    output_dtype: str | None = "float",
+    output_dtype: str | None = None,
     replace_zeros: str | None = None,
     runner: Runner | None = None,
 ) -> AntsN4BiasFieldCorrectionFsOutputs:
     """
-    Runs N4 (nonparameteric, nonuniform normalization) retrospective bias correction
-    on an image. This program wraps the AntsN4BiasFieldCorrection utility available
-    in the ANTs package.
+    AntsN4BiasFieldCorrectionFs
+    
+    Runs N4 (nonparameteric, nonuniform normalization) retrospective bias
+    correction on an image. This program wraps the AntsN4BiasFieldCorrection
+    utility available in the ANTs package.
     
     Author: FreeSurfer Developers
     
@@ -246,8 +230,6 @@ def ants_n4_bias_field_correction_fs(
     Returns:
         NamedTuple of outputs (described in `AntsN4BiasFieldCorrectionFsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(ANTS_N4_BIAS_FIELD_CORRECTION_FS_METADATA)
     params = ants_n4_bias_field_correction_fs_params(
         input_file=input_file,
         output_file=output_file,
@@ -257,13 +239,13 @@ def ants_n4_bias_field_correction_fs(
         output_dtype=output_dtype,
         replace_zeros=replace_zeros,
     )
-    return ants_n4_bias_field_correction_fs_execute(params, execution)
+    return ants_n4_bias_field_correction_fs_execute(params, runner)
 
 
 __all__ = [
     "ANTS_N4_BIAS_FIELD_CORRECTION_FS_METADATA",
     "AntsN4BiasFieldCorrectionFsOutputs",
-    "AntsN4BiasFieldCorrectionFsParameters",
     "ants_n4_bias_field_correction_fs",
+    "ants_n4_bias_field_correction_fs_execute",
     "ants_n4_bias_field_correction_fs_params",
 ]

niwrap_freesurfer/freesurfer/aparc2feat.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 APARC2FEAT_METADATA = Metadata(
-    id="53160d8704e92c1e9f62f27dba6616b608c7216b.boutiques",
+    id="06bbc3b060e19e5a1544cd8e91a4d953880fd77c.boutiques",
     name="aparc2feat",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,19 @@ APARC2FEAT_METADATA = Metadata(
 
 
 Aparc2featParameters = typing.TypedDict('Aparc2featParameters', {
-    "__STYXTYPE__": typing.Literal["aparc2feat"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/aparc2feat"]],
+    "feat_directories": str,
+    "featdirfile": typing.NotRequired[InputPathType | None],
+    "hemi": typing.NotRequired[str | None],
+    "annot": typing.NotRequired[str | None],
+    "annot_a2005s_flag": bool,
+    "annot_a2009s_flag": bool,
+    "debug_flag": bool,
+    "help_flag": bool,
+    "version_flag": bool,
+})
+Aparc2featParametersTagged = typing.TypedDict('Aparc2featParametersTagged', {
+    "@type": typing.Literal["freesurfer/aparc2feat"],
     "feat_directories": str,
     "featdirfile": typing.NotRequired[InputPathType | None],
     "hemi": typing.NotRequired[str | None],
@@ -25,43 +37,11 @@ Aparc2featParameters = typing.TypedDict('Aparc2featParameters', {
     "help_flag": bool,
     "version_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 {
-        "aparc2feat": aparc2feat_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 {
-        "aparc2feat": aparc2feat_outputs,
-    }.get(t)
 
 
 class Aparc2featOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `aparc2feat(...)`.
+    Output object returned when calling `Aparc2featParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -81,7 +61,7 @@ def aparc2feat_params(
     debug_flag: bool = False,
     help_flag: bool = False,
     version_flag: bool = False,
-) -> Aparc2featParameters:
+) -> Aparc2featParametersTagged:
     """
     Build parameters.
     
@@ -101,7 +81,7 @@ def aparc2feat_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "aparc2feat",
+        "@type": "freesurfer/aparc2feat",
         "feat_directories": feat_directories,
         "annot_a2005s_flag": annot_a2005s_flag,
         "annot_a2009s_flag": annot_a2009s_flag,
@@ -135,32 +115,32 @@ def aparc2feat_cargs(
     cargs.append("aparc2feat")
     cargs.extend([
         "--feat",
-        params.get("feat_directories")
+        params.get("feat_directories", None)
     ])
-    if params.get("featdirfile") is not None:
+    if params.get("featdirfile", None) is not None:
         cargs.extend([
             "--featdirfile",
-            execution.input_file(params.get("featdirfile"))
+            execution.input_file(params.get("featdirfile", None))
         ])
-    if params.get("hemi") is not None:
+    if params.get("hemi", None) is not None:
         cargs.extend([
             "--hemi",
-            params.get("hemi")
+            params.get("hemi", None)
         ])
-    if params.get("annot") is not None:
+    if params.get("annot", None) is not None:
         cargs.extend([
             "--annot",
-            params.get("annot")
+            params.get("annot", None)
         ])
-    if params.get("annot_a2005s_flag"):
+    if params.get("annot_a2005s_flag", False):
         cargs.append("--a2005s")
-    if params.get("annot_a2009s_flag"):
+    if params.get("annot_a2009s_flag", False):
         cargs.append("--a2009s")
-    if params.get("debug_flag"):
+    if params.get("debug_flag", False):
         cargs.append("--debug")
-    if params.get("help_flag"):
+    if params.get("help_flag", False):
         cargs.append("--help")
-    if params.get("version_flag"):
+    if params.get("version_flag", False):
         cargs.append("--version")
     return cargs
 
@@ -180,19 +160,21 @@ def aparc2feat_outputs(
     """
     ret = Aparc2featOutputs(
         root=execution.output_file("."),
-        lh_aparc_output=execution.output_file(params.get("feat_directories") + "/reg/freesurfer/lh.aparc.nii.gz"),
-        rh_aparc_output=execution.output_file(params.get("feat_directories") + "/reg/freesurfer/rh.aparc.nii.gz"),
+        lh_aparc_output=execution.output_file(params.get("feat_directories", None) + "/reg/freesurfer/lh.aparc.nii.gz"),
+        rh_aparc_output=execution.output_file(params.get("feat_directories", None) + "/reg/freesurfer/rh.aparc.nii.gz"),
     )
     return ret
 
 
 def aparc2feat_execute(
     params: Aparc2featParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Aparc2featOutputs:
     """
-    Resamples the FreeSurfer automatic cortical segmentation to the FEAT functional
-    space.
+    aparc2feat
+    
+    Resamples the FreeSurfer automatic cortical segmentation to the FEAT
+    functional space.
     
     Author: FreeSurfer Developers
     
@@ -200,10 +182,12 @@ def aparc2feat_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Aparc2featOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(APARC2FEAT_METADATA)
     params = execution.params(params)
     cargs = aparc2feat_cargs(params, execution)
     ret = aparc2feat_outputs(params, execution)
@@ -224,8 +208,10 @@ def aparc2feat(
     runner: Runner | None = None,
 ) -> Aparc2featOutputs:
     """
-    Resamples the FreeSurfer automatic cortical segmentation to the FEAT functional
-    space.
+    aparc2feat
+    
+    Resamples the FreeSurfer automatic cortical segmentation to the FEAT
+    functional space.
     
     Author: FreeSurfer Developers
     
@@ -247,8 +233,6 @@ def aparc2feat(
     Returns:
         NamedTuple of outputs (described in `Aparc2featOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(APARC2FEAT_METADATA)
     params = aparc2feat_params(
         feat_directories=feat_directories,
         featdirfile=featdirfile,
@@ -260,13 +244,13 @@ def aparc2feat(
         help_flag=help_flag,
         version_flag=version_flag,
     )
-    return aparc2feat_execute(params, execution)
+    return aparc2feat_execute(params, runner)
 
 
 __all__ = [
     "APARC2FEAT_METADATA",
     "Aparc2featOutputs",
-    "Aparc2featParameters",
     "aparc2feat",
+    "aparc2feat_execute",
     "aparc2feat_params",
 ]