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

niwrap_freesurfer/freesurfer/wm_anat_snr.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 WM_ANAT_SNR_METADATA = Metadata(
-    id="720d73c797ea6b11df6f56d663b8a31bbc7866b2.boutiques",
+    id="3893529b0bfaaaa154cf69dfd9caf679b5ffd38a.boutiques",
     name="wm-anat-snr",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,17 @@ WM_ANAT_SNR_METADATA = Metadata(
 
 
 WmAnatSnrParameters = typing.TypedDict('WmAnatSnrParameters', {
-    "__STYXTYPE__": typing.Literal["wm-anat-snr"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/wm-anat-snr"]],
+    "subject": str,
+    "output_file": str,
+    "force": bool,
+    "nerode": typing.NotRequired[int | None],
+    "tmp_dir": typing.NotRequired[str | None],
+    "cleanup": bool,
+    "no_cleanup": bool,
+})
+WmAnatSnrParametersTagged = typing.TypedDict('WmAnatSnrParametersTagged', {
+    "@type": typing.Literal["freesurfer/wm-anat-snr"],
     "subject": str,
     "output_file": str,
     "force": bool,
@@ -23,43 +33,11 @@ WmAnatSnrParameters = typing.TypedDict('WmAnatSnrParameters', {
     "cleanup": bool,
     "no_cleanup": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "wm-anat-snr": wm_anat_snr_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 {
-        "wm-anat-snr": wm_anat_snr_outputs,
-    }.get(t)
 
 
 class WmAnatSnrOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `wm_anat_snr(...)`.
+    Output object returned when calling `WmAnatSnrParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +53,7 @@ def wm_anat_snr_params(
     tmp_dir: str | None = None,
     cleanup: bool = False,
     no_cleanup: bool = False,
-) -> WmAnatSnrParameters:
+) -> WmAnatSnrParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +69,7 @@ def wm_anat_snr_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "wm-anat-snr",
+        "@type": "freesurfer/wm-anat-snr",
         "subject": subject,
         "output_file": output_file,
         "force": force,
@@ -122,27 +100,27 @@ def wm_anat_snr_cargs(
     cargs.append("wm-anat-snr")
     cargs.extend([
         "--s",
-        params.get("subject")
+        params.get("subject", None)
     ])
     cargs.extend([
         "--o",
-        params.get("output_file")
+        params.get("output_file", None)
     ])
-    if params.get("force"):
+    if params.get("force", False):
         cargs.append("--force")
-    if params.get("nerode") is not None:
+    if params.get("nerode", None) is not None:
         cargs.extend([
             "--nerode",
-            str(params.get("nerode"))
+            str(params.get("nerode", None))
         ])
-    if params.get("tmp_dir") is not None:
+    if params.get("tmp_dir", None) is not None:
         cargs.extend([
             "--tmp",
-            params.get("tmp_dir")
+            params.get("tmp_dir", None)
         ])
-    if params.get("cleanup"):
+    if params.get("cleanup", False):
         cargs.append("--cleanup")
-    if params.get("no_cleanup"):
+    if params.get("no_cleanup", False):
         cargs.append("--no-cleanup")
     return cargs
 
@@ -162,16 +140,18 @@ def wm_anat_snr_outputs(
     """
     ret = WmAnatSnrOutputs(
         root=execution.output_file("."),
-        output_datafile=execution.output_file(params.get("output_file")),
+        output_datafile=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def wm_anat_snr_execute(
     params: WmAnatSnrParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> WmAnatSnrOutputs:
     """
+    wm-anat-snr
+    
     Measures the anatomical SNR in white matter (WM) for quality assurance (QA).
     This is an experimental metric.
     
@@ -181,10 +161,12 @@ def wm_anat_snr_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `WmAnatSnrOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(WM_ANAT_SNR_METADATA)
     params = execution.params(params)
     cargs = wm_anat_snr_cargs(params, execution)
     ret = wm_anat_snr_outputs(params, execution)
@@ -203,6 +185,8 @@ def wm_anat_snr(
     runner: Runner | None = None,
 ) -> WmAnatSnrOutputs:
     """
+    wm-anat-snr
+    
     Measures the anatomical SNR in white matter (WM) for quality assurance (QA).
     This is an experimental metric.
     
@@ -222,8 +206,6 @@ def wm_anat_snr(
     Returns:
         NamedTuple of outputs (described in `WmAnatSnrOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(WM_ANAT_SNR_METADATA)
     params = wm_anat_snr_params(
         subject=subject,
         output_file=output_file,
@@ -233,13 +215,13 @@ def wm_anat_snr(
         cleanup=cleanup,
         no_cleanup=no_cleanup,
     )
-    return wm_anat_snr_execute(params, execution)
+    return wm_anat_snr_execute(params, runner)
 
 
 __all__ = [
     "WM_ANAT_SNR_METADATA",
     "WmAnatSnrOutputs",
-    "WmAnatSnrParameters",
     "wm_anat_snr",
+    "wm_anat_snr_execute",
     "wm_anat_snr_params",
 ]

niwrap_freesurfer/freesurfer/wmedits2surf.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 WMEDITS2SURF_METADATA = Metadata(
-    id="0c7cb381e9d90786951e70e4d39e8ecbb9e43b31.boutiques",
+    id="b306315ee534cde2a22d9d0e4063c4f878433302.boutiques",
     name="wmedits2surf",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,20 @@ WMEDITS2SURF_METADATA = Metadata(
 
 
 Wmedits2surfParameters = typing.TypedDict('Wmedits2surfParameters', {
-    "__STYXTYPE__": typing.Literal["wmedits2surf"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/wmedits2surf"]],
+    "subject": str,
+    "self": bool,
+    "overwrite": bool,
+    "tmp_dir": typing.NotRequired[str | None],
+    "cleanup": bool,
+    "no_cleanup": bool,
+    "debug": bool,
+    "lh": bool,
+    "rh": bool,
+    "no_surfs": bool,
+})
+Wmedits2surfParametersTagged = typing.TypedDict('Wmedits2surfParametersTagged', {
+    "@type": typing.Literal["freesurfer/wmedits2surf"],
     "subject": str,
     "self": bool,
     "overwrite": bool,
@@ -26,43 +39,11 @@ Wmedits2surfParameters = typing.TypedDict('Wmedits2surfParameters', {
     "rh": bool,
     "no_surfs": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "wmedits2surf": wmedits2surf_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 {
-        "wmedits2surf": wmedits2surf_outputs,
-    }.get(t)
 
 
 class Wmedits2surfOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `wmedits2surf(...)`.
+    Output object returned when calling `Wmedits2surfParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -91,7 +72,7 @@ def wmedits2surf_params(
     lh: bool = False,
     rh: bool = False,
     no_surfs: bool = False,
-) -> Wmedits2surfParameters:
+) -> Wmedits2surfParametersTagged:
     """
     Build parameters.
     
@@ -109,7 +90,7 @@ def wmedits2surf_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "wmedits2surf",
+        "@type": "freesurfer/wmedits2surf",
         "subject": subject,
         "self": self,
         "overwrite": overwrite,
@@ -142,28 +123,28 @@ def wmedits2surf_cargs(
     cargs.append("wmedits2surf")
     cargs.extend([
         "--s",
-        params.get("subject")
+        params.get("subject", None)
     ])
-    if params.get("self"):
+    if params.get("self", False):
         cargs.append("--self")
-    if params.get("overwrite"):
+    if params.get("overwrite", False):
         cargs.append("--overwrite")
-    if params.get("tmp_dir") is not None:
+    if params.get("tmp_dir", None) is not None:
         cargs.extend([
             "--tmp",
-            params.get("tmp_dir")
+            params.get("tmp_dir", None)
         ])
-    if params.get("cleanup"):
+    if params.get("cleanup", False):
         cargs.append("--cleanup")
-    if params.get("no_cleanup"):
+    if params.get("no_cleanup", False):
         cargs.append("--no-cleanup")
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
-    if params.get("lh"):
+    if params.get("lh", False):
         cargs.append("--lh")
-    if params.get("rh"):
+    if params.get("rh", False):
         cargs.append("--rh")
-    if params.get("no_surfs"):
+    if params.get("no_surfs", False):
         cargs.append("--no-surfs")
     return cargs
 
@@ -195,9 +176,11 @@ def wmedits2surf_outputs(
 
 def wmedits2surf_execute(
     params: Wmedits2surfParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Wmedits2surfOutputs:
     """
+    wmedits2surf
+    
     Computes binary maps of surface locations where the wm.mgz has been edited.
     Creates files for each hemisphere for each type of edit.
     
@@ -207,10 +190,12 @@ def wmedits2surf_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Wmedits2surfOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(WMEDITS2SURF_METADATA)
     params = execution.params(params)
     cargs = wmedits2surf_cargs(params, execution)
     ret = wmedits2surf_outputs(params, execution)
@@ -232,6 +217,8 @@ def wmedits2surf(
     runner: Runner | None = None,
 ) -> Wmedits2surfOutputs:
     """
+    wmedits2surf
+    
     Computes binary maps of surface locations where the wm.mgz has been edited.
     Creates files for each hemisphere for each type of edit.
     
@@ -253,8 +240,6 @@ def wmedits2surf(
     Returns:
         NamedTuple of outputs (described in `Wmedits2surfOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(WMEDITS2SURF_METADATA)
     params = wmedits2surf_params(
         subject=subject,
         self=self,
@@ -267,13 +252,13 @@ def wmedits2surf(
         rh=rh,
         no_surfs=no_surfs,
     )
-    return wmedits2surf_execute(params, execution)
+    return wmedits2surf_execute(params, runner)
 
 
 __all__ = [
     "WMEDITS2SURF_METADATA",
     "Wmedits2surfOutputs",
-    "Wmedits2surfParameters",
     "wmedits2surf",
+    "wmedits2surf_execute",
     "wmedits2surf_params",
 ]

niwrap_freesurfer/freesurfer/wmsaseg.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 WMSASEG_METADATA = Metadata(
-    id="13c0a73656eaf08524d7d485d6d8e1f97aef6a38.boutiques",
+    id="dc03aa6f6f16bc8b5912ca6532979e9cc7ed9e4d.boutiques",
     name="wmsaseg",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,21 @@ WMSASEG_METADATA = Metadata(
 
 
 WmsasegParameters = typing.TypedDict('WmsasegParameters', {
-    "__STYXTYPE__": typing.Literal["wmsaseg"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/wmsaseg"]],
+    "subject": str,
+    "source_orig": typing.NotRequired[str | None],
+    "source_long": bool,
+    "output_subdir": typing.NotRequired[str | None],
+    "gca_file": typing.NotRequired[InputPathType | None],
+    "no_reg": bool,
+    "no_canorm": bool,
+    "init_spm": bool,
+    "reg_only": bool,
+    "halo1": bool,
+    "halo2": bool,
+})
+WmsasegParametersTagged = typing.TypedDict('WmsasegParametersTagged', {
+    "@type": typing.Literal["freesurfer/wmsaseg"],
     "subject": str,
     "source_orig": typing.NotRequired[str | None],
     "source_long": bool,
@@ -27,43 +41,11 @@ WmsasegParameters = typing.TypedDict('WmsasegParameters', {
     "halo1": bool,
     "halo2": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "wmsaseg": wmsaseg_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 {
-        "wmsaseg": wmsaseg_outputs,
-    }.get(t)
 
 
 class WmsasegOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `wmsaseg(...)`.
+    Output object returned when calling `WmsasegParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -85,7 +67,7 @@ def wmsaseg_params(
     reg_only: bool = False,
     halo1: bool = False,
     halo2: bool = False,
-) -> WmsasegParameters:
+) -> WmsasegParametersTagged:
     """
     Build parameters.
     
@@ -105,7 +87,7 @@ def wmsaseg_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "wmsaseg",
+        "@type": "freesurfer/wmsaseg",
         "subject": subject,
         "source_long": source_long,
         "no_reg": no_reg,
@@ -141,36 +123,36 @@ def wmsaseg_cargs(
     cargs.append("wmsaseg")
     cargs.extend([
         "-s",
-        params.get("subject")
+        params.get("subject", None)
     ])
-    if params.get("source_orig") is not None:
+    if params.get("source_orig", None) is not None:
         cargs.extend([
             "--s+orig",
-            params.get("source_orig")
+            params.get("source_orig", None)
         ])
-    if params.get("source_long"):
+    if params.get("source_long", False):
         cargs.append("--s+long")
-    if params.get("output_subdir") is not None:
+    if params.get("output_subdir", None) is not None:
         cargs.extend([
             "--sub",
-            params.get("output_subdir")
+            params.get("output_subdir", None)
         ])
-    if params.get("gca_file") is not None:
+    if params.get("gca_file", None) is not None:
         cargs.extend([
             "--gca",
-            execution.input_file(params.get("gca_file"))
+            execution.input_file(params.get("gca_file", None))
         ])
-    if params.get("no_reg"):
+    if params.get("no_reg", False):
         cargs.append("--no-reg")
-    if params.get("no_canorm"):
+    if params.get("no_canorm", False):
         cargs.append("--no-canorm")
-    if params.get("init_spm"):
+    if params.get("init_spm", False):
         cargs.append("--init-spm")
-    if params.get("reg_only"):
+    if params.get("reg_only", False):
         cargs.append("--reg-only")
-    if params.get("halo1"):
+    if params.get("halo1", False):
         cargs.append("--halo1")
-    if params.get("halo2"):
+    if params.get("halo2", False):
         cargs.append("--halo2")
     return cargs
 
@@ -190,17 +172,19 @@ def wmsaseg_outputs(
     """
     ret = WmsasegOutputs(
         root=execution.output_file("."),
-        t1_canorm=execution.output_file(params.get("output_subdir") + "/T1.canorm.mgz") if (params.get("output_subdir") is not None) else None,
-        wmsa_lta=execution.output_file(params.get("output_subdir") + "/wmsa.lta") if (params.get("output_subdir") is not None) else None,
+        t1_canorm=execution.output_file(params.get("output_subdir", None) + "/T1.canorm.mgz") if (params.get("output_subdir") is not None) else None,
+        wmsa_lta=execution.output_file(params.get("output_subdir", None) + "/wmsa.lta") if (params.get("output_subdir") is not None) else None,
     )
     return ret
 
 
 def wmsaseg_execute(
     params: WmsasegParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> WmsasegOutputs:
     """
+    wmsaseg
+    
     White Matter Hyperintensity Segmentation Tool.
     
     Author: FreeSurfer Developers
@@ -209,10 +193,12 @@ def wmsaseg_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `WmsasegOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(WMSASEG_METADATA)
     params = execution.params(params)
     cargs = wmsaseg_cargs(params, execution)
     ret = wmsaseg_outputs(params, execution)
@@ -235,6 +221,8 @@ def wmsaseg(
     runner: Runner | None = None,
 ) -> WmsasegOutputs:
     """
+    wmsaseg
+    
     White Matter Hyperintensity Segmentation Tool.
     
     Author: FreeSurfer Developers
@@ -257,8 +245,6 @@ def wmsaseg(
     Returns:
         NamedTuple of outputs (described in `WmsasegOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(WMSASEG_METADATA)
     params = wmsaseg_params(
         subject=subject,
         source_orig=source_orig,
@@ -272,13 +258,13 @@ def wmsaseg(
         halo1=halo1,
         halo2=halo2,
     )
-    return wmsaseg_execute(params, execution)
+    return wmsaseg_execute(params, runner)
 
 
 __all__ = [
     "WMSASEG_METADATA",
     "WmsasegOutputs",
-    "WmsasegParameters",
     "wmsaseg",
+    "wmsaseg_execute",
     "wmsaseg_params",
 ]