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

niwrap_freesurfer/freesurfer/seg2filled.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SEG2FILLED_METADATA = Metadata(
-    id="1593b1d76e0b989c3692731ac5705d0a7ce06564.boutiques",
+    id="3d9ced8d4db53346a6df52570992a83793860107.boutiques",
     name="seg2filled",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,17 @@ SEG2FILLED_METADATA = Metadata(
 
 
 Seg2filledParameters = typing.TypedDict('Seg2filledParameters', {
-    "__STYXTYPE__": typing.Literal["seg2filled"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/seg2filled"]],
+    "seg_file": InputPathType,
+    "norm_file": InputPathType,
+    "output_file": str,
+    "ndil": typing.NotRequired[int | None],
+    "cavity_flag": bool,
+    "surf_name": typing.NotRequired[str | None],
+    "surf_dir": typing.NotRequired[str | None],
+})
+Seg2filledParametersTagged = typing.TypedDict('Seg2filledParametersTagged', {
+    "@type": typing.Literal["freesurfer/seg2filled"],
     "seg_file": InputPathType,
     "norm_file": InputPathType,
     "output_file": str,
@@ -23,43 +33,11 @@ Seg2filledParameters = typing.TypedDict('Seg2filledParameters', {
     "surf_name": typing.NotRequired[str | None],
     "surf_dir": 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 {
-        "seg2filled": seg2filled_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 {
-        "seg2filled": seg2filled_outputs,
-    }.get(t)
 
 
 class Seg2filledOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `seg2filled(...)`.
+    Output object returned when calling `Seg2filledParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +53,7 @@ def seg2filled_params(
     cavity_flag: bool = False,
     surf_name: str | None = None,
     surf_dir: str | None = None,
-) -> Seg2filledParameters:
+) -> Seg2filledParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +69,7 @@ def seg2filled_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "seg2filled",
+        "@type": "freesurfer/seg2filled",
         "seg_file": seg_file,
         "norm_file": norm_file,
         "output_file": output_file,
@@ -123,32 +101,32 @@ def seg2filled_cargs(
     cargs.append("seg2filled")
     cargs.extend([
         "-seg",
-        execution.input_file(params.get("seg_file"))
+        execution.input_file(params.get("seg_file", None))
     ])
     cargs.extend([
         "-norm",
-        execution.input_file(params.get("norm_file"))
+        execution.input_file(params.get("norm_file", None))
     ])
     cargs.extend([
         "-o",
-        params.get("output_file")
+        params.get("output_file", None)
     ])
-    if params.get("ndil") is not None:
+    if params.get("ndil", None) is not None:
         cargs.extend([
             "--ndil",
-            str(params.get("ndil"))
+            str(params.get("ndil", None))
         ])
-    if params.get("cavity_flag"):
+    if params.get("cavity_flag", False):
         cargs.append("--cavity")
-    if params.get("surf_name") is not None:
+    if params.get("surf_name", None) is not None:
         cargs.extend([
             "--surf",
-            params.get("surf_name")
+            params.get("surf_name", None)
         ])
-    if params.get("surf_dir") is not None:
+    if params.get("surf_dir", None) is not None:
         cargs.extend([
             "--surfdir",
-            params.get("surf_dir")
+            params.get("surf_dir", None)
         ])
     return cargs
 
@@ -168,17 +146,20 @@ def seg2filled_outputs(
     """
     ret = Seg2filledOutputs(
         root=execution.output_file("."),
-        out_filled_mgz=execution.output_file(params.get("output_file")),
+        out_filled_mgz=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def seg2filled_execute(
     params: Seg2filledParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Seg2filledOutputs:
     """
-    Creates a filled.mgz from an aseg-style segmentation using SAMSEG segmentation.
+    seg2filled
+    
+    Creates a filled.mgz from an aseg-style segmentation using SAMSEG
+    segmentation.
     
     Author: FreeSurfer Developers
     
@@ -186,10 +167,12 @@ def seg2filled_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Seg2filledOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SEG2FILLED_METADATA)
     params = execution.params(params)
     cargs = seg2filled_cargs(params, execution)
     ret = seg2filled_outputs(params, execution)
@@ -208,7 +191,10 @@ def seg2filled(
     runner: Runner | None = None,
 ) -> Seg2filledOutputs:
     """
-    Creates a filled.mgz from an aseg-style segmentation using SAMSEG segmentation.
+    seg2filled
+    
+    Creates a filled.mgz from an aseg-style segmentation using SAMSEG
+    segmentation.
     
     Author: FreeSurfer Developers
     
@@ -226,8 +212,6 @@ def seg2filled(
     Returns:
         NamedTuple of outputs (described in `Seg2filledOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SEG2FILLED_METADATA)
     params = seg2filled_params(
         seg_file=seg_file,
         norm_file=norm_file,
@@ -237,13 +221,13 @@ def seg2filled(
         surf_name=surf_name,
         surf_dir=surf_dir,
     )
-    return seg2filled_execute(params, execution)
+    return seg2filled_execute(params, runner)
 
 
 __all__ = [
     "SEG2FILLED_METADATA",
     "Seg2filledOutputs",
-    "Seg2filledParameters",
     "seg2filled",
+    "seg2filled_execute",
     "seg2filled_params",
 ]

niwrap_freesurfer/freesurfer/seg2recon.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SEG2RECON_METADATA = Metadata(
-    id="a2f2b008cac59cb84f112380cce351f9ae9e939d.boutiques",
+    id="22df8aaa390ed4db847c18846a8feb2c642ed1eb.boutiques",
     name="seg2recon",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,24 @@ SEG2RECON_METADATA = Metadata(
 
 
 Seg2reconParameters = typing.TypedDict('Seg2reconParameters', {
-    "__STYXTYPE__": typing.Literal["seg2recon"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/seg2recon"]],
+    "subject": str,
+    "segvol": InputPathType,
+    "inputvol": InputPathType,
+    "ctab": typing.NotRequired[InputPathType | None],
+    "ndilate": typing.NotRequired[float | None],
+    "threads": typing.NotRequired[float | None],
+    "force_update": bool,
+    "no_cc": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "headmask": typing.NotRequired[InputPathType | None],
+    "thresh": typing.NotRequired[float | None],
+    "expert": typing.NotRequired[InputPathType | None],
+    "rca": bool,
+    "no_bias_field_cor": bool,
+})
+Seg2reconParametersTagged = typing.TypedDict('Seg2reconParametersTagged', {
+    "@type": typing.Literal["freesurfer/seg2recon"],
     "subject": str,
     "segvol": InputPathType,
     "inputvol": InputPathType,
@@ -30,43 +47,11 @@ Seg2reconParameters = typing.TypedDict('Seg2reconParameters', {
     "rca": bool,
     "no_bias_field_cor": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "seg2recon": seg2recon_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 {
-        "seg2recon": seg2recon_outputs,
-    }.get(t)
 
 
 class Seg2reconOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `seg2recon(...)`.
+    Output object returned when calling `Seg2reconParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -93,7 +78,7 @@ def seg2recon_params(
     expert: InputPathType | None = None,
     rca: bool = False,
     no_bias_field_cor: bool = False,
-) -> Seg2reconParameters:
+) -> Seg2reconParametersTagged:
     """
     Build parameters.
     
@@ -120,7 +105,7 @@ def seg2recon_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "seg2recon",
+        "@type": "freesurfer/seg2recon",
         "subject": subject,
         "segvol": segvol,
         "inputvol": inputvol,
@@ -163,58 +148,58 @@ def seg2recon_cargs(
     cargs.append("seg2recon")
     cargs.extend([
         "-s",
-        params.get("subject")
+        params.get("subject", None)
     ])
     cargs.extend([
         "-seg",
-        execution.input_file(params.get("segvol"))
+        execution.input_file(params.get("segvol", None))
     ])
     cargs.extend([
         "-i",
-        execution.input_file(params.get("inputvol"))
+        execution.input_file(params.get("inputvol", None))
     ])
-    if params.get("ctab") is not None:
+    if params.get("ctab", None) is not None:
         cargs.extend([
             "-ctab",
-            execution.input_file(params.get("ctab"))
+            execution.input_file(params.get("ctab", None))
         ])
-    if params.get("ndilate") is not None:
+    if params.get("ndilate", None) is not None:
         cargs.extend([
             "--ndilate",
-            str(params.get("ndilate"))
+            str(params.get("ndilate", None))
         ])
-    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("force_update"):
+    if params.get("force_update", False):
         cargs.append("--force-update")
-    if params.get("no_cc"):
+    if params.get("no_cc", False):
         cargs.append("--no-cc")
-    if params.get("mask") is not None:
+    if params.get("mask", None) is not None:
         cargs.extend([
             "--m",
-            execution.input_file(params.get("mask"))
+            execution.input_file(params.get("mask", None))
         ])
-    if params.get("headmask") is not None:
+    if params.get("headmask", None) is not None:
         cargs.extend([
             "--h",
-            execution.input_file(params.get("headmask"))
+            execution.input_file(params.get("headmask", None))
         ])
-    if params.get("thresh") is not None:
+    if params.get("thresh", None) is not None:
         cargs.extend([
             "--thresh",
-            str(params.get("thresh"))
+            str(params.get("thresh", None))
         ])
-    if params.get("expert") is not None:
+    if params.get("expert", None) is not None:
         cargs.extend([
             "--expert",
-            execution.input_file(params.get("expert"))
+            execution.input_file(params.get("expert", None))
         ])
-    if params.get("rca"):
+    if params.get("rca", False):
         cargs.append("--rca")
-    if params.get("no_bias_field_cor"):
+    if params.get("no_bias_field_cor", False):
         cargs.append("--no-bias-field-cor")
     return cargs
 
@@ -234,20 +219,22 @@ def seg2recon_outputs(
     """
     ret = Seg2reconOutputs(
         root=execution.output_file("."),
-        aseg_auto_mgz=execution.output_file(params.get("subject") + "/aseg.auto.mgz"),
-        nu_mgz=execution.output_file(params.get("subject") + "/nu.mgz"),
-        brainmask_mgz=execution.output_file(params.get("subject") + "/brainmask.mgz"),
+        aseg_auto_mgz=execution.output_file(params.get("subject", None) + "/aseg.auto.mgz"),
+        nu_mgz=execution.output_file(params.get("subject", None) + "/nu.mgz"),
+        brainmask_mgz=execution.output_file(params.get("subject", None) + "/brainmask.mgz"),
     )
     return ret
 
 
 def seg2recon_execute(
     params: Seg2reconParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Seg2reconOutputs:
     """
-    Creates and populates a subjects directory from an input image and segmentation
-    suitable for running recon-all.
+    seg2recon
+    
+    Creates and populates a subjects directory from an input image and
+    segmentation suitable for running recon-all.
     
     Author: FreeSurfer Developers
     
@@ -255,10 +242,12 @@ def seg2recon_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Seg2reconOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SEG2RECON_METADATA)
     params = execution.params(params)
     cargs = seg2recon_cargs(params, execution)
     ret = seg2recon_outputs(params, execution)
@@ -284,8 +273,10 @@ def seg2recon(
     runner: Runner | None = None,
 ) -> Seg2reconOutputs:
     """
-    Creates and populates a subjects directory from an input image and segmentation
-    suitable for running recon-all.
+    seg2recon
+    
+    Creates and populates a subjects directory from an input image and
+    segmentation suitable for running recon-all.
     
     Author: FreeSurfer Developers
     
@@ -314,8 +305,6 @@ def seg2recon(
     Returns:
         NamedTuple of outputs (described in `Seg2reconOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SEG2RECON_METADATA)
     params = seg2recon_params(
         subject=subject,
         segvol=segvol,
@@ -332,13 +321,13 @@ def seg2recon(
         rca=rca,
         no_bias_field_cor=no_bias_field_cor,
     )
-    return seg2recon_execute(params, execution)
+    return seg2recon_execute(params, runner)
 
 
 __all__ = [
     "SEG2RECON_METADATA",
     "Seg2reconOutputs",
-    "Seg2reconParameters",
     "seg2recon",
+    "seg2recon_execute",
     "seg2recon_params",
 ]

niwrap_freesurfer/freesurfer/segment_bs_sh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SEGMENT_BS_SH_METADATA = Metadata(
-    id="ea5de6d87d6861bdf790a471d88443f6b20986d7.boutiques",
+    id="3915aa673c1184ad6e921ee72eab975737034168.boutiques",
     name="segmentBS.sh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,53 +14,26 @@ SEGMENT_BS_SH_METADATA = Metadata(
 
 
 SegmentBsShParameters = typing.TypedDict('SegmentBsShParameters', {
-    "__STYXTYPE__": typing.Literal["segmentBS.sh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/segmentBS.sh"]],
+    "matlab_runtime": typing.NotRequired[str | None],
+})
+SegmentBsShParametersTagged = typing.TypedDict('SegmentBsShParametersTagged', {
+    "@type": typing.Literal["freesurfer/segmentBS.sh"],
     "matlab_runtime": 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 {
-        "segmentBS.sh": segment_bs_sh_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 SegmentBsShOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `segment_bs_sh(...)`.
+    Output object returned when calling `SegmentBsShParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
 
 
 def segment_bs_sh_params(
-    matlab_runtime: str | None = "/usr/local/freesurfer/MCRv97",
-) -> SegmentBsShParameters:
+    matlab_runtime: str | None = None,
+) -> SegmentBsShParametersTagged:
     """
     Build parameters.
     
@@ -71,7 +44,7 @@ def segment_bs_sh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "segmentBS.sh",
+        "@type": "freesurfer/segmentBS.sh",
     }
     if matlab_runtime is not None:
         params["matlab_runtime"] = matlab_runtime
@@ -93,8 +66,8 @@ def segment_bs_sh_cargs(
     """
     cargs = []
     cargs.append("segmentBS.sh")
-    if params.get("matlab_runtime") is not None:
-        cargs.append(params.get("matlab_runtime"))
+    if params.get("matlab_runtime", None) is not None:
+        cargs.append(params.get("matlab_runtime", None))
     return cargs
 
 
@@ -119,9 +92,11 @@ def segment_bs_sh_outputs(
 
 def segment_bs_sh_execute(
     params: SegmentBsShParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SegmentBsShOutputs:
     """
+    segmentBS.sh
+    
     Segmentation tool for hippocampal/amygdala and brainstem modules.
     
     Author: FreeSurfer Developers
@@ -130,10 +105,12 @@ def segment_bs_sh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SegmentBsShOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SEGMENT_BS_SH_METADATA)
     params = execution.params(params)
     cargs = segment_bs_sh_cargs(params, execution)
     ret = segment_bs_sh_outputs(params, execution)
@@ -142,10 +119,12 @@ def segment_bs_sh_execute(
 
 
 def segment_bs_sh(
-    matlab_runtime: str | None = "/usr/local/freesurfer/MCRv97",
+    matlab_runtime: str | None = None,
     runner: Runner | None = None,
 ) -> SegmentBsShOutputs:
     """
+    segmentBS.sh
+    
     Segmentation tool for hippocampal/amygdala and brainstem modules.
     
     Author: FreeSurfer Developers
@@ -159,18 +138,16 @@ def segment_bs_sh(
     Returns:
         NamedTuple of outputs (described in `SegmentBsShOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SEGMENT_BS_SH_METADATA)
     params = segment_bs_sh_params(
         matlab_runtime=matlab_runtime,
     )
-    return segment_bs_sh_execute(params, execution)
+    return segment_bs_sh_execute(params, runner)
 
 
 __all__ = [
     "SEGMENT_BS_SH_METADATA",
     "SegmentBsShOutputs",
-    "SegmentBsShParameters",
     "segment_bs_sh",
+    "segment_bs_sh_execute",
     "segment_bs_sh_params",
 ]