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

niwrap_freesurfer/freesurfer/mideface.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MIDEFACE_METADATA = Metadata(
-    id="103c9c8e1c2adfa740ce06f20222e2baa57571f0.boutiques",
+    id="0687e5e05c5e03fafe6833cb1799a3357f75f896.boutiques",
     name="mideface",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,40 @@ MIDEFACE_METADATA = Metadata(
 
 
 MidefaceParameters = typing.TypedDict('MidefaceParameters', {
-    "__STYXTYPE__": typing.Literal["mideface"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mideface"]],
+    "input_volume": InputPathType,
+    "output_volume": str,
+    "facemask": typing.NotRequired[InputPathType | None],
+    "output_dir": typing.NotRequired[str | None],
+    "exclusion_mask": typing.NotRequired[InputPathType | None],
+    "samseg_ndilations": typing.NotRequired[float | None],
+    "samseg_json": typing.NotRequired[str | None],
+    "samseg_fast": bool,
+    "no_samseg_fast": bool,
+    "init_reg": typing.NotRequired[InputPathType | None],
+    "synthseg_ndilations": typing.NotRequired[float | None],
+    "fill_const": typing.NotRequired[list[float] | None],
+    "fill_zero": bool,
+    "fhi": typing.NotRequired[float | None],
+    "no_ears": bool,
+    "back_of_head": bool,
+    "forehead": bool,
+    "pics": bool,
+    "code": typing.NotRequired[str | None],
+    "image_convert": typing.NotRequired[str | None],
+    "no_post": bool,
+    "threads": typing.NotRequired[float | None],
+    "force": bool,
+    "output_format": typing.NotRequired[str | None],
+    "atlas": typing.NotRequired[str | None],
+    "expert": typing.NotRequired[str | None],
+    "display_no": typing.NotRequired[float | None],
+    "apply_volume": typing.NotRequired[str | None],
+    "check_volume": typing.NotRequired[InputPathType | None],
+    "check_output_file": typing.NotRequired[InputPathType | None],
+})
+MidefaceParametersTagged = typing.TypedDict('MidefaceParametersTagged', {
+    "@type": typing.Literal["freesurfer/mideface"],
     "input_volume": InputPathType,
     "output_volume": str,
     "facemask": typing.NotRequired[InputPathType | None],
@@ -46,43 +79,11 @@ MidefaceParameters = typing.TypedDict('MidefaceParameters', {
     "check_volume": typing.NotRequired[InputPathType | None],
     "check_output_file": typing.NotRequired[InputPathType | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mideface": mideface_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 {
-        "mideface": mideface_outputs,
-    }.get(t)
 
 
 class MidefaceOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mideface(...)`.
+    Output object returned when calling `MidefaceParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -123,7 +124,7 @@ def mideface_params(
     apply_volume: str | None = None,
     check_volume: InputPathType | None = None,
     check_output_file: InputPathType | None = None,
-) -> MidefaceParameters:
+) -> MidefaceParametersTagged:
     """
     Build parameters.
     
@@ -162,7 +163,7 @@ def mideface_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mideface",
+        "@type": "freesurfer/mideface",
         "input_volume": input_volume,
         "output_volume": output_volume,
         "samseg_fast": samseg_fast,
@@ -233,124 +234,124 @@ def mideface_cargs(
     cargs.append("mideface")
     cargs.extend([
         "--i",
-        execution.input_file(params.get("input_volume"))
+        execution.input_file(params.get("input_volume", None))
     ])
     cargs.extend([
         "--o",
-        params.get("output_volume")
+        params.get("output_volume", None)
     ])
-    if params.get("facemask") is not None:
+    if params.get("facemask", None) is not None:
         cargs.extend([
             "--facemask",
-            execution.input_file(params.get("facemask"))
+            execution.input_file(params.get("facemask", None))
         ])
-    if params.get("output_dir") is not None:
+    if params.get("output_dir", None) is not None:
         cargs.extend([
             "--odir",
-            params.get("output_dir")
+            params.get("output_dir", None)
         ])
-    if params.get("exclusion_mask") is not None:
+    if params.get("exclusion_mask", None) is not None:
         cargs.extend([
             "--xmask",
-            execution.input_file(params.get("exclusion_mask"))
+            execution.input_file(params.get("exclusion_mask", None))
         ])
-    if params.get("samseg_ndilations") is not None:
+    if params.get("samseg_ndilations", None) is not None:
         cargs.extend([
             "--xmask-samseg",
-            str(params.get("samseg_ndilations"))
+            str(params.get("samseg_ndilations", None))
         ])
-    if params.get("samseg_json") is not None:
+    if params.get("samseg_json", None) is not None:
         cargs.extend([
             "--samseg-json",
-            params.get("samseg_json")
+            params.get("samseg_json", None)
         ])
-    if params.get("samseg_fast"):
+    if params.get("samseg_fast", False):
         cargs.append("--samseg-fast")
-    if params.get("no_samseg_fast"):
+    if params.get("no_samseg_fast", False):
         cargs.append("--no-samseg-fast")
-    if params.get("init_reg") is not None:
+    if params.get("init_reg", None) is not None:
         cargs.extend([
             "--init-reg",
-            execution.input_file(params.get("init_reg"))
+            execution.input_file(params.get("init_reg", None))
         ])
-    if params.get("synthseg_ndilations") is not None:
+    if params.get("synthseg_ndilations", None) is not None:
         cargs.extend([
             "--xmask-synthseg",
-            str(params.get("synthseg_ndilations"))
+            str(params.get("synthseg_ndilations", None))
         ])
-    if params.get("fill_const") is not None:
+    if params.get("fill_const", None) is not None:
         cargs.extend([
             "--fill-const",
-            *map(str, params.get("fill_const"))
+            *map(str, params.get("fill_const", None))
         ])
-    if params.get("fill_zero"):
+    if params.get("fill_zero", False):
         cargs.append("--fill-zero")
-    if params.get("fhi") is not None:
+    if params.get("fhi", None) is not None:
         cargs.extend([
             "--fhi",
-            str(params.get("fhi"))
+            str(params.get("fhi", None))
         ])
-    if params.get("no_ears"):
+    if params.get("no_ears", False):
         cargs.append("--no-ears")
-    if params.get("back_of_head"):
+    if params.get("back_of_head", False):
         cargs.append("--back-of-head")
-    if params.get("forehead"):
+    if params.get("forehead", False):
         cargs.append("--forehead")
-    if params.get("pics"):
+    if params.get("pics", False):
         cargs.append("--pics")
-    if params.get("code") is not None:
+    if params.get("code", None) is not None:
         cargs.extend([
             "--code",
-            params.get("code")
+            params.get("code", None)
         ])
-    if params.get("image_convert") is not None:
+    if params.get("image_convert", None) is not None:
         cargs.extend([
             "--imconvert",
-            params.get("image_convert")
+            params.get("image_convert", None)
         ])
-    if params.get("no_post"):
+    if params.get("no_post", False):
         cargs.append("--no-post")
-    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"):
+    if params.get("force", False):
         cargs.append("--force")
-    if params.get("output_format") is not None:
+    if params.get("output_format", None) is not None:
         cargs.extend([
             "--nii --nii.gz --mgz",
-            params.get("output_format")
+            params.get("output_format", None)
         ])
-    if params.get("atlas") is not None:
+    if params.get("atlas", None) is not None:
         cargs.extend([
             "--atlas",
-            params.get("atlas")
+            params.get("atlas", 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("display_no") is not None:
+    if params.get("display_no", None) is not None:
         cargs.extend([
             "--display",
-            str(params.get("display_no"))
+            str(params.get("display_no", None))
         ])
-    if params.get("apply_volume") is not None:
+    if params.get("apply_volume", None) is not None:
         cargs.extend([
             "--apply",
-            params.get("apply_volume")
+            params.get("apply_volume", None)
         ])
-    if params.get("check_volume") is not None:
+    if params.get("check_volume", None) is not None:
         cargs.extend([
             "--check",
-            execution.input_file(params.get("check_volume"))
+            execution.input_file(params.get("check_volume", None))
         ])
-    if params.get("check_output_file") is not None:
+    if params.get("check_output_file", None) is not None:
         cargs.extend([
             "--check",
-            execution.input_file(params.get("check_output_file"))
+            execution.input_file(params.get("check_output_file", None))
         ])
     return cargs
 
@@ -370,17 +371,19 @@ def mideface_outputs(
     """
     ret = MidefaceOutputs(
         root=execution.output_file("."),
-        defaced_output=execution.output_file(params.get("output_volume")),
-        facemask_output=execution.output_file(pathlib.Path(params.get("facemask")).name) if (params.get("facemask") is not None) else None,
+        defaced_output=execution.output_file(params.get("output_volume", None)),
+        facemask_output=execution.output_file(pathlib.Path(params.get("facemask", None)).name) if (params.get("facemask") is not None) else None,
     )
     return ret
 
 
 def mideface_execute(
     params: MidefaceParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MidefaceOutputs:
     """
+    mideface
+    
     Minimally invasive defacing tool.
     
     Author: FreeSurfer Developers
@@ -389,10 +392,12 @@ def mideface_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MidefaceOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MIDEFACE_METADATA)
     params = execution.params(params)
     cargs = mideface_cargs(params, execution)
     ret = mideface_outputs(params, execution)
@@ -434,6 +439,8 @@ def mideface(
     runner: Runner | None = None,
 ) -> MidefaceOutputs:
     """
+    mideface
+    
     Minimally invasive defacing tool.
     
     Author: FreeSurfer Developers
@@ -475,8 +482,6 @@ def mideface(
     Returns:
         NamedTuple of outputs (described in `MidefaceOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MIDEFACE_METADATA)
     params = mideface_params(
         input_volume=input_volume,
         output_volume=output_volume,
@@ -509,13 +514,13 @@ def mideface(
         check_volume=check_volume,
         check_output_file=check_output_file,
     )
-    return mideface_execute(params, execution)
+    return mideface_execute(params, runner)
 
 
 __all__ = [
     "MIDEFACE_METADATA",
     "MidefaceOutputs",
-    "MidefaceParameters",
     "mideface",
+    "mideface_execute",
     "mideface_params",
 ]

niwrap_freesurfer/freesurfer/minc2seqinfo.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MINC2SEQINFO_METADATA = Metadata(
-    id="d57928aac7b425a7a859150e95ea57280a4d9604.boutiques",
+    id="40252e04328965715491d4e0d301dc7e8b671e34.boutiques",
     name="minc2seqinfo",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ MINC2SEQINFO_METADATA = Metadata(
 
 
 Minc2seqinfoParameters = typing.TypedDict('Minc2seqinfoParameters', {
-    "__STYXTYPE__": typing.Literal["minc2seqinfo"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/minc2seqinfo"]],
+    "mincfile": InputPathType,
+    "seqinfofile": str,
+})
+Minc2seqinfoParametersTagged = typing.TypedDict('Minc2seqinfoParametersTagged', {
+    "@type": typing.Literal["freesurfer/minc2seqinfo"],
     "mincfile": InputPathType,
     "seqinfofile": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "minc2seqinfo": minc2seqinfo_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 {
-        "minc2seqinfo": minc2seqinfo_outputs,
-    }.get(t)
 
 
 class Minc2seqinfoOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `minc2seqinfo(...)`.
+    Output object returned when calling `Minc2seqinfoParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class Minc2seqinfoOutputs(typing.NamedTuple):
 def minc2seqinfo_params(
     mincfile: InputPathType,
     seqinfofile: str,
-) -> Minc2seqinfoParameters:
+) -> Minc2seqinfoParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def minc2seqinfo_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "minc2seqinfo",
+        "@type": "freesurfer/minc2seqinfo",
         "mincfile": mincfile,
         "seqinfofile": seqinfofile,
     }
@@ -98,8 +71,8 @@ def minc2seqinfo_cargs(
     """
     cargs = []
     cargs.append("minc2seqinfo")
-    cargs.append(execution.input_file(params.get("mincfile")))
-    cargs.append(params.get("seqinfofile"))
+    cargs.append(execution.input_file(params.get("mincfile", None)))
+    cargs.append(params.get("seqinfofile", None))
     return cargs
 
 
@@ -118,16 +91,18 @@ def minc2seqinfo_outputs(
     """
     ret = Minc2seqinfoOutputs(
         root=execution.output_file("."),
-        out_seqinfofile=execution.output_file(params.get("seqinfofile")),
+        out_seqinfofile=execution.output_file(params.get("seqinfofile", None)),
     )
     return ret
 
 
 def minc2seqinfo_execute(
     params: Minc2seqinfoParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Minc2seqinfoOutputs:
     """
+    minc2seqinfo
+    
     Tool for extracting sequence information from MINC files.
     
     Author: FreeSurfer Developers
@@ -136,10 +111,12 @@ def minc2seqinfo_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Minc2seqinfoOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MINC2SEQINFO_METADATA)
     params = execution.params(params)
     cargs = minc2seqinfo_cargs(params, execution)
     ret = minc2seqinfo_outputs(params, execution)
@@ -153,6 +130,8 @@ def minc2seqinfo(
     runner: Runner | None = None,
 ) -> Minc2seqinfoOutputs:
     """
+    minc2seqinfo
+    
     Tool for extracting sequence information from MINC files.
     
     Author: FreeSurfer Developers
@@ -166,19 +145,17 @@ def minc2seqinfo(
     Returns:
         NamedTuple of outputs (described in `Minc2seqinfoOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MINC2SEQINFO_METADATA)
     params = minc2seqinfo_params(
         mincfile=mincfile,
         seqinfofile=seqinfofile,
     )
-    return minc2seqinfo_execute(params, execution)
+    return minc2seqinfo_execute(params, runner)
 
 
 __all__ = [
     "MINC2SEQINFO_METADATA",
     "Minc2seqinfoOutputs",
-    "Minc2seqinfoParameters",
     "minc2seqinfo",
+    "minc2seqinfo_execute",
     "minc2seqinfo_params",
 ]