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

niwrap_freesurfer/freesurfer/mkheadsurf.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MKHEADSURF_METADATA = Metadata(
-    id="adf4edc7e96dd75c3a827ac0d7019c78d16c36c0.boutiques",
+    id="1cfc94620745a88f35a5393a7c822c27660f72fa.boutiques",
     name="mkheadsurf",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,37 @@ MKHEADSURF_METADATA = Metadata(
 
 
 MkheadsurfParameters = typing.TypedDict('MkheadsurfParameters', {
-    "__STYXTYPE__": typing.Literal["mkheadsurf"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mkheadsurf"]],
+    "input_vol": InputPathType,
+    "output_vol": str,
+    "output_surf": str,
+    "subject_id": str,
+    "nsmooth": typing.NotRequired[float | None],
+    "noseghead": bool,
+    "thresh1": typing.NotRequired[float | None],
+    "thresh2": typing.NotRequired[float | None],
+    "nhitsmin": typing.NotRequired[float | None],
+    "ndilate": typing.NotRequired[float | None],
+    "nerode": typing.NotRequired[float | None],
+    "fillval": typing.NotRequired[float | None],
+    "fhi": typing.NotRequired[float | None],
+    "no_rescale": bool,
+    "no_fill_holes_islands": bool,
+    "or_mask": typing.NotRequired[InputPathType | None],
+    "tessellation_method": typing.NotRequired[str | None],
+    "inflate": bool,
+    "curv": bool,
+    "srcvol": typing.NotRequired[str | None],
+    "headvol": typing.NotRequired[str | None],
+    "headsurf": typing.NotRequired[str | None],
+    "smheadsurf": typing.NotRequired[str | None],
+    "hemi": typing.NotRequired[str | None],
+    "subjects_dir": typing.NotRequired[str | None],
+    "umask": typing.NotRequired[float | None],
+    "logfile": typing.NotRequired[str | None],
+})
+MkheadsurfParametersTagged = typing.TypedDict('MkheadsurfParametersTagged', {
+    "@type": typing.Literal["freesurfer/mkheadsurf"],
     "input_vol": InputPathType,
     "output_vol": str,
     "output_surf": str,
@@ -43,42 +73,11 @@ MkheadsurfParameters = typing.TypedDict('MkheadsurfParameters', {
     "umask": typing.NotRequired[float | None],
     "logfile": 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 {
-        "mkheadsurf": mkheadsurf_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 MkheadsurfOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mkheadsurf(...)`.
+    Output object returned when calling `MkheadsurfParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -112,7 +111,7 @@ def mkheadsurf_params(
     subjects_dir: str | None = None,
     umask: float | None = None,
     logfile: str | None = None,
-) -> MkheadsurfParameters:
+) -> MkheadsurfParametersTagged:
     """
     Build parameters.
     
@@ -149,7 +148,7 @@ def mkheadsurf_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mkheadsurf",
+        "@type": "freesurfer/mkheadsurf",
         "input_vol": input_vol,
         "output_vol": output_vol,
         "output_surf": output_surf,
@@ -216,119 +215,119 @@ def mkheadsurf_cargs(
     cargs.append("mkheadsurf")
     cargs.extend([
         "-i",
-        execution.input_file(params.get("input_vol"))
+        execution.input_file(params.get("input_vol", None))
     ])
     cargs.extend([
         "-o",
-        params.get("output_vol")
+        params.get("output_vol", None)
     ])
     cargs.extend([
         "-surf",
-        params.get("output_surf")
+        params.get("output_surf", None)
     ])
     cargs.extend([
         "-s",
-        params.get("subject_id")
+        params.get("subject_id", None)
     ])
-    if params.get("nsmooth") is not None:
+    if params.get("nsmooth", None) is not None:
         cargs.extend([
             "-nsmooth",
-            str(params.get("nsmooth"))
+            str(params.get("nsmooth", None))
         ])
-    if params.get("noseghead"):
+    if params.get("noseghead", False):
         cargs.append("-noseghead")
-    if params.get("thresh1") is not None:
+    if params.get("thresh1", None) is not None:
         cargs.extend([
             "-thresh1",
-            str(params.get("thresh1"))
+            str(params.get("thresh1", None))
         ])
-    if params.get("thresh2") is not None:
+    if params.get("thresh2", None) is not None:
         cargs.extend([
             "-thresh2",
-            str(params.get("thresh2"))
+            str(params.get("thresh2", None))
         ])
-    if params.get("nhitsmin") is not None:
+    if params.get("nhitsmin", None) is not None:
         cargs.extend([
             "-nhitsmin",
-            str(params.get("nhitsmin"))
+            str(params.get("nhitsmin", 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("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("fillval") is not None:
+    if params.get("fillval", None) is not None:
         cargs.extend([
             "-fillval",
-            str(params.get("fillval"))
+            str(params.get("fillval", None))
         ])
-    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_rescale"):
+    if params.get("no_rescale", False):
         cargs.append("-no-rescale")
-    if params.get("no_fill_holes_islands"):
+    if params.get("no_fill_holes_islands", False):
         cargs.append("-no-fill-holes-islands")
-    if params.get("or_mask") is not None:
+    if params.get("or_mask", None) is not None:
         cargs.extend([
             "-or-mask",
-            execution.input_file(params.get("or_mask"))
+            execution.input_file(params.get("or_mask", None))
         ])
-    if params.get("tessellation_method") is not None:
+    if params.get("tessellation_method", None) is not None:
         cargs.extend([
             "-tess",
-            params.get("tessellation_method")
+            params.get("tessellation_method", None)
         ])
-    if params.get("inflate"):
+    if params.get("inflate", False):
         cargs.append("-inflate")
-    if params.get("curv"):
+    if params.get("curv", False):
         cargs.append("-curv")
-    if params.get("srcvol") is not None:
+    if params.get("srcvol", None) is not None:
         cargs.extend([
             "-srcvol",
-            params.get("srcvol")
+            params.get("srcvol", None)
         ])
-    if params.get("headvol") is not None:
+    if params.get("headvol", None) is not None:
         cargs.extend([
             "-headvol",
-            params.get("headvol")
+            params.get("headvol", None)
         ])
-    if params.get("headsurf") is not None:
+    if params.get("headsurf", None) is not None:
         cargs.extend([
             "-headsurf",
-            params.get("headsurf")
+            params.get("headsurf", None)
         ])
-    if params.get("smheadsurf") is not None:
+    if params.get("smheadsurf", None) is not None:
         cargs.extend([
             "-smheadsurf",
-            params.get("smheadsurf")
+            params.get("smheadsurf", 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("subjects_dir") is not None:
+    if params.get("subjects_dir", None) is not None:
         cargs.extend([
             "-sd",
-            params.get("subjects_dir")
+            params.get("subjects_dir", None)
         ])
-    if params.get("umask") is not None:
+    if params.get("umask", None) is not None:
         cargs.extend([
             "-umask",
-            str(params.get("umask"))
+            str(params.get("umask", None))
         ])
-    if params.get("logfile") is not None:
+    if params.get("logfile", None) is not None:
         cargs.extend([
             "-log",
-            params.get("logfile")
+            params.get("logfile", None)
         ])
     return cargs
 
@@ -354,11 +353,13 @@ def mkheadsurf_outputs(
 
 def mkheadsurf_execute(
     params: MkheadsurfParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MkheadsurfOutputs:
     """
-    Segment and create a surface representation of the head for visualization and
-    further processing.
+    mkheadsurf
+    
+    Segment and create a surface representation of the head for visualization
+    and further processing.
     
     Author: FreeSurfer Developers
     
@@ -366,10 +367,12 @@ def mkheadsurf_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MkheadsurfOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MKHEADSURF_METADATA)
     params = execution.params(params)
     cargs = mkheadsurf_cargs(params, execution)
     ret = mkheadsurf_outputs(params, execution)
@@ -408,8 +411,10 @@ def mkheadsurf(
     runner: Runner | None = None,
 ) -> MkheadsurfOutputs:
     """
-    Segment and create a surface representation of the head for visualization and
-    further processing.
+    mkheadsurf
+    
+    Segment and create a surface representation of the head for visualization
+    and further processing.
     
     Author: FreeSurfer Developers
     
@@ -448,8 +453,6 @@ def mkheadsurf(
     Returns:
         NamedTuple of outputs (described in `MkheadsurfOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MKHEADSURF_METADATA)
     params = mkheadsurf_params(
         input_vol=input_vol,
         output_vol=output_vol,
@@ -479,13 +482,13 @@ def mkheadsurf(
         umask=umask,
         logfile=logfile,
     )
-    return mkheadsurf_execute(params, execution)
+    return mkheadsurf_execute(params, runner)
 
 
 __all__ = [
     "MKHEADSURF_METADATA",
     "MkheadsurfOutputs",
-    "MkheadsurfParameters",
     "mkheadsurf",
+    "mkheadsurf_execute",
     "mkheadsurf_params",
 ]

niwrap_freesurfer/freesurfer/mkima_index_tcl.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MKIMA_INDEX_TCL_METADATA = Metadata(
-    id="d22dfd37da5b994e6395a605a77c2fb31a66cdd0.boutiques",
+    id="86be0aef995f956ba52b06d4b0b72917946939dd.boutiques",
     name="mkima_index.tcl",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ MKIMA_INDEX_TCL_METADATA = Metadata(
 
 
 MkimaIndexTclParameters = typing.TypedDict('MkimaIndexTclParameters', {
-    "__STYXTYPE__": typing.Literal["mkima_index.tcl"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mkima_index.tcl"]],
+    "input_file": InputPathType,
+    "output_flag": bool,
+})
+MkimaIndexTclParametersTagged = typing.TypedDict('MkimaIndexTclParametersTagged', {
+    "@type": typing.Literal["freesurfer/mkima_index.tcl"],
     "input_file": InputPathType,
     "output_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 {
-        "mkima_index.tcl": mkima_index_tcl_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 {
-        "mkima_index.tcl": mkima_index_tcl_outputs,
-    }.get(t)
 
 
 class MkimaIndexTclOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mkima_index_tcl(...)`.
+    Output object returned when calling `MkimaIndexTclParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class MkimaIndexTclOutputs(typing.NamedTuple):
 def mkima_index_tcl_params(
     input_file: InputPathType,
     output_flag: bool = False,
-) -> MkimaIndexTclParameters:
+) -> MkimaIndexTclParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def mkima_index_tcl_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mkima_index.tcl",
+        "@type": "freesurfer/mkima_index.tcl",
         "input_file": input_file,
         "output_flag": output_flag,
     }
@@ -98,8 +71,8 @@ def mkima_index_tcl_cargs(
     """
     cargs = []
     cargs.append("mkima_index.tcl")
-    cargs.append(execution.input_file(params.get("input_file")))
-    if params.get("output_flag"):
+    cargs.append(execution.input_file(params.get("input_file", None)))
+    if params.get("output_flag", False):
         cargs.append("-o")
     return cargs
 
@@ -119,16 +92,18 @@ def mkima_index_tcl_outputs(
     """
     ret = MkimaIndexTclOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(pathlib.Path(params.get("input_file")).name + "_index_output"),
+        output_file=execution.output_file(pathlib.Path(params.get("input_file", None)).name + "_index_output"),
     )
     return ret
 
 
 def mkima_index_tcl_execute(
     params: MkimaIndexTclParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MkimaIndexTclOutputs:
     """
+    mkima_index.tcl
+    
     A command-line tool for handling mkima index operations.
     
     Author: FreeSurfer Developers
@@ -137,10 +112,12 @@ def mkima_index_tcl_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MkimaIndexTclOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MKIMA_INDEX_TCL_METADATA)
     params = execution.params(params)
     cargs = mkima_index_tcl_cargs(params, execution)
     ret = mkima_index_tcl_outputs(params, execution)
@@ -154,6 +131,8 @@ def mkima_index_tcl(
     runner: Runner | None = None,
 ) -> MkimaIndexTclOutputs:
     """
+    mkima_index.tcl
+    
     A command-line tool for handling mkima index operations.
     
     Author: FreeSurfer Developers
@@ -167,19 +146,17 @@ def mkima_index_tcl(
     Returns:
         NamedTuple of outputs (described in `MkimaIndexTclOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MKIMA_INDEX_TCL_METADATA)
     params = mkima_index_tcl_params(
         input_file=input_file,
         output_flag=output_flag,
     )
-    return mkima_index_tcl_execute(params, execution)
+    return mkima_index_tcl_execute(params, runner)
 
 
 __all__ = [
     "MKIMA_INDEX_TCL_METADATA",
     "MkimaIndexTclOutputs",
-    "MkimaIndexTclParameters",
     "mkima_index_tcl",
+    "mkima_index_tcl_execute",
     "mkima_index_tcl_params",
 ]

niwrap_freesurfer/freesurfer/mkmnc_index_tcl.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MKMNC_INDEX_TCL_METADATA = Metadata(
-    id="39f69e657a2149c0bb1bf748e98c328cb84fde74.boutiques",
+    id="a3e1a6ec38b7ba691a9575b1adcc081ab15b3fda.boutiques",
     name="mkmnc_index.tcl",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ MKMNC_INDEX_TCL_METADATA = Metadata(
 
 
 MkmncIndexTclParameters = typing.TypedDict('MkmncIndexTclParameters', {
-    "__STYXTYPE__": typing.Literal["mkmnc_index.tcl"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mkmnc_index.tcl"]],
+    "infile": InputPathType,
+    "outfile": str,
+})
+MkmncIndexTclParametersTagged = typing.TypedDict('MkmncIndexTclParametersTagged', {
+    "@type": typing.Literal["freesurfer/mkmnc_index.tcl"],
     "infile": InputPathType,
     "outfile": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mkmnc_index.tcl": mkmnc_index_tcl_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 {
-        "mkmnc_index.tcl": mkmnc_index_tcl_outputs,
-    }.get(t)
 
 
 class MkmncIndexTclOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mkmnc_index_tcl(...)`.
+    Output object returned when calling `MkmncIndexTclParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class MkmncIndexTclOutputs(typing.NamedTuple):
 def mkmnc_index_tcl_params(
     infile: InputPathType,
     outfile: str,
-) -> MkmncIndexTclParameters:
+) -> MkmncIndexTclParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def mkmnc_index_tcl_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mkmnc_index.tcl",
+        "@type": "freesurfer/mkmnc_index.tcl",
         "infile": infile,
         "outfile": outfile,
     }
@@ -98,8 +71,8 @@ def mkmnc_index_tcl_cargs(
     """
     cargs = []
     cargs.append("mkmnc_index.tcl")
-    cargs.append(execution.input_file(params.get("infile")))
-    cargs.append(params.get("outfile"))
+    cargs.append(execution.input_file(params.get("infile", None)))
+    cargs.append(params.get("outfile", None))
     return cargs
 
 
@@ -118,16 +91,18 @@ def mkmnc_index_tcl_outputs(
     """
     ret = MkmncIndexTclOutputs(
         root=execution.output_file("."),
-        indexfile=execution.output_file(params.get("outfile")),
+        indexfile=execution.output_file(params.get("outfile", None)),
     )
     return ret
 
 
 def mkmnc_index_tcl_execute(
     params: MkmncIndexTclParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MkmncIndexTclOutputs:
     """
+    mkmnc_index.tcl
+    
     A tool for creating MINC indices.
     
     Author: FreeSurfer Developers
@@ -136,10 +111,12 @@ def mkmnc_index_tcl_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MkmncIndexTclOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MKMNC_INDEX_TCL_METADATA)
     params = execution.params(params)
     cargs = mkmnc_index_tcl_cargs(params, execution)
     ret = mkmnc_index_tcl_outputs(params, execution)
@@ -153,6 +130,8 @@ def mkmnc_index_tcl(
     runner: Runner | None = None,
 ) -> MkmncIndexTclOutputs:
     """
+    mkmnc_index.tcl
+    
     A tool for creating MINC indices.
     
     Author: FreeSurfer Developers
@@ -166,19 +145,17 @@ def mkmnc_index_tcl(
     Returns:
         NamedTuple of outputs (described in `MkmncIndexTclOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MKMNC_INDEX_TCL_METADATA)
     params = mkmnc_index_tcl_params(
         infile=infile,
         outfile=outfile,
     )
-    return mkmnc_index_tcl_execute(params, execution)
+    return mkmnc_index_tcl_execute(params, runner)
 
 
 __all__ = [
     "MKMNC_INDEX_TCL_METADATA",
     "MkmncIndexTclOutputs",
-    "MkmncIndexTclParameters",
     "mkmnc_index_tcl",
+    "mkmnc_index_tcl_execute",
     "mkmnc_index_tcl_params",
 ]