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

niwrap_freesurfer/freesurfer/fspalm.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FSPALM_METADATA = Metadata(
-    id="6423174c0a141ab40ff807e3980bfa4f3ce57b18.boutiques",
+    id="cf8e3d88104ed079f77f6b32ec9e15dfe608166a.boutiques",
     name="fspalm",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,24 @@ FSPALM_METADATA = Metadata(
 
 
 FspalmParameters = typing.TypedDict('FspalmParameters', {
-    "__STYXTYPE__": typing.Literal["fspalm"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fspalm"]],
+    "glmdir": str,
+    "cft": float,
+    "cwp": float,
+    "onetail": bool,
+    "twotail": bool,
+    "name": typing.NotRequired[str | None],
+    "iters": typing.NotRequired[float | None],
+    "monly": bool,
+    "pponly": bool,
+    "octave": bool,
+    "centroid": bool,
+    "2spaces": bool,
+    "3spaces": bool,
+    "pargs": typing.NotRequired[str | None],
+})
+FspalmParametersTagged = typing.TypedDict('FspalmParametersTagged', {
+    "@type": typing.Literal["freesurfer/fspalm"],
     "glmdir": str,
     "cft": float,
     "cwp": float,
@@ -30,42 +47,11 @@ FspalmParameters = typing.TypedDict('FspalmParameters', {
     "3spaces": bool,
     "pargs": 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 {
-        "fspalm": fspalm_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 FspalmOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fspalm(...)`.
+    Output object returned when calling `FspalmParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -86,7 +72,7 @@ def fspalm_params(
     v_2spaces: bool = False,
     v_3spaces: bool = False,
     pargs: str | None = None,
-) -> FspalmParameters:
+) -> FspalmParametersTagged:
     """
     Build parameters.
     
@@ -109,7 +95,7 @@ def fspalm_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fspalm",
+        "@type": "freesurfer/fspalm",
         "glmdir": glmdir,
         "cft": cft,
         "cwp": cwp,
@@ -148,46 +134,46 @@ def fspalm_cargs(
     cargs.append("fspalm")
     cargs.extend([
         "--glmdir",
-        params.get("glmdir")
+        params.get("glmdir", None)
     ])
     cargs.extend([
         "--cft",
-        str(params.get("cft"))
+        str(params.get("cft", None))
     ])
     cargs.extend([
         "--cwp",
-        str(params.get("cwp"))
+        str(params.get("cwp", None))
     ])
-    if params.get("onetail"):
+    if params.get("onetail", False):
         cargs.append("--onetail")
-    if params.get("twotail"):
+    if params.get("twotail", False):
         cargs.append("--twotail")
-    if params.get("name") is not None:
+    if params.get("name", None) is not None:
         cargs.extend([
             "--name",
-            params.get("name")
+            params.get("name", None)
         ])
-    if params.get("iters") is not None:
+    if params.get("iters", None) is not None:
         cargs.extend([
             "--iters",
-            str(params.get("iters"))
+            str(params.get("iters", None))
         ])
-    if params.get("monly"):
+    if params.get("monly", False):
         cargs.append("--monly")
-    if params.get("pponly"):
+    if params.get("pponly", False):
         cargs.append("--pponly")
-    if params.get("octave"):
+    if params.get("octave", False):
         cargs.append("--octave")
-    if params.get("centroid"):
+    if params.get("centroid", False):
         cargs.append("--centroid")
-    if params.get("2spaces"):
+    if params.get("2spaces", False):
         cargs.append("--2spaces")
-    if params.get("3spaces"):
+    if params.get("3spaces", False):
         cargs.append("--3spaces")
-    if params.get("pargs") is not None:
+    if params.get("pargs", None) is not None:
         cargs.extend([
             "--pargs",
-            params.get("pargs")
+            params.get("pargs", None)
         ])
     return cargs
 
@@ -213,9 +199,11 @@ def fspalm_outputs(
 
 def fspalm_execute(
     params: FspalmParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FspalmOutputs:
     """
+    fspalm
+    
     Prepares and analyzes the output of mri_glmfit for Permutation Analysis of
     Linear Models (PALM) to correct for multiple comparisons.
     
@@ -225,10 +213,12 @@ def fspalm_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FspalmOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FSPALM_METADATA)
     params = execution.params(params)
     cargs = fspalm_cargs(params, execution)
     ret = fspalm_outputs(params, execution)
@@ -254,6 +244,8 @@ def fspalm(
     runner: Runner | None = None,
 ) -> FspalmOutputs:
     """
+    fspalm
+    
     Prepares and analyzes the output of mri_glmfit for Permutation Analysis of
     Linear Models (PALM) to correct for multiple comparisons.
     
@@ -280,8 +272,6 @@ def fspalm(
     Returns:
         NamedTuple of outputs (described in `FspalmOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FSPALM_METADATA)
     params = fspalm_params(
         glmdir=glmdir,
         cft=cft,
@@ -298,13 +288,13 @@ def fspalm(
         v_3spaces=v_3spaces,
         pargs=pargs,
     )
-    return fspalm_execute(params, execution)
+    return fspalm_execute(params, runner)
 
 
 __all__ = [
     "FSPALM_METADATA",
     "FspalmOutputs",
-    "FspalmParameters",
     "fspalm",
+    "fspalm_execute",
     "fspalm_params",
 ]

niwrap_freesurfer/freesurfer/fsr_coreg.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FSR_COREG_METADATA = Metadata(
-    id="b6136f2ba4c2e2f78f88acaab07f5da54d1d4acf.boutiques",
+    id="68ee39ecf693d112ce9b553262afcc9d6d2b5b02.boutiques",
     name="fsr-coreg",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ FSR_COREG_METADATA = Metadata(
 
 
 FsrCoregParameters = typing.TypedDict('FsrCoregParameters', {
-    "__STYXTYPE__": typing.Literal["fsr-coreg"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fsr-coreg"]],
+    "import_dir": str,
+    "reference_mode": str,
+    "num_threads": typing.NotRequired[float | None],
+    "force_update": bool,
+    "output_dir": typing.NotRequired[str | None],
+    "expert_options": typing.NotRequired[InputPathType | None],
+})
+FsrCoregParametersTagged = typing.TypedDict('FsrCoregParametersTagged', {
+    "@type": typing.Literal["freesurfer/fsr-coreg"],
     "import_dir": str,
     "reference_mode": str,
     "num_threads": typing.NotRequired[float | None],
@@ -22,43 +31,11 @@ FsrCoregParameters = typing.TypedDict('FsrCoregParameters', {
     "output_dir": typing.NotRequired[str | None],
     "expert_options": 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 {
-        "fsr-coreg": fsr_coreg_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 {
-        "fsr-coreg": fsr_coreg_outputs,
-    }.get(t)
 
 
 class FsrCoregOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fsr_coreg(...)`.
+    Output object returned when calling `FsrCoregParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +52,7 @@ def fsr_coreg_params(
     force_update: bool = False,
     output_dir: str | None = None,
     expert_options: InputPathType | None = None,
-) -> FsrCoregParameters:
+) -> FsrCoregParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +68,7 @@ def fsr_coreg_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fsr-coreg",
+        "@type": "freesurfer/fsr-coreg",
         "import_dir": import_dir,
         "reference_mode": reference_mode,
         "force_update": force_update,
@@ -122,28 +99,28 @@ def fsr_coreg_cargs(
     cargs.append("fsr-coreg")
     cargs.extend([
         "--i",
-        params.get("import_dir")
+        params.get("import_dir", None)
     ])
     cargs.extend([
         "--ref",
-        params.get("reference_mode")
+        params.get("reference_mode", None)
     ])
-    if params.get("num_threads") is not None:
+    if params.get("num_threads", None) is not None:
         cargs.extend([
             "--threads",
-            str(params.get("num_threads"))
+            str(params.get("num_threads", None))
         ])
-    if params.get("force_update"):
+    if params.get("force_update", False):
         cargs.append("--force-update")
-    if params.get("output_dir") is not None:
+    if params.get("output_dir", None) is not None:
         cargs.extend([
             "--o",
-            params.get("output_dir")
+            params.get("output_dir", None)
         ])
-    if params.get("expert_options") is not None:
+    if params.get("expert_options", None) is not None:
         cargs.extend([
             "--expert",
-            execution.input_file(params.get("expert_options"))
+            execution.input_file(params.get("expert_options", None))
         ])
     return cargs
 
@@ -163,17 +140,19 @@ def fsr_coreg_outputs(
     """
     ret = FsrCoregOutputs(
         root=execution.output_file("."),
-        aligned_volume=execution.output_file(params.get("output_dir") + "/mode.mgz") if (params.get("output_dir") is not None) else None,
-        registration_transform=execution.output_file(params.get("output_dir") + "/mode.reg-to-ref.lta") if (params.get("output_dir") is not None) else None,
+        aligned_volume=execution.output_file(params.get("output_dir", None) + "/mode.mgz") if (params.get("output_dir") is not None) else None,
+        registration_transform=execution.output_file(params.get("output_dir", None) + "/mode.reg-to-ref.lta") if (params.get("output_dir") is not None) else None,
     )
     return ret
 
 
 def fsr_coreg_execute(
     params: FsrCoregParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FsrCoregOutputs:
     """
+    fsr-coreg
+    
     Co-registers input data in preparation for FreeSurfer analysis.
     
     Author: FreeSurfer Developers
@@ -182,10 +161,12 @@ def fsr_coreg_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FsrCoregOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FSR_COREG_METADATA)
     params = execution.params(params)
     cargs = fsr_coreg_cargs(params, execution)
     ret = fsr_coreg_outputs(params, execution)
@@ -203,6 +184,8 @@ def fsr_coreg(
     runner: Runner | None = None,
 ) -> FsrCoregOutputs:
     """
+    fsr-coreg
+    
     Co-registers input data in preparation for FreeSurfer analysis.
     
     Author: FreeSurfer Developers
@@ -221,8 +204,6 @@ def fsr_coreg(
     Returns:
         NamedTuple of outputs (described in `FsrCoregOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FSR_COREG_METADATA)
     params = fsr_coreg_params(
         import_dir=import_dir,
         reference_mode=reference_mode,
@@ -231,13 +212,13 @@ def fsr_coreg(
         output_dir=output_dir,
         expert_options=expert_options,
     )
-    return fsr_coreg_execute(params, execution)
+    return fsr_coreg_execute(params, runner)
 
 
 __all__ = [
     "FSR_COREG_METADATA",
     "FsrCoregOutputs",
-    "FsrCoregParameters",
     "fsr_coreg",
+    "fsr_coreg_execute",
     "fsr_coreg_params",
 ]

niwrap_freesurfer/freesurfer/fsr_getxopts.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FSR_GETXOPTS_METADATA = Metadata(
-    id="6f917a3a241b51bdf055cbebf239e7fdeaf6d675.boutiques",
+    id="99d8c486b8e278b01e051129f89738f615f5b4b0.boutiques",
     name="fsr-getxopts",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ FSR_GETXOPTS_METADATA = Metadata(
 
 
 FsrGetxoptsParameters = typing.TypedDict('FsrGetxoptsParameters', {
-    "__STYXTYPE__": typing.Literal["fsr-getxopts"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fsr-getxopts"]],
+    "help": bool,
+})
+FsrGetxoptsParametersTagged = typing.TypedDict('FsrGetxoptsParametersTagged', {
+    "@type": typing.Literal["freesurfer/fsr-getxopts"],
     "help": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fsr-getxopts": fsr_getxopts_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 FsrGetxoptsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fsr_getxopts(...)`.
+    Output object returned when calling `FsrGetxoptsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class FsrGetxoptsOutputs(typing.NamedTuple):
 
 def fsr_getxopts_params(
     help_: bool = False,
-) -> FsrGetxoptsParameters:
+) -> FsrGetxoptsParametersTagged:
     """
     Build parameters.
     
@@ -70,7 +43,7 @@ def fsr_getxopts_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fsr-getxopts",
+        "@type": "freesurfer/fsr-getxopts",
         "help": help_,
     }
     return params
@@ -91,7 +64,7 @@ def fsr_getxopts_cargs(
     """
     cargs = []
     cargs.append("fsr-getxopts")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("--help")
     return cargs
 
@@ -117,9 +90,11 @@ def fsr_getxopts_outputs(
 
 def fsr_getxopts_execute(
     params: FsrGetxoptsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FsrGetxoptsOutputs:
     """
+    fsr-getxopts
+    
     Tool to retrieve extended options for a specific context or configuration.
     
     Author: FreeSurfer Developers
@@ -128,10 +103,12 @@ def fsr_getxopts_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FsrGetxoptsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FSR_GETXOPTS_METADATA)
     params = execution.params(params)
     cargs = fsr_getxopts_cargs(params, execution)
     ret = fsr_getxopts_outputs(params, execution)
@@ -144,6 +121,8 @@ def fsr_getxopts(
     runner: Runner | None = None,
 ) -> FsrGetxoptsOutputs:
     """
+    fsr-getxopts
+    
     Tool to retrieve extended options for a specific context or configuration.
     
     Author: FreeSurfer Developers
@@ -156,18 +135,16 @@ def fsr_getxopts(
     Returns:
         NamedTuple of outputs (described in `FsrGetxoptsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FSR_GETXOPTS_METADATA)
     params = fsr_getxopts_params(
         help_=help_,
     )
-    return fsr_getxopts_execute(params, execution)
+    return fsr_getxopts_execute(params, runner)
 
 
 __all__ = [
     "FSR_GETXOPTS_METADATA",
     "FsrGetxoptsOutputs",
-    "FsrGetxoptsParameters",
     "fsr_getxopts",
+    "fsr_getxopts_execute",
     "fsr_getxopts_params",
 ]