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

niwrap_afni/afni/v_3drefit.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DREFIT_METADATA = Metadata(
-    id="3f540f91056434ebd87b76f91b70964cf1dec091.boutiques",
+    id="1b32a8e5d836e884c437e83b1af640f8bc0937f0.boutiques",
     name="3drefit",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,27 @@ V_3DREFIT_METADATA = Metadata(
 
 
 V3drefitParameters = typing.TypedDict('V3drefitParameters', {
-    "__STYXTYPE__": typing.Literal["3drefit"],
+    "@type": typing.NotRequired[typing.Literal["afni/3drefit"]],
+    "atrcopy": typing.NotRequired[list[str] | None],
+    "atrfloat": typing.NotRequired[list[str] | None],
+    "atrint": typing.NotRequired[list[str] | None],
+    "atrstring": typing.NotRequired[list[str] | None],
+    "deoblique": bool,
+    "duporigin_file": typing.NotRequired[InputPathType | None],
+    "in_file": InputPathType,
+    "nosaveatr": bool,
+    "saveatr": bool,
+    "space": typing.NotRequired[typing.Literal["TLRC", "MNI", "ORIG"] | None],
+    "xdel": typing.NotRequired[float | None],
+    "xorigin": typing.NotRequired[str | None],
+    "xyzscale": typing.NotRequired[float | None],
+    "ydel": typing.NotRequired[float | None],
+    "yorigin": typing.NotRequired[str | None],
+    "zdel": typing.NotRequired[float | None],
+    "zorigin": typing.NotRequired[str | None],
+})
+V3drefitParametersTagged = typing.TypedDict('V3drefitParametersTagged', {
+    "@type": typing.Literal["afni/3drefit"],
     "atrcopy": typing.NotRequired[list[str] | None],
     "atrfloat": typing.NotRequired[list[str] | None],
     "atrint": typing.NotRequired[list[str] | None],
@@ -33,43 +53,11 @@ V3drefitParameters = typing.TypedDict('V3drefitParameters', {
     "zdel": typing.NotRequired[float | None],
     "zorigin": 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 {
-        "3drefit": v_3drefit_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 {
-        "3drefit": v_3drefit_outputs,
-    }.get(t)
 
 
 class V3drefitOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3drefit(...)`.
+    Output object returned when calling `V3drefitParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -95,7 +83,7 @@ def v_3drefit_params(
     yorigin: str | None = None,
     zdel: float | None = None,
     zorigin: str | None = None,
-) -> V3drefitParameters:
+) -> V3drefitParametersTagged:
     """
     Build parameters.
     
@@ -138,7 +126,7 @@ def v_3drefit_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3drefit",
+        "@type": "afni/3drefit",
         "deoblique": deoblique,
         "in_file": in_file,
         "nosaveatr": nosaveatr,
@@ -188,77 +176,77 @@ def v_3drefit_cargs(
     """
     cargs = []
     cargs.append("3drefit")
-    if params.get("atrcopy") is not None:
+    if params.get("atrcopy", None) is not None:
         cargs.extend([
             "-atrcopy",
-            *params.get("atrcopy")
+            *params.get("atrcopy", None)
         ])
-    if params.get("atrfloat") is not None:
+    if params.get("atrfloat", None) is not None:
         cargs.extend([
             "-atrfloat",
-            *params.get("atrfloat")
+            *params.get("atrfloat", None)
         ])
-    if params.get("atrint") is not None:
+    if params.get("atrint", None) is not None:
         cargs.extend([
             "-atrint",
-            *params.get("atrint")
+            *params.get("atrint", None)
         ])
-    if params.get("atrstring") is not None:
+    if params.get("atrstring", None) is not None:
         cargs.extend([
             "-atrstring",
-            *params.get("atrstring")
+            *params.get("atrstring", None)
         ])
-    if params.get("deoblique"):
+    if params.get("deoblique", False):
         cargs.append("-deoblique")
-    if params.get("duporigin_file") is not None:
+    if params.get("duporigin_file", None) is not None:
         cargs.extend([
             "-duporigin",
-            execution.input_file(params.get("duporigin_file"))
+            execution.input_file(params.get("duporigin_file", None))
         ])
-    cargs.append(execution.input_file(params.get("in_file"), mutable=True))
-    if params.get("nosaveatr"):
+    cargs.append(execution.input_file(params.get("in_file", None), mutable=True))
+    if params.get("nosaveatr", False):
         cargs.append("-nosaveatr")
-    if params.get("saveatr"):
+    if params.get("saveatr", False):
         cargs.append("-saveatr")
-    if params.get("space") is not None:
+    if params.get("space", None) is not None:
         cargs.extend([
             "-space",
-            params.get("space")
+            params.get("space", None)
         ])
-    if params.get("xdel") is not None:
+    if params.get("xdel", None) is not None:
         cargs.extend([
             "-xdel",
-            str(params.get("xdel"))
+            str(params.get("xdel", None))
         ])
-    if params.get("xorigin") is not None:
+    if params.get("xorigin", None) is not None:
         cargs.extend([
             "-xorigin",
-            params.get("xorigin")
+            params.get("xorigin", None)
         ])
-    if params.get("xyzscale") is not None:
+    if params.get("xyzscale", None) is not None:
         cargs.extend([
             "-xyzscale",
-            str(params.get("xyzscale"))
+            str(params.get("xyzscale", None))
         ])
-    if params.get("ydel") is not None:
+    if params.get("ydel", None) is not None:
         cargs.extend([
             "-ydel",
-            str(params.get("ydel"))
+            str(params.get("ydel", None))
         ])
-    if params.get("yorigin") is not None:
+    if params.get("yorigin", None) is not None:
         cargs.extend([
             "-yorigin",
-            params.get("yorigin")
+            params.get("yorigin", None)
         ])
-    if params.get("zdel") is not None:
+    if params.get("zdel", None) is not None:
         cargs.extend([
             "-zdel",
-            str(params.get("zdel"))
+            str(params.get("zdel", None))
         ])
-    if params.get("zorigin") is not None:
+    if params.get("zorigin", None) is not None:
         cargs.extend([
             "-zorigin",
-            params.get("zorigin")
+            params.get("zorigin", None)
         ])
     return cargs
 
@@ -285,9 +273,11 @@ def v_3drefit_outputs(
 
 def v_3drefit_execute(
     params: V3drefitParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3drefitOutputs:
     """
+    3drefit
+    
     Changes some of the information inside a 3D dataset's header.
     
     Author: AFNI Developers
@@ -296,10 +286,12 @@ def v_3drefit_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3drefitOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DREFIT_METADATA)
     params = execution.params(params)
     cargs = v_3drefit_cargs(params, execution)
     ret = v_3drefit_outputs(params, execution)
@@ -328,6 +320,8 @@ def v_3drefit(
     runner: Runner | None = None,
 ) -> V3drefitOutputs:
     """
+    3drefit
+    
     Changes some of the information inside a 3D dataset's header.
     
     Author: AFNI Developers
@@ -373,8 +367,6 @@ def v_3drefit(
     Returns:
         NamedTuple of outputs (described in `V3drefitOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DREFIT_METADATA)
     params = v_3drefit_params(
         atrcopy=atrcopy,
         atrfloat=atrfloat,
@@ -394,13 +386,13 @@ def v_3drefit(
         zdel=zdel,
         zorigin=zorigin,
     )
-    return v_3drefit_execute(params, execution)
+    return v_3drefit_execute(params, runner)
 
 
 __all__ = [
     "V3drefitOutputs",
-    "V3drefitParameters",
     "V_3DREFIT_METADATA",
     "v_3drefit",
+    "v_3drefit_execute",
     "v_3drefit_params",
 ]

niwrap_afni/afni/v_3drename.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DRENAME_METADATA = Metadata(
-    id="3c508d8f5e6d69689dd267857ef13efbf3693249.boutiques",
+    id="eeef400f9b4b64ede0cc383d564700f2178aa410.boutiques",
     name="3drename",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,46 +14,20 @@ V_3DRENAME_METADATA = Metadata(
 
 
 V3drenameParameters = typing.TypedDict('V3drenameParameters', {
-    "__STYXTYPE__": typing.Literal["3drename"],
+    "@type": typing.NotRequired[typing.Literal["afni/3drename"]],
+    "old_prefix": str,
+    "new_prefix": str,
+})
+V3drenameParametersTagged = typing.TypedDict('V3drenameParametersTagged', {
+    "@type": typing.Literal["afni/3drename"],
     "old_prefix": str,
     "new_prefix": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3drename": v_3drename_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 V3drenameOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3drename(...)`.
+    Output object returned when calling `V3drenameParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -62,7 +36,7 @@ class V3drenameOutputs(typing.NamedTuple):
 def v_3drename_params(
     old_prefix: str,
     new_prefix: str,
-) -> V3drenameParameters:
+) -> V3drenameParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +47,7 @@ def v_3drename_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3drename",
+        "@type": "afni/3drename",
         "old_prefix": old_prefix,
         "new_prefix": new_prefix,
     }
@@ -95,8 +69,8 @@ def v_3drename_cargs(
     """
     cargs = []
     cargs.append("3drename")
-    cargs.append(params.get("old_prefix"))
-    cargs.append(params.get("new_prefix"))
+    cargs.append(params.get("old_prefix", None))
+    cargs.append(params.get("new_prefix", None))
     return cargs
 
 
@@ -121,9 +95,11 @@ def v_3drename_outputs(
 
 def v_3drename_execute(
     params: V3drenameParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3drenameOutputs:
     """
+    3drename
+    
     Tool to rename AFNI datasets by changing the dataset prefix.
     
     Author: AFNI Developers
@@ -132,10 +108,12 @@ def v_3drename_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3drenameOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DRENAME_METADATA)
     params = execution.params(params)
     cargs = v_3drename_cargs(params, execution)
     ret = v_3drename_outputs(params, execution)
@@ -149,6 +127,8 @@ def v_3drename(
     runner: Runner | None = None,
 ) -> V3drenameOutputs:
     """
+    3drename
+    
     Tool to rename AFNI datasets by changing the dataset prefix.
     
     Author: AFNI Developers
@@ -162,19 +142,17 @@ def v_3drename(
     Returns:
         NamedTuple of outputs (described in `V3drenameOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DRENAME_METADATA)
     params = v_3drename_params(
         old_prefix=old_prefix,
         new_prefix=new_prefix,
     )
-    return v_3drename_execute(params, execution)
+    return v_3drename_execute(params, runner)
 
 
 __all__ = [
     "V3drenameOutputs",
-    "V3drenameParameters",
     "V_3DRENAME_METADATA",
     "v_3drename",
+    "v_3drename_execute",
     "v_3drename_params",
 ]

niwrap_afni/afni/v_3dresample.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DRESAMPLE_METADATA = Metadata(
-    id="c0aa0fa9560446a135dad492fcfd16c35e59d09a.boutiques",
+    id="8a3913d033c0e71a4bd6f9bad072454f5fd37c5b.boutiques",
     name="3dresample",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,17 @@ V_3DRESAMPLE_METADATA = Metadata(
 
 
 V3dresampleParameters = typing.TypedDict('V3dresampleParameters', {
-    "__STYXTYPE__": typing.Literal["3dresample"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dresample"]],
+    "in_file": InputPathType,
+    "master": typing.NotRequired[InputPathType | None],
+    "orientation": typing.NotRequired[typing.Literal["AIL", "AIR", "ASL", "ASR", "PIL", "PIR", "PSL", "PSR", "ALI", "ALS", "ARI", "ARS", "PLI", "PLS", "PRI", "PRS", "IAL", "IAR", "IPL", "IPR", "SAL", "SAR", "SPL", "SPR", "ILA", "ILP", "IRA", "IRP", "SLA", "SLP", "SRA", "SRP", "LAI", "LAS", "LPI", "LPS", "RAI", "RAS", "RPI", "RPS", "LIA", "LIP", "LSA", "LSP", "RIA", "RIP", "RSA", "RSP"] | None],
+    "prefix": str,
+    "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
+    "resample_mode": typing.NotRequired[typing.Literal["NN", "Li", "Cu", "Bk"] | None],
+    "voxel_size": typing.NotRequired[list[float] | None],
+})
+V3dresampleParametersTagged = typing.TypedDict('V3dresampleParametersTagged', {
+    "@type": typing.Literal["afni/3dresample"],
     "in_file": InputPathType,
     "master": typing.NotRequired[InputPathType | None],
     "orientation": typing.NotRequired[typing.Literal["AIL", "AIR", "ASL", "ASR", "PIL", "PIR", "PSL", "PSR", "ALI", "ALS", "ARI", "ARS", "PLI", "PLS", "PRI", "PRS", "IAL", "IAR", "IPL", "IPR", "SAL", "SAR", "SPL", "SPR", "ILA", "ILP", "IRA", "IRP", "SLA", "SLP", "SRA", "SRP", "LAI", "LAS", "LPI", "LPS", "RAI", "RAS", "RPI", "RPS", "LIA", "LIP", "LSA", "LSP", "RIA", "RIP", "RSA", "RSP"] | None],
@@ -23,43 +33,11 @@ V3dresampleParameters = typing.TypedDict('V3dresampleParameters', {
     "resample_mode": typing.NotRequired[typing.Literal["NN", "Li", "Cu", "Bk"] | None],
     "voxel_size": typing.NotRequired[list[float] | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dresample": v_3dresample_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 {
-        "3dresample": v_3dresample_outputs,
-    }.get(t)
 
 
 class V3dresampleOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3dresample(...)`.
+    Output object returned when calling `V3dresampleParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +53,7 @@ def v_3dresample_params(
     outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
     resample_mode: typing.Literal["NN", "Li", "Cu", "Bk"] | None = None,
     voxel_size: list[float] | None = None,
-) -> V3dresampleParameters:
+) -> V3dresampleParametersTagged:
     """
     Build parameters.
     
@@ -93,7 +71,7 @@ def v_3dresample_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dresample",
+        "@type": "afni/3dresample",
         "in_file": in_file,
         "prefix": prefix,
     }
@@ -127,33 +105,33 @@ def v_3dresample_cargs(
     cargs.append("3dresample")
     cargs.extend([
         "-inset",
-        execution.input_file(params.get("in_file"))
+        execution.input_file(params.get("in_file", None))
     ])
-    if params.get("master") is not None:
+    if params.get("master", None) is not None:
         cargs.extend([
             "-master",
-            execution.input_file(params.get("master"))
+            execution.input_file(params.get("master", None))
         ])
-    if params.get("orientation") is not None:
+    if params.get("orientation", None) is not None:
         cargs.extend([
             "-orient",
-            params.get("orientation")
+            params.get("orientation", None)
         ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("outputtype") is not None:
-        cargs.append(params.get("outputtype"))
-    if params.get("resample_mode") is not None:
+    if params.get("outputtype", None) is not None:
+        cargs.append(params.get("outputtype", None))
+    if params.get("resample_mode", None) is not None:
         cargs.extend([
             "-rmode",
-            params.get("resample_mode")
+            params.get("resample_mode", None)
         ])
-    if params.get("voxel_size") is not None:
+    if params.get("voxel_size", None) is not None:
         cargs.extend([
             "-dxyz",
-            *map(str, params.get("voxel_size"))
+            *map(str, params.get("voxel_size", None))
         ])
     return cargs
 
@@ -173,16 +151,18 @@ def v_3dresample_outputs(
     """
     ret = V3dresampleOutputs(
         root=execution.output_file("."),
-        out_file=execution.output_file(params.get("prefix")),
+        out_file=execution.output_file(params.get("prefix", None)),
     )
     return ret
 
 
 def v_3dresample_execute(
     params: V3dresampleParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dresampleOutputs:
     """
+    3dresample
+    
     Resample or reorient an image using AFNI 3dresample command.
     
     Author: AFNI Developers
@@ -191,10 +171,12 @@ def v_3dresample_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dresampleOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DRESAMPLE_METADATA)
     params = execution.params(params)
     cargs = v_3dresample_cargs(params, execution)
     ret = v_3dresample_outputs(params, execution)
@@ -213,6 +195,8 @@ def v_3dresample(
     runner: Runner | None = None,
 ) -> V3dresampleOutputs:
     """
+    3dresample
+    
     Resample or reorient an image using AFNI 3dresample command.
     
     Author: AFNI Developers
@@ -233,8 +217,6 @@ def v_3dresample(
     Returns:
         NamedTuple of outputs (described in `V3dresampleOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DRESAMPLE_METADATA)
     params = v_3dresample_params(
         in_file=in_file,
         master=master,
@@ -244,13 +226,13 @@ def v_3dresample(
         resample_mode=resample_mode,
         voxel_size=voxel_size,
     )
-    return v_3dresample_execute(params, execution)
+    return v_3dresample_execute(params, runner)
 
 
 __all__ = [
     "V3dresampleOutputs",
-    "V3dresampleParameters",
     "V_3DRESAMPLE_METADATA",
     "v_3dresample",
+    "v_3dresample_execute",
     "v_3dresample_params",
 ]