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

niwrap_afni/afni/v_3d_afnito3_d.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_AFNITO3_D_METADATA = Metadata(
-    id="f3d62c030e84253c6f88c8840150b3d8b1429f7e.boutiques",
+    id="a3feeeaeb8207dce6a8840c782ee3145d385033f.boutiques",
     name="3dAFNIto3D",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,49 +14,24 @@ V_3D_AFNITO3_D_METADATA = Metadata(
 
 
 V3dAfnito3DParameters = typing.TypedDict('V3dAfnito3DParameters', {
-    "__STYXTYPE__": typing.Literal["3dAFNIto3D"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dAFNIto3D"]],
+    "dataset": InputPathType,
+    "prefix": typing.NotRequired[str | None],
+    "binary": bool,
+    "text": bool,
+})
+V3dAfnito3DParametersTagged = typing.TypedDict('V3dAfnito3DParametersTagged', {
+    "@type": typing.Literal["afni/3dAFNIto3D"],
     "dataset": InputPathType,
     "prefix": typing.NotRequired[str | None],
     "binary": bool,
     "text": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dAFNIto3D": v_3d_afnito3_d_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 {
-        "3dAFNIto3D": v_3d_afnito3_d_outputs,
-    }.get(t)
 
 
 class V3dAfnito3DOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_afnito3_d(...)`.
+    Output object returned when calling `V3dAfnito3DParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def v_3d_afnito3_d_params(
     prefix: str | None = None,
     binary: bool = False,
     text: bool = False,
-) -> V3dAfnito3DParameters:
+) -> V3dAfnito3DParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +57,7 @@ def v_3d_afnito3_d_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dAFNIto3D",
+        "@type": "afni/3dAFNIto3D",
         "dataset": dataset,
         "binary": binary,
         "text": text,
@@ -107,15 +82,15 @@ def v_3d_afnito3_d_cargs(
     """
     cargs = []
     cargs.append("3dAFNIto3D")
-    cargs.append(execution.input_file(params.get("dataset")))
-    if params.get("prefix") is not None:
+    cargs.append(execution.input_file(params.get("dataset", None)))
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("prefix")
+            params.get("prefix", None)
         ])
-    if params.get("binary"):
+    if params.get("binary", False):
         cargs.append("-bin")
-    if params.get("text"):
+    if params.get("text", False):
         cargs.append("-txt")
     return cargs
 
@@ -135,16 +110,18 @@ def v_3d_afnito3_d_outputs(
     """
     ret = V3dAfnito3DOutputs(
         root=execution.output_file("."),
-        outfile=execution.output_file(params.get("prefix") + ".3D") if (params.get("prefix") is not None) else None,
+        outfile=execution.output_file(params.get("prefix", None) + ".3D") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_afnito3_d_execute(
     params: V3dAfnito3DParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dAfnito3DOutputs:
     """
+    3dAFNIto3D
+    
     Reads in an AFNI dataset, and writes it out as a 3D file.
     
     Author: AFNI Developers
@@ -153,10 +130,12 @@ def v_3d_afnito3_d_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dAfnito3DOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_AFNITO3_D_METADATA)
     params = execution.params(params)
     cargs = v_3d_afnito3_d_cargs(params, execution)
     ret = v_3d_afnito3_d_outputs(params, execution)
@@ -172,6 +151,8 @@ def v_3d_afnito3_d(
     runner: Runner | None = None,
 ) -> V3dAfnito3DOutputs:
     """
+    3dAFNIto3D
+    
     Reads in an AFNI dataset, and writes it out as a 3D file.
     
     Author: AFNI Developers
@@ -187,21 +168,19 @@ def v_3d_afnito3_d(
     Returns:
         NamedTuple of outputs (described in `V3dAfnito3DOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_AFNITO3_D_METADATA)
     params = v_3d_afnito3_d_params(
         dataset=dataset,
         prefix=prefix,
         binary=binary,
         text=text,
     )
-    return v_3d_afnito3_d_execute(params, execution)
+    return v_3d_afnito3_d_execute(params, runner)
 
 
 __all__ = [
     "V3dAfnito3DOutputs",
-    "V3dAfnito3DParameters",
     "V_3D_AFNITO3_D_METADATA",
     "v_3d_afnito3_d",
+    "v_3d_afnito3_d_execute",
     "v_3d_afnito3_d_params",
 ]

niwrap_afni/afni/v_3d_afnito_analyze.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_AFNITO_ANALYZE_METADATA = Metadata(
-    id="548e038af121070312e4a78291d268ecc7822165.boutiques",
+    id="9b1a20e4e17df734ff8c36adb88c21b1c7cfb1bd.boutiques",
     name="3dAFNItoANALYZE",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,49 +14,24 @@ V_3D_AFNITO_ANALYZE_METADATA = Metadata(
 
 
 V3dAfnitoAnalyzeParameters = typing.TypedDict('V3dAfnitoAnalyzeParameters', {
-    "__STYXTYPE__": typing.Literal["3dAFNItoANALYZE"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dAFNItoANALYZE"]],
+    "4d_option": bool,
+    "orient_option": typing.NotRequired[str | None],
+    "output_name": str,
+    "afni_dataset": InputPathType,
+})
+V3dAfnitoAnalyzeParametersTagged = typing.TypedDict('V3dAfnitoAnalyzeParametersTagged', {
+    "@type": typing.Literal["afni/3dAFNItoANALYZE"],
     "4d_option": bool,
     "orient_option": typing.NotRequired[str | None],
     "output_name": str,
     "afni_dataset": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dAFNItoANALYZE": v_3d_afnito_analyze_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 {
-        "3dAFNItoANALYZE": v_3d_afnito_analyze_outputs,
-    }.get(t)
 
 
 class V3dAfnitoAnalyzeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_afnito_analyze(...)`.
+    Output object returned when calling `V3dAfnitoAnalyzeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +50,7 @@ def v_3d_afnito_analyze_params(
     afni_dataset: InputPathType,
     v_4d_option: bool = False,
     orient_option: str | None = None,
-) -> V3dAfnitoAnalyzeParameters:
+) -> V3dAfnitoAnalyzeParametersTagged:
     """
     Build parameters.
     
@@ -90,7 +65,7 @@ def v_3d_afnito_analyze_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dAFNItoANALYZE",
+        "@type": "afni/3dAFNItoANALYZE",
         "4d_option": v_4d_option,
         "output_name": output_name,
         "afni_dataset": afni_dataset,
@@ -115,15 +90,15 @@ def v_3d_afnito_analyze_cargs(
     """
     cargs = []
     cargs.append("3dAFNItoANALYZE")
-    if params.get("4d_option"):
+    if params.get("4d_option", False):
         cargs.append("-4D")
-    if params.get("orient_option") is not None:
+    if params.get("orient_option", None) is not None:
         cargs.extend([
             "-orient",
-            params.get("orient_option")
+            params.get("orient_option", None)
         ])
-    cargs.append(params.get("output_name"))
-    cargs.append(execution.input_file(params.get("afni_dataset")))
+    cargs.append(params.get("output_name", None))
+    cargs.append(execution.input_file(params.get("afni_dataset", None)))
     return cargs
 
 
@@ -142,19 +117,21 @@ def v_3d_afnito_analyze_outputs(
     """
     ret = V3dAfnitoAnalyzeOutputs(
         root=execution.output_file("."),
-        output_hdr_file=execution.output_file(params.get("output_name") + "_[INDEX].hdr"),
-        output_img_file=execution.output_file(params.get("output_name") + "_[INDEX].img"),
-        output_4d_hdr_file=execution.output_file(params.get("output_name") + ".hdr"),
-        output_4d_img_file=execution.output_file(params.get("output_name") + ".img"),
+        output_hdr_file=execution.output_file(params.get("output_name", None) + "_[INDEX].hdr"),
+        output_img_file=execution.output_file(params.get("output_name", None) + "_[INDEX].img"),
+        output_4d_hdr_file=execution.output_file(params.get("output_name", None) + ".hdr"),
+        output_4d_img_file=execution.output_file(params.get("output_name", None) + ".img"),
     )
     return ret
 
 
 def v_3d_afnito_analyze_execute(
     params: V3dAfnitoAnalyzeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dAfnitoAnalyzeOutputs:
     """
+    3dAFNItoANALYZE
+    
     Writes AFNI dataset to ANALYZE 7.5 format .hdr/.img file pairs.
     
     Author: AFNI Developers
@@ -163,10 +140,12 @@ def v_3d_afnito_analyze_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dAfnitoAnalyzeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_AFNITO_ANALYZE_METADATA)
     params = execution.params(params)
     cargs = v_3d_afnito_analyze_cargs(params, execution)
     ret = v_3d_afnito_analyze_outputs(params, execution)
@@ -182,6 +161,8 @@ def v_3d_afnito_analyze(
     runner: Runner | None = None,
 ) -> V3dAfnitoAnalyzeOutputs:
     """
+    3dAFNItoANALYZE
+    
     Writes AFNI dataset to ANALYZE 7.5 format .hdr/.img file pairs.
     
     Author: AFNI Developers
@@ -199,21 +180,19 @@ def v_3d_afnito_analyze(
     Returns:
         NamedTuple of outputs (described in `V3dAfnitoAnalyzeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_AFNITO_ANALYZE_METADATA)
     params = v_3d_afnito_analyze_params(
         v_4d_option=v_4d_option,
         orient_option=orient_option,
         output_name=output_name,
         afni_dataset=afni_dataset,
     )
-    return v_3d_afnito_analyze_execute(params, execution)
+    return v_3d_afnito_analyze_execute(params, runner)
 
 
 __all__ = [
     "V3dAfnitoAnalyzeOutputs",
-    "V3dAfnitoAnalyzeParameters",
     "V_3D_AFNITO_ANALYZE_METADATA",
     "v_3d_afnito_analyze",
+    "v_3d_afnito_analyze_execute",
     "v_3d_afnito_analyze_params",
 ]

niwrap_afni/afni/v_3d_afnito_nifti.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_AFNITO_NIFTI_METADATA = Metadata(
-    id="b662117c7046300507a477f8a780feba9be8f57f.boutiques",
+    id="a7bea0118332764560ff63140180ab8a368e1655.boutiques",
     name="3dAFNItoNIFTI",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,18 @@ V_3D_AFNITO_NIFTI_METADATA = Metadata(
 
 
 V3dAfnitoNiftiParameters = typing.TypedDict('V3dAfnitoNiftiParameters', {
-    "__STYXTYPE__": typing.Literal["3dAFNItoNIFTI"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dAFNItoNIFTI"]],
+    "input_dataset": InputPathType,
+    "prefix": typing.NotRequired[str | None],
+    "verbose": bool,
+    "force_float": bool,
+    "pure": bool,
+    "denote": bool,
+    "oldid": bool,
+    "newid": bool,
+})
+V3dAfnitoNiftiParametersTagged = typing.TypedDict('V3dAfnitoNiftiParametersTagged', {
+    "@type": typing.Literal["afni/3dAFNItoNIFTI"],
     "input_dataset": InputPathType,
     "prefix": typing.NotRequired[str | None],
     "verbose": bool,
@@ -24,43 +35,11 @@ V3dAfnitoNiftiParameters = typing.TypedDict('V3dAfnitoNiftiParameters', {
     "oldid": bool,
     "newid": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dAFNItoNIFTI": v_3d_afnito_nifti_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 {
-        "3dAFNItoNIFTI": v_3d_afnito_nifti_outputs,
-    }.get(t)
 
 
 class V3dAfnitoNiftiOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_afnito_nifti(...)`.
+    Output object returned when calling `V3dAfnitoNiftiParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -77,7 +56,7 @@ def v_3d_afnito_nifti_params(
     denote: bool = False,
     oldid: bool = False,
     newid: bool = False,
-) -> V3dAfnitoNiftiParameters:
+) -> V3dAfnitoNiftiParametersTagged:
     """
     Build parameters.
     
@@ -95,7 +74,7 @@ def v_3d_afnito_nifti_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dAFNItoNIFTI",
+        "@type": "afni/3dAFNItoNIFTI",
         "input_dataset": input_dataset,
         "verbose": verbose,
         "force_float": force_float,
@@ -124,23 +103,23 @@ def v_3d_afnito_nifti_cargs(
     """
     cargs = []
     cargs.append("3dAFNItoNIFTI")
-    cargs.append(execution.input_file(params.get("input_dataset")))
-    if params.get("prefix") is not None:
+    cargs.append(execution.input_file(params.get("input_dataset", None)))
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("prefix")
+            params.get("prefix", None)
         ])
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-verb")
-    if params.get("force_float"):
+    if params.get("force_float", False):
         cargs.append("-float")
-    if params.get("pure"):
+    if params.get("pure", False):
         cargs.append("-pure")
-    if params.get("denote"):
+    if params.get("denote", False):
         cargs.append("-denote")
-    if params.get("oldid"):
+    if params.get("oldid", False):
         cargs.append("-oldid")
-    if params.get("newid"):
+    if params.get("newid", False):
         cargs.append("-newid")
     return cargs
 
@@ -160,16 +139,18 @@ def v_3d_afnito_nifti_outputs(
     """
     ret = V3dAfnitoNiftiOutputs(
         root=execution.output_file("."),
-        output_nifti=execution.output_file(params.get("prefix") + ".nii") if (params.get("prefix") is not None) else None,
+        output_nifti=execution.output_file(params.get("prefix", None) + ".nii") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_afnito_nifti_execute(
     params: V3dAfnitoNiftiParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dAfnitoNiftiOutputs:
     """
+    3dAFNItoNIFTI
+    
     Converts an AFNI dataset to a NIfTI-1.1 file.
     
     Author: AFNI Developers
@@ -178,10 +159,12 @@ def v_3d_afnito_nifti_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dAfnitoNiftiOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_AFNITO_NIFTI_METADATA)
     params = execution.params(params)
     cargs = v_3d_afnito_nifti_cargs(params, execution)
     ret = v_3d_afnito_nifti_outputs(params, execution)
@@ -201,6 +184,8 @@ def v_3d_afnito_nifti(
     runner: Runner | None = None,
 ) -> V3dAfnitoNiftiOutputs:
     """
+    3dAFNItoNIFTI
+    
     Converts an AFNI dataset to a NIfTI-1.1 file.
     
     Author: AFNI Developers
@@ -221,8 +206,6 @@ def v_3d_afnito_nifti(
     Returns:
         NamedTuple of outputs (described in `V3dAfnitoNiftiOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_AFNITO_NIFTI_METADATA)
     params = v_3d_afnito_nifti_params(
         input_dataset=input_dataset,
         prefix=prefix,
@@ -233,13 +216,13 @@ def v_3d_afnito_nifti(
         oldid=oldid,
         newid=newid,
     )
-    return v_3d_afnito_nifti_execute(params, execution)
+    return v_3d_afnito_nifti_execute(params, runner)
 
 
 __all__ = [
     "V3dAfnitoNiftiOutputs",
-    "V3dAfnitoNiftiParameters",
     "V_3D_AFNITO_NIFTI_METADATA",
     "v_3d_afnito_nifti",
+    "v_3d_afnito_nifti_execute",
     "v_3d_afnito_nifti_params",
 ]