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

niwrap_afni/afni/v_3dbucket.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DBUCKET_METADATA = Metadata(
-    id="209f280cf80f67eec54b9e248d877666d290d19c.boutiques",
+    id="e8cc2881149d3136709a0708be9b84949d81918c.boutiques",
     name="3dbucket",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,20 @@ V_3DBUCKET_METADATA = Metadata(
 
 
 V3dbucketParameters = typing.TypedDict('V3dbucketParameters', {
-    "__STYXTYPE__": typing.Literal["3dbucket"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dbucket"]],
+    "prefix": typing.NotRequired[str | None],
+    "output": typing.NotRequired[str | None],
+    "session": typing.NotRequired[str | None],
+    "glueto": typing.NotRequired[str | None],
+    "aglueto": typing.NotRequired[str | None],
+    "dry": bool,
+    "verbose": bool,
+    "fbuc": bool,
+    "abuc": bool,
+    "input_files": list[str],
+})
+V3dbucketParametersTagged = typing.TypedDict('V3dbucketParametersTagged', {
+    "@type": typing.Literal["afni/3dbucket"],
     "prefix": typing.NotRequired[str | None],
     "output": typing.NotRequired[str | None],
     "session": typing.NotRequired[str | None],
@@ -26,42 +39,11 @@ V3dbucketParameters = typing.TypedDict('V3dbucketParameters', {
     "abuc": bool,
     "input_files": list[str],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dbucket": v_3dbucket_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 V3dbucketOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3dbucket(...)`.
+    Output object returned when calling `V3dbucketParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -78,7 +60,7 @@ def v_3dbucket_params(
     verbose: bool = False,
     fbuc: bool = False,
     abuc: bool = False,
-) -> V3dbucketParameters:
+) -> V3dbucketParametersTagged:
     """
     Build parameters.
     
@@ -100,7 +82,7 @@ def v_3dbucket_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dbucket",
+        "@type": "afni/3dbucket",
         "dry": dry,
         "verbose": verbose,
         "fbuc": fbuc,
@@ -135,40 +117,40 @@ def v_3dbucket_cargs(
     """
     cargs = []
     cargs.append("3dbucket")
-    if params.get("prefix") is not None:
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("prefix")
+            params.get("prefix", None)
         ])
-    if params.get("output") is not None:
+    if params.get("output", None) is not None:
         cargs.extend([
             "-output",
-            params.get("output")
+            params.get("output", None)
         ])
-    if params.get("session") is not None:
+    if params.get("session", None) is not None:
         cargs.extend([
             "-session",
-            params.get("session")
+            params.get("session", None)
         ])
-    if params.get("glueto") is not None:
+    if params.get("glueto", None) is not None:
         cargs.extend([
             "-glueto",
-            params.get("glueto")
+            params.get("glueto", None)
         ])
-    if params.get("aglueto") is not None:
+    if params.get("aglueto", None) is not None:
         cargs.extend([
             "-aglueto",
-            params.get("aglueto")
+            params.get("aglueto", None)
         ])
-    if params.get("dry"):
+    if params.get("dry", False):
         cargs.append("-dry")
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-verb")
-    if params.get("fbuc"):
+    if params.get("fbuc", False):
         cargs.append("-fbuc")
-    if params.get("abuc"):
+    if params.get("abuc", False):
         cargs.append("-abuc")
-    cargs.extend(params.get("input_files"))
+    cargs.extend(params.get("input_files", None))
     return cargs
 
 
@@ -193,9 +175,11 @@ def v_3dbucket_outputs(
 
 def v_3dbucket_execute(
     params: V3dbucketParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dbucketOutputs:
     """
+    3dbucket
+    
     Concatenate sub-bricks from input datasets into one big bucket dataset.
     
     Author: AFNI Developers
@@ -204,10 +188,12 @@ def v_3dbucket_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dbucketOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DBUCKET_METADATA)
     params = execution.params(params)
     cargs = v_3dbucket_cargs(params, execution)
     ret = v_3dbucket_outputs(params, execution)
@@ -229,6 +215,8 @@ def v_3dbucket(
     runner: Runner | None = None,
 ) -> V3dbucketOutputs:
     """
+    3dbucket
+    
     Concatenate sub-bricks from input datasets into one big bucket dataset.
     
     Author: AFNI Developers
@@ -253,8 +241,6 @@ def v_3dbucket(
     Returns:
         NamedTuple of outputs (described in `V3dbucketOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DBUCKET_METADATA)
     params = v_3dbucket_params(
         prefix=prefix,
         output=output,
@@ -267,13 +253,13 @@ def v_3dbucket(
         abuc=abuc,
         input_files=input_files,
     )
-    return v_3dbucket_execute(params, execution)
+    return v_3dbucket_execute(params, runner)
 
 
 __all__ = [
     "V3dbucketOutputs",
-    "V3dbucketParameters",
     "V_3DBUCKET_METADATA",
     "v_3dbucket",
+    "v_3dbucket_execute",
     "v_3dbucket_params",
 ]

niwrap_afni/afni/v_3dcalc.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DCALC_METADATA = Metadata(
-    id="34983276632d5f12085998aa5812bfe380a32306.boutiques",
+    id="4ecc4bd9710b038a889275d36ce45265ee4b3f81.boutiques",
     name="3dcalc",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,20 @@ V_3DCALC_METADATA = Metadata(
 
 
 V3dcalcParameters = typing.TypedDict('V3dcalcParameters', {
-    "__STYXTYPE__": typing.Literal["3dcalc"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dcalc"]],
+    "in_file_a": InputPathType,
+    "in_file_b": typing.NotRequired[InputPathType | None],
+    "in_file_c": typing.NotRequired[InputPathType | None],
+    "other": typing.NotRequired[InputPathType | None],
+    "overwrite": bool,
+    "single_idx": typing.NotRequired[int | None],
+    "start_idx": typing.NotRequired[int | None],
+    "stop_idx": typing.NotRequired[int | None],
+    "expr": str,
+    "prefix": typing.NotRequired[str | None],
+})
+V3dcalcParametersTagged = typing.TypedDict('V3dcalcParametersTagged', {
+    "@type": typing.Literal["afni/3dcalc"],
     "in_file_a": InputPathType,
     "in_file_b": typing.NotRequired[InputPathType | None],
     "in_file_c": typing.NotRequired[InputPathType | None],
@@ -26,43 +39,11 @@ V3dcalcParameters = typing.TypedDict('V3dcalcParameters', {
     "expr": str,
     "prefix": 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 {
-        "3dcalc": v_3dcalc_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 {
-        "3dcalc": v_3dcalc_outputs,
-    }.get(t)
 
 
 class V3dcalcOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3dcalc(...)`.
+    Output object returned when calling `V3dcalcParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -81,7 +62,7 @@ def v_3dcalc_params(
     start_idx: int | None = None,
     stop_idx: int | None = None,
     prefix: str | None = None,
-) -> V3dcalcParameters:
+) -> V3dcalcParametersTagged:
     """
     Build parameters.
     
@@ -100,7 +81,7 @@ def v_3dcalc_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dcalc",
+        "@type": "afni/3dcalc",
         "in_file_a": in_file_a,
         "overwrite": overwrite,
         "expr": expr,
@@ -139,36 +120,36 @@ def v_3dcalc_cargs(
     cargs.append("3dcalc")
     cargs.extend([
         "-a",
-        execution.input_file(params.get("in_file_a"))
+        execution.input_file(params.get("in_file_a", None))
     ])
-    if params.get("in_file_b") is not None:
+    if params.get("in_file_b", None) is not None:
         cargs.extend([
             "-b",
-            execution.input_file(params.get("in_file_b"))
+            execution.input_file(params.get("in_file_b", None))
         ])
-    if params.get("in_file_c") is not None:
+    if params.get("in_file_c", None) is not None:
         cargs.extend([
             "-c",
-            execution.input_file(params.get("in_file_c"))
+            execution.input_file(params.get("in_file_c", None))
         ])
-    if params.get("other") is not None:
-        cargs.append(execution.input_file(params.get("other")))
-    if params.get("overwrite"):
+    if params.get("other", None) is not None:
+        cargs.append(execution.input_file(params.get("other", None)))
+    if params.get("overwrite", False):
         cargs.append("-overwrite")
-    if params.get("single_idx") is not None:
-        cargs.append(str(params.get("single_idx")))
-    if params.get("start_idx") is not None:
-        cargs.append(str(params.get("start_idx")))
-    if params.get("stop_idx") is not None:
-        cargs.append(str(params.get("stop_idx")))
+    if params.get("single_idx", None) is not None:
+        cargs.append(str(params.get("single_idx", None)))
+    if params.get("start_idx", None) is not None:
+        cargs.append(str(params.get("start_idx", None)))
+    if params.get("stop_idx", None) is not None:
+        cargs.append(str(params.get("stop_idx", None)))
     cargs.extend([
         "-expr",
-        params.get("expr")
+        params.get("expr", None)
     ])
-    if params.get("prefix") is not None:
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("prefix")
+            params.get("prefix", None)
         ])
     return cargs
 
@@ -188,16 +169,18 @@ def v_3dcalc_outputs(
     """
     ret = V3dcalcOutputs(
         root=execution.output_file("."),
-        out_file=execution.output_file(params.get("prefix")) if (params.get("prefix") is not None) else None,
+        out_file=execution.output_file(params.get("prefix", None)) if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3dcalc_execute(
     params: V3dcalcParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dcalcOutputs:
     """
+    3dcalc
+    
     AFNI's calculator program.
     
     Author: AFNI Developers
@@ -206,10 +189,12 @@ def v_3dcalc_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dcalcOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DCALC_METADATA)
     params = execution.params(params)
     cargs = v_3dcalc_cargs(params, execution)
     ret = v_3dcalc_outputs(params, execution)
@@ -231,6 +216,8 @@ def v_3dcalc(
     runner: Runner | None = None,
 ) -> V3dcalcOutputs:
     """
+    3dcalc
+    
     AFNI's calculator program.
     
     Author: AFNI Developers
@@ -252,8 +239,6 @@ def v_3dcalc(
     Returns:
         NamedTuple of outputs (described in `V3dcalcOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DCALC_METADATA)
     params = v_3dcalc_params(
         in_file_a=in_file_a,
         in_file_b=in_file_b,
@@ -266,13 +251,13 @@ def v_3dcalc(
         expr=expr,
         prefix=prefix,
     )
-    return v_3dcalc_execute(params, execution)
+    return v_3dcalc_execute(params, runner)
 
 
 __all__ = [
     "V3dcalcOutputs",
-    "V3dcalcParameters",
     "V_3DCALC_METADATA",
     "v_3dcalc",
+    "v_3dcalc_execute",
     "v_3dcalc_params",
 ]

niwrap_afni/afni/v_3dclust.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DCLUST_METADATA = Metadata(
-    id="6ce131d0cf527a3a2a6df4f0ddf952eefa164b8c.boutiques",
+    id="bb71dd389ead7c86b04372e27cd788efc250aed1.boutiques",
     name="3dclust",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,30 @@ V_3DCLUST_METADATA = Metadata(
 
 
 V3dclustParameters = typing.TypedDict('V3dclustParameters', {
-    "__STYXTYPE__": typing.Literal["3dclust"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dclust"]],
+    "rmm": typing.NotRequired[float | None],
+    "vmul": typing.NotRequired[float | None],
+    "datasets": list[InputPathType],
+    "nn1": bool,
+    "nn2": bool,
+    "nn3": bool,
+    "noabs": bool,
+    "summarize": bool,
+    "nosum": bool,
+    "verb": bool,
+    "oned_format": bool,
+    "no_oned_format": bool,
+    "quiet": bool,
+    "mni": bool,
+    "isovalue": bool,
+    "isomerge": bool,
+    "inmask": bool,
+    "prefix": typing.NotRequired[str | None],
+    "savemask": typing.NotRequired[str | None],
+    "binary": bool,
+})
+V3dclustParametersTagged = typing.TypedDict('V3dclustParametersTagged', {
+    "@type": typing.Literal["afni/3dclust"],
     "rmm": typing.NotRequired[float | None],
     "vmul": typing.NotRequired[float | None],
     "datasets": list[InputPathType],
@@ -36,43 +59,11 @@ V3dclustParameters = typing.TypedDict('V3dclustParameters', {
     "savemask": typing.NotRequired[str | None],
     "binary": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dclust": v_3dclust_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 {
-        "3dclust": v_3dclust_outputs,
-    }.get(t)
 
 
 class V3dclustOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3dclust(...)`.
+    Output object returned when calling `V3dclustParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -103,7 +94,7 @@ def v_3dclust_params(
     prefix: str | None = None,
     savemask: str | None = None,
     binary: bool = False,
-) -> V3dclustParameters:
+) -> V3dclustParametersTagged:
     """
     Build parameters.
     
@@ -142,7 +133,7 @@ def v_3dclust_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dclust",
+        "@type": "afni/3dclust",
         "datasets": datasets,
         "nn1": nn1,
         "nn2": nn2,
@@ -186,50 +177,50 @@ def v_3dclust_cargs(
     """
     cargs = []
     cargs.append("3dclust")
-    if params.get("rmm") is not None:
-        cargs.append(str(params.get("rmm")))
-    if params.get("vmul") is not None:
-        cargs.append(str(params.get("vmul")))
-    cargs.extend([execution.input_file(f) for f in params.get("datasets")])
-    if params.get("nn1"):
+    if params.get("rmm", None) is not None:
+        cargs.append(str(params.get("rmm", None)))
+    if params.get("vmul", None) is not None:
+        cargs.append(str(params.get("vmul", None)))
+    cargs.extend([execution.input_file(f) for f in params.get("datasets", None)])
+    if params.get("nn1", False):
         cargs.append("-NN1")
-    if params.get("nn2"):
+    if params.get("nn2", False):
         cargs.append("-NN2")
-    if params.get("nn3"):
+    if params.get("nn3", False):
         cargs.append("-NN3")
-    if params.get("noabs"):
+    if params.get("noabs", False):
         cargs.append("-noabs")
-    if params.get("summarize"):
+    if params.get("summarize", False):
         cargs.append("-summarize")
-    if params.get("nosum"):
+    if params.get("nosum", False):
         cargs.append("-nosum")
-    if params.get("verb"):
+    if params.get("verb", False):
         cargs.append("-verb")
-    if params.get("oned_format"):
+    if params.get("oned_format", False):
         cargs.append("-1Dformat")
-    if params.get("no_oned_format"):
+    if params.get("no_oned_format", False):
         cargs.append("-no_1Dformat")
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
-    if params.get("mni"):
+    if params.get("mni", False):
         cargs.append("-mni")
-    if params.get("isovalue"):
+    if params.get("isovalue", False):
         cargs.append("-isovalue")
-    if params.get("isomerge"):
+    if params.get("isomerge", False):
         cargs.append("-isomerge")
-    if params.get("inmask"):
+    if params.get("inmask", False):
         cargs.append("-inmask")
-    if params.get("prefix") is not None:
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("prefix")
+            params.get("prefix", None)
         ])
-    if params.get("savemask") is not None:
+    if params.get("savemask", None) is not None:
         cargs.extend([
             "-savemask",
-            params.get("savemask")
+            params.get("savemask", None)
         ])
-    if params.get("binary"):
+    if params.get("binary", False):
         cargs.append("-binary")
     return cargs
 
@@ -249,17 +240,19 @@ def v_3dclust_outputs(
     """
     ret = V3dclustOutputs(
         root=execution.output_file("."),
-        prefixed_output=execution.output_file(params.get("prefix") + ".nii.gz") if (params.get("prefix") is not None) else None,
-        ordered_mask_output=execution.output_file(params.get("savemask") + ".nii.gz") if (params.get("savemask") is not None) else None,
+        prefixed_output=execution.output_file(params.get("prefix", None) + ".nii.gz") if (params.get("prefix") is not None) else None,
+        ordered_mask_output=execution.output_file(params.get("savemask", None) + ".nii.gz") if (params.get("savemask") is not None) else None,
     )
     return ret
 
 
 def v_3dclust_execute(
     params: V3dclustParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dclustOutputs:
     """
+    3dclust
+    
     Performs simple-minded cluster detection in 3D datasets.
     
     Author: AFNI Developers
@@ -268,10 +261,12 @@ def v_3dclust_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dclustOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DCLUST_METADATA)
     params = execution.params(params)
     cargs = v_3dclust_cargs(params, execution)
     ret = v_3dclust_outputs(params, execution)
@@ -303,6 +298,8 @@ def v_3dclust(
     runner: Runner | None = None,
 ) -> V3dclustOutputs:
     """
+    3dclust
+    
     Performs simple-minded cluster detection in 3D datasets.
     
     Author: AFNI Developers
@@ -344,8 +341,6 @@ def v_3dclust(
     Returns:
         NamedTuple of outputs (described in `V3dclustOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DCLUST_METADATA)
     params = v_3dclust_params(
         rmm=rmm,
         vmul=vmul,
@@ -368,13 +363,13 @@ def v_3dclust(
         savemask=savemask,
         binary=binary,
     )
-    return v_3dclust_execute(params, execution)
+    return v_3dclust_execute(params, runner)
 
 
 __all__ = [
     "V3dclustOutputs",
-    "V3dclustParameters",
     "V_3DCLUST_METADATA",
     "v_3dclust",
+    "v_3dclust_execute",
     "v_3dclust_params",
 ]