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

niwrap_afni/afni/v_3dmaskdump.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DMASKDUMP_METADATA = Metadata(
-    id="556f8c8bdddd5a68c68e0dbd728e6850a7d7f648.boutiques",
+    id="592e963676fc4ef445e35ff95c09c2b7fb061059.boutiques",
     name="3dmaskdump",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,30 @@ V_3DMASKDUMP_METADATA = Metadata(
 
 
 V3dmaskdumpParameters = typing.TypedDict('V3dmaskdumpParameters', {
-    "__STYXTYPE__": typing.Literal["3dmaskdump"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dmaskdump"]],
+    "input_files": list[InputPathType],
+    "mask_dataset": typing.NotRequired[InputPathType | None],
+    "mask_range": typing.NotRequired[list[str] | None],
+    "output_index": bool,
+    "output_noijk": bool,
+    "output_xyz": bool,
+    "output_filename": typing.NotRequired[str | None],
+    "calc_mask_opts": typing.NotRequired[str | None],
+    "xbox_coords": typing.NotRequired[str | None],
+    "dbox_coords": typing.NotRequired[str | None],
+    "nbox_coords": typing.NotRequired[str | None],
+    "ibox_coords": typing.NotRequired[str | None],
+    "xball_coords": typing.NotRequired[str | None],
+    "dball_coords": typing.NotRequired[str | None],
+    "nball_coords": typing.NotRequired[str | None],
+    "nozero_output": bool,
+    "random_voxels": typing.NotRequired[float | None],
+    "random_seed": typing.NotRequired[float | None],
+    "output_niml": typing.NotRequired[str | None],
+    "quiet_mode": bool,
+})
+V3dmaskdumpParametersTagged = typing.TypedDict('V3dmaskdumpParametersTagged', {
+    "@type": typing.Literal["afni/3dmaskdump"],
     "input_files": list[InputPathType],
     "mask_dataset": typing.NotRequired[InputPathType | None],
     "mask_range": typing.NotRequired[list[str] | None],
@@ -36,43 +59,11 @@ V3dmaskdumpParameters = typing.TypedDict('V3dmaskdumpParameters', {
     "output_niml": typing.NotRequired[str | None],
     "quiet_mode": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dmaskdump": v_3dmaskdump_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 {
-        "3dmaskdump": v_3dmaskdump_outputs,
-    }.get(t)
 
 
 class V3dmaskdumpOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3dmaskdump(...)`.
+    Output object returned when calling `V3dmaskdumpParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -101,7 +92,7 @@ def v_3dmaskdump_params(
     random_seed: float | None = None,
     output_niml: str | None = None,
     quiet_mode: bool = False,
-) -> V3dmaskdumpParameters:
+) -> V3dmaskdumpParametersTagged:
     """
     Build parameters.
     
@@ -140,7 +131,7 @@ def v_3dmaskdump_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dmaskdump",
+        "@type": "afni/3dmaskdump",
         "input_files": input_files,
         "output_index": output_index,
         "output_noijk": output_noijk,
@@ -194,86 +185,86 @@ def v_3dmaskdump_cargs(
     """
     cargs = []
     cargs.append("3dmaskdump")
-    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
-    if params.get("mask_dataset") is not None:
+    cargs.extend([execution.input_file(f) for f in params.get("input_files", None)])
+    if params.get("mask_dataset", None) is not None:
         cargs.extend([
             "-mask",
-            execution.input_file(params.get("mask_dataset"))
+            execution.input_file(params.get("mask_dataset", None))
         ])
-    if params.get("mask_range") is not None:
+    if params.get("mask_range", None) is not None:
         cargs.extend([
             "-mrange",
-            *params.get("mask_range")
+            *params.get("mask_range", None)
         ])
-    if params.get("output_index"):
+    if params.get("output_index", False):
         cargs.append("-index")
-    if params.get("output_noijk"):
+    if params.get("output_noijk", False):
         cargs.append("-noijk")
-    if params.get("output_xyz"):
+    if params.get("output_xyz", False):
         cargs.append("-xyz")
-    if params.get("output_filename") is not None:
+    if params.get("output_filename", None) is not None:
         cargs.extend([
             "-o",
-            params.get("output_filename")
+            params.get("output_filename", None)
         ])
-    if params.get("calc_mask_opts") is not None:
+    if params.get("calc_mask_opts", None) is not None:
         cargs.extend([
             "-cmask",
-            params.get("calc_mask_opts")
+            params.get("calc_mask_opts", None)
         ])
-    if params.get("xbox_coords") is not None:
+    if params.get("xbox_coords", None) is not None:
         cargs.extend([
             "-xbox",
-            params.get("xbox_coords")
+            params.get("xbox_coords", None)
         ])
-    if params.get("dbox_coords") is not None:
+    if params.get("dbox_coords", None) is not None:
         cargs.extend([
             "-dbox",
-            params.get("dbox_coords")
+            params.get("dbox_coords", None)
         ])
-    if params.get("nbox_coords") is not None:
+    if params.get("nbox_coords", None) is not None:
         cargs.extend([
             "-nbox",
-            params.get("nbox_coords")
+            params.get("nbox_coords", None)
         ])
-    if params.get("ibox_coords") is not None:
+    if params.get("ibox_coords", None) is not None:
         cargs.extend([
             "-ibox",
-            params.get("ibox_coords")
+            params.get("ibox_coords", None)
         ])
-    if params.get("xball_coords") is not None:
+    if params.get("xball_coords", None) is not None:
         cargs.extend([
             "-xball",
-            params.get("xball_coords")
+            params.get("xball_coords", None)
         ])
-    if params.get("dball_coords") is not None:
+    if params.get("dball_coords", None) is not None:
         cargs.extend([
             "-dball",
-            params.get("dball_coords")
+            params.get("dball_coords", None)
         ])
-    if params.get("nball_coords") is not None:
+    if params.get("nball_coords", None) is not None:
         cargs.extend([
             "-nball",
-            params.get("nball_coords")
+            params.get("nball_coords", None)
         ])
-    if params.get("nozero_output"):
+    if params.get("nozero_output", False):
         cargs.append("-nozero")
-    if params.get("random_voxels") is not None:
+    if params.get("random_voxels", None) is not None:
         cargs.extend([
             "-n_rand",
-            str(params.get("random_voxels"))
+            str(params.get("random_voxels", None))
         ])
-    if params.get("random_seed") is not None:
+    if params.get("random_seed", None) is not None:
         cargs.extend([
             "-n_randseed",
-            str(params.get("random_seed"))
+            str(params.get("random_seed", None))
         ])
-    if params.get("output_niml") is not None:
+    if params.get("output_niml", None) is not None:
         cargs.extend([
             "-niml",
-            params.get("output_niml")
+            params.get("output_niml", None)
         ])
-    if params.get("quiet_mode"):
+    if params.get("quiet_mode", False):
         cargs.append("-quiet")
     return cargs
 
@@ -293,16 +284,18 @@ def v_3dmaskdump_outputs(
     """
     ret = V3dmaskdumpOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("output_filename")) if (params.get("output_filename") is not None) else None,
+        output_file=execution.output_file(params.get("output_filename", None)) if (params.get("output_filename") is not None) else None,
     )
     return ret
 
 
 def v_3dmaskdump_execute(
     params: V3dmaskdumpParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dmaskdumpOutputs:
     """
+    3dmaskdump
+    
     Outputs voxel values from AFNI datasets satisfying mask criteria to an ASCII
     file.
     
@@ -312,10 +305,12 @@ def v_3dmaskdump_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dmaskdumpOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DMASKDUMP_METADATA)
     params = execution.params(params)
     cargs = v_3dmaskdump_cargs(params, execution)
     ret = v_3dmaskdump_outputs(params, execution)
@@ -347,6 +342,8 @@ def v_3dmaskdump(
     runner: Runner | None = None,
 ) -> V3dmaskdumpOutputs:
     """
+    3dmaskdump
+    
     Outputs voxel values from AFNI datasets satisfying mask criteria to an ASCII
     file.
     
@@ -389,8 +386,6 @@ def v_3dmaskdump(
     Returns:
         NamedTuple of outputs (described in `V3dmaskdumpOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DMASKDUMP_METADATA)
     params = v_3dmaskdump_params(
         input_files=input_files,
         mask_dataset=mask_dataset,
@@ -413,13 +408,13 @@ def v_3dmaskdump(
         output_niml=output_niml,
         quiet_mode=quiet_mode,
     )
-    return v_3dmaskdump_execute(params, execution)
+    return v_3dmaskdump_execute(params, runner)
 
 
 __all__ = [
     "V3dmaskdumpOutputs",
-    "V3dmaskdumpParameters",
     "V_3DMASKDUMP_METADATA",
     "v_3dmaskdump",
+    "v_3dmaskdump_execute",
     "v_3dmaskdump_params",
 ]

niwrap_afni/afni/v_3dmatcalc.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DMATCALC_METADATA = Metadata(
-    id="b12640a251db3b73fc81eee4373e39cfe399c403.boutiques",
+    id="8f178bdc30988773d64483c60aa601e33c83d9f6.boutiques",
     name="3dmatcalc",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,49 +14,24 @@ V_3DMATCALC_METADATA = Metadata(
 
 
 V3dmatcalcParameters = typing.TypedDict('V3dmatcalcParameters', {
-    "__STYXTYPE__": typing.Literal["3dmatcalc"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dmatcalc"]],
+    "input_dataset": InputPathType,
+    "input_matrix": InputPathType,
+    "output_dataset": str,
+    "mask": typing.NotRequired[InputPathType | None],
+})
+V3dmatcalcParametersTagged = typing.TypedDict('V3dmatcalcParametersTagged', {
+    "@type": typing.Literal["afni/3dmatcalc"],
     "input_dataset": InputPathType,
     "input_matrix": InputPathType,
     "output_dataset": str,
     "mask": 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 {
-        "3dmatcalc": v_3dmatcalc_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 {
-        "3dmatcalc": v_3dmatcalc_outputs,
-    }.get(t)
 
 
 class V3dmatcalcOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3dmatcalc(...)`.
+    Output object returned when calling `V3dmatcalcParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +46,7 @@ def v_3dmatcalc_params(
     input_matrix: InputPathType,
     output_dataset: str,
     mask: InputPathType | None = None,
-) -> V3dmatcalcParameters:
+) -> V3dmatcalcParametersTagged:
     """
     Build parameters.
     
@@ -86,7 +61,7 @@ def v_3dmatcalc_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dmatcalc",
+        "@type": "afni/3dmatcalc",
         "input_dataset": input_dataset,
         "input_matrix": input_matrix,
         "output_dataset": output_dataset,
@@ -113,20 +88,20 @@ def v_3dmatcalc_cargs(
     cargs.append("3dmatcalc")
     cargs.extend([
         "-input",
-        execution.input_file(params.get("input_dataset"))
+        execution.input_file(params.get("input_dataset", None))
     ])
     cargs.extend([
         "-matrix",
-        execution.input_file(params.get("input_matrix"))
+        execution.input_file(params.get("input_matrix", None))
     ])
     cargs.extend([
         "-prefix",
-        params.get("output_dataset")
+        params.get("output_dataset", None)
     ])
-    if params.get("mask") is not None:
+    if params.get("mask", None) is not None:
         cargs.extend([
             "-mask",
-            execution.input_file(params.get("mask"))
+            execution.input_file(params.get("mask", None))
         ])
     return cargs
 
@@ -146,17 +121,19 @@ def v_3dmatcalc_outputs(
     """
     ret = V3dmatcalcOutputs(
         root=execution.output_file("."),
-        output_header=execution.output_file(params.get("output_dataset") + "+tlrc.HEAD"),
-        output_brick=execution.output_file(params.get("output_dataset") + "+tlrc.BRIK"),
+        output_header=execution.output_file(params.get("output_dataset", None) + "+tlrc.HEAD"),
+        output_brick=execution.output_file(params.get("output_dataset", None) + "+tlrc.BRIK"),
     )
     return ret
 
 
 def v_3dmatcalc_execute(
     params: V3dmatcalcParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dmatcalcOutputs:
     """
+    3dmatcalc
+    
     Apply a matrix to a dataset, voxel-by-voxel, to produce a new dataset.
     
     Author: AFNI Developers
@@ -165,10 +142,12 @@ def v_3dmatcalc_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dmatcalcOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DMATCALC_METADATA)
     params = execution.params(params)
     cargs = v_3dmatcalc_cargs(params, execution)
     ret = v_3dmatcalc_outputs(params, execution)
@@ -184,6 +163,8 @@ def v_3dmatcalc(
     runner: Runner | None = None,
 ) -> V3dmatcalcOutputs:
     """
+    3dmatcalc
+    
     Apply a matrix to a dataset, voxel-by-voxel, to produce a new dataset.
     
     Author: AFNI Developers
@@ -201,21 +182,19 @@ def v_3dmatcalc(
     Returns:
         NamedTuple of outputs (described in `V3dmatcalcOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DMATCALC_METADATA)
     params = v_3dmatcalc_params(
         input_dataset=input_dataset,
         input_matrix=input_matrix,
         output_dataset=output_dataset,
         mask=mask,
     )
-    return v_3dmatcalc_execute(params, execution)
+    return v_3dmatcalc_execute(params, runner)
 
 
 __all__ = [
     "V3dmatcalcOutputs",
-    "V3dmatcalcParameters",
     "V_3DMATCALC_METADATA",
     "v_3dmatcalc",
+    "v_3dmatcalc_execute",
     "v_3dmatcalc_params",
 ]

niwrap_afni/afni/v_3dmatmult.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DMATMULT_METADATA = Metadata(
-    id="4c01ec090b313da194a5a2b7eb8c0d0439e1e624.boutiques",
+    id="025bcf26f324d0334be68bee9d41585c8c6c570d.boutiques",
     name="3dmatmult",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,50 +14,26 @@ V_3DMATMULT_METADATA = Metadata(
 
 
 V3dmatmultParameters = typing.TypedDict('V3dmatmultParameters', {
-    "__STYXTYPE__": typing.Literal["3dmatmult"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dmatmult"]],
+    "inputA": InputPathType,
+    "inputB": InputPathType,
+    "prefix": str,
+    "datum": typing.NotRequired[str | None],
+    "verb": typing.NotRequired[float | None],
+})
+V3dmatmultParametersTagged = typing.TypedDict('V3dmatmultParametersTagged', {
+    "@type": typing.Literal["afni/3dmatmult"],
     "inputA": InputPathType,
     "inputB": InputPathType,
     "prefix": str,
     "datum": typing.NotRequired[str | None],
     "verb": typing.NotRequired[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 {
-        "3dmatmult": v_3dmatmult_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 {
-        "3dmatmult": v_3dmatmult_outputs,
-    }.get(t)
 
 
 class V3dmatmultOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3dmatmult(...)`.
+    Output object returned when calling `V3dmatmultParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +47,7 @@ def v_3dmatmult_params(
     prefix: str,
     datum: str | None = None,
     verb: float | None = None,
-) -> V3dmatmultParameters:
+) -> V3dmatmultParametersTagged:
     """
     Build parameters.
     
@@ -85,7 +61,7 @@ def v_3dmatmult_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dmatmult",
+        "@type": "afni/3dmatmult",
         "inputA": input_a,
         "inputB": input_b,
         "prefix": prefix,
@@ -114,25 +90,25 @@ def v_3dmatmult_cargs(
     cargs.append("3dmatmult")
     cargs.extend([
         "-inputA",
-        execution.input_file(params.get("inputA"))
+        execution.input_file(params.get("inputA", None))
     ])
     cargs.extend([
         "-inputB",
-        execution.input_file(params.get("inputB"))
+        execution.input_file(params.get("inputB", None))
     ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("datum") is not None:
+    if params.get("datum", None) is not None:
         cargs.extend([
             "-datum",
-            params.get("datum")
+            params.get("datum", None)
         ])
-    if params.get("verb") is not None:
+    if params.get("verb", None) is not None:
         cargs.extend([
             "-verb",
-            str(params.get("verb"))
+            str(params.get("verb", None))
         ])
     return cargs
 
@@ -152,16 +128,18 @@ def v_3dmatmult_outputs(
     """
     ret = V3dmatmultOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("prefix")),
+        output_file=execution.output_file(params.get("prefix", None)),
     )
     return ret
 
 
 def v_3dmatmult_execute(
     params: V3dmatmultParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dmatmultOutputs:
     """
+    3dmatmult
+    
     Multiply AFNI datasets slice-by-slice as matrices.
     
     Author: AFNI Developers
@@ -170,10 +148,12 @@ def v_3dmatmult_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dmatmultOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DMATMULT_METADATA)
     params = execution.params(params)
     cargs = v_3dmatmult_cargs(params, execution)
     ret = v_3dmatmult_outputs(params, execution)
@@ -190,6 +170,8 @@ def v_3dmatmult(
     runner: Runner | None = None,
 ) -> V3dmatmultOutputs:
     """
+    3dmatmult
+    
     Multiply AFNI datasets slice-by-slice as matrices.
     
     Author: AFNI Developers
@@ -206,8 +188,6 @@ def v_3dmatmult(
     Returns:
         NamedTuple of outputs (described in `V3dmatmultOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DMATMULT_METADATA)
     params = v_3dmatmult_params(
         input_a=input_a,
         input_b=input_b,
@@ -215,13 +195,13 @@ def v_3dmatmult(
         datum=datum,
         verb=verb,
     )
-    return v_3dmatmult_execute(params, execution)
+    return v_3dmatmult_execute(params, runner)
 
 
 __all__ = [
     "V3dmatmultOutputs",
-    "V3dmatmultParameters",
     "V_3DMATMULT_METADATA",
     "v_3dmatmult",
+    "v_3dmatmult_execute",
     "v_3dmatmult_params",
 ]