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

niwrap_afni/afni/v_3d_zcat.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_ZCAT_METADATA = Metadata(
-    id="f09932d1f0c48de36aaac052798af4aa5ecaae6f.boutiques",
+    id="f8b6d970d79a1b34aa5cdfe38573a01caa7d1505.boutiques",
     name="3dZcat",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,17 @@ V_3D_ZCAT_METADATA = Metadata(
 
 
 V3dZcatParameters = typing.TypedDict('V3dZcatParameters', {
-    "__STYXTYPE__": typing.Literal["3dZcat"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dZcat"]],
+    "prefix": typing.NotRequired[str | None],
+    "datum": typing.NotRequired[typing.Literal["byte", "short", "float"] | None],
+    "fscale": bool,
+    "nscale": bool,
+    "verb": bool,
+    "frugal": bool,
+    "input_files": list[InputPathType],
+})
+V3dZcatParametersTagged = typing.TypedDict('V3dZcatParametersTagged', {
+    "@type": typing.Literal["afni/3dZcat"],
     "prefix": typing.NotRequired[str | None],
     "datum": typing.NotRequired[typing.Literal["byte", "short", "float"] | None],
     "fscale": bool,
@@ -23,43 +33,11 @@ V3dZcatParameters = typing.TypedDict('V3dZcatParameters', {
     "frugal": bool,
     "input_files": list[InputPathType],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dZcat": v_3d_zcat_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 {
-        "3dZcat": v_3d_zcat_outputs,
-    }.get(t)
 
 
 class V3dZcatOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_zcat(...)`.
+    Output object returned when calling `V3dZcatParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -77,7 +55,7 @@ def v_3d_zcat_params(
     nscale: bool = False,
     verb: bool = False,
     frugal: bool = False,
-) -> V3dZcatParameters:
+) -> V3dZcatParametersTagged:
     """
     Build parameters.
     
@@ -102,7 +80,7 @@ def v_3d_zcat_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dZcat",
+        "@type": "afni/3dZcat",
         "fscale": fscale,
         "nscale": nscale,
         "verb": verb,
@@ -131,25 +109,25 @@ def v_3d_zcat_cargs(
     """
     cargs = []
     cargs.append("3dZcat")
-    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("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("fscale"):
+    if params.get("fscale", False):
         cargs.append("-fscale")
-    if params.get("nscale"):
+    if params.get("nscale", False):
         cargs.append("-nscale")
-    if params.get("verb"):
+    if params.get("verb", False):
         cargs.append("-verb")
-    if params.get("frugal"):
+    if params.get("frugal", False):
         cargs.append("-frugal")
-    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
+    cargs.extend([execution.input_file(f) for f in params.get("input_files", None)])
     return cargs
 
 
@@ -168,17 +146,19 @@ def v_3d_zcat_outputs(
     """
     ret = V3dZcatOutputs(
         root=execution.output_file("."),
-        out_head=execution.output_file(params.get("prefix") + "+orig.HEAD") if (params.get("prefix") is not None) else None,
-        out_brik=execution.output_file(params.get("prefix") + "+orig.BRIK") if (params.get("prefix") is not None) else None,
+        out_head=execution.output_file(params.get("prefix", None) + "+orig.HEAD") if (params.get("prefix") is not None) else None,
+        out_brik=execution.output_file(params.get("prefix", None) + "+orig.BRIK") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_zcat_execute(
     params: V3dZcatParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dZcatOutputs:
     """
+    3dZcat
+    
     Concatenates datasets in the slice (z) direction.
     
     Author: AFNI Developers
@@ -187,10 +167,12 @@ def v_3d_zcat_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dZcatOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_ZCAT_METADATA)
     params = execution.params(params)
     cargs = v_3d_zcat_cargs(params, execution)
     ret = v_3d_zcat_outputs(params, execution)
@@ -209,6 +191,8 @@ def v_3d_zcat(
     runner: Runner | None = None,
 ) -> V3dZcatOutputs:
     """
+    3dZcat
+    
     Concatenates datasets in the slice (z) direction.
     
     Author: AFNI Developers
@@ -236,8 +220,6 @@ def v_3d_zcat(
     Returns:
         NamedTuple of outputs (described in `V3dZcatOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_ZCAT_METADATA)
     params = v_3d_zcat_params(
         prefix=prefix,
         datum=datum,
@@ -247,13 +229,13 @@ def v_3d_zcat(
         frugal=frugal,
         input_files=input_files,
     )
-    return v_3d_zcat_execute(params, execution)
+    return v_3d_zcat_execute(params, runner)
 
 
 __all__ = [
     "V3dZcatOutputs",
-    "V3dZcatParameters",
     "V_3D_ZCAT_METADATA",
     "v_3d_zcat",
+    "v_3d_zcat_execute",
     "v_3d_zcat_params",
 ]

niwrap_afni/afni/v_3d_zcutup.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_ZCUTUP_METADATA = Metadata(
-    id="da952f2c6d1682e69ef1ef9b1f9dce9d5eeaa1da.boutiques",
+    id="7f841bd4dfbc27b4d2e1ea682e9cf137e9548bea.boutiques",
     name="3dZcutup",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,48 +14,22 @@ V_3D_ZCUTUP_METADATA = Metadata(
 
 
 V3dZcutupParameters = typing.TypedDict('V3dZcutupParameters', {
-    "__STYXTYPE__": typing.Literal["3dZcutup"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dZcutup"]],
+    "keep_slices": str,
+    "prefix": typing.NotRequired[str | None],
+    "dataset": InputPathType,
+})
+V3dZcutupParametersTagged = typing.TypedDict('V3dZcutupParametersTagged', {
+    "@type": typing.Literal["afni/3dZcutup"],
     "keep_slices": str,
     "prefix": typing.NotRequired[str | None],
     "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 {
-        "3dZcutup": v_3d_zcutup_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 {
-        "3dZcutup": v_3d_zcutup_outputs,
-    }.get(t)
 
 
 class V3dZcutupOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_zcutup(...)`.
+    Output object returned when calling `V3dZcutupParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +43,7 @@ def v_3d_zcutup_params(
     keep_slices: str,
     dataset: InputPathType,
     prefix: str | None = None,
-) -> V3dZcutupParameters:
+) -> V3dZcutupParametersTagged:
     """
     Build parameters.
     
@@ -84,7 +58,7 @@ def v_3d_zcutup_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dZcutup",
+        "@type": "afni/3dZcutup",
         "keep_slices": keep_slices,
         "dataset": dataset,
     }
@@ -110,14 +84,14 @@ def v_3d_zcutup_cargs(
     cargs.append("3dZcutup")
     cargs.extend([
         "-keep",
-        params.get("keep_slices")
+        params.get("keep_slices", 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)
         ])
-    cargs.append(execution.input_file(params.get("dataset")))
+    cargs.append(execution.input_file(params.get("dataset", None)))
     return cargs
 
 
@@ -136,17 +110,19 @@ def v_3d_zcutup_outputs(
     """
     ret = V3dZcutupOutputs(
         root=execution.output_file("."),
-        output_head=execution.output_file(params.get("prefix") + "+orig.HEAD") if (params.get("prefix") is not None) else None,
-        output_brik=execution.output_file(params.get("prefix") + "+orig.BRIK") if (params.get("prefix") is not None) else None,
+        output_head=execution.output_file(params.get("prefix", None) + "+orig.HEAD") if (params.get("prefix") is not None) else None,
+        output_brik=execution.output_file(params.get("prefix", None) + "+orig.BRIK") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_zcutup_execute(
     params: V3dZcutupParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dZcutupOutputs:
     """
+    3dZcutup
+    
     Cut slices off a dataset in its z-direction and write a new dataset.
     
     Author: AFNI Developers
@@ -155,10 +131,12 @@ def v_3d_zcutup_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dZcutupOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_ZCUTUP_METADATA)
     params = execution.params(params)
     cargs = v_3d_zcutup_cargs(params, execution)
     ret = v_3d_zcutup_outputs(params, execution)
@@ -173,6 +151,8 @@ def v_3d_zcutup(
     runner: Runner | None = None,
 ) -> V3dZcutupOutputs:
     """
+    3dZcutup
+    
     Cut slices off a dataset in its z-direction and write a new dataset.
     
     Author: AFNI Developers
@@ -190,20 +170,18 @@ def v_3d_zcutup(
     Returns:
         NamedTuple of outputs (described in `V3dZcutupOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_ZCUTUP_METADATA)
     params = v_3d_zcutup_params(
         keep_slices=keep_slices,
         prefix=prefix,
         dataset=dataset,
     )
-    return v_3d_zcutup_execute(params, execution)
+    return v_3d_zcutup_execute(params, runner)
 
 
 __all__ = [
     "V3dZcutupOutputs",
-    "V3dZcutupParameters",
     "V_3D_ZCUTUP_METADATA",
     "v_3d_zcutup",
+    "v_3d_zcutup_execute",
     "v_3d_zcutup_params",
 ]

niwrap_afni/afni/v_3d_zeropad.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_ZEROPAD_METADATA = Metadata(
-    id="8becb29cf5d687af1a0c52c165ec0b440d32f49e.boutiques",
+    id="4fa7de0aae4ebc4468329b27d1522e9ee05fa450.boutiques",
     name="3dZeropad",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,25 @@ V_3D_ZEROPAD_METADATA = Metadata(
 
 
 V3dZeropadParameters = typing.TypedDict('V3dZeropadParameters', {
-    "__STYXTYPE__": typing.Literal["3dZeropad"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dZeropad"]],
+    "dataset": InputPathType,
+    "I": typing.NotRequired[float | None],
+    "S": typing.NotRequired[float | None],
+    "A": typing.NotRequired[float | None],
+    "P": typing.NotRequired[float | None],
+    "L": typing.NotRequired[float | None],
+    "R": typing.NotRequired[float | None],
+    "z": typing.NotRequired[float | None],
+    "RL": typing.NotRequired[float | None],
+    "AP": typing.NotRequired[float | None],
+    "IS": typing.NotRequired[float | None],
+    "pad2even": bool,
+    "mm_flag": bool,
+    "master_dataset": typing.NotRequired[InputPathType | None],
+    "prefix": typing.NotRequired[str | None],
+})
+V3dZeropadParametersTagged = typing.TypedDict('V3dZeropadParametersTagged', {
+    "@type": typing.Literal["afni/3dZeropad"],
     "dataset": InputPathType,
     "I": typing.NotRequired[float | None],
     "S": typing.NotRequired[float | None],
@@ -31,43 +49,11 @@ V3dZeropadParameters = typing.TypedDict('V3dZeropadParameters', {
     "master_dataset": typing.NotRequired[InputPathType | None],
     "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 {
-        "3dZeropad": v_3d_zeropad_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 {
-        "3dZeropad": v_3d_zeropad_outputs,
-    }.get(t)
 
 
 class V3dZeropadOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_zeropad(...)`.
+    Output object returned when calling `V3dZeropadParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -93,7 +79,7 @@ def v_3d_zeropad_params(
     mm_flag: bool = False,
     master_dataset: InputPathType | None = None,
     prefix: str | None = None,
-) -> V3dZeropadParameters:
+) -> V3dZeropadParametersTagged:
     """
     Build parameters.
     
@@ -125,7 +111,7 @@ def v_3d_zeropad_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dZeropad",
+        "@type": "afni/3dZeropad",
         "dataset": dataset,
         "pad2even": pad2even,
         "mm_flag": mm_flag,
@@ -172,70 +158,70 @@ def v_3d_zeropad_cargs(
     """
     cargs = []
     cargs.append("3dZeropad")
-    cargs.append(execution.input_file(params.get("dataset")))
-    if params.get("I") is not None:
+    cargs.append(execution.input_file(params.get("dataset", None)))
+    if params.get("I", None) is not None:
         cargs.extend([
             "-I",
-            str(params.get("I"))
+            str(params.get("I", None))
         ])
-    if params.get("S") is not None:
+    if params.get("S", None) is not None:
         cargs.extend([
             "-S",
-            str(params.get("S"))
+            str(params.get("S", None))
         ])
-    if params.get("A") is not None:
+    if params.get("A", None) is not None:
         cargs.extend([
             "-A",
-            str(params.get("A"))
+            str(params.get("A", None))
         ])
-    if params.get("P") is not None:
+    if params.get("P", None) is not None:
         cargs.extend([
             "-P",
-            str(params.get("P"))
+            str(params.get("P", None))
         ])
-    if params.get("L") is not None:
+    if params.get("L", None) is not None:
         cargs.extend([
             "-L",
-            str(params.get("L"))
+            str(params.get("L", None))
         ])
-    if params.get("R") is not None:
+    if params.get("R", None) is not None:
         cargs.extend([
             "-R",
-            str(params.get("R"))
+            str(params.get("R", None))
         ])
-    if params.get("z") is not None:
+    if params.get("z", None) is not None:
         cargs.extend([
             "-z",
-            str(params.get("z"))
+            str(params.get("z", None))
         ])
-    if params.get("RL") is not None:
+    if params.get("RL", None) is not None:
         cargs.extend([
             "-RL",
-            str(params.get("RL"))
+            str(params.get("RL", None))
         ])
-    if params.get("AP") is not None:
+    if params.get("AP", None) is not None:
         cargs.extend([
             "-AP",
-            str(params.get("AP"))
+            str(params.get("AP", None))
         ])
-    if params.get("IS") is not None:
+    if params.get("IS", None) is not None:
         cargs.extend([
             "-IS",
-            str(params.get("IS"))
+            str(params.get("IS", None))
         ])
-    if params.get("pad2even"):
+    if params.get("pad2even", False):
         cargs.append("-pad2evens")
-    if params.get("mm_flag"):
+    if params.get("mm_flag", False):
         cargs.append("-mm")
-    if params.get("master_dataset") is not None:
+    if params.get("master_dataset", None) is not None:
         cargs.extend([
             "-master",
-            execution.input_file(params.get("master_dataset"))
+            execution.input_file(params.get("master_dataset", 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
 
@@ -255,17 +241,19 @@ def v_3d_zeropad_outputs(
     """
     ret = V3dZeropadOutputs(
         root=execution.output_file("."),
-        output_dataset_brik=execution.output_file(params.get("prefix") + "+orig.BRIK") if (params.get("prefix") is not None) else None,
-        output_dataset_head=execution.output_file(params.get("prefix") + "+orig.HEAD") if (params.get("prefix") is not None) else None,
+        output_dataset_brik=execution.output_file(params.get("prefix", None) + "+orig.BRIK") if (params.get("prefix") is not None) else None,
+        output_dataset_head=execution.output_file(params.get("prefix", None) + "+orig.HEAD") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_zeropad_execute(
     params: V3dZeropadParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dZeropadOutputs:
     """
+    3dZeropad
+    
     Adds planes of zeros to a dataset (i.e., pads it out). Negative 'add' count
     means to cut a dataset down in size.
     
@@ -275,10 +263,12 @@ def v_3d_zeropad_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dZeropadOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_ZEROPAD_METADATA)
     params = execution.params(params)
     cargs = v_3d_zeropad_cargs(params, execution)
     ret = v_3d_zeropad_outputs(params, execution)
@@ -305,6 +295,8 @@ def v_3d_zeropad(
     runner: Runner | None = None,
 ) -> V3dZeropadOutputs:
     """
+    3dZeropad
+    
     Adds planes of zeros to a dataset (i.e., pads it out). Negative 'add' count
     means to cut a dataset down in size.
     
@@ -340,8 +332,6 @@ def v_3d_zeropad(
     Returns:
         NamedTuple of outputs (described in `V3dZeropadOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_ZEROPAD_METADATA)
     params = v_3d_zeropad_params(
         dataset=dataset,
         i=i,
@@ -359,13 +349,13 @@ def v_3d_zeropad(
         master_dataset=master_dataset,
         prefix=prefix,
     )
-    return v_3d_zeropad_execute(params, execution)
+    return v_3d_zeropad_execute(params, runner)
 
 
 __all__ = [
     "V3dZeropadOutputs",
-    "V3dZeropadParameters",
     "V_3D_ZEROPAD_METADATA",
     "v_3d_zeropad",
+    "v_3d_zeropad_execute",
     "v_3d_zeropad_params",
 ]