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

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",
 ]

niwrap_afni/afni/v_3d_zipper_zapper.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_ZIPPER_ZAPPER_METADATA = Metadata(
-    id="7251c6575169756127e2528815aed08a88f0f0f8.boutiques",
+    id="39018d2cee2f860298e557f60f6ddf79a0d96337.boutiques",
     name="3dZipperZapper",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,26 @@ V_3D_ZIPPER_ZAPPER_METADATA = Metadata(
 
 
 V3dZipperZapperParameters = typing.TypedDict('V3dZipperZapperParameters', {
-    "__STYXTYPE__": typing.Literal["3dZipperZapper"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dZipperZapper"]],
+    "input_file": InputPathType,
+    "output_prefix": str,
+    "mask_file": typing.NotRequired[InputPathType | None],
+    "min_slice_nvox": typing.NotRequired[float | None],
+    "min_streak_len": typing.NotRequired[float | None],
+    "do_out_slice_param": bool,
+    "no_out_bad_mask": bool,
+    "no_out_text_vals": bool,
+    "dont_use_streak": bool,
+    "dont_use_drop": bool,
+    "dont_use_corr": bool,
+    "min_streak_val": typing.NotRequired[float | None],
+    "min_drop_frac": typing.NotRequired[float | None],
+    "min_drop_diff": typing.NotRequired[float | None],
+    "min_corr_len": typing.NotRequired[float | None],
+    "min_corr_corr": typing.NotRequired[float | None],
+})
+V3dZipperZapperParametersTagged = typing.TypedDict('V3dZipperZapperParametersTagged', {
+    "@type": typing.Literal["afni/3dZipperZapper"],
     "input_file": InputPathType,
     "output_prefix": str,
     "mask_file": typing.NotRequired[InputPathType | None],
@@ -32,43 +51,11 @@ V3dZipperZapperParameters = typing.TypedDict('V3dZipperZapperParameters', {
     "min_corr_len": typing.NotRequired[float | None],
     "min_corr_corr": 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 {
-        "3dZipperZapper": v_3d_zipper_zapper_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 {
-        "3dZipperZapper": v_3d_zipper_zapper_outputs,
-    }.get(t)
 
 
 class V3dZipperZapperOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_zipper_zapper(...)`.
+    Output object returned when calling `V3dZipperZapperParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -101,7 +88,7 @@ def v_3d_zipper_zapper_params(
     min_drop_diff: float | None = None,
     min_corr_len: float | None = None,
     min_corr_corr: float | None = None,
-) -> V3dZipperZapperParameters:
+) -> V3dZipperZapperParametersTagged:
     """
     Build parameters.
     
@@ -139,7 +126,7 @@ def v_3d_zipper_zapper_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dZipperZapper",
+        "@type": "afni/3dZipperZapper",
         "input_file": input_file,
         "output_prefix": output_prefix,
         "do_out_slice_param": do_out_slice_param,
@@ -185,63 +172,63 @@ def v_3d_zipper_zapper_cargs(
     cargs.append("3dZipperZapper")
     cargs.extend([
         "-input",
-        execution.input_file(params.get("input_file"))
+        execution.input_file(params.get("input_file", None))
     ])
     cargs.extend([
         "-prefix",
-        params.get("output_prefix")
+        params.get("output_prefix", None)
     ])
-    if params.get("mask_file") is not None:
+    if params.get("mask_file", None) is not None:
         cargs.extend([
             "-mask",
-            execution.input_file(params.get("mask_file"))
+            execution.input_file(params.get("mask_file", None))
         ])
-    if params.get("min_slice_nvox") is not None:
+    if params.get("min_slice_nvox", None) is not None:
         cargs.extend([
             "-min_slice_nvox",
-            str(params.get("min_slice_nvox"))
+            str(params.get("min_slice_nvox", None))
         ])
-    if params.get("min_streak_len") is not None:
+    if params.get("min_streak_len", None) is not None:
         cargs.extend([
             "-min_streak_len",
-            str(params.get("min_streak_len"))
+            str(params.get("min_streak_len", None))
         ])
-    if params.get("do_out_slice_param"):
+    if params.get("do_out_slice_param", False):
         cargs.append("-do_out_slice_param")
-    if params.get("no_out_bad_mask"):
+    if params.get("no_out_bad_mask", False):
         cargs.append("-no_out_bad_mask")
-    if params.get("no_out_text_vals"):
+    if params.get("no_out_text_vals", False):
         cargs.append("-no_out_text_vals")
-    if params.get("dont_use_streak"):
+    if params.get("dont_use_streak", False):
         cargs.append("-dont_use_streak")
-    if params.get("dont_use_drop"):
+    if params.get("dont_use_drop", False):
         cargs.append("-dont_use_drop")
-    if params.get("dont_use_corr"):
+    if params.get("dont_use_corr", False):
         cargs.append("-dont_use_corr")
-    if params.get("min_streak_val") is not None:
+    if params.get("min_streak_val", None) is not None:
         cargs.extend([
             "-min_streak_val",
-            str(params.get("min_streak_val"))
+            str(params.get("min_streak_val", None))
         ])
-    if params.get("min_drop_frac") is not None:
+    if params.get("min_drop_frac", None) is not None:
         cargs.extend([
             "-min_drop_frac",
-            str(params.get("min_drop_frac"))
+            str(params.get("min_drop_frac", None))
         ])
-    if params.get("min_drop_diff") is not None:
+    if params.get("min_drop_diff", None) is not None:
         cargs.extend([
             "-min_drop_diff",
-            str(params.get("min_drop_diff"))
+            str(params.get("min_drop_diff", None))
         ])
-    if params.get("min_corr_len") is not None:
+    if params.get("min_corr_len", None) is not None:
         cargs.extend([
             "-min_corr_len",
-            str(params.get("min_corr_len"))
+            str(params.get("min_corr_len", None))
         ])
-    if params.get("min_corr_corr") is not None:
+    if params.get("min_corr_corr", None) is not None:
         cargs.extend([
             "-min_corr_corr",
-            str(params.get("min_corr_corr"))
+            str(params.get("min_corr_corr", None))
         ])
     return cargs
 
@@ -261,20 +248,22 @@ def v_3d_zipper_zapper_outputs(
     """
     ret = V3dZipperZapperOutputs(
         root=execution.output_file("."),
-        bad_slice_mask=execution.output_file(params.get("output_prefix") + "_badmask.nii.gz"),
-        bad_volumes_list=execution.output_file(params.get("output_prefix") + "_badvols.1D"),
-        per_volume_params=execution.output_file(params.get("output_prefix") + "_param.1D"),
-        calculated_slices=execution.output_file(params.get("output_prefix") + "_sli.1D"),
-        good_volumes_selector=execution.output_file(params.get("output_prefix") + "_goodvols.txt"),
+        bad_slice_mask=execution.output_file(params.get("output_prefix", None) + "_badmask.nii.gz"),
+        bad_volumes_list=execution.output_file(params.get("output_prefix", None) + "_badvols.1D"),
+        per_volume_params=execution.output_file(params.get("output_prefix", None) + "_param.1D"),
+        calculated_slices=execution.output_file(params.get("output_prefix", None) + "_sli.1D"),
+        good_volumes_selector=execution.output_file(params.get("output_prefix", None) + "_goodvols.txt"),
     )
     return ret
 
 
 def v_3d_zipper_zapper_execute(
     params: V3dZipperZapperParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dZipperZapperOutputs:
     """
+    3dZipperZapper
+    
     A basic program to highlight problematic volumes in data sets, especially
     EPI/DWI data sets with interleaved acquisition.
     
@@ -284,10 +273,12 @@ def v_3d_zipper_zapper_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dZipperZapperOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_ZIPPER_ZAPPER_METADATA)
     params = execution.params(params)
     cargs = v_3d_zipper_zapper_cargs(params, execution)
     ret = v_3d_zipper_zapper_outputs(params, execution)
@@ -315,6 +306,8 @@ def v_3d_zipper_zapper(
     runner: Runner | None = None,
 ) -> V3dZipperZapperOutputs:
     """
+    3dZipperZapper
+    
     A basic program to highlight problematic volumes in data sets, especially
     EPI/DWI data sets with interleaved acquisition.
     
@@ -356,8 +349,6 @@ def v_3d_zipper_zapper(
     Returns:
         NamedTuple of outputs (described in `V3dZipperZapperOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_ZIPPER_ZAPPER_METADATA)
     params = v_3d_zipper_zapper_params(
         input_file=input_file,
         output_prefix=output_prefix,
@@ -376,13 +367,13 @@ def v_3d_zipper_zapper(
         min_corr_len=min_corr_len,
         min_corr_corr=min_corr_corr,
     )
-    return v_3d_zipper_zapper_execute(params, execution)
+    return v_3d_zipper_zapper_execute(params, runner)
 
 
 __all__ = [
     "V3dZipperZapperOutputs",
-    "V3dZipperZapperParameters",
     "V_3D_ZIPPER_ZAPPER_METADATA",
     "v_3d_zipper_zapper",
+    "v_3d_zipper_zapper_execute",
     "v_3d_zipper_zapper_params",
 ]