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

niwrap_afni/afni/v_3d_rsfc.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_RSFC_METADATA = Metadata(
-    id="3744bd8abe61303eddd78489bba2b70611a8f241.boutiques",
+    id="156b536f6615a0cd1a6826bf0e798b84ac6b4756.boutiques",
     name="3dRSFC",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,34 @@ V_3D_RSFC_METADATA = Metadata(
 
 
 V3dRsfcParameters = typing.TypedDict('V3dRsfcParameters', {
-    "__STYXTYPE__": typing.Literal["3dRSFC"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dRSFC"]],
+    "fbot": float,
+    "ftop": float,
+    "input_dataset": InputPathType,
+    "despike": bool,
+    "ort_file": typing.NotRequired[InputPathType | None],
+    "dsort_file": typing.NotRequired[InputPathType | None],
+    "nodetrend": bool,
+    "time_step": typing.NotRequired[float | None],
+    "nfft": typing.NotRequired[int | None],
+    "norm": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "automask": bool,
+    "blur": typing.NotRequired[float | None],
+    "localpv": typing.NotRequired[float | None],
+    "input_alt": typing.NotRequired[InputPathType | None],
+    "band": typing.NotRequired[list[float] | None],
+    "prefix": typing.NotRequired[str | None],
+    "quiet": bool,
+    "no_rs_out": bool,
+    "un_bandpass_out": bool,
+    "no_rsfa": bool,
+    "bp_at_end": bool,
+    "notrans": bool,
+    "nosat": bool,
+})
+V3dRsfcParametersTagged = typing.TypedDict('V3dRsfcParametersTagged', {
+    "@type": typing.Literal["afni/3dRSFC"],
     "fbot": float,
     "ftop": float,
     "input_dataset": InputPathType,
@@ -40,43 +67,11 @@ V3dRsfcParameters = typing.TypedDict('V3dRsfcParameters', {
     "notrans": bool,
     "nosat": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dRSFC": v_3d_rsfc_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 {
-        "3dRSFC": v_3d_rsfc_outputs,
-    }.get(t)
 
 
 class V3dRsfcOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_rsfc(...)`.
+    Output object returned when calling `V3dRsfcParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -111,7 +106,7 @@ def v_3d_rsfc_params(
     bp_at_end: bool = False,
     notrans: bool = False,
     nosat: bool = False,
-) -> V3dRsfcParameters:
+) -> V3dRsfcParametersTagged:
     """
     Build parameters.
     
@@ -147,7 +142,7 @@ def v_3d_rsfc_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dRSFC",
+        "@type": "afni/3dRSFC",
         "fbot": fbot,
         "ftop": ftop,
         "input_dataset": input_dataset,
@@ -201,80 +196,80 @@ def v_3d_rsfc_cargs(
     """
     cargs = []
     cargs.append("3dRSFC")
-    cargs.append(str(params.get("fbot")))
-    cargs.append(str(params.get("ftop")))
-    cargs.append(execution.input_file(params.get("input_dataset")))
-    if params.get("despike"):
+    cargs.append(str(params.get("fbot", None)))
+    cargs.append(str(params.get("ftop", None)))
+    cargs.append(execution.input_file(params.get("input_dataset", None)))
+    if params.get("despike", False):
         cargs.append("-despike")
-    if params.get("ort_file") is not None:
+    if params.get("ort_file", None) is not None:
         cargs.extend([
             "-ort",
-            execution.input_file(params.get("ort_file"))
+            execution.input_file(params.get("ort_file", None))
         ])
-    if params.get("dsort_file") is not None:
+    if params.get("dsort_file", None) is not None:
         cargs.extend([
             "-dsort",
-            execution.input_file(params.get("dsort_file"))
+            execution.input_file(params.get("dsort_file", None))
         ])
-    if params.get("nodetrend"):
+    if params.get("nodetrend", False):
         cargs.append("-nodetrend")
-    if params.get("time_step") is not None:
+    if params.get("time_step", None) is not None:
         cargs.extend([
             "-dt",
-            str(params.get("time_step"))
+            str(params.get("time_step", None))
         ])
-    if params.get("nfft") is not None:
+    if params.get("nfft", None) is not None:
         cargs.extend([
             "-nfft",
-            str(params.get("nfft"))
+            str(params.get("nfft", None))
         ])
-    if params.get("norm"):
+    if params.get("norm", False):
         cargs.append("-norm")
-    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))
         ])
-    if params.get("automask"):
+    if params.get("automask", False):
         cargs.append("-automask")
-    if params.get("blur") is not None:
+    if params.get("blur", None) is not None:
         cargs.extend([
             "-blur",
-            str(params.get("blur"))
+            str(params.get("blur", None))
         ])
-    if params.get("localpv") is not None:
+    if params.get("localpv", None) is not None:
         cargs.extend([
             "-localPV",
-            str(params.get("localpv"))
+            str(params.get("localpv", None))
         ])
-    if params.get("input_alt") is not None:
+    if params.get("input_alt", None) is not None:
         cargs.extend([
             "-input",
-            execution.input_file(params.get("input_alt"))
+            execution.input_file(params.get("input_alt", None))
         ])
-    if params.get("band") is not None:
+    if params.get("band", None) is not None:
         cargs.extend([
             "-band",
-            *map(str, params.get("band"))
+            *map(str, params.get("band", 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)
         ])
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
-    if params.get("no_rs_out"):
+    if params.get("no_rs_out", False):
         cargs.append("-no_rs_out")
-    if params.get("un_bandpass_out"):
+    if params.get("un_bandpass_out", False):
         cargs.append("-un_bp_out")
-    if params.get("no_rsfa"):
+    if params.get("no_rsfa", False):
         cargs.append("-no_rsfa")
-    if params.get("bp_at_end"):
+    if params.get("bp_at_end", False):
         cargs.append("-bp_at_end")
-    if params.get("notrans"):
+    if params.get("notrans", False):
         cargs.append("-notrans")
-    if params.get("nosat"):
+    if params.get("nosat", False):
         cargs.append("-nosat")
     return cargs
 
@@ -294,17 +289,19 @@ def v_3d_rsfc_outputs(
     """
     ret = V3dRsfcOutputs(
         root=execution.output_file("."),
-        filtered_time_series=execution.output_file(params.get("prefix") + "_LFF+orig.*") if (params.get("prefix") is not None) else None,
-        un_bandpassed_series=execution.output_file(params.get("prefix") + "_unBP+orig.*") if (params.get("prefix") is not None) else None,
+        filtered_time_series=execution.output_file(params.get("prefix", None) + "_LFF+orig") if (params.get("prefix") is not None) else None,
+        un_bandpassed_series=execution.output_file(params.get("prefix", None) + "_unBP+orig") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_rsfc_execute(
     params: V3dRsfcParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dRsfcOutputs:
     """
+    3dRSFC
+    
     Program to calculate common resting state functional connectivity (RSFC)
     parameters.
     
@@ -314,10 +311,12 @@ def v_3d_rsfc_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dRsfcOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_RSFC_METADATA)
     params = execution.params(params)
     cargs = v_3d_rsfc_cargs(params, execution)
     ret = v_3d_rsfc_outputs(params, execution)
@@ -353,6 +352,8 @@ def v_3d_rsfc(
     runner: Runner | None = None,
 ) -> V3dRsfcOutputs:
     """
+    3dRSFC
+    
     Program to calculate common resting state functional connectivity (RSFC)
     parameters.
     
@@ -392,8 +393,6 @@ def v_3d_rsfc(
     Returns:
         NamedTuple of outputs (described in `V3dRsfcOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_RSFC_METADATA)
     params = v_3d_rsfc_params(
         fbot=fbot,
         ftop=ftop,
@@ -420,13 +419,13 @@ def v_3d_rsfc(
         notrans=notrans,
         nosat=nosat,
     )
-    return v_3d_rsfc_execute(params, execution)
+    return v_3d_rsfc_execute(params, runner)
 
 
 __all__ = [
     "V3dRsfcOutputs",
-    "V3dRsfcParameters",
     "V_3D_RSFC_METADATA",
     "v_3d_rsfc",
+    "v_3d_rsfc_execute",
     "v_3d_rsfc_params",
 ]

niwrap_afni/afni/v_3d_seg.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_SEG_METADATA = Metadata(
-    id="45ea7914f43838d036104b817cbe78bed257a1ac.boutiques",
+    id="e801d19e26c3d04a8a07ae8868f21f36e6c05921.boutiques",
     name="3dSeg",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,29 @@ V_3D_SEG_METADATA = Metadata(
 
 
 V3dSegParameters = typing.TypedDict('V3dSegParameters', {
-    "__STYXTYPE__": typing.Literal["3dSeg"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dSeg"]],
+    "anat": InputPathType,
+    "mask": typing.NotRequired[str | None],
+    "blur_meth": typing.NotRequired[str | None],
+    "bias_fwhm": typing.NotRequired[float | None],
+    "classes": typing.NotRequired[str | None],
+    "Bmrf": typing.NotRequired[float | None],
+    "bias_classes": typing.NotRequired[str | None],
+    "prefix": typing.NotRequired[str | None],
+    "overwrite": bool,
+    "debug": typing.NotRequired[float | None],
+    "mixfrac": typing.NotRequired[str | None],
+    "mixfloor": typing.NotRequired[float | None],
+    "gold": typing.NotRequired[InputPathType | None],
+    "gold_bias": typing.NotRequired[InputPathType | None],
+    "main_N": typing.NotRequired[float | None],
+    "cset": typing.NotRequired[InputPathType | None],
+    "labeltable": typing.NotRequired[InputPathType | None],
+    "vox_debug": typing.NotRequired[str | None],
+    "vox_debug_file": typing.NotRequired[str | None],
+})
+V3dSegParametersTagged = typing.TypedDict('V3dSegParametersTagged', {
+    "@type": typing.Literal["afni/3dSeg"],
     "anat": InputPathType,
     "mask": typing.NotRequired[str | None],
     "blur_meth": typing.NotRequired[str | None],
@@ -35,43 +57,11 @@ V3dSegParameters = typing.TypedDict('V3dSegParameters', {
     "vox_debug": typing.NotRequired[str | None],
     "vox_debug_file": 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 {
-        "3dSeg": v_3d_seg_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 {
-        "3dSeg": v_3d_seg_outputs,
-    }.get(t)
 
 
 class V3dSegOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_seg(...)`.
+    Output object returned when calling `V3dSegParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -103,7 +93,7 @@ def v_3d_seg_params(
     labeltable: InputPathType | None = None,
     vox_debug: str | None = None,
     vox_debug_file: str | None = None,
-) -> V3dSegParameters:
+) -> V3dSegParametersTagged:
     """
     Build parameters.
     
@@ -141,7 +131,7 @@ def v_3d_seg_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dSeg",
+        "@type": "afni/3dSeg",
         "anat": anat,
         "overwrite": overwrite,
     }
@@ -199,94 +189,94 @@ def v_3d_seg_cargs(
     cargs.append("3dSeg")
     cargs.extend([
         "-anat",
-        execution.input_file(params.get("anat"))
+        execution.input_file(params.get("anat", None))
     ])
-    if params.get("mask") is not None:
+    if params.get("mask", None) is not None:
         cargs.extend([
             "-mask",
-            params.get("mask")
+            params.get("mask", None)
         ])
-    if params.get("blur_meth") is not None:
+    if params.get("blur_meth", None) is not None:
         cargs.extend([
             "-blur_meth",
-            params.get("blur_meth")
+            params.get("blur_meth", None)
         ])
-    if params.get("bias_fwhm") is not None:
+    if params.get("bias_fwhm", None) is not None:
         cargs.extend([
             "-bias_fwhm",
-            str(params.get("bias_fwhm"))
+            str(params.get("bias_fwhm", None))
         ])
-    if params.get("classes") is not None:
+    if params.get("classes", None) is not None:
         cargs.extend([
             "-classes",
-            params.get("classes")
+            params.get("classes", None)
         ])
-    if params.get("Bmrf") is not None:
+    if params.get("Bmrf", None) is not None:
         cargs.extend([
             "-Bmrf",
-            str(params.get("Bmrf"))
+            str(params.get("Bmrf", None))
         ])
-    if params.get("bias_classes") is not None:
+    if params.get("bias_classes", None) is not None:
         cargs.extend([
             "-bias_classes",
-            params.get("bias_classes")
+            params.get("bias_classes", 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)
         ])
-    if params.get("overwrite"):
+    if params.get("overwrite", False):
         cargs.append("-overwrite")
-    if params.get("debug") is not None:
+    if params.get("debug", None) is not None:
         cargs.extend([
             "-debug",
-            str(params.get("debug"))
+            str(params.get("debug", None))
         ])
-    if params.get("mixfrac") is not None:
+    if params.get("mixfrac", None) is not None:
         cargs.extend([
             "-mixfrac",
-            params.get("mixfrac")
+            params.get("mixfrac", None)
         ])
-    if params.get("mixfloor") is not None:
+    if params.get("mixfloor", None) is not None:
         cargs.extend([
             "-mixfloor",
-            str(params.get("mixfloor"))
+            str(params.get("mixfloor", None))
         ])
-    if params.get("gold") is not None:
+    if params.get("gold", None) is not None:
         cargs.extend([
             "-gold",
-            execution.input_file(params.get("gold"))
+            execution.input_file(params.get("gold", None))
         ])
-    if params.get("gold_bias") is not None:
+    if params.get("gold_bias", None) is not None:
         cargs.extend([
             "-gold_bias",
-            execution.input_file(params.get("gold_bias"))
+            execution.input_file(params.get("gold_bias", None))
         ])
-    if params.get("main_N") is not None:
+    if params.get("main_N", None) is not None:
         cargs.extend([
             "-main_N",
-            str(params.get("main_N"))
+            str(params.get("main_N", None))
         ])
-    if params.get("cset") is not None:
+    if params.get("cset", None) is not None:
         cargs.extend([
             "-cset",
-            execution.input_file(params.get("cset"))
+            execution.input_file(params.get("cset", None))
         ])
-    if params.get("labeltable") is not None:
+    if params.get("labeltable", None) is not None:
         cargs.extend([
             "-labeltable",
-            execution.input_file(params.get("labeltable"))
+            execution.input_file(params.get("labeltable", None))
         ])
-    if params.get("vox_debug") is not None:
+    if params.get("vox_debug", None) is not None:
         cargs.extend([
             "-vox_debug",
-            params.get("vox_debug")
+            params.get("vox_debug", None)
         ])
-    if params.get("vox_debug_file") is not None:
+    if params.get("vox_debug_file", None) is not None:
         cargs.extend([
             "-vox_debug_file",
-            params.get("vox_debug_file")
+            params.get("vox_debug_file", None)
         ])
     return cargs
 
@@ -306,20 +296,22 @@ def v_3d_seg_outputs(
     """
     ret = V3dSegOutputs(
         root=execution.output_file("."),
-        segmented_volume=execution.output_file(params.get("prefix") + "_Segsy+orig.HEAD") if (params.get("prefix") is not None) else None,
-        bias_field=execution.output_file(params.get("prefix") + "_BiasField+orig.HEAD") if (params.get("prefix") is not None) else None,
-        classified_volume=execution.output_file(params.get("prefix") + "_Classes+orig.HEAD") if (params.get("prefix") is not None) else None,
+        segmented_volume=execution.output_file(params.get("prefix", None) + "_Segsy+orig.HEAD") if (params.get("prefix") is not None) else None,
+        bias_field=execution.output_file(params.get("prefix", None) + "_BiasField+orig.HEAD") if (params.get("prefix") is not None) else None,
+        classified_volume=execution.output_file(params.get("prefix", None) + "_Classes+orig.HEAD") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_seg_execute(
     params: V3dSegParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dSegOutputs:
     """
-    Segments brain volumes into tissue classes with optional global and voxelwise
-    priors.
+    3dSeg
+    
+    Segments brain volumes into tissue classes with optional global and
+    voxelwise priors.
     
     Author: AFNI Developers
     
@@ -327,10 +319,12 @@ def v_3d_seg_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dSegOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_SEG_METADATA)
     params = execution.params(params)
     cargs = v_3d_seg_cargs(params, execution)
     ret = v_3d_seg_outputs(params, execution)
@@ -361,8 +355,10 @@ def v_3d_seg(
     runner: Runner | None = None,
 ) -> V3dSegOutputs:
     """
-    Segments brain volumes into tissue classes with optional global and voxelwise
-    priors.
+    3dSeg
+    
+    Segments brain volumes into tissue classes with optional global and
+    voxelwise priors.
     
     Author: AFNI Developers
     
@@ -402,8 +398,6 @@ def v_3d_seg(
     Returns:
         NamedTuple of outputs (described in `V3dSegOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_SEG_METADATA)
     params = v_3d_seg_params(
         anat=anat,
         mask=mask,
@@ -425,13 +419,13 @@ def v_3d_seg(
         vox_debug=vox_debug,
         vox_debug_file=vox_debug_file,
     )
-    return v_3d_seg_execute(params, execution)
+    return v_3d_seg_execute(params, runner)
 
 
 __all__ = [
     "V3dSegOutputs",
-    "V3dSegParameters",
     "V_3D_SEG_METADATA",
     "v_3d_seg",
+    "v_3d_seg_execute",
     "v_3d_seg_params",
 ]