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

niwrap_afni/afni/meica_py.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MEICA_PY_METADATA = Metadata(
-    id="0ef40c9e3811e940f045cb9c834086f22bf505b2.boutiques",
+    id="b446f47c0652504fc62596ad7811f616934e7136.boutiques",
     name="meica.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,18 @@ MEICA_PY_METADATA = Metadata(
 
 
 MeicaPyParameters = typing.TypedDict('MeicaPyParameters', {
-    "__STYXTYPE__": typing.Literal["meica.py"],
+    "@type": typing.NotRequired[typing.Literal["afni/meica.py"]],
+    "infile": InputPathType,
+    "echo_times": str,
+    "affine": str,
+    "output_directory": str,
+    "components": typing.NotRequired[float | None],
+    "talairach": bool,
+    "threshold": typing.NotRequired[float | None],
+    "debug": bool,
+})
+MeicaPyParametersTagged = typing.TypedDict('MeicaPyParametersTagged', {
+    "@type": typing.Literal["afni/meica.py"],
     "infile": InputPathType,
     "echo_times": str,
     "affine": str,
@@ -24,43 +35,11 @@ MeicaPyParameters = typing.TypedDict('MeicaPyParameters', {
     "threshold": typing.NotRequired[float | None],
     "debug": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "meica.py": meica_py_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 {
-        "meica.py": meica_py_outputs,
-    }.get(t)
 
 
 class MeicaPyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `meica_py(...)`.
+    Output object returned when calling `MeicaPyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -79,7 +58,7 @@ def meica_py_params(
     talairach: bool = False,
     threshold: float | None = None,
     debug: bool = False,
-) -> MeicaPyParameters:
+) -> MeicaPyParametersTagged:
     """
     Build parameters.
     
@@ -96,7 +75,7 @@ def meica_py_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "meica.py",
+        "@type": "afni/meica.py",
         "infile": infile,
         "echo_times": echo_times,
         "affine": affine,
@@ -128,33 +107,33 @@ def meica_py_cargs(
     cargs.append("meica.py")
     cargs.extend([
         "-d",
-        execution.input_file(params.get("infile"))
+        execution.input_file(params.get("infile", None))
     ])
     cargs.extend([
         "-e",
-        params.get("echo_times")
+        params.get("echo_times", None)
     ])
     cargs.extend([
         "-a",
-        params.get("affine")
+        params.get("affine", None)
     ])
     cargs.extend([
         "-o",
-        params.get("output_directory")
+        params.get("output_directory", None)
     ])
-    if params.get("components") is not None:
+    if params.get("components", None) is not None:
         cargs.extend([
             "-c",
-            str(params.get("components"))
+            str(params.get("components", None))
         ])
-    if params.get("talairach"):
+    if params.get("talairach", False):
         cargs.append("-t")
-    if params.get("threshold") is not None:
+    if params.get("threshold", None) is not None:
         cargs.extend([
             "--thresh",
-            str(params.get("threshold"))
+            str(params.get("threshold", None))
         ])
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
     return cargs
 
@@ -174,17 +153,19 @@ def meica_py_outputs(
     """
     ret = MeicaPyOutputs(
         root=execution.output_file("."),
-        cleaned_bold=execution.output_file(params.get("output_directory") + "/cleaned_bold.nii.gz"),
-        components_output=execution.output_file(params.get("output_directory") + "/components.nii.gz"),
+        cleaned_bold=execution.output_file(params.get("output_directory", None) + "/cleaned_bold.nii.gz"),
+        components_output=execution.output_file(params.get("output_directory", None) + "/components.nii.gz"),
     )
     return ret
 
 
 def meica_py_execute(
     params: MeicaPyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MeicaPyOutputs:
     """
+    meica.py
+    
     Multi-Echo Independent Component Analysis for fMRI denoising.
     
     Author: AFNI Developers
@@ -193,10 +174,12 @@ def meica_py_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MeicaPyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MEICA_PY_METADATA)
     params = execution.params(params)
     cargs = meica_py_cargs(params, execution)
     ret = meica_py_outputs(params, execution)
@@ -216,6 +199,8 @@ def meica_py(
     runner: Runner | None = None,
 ) -> MeicaPyOutputs:
     """
+    meica.py
+    
     Multi-Echo Independent Component Analysis for fMRI denoising.
     
     Author: AFNI Developers
@@ -235,8 +220,6 @@ def meica_py(
     Returns:
         NamedTuple of outputs (described in `MeicaPyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MEICA_PY_METADATA)
     params = meica_py_params(
         infile=infile,
         echo_times=echo_times,
@@ -247,13 +230,13 @@ def meica_py(
         threshold=threshold,
         debug=debug,
     )
-    return meica_py_execute(params, execution)
+    return meica_py_execute(params, runner)
 
 
 __all__ = [
     "MEICA_PY_METADATA",
     "MeicaPyOutputs",
-    "MeicaPyParameters",
     "meica_py",
+    "meica_py_execute",
     "meica_py_params",
 ]

niwrap_afni/afni/myget.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MYGET_METADATA = Metadata(
-    id="e02e3476f488deccf0d90ec8d75f3911d20f2f0e.boutiques",
+    id="6924b5dd88139a6314a9d06a406e8d99114cb986.boutiques",
     name="myget",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,48 +14,22 @@ MYGET_METADATA = Metadata(
 
 
 MygetParameters = typing.TypedDict('MygetParameters', {
-    "__STYXTYPE__": typing.Literal["myget"],
+    "@type": typing.NotRequired[typing.Literal["afni/myget"]],
+    "protocol_version": typing.NotRequired[typing.Literal["-1", "-1.1"] | None],
+    "url": str,
+    "output_file": str,
+})
+MygetParametersTagged = typing.TypedDict('MygetParametersTagged', {
+    "@type": typing.Literal["afni/myget"],
     "protocol_version": typing.NotRequired[typing.Literal["-1", "-1.1"] | None],
     "url": str,
     "output_file": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "myget": myget_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 {
-        "myget": myget_outputs,
-    }.get(t)
 
 
 class MygetOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `myget(...)`.
+    Output object returned when calling `MygetParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def myget_params(
     url: str,
     output_file: str,
     protocol_version: typing.Literal["-1", "-1.1"] | None = None,
-) -> MygetParameters:
+) -> MygetParametersTagged:
     """
     Build parameters.
     
@@ -80,7 +54,7 @@ def myget_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "myget",
+        "@type": "afni/myget",
         "url": url,
         "output_file": output_file,
     }
@@ -104,12 +78,12 @@ def myget_cargs(
     """
     cargs = []
     cargs.append("myget")
-    if params.get("protocol_version") is not None:
-        cargs.append(params.get("protocol_version"))
-    cargs.append(params.get("url"))
+    if params.get("protocol_version", None) is not None:
+        cargs.append(params.get("protocol_version", None))
+    cargs.append(params.get("url", None))
     cargs.extend([
         ">",
-        params.get("output_file")
+        params.get("output_file", None)
     ])
     return cargs
 
@@ -129,16 +103,18 @@ def myget_outputs(
     """
     ret = MygetOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("output_file")),
+        output_file=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def myget_execute(
     params: MygetParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MygetOutputs:
     """
+    myget
+    
     A simple file downloader from a URL.
     
     Author: AFNI Developers
@@ -147,10 +123,12 @@ def myget_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MygetOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MYGET_METADATA)
     params = execution.params(params)
     cargs = myget_cargs(params, execution)
     ret = myget_outputs(params, execution)
@@ -165,6 +143,8 @@ def myget(
     runner: Runner | None = None,
 ) -> MygetOutputs:
     """
+    myget
+    
     A simple file downloader from a URL.
     
     Author: AFNI Developers
@@ -180,20 +160,18 @@ def myget(
     Returns:
         NamedTuple of outputs (described in `MygetOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MYGET_METADATA)
     params = myget_params(
         protocol_version=protocol_version,
         url=url,
         output_file=output_file,
     )
-    return myget_execute(params, execution)
+    return myget_execute(params, runner)
 
 
 __all__ = [
     "MYGET_METADATA",
     "MygetOutputs",
-    "MygetParameters",
     "myget",
+    "myget_execute",
     "myget_params",
 ]

niwrap_afni/afni/neuro_deconvolve_py.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 NEURO_DECONVOLVE_PY_METADATA = Metadata(
-    id="154583959fdfd006d275bd6d8f9c6a8e067b7747.boutiques",
+    id="68370abf4e1ff88106fda189b221bf2ee052bc8b.boutiques",
     name="neuro_deconvolve.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,20 @@ NEURO_DECONVOLVE_PY_METADATA = Metadata(
 
 
 NeuroDeconvolvePyParameters = typing.TypedDict('NeuroDeconvolvePyParameters', {
-    "__STYXTYPE__": typing.Literal["neuro_deconvolve.py"],
+    "@type": typing.NotRequired[typing.Literal["afni/neuro_deconvolve.py"]],
+    "input_file": InputPathType,
+    "prefix": str,
+    "script": str,
+    "kernel": typing.NotRequired[str | None],
+    "kernel_file": typing.NotRequired[str | None],
+    "mask_dset": typing.NotRequired[InputPathType | None],
+    "old_style": bool,
+    "tr": typing.NotRequired[float | None],
+    "tr_nup": typing.NotRequired[float | None],
+    "verbosity": typing.NotRequired[float | None],
+})
+NeuroDeconvolvePyParametersTagged = typing.TypedDict('NeuroDeconvolvePyParametersTagged', {
+    "@type": typing.Literal["afni/neuro_deconvolve.py"],
     "input_file": InputPathType,
     "prefix": str,
     "script": str,
@@ -26,43 +39,11 @@ NeuroDeconvolvePyParameters = typing.TypedDict('NeuroDeconvolvePyParameters', {
     "tr_nup": typing.NotRequired[float | None],
     "verbosity": 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 {
-        "neuro_deconvolve.py": neuro_deconvolve_py_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 {
-        "neuro_deconvolve.py": neuro_deconvolve_py_outputs,
-    }.get(t)
 
 
 class NeuroDeconvolvePyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `neuro_deconvolve_py(...)`.
+    Output object returned when calling `NeuroDeconvolvePyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -85,7 +66,7 @@ def neuro_deconvolve_py_params(
     tr: float | None = None,
     tr_nup: float | None = None,
     verbosity: float | None = None,
-) -> NeuroDeconvolvePyParameters:
+) -> NeuroDeconvolvePyParametersTagged:
     """
     Build parameters.
     
@@ -106,7 +87,7 @@ def neuro_deconvolve_py_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "neuro_deconvolve.py",
+        "@type": "afni/neuro_deconvolve.py",
         "input_file": input_file,
         "prefix": prefix,
         "script": script,
@@ -142,40 +123,40 @@ def neuro_deconvolve_py_cargs(
     """
     cargs = []
     cargs.append("neuro_deconvolve.py")
-    cargs.append(execution.input_file(params.get("input_file")))
-    cargs.append(params.get("prefix"))
-    cargs.append(params.get("script"))
-    if params.get("kernel") is not None:
+    cargs.append(execution.input_file(params.get("input_file", None)))
+    cargs.append(params.get("prefix", None))
+    cargs.append(params.get("script", None))
+    if params.get("kernel", None) is not None:
         cargs.extend([
             "-kernel",
-            params.get("kernel")
+            params.get("kernel", None)
         ])
-    if params.get("kernel_file") is not None:
+    if params.get("kernel_file", None) is not None:
         cargs.extend([
             "-kernel_file",
-            params.get("kernel_file")
+            params.get("kernel_file", None)
         ])
-    if params.get("mask_dset") is not None:
+    if params.get("mask_dset", None) is not None:
         cargs.extend([
             "-mask_dset",
-            execution.input_file(params.get("mask_dset"))
+            execution.input_file(params.get("mask_dset", None))
         ])
-    if params.get("old_style"):
+    if params.get("old_style", False):
         cargs.append("-old")
-    if params.get("tr") is not None:
+    if params.get("tr", None) is not None:
         cargs.extend([
             "-tr",
-            str(params.get("tr"))
+            str(params.get("tr", None))
         ])
-    if params.get("tr_nup") is not None:
+    if params.get("tr_nup", None) is not None:
         cargs.extend([
             "-tr_nup",
-            str(params.get("tr_nup"))
+            str(params.get("tr_nup", None))
         ])
-    if params.get("verbosity") is not None:
+    if params.get("verbosity", None) is not None:
         cargs.extend([
             "-verb",
-            str(params.get("verbosity"))
+            str(params.get("verbosity", None))
         ])
     return cargs
 
@@ -195,20 +176,22 @@ def neuro_deconvolve_py_outputs(
     """
     ret = NeuroDeconvolvePyOutputs(
         root=execution.output_file("."),
-        output_head=execution.output_file(params.get("prefix") + "+orig.HEAD"),
-        output_brik=execution.output_file(params.get("prefix") + "+orig.BRIK"),
-        kernel_file_out=execution.output_file(params.get("kernel_file")) if (params.get("kernel_file") is not None) else None,
+        output_head=execution.output_file(params.get("prefix", None) + "+orig.HEAD"),
+        output_brik=execution.output_file(params.get("prefix", None) + "+orig.BRIK"),
+        kernel_file_out=execution.output_file(params.get("kernel_file", None)) if (params.get("kernel_file") is not None) else None,
     )
     return ret
 
 
 def neuro_deconvolve_py_execute(
     params: NeuroDeconvolvePyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> NeuroDeconvolvePyOutputs:
     """
-    Generate a script to apply 3dTfitter to deconvolve an MRI signal (BOLD response
-    curve) into a neuro response curve.
+    neuro_deconvolve.py
+    
+    Generate a script to apply 3dTfitter to deconvolve an MRI signal (BOLD
+    response curve) into a neuro response curve.
     
     Author: AFNI Developers
     
@@ -216,10 +199,12 @@ def neuro_deconvolve_py_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `NeuroDeconvolvePyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(NEURO_DECONVOLVE_PY_METADATA)
     params = execution.params(params)
     cargs = neuro_deconvolve_py_cargs(params, execution)
     ret = neuro_deconvolve_py_outputs(params, execution)
@@ -241,8 +226,10 @@ def neuro_deconvolve_py(
     runner: Runner | None = None,
 ) -> NeuroDeconvolvePyOutputs:
     """
-    Generate a script to apply 3dTfitter to deconvolve an MRI signal (BOLD response
-    curve) into a neuro response curve.
+    neuro_deconvolve.py
+    
+    Generate a script to apply 3dTfitter to deconvolve an MRI signal (BOLD
+    response curve) into a neuro response curve.
     
     Author: AFNI Developers
     
@@ -265,8 +252,6 @@ def neuro_deconvolve_py(
     Returns:
         NamedTuple of outputs (described in `NeuroDeconvolvePyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(NEURO_DECONVOLVE_PY_METADATA)
     params = neuro_deconvolve_py_params(
         input_file=input_file,
         prefix=prefix,
@@ -279,13 +264,13 @@ def neuro_deconvolve_py(
         tr_nup=tr_nup,
         verbosity=verbosity,
     )
-    return neuro_deconvolve_py_execute(params, execution)
+    return neuro_deconvolve_py_execute(params, runner)
 
 
 __all__ = [
     "NEURO_DECONVOLVE_PY_METADATA",
     "NeuroDeconvolvePyOutputs",
-    "NeuroDeconvolvePyParameters",
     "neuro_deconvolve_py",
+    "neuro_deconvolve_py_execute",
     "neuro_deconvolve_py_params",
 ]