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

niwrap_afni/afni/v_3ddelay.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DDELAY_METADATA = Metadata(
-    id="2d26920b8cdbf0a89ad3b54faeeb0771184e4e3d.boutiques",
+    id="9f445bfd4e22e8acf1539bc36a66ae74a99fda8c.boutiques",
     name="3ddelay",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,34 @@ V_3DDELAY_METADATA = Metadata(
 
 
 V3ddelayParameters = typing.TypedDict('V3ddelayParameters', {
-    "__STYXTYPE__": typing.Literal["3ddelay"],
+    "@type": typing.NotRequired[typing.Literal["afni/3ddelay"]],
+    "input_file": InputPathType,
+    "reference_file": InputPathType,
+    "sampling_freq": float,
+    "stim_period": float,
+    "prefix": typing.NotRequired[str | None],
+    "polort": typing.NotRequired[float | None],
+    "nodtrnd": bool,
+    "units_seconds": bool,
+    "units_degrees": bool,
+    "units_radians": bool,
+    "phzwrp": bool,
+    "nophzwrp": bool,
+    "phzreverse": bool,
+    "phzscale": typing.NotRequired[float | None],
+    "bias": bool,
+    "nobias": bool,
+    "dsamp": bool,
+    "nodsamp": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "nfirst": typing.NotRequired[float | None],
+    "nlast": typing.NotRequired[float | None],
+    "co": typing.NotRequired[float | None],
+    "asc": typing.NotRequired[str | None],
+    "ascts": typing.NotRequired[str | None],
+})
+V3ddelayParametersTagged = typing.TypedDict('V3ddelayParametersTagged', {
+    "@type": typing.Literal["afni/3ddelay"],
     "input_file": InputPathType,
     "reference_file": InputPathType,
     "sampling_freq": float,
@@ -40,43 +67,11 @@ V3ddelayParameters = typing.TypedDict('V3ddelayParameters', {
     "asc": typing.NotRequired[str | None],
     "ascts": 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 {
-        "3ddelay": v_3ddelay_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 {
-        "3ddelay": v_3ddelay_outputs,
-    }.get(t)
 
 
 class V3ddelayOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3ddelay(...)`.
+    Output object returned when calling `V3ddelayParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -115,7 +110,7 @@ def v_3ddelay_params(
     co: float | None = None,
     asc: str | None = None,
     ascts: str | None = None,
-) -> V3ddelayParameters:
+) -> V3ddelayParametersTagged:
     """
     Build parameters.
     
@@ -153,7 +148,7 @@ def v_3ddelay_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3ddelay",
+        "@type": "afni/3ddelay",
         "input_file": input_file,
         "reference_file": reference_file,
         "sampling_freq": sampling_freq,
@@ -206,82 +201,82 @@ def v_3ddelay_cargs(
     """
     cargs = []
     cargs.append("3ddelay")
-    cargs.append(execution.input_file(params.get("input_file")))
-    cargs.append(execution.input_file(params.get("reference_file")))
+    cargs.append(execution.input_file(params.get("input_file", None)))
+    cargs.append(execution.input_file(params.get("reference_file", None)))
     cargs.extend([
         "-fs",
-        str(params.get("sampling_freq"))
+        str(params.get("sampling_freq", None))
     ])
     cargs.extend([
         "-T",
-        str(params.get("stim_period"))
+        str(params.get("stim_period", 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("polort") is not None:
+    if params.get("polort", None) is not None:
         cargs.extend([
             "-polort",
-            str(params.get("polort"))
+            str(params.get("polort", None))
         ])
-    if params.get("nodtrnd"):
+    if params.get("nodtrnd", False):
         cargs.append("-nodtrnd")
-    if params.get("units_seconds"):
+    if params.get("units_seconds", False):
         cargs.append("-uS")
-    if params.get("units_degrees"):
+    if params.get("units_degrees", False):
         cargs.append("-uD")
-    if params.get("units_radians"):
+    if params.get("units_radians", False):
         cargs.append("-uR")
-    if params.get("phzwrp"):
+    if params.get("phzwrp", False):
         cargs.append("-phzwrp")
-    if params.get("nophzwrp"):
+    if params.get("nophzwrp", False):
         cargs.append("-nophzwrp")
-    if params.get("phzreverse"):
+    if params.get("phzreverse", False):
         cargs.append("-phzreverse")
-    if params.get("phzscale") is not None:
+    if params.get("phzscale", None) is not None:
         cargs.extend([
             "-phzscale",
-            str(params.get("phzscale"))
+            str(params.get("phzscale", None))
         ])
-    if params.get("bias"):
+    if params.get("bias", False):
         cargs.append("-bias")
-    if params.get("nobias"):
+    if params.get("nobias", False):
         cargs.append("-nobias")
-    if params.get("dsamp"):
+    if params.get("dsamp", False):
         cargs.append("-dsamp")
-    if params.get("nodsamp"):
+    if params.get("nodsamp", False):
         cargs.append("-nodsamp")
-    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("nfirst") is not None:
+    if params.get("nfirst", None) is not None:
         cargs.extend([
             "-nfirst",
-            str(params.get("nfirst"))
+            str(params.get("nfirst", None))
         ])
-    if params.get("nlast") is not None:
+    if params.get("nlast", None) is not None:
         cargs.extend([
             "-nlast",
-            str(params.get("nlast"))
+            str(params.get("nlast", None))
         ])
-    if params.get("co") is not None:
+    if params.get("co", None) is not None:
         cargs.extend([
             "-co",
-            str(params.get("co"))
+            str(params.get("co", None))
         ])
-    if params.get("asc") is not None:
+    if params.get("asc", None) is not None:
         cargs.extend([
             "-asc",
-            params.get("asc")
+            params.get("asc", None)
         ])
-    if params.get("ascts") is not None:
+    if params.get("ascts", None) is not None:
         cargs.extend([
             "-ascts",
-            params.get("ascts")
+            params.get("ascts", None)
         ])
     return cargs
 
@@ -301,21 +296,23 @@ def v_3ddelay_outputs(
     """
     ret = V3ddelayOutputs(
         root=execution.output_file("."),
-        output_brick=execution.output_file(params.get("prefix") + ".DEL+orig.BRIK") if (params.get("prefix") is not None) else None,
-        output_asc=execution.output_file(params.get("prefix") + ".ASC") if (params.get("prefix") is not None) else None,
-        output_asc_log=execution.output_file(params.get("prefix") + ".ASC.log") if (params.get("prefix") is not None) else None,
-        output_asc_ts=execution.output_file(params.get("prefix") + ".ASC.ts") if (params.get("prefix") is not None) else None,
+        output_brick=execution.output_file(params.get("prefix", None) + ".DEL+orig.BRIK") if (params.get("prefix") is not None) else None,
+        output_asc=execution.output_file(params.get("prefix", None) + ".ASC") if (params.get("prefix") is not None) else None,
+        output_asc_log=execution.output_file(params.get("prefix", None) + ".ASC.log") if (params.get("prefix") is not None) else None,
+        output_asc_ts=execution.output_file(params.get("prefix", None) + ".ASC.ts") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3ddelay_execute(
     params: V3ddelayParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3ddelayOutputs:
     """
-    Estimates the time delay between each voxel time series in a 3D+time dataset and
-    a reference time series.
+    3ddelay
+    
+    Estimates the time delay between each voxel time series in a 3D+time dataset
+    and a reference time series.
     
     Author: AFNI Developers
     
@@ -323,10 +320,12 @@ def v_3ddelay_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3ddelayOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DDELAY_METADATA)
     params = execution.params(params)
     cargs = v_3ddelay_cargs(params, execution)
     ret = v_3ddelay_outputs(params, execution)
@@ -362,8 +361,10 @@ def v_3ddelay(
     runner: Runner | None = None,
 ) -> V3ddelayOutputs:
     """
-    Estimates the time delay between each voxel time series in a 3D+time dataset and
-    a reference time series.
+    3ddelay
+    
+    Estimates the time delay between each voxel time series in a 3D+time dataset
+    and a reference time series.
     
     Author: AFNI Developers
     
@@ -403,8 +404,6 @@ def v_3ddelay(
     Returns:
         NamedTuple of outputs (described in `V3ddelayOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DDELAY_METADATA)
     params = v_3ddelay_params(
         input_file=input_file,
         reference_file=reference_file,
@@ -431,13 +430,13 @@ def v_3ddelay(
         asc=asc,
         ascts=ascts,
     )
-    return v_3ddelay_execute(params, execution)
+    return v_3ddelay_execute(params, runner)
 
 
 __all__ = [
     "V3ddelayOutputs",
-    "V3ddelayParameters",
     "V_3DDELAY_METADATA",
     "v_3ddelay",
+    "v_3ddelay_execute",
     "v_3ddelay_params",
 ]

niwrap_afni/afni/v_3ddot.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DDOT_METADATA = Metadata(
-    id="4a668d35fe20645df0c5d29ea0e2920f566ca390.boutiques",
+    id="75b04eb5f9c166f057a0c9581a386025f83e4db7.boutiques",
     name="3ddot",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,25 @@ V_3DDOT_METADATA = Metadata(
 
 
 V3ddotParameters = typing.TypedDict('V3ddotParameters', {
-    "__STYXTYPE__": typing.Literal["3ddot"],
+    "@type": typing.NotRequired[typing.Literal["afni/3ddot"]],
+    "input_datasets": list[InputPathType],
+    "mask": typing.NotRequired[InputPathType | None],
+    "mrange": typing.NotRequired[list[float] | None],
+    "demean": bool,
+    "docor": bool,
+    "dodot": bool,
+    "docoef": bool,
+    "dosums": bool,
+    "doeta2": bool,
+    "dodice": bool,
+    "show_labels": bool,
+    "upper": bool,
+    "full": bool,
+    "1D": bool,
+    "NIML": bool,
+})
+V3ddotParametersTagged = typing.TypedDict('V3ddotParametersTagged', {
+    "@type": typing.Literal["afni/3ddot"],
     "input_datasets": list[InputPathType],
     "mask": typing.NotRequired[InputPathType | None],
     "mrange": typing.NotRequired[list[float] | None],
@@ -31,43 +49,11 @@ V3ddotParameters = typing.TypedDict('V3ddotParameters', {
     "1D": bool,
     "NIML": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3ddot": v_3ddot_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 {
-        "3ddot": v_3ddot_outputs,
-    }.get(t)
 
 
 class V3ddotOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3ddot(...)`.
+    Output object returned when calling `V3ddotParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -91,7 +77,7 @@ def v_3ddot_params(
     full: bool = False,
     v_1_d: bool = False,
     niml: bool = False,
-) -> V3ddotParameters:
+) -> V3ddotParametersTagged:
     """
     Build parameters.
     
@@ -121,7 +107,7 @@ def v_3ddot_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3ddot",
+        "@type": "afni/3ddot",
         "input_datasets": input_datasets,
         "demean": demean,
         "docor": docor,
@@ -158,40 +144,40 @@ def v_3ddot_cargs(
     """
     cargs = []
     cargs.append("3ddot")
-    cargs.extend([execution.input_file(f) for f in params.get("input_datasets")])
-    if params.get("mask") is not None:
+    cargs.extend([execution.input_file(f) for f in params.get("input_datasets", 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("mrange") is not None:
+    if params.get("mrange", None) is not None:
         cargs.extend([
             "-mrange",
-            *map(str, params.get("mrange"))
+            *map(str, params.get("mrange", None))
         ])
-    if params.get("demean"):
+    if params.get("demean", False):
         cargs.append("-demean")
-    if params.get("docor"):
+    if params.get("docor", False):
         cargs.append("-docor")
-    if params.get("dodot"):
+    if params.get("dodot", False):
         cargs.append("-dodot")
-    if params.get("docoef"):
+    if params.get("docoef", False):
         cargs.append("-docoef")
-    if params.get("dosums"):
+    if params.get("dosums", False):
         cargs.append("-dosums")
-    if params.get("doeta2"):
+    if params.get("doeta2", False):
         cargs.append("-doeta2")
-    if params.get("dodice"):
+    if params.get("dodice", False):
         cargs.append("-dodice")
-    if params.get("show_labels"):
+    if params.get("show_labels", False):
         cargs.append("-show_labels")
-    if params.get("upper"):
+    if params.get("upper", False):
         cargs.append("-upper")
-    if params.get("full"):
+    if params.get("full", False):
         cargs.append("-full")
-    if params.get("1D"):
+    if params.get("1D", False):
         cargs.append("-1D")
-    if params.get("NIML"):
+    if params.get("NIML", False):
         cargs.append("-NIML")
     return cargs
 
@@ -218,9 +204,11 @@ def v_3ddot_outputs(
 
 def v_3ddot_execute(
     params: V3ddotParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3ddotOutputs:
     """
+    3ddot
+    
     Computes correlation coefficients between sub-brick pairs.
     
     Author: AFNI Developers
@@ -229,10 +217,12 @@ def v_3ddot_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3ddotOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DDOT_METADATA)
     params = execution.params(params)
     cargs = v_3ddot_cargs(params, execution)
     ret = v_3ddot_outputs(params, execution)
@@ -259,6 +249,8 @@ def v_3ddot(
     runner: Runner | None = None,
 ) -> V3ddotOutputs:
     """
+    3ddot
+    
     Computes correlation coefficients between sub-brick pairs.
     
     Author: AFNI Developers
@@ -291,8 +283,6 @@ def v_3ddot(
     Returns:
         NamedTuple of outputs (described in `V3ddotOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DDOT_METADATA)
     params = v_3ddot_params(
         input_datasets=input_datasets,
         mask=mask,
@@ -310,13 +300,13 @@ def v_3ddot(
         v_1_d=v_1_d,
         niml=niml,
     )
-    return v_3ddot_execute(params, execution)
+    return v_3ddot_execute(params, runner)
 
 
 __all__ = [
     "V3ddotOutputs",
-    "V3ddotParameters",
     "V_3DDOT_METADATA",
     "v_3ddot",
+    "v_3ddot_execute",
     "v_3ddot_params",
 ]

niwrap_afni/afni/v_3ddot_beta.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DDOT_BETA_METADATA = Metadata(
-    id="713d46495fc511b0c705f51aedcff3425be6c314.boutiques",
+    id="29f85c73d1e8013050b3f32ac425b1405e6a97d0.boutiques",
     name="3ddot_beta",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,49 +14,24 @@ V_3DDOT_BETA_METADATA = Metadata(
 
 
 V3ddotBetaParameters = typing.TypedDict('V3ddotBetaParameters', {
-    "__STYXTYPE__": typing.Literal["3ddot_beta"],
+    "@type": typing.NotRequired[typing.Literal["afni/3ddot_beta"]],
+    "input_file": InputPathType,
+    "prefix": str,
+    "doeta2": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+})
+V3ddotBetaParametersTagged = typing.TypedDict('V3ddotBetaParametersTagged', {
+    "@type": typing.Literal["afni/3ddot_beta"],
     "input_file": InputPathType,
     "prefix": str,
     "doeta2": bool,
     "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 {
-        "3ddot_beta": v_3ddot_beta_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 {
-        "3ddot_beta": v_3ddot_beta_outputs,
-    }.get(t)
 
 
 class V3ddotBetaOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3ddot_beta(...)`.
+    Output object returned when calling `V3ddotBetaParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def v_3ddot_beta_params(
     prefix: str,
     doeta2: bool = False,
     mask: InputPathType | None = None,
-) -> V3ddotBetaParameters:
+) -> V3ddotBetaParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +57,7 @@ def v_3ddot_beta_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3ddot_beta",
+        "@type": "afni/3ddot_beta",
         "input_file": input_file,
         "prefix": prefix,
         "doeta2": doeta2,
@@ -109,18 +84,18 @@ def v_3ddot_beta_cargs(
     cargs.append("3ddot_beta")
     cargs.extend([
         "-input",
-        execution.input_file(params.get("input_file"))
+        execution.input_file(params.get("input_file", None))
     ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("doeta2"):
+    if params.get("doeta2", False):
         cargs.append("-doeta2")
-    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
 
@@ -140,16 +115,18 @@ def v_3ddot_beta_outputs(
     """
     ret = V3ddotBetaOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("prefix") + "_eta2.dat"),
+        output_file=execution.output_file(params.get("prefix", None) + "_eta2.dat"),
     )
     return ret
 
 
 def v_3ddot_beta_execute(
     params: V3ddotBetaParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3ddotBetaOutputs:
     """
+    3ddot_beta
+    
     Beta version of updating 3ddot, currently only performing eta2 tests and
     outputting a full matrix to a text file.
     
@@ -159,10 +136,12 @@ def v_3ddot_beta_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3ddotBetaOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DDOT_BETA_METADATA)
     params = execution.params(params)
     cargs = v_3ddot_beta_cargs(params, execution)
     ret = v_3ddot_beta_outputs(params, execution)
@@ -178,6 +157,8 @@ def v_3ddot_beta(
     runner: Runner | None = None,
 ) -> V3ddotBetaOutputs:
     """
+    3ddot_beta
+    
     Beta version of updating 3ddot, currently only performing eta2 tests and
     outputting a full matrix to a text file.
     
@@ -194,21 +175,19 @@ def v_3ddot_beta(
     Returns:
         NamedTuple of outputs (described in `V3ddotBetaOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DDOT_BETA_METADATA)
     params = v_3ddot_beta_params(
         input_file=input_file,
         prefix=prefix,
         doeta2=doeta2,
         mask=mask,
     )
-    return v_3ddot_beta_execute(params, execution)
+    return v_3ddot_beta_execute(params, runner)
 
 
 __all__ = [
     "V3ddotBetaOutputs",
-    "V3ddotBetaParameters",
     "V_3DDOT_BETA_METADATA",
     "v_3ddot_beta",
+    "v_3ddot_beta_execute",
     "v_3ddot_beta_params",
 ]