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

niwrap_afni/afni/v_3d_brain_voyagerto_afni.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_BRAIN_VOYAGERTO_AFNI_METADATA = Metadata(
-    id="5fa4482f1d05556b8c1f6948d6ca7a34ed478089.boutiques",
+    id="286218a64fa6e1151307ace8ad14804dacd20778.boutiques",
     name="3dBRAIN_VOYAGERtoAFNI",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,24 @@ V_3D_BRAIN_VOYAGERTO_AFNI_METADATA = Metadata(
 
 
 V3dBrainVoyagertoAfniParameters = typing.TypedDict('V3dBrainVoyagertoAfniParameters', {
-    "__STYXTYPE__": typing.Literal["3dBRAIN_VOYAGERtoAFNI"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dBRAIN_VOYAGERtoAFNI"]],
+    "input_file": InputPathType,
+    "force_byte_swap": bool,
+    "brainvoyager_qx": bool,
+    "tlrc_space": bool,
+    "acpc_space": bool,
+    "orig_space": bool,
+    "prefix": typing.NotRequired[str | None],
+    "novolreg": bool,
+    "noxform": bool,
+    "set_environment": typing.NotRequired[str | None],
+    "trace_debugging": bool,
+    "trace_extreme_debugging": bool,
+    "turn_off_memory_tracing": bool,
+    "turn_on_memory_tracing": bool,
+})
+V3dBrainVoyagertoAfniParametersTagged = typing.TypedDict('V3dBrainVoyagertoAfniParametersTagged', {
+    "@type": typing.Literal["afni/3dBRAIN_VOYAGERtoAFNI"],
     "input_file": InputPathType,
     "force_byte_swap": bool,
     "brainvoyager_qx": bool,
@@ -30,43 +47,11 @@ V3dBrainVoyagertoAfniParameters = typing.TypedDict('V3dBrainVoyagertoAfniParamet
     "turn_off_memory_tracing": bool,
     "turn_on_memory_tracing": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dBRAIN_VOYAGERtoAFNI": v_3d_brain_voyagerto_afni_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 {
-        "3dBRAIN_VOYAGERtoAFNI": v_3d_brain_voyagerto_afni_outputs,
-    }.get(t)
 
 
 class V3dBrainVoyagertoAfniOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_brain_voyagerto_afni(...)`.
+    Output object returned when calling `V3dBrainVoyagertoAfniParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -91,7 +76,7 @@ def v_3d_brain_voyagerto_afni_params(
     trace_extreme_debugging: bool = False,
     turn_off_memory_tracing: bool = False,
     turn_on_memory_tracing: bool = False,
-) -> V3dBrainVoyagertoAfniParameters:
+) -> V3dBrainVoyagertoAfniParametersTagged:
     """
     Build parameters.
     
@@ -116,7 +101,7 @@ def v_3d_brain_voyagerto_afni_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dBRAIN_VOYAGERtoAFNI",
+        "@type": "afni/3dBRAIN_VOYAGERtoAFNI",
         "input_file": input_file,
         "force_byte_swap": force_byte_swap,
         "brainvoyager_qx": brainvoyager_qx,
@@ -154,39 +139,39 @@ def v_3d_brain_voyagerto_afni_cargs(
     cargs.append("3dBRAIN_VOYAGERtoAFNI")
     cargs.extend([
         "--input",
-        execution.input_file(params.get("input_file"))
+        execution.input_file(params.get("input_file", None))
     ])
-    if params.get("force_byte_swap"):
+    if params.get("force_byte_swap", False):
         cargs.append("-bs")
-    if params.get("brainvoyager_qx"):
+    if params.get("brainvoyager_qx", False):
         cargs.append("-qx")
-    if params.get("tlrc_space"):
+    if params.get("tlrc_space", False):
         cargs.append("-tlrc")
-    if params.get("acpc_space"):
+    if params.get("acpc_space", False):
         cargs.append("-acpc")
-    if params.get("orig_space"):
+    if params.get("orig_space", False):
         cargs.append("-orig")
-    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("novolreg"):
+    if params.get("novolreg", False):
         cargs.append("-novolreg")
-    if params.get("noxform"):
+    if params.get("noxform", False):
         cargs.append("-noxform")
-    if params.get("set_environment") is not None:
+    if params.get("set_environment", None) is not None:
         cargs.extend([
             "-setenv",
-            params.get("set_environment")
+            params.get("set_environment", None)
         ])
-    if params.get("trace_debugging"):
+    if params.get("trace_debugging", False):
         cargs.append("-trace")
-    if params.get("trace_extreme_debugging"):
+    if params.get("trace_extreme_debugging", False):
         cargs.append("-TRACE")
-    if params.get("turn_off_memory_tracing"):
+    if params.get("turn_off_memory_tracing", False):
         cargs.append("-nomall")
-    if params.get("turn_on_memory_tracing"):
+    if params.get("turn_on_memory_tracing", False):
         cargs.append("-yesmall")
     return cargs
 
@@ -214,11 +199,13 @@ def v_3d_brain_voyagerto_afni_outputs(
 
 def v_3d_brain_voyagerto_afni_execute(
     params: V3dBrainVoyagertoAfniParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dBrainVoyagertoAfniOutputs:
     """
-    Converts a BrainVoyager vmr dataset to AFNI's BRIK format based on information
-    from BrainVoyager's website.
+    3dBRAIN_VOYAGERtoAFNI
+    
+    Converts a BrainVoyager vmr dataset to AFNI's BRIK format based on
+    information from BrainVoyager's website.
     
     Author: AFNI Developers
     
@@ -226,10 +213,12 @@ def v_3d_brain_voyagerto_afni_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dBrainVoyagertoAfniOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_BRAIN_VOYAGERTO_AFNI_METADATA)
     params = execution.params(params)
     cargs = v_3d_brain_voyagerto_afni_cargs(params, execution)
     ret = v_3d_brain_voyagerto_afni_outputs(params, execution)
@@ -255,8 +244,10 @@ def v_3d_brain_voyagerto_afni(
     runner: Runner | None = None,
 ) -> V3dBrainVoyagertoAfniOutputs:
     """
-    Converts a BrainVoyager vmr dataset to AFNI's BRIK format based on information
-    from BrainVoyager's website.
+    3dBRAIN_VOYAGERtoAFNI
+    
+    Converts a BrainVoyager vmr dataset to AFNI's BRIK format based on
+    information from BrainVoyager's website.
     
     Author: AFNI Developers
     
@@ -283,8 +274,6 @@ def v_3d_brain_voyagerto_afni(
     Returns:
         NamedTuple of outputs (described in `V3dBrainVoyagertoAfniOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_BRAIN_VOYAGERTO_AFNI_METADATA)
     params = v_3d_brain_voyagerto_afni_params(
         input_file=input_file,
         force_byte_swap=force_byte_swap,
@@ -301,13 +290,13 @@ def v_3d_brain_voyagerto_afni(
         turn_off_memory_tracing=turn_off_memory_tracing,
         turn_on_memory_tracing=turn_on_memory_tracing,
     )
-    return v_3d_brain_voyagerto_afni_execute(params, execution)
+    return v_3d_brain_voyagerto_afni_execute(params, runner)
 
 
 __all__ = [
     "V3dBrainVoyagertoAfniOutputs",
-    "V3dBrainVoyagertoAfniParameters",
     "V_3D_BRAIN_VOYAGERTO_AFNI_METADATA",
     "v_3d_brain_voyagerto_afni",
+    "v_3d_brain_voyagerto_afni_execute",
     "v_3d_brain_voyagerto_afni_params",
 ]

niwrap_afni/afni/v_3d_brick_stat.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_BRICK_STAT_METADATA = Metadata(
-    id="a69dcfae94945e2d6a2a10deecf9753b5bb81503.boutiques",
+    id="e3c343d74218f80738d6518abc69819afe7c7458.boutiques",
     name="3dBrickStat",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,40 @@ V_3D_BRICK_STAT_METADATA = Metadata(
 
 
 V3dBrickStatParameters = typing.TypedDict('V3dBrickStatParameters', {
-    "__STYXTYPE__": typing.Literal["3dBrickStat"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dBrickStat"]],
+    "dataset": str,
+    "quick": bool,
+    "slow": bool,
+    "min": bool,
+    "max": bool,
+    "mean": bool,
+    "sum": bool,
+    "var": bool,
+    "stdev": bool,
+    "count": bool,
+    "volume": bool,
+    "positive": bool,
+    "negative": bool,
+    "zero": bool,
+    "non_positive": bool,
+    "non_negative": bool,
+    "non_zero": bool,
+    "absolute": bool,
+    "nan": bool,
+    "nonan": bool,
+    "mask": typing.NotRequired[str | None],
+    "mrange": typing.NotRequired[list[float] | None],
+    "mvalue": typing.NotRequired[float | None],
+    "automask": bool,
+    "percentile": typing.NotRequired[list[float] | None],
+    "perclist": typing.NotRequired[list[float] | None],
+    "median": bool,
+    "perc_quiet": bool,
+    "ver": bool,
+    "help": bool,
+})
+V3dBrickStatParametersTagged = typing.TypedDict('V3dBrickStatParametersTagged', {
+    "@type": typing.Literal["afni/3dBrickStat"],
     "dataset": str,
     "quick": bool,
     "slow": bool,
@@ -46,43 +79,11 @@ V3dBrickStatParameters = typing.TypedDict('V3dBrickStatParameters', {
     "ver": bool,
     "help": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dBrickStat": v_3d_brick_stat_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 {
-        "3dBrickStat": v_3d_brick_stat_outputs,
-    }.get(t)
 
 
 class V3dBrickStatOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_brick_stat(...)`.
+    Output object returned when calling `V3dBrickStatParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -121,7 +122,7 @@ def v_3d_brick_stat_params(
     perc_quiet: bool = False,
     ver: bool = False,
     help_: bool = False,
-) -> V3dBrickStatParameters:
+) -> V3dBrickStatParametersTagged:
     """
     Build parameters.
     
@@ -163,7 +164,7 @@ def v_3d_brick_stat_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dBrickStat",
+        "@type": "afni/3dBrickStat",
         "dataset": dataset,
         "quick": quick,
         "slow": slow,
@@ -218,79 +219,79 @@ def v_3d_brick_stat_cargs(
     """
     cargs = []
     cargs.append("3dBrickStat")
-    cargs.append(params.get("dataset"))
-    if params.get("quick"):
+    cargs.append(params.get("dataset", None))
+    if params.get("quick", False):
         cargs.append("-quick")
-    if params.get("slow"):
+    if params.get("slow", False):
         cargs.append("-slow")
-    if params.get("min"):
+    if params.get("min", False):
         cargs.append("-min")
-    if params.get("max"):
+    if params.get("max", False):
         cargs.append("-max")
-    if params.get("mean"):
+    if params.get("mean", False):
         cargs.append("-mean")
-    if params.get("sum"):
+    if params.get("sum", False):
         cargs.append("-sum")
-    if params.get("var"):
+    if params.get("var", False):
         cargs.append("-var")
-    if params.get("stdev"):
+    if params.get("stdev", False):
         cargs.append("-stdev")
-    if params.get("count"):
+    if params.get("count", False):
         cargs.append("-count")
-    if params.get("volume"):
+    if params.get("volume", False):
         cargs.append("-volume")
-    if params.get("positive"):
+    if params.get("positive", False):
         cargs.append("-positive")
-    if params.get("negative"):
+    if params.get("negative", False):
         cargs.append("-negative")
-    if params.get("zero"):
+    if params.get("zero", False):
         cargs.append("-zero")
-    if params.get("non_positive"):
+    if params.get("non_positive", False):
         cargs.append("-non-positive")
-    if params.get("non_negative"):
+    if params.get("non_negative", False):
         cargs.append("-non-negative")
-    if params.get("non_zero"):
+    if params.get("non_zero", False):
         cargs.append("-non-zero")
-    if params.get("absolute"):
+    if params.get("absolute", False):
         cargs.append("-absolute")
-    if params.get("nan"):
+    if params.get("nan", False):
         cargs.append("-nan")
-    if params.get("nonan"):
+    if params.get("nonan", False):
         cargs.append("-nonan")
-    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("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("mvalue") is not None:
+    if params.get("mvalue", None) is not None:
         cargs.extend([
             "-mvalue",
-            str(params.get("mvalue"))
+            str(params.get("mvalue", None))
         ])
-    if params.get("automask"):
+    if params.get("automask", False):
         cargs.append("-automask")
-    if params.get("percentile") is not None:
+    if params.get("percentile", None) is not None:
         cargs.extend([
             "-percentile",
-            *map(str, params.get("percentile"))
+            *map(str, params.get("percentile", None))
         ])
-    if params.get("perclist") is not None:
+    if params.get("perclist", None) is not None:
         cargs.extend([
             "-perclist",
-            *map(str, params.get("perclist"))
+            *map(str, params.get("perclist", None))
         ])
-    if params.get("median"):
+    if params.get("median", False):
         cargs.append("-median")
-    if params.get("perc_quiet"):
+    if params.get("perc_quiet", False):
         cargs.append("-perc_quiet")
-    if params.get("ver"):
+    if params.get("ver", False):
         cargs.append("-ver")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
     return cargs
 
@@ -317,9 +318,11 @@ def v_3d_brick_stat_outputs(
 
 def v_3d_brick_stat_execute(
     params: V3dBrickStatParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dBrickStatOutputs:
     """
+    3dBrickStat
+    
     Compute voxel statistics of an input dataset.
     
     Author: AFNI Developers
@@ -328,10 +331,12 @@ def v_3d_brick_stat_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dBrickStatOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_BRICK_STAT_METADATA)
     params = execution.params(params)
     cargs = v_3d_brick_stat_cargs(params, execution)
     ret = v_3d_brick_stat_outputs(params, execution)
@@ -373,6 +378,8 @@ def v_3d_brick_stat(
     runner: Runner | None = None,
 ) -> V3dBrickStatOutputs:
     """
+    3dBrickStat
+    
     Compute voxel statistics of an input dataset.
     
     Author: AFNI Developers
@@ -417,8 +424,6 @@ def v_3d_brick_stat(
     Returns:
         NamedTuple of outputs (described in `V3dBrickStatOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_BRICK_STAT_METADATA)
     params = v_3d_brick_stat_params(
         dataset=dataset,
         quick=quick,
@@ -451,13 +456,13 @@ def v_3d_brick_stat(
         ver=ver,
         help_=help_,
     )
-    return v_3d_brick_stat_execute(params, execution)
+    return v_3d_brick_stat_execute(params, runner)
 
 
 __all__ = [
     "V3dBrickStatOutputs",
-    "V3dBrickStatParameters",
     "V_3D_BRICK_STAT_METADATA",
     "v_3d_brick_stat",
+    "v_3d_brick_stat_execute",
     "v_3d_brick_stat_params",
 ]

niwrap_afni/afni/v_3d_clip_level.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_CLIP_LEVEL_METADATA = Metadata(
-    id="88bdbec4ad5f8ad542e0aad8dde4036aca9e4e12.boutiques",
+    id="fd4a8baf337596ea9a1bc436e3a61d90b89ee692.boutiques",
     name="3dClipLevel",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,48 +14,24 @@ V_3D_CLIP_LEVEL_METADATA = Metadata(
 
 
 V3dClipLevelParameters = typing.TypedDict('V3dClipLevelParameters', {
-    "__STYXTYPE__": typing.Literal["3dClipLevel"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dClipLevel"]],
+    "dataset": InputPathType,
+    "mfrac": typing.NotRequired[float | None],
+    "doall": bool,
+    "grad": typing.NotRequired[str | None],
+})
+V3dClipLevelParametersTagged = typing.TypedDict('V3dClipLevelParametersTagged', {
+    "@type": typing.Literal["afni/3dClipLevel"],
     "dataset": InputPathType,
     "mfrac": typing.NotRequired[float | None],
     "doall": bool,
     "grad": 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 {
-        "3dClipLevel": v_3d_clip_level_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 {
-    }.get(t)
 
 
 class V3dClipLevelOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_clip_level(...)`.
+    Output object returned when calling `V3dClipLevelParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -66,7 +42,7 @@ def v_3d_clip_level_params(
     mfrac: float | None = None,
     doall: bool = False,
     grad: str | None = None,
-) -> V3dClipLevelParameters:
+) -> V3dClipLevelParametersTagged:
     """
     Build parameters.
     
@@ -80,7 +56,7 @@ def v_3d_clip_level_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dClipLevel",
+        "@type": "afni/3dClipLevel",
         "dataset": dataset,
         "doall": doall,
     }
@@ -106,18 +82,18 @@ def v_3d_clip_level_cargs(
     """
     cargs = []
     cargs.append("3dClipLevel")
-    cargs.append(execution.input_file(params.get("dataset")))
-    if params.get("mfrac") is not None:
+    cargs.append(execution.input_file(params.get("dataset", None)))
+    if params.get("mfrac", None) is not None:
         cargs.extend([
             "-mfrac",
-            str(params.get("mfrac"))
+            str(params.get("mfrac", None))
         ])
-    if params.get("doall"):
+    if params.get("doall", False):
         cargs.append("-doall")
-    if params.get("grad") is not None:
+    if params.get("grad", None) is not None:
         cargs.extend([
             "-grad",
-            params.get("grad")
+            params.get("grad", None)
         ])
     return cargs
 
@@ -143,11 +119,13 @@ def v_3d_clip_level_outputs(
 
 def v_3d_clip_level_execute(
     params: V3dClipLevelParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dClipLevelOutputs:
     """
-    Estimates the value at which to clip the anatomical dataset so that background
-    regions are set to zero.
+    3dClipLevel
+    
+    Estimates the value at which to clip the anatomical dataset so that
+    background regions are set to zero.
     
     Author: AFNI Developers
     
@@ -155,10 +133,12 @@ def v_3d_clip_level_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dClipLevelOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_CLIP_LEVEL_METADATA)
     params = execution.params(params)
     cargs = v_3d_clip_level_cargs(params, execution)
     ret = v_3d_clip_level_outputs(params, execution)
@@ -174,8 +154,10 @@ def v_3d_clip_level(
     runner: Runner | None = None,
 ) -> V3dClipLevelOutputs:
     """
-    Estimates the value at which to clip the anatomical dataset so that background
-    regions are set to zero.
+    3dClipLevel
+    
+    Estimates the value at which to clip the anatomical dataset so that
+    background regions are set to zero.
     
     Author: AFNI Developers
     
@@ -191,21 +173,19 @@ def v_3d_clip_level(
     Returns:
         NamedTuple of outputs (described in `V3dClipLevelOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_CLIP_LEVEL_METADATA)
     params = v_3d_clip_level_params(
         dataset=dataset,
         mfrac=mfrac,
         doall=doall,
         grad=grad,
     )
-    return v_3d_clip_level_execute(params, execution)
+    return v_3d_clip_level_execute(params, runner)
 
 
 __all__ = [
     "V3dClipLevelOutputs",
-    "V3dClipLevelParameters",
     "V_3D_CLIP_LEVEL_METADATA",
     "v_3d_clip_level",
+    "v_3d_clip_level_execute",
     "v_3d_clip_level_params",
 ]