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

niwrap_afni/afni/spharm_reco.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SPHARM_RECO_METADATA = Metadata(
-    id="33f63f74ec6a7870069eec599fbb3c35bec65ba8.boutiques",
+    id="9f0ea5185e1a3e81f01bb8b4609838f587122cf5.boutiques",
     name="SpharmReco",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,18 @@ SPHARM_RECO_METADATA = Metadata(
 
 
 SpharmRecoParameters = typing.TypedDict('SpharmRecoParameters', {
-    "__STYXTYPE__": typing.Literal["SpharmReco"],
+    "@type": typing.NotRequired[typing.Literal["afni/SpharmReco"]],
+    "input_surface": str,
+    "decomposition_order": float,
+    "bases_prefix": str,
+    "coefficients": list[InputPathType],
+    "output_prefix": typing.NotRequired[str | None],
+    "output_surface": typing.NotRequired[list[str] | None],
+    "debug": typing.NotRequired[float | None],
+    "smoothing": typing.NotRequired[float | None],
+})
+SpharmRecoParametersTagged = typing.TypedDict('SpharmRecoParametersTagged', {
+    "@type": typing.Literal["afni/SpharmReco"],
     "input_surface": str,
     "decomposition_order": float,
     "bases_prefix": str,
@@ -24,42 +35,11 @@ SpharmRecoParameters = typing.TypedDict('SpharmRecoParameters', {
     "debug": typing.NotRequired[float | None],
     "smoothing": 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 {
-        "SpharmReco": spharm_reco_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 SpharmRecoOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `spharm_reco(...)`.
+    Output object returned when calling `SpharmRecoParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -74,7 +54,7 @@ def spharm_reco_params(
     output_surface: list[str] | None = None,
     debug: float | None = None,
     smoothing: float | None = None,
-) -> SpharmRecoParameters:
+) -> SpharmRecoParametersTagged:
     """
     Build parameters.
     
@@ -97,7 +77,7 @@ def spharm_reco_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "SpharmReco",
+        "@type": "afni/SpharmReco",
         "input_surface": input_surface,
         "decomposition_order": decomposition_order,
         "bases_prefix": bases_prefix,
@@ -131,39 +111,39 @@ def spharm_reco_cargs(
     cargs.append("SpharmReco")
     cargs.extend([
         "-i_TYPE",
-        params.get("input_surface")
+        params.get("input_surface", None)
     ])
     cargs.extend([
         "-l",
-        str(params.get("decomposition_order"))
+        str(params.get("decomposition_order", None))
     ])
     cargs.extend([
         "-bases_prefix",
-        params.get("bases_prefix")
+        params.get("bases_prefix", None)
     ])
     cargs.extend([
         "-coef",
-        *[execution.input_file(f) for f in params.get("coefficients")]
+        *[execution.input_file(f) for f in params.get("coefficients", None)]
     ])
-    if params.get("output_prefix") is not None:
+    if params.get("output_prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("output_prefix")
+            params.get("output_prefix", None)
         ])
-    if params.get("output_surface") is not None:
+    if params.get("output_surface", None) is not None:
         cargs.extend([
             "-o_TYPE",
-            *params.get("output_surface")
+            *params.get("output_surface", None)
         ])
-    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("smoothing") is not None:
+    if params.get("smoothing", None) is not None:
         cargs.extend([
             "-sigma",
-            str(params.get("smoothing"))
+            str(params.get("smoothing", None))
         ])
     return cargs
 
@@ -189,9 +169,11 @@ def spharm_reco_outputs(
 
 def spharm_reco_execute(
     params: SpharmRecoParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SpharmRecoOutputs:
     """
+    SpharmReco
+    
     Spherical Harmonics Reconstruction from a set of harmonics and their
     corresponding coefficients.
     
@@ -201,10 +183,12 @@ def spharm_reco_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SpharmRecoOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SPHARM_RECO_METADATA)
     params = execution.params(params)
     cargs = spharm_reco_cargs(params, execution)
     ret = spharm_reco_outputs(params, execution)
@@ -224,6 +208,8 @@ def spharm_reco(
     runner: Runner | None = None,
 ) -> SpharmRecoOutputs:
     """
+    SpharmReco
+    
     Spherical Harmonics Reconstruction from a set of harmonics and their
     corresponding coefficients.
     
@@ -250,8 +236,6 @@ def spharm_reco(
     Returns:
         NamedTuple of outputs (described in `SpharmRecoOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SPHARM_RECO_METADATA)
     params = spharm_reco_params(
         input_surface=input_surface,
         decomposition_order=decomposition_order,
@@ -262,13 +246,13 @@ def spharm_reco(
         debug=debug,
         smoothing=smoothing,
     )
-    return spharm_reco_execute(params, execution)
+    return spharm_reco_execute(params, runner)
 
 
 __all__ = [
     "SPHARM_RECO_METADATA",
     "SpharmRecoOutputs",
-    "SpharmRecoParameters",
     "spharm_reco",
+    "spharm_reco_execute",
     "spharm_reco_params",
 ]

niwrap_afni/afni/stimband.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 STIMBAND_METADATA = Metadata(
-    id="0fd66dc3c918c574a8c27c7cb16b3f971f5ac250.boutiques",
+    id="f6ebe684f2c7f744813c6cc085872acc2191fa80.boutiques",
     name="stimband",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,16 @@ STIMBAND_METADATA = Metadata(
 
 
 StimbandParameters = typing.TypedDict('StimbandParameters', {
-    "__STYXTYPE__": typing.Literal["stimband"],
+    "@type": typing.NotRequired[typing.Literal["afni/stimband"]],
+    "verbose_flag": bool,
+    "matrixfiles": list[InputPathType],
+    "additional_matrixfiles": typing.NotRequired[list[InputPathType] | None],
+    "min_freq": typing.NotRequired[float | None],
+    "min_bwidth": typing.NotRequired[float | None],
+    "min_pow": typing.NotRequired[float | None],
+})
+StimbandParametersTagged = typing.TypedDict('StimbandParametersTagged', {
+    "@type": typing.Literal["afni/stimband"],
     "verbose_flag": bool,
     "matrixfiles": list[InputPathType],
     "additional_matrixfiles": typing.NotRequired[list[InputPathType] | None],
@@ -22,43 +31,11 @@ StimbandParameters = typing.TypedDict('StimbandParameters', {
     "min_bwidth": typing.NotRequired[float | None],
     "min_pow": 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 {
-        "stimband": stimband_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 {
-        "stimband": stimband_outputs,
-    }.get(t)
 
 
 class StimbandOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `stimband(...)`.
+    Output object returned when calling `StimbandParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -74,7 +51,7 @@ def stimband_params(
     min_freq: float | None = None,
     min_bwidth: float | None = None,
     min_pow: float | None = None,
-) -> StimbandParameters:
+) -> StimbandParametersTagged:
     """
     Build parameters.
     
@@ -93,7 +70,7 @@ def stimband_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "stimband",
+        "@type": "afni/stimband",
         "verbose_flag": verbose_flag,
         "matrixfiles": matrixfiles,
     }
@@ -123,28 +100,28 @@ def stimband_cargs(
     """
     cargs = []
     cargs.append("stimband")
-    if params.get("verbose_flag"):
+    if params.get("verbose_flag", False):
         cargs.append("-verb")
-    cargs.extend([execution.input_file(f) for f in params.get("matrixfiles")])
-    if params.get("additional_matrixfiles") is not None:
+    cargs.extend([execution.input_file(f) for f in params.get("matrixfiles", None)])
+    if params.get("additional_matrixfiles", None) is not None:
         cargs.extend([
             "-matrix",
-            *[execution.input_file(f) for f in params.get("additional_matrixfiles")]
+            *[execution.input_file(f) for f in params.get("additional_matrixfiles", None)]
         ])
-    if params.get("min_freq") is not None:
+    if params.get("min_freq", None) is not None:
         cargs.extend([
             "-min_freq",
-            str(params.get("min_freq"))
+            str(params.get("min_freq", None))
         ])
-    if params.get("min_bwidth") is not None:
+    if params.get("min_bwidth", None) is not None:
         cargs.extend([
             "-min_bwidth",
-            str(params.get("min_bwidth"))
+            str(params.get("min_bwidth", None))
         ])
-    if params.get("min_pow") is not None:
+    if params.get("min_pow", None) is not None:
         cargs.extend([
             "-min_pow",
-            str(params.get("min_pow"))
+            str(params.get("min_pow", None))
         ])
     return cargs
 
@@ -171,9 +148,11 @@ def stimband_outputs(
 
 def stimband_execute(
     params: StimbandParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> StimbandOutputs:
     """
+    stimband
+    
     Determines frequency band covering at least 90% of the 'power' (|FFT|^2) of
     stimulus columns from X.nocensor.xmat.1D files.
     
@@ -183,10 +162,12 @@ def stimband_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `StimbandOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(STIMBAND_METADATA)
     params = execution.params(params)
     cargs = stimband_cargs(params, execution)
     ret = stimband_outputs(params, execution)
@@ -204,6 +185,8 @@ def stimband(
     runner: Runner | None = None,
 ) -> StimbandOutputs:
     """
+    stimband
+    
     Determines frequency band covering at least 90% of the 'power' (|FFT|^2) of
     stimulus columns from X.nocensor.xmat.1D files.
     
@@ -226,8 +209,6 @@ def stimband(
     Returns:
         NamedTuple of outputs (described in `StimbandOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(STIMBAND_METADATA)
     params = stimband_params(
         verbose_flag=verbose_flag,
         matrixfiles=matrixfiles,
@@ -236,13 +217,13 @@ def stimband(
         min_bwidth=min_bwidth,
         min_pow=min_pow,
     )
-    return stimband_execute(params, execution)
+    return stimband_execute(params, runner)
 
 
 __all__ = [
     "STIMBAND_METADATA",
     "StimbandOutputs",
-    "StimbandParameters",
     "stimband",
+    "stimband_execute",
     "stimband_params",
 ]

niwrap_afni/afni/strblast.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 STRBLAST_METADATA = Metadata(
-    id="f32f04cd48a95c18324b547f5e4333f3e6c5f926.boutiques",
+    id="979e93554e0c9bc2129eb838cda90544cca19b0e.boutiques",
     name="strblast",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,17 @@ STRBLAST_METADATA = Metadata(
 
 
 StrblastParameters = typing.TypedDict('StrblastParameters', {
-    "__STYXTYPE__": typing.Literal["strblast"],
+    "@type": typing.NotRequired[typing.Literal["afni/strblast"]],
+    "targetstring": str,
+    "input_files": list[InputPathType],
+    "new_char": typing.NotRequired[str | None],
+    "new_string": typing.NotRequired[str | None],
+    "unescape": bool,
+    "quiet": bool,
+    "help": bool,
+})
+StrblastParametersTagged = typing.TypedDict('StrblastParametersTagged', {
+    "@type": typing.Literal["afni/strblast"],
     "targetstring": str,
     "input_files": list[InputPathType],
     "new_char": typing.NotRequired[str | None],
@@ -23,42 +33,11 @@ StrblastParameters = typing.TypedDict('StrblastParameters', {
     "quiet": 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 {
-        "strblast": strblast_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 StrblastOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `strblast(...)`.
+    Output object returned when calling `StrblastParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -72,7 +51,7 @@ def strblast_params(
     unescape: bool = False,
     quiet: bool = False,
     help_: bool = False,
-) -> StrblastParameters:
+) -> StrblastParametersTagged:
     """
     Build parameters.
     
@@ -90,7 +69,7 @@ def strblast_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "strblast",
+        "@type": "afni/strblast",
         "targetstring": targetstring,
         "input_files": input_files,
         "unescape": unescape,
@@ -119,23 +98,23 @@ def strblast_cargs(
     """
     cargs = []
     cargs.append("strblast")
-    cargs.append(params.get("targetstring"))
-    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
-    if params.get("new_char") is not None:
+    cargs.append(params.get("targetstring", None))
+    cargs.extend([execution.input_file(f) for f in params.get("input_files", None)])
+    if params.get("new_char", None) is not None:
         cargs.extend([
             "-new_char",
-            params.get("new_char")
+            params.get("new_char", None)
         ])
-    if params.get("new_string") is not None:
+    if params.get("new_string", None) is not None:
         cargs.extend([
             "-new_string",
-            params.get("new_string")
+            params.get("new_string", None)
         ])
-    if params.get("unescape"):
+    if params.get("unescape", False):
         cargs.append("-unescape")
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
     return cargs
 
@@ -161,11 +140,13 @@ def strblast_outputs(
 
 def strblast_execute(
     params: StrblastParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> StrblastOutputs:
     """
-    Finds exact copies of the target string in each of the input files, and replaces
-    all characters with some junk string.
+    strblast
+    
+    Finds exact copies of the target string in each of the input files, and
+    replaces all characters with some junk string.
     
     Author: AFNI Developers
     
@@ -173,10 +154,12 @@ def strblast_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `StrblastOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(STRBLAST_METADATA)
     params = execution.params(params)
     cargs = strblast_cargs(params, execution)
     ret = strblast_outputs(params, execution)
@@ -195,8 +178,10 @@ def strblast(
     runner: Runner | None = None,
 ) -> StrblastOutputs:
     """
-    Finds exact copies of the target string in each of the input files, and replaces
-    all characters with some junk string.
+    strblast
+    
+    Finds exact copies of the target string in each of the input files, and
+    replaces all characters with some junk string.
     
     Author: AFNI Developers
     
@@ -216,8 +201,6 @@ def strblast(
     Returns:
         NamedTuple of outputs (described in `StrblastOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(STRBLAST_METADATA)
     params = strblast_params(
         targetstring=targetstring,
         input_files=input_files,
@@ -227,13 +210,13 @@ def strblast(
         quiet=quiet,
         help_=help_,
     )
-    return strblast_execute(params, execution)
+    return strblast_execute(params, runner)
 
 
 __all__ = [
     "STRBLAST_METADATA",
     "StrblastOutputs",
-    "StrblastParameters",
     "strblast",
+    "strblast_execute",
     "strblast_params",
 ]