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

niwrap_afni/afni/rsfgen.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 RSFGEN_METADATA = Metadata(
-    id="11b25a34307a16d17dd031e0865f508903b6754c.boutiques",
+    id="f57a291faa4a03d6574ad3f56ebfc4cc2c0004ca.boutiques",
     name="RSFgen",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,23 @@ RSFGEN_METADATA = Metadata(
 
 
 RsfgenParameters = typing.TypedDict('RsfgenParameters', {
-    "__STYXTYPE__": typing.Literal["RSFgen"],
+    "@type": typing.NotRequired[typing.Literal["afni/RSFgen"]],
+    "length": int,
+    "num_experimental_conditions": int,
+    "block_length": typing.NotRequired[str | None],
+    "random_seed": typing.NotRequired[float | None],
+    "suppress_output_flag": bool,
+    "single_file_flag": bool,
+    "single_column_flag": bool,
+    "output_prefix": typing.NotRequired[str | None],
+    "num_reps": typing.NotRequired[str | None],
+    "permutation_seed": typing.NotRequired[float | None],
+    "markov_file": typing.NotRequired[InputPathType | None],
+    "prob_zero": typing.NotRequired[float | None],
+    "input_table": typing.NotRequired[InputPathType | None],
+})
+RsfgenParametersTagged = typing.TypedDict('RsfgenParametersTagged', {
+    "@type": typing.Literal["afni/RSFgen"],
     "length": int,
     "num_experimental_conditions": int,
     "block_length": typing.NotRequired[str | None],
@@ -29,43 +45,11 @@ RsfgenParameters = typing.TypedDict('RsfgenParameters', {
     "prob_zero": typing.NotRequired[float | None],
     "input_table": 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 {
-        "RSFgen": rsfgen_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 {
-        "RSFgen": rsfgen_outputs,
-    }.get(t)
 
 
 class RsfgenOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `rsfgen(...)`.
+    Output object returned when calling `RsfgenParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -88,7 +72,7 @@ def rsfgen_params(
     markov_file: InputPathType | None = None,
     prob_zero: float | None = None,
     input_table: InputPathType | None = None,
-) -> RsfgenParameters:
+) -> RsfgenParametersTagged:
     """
     Build parameters.
     
@@ -114,7 +98,7 @@ def rsfgen_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "RSFgen",
+        "@type": "afni/RSFgen",
         "length": length,
         "num_experimental_conditions": num_experimental_conditions,
         "suppress_output_flag": suppress_output_flag,
@@ -157,57 +141,57 @@ def rsfgen_cargs(
     cargs.append("RSFgen")
     cargs.extend([
         "-nt",
-        str(params.get("length"))
+        str(params.get("length", None))
     ])
     cargs.extend([
         "-num_stimts",
-        str(params.get("num_experimental_conditions"))
+        str(params.get("num_experimental_conditions", None))
     ])
-    if params.get("block_length") is not None:
+    if params.get("block_length", None) is not None:
         cargs.extend([
             "-nblock",
-            params.get("block_length")
+            params.get("block_length", None)
         ])
-    if params.get("random_seed") is not None:
+    if params.get("random_seed", None) is not None:
         cargs.extend([
             "-seed",
-            str(params.get("random_seed"))
+            str(params.get("random_seed", None))
         ])
-    if params.get("suppress_output_flag"):
+    if params.get("suppress_output_flag", False):
         cargs.append("-quiet")
-    if params.get("single_file_flag"):
+    if params.get("single_file_flag", False):
         cargs.append("-one_file")
-    if params.get("single_column_flag"):
+    if params.get("single_column_flag", False):
         cargs.append("-one_col")
-    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("num_reps") is not None:
+    if params.get("num_reps", None) is not None:
         cargs.extend([
             "-nreps",
-            params.get("num_reps")
+            params.get("num_reps", None)
         ])
-    if params.get("permutation_seed") is not None:
+    if params.get("permutation_seed", None) is not None:
         cargs.extend([
             "-pseed",
-            str(params.get("permutation_seed"))
+            str(params.get("permutation_seed", None))
         ])
-    if params.get("markov_file") is not None:
+    if params.get("markov_file", None) is not None:
         cargs.extend([
             "-markov",
-            execution.input_file(params.get("markov_file"))
+            execution.input_file(params.get("markov_file", None))
         ])
-    if params.get("prob_zero") is not None:
+    if params.get("prob_zero", None) is not None:
         cargs.extend([
             "-pzero",
-            str(params.get("prob_zero"))
+            str(params.get("prob_zero", None))
         ])
-    if params.get("input_table") is not None:
+    if params.get("input_table", None) is not None:
         cargs.extend([
             "-table",
-            execution.input_file(params.get("input_table"))
+            execution.input_file(params.get("input_table", None))
         ])
     return cargs
 
@@ -227,16 +211,18 @@ def rsfgen_outputs(
     """
     ret = RsfgenOutputs(
         root=execution.output_file("."),
-        output_files=execution.output_file(params.get("output_prefix") + "1.1D") if (params.get("output_prefix") is not None) else None,
+        output_files=execution.output_file(params.get("output_prefix", None) + "1.1D") if (params.get("output_prefix") is not None) else None,
     )
     return ret
 
 
 def rsfgen_execute(
     params: RsfgenParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> RsfgenOutputs:
     """
+    RSFgen
+    
     Program to generate random stimulus functions.
     
     Author: AFNI Developers
@@ -245,10 +231,12 @@ def rsfgen_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `RsfgenOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(RSFGEN_METADATA)
     params = execution.params(params)
     cargs = rsfgen_cargs(params, execution)
     ret = rsfgen_outputs(params, execution)
@@ -273,6 +261,8 @@ def rsfgen(
     runner: Runner | None = None,
 ) -> RsfgenOutputs:
     """
+    RSFgen
+    
     Program to generate random stimulus functions.
     
     Author: AFNI Developers
@@ -301,8 +291,6 @@ def rsfgen(
     Returns:
         NamedTuple of outputs (described in `RsfgenOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(RSFGEN_METADATA)
     params = rsfgen_params(
         length=length,
         num_experimental_conditions=num_experimental_conditions,
@@ -318,13 +306,13 @@ def rsfgen(
         prob_zero=prob_zero,
         input_table=input_table,
     )
-    return rsfgen_execute(params, execution)
+    return rsfgen_execute(params, runner)
 
 
 __all__ = [
     "RSFGEN_METADATA",
     "RsfgenOutputs",
-    "RsfgenParameters",
     "rsfgen",
+    "rsfgen_execute",
     "rsfgen_params",
 ]

niwrap_afni/afni/rtfeedme.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 RTFEEDME_METADATA = Metadata(
-    id="10a9c1f1dd1351e0a684111b51d759ea5478ae34.boutiques",
+    id="031662f7ace1e435c0c343699a3380e8eef5d84a.boutiques",
     name="rtfeedme",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,21 @@ RTFEEDME_METADATA = Metadata(
 
 
 RtfeedmeParameters = typing.TypedDict('RtfeedmeParameters', {
-    "__STYXTYPE__": typing.Literal["rtfeedme"],
+    "@type": typing.NotRequired[typing.Literal["afni/rtfeedme"]],
+    "datasets": list[InputPathType],
+    "host": typing.NotRequired[str | None],
+    "interval_ms": typing.NotRequired[float | None],
+    "send_3d": bool,
+    "buffer_mb": typing.NotRequired[float | None],
+    "verbose": bool,
+    "swap_bytes": bool,
+    "nz_fake": typing.NotRequired[float | None],
+    "drive_cmd": typing.NotRequired[list[str] | None],
+    "note": typing.NotRequired[list[str] | None],
+    "yrange": typing.NotRequired[float | None],
+})
+RtfeedmeParametersTagged = typing.TypedDict('RtfeedmeParametersTagged', {
+    "@type": typing.Literal["afni/rtfeedme"],
     "datasets": list[InputPathType],
     "host": typing.NotRequired[str | None],
     "interval_ms": typing.NotRequired[float | None],
@@ -27,42 +41,11 @@ RtfeedmeParameters = typing.TypedDict('RtfeedmeParameters', {
     "note": typing.NotRequired[list[str] | None],
     "yrange": 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 {
-        "rtfeedme": rtfeedme_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 RtfeedmeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `rtfeedme(...)`.
+    Output object returned when calling `RtfeedmeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -80,7 +63,7 @@ def rtfeedme_params(
     drive_cmd: list[str] | None = None,
     note: list[str] | None = None,
     yrange: float | None = None,
-) -> RtfeedmeParameters:
+) -> RtfeedmeParametersTagged:
     """
     Build parameters.
     
@@ -109,7 +92,7 @@ def rtfeedme_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "rtfeedme",
+        "@type": "afni/rtfeedme",
         "datasets": datasets,
         "send_3d": send_3d,
         "verbose": verbose,
@@ -147,47 +130,47 @@ def rtfeedme_cargs(
     """
     cargs = []
     cargs.append("rtfeedme")
-    cargs.extend([execution.input_file(f) for f in params.get("datasets")])
-    if params.get("host") is not None:
+    cargs.extend([execution.input_file(f) for f in params.get("datasets", None)])
+    if params.get("host", None) is not None:
         cargs.extend([
             "-host",
-            params.get("host")
+            params.get("host", None)
         ])
-    if params.get("interval_ms") is not None:
+    if params.get("interval_ms", None) is not None:
         cargs.extend([
             "-dt",
-            str(params.get("interval_ms"))
+            str(params.get("interval_ms", None))
         ])
-    if params.get("send_3d"):
+    if params.get("send_3d", False):
         cargs.append("-3D")
-    if params.get("buffer_mb") is not None:
+    if params.get("buffer_mb", None) is not None:
         cargs.extend([
             "-buf",
-            str(params.get("buffer_mb"))
+            str(params.get("buffer_mb", None))
         ])
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-verbose")
-    if params.get("swap_bytes"):
+    if params.get("swap_bytes", False):
         cargs.append("-swap2")
-    if params.get("nz_fake") is not None:
+    if params.get("nz_fake", None) is not None:
         cargs.extend([
             "-nzfake",
-            str(params.get("nz_fake"))
+            str(params.get("nz_fake", None))
         ])
-    if params.get("drive_cmd") is not None:
+    if params.get("drive_cmd", None) is not None:
         cargs.extend([
             "-drive",
-            *params.get("drive_cmd")
+            *params.get("drive_cmd", None)
         ])
-    if params.get("note") is not None:
+    if params.get("note", None) is not None:
         cargs.extend([
             "-note",
-            *params.get("note")
+            *params.get("note", None)
         ])
-    if params.get("yrange") is not None:
+    if params.get("yrange", None) is not None:
         cargs.extend([
             "-gyr",
-            str(params.get("yrange"))
+            str(params.get("yrange", None))
         ])
     return cargs
 
@@ -213,9 +196,11 @@ def rtfeedme_outputs(
 
 def rtfeedme_execute(
     params: RtfeedmeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> RtfeedmeOutputs:
     """
+    rtfeedme
+    
     Test the real-time plugin by sending all the bricks in 'dataset' to AFNI.
     
     Author: AFNI Developers
@@ -224,10 +209,12 @@ def rtfeedme_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `RtfeedmeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(RTFEEDME_METADATA)
     params = execution.params(params)
     cargs = rtfeedme_cargs(params, execution)
     ret = rtfeedme_outputs(params, execution)
@@ -250,6 +237,8 @@ def rtfeedme(
     runner: Runner | None = None,
 ) -> RtfeedmeOutputs:
     """
+    rtfeedme
+    
     Test the real-time plugin by sending all the bricks in 'dataset' to AFNI.
     
     Author: AFNI Developers
@@ -281,8 +270,6 @@ def rtfeedme(
     Returns:
         NamedTuple of outputs (described in `RtfeedmeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(RTFEEDME_METADATA)
     params = rtfeedme_params(
         datasets=datasets,
         host=host,
@@ -296,13 +283,13 @@ def rtfeedme(
         note=note,
         yrange=yrange,
     )
-    return rtfeedme_execute(params, execution)
+    return rtfeedme_execute(params, runner)
 
 
 __all__ = [
     "RTFEEDME_METADATA",
     "RtfeedmeOutputs",
-    "RtfeedmeParameters",
     "rtfeedme",
+    "rtfeedme_execute",
     "rtfeedme_params",
 ]

niwrap_afni/afni/samp_bias.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SAMP_BIAS_METADATA = Metadata(
-    id="73bcedebddacb73e50fa496ef2f4a5a44b29fdd5.boutiques",
+    id="4faddcdab52d97992d0c7bcd367e7c5071d25515.boutiques",
     name="SampBias",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,17 @@ SAMP_BIAS_METADATA = Metadata(
 
 
 SampBiasParameters = typing.TypedDict('SampBiasParameters', {
-    "__STYXTYPE__": typing.Literal["SampBias"],
+    "@type": typing.NotRequired[typing.Literal["afni/SampBias"]],
+    "specfile": InputPathType,
+    "surfname": str,
+    "plimit": typing.NotRequired[float | None],
+    "dlimit": typing.NotRequired[float | None],
+    "outfile": str,
+    "prefix": typing.NotRequired[str | None],
+    "segdo": typing.NotRequired[str | None],
+})
+SampBiasParametersTagged = typing.TypedDict('SampBiasParametersTagged', {
+    "@type": typing.Literal["afni/SampBias"],
     "specfile": InputPathType,
     "surfname": str,
     "plimit": typing.NotRequired[float | None],
@@ -23,43 +33,11 @@ SampBiasParameters = typing.TypedDict('SampBiasParameters', {
     "prefix": typing.NotRequired[str | None],
     "segdo": 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 {
-        "SampBias": samp_bias_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 {
-        "SampBias": samp_bias_outputs,
-    }.get(t)
 
 
 class SampBiasOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `samp_bias(...)`.
+    Output object returned when calling `SampBiasParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -77,7 +55,7 @@ def samp_bias_params(
     dlimit: float | None = None,
     prefix: str | None = None,
     segdo: str | None = None,
-) -> SampBiasParameters:
+) -> SampBiasParametersTagged:
     """
     Build parameters.
     
@@ -94,7 +72,7 @@ def samp_bias_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "SampBias",
+        "@type": "afni/SampBias",
         "specfile": specfile,
         "surfname": surfname,
         "outfile": outfile,
@@ -127,35 +105,35 @@ def samp_bias_cargs(
     cargs.append("SampBias")
     cargs.extend([
         "-spec",
-        execution.input_file(params.get("specfile"))
+        execution.input_file(params.get("specfile", None))
     ])
     cargs.extend([
         "-surf",
-        params.get("surfname")
+        params.get("surfname", None)
     ])
-    if params.get("plimit") is not None:
+    if params.get("plimit", None) is not None:
         cargs.extend([
             "-plimit",
-            str(params.get("plimit"))
+            str(params.get("plimit", None))
         ])
-    if params.get("dlimit") is not None:
+    if params.get("dlimit", None) is not None:
         cargs.extend([
             "-dlimit",
-            str(params.get("dlimit"))
+            str(params.get("dlimit", None))
         ])
     cargs.extend([
         "-out",
-        params.get("outfile")
+        params.get("outfile", 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("segdo") is not None:
+    if params.get("segdo", None) is not None:
         cargs.extend([
             "-segdo",
-            params.get("segdo")
+            params.get("segdo", None)
         ])
     return cargs
 
@@ -175,19 +153,21 @@ def samp_bias_outputs(
     """
     ret = SampBiasOutputs(
         root=execution.output_file("."),
-        out_1_d=execution.output_file(params.get("outfile") + ".1D"),
-        out_prefix=execution.output_file(params.get("prefix")) if (params.get("prefix") is not None) else None,
+        out_1_d=execution.output_file(params.get("outfile", None) + ".1D"),
+        out_prefix=execution.output_file(params.get("prefix", None)) if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def samp_bias_execute(
     params: SampBiasParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SampBiasOutputs:
     """
-    SampBias is a tool for sampling bias resultant segments between paired nodes on
-    anatomical surfaces.
+    SampBias
+    
+    SampBias is a tool for sampling bias resultant segments between paired nodes
+    on anatomical surfaces.
     
     Author: AFNI Developers
     
@@ -195,10 +175,12 @@ def samp_bias_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SampBiasOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SAMP_BIAS_METADATA)
     params = execution.params(params)
     cargs = samp_bias_cargs(params, execution)
     ret = samp_bias_outputs(params, execution)
@@ -217,8 +199,10 @@ def samp_bias(
     runner: Runner | None = None,
 ) -> SampBiasOutputs:
     """
-    SampBias is a tool for sampling bias resultant segments between paired nodes on
-    anatomical surfaces.
+    SampBias
+    
+    SampBias is a tool for sampling bias resultant segments between paired nodes
+    on anatomical surfaces.
     
     Author: AFNI Developers
     
@@ -237,8 +221,6 @@ def samp_bias(
     Returns:
         NamedTuple of outputs (described in `SampBiasOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SAMP_BIAS_METADATA)
     params = samp_bias_params(
         specfile=specfile,
         surfname=surfname,
@@ -248,13 +230,13 @@ def samp_bias(
         prefix=prefix,
         segdo=segdo,
     )
-    return samp_bias_execute(params, execution)
+    return samp_bias_execute(params, runner)
 
 
 __all__ = [
     "SAMP_BIAS_METADATA",
     "SampBiasOutputs",
-    "SampBiasParameters",
     "samp_bias",
+    "samp_bias_execute",
     "samp_bias_params",
 ]