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

niwrap_afni/afni/firdesign.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FIRDESIGN_METADATA = Metadata(
-    id="a74504adf0b49ec5a0615bc609bf67d8b73823f0.boutiques",
+    id="0c4ea34db1930ae230e4105a67970c789ca0a3f2.boutiques",
     name="FIRdesign",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,16 @@ FIRDESIGN_METADATA = Metadata(
 
 
 FirdesignParameters = typing.TypedDict('FirdesignParameters', {
-    "__STYXTYPE__": typing.Literal["FIRdesign"],
+    "@type": typing.NotRequired[typing.Literal["afni/FIRdesign"]],
+    "fbot": float,
+    "ftop": float,
+    "ntap": float,
+    "tr": typing.NotRequired[float | None],
+    "alternative_band": typing.NotRequired[list[float] | None],
+    "alternative_ntap": typing.NotRequired[float | None],
+})
+FirdesignParametersTagged = typing.TypedDict('FirdesignParametersTagged', {
+    "@type": typing.Literal["afni/FIRdesign"],
     "fbot": float,
     "ftop": float,
     "ntap": float,
@@ -22,42 +31,11 @@ FirdesignParameters = typing.TypedDict('FirdesignParameters', {
     "alternative_band": typing.NotRequired[list[float] | None],
     "alternative_ntap": 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 {
-        "FIRdesign": firdesign_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 FirdesignOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `firdesign(...)`.
+    Output object returned when calling `FirdesignParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -70,7 +48,7 @@ def firdesign_params(
     tr: float | None = None,
     alternative_band: list[float] | None = None,
     alternative_ntap: float | None = None,
-) -> FirdesignParameters:
+) -> FirdesignParametersTagged:
     """
     Build parameters.
     
@@ -87,7 +65,7 @@ def firdesign_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "FIRdesign",
+        "@type": "afni/FIRdesign",
         "fbot": fbot,
         "ftop": ftop,
         "ntap": ntap,
@@ -116,23 +94,23 @@ def firdesign_cargs(
     """
     cargs = []
     cargs.append("FIRdesign")
-    cargs.append(str(params.get("fbot")))
-    cargs.append(str(params.get("ftop")))
-    cargs.append(str(params.get("ntap")))
-    if params.get("tr") is not None:
+    cargs.append(str(params.get("fbot", None)))
+    cargs.append(str(params.get("ftop", None)))
+    cargs.append(str(params.get("ntap", None)))
+    if params.get("tr", None) is not None:
         cargs.extend([
             "-TR",
-            str(params.get("tr"))
+            str(params.get("tr", None))
         ])
-    if params.get("alternative_band") is not None:
+    if params.get("alternative_band", None) is not None:
         cargs.extend([
             "-band",
-            *map(str, params.get("alternative_band"))
+            *map(str, params.get("alternative_band", None))
         ])
-    if params.get("alternative_ntap") is not None:
+    if params.get("alternative_ntap", None) is not None:
         cargs.extend([
             "-ntap",
-            str(params.get("alternative_ntap"))
+            str(params.get("alternative_ntap", None))
         ])
     return cargs
 
@@ -158,9 +136,11 @@ def firdesign_outputs(
 
 def firdesign_execute(
     params: FirdesignParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FirdesignOutputs:
     """
+    FIRdesign
+    
     Uses the Remez algorithm to calculate the FIR filter weights for a bandpass
     filter; results are written to stdout in an unadorned (no header) column of
     numbers.
@@ -171,10 +151,12 @@ def firdesign_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FirdesignOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIRDESIGN_METADATA)
     params = execution.params(params)
     cargs = firdesign_cargs(params, execution)
     ret = firdesign_outputs(params, execution)
@@ -192,6 +174,8 @@ def firdesign(
     runner: Runner | None = None,
 ) -> FirdesignOutputs:
     """
+    FIRdesign
+    
     Uses the Remez algorithm to calculate the FIR filter weights for a bandpass
     filter; results are written to stdout in an unadorned (no header) column of
     numbers.
@@ -213,8 +197,6 @@ def firdesign(
     Returns:
         NamedTuple of outputs (described in `FirdesignOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FIRDESIGN_METADATA)
     params = firdesign_params(
         fbot=fbot,
         ftop=ftop,
@@ -223,13 +205,13 @@ def firdesign(
         alternative_band=alternative_band,
         alternative_ntap=alternative_ntap,
     )
-    return firdesign_execute(params, execution)
+    return firdesign_execute(params, runner)
 
 
 __all__ = [
     "FIRDESIGN_METADATA",
     "FirdesignOutputs",
-    "FirdesignParameters",
     "firdesign",
+    "firdesign_execute",
     "firdesign_params",
 ]

niwrap_afni/afni/float_scan.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FLOAT_SCAN_METADATA = Metadata(
-    id="28d4eadc825c8d2737bbbea46fd718d9d9a73f5d.boutiques",
+    id="736559794aec1b67724d54af3dc33b4693f7d27e.boutiques",
     name="float_scan",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,49 +14,24 @@ FLOAT_SCAN_METADATA = Metadata(
 
 
 FloatScanParameters = typing.TypedDict('FloatScanParameters', {
-    "__STYXTYPE__": typing.Literal["float_scan"],
+    "@type": typing.NotRequired[typing.Literal["afni/float_scan"]],
+    "fix_illegal_values": bool,
+    "verbose_mode": bool,
+    "skip_count": typing.NotRequired[int | None],
+    "input_file": InputPathType,
+})
+FloatScanParametersTagged = typing.TypedDict('FloatScanParametersTagged', {
+    "@type": typing.Literal["afni/float_scan"],
     "fix_illegal_values": bool,
     "verbose_mode": bool,
     "skip_count": typing.NotRequired[int | None],
     "input_file": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "float_scan": float_scan_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 {
-        "float_scan": float_scan_outputs,
-    }.get(t)
 
 
 class FloatScanOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `float_scan(...)`.
+    Output object returned when calling `FloatScanParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def float_scan_params(
     fix_illegal_values: bool = False,
     verbose_mode: bool = False,
     skip_count: int | None = None,
-) -> FloatScanParameters:
+) -> FloatScanParametersTagged:
     """
     Build parameters.
     
@@ -84,7 +59,7 @@ def float_scan_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "float_scan",
+        "@type": "afni/float_scan",
         "fix_illegal_values": fix_illegal_values,
         "verbose_mode": verbose_mode,
         "input_file": input_file,
@@ -109,16 +84,16 @@ def float_scan_cargs(
     """
     cargs = []
     cargs.append("float_scan")
-    if params.get("fix_illegal_values"):
+    if params.get("fix_illegal_values", False):
         cargs.append("-fix")
-    if params.get("verbose_mode"):
+    if params.get("verbose_mode", False):
         cargs.append("-v")
-    if params.get("skip_count") is not None:
+    if params.get("skip_count", None) is not None:
         cargs.extend([
             "-skip",
-            str(params.get("skip_count"))
+            str(params.get("skip_count", None))
         ])
-    cargs.append(execution.input_file(params.get("input_file")))
+    cargs.append(execution.input_file(params.get("input_file", None)))
     return cargs
 
 
@@ -144,9 +119,11 @@ def float_scan_outputs(
 
 def float_scan_execute(
     params: FloatScanParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FloatScanOutputs:
     """
+    float_scan
+    
     Scans the input file of IEEE floating point numbers for illegal values:
     infinities and not-a-number (NaN) values.
     
@@ -156,10 +133,12 @@ def float_scan_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FloatScanOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FLOAT_SCAN_METADATA)
     params = execution.params(params)
     cargs = float_scan_cargs(params, execution)
     ret = float_scan_outputs(params, execution)
@@ -175,6 +154,8 @@ def float_scan(
     runner: Runner | None = None,
 ) -> FloatScanOutputs:
     """
+    float_scan
+    
     Scans the input file of IEEE floating point numbers for illegal values:
     infinities and not-a-number (NaN) values.
     
@@ -193,21 +174,19 @@ def float_scan(
     Returns:
         NamedTuple of outputs (described in `FloatScanOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FLOAT_SCAN_METADATA)
     params = float_scan_params(
         fix_illegal_values=fix_illegal_values,
         verbose_mode=verbose_mode,
         skip_count=skip_count,
         input_file=input_file,
     )
-    return float_scan_execute(params, execution)
+    return float_scan_execute(params, runner)
 
 
 __all__ = [
     "FLOAT_SCAN_METADATA",
     "FloatScanOutputs",
-    "FloatScanParameters",
     "float_scan",
+    "float_scan_execute",
     "float_scan_params",
 ]

niwrap_afni/afni/from3d.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FROM3D_METADATA = Metadata(
-    id="86c7a2fb13a1802f4e1927d75aef4bb109495c45.boutiques",
+    id="350eb8e371fbf27418afd1384aa7ae411057de32.boutiques",
     name="from3d",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,20 @@ FROM3D_METADATA = Metadata(
 
 
 From3dParameters = typing.TypedDict('From3dParameters', {
-    "__STYXTYPE__": typing.Literal["from3d"],
+    "@type": typing.NotRequired[typing.Literal["afni/from3d"]],
+    "verbose": bool,
+    "nsize": bool,
+    "raw": bool,
+    "float": bool,
+    "zfirst": typing.NotRequired[float | None],
+    "zlast": typing.NotRequired[float | None],
+    "tfirst": typing.NotRequired[float | None],
+    "tlast": typing.NotRequired[float | None],
+    "input": InputPathType,
+    "prefix": str,
+})
+From3dParametersTagged = typing.TypedDict('From3dParametersTagged', {
+    "@type": typing.Literal["afni/from3d"],
     "verbose": bool,
     "nsize": bool,
     "raw": bool,
@@ -26,48 +39,14 @@ From3dParameters = typing.TypedDict('From3dParameters', {
     "input": InputPathType,
     "prefix": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "from3d": from3d_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 {
-        "from3d": from3d_outputs,
-    }.get(t)
 
 
 class From3dOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `from3d(...)`.
+    Output object returned when calling `From3dParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    extracted_images: OutputPathType
-    """Extracted 2D images from the 3D dataset"""
 
 
 def from3d_params(
@@ -81,7 +60,7 @@ def from3d_params(
     zlast: float | None = None,
     tfirst: float | None = None,
     tlast: float | None = None,
-) -> From3dParameters:
+) -> From3dParametersTagged:
     """
     Build parameters.
     
@@ -107,7 +86,7 @@ def from3d_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "from3d",
+        "@type": "afni/from3d",
         "verbose": verbose,
         "nsize": nsize,
         "raw": raw,
@@ -141,41 +120,41 @@ def from3d_cargs(
     """
     cargs = []
     cargs.append("from3d")
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-v")
-    if params.get("nsize"):
+    if params.get("nsize", False):
         cargs.append("-nsize")
-    if params.get("raw"):
+    if params.get("raw", False):
         cargs.append("-raw")
-    if params.get("float"):
+    if params.get("float", False):
         cargs.append("-float")
-    if params.get("zfirst") is not None:
+    if params.get("zfirst", None) is not None:
         cargs.extend([
             "-zfirst",
-            str(params.get("zfirst"))
+            str(params.get("zfirst", None))
         ])
-    if params.get("zlast") is not None:
+    if params.get("zlast", None) is not None:
         cargs.extend([
             "-zlast",
-            str(params.get("zlast"))
+            str(params.get("zlast", None))
         ])
-    if params.get("tfirst") is not None:
+    if params.get("tfirst", None) is not None:
         cargs.extend([
             "-tfirst",
-            str(params.get("tfirst"))
+            str(params.get("tfirst", None))
         ])
-    if params.get("tlast") is not None:
+    if params.get("tlast", None) is not None:
         cargs.extend([
             "-tlast",
-            str(params.get("tlast"))
+            str(params.get("tlast", None))
         ])
     cargs.extend([
         "-input",
-        execution.input_file(params.get("input"))
+        execution.input_file(params.get("input", None))
     ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
     return cargs
 
@@ -195,16 +174,17 @@ def from3d_outputs(
     """
     ret = From3dOutputs(
         root=execution.output_file("."),
-        extracted_images=execution.output_file(params.get("prefix") + "*.img"),
     )
     return ret
 
 
 def from3d_execute(
     params: From3dParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> From3dOutputs:
     """
+    from3d
+    
     Extract 2D image files from a 3D AFNI dataset.
     
     Author: AFNI Developers
@@ -213,10 +193,12 @@ def from3d_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `From3dOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FROM3D_METADATA)
     params = execution.params(params)
     cargs = from3d_cargs(params, execution)
     ret = from3d_outputs(params, execution)
@@ -238,6 +220,8 @@ def from3d(
     runner: Runner | None = None,
 ) -> From3dOutputs:
     """
+    from3d
+    
     Extract 2D image files from a 3D AFNI dataset.
     
     Author: AFNI Developers
@@ -266,8 +250,6 @@ def from3d(
     Returns:
         NamedTuple of outputs (described in `From3dOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FROM3D_METADATA)
     params = from3d_params(
         verbose=verbose,
         nsize=nsize,
@@ -280,13 +262,13 @@ def from3d(
         input_=input_,
         prefix=prefix,
     )
-    return from3d_execute(params, execution)
+    return from3d_execute(params, runner)
 
 
 __all__ = [
     "FROM3D_METADATA",
     "From3dOutputs",
-    "From3dParameters",
     "from3d",
+    "from3d_execute",
     "from3d_params",
 ]