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

niwrap_afni/afni/imreg.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 IMREG_METADATA = Metadata(
-    id="818a93bfe29ae4f138331b2556d371211371266b.boutiques",
+    id="f9b37911bbee55f16e00b06af7413164ae887501.boutiques",
     name="imreg",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,30 @@ IMREG_METADATA = Metadata(
 
 
 ImregParameters = typing.TypedDict('ImregParameters', {
-    "__STYXTYPE__": typing.Literal["imreg"],
+    "@type": typing.NotRequired[typing.Literal["afni/imreg"]],
+    "base_image": str,
+    "image_sequence": list[InputPathType],
+    "nowrite": bool,
+    "prefix": typing.NotRequired[str | None],
+    "suffix": typing.NotRequired[str | None],
+    "start": typing.NotRequired[float | None],
+    "step": typing.NotRequired[float | None],
+    "flim": bool,
+    "keepsize": bool,
+    "quiet": bool,
+    "debug": bool,
+    "dprefix": typing.NotRequired[str | None],
+    "bilinear": bool,
+    "modes": typing.NotRequired[str | None],
+    "mlcf": bool,
+    "wtim": typing.NotRequired[InputPathType | None],
+    "dfspace": bool,
+    "cmass": bool,
+    "fine": typing.NotRequired[list[float] | None],
+    "nofine": bool,
+})
+ImregParametersTagged = typing.TypedDict('ImregParametersTagged', {
+    "@type": typing.Literal["afni/imreg"],
     "base_image": str,
     "image_sequence": list[InputPathType],
     "nowrite": bool,
@@ -36,43 +59,11 @@ ImregParameters = typing.TypedDict('ImregParameters', {
     "fine": typing.NotRequired[list[float] | None],
     "nofine": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "imreg": imreg_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 {
-        "imreg": imreg_outputs,
-    }.get(t)
 
 
 class ImregOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `imreg(...)`.
+    Output object returned when calling `ImregParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -107,7 +98,7 @@ def imreg_params(
     cmass: bool = False,
     fine: list[float] | None = None,
     nofine: bool = False,
-) -> ImregParameters:
+) -> ImregParametersTagged:
     """
     Build parameters.
     
@@ -137,7 +128,7 @@ def imreg_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "imreg",
+        "@type": "afni/imreg",
         "base_image": base_image,
         "image_sequence": image_sequence,
         "nowrite": nowrite,
@@ -185,67 +176,67 @@ def imreg_cargs(
     """
     cargs = []
     cargs.append("imreg")
-    cargs.append(params.get("base_image"))
-    cargs.extend([execution.input_file(f) for f in params.get("image_sequence")])
-    if params.get("nowrite"):
+    cargs.append(params.get("base_image", None))
+    cargs.extend([execution.input_file(f) for f in params.get("image_sequence", None)])
+    if params.get("nowrite", False):
         cargs.append("-nowrite")
-    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("suffix") is not None:
+    if params.get("suffix", None) is not None:
         cargs.extend([
             "-suffix",
-            params.get("suffix")
+            params.get("suffix", None)
         ])
-    if params.get("start") is not None:
+    if params.get("start", None) is not None:
         cargs.extend([
             "-start",
-            str(params.get("start"))
+            str(params.get("start", None))
         ])
-    if params.get("step") is not None:
+    if params.get("step", None) is not None:
         cargs.extend([
             "-step",
-            str(params.get("step"))
+            str(params.get("step", None))
         ])
-    if params.get("flim"):
+    if params.get("flim", False):
         cargs.append("-flim")
-    if params.get("keepsize"):
+    if params.get("keepsize", False):
         cargs.append("-keepsize")
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("-debug")
-    if params.get("dprefix") is not None:
+    if params.get("dprefix", None) is not None:
         cargs.extend([
             "-dprefix",
-            params.get("dprefix")
+            params.get("dprefix", None)
         ])
-    if params.get("bilinear"):
+    if params.get("bilinear", False):
         cargs.append("-bilinear")
-    if params.get("modes") is not None:
+    if params.get("modes", None) is not None:
         cargs.extend([
             "-modes",
-            params.get("modes")
+            params.get("modes", None)
         ])
-    if params.get("mlcf"):
+    if params.get("mlcf", False):
         cargs.append("-mlcF")
-    if params.get("wtim") is not None:
+    if params.get("wtim", None) is not None:
         cargs.extend([
             "-wtim",
-            execution.input_file(params.get("wtim"))
+            execution.input_file(params.get("wtim", None))
         ])
-    if params.get("dfspace"):
+    if params.get("dfspace", False):
         cargs.append("-dfspace")
-    if params.get("cmass"):
+    if params.get("cmass", False):
         cargs.append("-cmass")
-    if params.get("fine") is not None:
+    if params.get("fine", None) is not None:
         cargs.extend([
             "-fine",
-            *map(str, params.get("fine"))
+            *map(str, params.get("fine", None))
         ])
-    if params.get("nofine"):
+    if params.get("nofine", False):
         cargs.append("-nofine")
     return cargs
 
@@ -265,19 +256,21 @@ def imreg_outputs(
     """
     ret = ImregOutputs(
         root=execution.output_file("."),
-        registered_images=execution.output_file(params.get("prefix") + ".[INDEX]." + params.get("suffix")) if (params.get("prefix") is not None and params.get("suffix") is not None) else None,
-        dx_file=execution.output_file(params.get("dprefix") + ".dx") if (params.get("dprefix") is not None) else None,
-        dy_file=execution.output_file(params.get("dprefix") + ".dy") if (params.get("dprefix") is not None) else None,
-        phi_file=execution.output_file(params.get("dprefix") + ".phi") if (params.get("dprefix") is not None) else None,
+        registered_images=execution.output_file(params.get("prefix", None) + ".[INDEX]." + params.get("suffix", None)) if (params.get("prefix") is not None and params.get("suffix") is not None) else None,
+        dx_file=execution.output_file(params.get("dprefix", None) + ".dx") if (params.get("dprefix") is not None) else None,
+        dy_file=execution.output_file(params.get("dprefix", None) + ".dy") if (params.get("dprefix") is not None) else None,
+        phi_file=execution.output_file(params.get("dprefix", None) + ".phi") if (params.get("dprefix") is not None) else None,
     )
     return ret
 
 
 def imreg_execute(
     params: ImregParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ImregOutputs:
     """
+    imreg
+    
     Registers each 2D image in 'image_sequence' to 'base_image'.
     
     Author: AFNI Developers
@@ -286,10 +279,12 @@ def imreg_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ImregOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(IMREG_METADATA)
     params = execution.params(params)
     cargs = imreg_cargs(params, execution)
     ret = imreg_outputs(params, execution)
@@ -321,6 +316,8 @@ def imreg(
     runner: Runner | None = None,
 ) -> ImregOutputs:
     """
+    imreg
+    
     Registers each 2D image in 'image_sequence' to 'base_image'.
     
     Author: AFNI Developers
@@ -353,8 +350,6 @@ def imreg(
     Returns:
         NamedTuple of outputs (described in `ImregOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(IMREG_METADATA)
     params = imreg_params(
         base_image=base_image,
         image_sequence=image_sequence,
@@ -377,13 +372,13 @@ def imreg(
         fine=fine,
         nofine=nofine,
     )
-    return imreg_execute(params, execution)
+    return imreg_execute(params, runner)
 
 
 __all__ = [
     "IMREG_METADATA",
     "ImregOutputs",
-    "ImregParameters",
     "imreg",
+    "imreg_execute",
     "imreg_params",
 ]

niwrap_afni/afni/imrotate.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 IMROTATE_METADATA = Metadata(
-    id="b1deba5a72945c551d4389c3320d0152b83b453a.boutiques",
+    id="68a8a871a455385d9e6b357b30b75c0ea9b3cc6d.boutiques",
     name="imrotate",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,17 @@ IMROTATE_METADATA = Metadata(
 
 
 ImrotateParameters = typing.TypedDict('ImrotateParameters', {
-    "__STYXTYPE__": typing.Literal["imrotate"],
+    "@type": typing.NotRequired[typing.Literal["afni/imrotate"]],
+    "linear_interpolation": bool,
+    "fourier_interpolation": bool,
+    "dx": float,
+    "dy": float,
+    "phi": float,
+    "input_image": InputPathType,
+    "output_image": str,
+})
+ImrotateParametersTagged = typing.TypedDict('ImrotateParametersTagged', {
+    "@type": typing.Literal["afni/imrotate"],
     "linear_interpolation": bool,
     "fourier_interpolation": bool,
     "dx": float,
@@ -23,43 +33,11 @@ ImrotateParameters = typing.TypedDict('ImrotateParameters', {
     "input_image": InputPathType,
     "output_image": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "imrotate": imrotate_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 {
-        "imrotate": imrotate_outputs,
-    }.get(t)
 
 
 class ImrotateOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `imrotate(...)`.
+    Output object returned when calling `ImrotateParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +53,7 @@ def imrotate_params(
     output_image: str,
     linear_interpolation: bool = False,
     fourier_interpolation: bool = False,
-) -> ImrotateParameters:
+) -> ImrotateParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +69,7 @@ def imrotate_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "imrotate",
+        "@type": "afni/imrotate",
         "linear_interpolation": linear_interpolation,
         "fourier_interpolation": fourier_interpolation,
         "dx": dx,
@@ -118,15 +96,15 @@ def imrotate_cargs(
     """
     cargs = []
     cargs.append("imrotate")
-    if params.get("linear_interpolation"):
+    if params.get("linear_interpolation", False):
         cargs.append("-linear")
-    if params.get("fourier_interpolation"):
+    if params.get("fourier_interpolation", False):
         cargs.append("-Fourier")
-    cargs.append(str(params.get("dx")))
-    cargs.append(str(params.get("dy")))
-    cargs.append(str(params.get("phi")))
-    cargs.append(execution.input_file(params.get("input_image")))
-    cargs.append(params.get("output_image"))
+    cargs.append(str(params.get("dx", None)))
+    cargs.append(str(params.get("dy", None)))
+    cargs.append(str(params.get("phi", None)))
+    cargs.append(execution.input_file(params.get("input_image", None)))
+    cargs.append(params.get("output_image", None))
     return cargs
 
 
@@ -145,16 +123,18 @@ def imrotate_outputs(
     """
     ret = ImrotateOutputs(
         root=execution.output_file("."),
-        output_image_file=execution.output_file(params.get("output_image")),
+        output_image_file=execution.output_file(params.get("output_image", None)),
     )
     return ret
 
 
 def imrotate_execute(
     params: ImrotateParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ImrotateOutputs:
     """
+    imrotate
+    
     Shifts and rotates an image.
     
     Author: AFNI Developers
@@ -163,10 +143,12 @@ def imrotate_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ImrotateOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(IMROTATE_METADATA)
     params = execution.params(params)
     cargs = imrotate_cargs(params, execution)
     ret = imrotate_outputs(params, execution)
@@ -185,6 +167,8 @@ def imrotate(
     runner: Runner | None = None,
 ) -> ImrotateOutputs:
     """
+    imrotate
+    
     Shifts and rotates an image.
     
     Author: AFNI Developers
@@ -203,8 +187,6 @@ def imrotate(
     Returns:
         NamedTuple of outputs (described in `ImrotateOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(IMROTATE_METADATA)
     params = imrotate_params(
         linear_interpolation=linear_interpolation,
         fourier_interpolation=fourier_interpolation,
@@ -214,13 +196,13 @@ def imrotate(
         input_image=input_image,
         output_image=output_image,
     )
-    return imrotate_execute(params, execution)
+    return imrotate_execute(params, runner)
 
 
 __all__ = [
     "IMROTATE_METADATA",
     "ImrotateOutputs",
-    "ImrotateParameters",
     "imrotate",
+    "imrotate_execute",
     "imrotate_params",
 ]

niwrap_afni/afni/imstack.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 IMSTACK_METADATA = Metadata(
-    id="d9dca2a7110a68c32c73fef2f7ffc0520892ff07.boutiques",
+    id="903eb8f0f9425899a698dfbbbf982f858818717b.boutiques",
     name="imstack",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,48 +14,22 @@ IMSTACK_METADATA = Metadata(
 
 
 ImstackParameters = typing.TypedDict('ImstackParameters', {
-    "__STYXTYPE__": typing.Literal["imstack"],
+    "@type": typing.NotRequired[typing.Literal["afni/imstack"]],
+    "image_files": list[InputPathType],
+    "data_type": typing.NotRequired[typing.Literal["short", "float"] | None],
+    "output_prefix": typing.NotRequired[str | None],
+})
+ImstackParametersTagged = typing.TypedDict('ImstackParametersTagged', {
+    "@type": typing.Literal["afni/imstack"],
     "image_files": list[InputPathType],
     "data_type": typing.NotRequired[typing.Literal["short", "float"] | None],
     "output_prefix": 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 {
-        "imstack": imstack_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 {
-        "imstack": imstack_outputs,
-    }.get(t)
 
 
 class ImstackOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `imstack(...)`.
+    Output object returned when calling `ImstackParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +43,7 @@ def imstack_params(
     image_files: list[InputPathType],
     data_type: typing.Literal["short", "float"] | None = None,
     output_prefix: str | None = None,
-) -> ImstackParameters:
+) -> ImstackParametersTagged:
     """
     Build parameters.
     
@@ -83,7 +57,7 @@ def imstack_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "imstack",
+        "@type": "afni/imstack",
         "image_files": image_files,
     }
     if data_type is not None:
@@ -108,16 +82,16 @@ def imstack_cargs(
     """
     cargs = []
     cargs.append("imstack")
-    cargs.extend([execution.input_file(f) for f in params.get("image_files")])
-    if params.get("data_type") is not None:
+    cargs.extend([execution.input_file(f) for f in params.get("image_files", None)])
+    if params.get("data_type", None) is not None:
         cargs.extend([
             "-datum",
-            params.get("data_type")
+            params.get("data_type", 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)
         ])
     return cargs
 
@@ -137,17 +111,19 @@ def imstack_outputs(
     """
     ret = ImstackOutputs(
         root=execution.output_file("."),
-        output_data_file=execution.output_file(params.get("output_prefix") + ".b" + params.get("data_type")) if (params.get("output_prefix") is not None and params.get("data_type") is not None) else None,
-        output_header_file=execution.output_file(params.get("output_prefix") + ".hdr") if (params.get("output_prefix") is not None) else None,
+        output_data_file=execution.output_file(params.get("output_prefix", None) + ".b" + params.get("data_type", None)) if (params.get("output_prefix") is not None and params.get("data_type") is not None) else None,
+        output_header_file=execution.output_file(params.get("output_prefix", None) + ".hdr") if (params.get("output_prefix") is not None) else None,
     )
     return ret
 
 
 def imstack_execute(
     params: ImstackParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ImstackOutputs:
     """
+    imstack
+    
     Stacks up a set of 2D images into one big file (a la MGH).
     
     Author: AFNI Developers
@@ -156,10 +132,12 @@ def imstack_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ImstackOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(IMSTACK_METADATA)
     params = execution.params(params)
     cargs = imstack_cargs(params, execution)
     ret = imstack_outputs(params, execution)
@@ -174,6 +152,8 @@ def imstack(
     runner: Runner | None = None,
 ) -> ImstackOutputs:
     """
+    imstack
+    
     Stacks up a set of 2D images into one big file (a la MGH).
     
     Author: AFNI Developers
@@ -190,20 +170,18 @@ def imstack(
     Returns:
         NamedTuple of outputs (described in `ImstackOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(IMSTACK_METADATA)
     params = imstack_params(
         image_files=image_files,
         data_type=data_type,
         output_prefix=output_prefix,
     )
-    return imstack_execute(params, execution)
+    return imstack_execute(params, runner)
 
 
 __all__ = [
     "IMSTACK_METADATA",
     "ImstackOutputs",
-    "ImstackParameters",
     "imstack",
+    "imstack_execute",
     "imstack_params",
 ]