niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/imand.py

@@ -0,0 +1,203 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+IMAND_METADATA = Metadata(
+    id="0afb6402a062c937d946cf010c86102b9c4a0c96.boutiques",
+    name="imand",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+ImandParameters = typing.TypedDict('ImandParameters', {
+    "__STYX_TYPE__": typing.Literal["imand"],
+    "threshold": typing.NotRequired[float | None],
+    "input_images": list[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 {
+        "imand": imand_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 {
+        "imand": imand_outputs,
+    }.get(t)
+
+
+class ImandOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `imand(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outfile: OutputPathType
+    """The resulting output image file."""
+
+
+def imand_params(
+    input_images: list[InputPathType],
+    output_image: str,
+    threshold: float | None = None,
+) -> ImandParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_images: Input images to be processed. Multiple input images can\
+            be specified.
+        output_image: Output image file.
+        threshold: Threshold value; only pixels above this value will be\
+            output. Optional.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "imand",
+        "input_images": input_images,
+        "output_image": output_image,
+    }
+    if threshold is not None:
+        params["threshold"] = threshold
+    return params
+
+
+def imand_cargs(
+    params: ImandParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("imand")
+    if params.get("threshold") is not None:
+        cargs.extend([
+            "--thresh",
+            str(params.get("threshold"))
+        ])
+    cargs.extend([execution.input_file(f) for f in params.get("input_images")])
+    cargs.append(params.get("output_image"))
+    return cargs
+
+
+def imand_outputs(
+    params: ImandParameters,
+    execution: Execution,
+) -> ImandOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = ImandOutputs(
+        root=execution.output_file("."),
+        outfile=execution.output_file(params.get("output_image")),
+    )
+    return ret
+
+
+def imand_execute(
+    params: ImandParameters,
+    execution: Execution,
+) -> ImandOutputs:
+    """
+    Image AND operation tool. Only pixels nonzero in all input images (and above the
+    threshold, if given) will be output.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `ImandOutputs`).
+    """
+    params = execution.params(params)
+    cargs = imand_cargs(params, execution)
+    ret = imand_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def imand(
+    input_images: list[InputPathType],
+    output_image: str,
+    threshold: float | None = None,
+    runner: Runner | None = None,
+) -> ImandOutputs:
+    """
+    Image AND operation tool. Only pixels nonzero in all input images (and above the
+    threshold, if given) will be output.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_images: Input images to be processed. Multiple input images can\
+            be specified.
+        output_image: Output image file.
+        threshold: Threshold value; only pixels above this value will be\
+            output. Optional.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `ImandOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(IMAND_METADATA)
+    params = imand_params(
+        threshold=threshold,
+        input_images=input_images,
+        output_image=output_image,
+    )
+    return imand_execute(params, execution)
+
+
+__all__ = [
+    "IMAND_METADATA",
+    "ImandOutputs",
+    "ImandParameters",
+    "imand",
+    "imand_params",
+]

niwrap_afni/afni/imaver.py

@@ -0,0 +1,201 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+IMAVER_METADATA = Metadata(
+    id="d40eed47338fed1128a04d1c60c1e336c6bcfad8.boutiques",
+    name="imaver",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+ImaverParameters = typing.TypedDict('ImaverParameters', {
+    "__STYX_TYPE__": typing.Literal["imaver"],
+    "out_ave": typing.NotRequired[str | None],
+    "out_sig": typing.NotRequired[str | None],
+    "input_images": list[InputPathType],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "imaver": imaver_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 {
+        "imaver": imaver_outputs,
+    }.get(t)
+
+
+class ImaverOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `imaver(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_ave_output: OutputPathType | None
+    """Output image file for averages (optional)"""
+    out_sig_output: OutputPathType | None
+    """Output image file for standard deviations (optional)"""
+
+
+def imaver_params(
+    input_images: list[InputPathType],
+    out_ave: str | None = None,
+    out_sig: str | None = None,
+) -> ImaverParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_images: Input image files for processing.
+        out_ave: Output average image file. Use '-' to skip output.
+        out_sig: Output standard deviation image file. Use '-' to skip output.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "imaver",
+        "input_images": input_images,
+    }
+    if out_ave is not None:
+        params["out_ave"] = out_ave
+    if out_sig is not None:
+        params["out_sig"] = out_sig
+    return params
+
+
+def imaver_cargs(
+    params: ImaverParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("imaver")
+    if params.get("out_ave") is not None:
+        cargs.append(params.get("out_ave"))
+    if params.get("out_sig") is not None:
+        cargs.append(params.get("out_sig"))
+    cargs.extend([execution.input_file(f) for f in params.get("input_images")])
+    return cargs
+
+
+def imaver_outputs(
+    params: ImaverParameters,
+    execution: Execution,
+) -> ImaverOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = ImaverOutputs(
+        root=execution.output_file("."),
+        out_ave_output=execution.output_file(params.get("out_ave")) if (params.get("out_ave") is not None) else None,
+        out_sig_output=execution.output_file(params.get("out_sig")) if (params.get("out_sig") is not None) else None,
+    )
+    return ret
+
+
+def imaver_execute(
+    params: ImaverParameters,
+    execution: Execution,
+) -> ImaverOutputs:
+    """
+    Computes the mean and standard deviation, pixel-by-pixel, of a whole bunch of
+    images.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `ImaverOutputs`).
+    """
+    params = execution.params(params)
+    cargs = imaver_cargs(params, execution)
+    ret = imaver_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def imaver(
+    input_images: list[InputPathType],
+    out_ave: str | None = None,
+    out_sig: str | None = None,
+    runner: Runner | None = None,
+) -> ImaverOutputs:
+    """
+    Computes the mean and standard deviation, pixel-by-pixel, of a whole bunch of
+    images.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_images: Input image files for processing.
+        out_ave: Output average image file. Use '-' to skip output.
+        out_sig: Output standard deviation image file. Use '-' to skip output.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `ImaverOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(IMAVER_METADATA)
+    params = imaver_params(
+        out_ave=out_ave,
+        out_sig=out_sig,
+        input_images=input_images,
+    )
+    return imaver_execute(params, execution)
+
+
+__all__ = [
+    "IMAVER_METADATA",
+    "ImaverOutputs",
+    "ImaverParameters",
+    "imaver",
+    "imaver_params",
+]

niwrap_afni/afni/imcalc.py

@@ -0,0 +1,235 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+IMCALC_METADATA = Metadata(
+    id="619429e3eb3a18d69af5e0d47edb5f5289323a19.boutiques",
+    name="imcalc",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+ImcalcParameters = typing.TypedDict('ImcalcParameters', {
+    "__STYX_TYPE__": typing.Literal["imcalc"],
+    "datum_type": typing.NotRequired[str | None],
+    "image_inputs": typing.NotRequired[list[InputPathType] | None],
+    "expression": str,
+    "output_name": 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 {
+        "imcalc": imcalc_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 {
+        "imcalc": imcalc_outputs,
+    }.get(t)
+
+
+class ImcalcOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `imcalc(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_image: OutputPathType | None
+    """Output image file produced after applying the expression to input
+    images"""
+
+
+def imcalc_params(
+    expression: str,
+    datum_type: str | None = None,
+    image_inputs: list[InputPathType] | None = None,
+    output_name: str | None = None,
+) -> ImcalcParameters:
+    """
+    Build parameters.
+    
+    Args:
+        expression: Apply the expression within quotes to the input images, one\
+            voxel at a time, to produce the output image. (e.g., "sqrt(a*b)" to\
+            compute the geometric mean).
+        datum_type: Coerce the output data to be stored as the given type:\
+            byte, short, or float. Default is the datum of the first input image on\
+            the command line.
+        image_inputs: Read image 'dname' and call the voxel values 'a' in the\
+            expression. 'a' may be any letter from 'a' to 'z'. If some letter name\
+            is used in the expression but not present in one of the image options\
+            here, then that variable is set to 0.
+        output_name: Use 'name' for the output image filename. Default is\
+            'imcalc.out'.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "imcalc",
+        "expression": expression,
+    }
+    if datum_type is not None:
+        params["datum_type"] = datum_type
+    if image_inputs is not None:
+        params["image_inputs"] = image_inputs
+    if output_name is not None:
+        params["output_name"] = output_name
+    return params
+
+
+def imcalc_cargs(
+    params: ImcalcParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("imcalc")
+    if params.get("datum_type") is not None:
+        cargs.extend([
+            "-datum type",
+            params.get("datum_type")
+        ])
+    if params.get("image_inputs") is not None:
+        cargs.extend([
+            "-a",
+            *[execution.input_file(f) for f in params.get("image_inputs")]
+        ])
+    cargs.extend([
+        "-expr",
+        params.get("expression")
+    ])
+    if params.get("output_name") is not None:
+        cargs.extend([
+            "-output",
+            params.get("output_name")
+        ])
+    return cargs
+
+
+def imcalc_outputs(
+    params: ImcalcParameters,
+    execution: Execution,
+) -> ImcalcOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = ImcalcOutputs(
+        root=execution.output_file("."),
+        output_image=execution.output_file(params.get("output_name")) if (params.get("output_name") is not None) else None,
+    )
+    return ret
+
+
+def imcalc_execute(
+    params: ImcalcParameters,
+    execution: Execution,
+) -> ImcalcOutputs:
+    """
+    Tool for arithmetic operations on 2D images, pixel-by-pixel.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `ImcalcOutputs`).
+    """
+    params = execution.params(params)
+    cargs = imcalc_cargs(params, execution)
+    ret = imcalc_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def imcalc(
+    expression: str,
+    datum_type: str | None = None,
+    image_inputs: list[InputPathType] | None = None,
+    output_name: str | None = None,
+    runner: Runner | None = None,
+) -> ImcalcOutputs:
+    """
+    Tool for arithmetic operations on 2D images, pixel-by-pixel.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        expression: Apply the expression within quotes to the input images, one\
+            voxel at a time, to produce the output image. (e.g., "sqrt(a*b)" to\
+            compute the geometric mean).
+        datum_type: Coerce the output data to be stored as the given type:\
+            byte, short, or float. Default is the datum of the first input image on\
+            the command line.
+        image_inputs: Read image 'dname' and call the voxel values 'a' in the\
+            expression. 'a' may be any letter from 'a' to 'z'. If some letter name\
+            is used in the expression but not present in one of the image options\
+            here, then that variable is set to 0.
+        output_name: Use 'name' for the output image filename. Default is\
+            'imcalc.out'.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `ImcalcOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(IMCALC_METADATA)
+    params = imcalc_params(
+        datum_type=datum_type,
+        image_inputs=image_inputs,
+        expression=expression,
+        output_name=output_name,
+    )
+    return imcalc_execute(params, execution)
+
+
+__all__ = [
+    "IMCALC_METADATA",
+    "ImcalcOutputs",
+    "ImcalcParameters",
+    "imcalc",
+    "imcalc_params",
+]