niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/imcutup.py

@@ -0,0 +1,241 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+IMCUTUP_METADATA = Metadata(
+    id="f7a6e708513c2d65a4c90feab343a1b3f974642a.boutiques",
+    name="imcutup",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+ImcutupParameters = typing.TypedDict('ImcutupParameters', {
+    "__STYX_TYPE__": typing.Literal["imcutup"],
+    "prefix": typing.NotRequired[str | None],
+    "xynum": bool,
+    "yxnum": bool,
+    "xynum_format": bool,
+    "yxnum_format": bool,
+    "nx": int,
+    "ny": int,
+    "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 {
+        "imcutup": imcutup_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 {
+        "imcutup": imcutup_outputs,
+    }.get(t)
+
+
+class ImcutupOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `imcutup(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_files: OutputPathType | None
+    """Output smaller images with the specified prefix numbering format."""
+
+
+def imcutup_params(
+    nx: int,
+    ny: int,
+    input_file: InputPathType,
+    prefix: str | None = None,
+    xynum: bool = False,
+    yxnum: bool = False,
+    xynum_format: bool = False,
+    yxnum_format: bool = False,
+) -> ImcutupParameters:
+    """
+    Build parameters.
+    
+    Args:
+        nx: Number of pixels along the x-dimension for the smaller images.
+        ny: Number of pixels along the y-dimension for the smaller images.
+        input_file: Input image filename. Must be a single 2D image.
+        prefix: Prefix the output files with the provided string.
+        xynum: Number the output images in x-first, then y (default behavior).
+        yxnum: Number the output images in y-first, then x.
+        xynum_format: 2D numbering in x.y format.
+        yxnum_format: 2D numbering in y.x format.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "imcutup",
+        "xynum": xynum,
+        "yxnum": yxnum,
+        "xynum_format": xynum_format,
+        "yxnum_format": yxnum_format,
+        "nx": nx,
+        "ny": ny,
+        "input_file": input_file,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    return params
+
+
+def imcutup_cargs(
+    params: ImcutupParameters,
+    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("imcutup")
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("xynum"):
+        cargs.append("-xynum")
+    if params.get("yxnum"):
+        cargs.append("-yxnum")
+    if params.get("xynum_format"):
+        cargs.append("-x.ynum")
+    if params.get("yxnum_format"):
+        cargs.append("-y.xnum")
+    cargs.append(str(params.get("nx")))
+    cargs.append(str(params.get("ny")))
+    cargs.append(execution.input_file(params.get("input_file")))
+    return cargs
+
+
+def imcutup_outputs(
+    params: ImcutupParameters,
+    execution: Execution,
+) -> ImcutupOutputs:
+    """
+    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 = ImcutupOutputs(
+        root=execution.output_file("."),
+        output_files=execution.output_file(params.get("prefix") + "*") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def imcutup_execute(
+    params: ImcutupParameters,
+    execution: Execution,
+) -> ImcutupOutputs:
+    """
+    Breaks up larger images into smaller image files of user-defined size.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `ImcutupOutputs`).
+    """
+    params = execution.params(params)
+    cargs = imcutup_cargs(params, execution)
+    ret = imcutup_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def imcutup(
+    nx: int,
+    ny: int,
+    input_file: InputPathType,
+    prefix: str | None = None,
+    xynum: bool = False,
+    yxnum: bool = False,
+    xynum_format: bool = False,
+    yxnum_format: bool = False,
+    runner: Runner | None = None,
+) -> ImcutupOutputs:
+    """
+    Breaks up larger images into smaller image files of user-defined size.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        nx: Number of pixels along the x-dimension for the smaller images.
+        ny: Number of pixels along the y-dimension for the smaller images.
+        input_file: Input image filename. Must be a single 2D image.
+        prefix: Prefix the output files with the provided string.
+        xynum: Number the output images in x-first, then y (default behavior).
+        yxnum: Number the output images in y-first, then x.
+        xynum_format: 2D numbering in x.y format.
+        yxnum_format: 2D numbering in y.x format.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `ImcutupOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(IMCUTUP_METADATA)
+    params = imcutup_params(
+        prefix=prefix,
+        xynum=xynum,
+        yxnum=yxnum,
+        xynum_format=xynum_format,
+        yxnum_format=yxnum_format,
+        nx=nx,
+        ny=ny,
+        input_file=input_file,
+    )
+    return imcutup_execute(params, execution)
+
+
+__all__ = [
+    "IMCUTUP_METADATA",
+    "ImcutupOutputs",
+    "ImcutupParameters",
+    "imcutup",
+    "imcutup_params",
+]

niwrap_afni/afni/imdump.py

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+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+IMDUMP_METADATA = Metadata(
+    id="7f8451c2da7ec8cbf2c32a069270cdd298deaee7.boutiques",
+    name="imdump",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+ImdumpParameters = typing.TypedDict('ImdumpParameters', {
+    "__STYX_TYPE__": typing.Literal["imdump"],
+    "input_image": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "imdump": imdump_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 {
+        "imdump": imdump_outputs,
+    }.get(t)
+
+
+class ImdumpOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `imdump(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    stdout: OutputPathType
+    """Nonzero pixels in the format: x-index y-index value, one pixel per
+    line."""
+
+
+def imdump_params(
+    input_image: InputPathType,
+) -> ImdumpParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_image: Input image file to be processed.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "imdump",
+        "input_image": input_image,
+    }
+    return params
+
+
+def imdump_cargs(
+    params: ImdumpParameters,
+    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("imdump")
+    cargs.append(execution.input_file(params.get("input_image")))
+    return cargs
+
+
+def imdump_outputs(
+    params: ImdumpParameters,
+    execution: Execution,
+) -> ImdumpOutputs:
+    """
+    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 = ImdumpOutputs(
+        root=execution.output_file("."),
+        stdout=execution.output_file("stdout.txt"),
+    )
+    return ret
+
+
+def imdump_execute(
+    params: ImdumpParameters,
+    execution: Execution,
+) -> ImdumpOutputs:
+    """
+    Prints out nonzero pixels in an image.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `ImdumpOutputs`).
+    """
+    params = execution.params(params)
+    cargs = imdump_cargs(params, execution)
+    ret = imdump_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def imdump(
+    input_image: InputPathType,
+    runner: Runner | None = None,
+) -> ImdumpOutputs:
+    """
+    Prints out nonzero pixels in an image.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_image: Input image file to be processed.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `ImdumpOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(IMDUMP_METADATA)
+    params = imdump_params(
+        input_image=input_image,
+    )
+    return imdump_execute(params, execution)
+
+
+__all__ = [
+    "IMDUMP_METADATA",
+    "ImdumpOutputs",
+    "ImdumpParameters",
+    "imdump",
+    "imdump_params",
+]

niwrap_afni/afni/immask.py

@@ -0,0 +1,223 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+IMMASK_METADATA = Metadata(
+    id="9c1f93c0cb09202023e9490b9f3feb5a319f6f59.boutiques",
+    name="immask",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+ImmaskParameters = typing.TypedDict('ImmaskParameters', {
+    "__STYX_TYPE__": typing.Literal["immask"],
+    "threshold": typing.NotRequired[float | None],
+    "mask_image": typing.NotRequired[InputPathType | None],
+    "positive_only": bool,
+    "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 {
+        "immask": immask_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 {
+        "immask": immask_outputs,
+    }.get(t)
+
+
+class ImmaskOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `immask(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """Masked output image"""
+
+
+def immask_params(
+    input_image: InputPathType,
+    output_image: str,
+    threshold: float | None = None,
+    mask_image: InputPathType | None = None,
+    positive_only: bool = False,
+) -> ImmaskParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_image: Input image to be masked.
+        output_image: Output image after masking.
+        threshold: Threshold value; all pixels with absolute value below this\
+            will be set to zero in the output image.
+        mask_image: Mask image; only locations that are nonzero in the mask\
+            image will be nonzero in the output image.
+        positive_only: Use only positive pixels from input image.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "immask",
+        "positive_only": positive_only,
+        "input_image": input_image,
+        "output_image": output_image,
+    }
+    if threshold is not None:
+        params["threshold"] = threshold
+    if mask_image is not None:
+        params["mask_image"] = mask_image
+    return params
+
+
+def immask_cargs(
+    params: ImmaskParameters,
+    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("immask")
+    if params.get("threshold") is not None:
+        cargs.extend([
+            "-thresh",
+            str(params.get("threshold"))
+        ])
+    if params.get("mask_image") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask_image"))
+        ])
+    if params.get("positive_only"):
+        cargs.append("-pos")
+    cargs.append(execution.input_file(params.get("input_image")))
+    cargs.append(params.get("output_image"))
+    return cargs
+
+
+def immask_outputs(
+    params: ImmaskParameters,
+    execution: Execution,
+) -> ImmaskOutputs:
+    """
+    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 = ImmaskOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("output_image")),
+    )
+    return ret
+
+
+def immask_execute(
+    params: ImmaskParameters,
+    execution: Execution,
+) -> ImmaskOutputs:
+    """
+    Masks the input image based on specified criteria and produces the output image.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `ImmaskOutputs`).
+    """
+    params = execution.params(params)
+    cargs = immask_cargs(params, execution)
+    ret = immask_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def immask(
+    input_image: InputPathType,
+    output_image: str,
+    threshold: float | None = None,
+    mask_image: InputPathType | None = None,
+    positive_only: bool = False,
+    runner: Runner | None = None,
+) -> ImmaskOutputs:
+    """
+    Masks the input image based on specified criteria and produces the output image.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_image: Input image to be masked.
+        output_image: Output image after masking.
+        threshold: Threshold value; all pixels with absolute value below this\
+            will be set to zero in the output image.
+        mask_image: Mask image; only locations that are nonzero in the mask\
+            image will be nonzero in the output image.
+        positive_only: Use only positive pixels from input image.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `ImmaskOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(IMMASK_METADATA)
+    params = immask_params(
+        threshold=threshold,
+        mask_image=mask_image,
+        positive_only=positive_only,
+        input_image=input_image,
+        output_image=output_image,
+    )
+    return immask_execute(params, execution)
+
+
+__all__ = [
+    "IMMASK_METADATA",
+    "ImmaskOutputs",
+    "ImmaskParameters",
+    "immask",
+    "immask_params",
+]