niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/imreg.py

@@ -0,0 +1,389 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+IMREG_METADATA = Metadata(
+    id="4ed217ec6db0c1ed0ca85263b118a5554ebb437a.boutiques",
+    name="imreg",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+ImregParameters = typing.TypedDict('ImregParameters', {
+    "__STYX_TYPE__": typing.Literal["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,
+})
+
+
+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(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    registered_images: OutputPathType | None
+    """Registered images"""
+    dx_file: OutputPathType | None
+    """Time series dx file"""
+    dy_file: OutputPathType | None
+    """Time series dy file"""
+    phi_file: OutputPathType | None
+    """Time series phi file"""
+
+
+def imreg_params(
+    base_image: str,
+    image_sequence: list[InputPathType],
+    nowrite: bool = False,
+    prefix: str | None = None,
+    suffix: str | None = None,
+    start: float | None = None,
+    step: float | None = None,
+    flim: bool = False,
+    keepsize: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    dprefix: str | None = None,
+    bilinear: bool = False,
+    modes: str | None = None,
+    mlcf: bool = False,
+    wtim: InputPathType | None = None,
+    dfspace: bool = False,
+    cmass: bool = False,
+    fine: list[float] | None = None,
+    nofine: bool = False,
+) -> ImregParameters:
+    """
+    Build parameters.
+    
+    Args:
+        base_image: Base image or method to determine base image ('+AVER' or\
+            '+count').
+        image_sequence: Sequence of images to be registered.
+        nowrite: Don't write outputs, just print progress reports.
+        prefix: Prefix for output file names.
+        suffix: Suffix for output file names.
+        start: Start index for output file names.
+        step: Step size for output file indices.
+        flim: Write output in mrilib floating point format.
+        keepsize: Preserve the original image size on output.
+        quiet: Don't write progress report messages.
+        debug: Write lots of debugging output.
+        dprefix: Prefix for dx, dy, and phi files.
+        bilinear: Use bilinear interpolation.
+        modes: Interpolation modes during coarse, fine, and registration phases.
+        mlcf: Equivalent to '-modes bilinear bicubic Fourier'.
+        wtim: Weighting image file.
+        dfspace: Use difiterated differential spatial method.
+        cmass: Align centers of mass of the images.
+        fine: Fine fit parameters: blur, dxy, dphi.
+        nofine: Turn off the 'fine' fit algorithm.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "imreg",
+        "base_image": base_image,
+        "image_sequence": image_sequence,
+        "nowrite": nowrite,
+        "flim": flim,
+        "keepsize": keepsize,
+        "quiet": quiet,
+        "debug": debug,
+        "bilinear": bilinear,
+        "mlcf": mlcf,
+        "dfspace": dfspace,
+        "cmass": cmass,
+        "nofine": nofine,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if suffix is not None:
+        params["suffix"] = suffix
+    if start is not None:
+        params["start"] = start
+    if step is not None:
+        params["step"] = step
+    if dprefix is not None:
+        params["dprefix"] = dprefix
+    if modes is not None:
+        params["modes"] = modes
+    if wtim is not None:
+        params["wtim"] = wtim
+    if fine is not None:
+        params["fine"] = fine
+    return params
+
+
+def imreg_cargs(
+    params: ImregParameters,
+    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("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("-nowrite")
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("suffix") is not None:
+        cargs.extend([
+            "-suffix",
+            params.get("suffix")
+        ])
+    if params.get("start") is not None:
+        cargs.extend([
+            "-start",
+            str(params.get("start"))
+        ])
+    if params.get("step") is not None:
+        cargs.extend([
+            "-step",
+            str(params.get("step"))
+        ])
+    if params.get("flim"):
+        cargs.append("-flim")
+    if params.get("keepsize"):
+        cargs.append("-keepsize")
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    if params.get("debug"):
+        cargs.append("-debug")
+    if params.get("dprefix") is not None:
+        cargs.extend([
+            "-dprefix",
+            params.get("dprefix")
+        ])
+    if params.get("bilinear"):
+        cargs.append("-bilinear")
+    if params.get("modes") is not None:
+        cargs.extend([
+            "-modes",
+            params.get("modes")
+        ])
+    if params.get("mlcf"):
+        cargs.append("-mlcF")
+    if params.get("wtim") is not None:
+        cargs.extend([
+            "-wtim",
+            execution.input_file(params.get("wtim"))
+        ])
+    if params.get("dfspace"):
+        cargs.append("-dfspace")
+    if params.get("cmass"):
+        cargs.append("-cmass")
+    if params.get("fine") is not None:
+        cargs.extend([
+            "-fine",
+            *map(str, params.get("fine"))
+        ])
+    if params.get("nofine"):
+        cargs.append("-nofine")
+    return cargs
+
+
+def imreg_outputs(
+    params: ImregParameters,
+    execution: Execution,
+) -> ImregOutputs:
+    """
+    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 = 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,
+    )
+    return ret
+
+
+def imreg_execute(
+    params: ImregParameters,
+    execution: Execution,
+) -> ImregOutputs:
+    """
+    Registers each 2D image in 'image_sequence' to 'base_image'.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `ImregOutputs`).
+    """
+    params = execution.params(params)
+    cargs = imreg_cargs(params, execution)
+    ret = imreg_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def imreg(
+    base_image: str,
+    image_sequence: list[InputPathType],
+    nowrite: bool = False,
+    prefix: str | None = None,
+    suffix: str | None = None,
+    start: float | None = None,
+    step: float | None = None,
+    flim: bool = False,
+    keepsize: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    dprefix: str | None = None,
+    bilinear: bool = False,
+    modes: str | None = None,
+    mlcf: bool = False,
+    wtim: InputPathType | None = None,
+    dfspace: bool = False,
+    cmass: bool = False,
+    fine: list[float] | None = None,
+    nofine: bool = False,
+    runner: Runner | None = None,
+) -> ImregOutputs:
+    """
+    Registers each 2D image in 'image_sequence' to 'base_image'.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        base_image: Base image or method to determine base image ('+AVER' or\
+            '+count').
+        image_sequence: Sequence of images to be registered.
+        nowrite: Don't write outputs, just print progress reports.
+        prefix: Prefix for output file names.
+        suffix: Suffix for output file names.
+        start: Start index for output file names.
+        step: Step size for output file indices.
+        flim: Write output in mrilib floating point format.
+        keepsize: Preserve the original image size on output.
+        quiet: Don't write progress report messages.
+        debug: Write lots of debugging output.
+        dprefix: Prefix for dx, dy, and phi files.
+        bilinear: Use bilinear interpolation.
+        modes: Interpolation modes during coarse, fine, and registration phases.
+        mlcf: Equivalent to '-modes bilinear bicubic Fourier'.
+        wtim: Weighting image file.
+        dfspace: Use difiterated differential spatial method.
+        cmass: Align centers of mass of the images.
+        fine: Fine fit parameters: blur, dxy, dphi.
+        nofine: Turn off the 'fine' fit algorithm.
+        runner: Command runner.
+    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,
+        nowrite=nowrite,
+        prefix=prefix,
+        suffix=suffix,
+        start=start,
+        step=step,
+        flim=flim,
+        keepsize=keepsize,
+        quiet=quiet,
+        debug=debug,
+        dprefix=dprefix,
+        bilinear=bilinear,
+        modes=modes,
+        mlcf=mlcf,
+        wtim=wtim,
+        dfspace=dfspace,
+        cmass=cmass,
+        fine=fine,
+        nofine=nofine,
+    )
+    return imreg_execute(params, execution)
+
+
+__all__ = [
+    "IMREG_METADATA",
+    "ImregOutputs",
+    "ImregParameters",
+    "imreg",
+    "imreg_params",
+]

niwrap_afni/afni/imrotate.py

@@ -0,0 +1,217 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+IMROTATE_METADATA = Metadata(
+    id="046eb12264816ed4b6d2246d2d697caf596e0670.boutiques",
+    name="imrotate",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+ImrotateParameters = typing.TypedDict('ImrotateParameters', {
+    "__STYX_TYPE__": typing.Literal["imrotate"],
+    "fourier_interpolation": bool,
+    "dx": float,
+    "dy": float,
+    "phi": float,
+    "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(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_image_file: OutputPathType
+    """Path to the output image file"""
+
+
+def imrotate_params(
+    dx: float,
+    dy: float,
+    phi: float,
+    input_image: InputPathType,
+    output_image: str,
+    fourier_interpolation: bool = False,
+) -> ImrotateParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dx: Pixels to shift rightwards (can be non-integer).
+        dy: Pixels to shift downwards (can be non-integer).
+        phi: Degrees to rotate clockwise.
+        input_image: Input image file.
+        output_image: Output image file.
+        fourier_interpolation: Use Fourier interpolation.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "imrotate",
+        "fourier_interpolation": fourier_interpolation,
+        "dx": dx,
+        "dy": dy,
+        "phi": phi,
+        "input_image": input_image,
+        "output_image": output_image,
+    }
+    return params
+
+
+def imrotate_cargs(
+    params: ImrotateParameters,
+    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("imrotate")
+    if params.get("fourier_interpolation"):
+        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"))
+    return cargs
+
+
+def imrotate_outputs(
+    params: ImrotateParameters,
+    execution: Execution,
+) -> ImrotateOutputs:
+    """
+    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 = ImrotateOutputs(
+        root=execution.output_file("."),
+        output_image_file=execution.output_file(params.get("output_image")),
+    )
+    return ret
+
+
+def imrotate_execute(
+    params: ImrotateParameters,
+    execution: Execution,
+) -> ImrotateOutputs:
+    """
+    Shifts and rotates 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 `ImrotateOutputs`).
+    """
+    params = execution.params(params)
+    cargs = imrotate_cargs(params, execution)
+    ret = imrotate_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def imrotate(
+    dx: float,
+    dy: float,
+    phi: float,
+    input_image: InputPathType,
+    output_image: str,
+    fourier_interpolation: bool = False,
+    runner: Runner | None = None,
+) -> ImrotateOutputs:
+    """
+    Shifts and rotates an image.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dx: Pixels to shift rightwards (can be non-integer).
+        dy: Pixels to shift downwards (can be non-integer).
+        phi: Degrees to rotate clockwise.
+        input_image: Input image file.
+        output_image: Output image file.
+        fourier_interpolation: Use Fourier interpolation.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `ImrotateOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(IMROTATE_METADATA)
+    params = imrotate_params(
+        fourier_interpolation=fourier_interpolation,
+        dx=dx,
+        dy=dy,
+        phi=phi,
+        input_image=input_image,
+        output_image=output_image,
+    )
+    return imrotate_execute(params, execution)
+
+
+__all__ = [
+    "IMROTATE_METADATA",
+    "ImrotateOutputs",
+    "ImrotateParameters",
+    "imrotate",
+    "imrotate_params",
+]