niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/fat_proc_axialize_anat.py

@@ -0,0 +1,415 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FAT_PROC_AXIALIZE_ANAT_METADATA = Metadata(
+    id="e138eb56e5029d03d449b78987c687adf3579333.boutiques",
+    name="fat_proc_axialize_anat",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+FatProcAxializeAnatParameters = typing.TypedDict('FatProcAxializeAnatParameters', {
+    "__STYX_TYPE__": typing.Literal["fat_proc_axialize_anat"],
+    "in_file": InputPathType,
+    "ref_file": InputPathType,
+    "prefix": str,
+    "mode_t2w": bool,
+    "mode_t1w": bool,
+    "workdir": typing.NotRequired[str | None],
+    "out_match_ref": bool,
+    "do_ceil_out": bool,
+    "extra_al_wtmask": typing.NotRequired[InputPathType | None],
+    "extra_al_cost": typing.NotRequired[str | None],
+    "extra_al_opts": typing.NotRequired[str | None],
+    "focus_mask": typing.NotRequired[InputPathType | None],
+    "focus_by_ss": bool,
+    "remove_inf_sli": typing.NotRequired[float | None],
+    "pre_align_center_mass": bool,
+    "pre_center_mass": bool,
+    "post_lr_symm": bool,
+    "no_pre_lr_symm": bool,
+    "no_clean": bool,
+    "qc_ulay_range": typing.NotRequired[list[float] | None],
+    "no_qc_view": bool,
+    "qc_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 {
+        "fat_proc_axialize_anat": fat_proc_axialize_anat_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 {
+        "fat_proc_axialize_anat": fat_proc_axialize_anat_outputs,
+    }.get(t)
+
+
+class FatProcAxializeAnatOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `fat_proc_axialize_anat(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """An anatomical data set that is regularly situated within its FOV
+    volume"""
+    working_directory: OutputPathType | None
+    """The working directory with intermediate files"""
+
+
+def fat_proc_axialize_anat_params(
+    in_file: InputPathType,
+    ref_file: InputPathType,
+    prefix: str,
+    mode_t2w: bool = False,
+    mode_t1w: bool = False,
+    workdir: str | None = None,
+    out_match_ref: bool = False,
+    do_ceil_out: bool = False,
+    extra_al_wtmask: InputPathType | None = None,
+    extra_al_cost: str | None = None,
+    extra_al_opts: str | None = None,
+    focus_mask: InputPathType | None = None,
+    focus_by_ss: bool = False,
+    remove_inf_sli: float | None = None,
+    pre_align_center_mass: bool = False,
+    pre_center_mass: bool = False,
+    post_lr_symm: bool = False,
+    no_pre_lr_symm: bool = False,
+    no_clean: bool = False,
+    qc_ulay_range: list[float] | None = None,
+    no_qc_view: bool = False,
+    qc_prefix: str | None = None,
+) -> FatProcAxializeAnatParameters:
+    """
+    Build parameters.
+    
+    Args:
+        in_file: Input anatomical volume full name.
+        ref_file: Reference volume full name, such as TT or MNI.
+        prefix: Output prefix for files and snapshots.
+        mode_t2w: Switch for T2-weighted image processing.
+        mode_t1w: Switch for T1-weighted image processing.
+        workdir: Name of the working subdirectory in the output directory.
+        out_match_ref: Match the final output volume space FOV and spatial\
+            resolution to the reference file.
+        do_ceil_out: Apply a ceiling based on the 98%ile value within an\
+            automasked volume.
+        extra_al_wtmask: Extra weight mask to emphasize specific parts for\
+            alignment.
+        extra_al_cost: Specify a cost function for 3dAllineate to use (default\
+            'lpa').
+        extra_al_opts: Extra options for 3dAllineate when applying the warp.
+        focus_mask: Input mask to focus processing and alignment.
+        focus_by_ss: Make a mask by simply skullstripping input data set.
+        remove_inf_sli: Remove a number of slices from the inferior part of the\
+            FOV.
+        pre_align_center_mass: Pre-align the centers of mass of the volumes.
+        pre_center_mass: Pre-recenter input center of mass to (0, 0, 0).
+        post_lr_symm: Apply post-alignment left-right symmetrization.
+        no_pre_lr_symm: Turn off pre-alignment left-right symmetrization.
+        no_clean: Do not remove working directory '__WORKING_axialize_anat'.
+        qc_ulay_range: Provide a min (UMIN) and max (UMAX) range for underlay\
+            grayscale bar.
+        no_qc_view: Turn off default QC image saving/viewing.
+        qc_prefix: Provide a prefix for QC outputs separate from the main\
+            prefix.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "fat_proc_axialize_anat",
+        "in_file": in_file,
+        "ref_file": ref_file,
+        "prefix": prefix,
+        "mode_t2w": mode_t2w,
+        "mode_t1w": mode_t1w,
+        "out_match_ref": out_match_ref,
+        "do_ceil_out": do_ceil_out,
+        "focus_by_ss": focus_by_ss,
+        "pre_align_center_mass": pre_align_center_mass,
+        "pre_center_mass": pre_center_mass,
+        "post_lr_symm": post_lr_symm,
+        "no_pre_lr_symm": no_pre_lr_symm,
+        "no_clean": no_clean,
+        "no_qc_view": no_qc_view,
+    }
+    if workdir is not None:
+        params["workdir"] = workdir
+    if extra_al_wtmask is not None:
+        params["extra_al_wtmask"] = extra_al_wtmask
+    if extra_al_cost is not None:
+        params["extra_al_cost"] = extra_al_cost
+    if extra_al_opts is not None:
+        params["extra_al_opts"] = extra_al_opts
+    if focus_mask is not None:
+        params["focus_mask"] = focus_mask
+    if remove_inf_sli is not None:
+        params["remove_inf_sli"] = remove_inf_sli
+    if qc_ulay_range is not None:
+        params["qc_ulay_range"] = qc_ulay_range
+    if qc_prefix is not None:
+        params["qc_prefix"] = qc_prefix
+    return params
+
+
+def fat_proc_axialize_anat_cargs(
+    params: FatProcAxializeAnatParameters,
+    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("fat_proc_axialize_anat")
+    cargs.append(execution.input_file(params.get("in_file")))
+    cargs.append(execution.input_file(params.get("ref_file")))
+    cargs.append(params.get("prefix"))
+    if params.get("mode_t2w"):
+        cargs.append("-mode_t2w")
+    if params.get("mode_t1w"):
+        cargs.append("-mode_t1w")
+    if params.get("workdir") is not None:
+        cargs.extend([
+            "-workdir",
+            params.get("workdir")
+        ])
+    if params.get("out_match_ref"):
+        cargs.append("-out_match_ref")
+    if params.get("do_ceil_out"):
+        cargs.append("-do_ceil_out")
+    if params.get("extra_al_wtmask") is not None:
+        cargs.extend([
+            "-extra_al_wtmask",
+            execution.input_file(params.get("extra_al_wtmask"))
+        ])
+    if params.get("extra_al_cost") is not None:
+        cargs.extend([
+            "-extra_al_cost",
+            params.get("extra_al_cost")
+        ])
+    if params.get("extra_al_opts") is not None:
+        cargs.extend([
+            "-extra_al_opts",
+            params.get("extra_al_opts")
+        ])
+    if params.get("focus_mask") is not None:
+        cargs.extend([
+            "-focus_mask",
+            execution.input_file(params.get("focus_mask"))
+        ])
+    if params.get("focus_by_ss"):
+        cargs.append("-focus_by_ss")
+    if params.get("remove_inf_sli") is not None:
+        cargs.extend([
+            "-remove_inf_sli",
+            str(params.get("remove_inf_sli"))
+        ])
+    if params.get("pre_align_center_mass"):
+        cargs.append("-pre_align_center_mass")
+    if params.get("pre_center_mass"):
+        cargs.append("-pre_center_mass")
+    if params.get("post_lr_symm"):
+        cargs.append("-post_lr_symm")
+    if params.get("no_pre_lr_symm"):
+        cargs.append("-no_pre_lr_symm")
+    if params.get("no_clean"):
+        cargs.append("-no_clean")
+    if params.get("qc_ulay_range") is not None:
+        cargs.extend([
+            "-qc1_ulay_range",
+            *map(str, params.get("qc_ulay_range"))
+        ])
+    if params.get("no_qc_view"):
+        cargs.append("-no_qc_view")
+    if params.get("qc_prefix") is not None:
+        cargs.extend([
+            "-qc_prefix",
+            params.get("qc_prefix")
+        ])
+    return cargs
+
+
+def fat_proc_axialize_anat_outputs(
+    params: FatProcAxializeAnatParameters,
+    execution: Execution,
+) -> FatProcAxializeAnatOutputs:
+    """
+    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 = FatProcAxializeAnatOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("prefix") + ".nii.gz"),
+        working_directory=execution.output_file(params.get("workdir")) if (params.get("workdir") is not None) else None,
+    )
+    return ret
+
+
+def fat_proc_axialize_anat_execute(
+    params: FatProcAxializeAnatParameters,
+    execution: Execution,
+) -> FatProcAxializeAnatOutputs:
+    """
+    Helps align the major axes of an anatomical volume to those of the volumetric
+    field of view.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `FatProcAxializeAnatOutputs`).
+    """
+    params = execution.params(params)
+    cargs = fat_proc_axialize_anat_cargs(params, execution)
+    ret = fat_proc_axialize_anat_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def fat_proc_axialize_anat(
+    in_file: InputPathType,
+    ref_file: InputPathType,
+    prefix: str,
+    mode_t2w: bool = False,
+    mode_t1w: bool = False,
+    workdir: str | None = None,
+    out_match_ref: bool = False,
+    do_ceil_out: bool = False,
+    extra_al_wtmask: InputPathType | None = None,
+    extra_al_cost: str | None = None,
+    extra_al_opts: str | None = None,
+    focus_mask: InputPathType | None = None,
+    focus_by_ss: bool = False,
+    remove_inf_sli: float | None = None,
+    pre_align_center_mass: bool = False,
+    pre_center_mass: bool = False,
+    post_lr_symm: bool = False,
+    no_pre_lr_symm: bool = False,
+    no_clean: bool = False,
+    qc_ulay_range: list[float] | None = None,
+    no_qc_view: bool = False,
+    qc_prefix: str | None = None,
+    runner: Runner | None = None,
+) -> FatProcAxializeAnatOutputs:
+    """
+    Helps align the major axes of an anatomical volume to those of the volumetric
+    field of view.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        in_file: Input anatomical volume full name.
+        ref_file: Reference volume full name, such as TT or MNI.
+        prefix: Output prefix for files and snapshots.
+        mode_t2w: Switch for T2-weighted image processing.
+        mode_t1w: Switch for T1-weighted image processing.
+        workdir: Name of the working subdirectory in the output directory.
+        out_match_ref: Match the final output volume space FOV and spatial\
+            resolution to the reference file.
+        do_ceil_out: Apply a ceiling based on the 98%ile value within an\
+            automasked volume.
+        extra_al_wtmask: Extra weight mask to emphasize specific parts for\
+            alignment.
+        extra_al_cost: Specify a cost function for 3dAllineate to use (default\
+            'lpa').
+        extra_al_opts: Extra options for 3dAllineate when applying the warp.
+        focus_mask: Input mask to focus processing and alignment.
+        focus_by_ss: Make a mask by simply skullstripping input data set.
+        remove_inf_sli: Remove a number of slices from the inferior part of the\
+            FOV.
+        pre_align_center_mass: Pre-align the centers of mass of the volumes.
+        pre_center_mass: Pre-recenter input center of mass to (0, 0, 0).
+        post_lr_symm: Apply post-alignment left-right symmetrization.
+        no_pre_lr_symm: Turn off pre-alignment left-right symmetrization.
+        no_clean: Do not remove working directory '__WORKING_axialize_anat'.
+        qc_ulay_range: Provide a min (UMIN) and max (UMAX) range for underlay\
+            grayscale bar.
+        no_qc_view: Turn off default QC image saving/viewing.
+        qc_prefix: Provide a prefix for QC outputs separate from the main\
+            prefix.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `FatProcAxializeAnatOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FAT_PROC_AXIALIZE_ANAT_METADATA)
+    params = fat_proc_axialize_anat_params(
+        in_file=in_file,
+        ref_file=ref_file,
+        prefix=prefix,
+        mode_t2w=mode_t2w,
+        mode_t1w=mode_t1w,
+        workdir=workdir,
+        out_match_ref=out_match_ref,
+        do_ceil_out=do_ceil_out,
+        extra_al_wtmask=extra_al_wtmask,
+        extra_al_cost=extra_al_cost,
+        extra_al_opts=extra_al_opts,
+        focus_mask=focus_mask,
+        focus_by_ss=focus_by_ss,
+        remove_inf_sli=remove_inf_sli,
+        pre_align_center_mass=pre_align_center_mass,
+        pre_center_mass=pre_center_mass,
+        post_lr_symm=post_lr_symm,
+        no_pre_lr_symm=no_pre_lr_symm,
+        no_clean=no_clean,
+        qc_ulay_range=qc_ulay_range,
+        no_qc_view=no_qc_view,
+        qc_prefix=qc_prefix,
+    )
+    return fat_proc_axialize_anat_execute(params, execution)
+
+
+__all__ = [
+    "FAT_PROC_AXIALIZE_ANAT_METADATA",
+    "FatProcAxializeAnatOutputs",
+    "FatProcAxializeAnatParameters",
+    "fat_proc_axialize_anat",
+    "fat_proc_axialize_anat_params",
+]