niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_zipper_zapper.py

@@ -0,0 +1,388 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_ZIPPER_ZAPPER_METADATA = Metadata(
+    id="345c0ab457fab3fd59e06829b589145ef0e78581.boutiques",
+    name="3dZipperZapper",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dZipperZapperParameters = typing.TypedDict('V3dZipperZapperParameters', {
+    "__STYX_TYPE__": typing.Literal["3dZipperZapper"],
+    "input_file": InputPathType,
+    "output_prefix": str,
+    "mask_file": typing.NotRequired[InputPathType | None],
+    "min_slice_nvox": typing.NotRequired[float | None],
+    "min_streak_len": typing.NotRequired[float | None],
+    "do_out_slice_param": bool,
+    "no_out_bad_mask": bool,
+    "no_out_text_vals": bool,
+    "dont_use_streak": bool,
+    "dont_use_drop": bool,
+    "dont_use_corr": bool,
+    "min_streak_val": typing.NotRequired[float | None],
+    "min_drop_frac": typing.NotRequired[float | None],
+    "min_drop_diff": typing.NotRequired[float | None],
+    "min_corr_len": typing.NotRequired[float | None],
+    "min_corr_corr": typing.NotRequired[float | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dZipperZapper": v_3d_zipper_zapper_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 {
+        "3dZipperZapper": v_3d_zipper_zapper_outputs,
+    }.get(t)
+
+
+class V3dZipperZapperOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_zipper_zapper(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    bad_slice_mask: OutputPathType
+    """Mask of potentially bad slices across the input dataset."""
+    bad_volumes_list: OutputPathType
+    """1D file containing a list of the bad volumes."""
+    per_volume_params: OutputPathType
+    """1D file of the per-volume parameters used to detect badness."""
+    calculated_slices: OutputPathType
+    """1D file of the slices within which calculations were made."""
+    good_volumes_selector: OutputPathType
+    """Text file with the selector string of *good* volumes."""
+
+
+def v_3d_zipper_zapper_params(
+    input_file: InputPathType,
+    output_prefix: str,
+    mask_file: InputPathType | None = None,
+    min_slice_nvox: float | None = None,
+    min_streak_len: float | None = None,
+    do_out_slice_param: bool = False,
+    no_out_bad_mask: bool = False,
+    no_out_text_vals: bool = False,
+    dont_use_streak: bool = False,
+    dont_use_drop: bool = False,
+    dont_use_corr: bool = False,
+    min_streak_val: float | None = None,
+    min_drop_frac: float | None = None,
+    min_drop_diff: float | None = None,
+    min_corr_len: float | None = None,
+    min_corr_corr: float | None = None,
+) -> V3dZipperZapperParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Input 3D+time file of DWIs or EPIs.
+        output_prefix: Prefix for output file name.
+        mask_file: Optional input of a single volume mask file, which gets\
+            applied to each volume in the input file.
+        min_slice_nvox: Set the minimum number of voxels to be in the mask for\
+            a given slice to be included in the calculations.
+        min_streak_len: Minimum number of slices in a row to look for\
+            fluctuations within.
+        do_out_slice_param: Output the map of slice parameters.
+        no_out_bad_mask: Do not output the mask of 'bad' slices.
+        no_out_text_vals: Do not output the 1D files of the slice parameter\
+            values.
+        dont_use_streak: Turn off the 'streak' criterion for identifying bad\
+            slices.
+        dont_use_drop: Turn off the 'drop' criterion for identifying bad\
+            slices.
+        dont_use_corr: Turn off the 'corr' criterion for identifying bad\
+            slices.
+        min_streak_val: Minimum magnitude of voxelwise relative differences to\
+            perhaps be problematic.
+        min_drop_frac: Minimum fraction for judging if the change in 'slice\
+            parameter' differences between neighboring slices might be a sign of\
+            badness.
+        min_drop_diff: Minimum 'slice parameter' value within a single slice\
+            that might be considered a bad sign.
+        min_corr_len: Minimum number of slices in a row to look for consecutive\
+            anticorrelations in brightness differences.
+        min_corr_corr: Threshold for the magnitude of anticorrelations to be\
+            considered potentially bad.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dZipperZapper",
+        "input_file": input_file,
+        "output_prefix": output_prefix,
+        "do_out_slice_param": do_out_slice_param,
+        "no_out_bad_mask": no_out_bad_mask,
+        "no_out_text_vals": no_out_text_vals,
+        "dont_use_streak": dont_use_streak,
+        "dont_use_drop": dont_use_drop,
+        "dont_use_corr": dont_use_corr,
+    }
+    if mask_file is not None:
+        params["mask_file"] = mask_file
+    if min_slice_nvox is not None:
+        params["min_slice_nvox"] = min_slice_nvox
+    if min_streak_len is not None:
+        params["min_streak_len"] = min_streak_len
+    if min_streak_val is not None:
+        params["min_streak_val"] = min_streak_val
+    if min_drop_frac is not None:
+        params["min_drop_frac"] = min_drop_frac
+    if min_drop_diff is not None:
+        params["min_drop_diff"] = min_drop_diff
+    if min_corr_len is not None:
+        params["min_corr_len"] = min_corr_len
+    if min_corr_corr is not None:
+        params["min_corr_corr"] = min_corr_corr
+    return params
+
+
+def v_3d_zipper_zapper_cargs(
+    params: V3dZipperZapperParameters,
+    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("3dZipperZapper")
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input_file"))
+    ])
+    cargs.extend([
+        "-prefix",
+        params.get("output_prefix")
+    ])
+    if params.get("mask_file") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask_file"))
+        ])
+    if params.get("min_slice_nvox") is not None:
+        cargs.extend([
+            "-min_slice_nvox",
+            str(params.get("min_slice_nvox"))
+        ])
+    if params.get("min_streak_len") is not None:
+        cargs.extend([
+            "-min_streak_len",
+            str(params.get("min_streak_len"))
+        ])
+    if params.get("do_out_slice_param"):
+        cargs.append("-do_out_slice_param")
+    if params.get("no_out_bad_mask"):
+        cargs.append("-no_out_bad_mask")
+    if params.get("no_out_text_vals"):
+        cargs.append("-no_out_text_vals")
+    if params.get("dont_use_streak"):
+        cargs.append("-dont_use_streak")
+    if params.get("dont_use_drop"):
+        cargs.append("-dont_use_drop")
+    if params.get("dont_use_corr"):
+        cargs.append("-dont_use_corr")
+    if params.get("min_streak_val") is not None:
+        cargs.extend([
+            "-min_streak_val",
+            str(params.get("min_streak_val"))
+        ])
+    if params.get("min_drop_frac") is not None:
+        cargs.extend([
+            "-min_drop_frac",
+            str(params.get("min_drop_frac"))
+        ])
+    if params.get("min_drop_diff") is not None:
+        cargs.extend([
+            "-min_drop_diff",
+            str(params.get("min_drop_diff"))
+        ])
+    if params.get("min_corr_len") is not None:
+        cargs.extend([
+            "-min_corr_len",
+            str(params.get("min_corr_len"))
+        ])
+    if params.get("min_corr_corr") is not None:
+        cargs.extend([
+            "-min_corr_corr",
+            str(params.get("min_corr_corr"))
+        ])
+    return cargs
+
+
+def v_3d_zipper_zapper_outputs(
+    params: V3dZipperZapperParameters,
+    execution: Execution,
+) -> V3dZipperZapperOutputs:
+    """
+    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 = V3dZipperZapperOutputs(
+        root=execution.output_file("."),
+        bad_slice_mask=execution.output_file(params.get("output_prefix") + "_badmask.nii.gz"),
+        bad_volumes_list=execution.output_file(params.get("output_prefix") + "_badvols.1D"),
+        per_volume_params=execution.output_file(params.get("output_prefix") + "_param.1D"),
+        calculated_slices=execution.output_file(params.get("output_prefix") + "_sli.1D"),
+        good_volumes_selector=execution.output_file(params.get("output_prefix") + "_goodvols.txt"),
+    )
+    return ret
+
+
+def v_3d_zipper_zapper_execute(
+    params: V3dZipperZapperParameters,
+    execution: Execution,
+) -> V3dZipperZapperOutputs:
+    """
+    A basic program to highlight problematic volumes in data sets, especially
+    EPI/DWI data sets with interleaved acquisition.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dZipperZapperOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_zipper_zapper_cargs(params, execution)
+    ret = v_3d_zipper_zapper_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_zipper_zapper(
+    input_file: InputPathType,
+    output_prefix: str,
+    mask_file: InputPathType | None = None,
+    min_slice_nvox: float | None = None,
+    min_streak_len: float | None = None,
+    do_out_slice_param: bool = False,
+    no_out_bad_mask: bool = False,
+    no_out_text_vals: bool = False,
+    dont_use_streak: bool = False,
+    dont_use_drop: bool = False,
+    dont_use_corr: bool = False,
+    min_streak_val: float | None = None,
+    min_drop_frac: float | None = None,
+    min_drop_diff: float | None = None,
+    min_corr_len: float | None = None,
+    min_corr_corr: float | None = None,
+    runner: Runner | None = None,
+) -> V3dZipperZapperOutputs:
+    """
+    A basic program to highlight problematic volumes in data sets, especially
+    EPI/DWI data sets with interleaved acquisition.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: Input 3D+time file of DWIs or EPIs.
+        output_prefix: Prefix for output file name.
+        mask_file: Optional input of a single volume mask file, which gets\
+            applied to each volume in the input file.
+        min_slice_nvox: Set the minimum number of voxels to be in the mask for\
+            a given slice to be included in the calculations.
+        min_streak_len: Minimum number of slices in a row to look for\
+            fluctuations within.
+        do_out_slice_param: Output the map of slice parameters.
+        no_out_bad_mask: Do not output the mask of 'bad' slices.
+        no_out_text_vals: Do not output the 1D files of the slice parameter\
+            values.
+        dont_use_streak: Turn off the 'streak' criterion for identifying bad\
+            slices.
+        dont_use_drop: Turn off the 'drop' criterion for identifying bad\
+            slices.
+        dont_use_corr: Turn off the 'corr' criterion for identifying bad\
+            slices.
+        min_streak_val: Minimum magnitude of voxelwise relative differences to\
+            perhaps be problematic.
+        min_drop_frac: Minimum fraction for judging if the change in 'slice\
+            parameter' differences between neighboring slices might be a sign of\
+            badness.
+        min_drop_diff: Minimum 'slice parameter' value within a single slice\
+            that might be considered a bad sign.
+        min_corr_len: Minimum number of slices in a row to look for consecutive\
+            anticorrelations in brightness differences.
+        min_corr_corr: Threshold for the magnitude of anticorrelations to be\
+            considered potentially bad.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dZipperZapperOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_ZIPPER_ZAPPER_METADATA)
+    params = v_3d_zipper_zapper_params(
+        input_file=input_file,
+        output_prefix=output_prefix,
+        mask_file=mask_file,
+        min_slice_nvox=min_slice_nvox,
+        min_streak_len=min_streak_len,
+        do_out_slice_param=do_out_slice_param,
+        no_out_bad_mask=no_out_bad_mask,
+        no_out_text_vals=no_out_text_vals,
+        dont_use_streak=dont_use_streak,
+        dont_use_drop=dont_use_drop,
+        dont_use_corr=dont_use_corr,
+        min_streak_val=min_streak_val,
+        min_drop_frac=min_drop_frac,
+        min_drop_diff=min_drop_diff,
+        min_corr_len=min_corr_len,
+        min_corr_corr=min_corr_corr,
+    )
+    return v_3d_zipper_zapper_execute(params, execution)
+
+
+__all__ = [
+    "V3dZipperZapperOutputs",
+    "V3dZipperZapperParameters",
+    "V_3D_ZIPPER_ZAPPER_METADATA",
+    "v_3d_zipper_zapper",
+    "v_3d_zipper_zapper_params",
+]

niwrap_afni/afni/v_3d_zregrid.py

@@ -0,0 +1,242 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_ZREGRID_METADATA = Metadata(
+    id="2597cdebba8fe75de8a28bb8bff140590938cb2b.boutiques",
+    name="3dZregrid",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dZregridParameters = typing.TypedDict('V3dZregridParameters', {
+    "__STYX_TYPE__": typing.Literal["3dZregrid"],
+    "z_thickness": typing.NotRequired[float | None],
+    "slice_count": typing.NotRequired[float | None],
+    "z_size": typing.NotRequired[float | None],
+    "prefix": typing.NotRequired[str | None],
+    "infile": InputPathType,
+    "verbose": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dZregrid": v_3d_zregrid_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 {
+        "3dZregrid": v_3d_zregrid_outputs,
+    }.get(t)
+
+
+class V3dZregridOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_zregrid(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outfile_head: OutputPathType | None
+    """Output dataset with new grid"""
+    outfile_brik: OutputPathType | None
+    """Output dataset with new grid"""
+
+
+def v_3d_zregrid_params(
+    infile: InputPathType,
+    z_thickness: float | None = None,
+    slice_count: float | None = None,
+    z_size: float | None = None,
+    prefix: str | None = None,
+    verbose: bool = False,
+) -> V3dZregridParameters:
+    """
+    Build parameters.
+    
+    Args:
+        infile: Input dataset.
+        z_thickness: Set slice thickness to D mm.
+        slice_count: Set slice count to N.
+        z_size: Set thickness of dataset (center-to-center of first and last\
+            slices) to Z mm.
+        prefix: Write result to dataset with prefix P.
+        verbose: Write progress reports to stderr.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dZregrid",
+        "infile": infile,
+        "verbose": verbose,
+    }
+    if z_thickness is not None:
+        params["z_thickness"] = z_thickness
+    if slice_count is not None:
+        params["slice_count"] = slice_count
+    if z_size is not None:
+        params["z_size"] = z_size
+    if prefix is not None:
+        params["prefix"] = prefix
+    return params
+
+
+def v_3d_zregrid_cargs(
+    params: V3dZregridParameters,
+    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("3dZregrid")
+    if params.get("z_thickness") is not None:
+        cargs.extend([
+            "-dz",
+            str(params.get("z_thickness"))
+        ])
+    if params.get("slice_count") is not None:
+        cargs.extend([
+            "-nz",
+            str(params.get("slice_count"))
+        ])
+    if params.get("z_size") is not None:
+        cargs.extend([
+            "-zsize",
+            str(params.get("z_size"))
+        ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    cargs.append(execution.input_file(params.get("infile")))
+    if params.get("verbose"):
+        cargs.append("-verb")
+    return cargs
+
+
+def v_3d_zregrid_outputs(
+    params: V3dZregridParameters,
+    execution: Execution,
+) -> V3dZregridOutputs:
+    """
+    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 = V3dZregridOutputs(
+        root=execution.output_file("."),
+        outfile_head=execution.output_file(params.get("prefix") + "+orig.HEAD") if (params.get("prefix") is not None) else None,
+        outfile_brik=execution.output_file(params.get("prefix") + "+orig.BRIK") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_zregrid_execute(
+    params: V3dZregridParameters,
+    execution: Execution,
+) -> V3dZregridOutputs:
+    """
+    Alters the input dataset's slice thickness and/or number.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dZregridOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_zregrid_cargs(params, execution)
+    ret = v_3d_zregrid_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_zregrid(
+    infile: InputPathType,
+    z_thickness: float | None = None,
+    slice_count: float | None = None,
+    z_size: float | None = None,
+    prefix: str | None = None,
+    verbose: bool = False,
+    runner: Runner | None = None,
+) -> V3dZregridOutputs:
+    """
+    Alters the input dataset's slice thickness and/or number.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        infile: Input dataset.
+        z_thickness: Set slice thickness to D mm.
+        slice_count: Set slice count to N.
+        z_size: Set thickness of dataset (center-to-center of first and last\
+            slices) to Z mm.
+        prefix: Write result to dataset with prefix P.
+        verbose: Write progress reports to stderr.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dZregridOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_ZREGRID_METADATA)
+    params = v_3d_zregrid_params(
+        z_thickness=z_thickness,
+        slice_count=slice_count,
+        z_size=z_size,
+        prefix=prefix,
+        infile=infile,
+        verbose=verbose,
+    )
+    return v_3d_zregrid_execute(params, execution)
+
+
+__all__ = [
+    "V3dZregridOutputs",
+    "V3dZregridParameters",
+    "V_3D_ZREGRID_METADATA",
+    "v_3d_zregrid",
+    "v_3d_zregrid_params",
+]