niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_roistats.py

@@ -0,0 +1,379 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_ROISTATS_METADATA = Metadata(
+    id="80281254f3598a961619f69119f1d0eb9b58f421.boutiques",
+    name="3dROIstats",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dRoistatsParameters = typing.TypedDict('V3dRoistatsParameters', {
+    "__STYX_TYPE__": typing.Literal["3dROIstats"],
+    "in_file": InputPathType,
+    "mask": typing.NotRequired[InputPathType | None],
+    "debug": bool,
+    "format1D": bool,
+    "format1DR": bool,
+    "mask_f2short": bool,
+    "mask_file": typing.NotRequired[InputPathType | None],
+    "nobriklab": bool,
+    "nomeanout": bool,
+    "num_roi": typing.NotRequired[int | None],
+    "quiet": bool,
+    "roisel": typing.NotRequired[InputPathType | None],
+    "stat": typing.NotRequired[list[InputPathType] | None],
+    "zerofill": 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 {
+        "3dROIstats": v_3d_roistats_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 {
+    }.get(t)
+
+
+class V3dRoistatsOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_roistats(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    stats: list[str]
+    """There will be one line of output for every sub-brick of every input
+    dataset. Across each line will be every statistic for every mask value. For
+    instance, if there 3 mask values (1,2,3), then the columns Mean_1, Mean_2
+    and Mean_3 will refer to the means across each mask value, respectively. If
+    4 statistics are requested, then there will be 12 stats displayed on each
+    line (4 for each mask region), besides the file and sub-brick number."""
+
+
+def v_3d_roistats_params(
+    in_file: InputPathType,
+    mask: InputPathType | None = None,
+    debug: bool = False,
+    format1_d: bool = False,
+    format1_dr: bool = False,
+    mask_f2short: bool = False,
+    mask_file: InputPathType | None = None,
+    nobriklab: bool = False,
+    nomeanout: bool = False,
+    num_roi: int | None = None,
+    quiet: bool = False,
+    roisel: InputPathType | None = None,
+    stat_: list[InputPathType] | None = None,
+    zerofill: str | None = None,
+) -> V3dRoistatsParameters:
+    """
+    Build parameters.
+    
+    Args:
+        in_file: Input dataset.
+        mask: Input mask.
+        debug: Print debug information.
+        format1_d: Output results in a 1d format that includes commented\
+            labels.
+        format1_dr: Output results in a 1d format that includes uncommented\
+            labels. may not work optimally with typical 1d functions, but is useful\
+            for r functions.
+        mask_f2short: Tells the program to convert a float mask to short\
+            integers, by simple rounding.
+        mask_file: Input mask.
+        nobriklab: Do not print the sub-brick label next to its index.
+        nomeanout: Do not include the (zero-inclusive) mean among computed\
+            stats.
+        num_roi: Forces the assumption that the mask dataset's rois are denoted\
+            by 1 to n inclusive. normally, the program figures out the rois on its\
+            own. this option is useful if a) you are certain that the mask dataset\
+            has no values outside the range [0 n], b) there may be some rois\
+            missing between [1 n] in the mask data-set and c) you want those\
+            columns in the output any-way so the output lines up with the output\
+            from other invocations of 3droistats.
+        quiet: Execute quietly.
+        roisel: Only considers rois denoted by values found in the specified\
+            file. note that the order of the rois as specified in the file is not\
+            preserved. so an sel.1d of '2 8 20' produces the same output as '8 20\
+            2'.
+        stat_: A list of items which are 'mean' or 'sum' or 'voxels' or\
+            'minmax' or 'sigma' or 'median' or 'mode' or 'summary' or 'zerominmax'\
+            or 'zerosigma' or 'zeromedian' or 'zeromode'. Statistics to compute.\
+            options include: * mean = compute the mean using only non_zero voxels.\
+            implies the opposite for the mean computed by default. * median =\
+            compute the median of nonzero voxels * mode = compute the mode of\
+            nonzero voxels. (integral valued sets only) * minmax = compute the\
+            min/max of nonzero voxels * sum = compute the sum using only nonzero\
+            voxels. * voxels = compute the number of nonzero voxels * sigma =\
+            compute the standard deviation of nonzero voxelsstatistics that include\
+            zero-valued voxels: * zerominmax = compute the min/max of all voxels. *\
+            zerosigma = compute the standard deviation of all voxels. * zeromedian\
+            = compute the median of all voxels. * zeromode = compute the mode of\
+            all voxels. * summary = only output a summary line with the grand mean\
+            across all briks in the input dataset. this option cannot be used with\
+            nomeanout.more that one option can be specified.
+        zerofill: For roi labels not found, use the provided string instead of\
+            a '0' in the output file. only active if `num_roi` is enabled.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dROIstats",
+        "in_file": in_file,
+        "debug": debug,
+        "format1D": format1_d,
+        "format1DR": format1_dr,
+        "mask_f2short": mask_f2short,
+        "nobriklab": nobriklab,
+        "nomeanout": nomeanout,
+        "quiet": quiet,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    if mask_file is not None:
+        params["mask_file"] = mask_file
+    if num_roi is not None:
+        params["num_roi"] = num_roi
+    if roisel is not None:
+        params["roisel"] = roisel
+    if stat_ is not None:
+        params["stat"] = stat_
+    if zerofill is not None:
+        params["zerofill"] = zerofill
+    return params
+
+
+def v_3d_roistats_cargs(
+    params: V3dRoistatsParameters,
+    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("3dROIstats")
+    cargs.append(execution.input_file(params.get("in_file")))
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    cargs.append("[OUT_FILE]")
+    if params.get("debug"):
+        cargs.append("-debug")
+    if params.get("format1D"):
+        cargs.append("-1Dformat")
+    if params.get("format1DR"):
+        cargs.append("-1DRformat")
+    if params.get("mask_f2short"):
+        cargs.append("-mask_f2short")
+    if params.get("mask_file") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask_file"))
+        ])
+    if params.get("nobriklab"):
+        cargs.append("-nobriklab")
+    if params.get("nomeanout"):
+        cargs.append("-nomeanout")
+    if params.get("num_roi") is not None:
+        cargs.extend([
+            "-numroi",
+            str(params.get("num_roi"))
+        ])
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    if params.get("roisel") is not None:
+        cargs.extend([
+            "-roisel",
+            execution.input_file(params.get("roisel"))
+        ])
+    if params.get("stat") is not None:
+        cargs.extend([execution.input_file(f) for f in params.get("stat")])
+    if params.get("zerofill") is not None:
+        cargs.extend([
+            "-zerofill",
+            params.get("zerofill")
+        ])
+    return cargs
+
+
+def v_3d_roistats_outputs(
+    params: V3dRoistatsParameters,
+    execution: Execution,
+) -> V3dRoistatsOutputs:
+    """
+    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 = V3dRoistatsOutputs(
+        root=execution.output_file("."),
+        stats=[],
+    )
+    return ret
+
+
+def v_3d_roistats_execute(
+    params: V3dRoistatsParameters,
+    execution: Execution,
+) -> V3dRoistatsOutputs:
+    """
+    Display statistics over masked regions.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dRoistatsOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_roistats_cargs(params, execution)
+    ret = v_3d_roistats_outputs(params, execution)
+    execution.run(cargs, handle_stdout=lambda s: ret.stats.append(s))
+    return ret
+
+
+def v_3d_roistats(
+    in_file: InputPathType,
+    mask: InputPathType | None = None,
+    debug: bool = False,
+    format1_d: bool = False,
+    format1_dr: bool = False,
+    mask_f2short: bool = False,
+    mask_file: InputPathType | None = None,
+    nobriklab: bool = False,
+    nomeanout: bool = False,
+    num_roi: int | None = None,
+    quiet: bool = False,
+    roisel: InputPathType | None = None,
+    stat_: list[InputPathType] | None = None,
+    zerofill: str | None = None,
+    runner: Runner | None = None,
+) -> V3dRoistatsOutputs:
+    """
+    Display statistics over masked regions.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        in_file: Input dataset.
+        mask: Input mask.
+        debug: Print debug information.
+        format1_d: Output results in a 1d format that includes commented\
+            labels.
+        format1_dr: Output results in a 1d format that includes uncommented\
+            labels. may not work optimally with typical 1d functions, but is useful\
+            for r functions.
+        mask_f2short: Tells the program to convert a float mask to short\
+            integers, by simple rounding.
+        mask_file: Input mask.
+        nobriklab: Do not print the sub-brick label next to its index.
+        nomeanout: Do not include the (zero-inclusive) mean among computed\
+            stats.
+        num_roi: Forces the assumption that the mask dataset's rois are denoted\
+            by 1 to n inclusive. normally, the program figures out the rois on its\
+            own. this option is useful if a) you are certain that the mask dataset\
+            has no values outside the range [0 n], b) there may be some rois\
+            missing between [1 n] in the mask data-set and c) you want those\
+            columns in the output any-way so the output lines up with the output\
+            from other invocations of 3droistats.
+        quiet: Execute quietly.
+        roisel: Only considers rois denoted by values found in the specified\
+            file. note that the order of the rois as specified in the file is not\
+            preserved. so an sel.1d of '2 8 20' produces the same output as '8 20\
+            2'.
+        stat_: A list of items which are 'mean' or 'sum' or 'voxels' or\
+            'minmax' or 'sigma' or 'median' or 'mode' or 'summary' or 'zerominmax'\
+            or 'zerosigma' or 'zeromedian' or 'zeromode'. Statistics to compute.\
+            options include: * mean = compute the mean using only non_zero voxels.\
+            implies the opposite for the mean computed by default. * median =\
+            compute the median of nonzero voxels * mode = compute the mode of\
+            nonzero voxels. (integral valued sets only) * minmax = compute the\
+            min/max of nonzero voxels * sum = compute the sum using only nonzero\
+            voxels. * voxels = compute the number of nonzero voxels * sigma =\
+            compute the standard deviation of nonzero voxelsstatistics that include\
+            zero-valued voxels: * zerominmax = compute the min/max of all voxels. *\
+            zerosigma = compute the standard deviation of all voxels. * zeromedian\
+            = compute the median of all voxels. * zeromode = compute the mode of\
+            all voxels. * summary = only output a summary line with the grand mean\
+            across all briks in the input dataset. this option cannot be used with\
+            nomeanout.more that one option can be specified.
+        zerofill: For roi labels not found, use the provided string instead of\
+            a '0' in the output file. only active if `num_roi` is enabled.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dRoistatsOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_ROISTATS_METADATA)
+    params = v_3d_roistats_params(
+        in_file=in_file,
+        mask=mask,
+        debug=debug,
+        format1_d=format1_d,
+        format1_dr=format1_dr,
+        mask_f2short=mask_f2short,
+        mask_file=mask_file,
+        nobriklab=nobriklab,
+        nomeanout=nomeanout,
+        num_roi=num_roi,
+        quiet=quiet,
+        roisel=roisel,
+        stat_=stat_,
+        zerofill=zerofill,
+    )
+    return v_3d_roistats_execute(params, execution)
+
+
+__all__ = [
+    "V3dRoistatsOutputs",
+    "V3dRoistatsParameters",
+    "V_3D_ROISTATS_METADATA",
+    "v_3d_roistats",
+    "v_3d_roistats_params",
+]

niwrap_afni/afni/v_3d_row_fillin.py

@@ -0,0 +1,231 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_ROW_FILLIN_METADATA = Metadata(
+    id="efdbcc5556b9f847fe0eba3e015856a0addd50be.boutiques",
+    name="3dRowFillin",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dRowFillinParameters = typing.TypedDict('V3dRowFillinParameters', {
+    "__STYX_TYPE__": typing.Literal["3dRowFillin"],
+    "maxgap": typing.NotRequired[float | None],
+    "dir": typing.NotRequired[str | None],
+    "binary": bool,
+    "prefix": typing.NotRequired[str | None],
+    "input_dataset": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dRowFillin": v_3d_row_fillin_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 {
+        "3dRowFillin": v_3d_row_fillin_outputs,
+    }.get(t)
+
+
+class V3dRowFillinOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_row_fillin(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_brik: OutputPathType | None
+    """Output dataset in BRIK format"""
+    output_head: OutputPathType | None
+    """Output dataset in HEAD format"""
+
+
+def v_3d_row_fillin_params(
+    input_dataset: InputPathType,
+    maxgap: float | None = None,
+    dir_: str | None = None,
+    binary: bool = False,
+    prefix: str | None = None,
+) -> V3dRowFillinParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_dataset: Input 3D dataset (e.g., dataset+orig).
+        maxgap: Set the maximum length of a blank region that will be filled in.
+        dir_: Set the direction of fill, e.g., A-P, P-A, I-S, S-I, L-R, R-L, x,\
+            y, z, XYZ.OR, XYZ.AND.
+        binary: Turn input dataset to binary (0 and 1) before filling in.\
+            Output will also be binary.
+        prefix: Set the prefix for the output dataset.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dRowFillin",
+        "binary": binary,
+        "input_dataset": input_dataset,
+    }
+    if maxgap is not None:
+        params["maxgap"] = maxgap
+    if dir_ is not None:
+        params["dir"] = dir_
+    if prefix is not None:
+        params["prefix"] = prefix
+    return params
+
+
+def v_3d_row_fillin_cargs(
+    params: V3dRowFillinParameters,
+    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("3dRowFillin")
+    if params.get("maxgap") is not None:
+        cargs.extend([
+            "-maxgap",
+            str(params.get("maxgap"))
+        ])
+    if params.get("dir") is not None:
+        cargs.extend([
+            "-dir",
+            params.get("dir")
+        ])
+    if params.get("binary"):
+        cargs.append("-binary")
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    cargs.append(execution.input_file(params.get("input_dataset")))
+    return cargs
+
+
+def v_3d_row_fillin_outputs(
+    params: V3dRowFillinParameters,
+    execution: Execution,
+) -> V3dRowFillinOutputs:
+    """
+    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 = V3dRowFillinOutputs(
+        root=execution.output_file("."),
+        output_brik=execution.output_file(params.get("prefix") + "+orig.BRIK") if (params.get("prefix") is not None) else None,
+        output_head=execution.output_file(params.get("prefix") + "+orig.HEAD") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_row_fillin_execute(
+    params: V3dRowFillinParameters,
+    execution: Execution,
+) -> V3dRowFillinOutputs:
+    """
+    Fills in blank regions in 1D rows extracted from a 3D dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dRowFillinOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_row_fillin_cargs(params, execution)
+    ret = v_3d_row_fillin_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_row_fillin(
+    input_dataset: InputPathType,
+    maxgap: float | None = None,
+    dir_: str | None = None,
+    binary: bool = False,
+    prefix: str | None = None,
+    runner: Runner | None = None,
+) -> V3dRowFillinOutputs:
+    """
+    Fills in blank regions in 1D rows extracted from a 3D dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_dataset: Input 3D dataset (e.g., dataset+orig).
+        maxgap: Set the maximum length of a blank region that will be filled in.
+        dir_: Set the direction of fill, e.g., A-P, P-A, I-S, S-I, L-R, R-L, x,\
+            y, z, XYZ.OR, XYZ.AND.
+        binary: Turn input dataset to binary (0 and 1) before filling in.\
+            Output will also be binary.
+        prefix: Set the prefix for the output dataset.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dRowFillinOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_ROW_FILLIN_METADATA)
+    params = v_3d_row_fillin_params(
+        maxgap=maxgap,
+        dir_=dir_,
+        binary=binary,
+        prefix=prefix,
+        input_dataset=input_dataset,
+    )
+    return v_3d_row_fillin_execute(params, execution)
+
+
+__all__ = [
+    "V3dRowFillinOutputs",
+    "V3dRowFillinParameters",
+    "V_3D_ROW_FILLIN_METADATA",
+    "v_3d_row_fillin",
+    "v_3d_row_fillin_params",
+]