niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3drefit.py

@@ -0,0 +1,406 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3DREFIT_METADATA = Metadata(
+    id="c64dae99a72b96a3fc2de9c362a4bcd4492ceffe.boutiques",
+    name="3drefit",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3drefitParameters = typing.TypedDict('V3drefitParameters', {
+    "__STYX_TYPE__": typing.Literal["3drefit"],
+    "atrcopy": typing.NotRequired[list[str] | None],
+    "atrfloat": typing.NotRequired[list[str] | None],
+    "atrint": typing.NotRequired[list[str] | None],
+    "atrstring": typing.NotRequired[list[str] | None],
+    "deoblique": bool,
+    "duporigin_file": typing.NotRequired[InputPathType | None],
+    "in_file": InputPathType,
+    "nosaveatr": bool,
+    "saveatr": bool,
+    "space": typing.NotRequired[typing.Literal["TLRC", "MNI", "ORIG"] | None],
+    "xdel": typing.NotRequired[float | None],
+    "xorigin": typing.NotRequired[str | None],
+    "xyzscale": typing.NotRequired[float | None],
+    "ydel": typing.NotRequired[float | None],
+    "yorigin": typing.NotRequired[str | None],
+    "zdel": typing.NotRequired[float | None],
+    "zorigin": 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 {
+        "3drefit": v_3drefit_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 {
+        "3drefit": v_3drefit_outputs,
+    }.get(t)
+
+
+class V3drefitOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3drefit(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_file: OutputPathType
+    """Output file."""
+
+
+def v_3drefit_params(
+    in_file: InputPathType,
+    atrcopy: list[str] | None = None,
+    atrfloat: list[str] | None = None,
+    atrint: list[str] | None = None,
+    atrstring: list[str] | None = None,
+    deoblique: bool = False,
+    duporigin_file: InputPathType | None = None,
+    nosaveatr: bool = False,
+    saveatr: bool = False,
+    space: typing.Literal["TLRC", "MNI", "ORIG"] | None = None,
+    xdel: float | None = None,
+    xorigin: str | None = None,
+    xyzscale: float | None = None,
+    ydel: float | None = None,
+    yorigin: str | None = None,
+    zdel: float | None = None,
+    zorigin: str | None = None,
+) -> V3drefitParameters:
+    """
+    Build parameters.
+    
+    Args:
+        in_file: Input file to 3drefit.
+        atrcopy: (file, string). Copy afni header attribute from the given file\
+            into the header of the dataset(s) being modified. for more information\
+            on afni header attributes, see documentation file readme.attributes.\
+            more than one '-atrcopy' option can be used. for afni advanced users\
+            only. do not use -atrcopy or -atrstring with other modification\
+            options. see also -copyaux.
+        atrfloat: (a string, a string). Create or modify floating point\
+            attributes. the input values may be specified as a single string in\
+            quotes or as a 1d filename or string, example '1 0.2 0 0 -0.2 1 0 0 0 0\
+            1 0' or flipz.1d or '1d:1,0.2,2@0,-0.2,1,2@0,2@0,1,0'.
+        atrint: (a string, a string). Create or modify integer attributes. the\
+            input values may be specified as a single string in quotes or as a 1d\
+            filename or string, example '1 0 0 0 0 1 0 0 0 0 1 0' or flipz.1d or\
+            '1d:1,0,2@0,-0,1,2@0,2@0,1,0'.
+        atrstring: (a string, a string). Copy the last given string into the\
+            dataset(s) being modified, giving it the attribute name given by the\
+            last string.to be safe, the last string should be in quotes.
+        deoblique: Replace current transformation matrix with cardinal matrix.
+        duporigin_file: Copies the xorigin, yorigin, and zorigin values from\
+            the header of the given dataset.
+        nosaveatr: Opposite of -saveatr.
+        saveatr: (default) copy the attributes that are known to afni into the\
+            dset->dblk structure thereby forcing changes to known attributes to be\
+            present in the output. this option only makes sense with -atrcopy.
+        space: 'tlrc' or 'mni' or 'orig'. Associates the dataset with a\
+            specific template type, e.g. tlrc, mni, orig.
+        xdel: New x voxel dimension in mm.
+        xorigin: X distance for edge voxel offset.
+        xyzscale: Scale the size of the dataset voxels by the given factor.
+        ydel: New y voxel dimension in mm.
+        yorigin: Y distance for edge voxel offset.
+        zdel: New z voxel dimension in mm.
+        zorigin: Z distance for edge voxel offset.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3drefit",
+        "deoblique": deoblique,
+        "in_file": in_file,
+        "nosaveatr": nosaveatr,
+        "saveatr": saveatr,
+    }
+    if atrcopy is not None:
+        params["atrcopy"] = atrcopy
+    if atrfloat is not None:
+        params["atrfloat"] = atrfloat
+    if atrint is not None:
+        params["atrint"] = atrint
+    if atrstring is not None:
+        params["atrstring"] = atrstring
+    if duporigin_file is not None:
+        params["duporigin_file"] = duporigin_file
+    if space is not None:
+        params["space"] = space
+    if xdel is not None:
+        params["xdel"] = xdel
+    if xorigin is not None:
+        params["xorigin"] = xorigin
+    if xyzscale is not None:
+        params["xyzscale"] = xyzscale
+    if ydel is not None:
+        params["ydel"] = ydel
+    if yorigin is not None:
+        params["yorigin"] = yorigin
+    if zdel is not None:
+        params["zdel"] = zdel
+    if zorigin is not None:
+        params["zorigin"] = zorigin
+    return params
+
+
+def v_3drefit_cargs(
+    params: V3drefitParameters,
+    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("3drefit")
+    if params.get("atrcopy") is not None:
+        cargs.extend([
+            "-atrcopy",
+            *params.get("atrcopy")
+        ])
+    if params.get("atrfloat") is not None:
+        cargs.extend([
+            "-atrfloat",
+            *params.get("atrfloat")
+        ])
+    if params.get("atrint") is not None:
+        cargs.extend([
+            "-atrint",
+            *params.get("atrint")
+        ])
+    if params.get("atrstring") is not None:
+        cargs.extend([
+            "-atrstring",
+            *params.get("atrstring")
+        ])
+    if params.get("deoblique"):
+        cargs.append("-deoblique")
+    if params.get("duporigin_file") is not None:
+        cargs.extend([
+            "-duporigin",
+            execution.input_file(params.get("duporigin_file"))
+        ])
+    cargs.append(execution.input_file(params.get("in_file"), mutable=True))
+    if params.get("nosaveatr"):
+        cargs.append("-nosaveatr")
+    if params.get("saveatr"):
+        cargs.append("-saveatr")
+    if params.get("space") is not None:
+        cargs.extend([
+            "-space",
+            params.get("space")
+        ])
+    if params.get("xdel") is not None:
+        cargs.extend([
+            "-xdel",
+            str(params.get("xdel"))
+        ])
+    if params.get("xorigin") is not None:
+        cargs.extend([
+            "-xorigin",
+            params.get("xorigin")
+        ])
+    if params.get("xyzscale") is not None:
+        cargs.extend([
+            "-xyzscale",
+            str(params.get("xyzscale"))
+        ])
+    if params.get("ydel") is not None:
+        cargs.extend([
+            "-ydel",
+            str(params.get("ydel"))
+        ])
+    if params.get("yorigin") is not None:
+        cargs.extend([
+            "-yorigin",
+            params.get("yorigin")
+        ])
+    if params.get("zdel") is not None:
+        cargs.extend([
+            "-zdel",
+            str(params.get("zdel"))
+        ])
+    if params.get("zorigin") is not None:
+        cargs.extend([
+            "-zorigin",
+            params.get("zorigin")
+        ])
+    return cargs
+
+
+def v_3drefit_outputs(
+    params: V3drefitParameters,
+    execution: Execution,
+) -> V3drefitOutputs:
+    """
+    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 = V3drefitOutputs(
+        root=execution.output_file("."),
+        out_file=execution.output_file("out_file"),
+    )
+    return ret
+
+
+def v_3drefit_execute(
+    params: V3drefitParameters,
+    execution: Execution,
+) -> V3drefitOutputs:
+    """
+    Changes some of the information inside a 3D dataset's header.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3drefitOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3drefit_cargs(params, execution)
+    ret = v_3drefit_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3drefit(
+    in_file: InputPathType,
+    atrcopy: list[str] | None = None,
+    atrfloat: list[str] | None = None,
+    atrint: list[str] | None = None,
+    atrstring: list[str] | None = None,
+    deoblique: bool = False,
+    duporigin_file: InputPathType | None = None,
+    nosaveatr: bool = False,
+    saveatr: bool = False,
+    space: typing.Literal["TLRC", "MNI", "ORIG"] | None = None,
+    xdel: float | None = None,
+    xorigin: str | None = None,
+    xyzscale: float | None = None,
+    ydel: float | None = None,
+    yorigin: str | None = None,
+    zdel: float | None = None,
+    zorigin: str | None = None,
+    runner: Runner | None = None,
+) -> V3drefitOutputs:
+    """
+    Changes some of the information inside a 3D dataset's header.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        in_file: Input file to 3drefit.
+        atrcopy: (file, string). Copy afni header attribute from the given file\
+            into the header of the dataset(s) being modified. for more information\
+            on afni header attributes, see documentation file readme.attributes.\
+            more than one '-atrcopy' option can be used. for afni advanced users\
+            only. do not use -atrcopy or -atrstring with other modification\
+            options. see also -copyaux.
+        atrfloat: (a string, a string). Create or modify floating point\
+            attributes. the input values may be specified as a single string in\
+            quotes or as a 1d filename or string, example '1 0.2 0 0 -0.2 1 0 0 0 0\
+            1 0' or flipz.1d or '1d:1,0.2,2@0,-0.2,1,2@0,2@0,1,0'.
+        atrint: (a string, a string). Create or modify integer attributes. the\
+            input values may be specified as a single string in quotes or as a 1d\
+            filename or string, example '1 0 0 0 0 1 0 0 0 0 1 0' or flipz.1d or\
+            '1d:1,0,2@0,-0,1,2@0,2@0,1,0'.
+        atrstring: (a string, a string). Copy the last given string into the\
+            dataset(s) being modified, giving it the attribute name given by the\
+            last string.to be safe, the last string should be in quotes.
+        deoblique: Replace current transformation matrix with cardinal matrix.
+        duporigin_file: Copies the xorigin, yorigin, and zorigin values from\
+            the header of the given dataset.
+        nosaveatr: Opposite of -saveatr.
+        saveatr: (default) copy the attributes that are known to afni into the\
+            dset->dblk structure thereby forcing changes to known attributes to be\
+            present in the output. this option only makes sense with -atrcopy.
+        space: 'tlrc' or 'mni' or 'orig'. Associates the dataset with a\
+            specific template type, e.g. tlrc, mni, orig.
+        xdel: New x voxel dimension in mm.
+        xorigin: X distance for edge voxel offset.
+        xyzscale: Scale the size of the dataset voxels by the given factor.
+        ydel: New y voxel dimension in mm.
+        yorigin: Y distance for edge voxel offset.
+        zdel: New z voxel dimension in mm.
+        zorigin: Z distance for edge voxel offset.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3drefitOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DREFIT_METADATA)
+    params = v_3drefit_params(
+        atrcopy=atrcopy,
+        atrfloat=atrfloat,
+        atrint=atrint,
+        atrstring=atrstring,
+        deoblique=deoblique,
+        duporigin_file=duporigin_file,
+        in_file=in_file,
+        nosaveatr=nosaveatr,
+        saveatr=saveatr,
+        space=space,
+        xdel=xdel,
+        xorigin=xorigin,
+        xyzscale=xyzscale,
+        ydel=ydel,
+        yorigin=yorigin,
+        zdel=zdel,
+        zorigin=zorigin,
+    )
+    return v_3drefit_execute(params, execution)
+
+
+__all__ = [
+    "V3drefitOutputs",
+    "V3drefitParameters",
+    "V_3DREFIT_METADATA",
+    "v_3drefit",
+    "v_3drefit_params",
+]

niwrap_afni/afni/v_3drename.py

@@ -0,0 +1,180 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3DRENAME_METADATA = Metadata(
+    id="3c508d8f5e6d69689dd267857ef13efbf3693249.boutiques",
+    name="3drename",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3drenameParameters = typing.TypedDict('V3drenameParameters', {
+    "__STYX_TYPE__": typing.Literal["3drename"],
+    "old_prefix": str,
+    "new_prefix": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3drename": v_3drename_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 V3drenameOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3drename(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v_3drename_params(
+    old_prefix: str,
+    new_prefix: str,
+) -> V3drenameParameters:
+    """
+    Build parameters.
+    
+    Args:
+        old_prefix: Old prefix of the datasets to rename.
+        new_prefix: New prefix for the datasets.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3drename",
+        "old_prefix": old_prefix,
+        "new_prefix": new_prefix,
+    }
+    return params
+
+
+def v_3drename_cargs(
+    params: V3drenameParameters,
+    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("3drename")
+    cargs.append(params.get("old_prefix"))
+    cargs.append(params.get("new_prefix"))
+    return cargs
+
+
+def v_3drename_outputs(
+    params: V3drenameParameters,
+    execution: Execution,
+) -> V3drenameOutputs:
+    """
+    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 = V3drenameOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v_3drename_execute(
+    params: V3drenameParameters,
+    execution: Execution,
+) -> V3drenameOutputs:
+    """
+    Tool to rename AFNI datasets by changing the dataset prefix.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3drenameOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3drename_cargs(params, execution)
+    ret = v_3drename_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3drename(
+    old_prefix: str,
+    new_prefix: str,
+    runner: Runner | None = None,
+) -> V3drenameOutputs:
+    """
+    Tool to rename AFNI datasets by changing the dataset prefix.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        old_prefix: Old prefix of the datasets to rename.
+        new_prefix: New prefix for the datasets.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3drenameOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DRENAME_METADATA)
+    params = v_3drename_params(
+        old_prefix=old_prefix,
+        new_prefix=new_prefix,
+    )
+    return v_3drename_execute(params, execution)
+
+
+__all__ = [
+    "V3drenameOutputs",
+    "V3drenameParameters",
+    "V_3DRENAME_METADATA",
+    "v_3drename",
+    "v_3drename_params",
+]