niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_tagalign.py

@@ -0,0 +1,342 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_TAGALIGN_METADATA = Metadata(
+    id="72f062732ebd3946f6103ba90212bf73566a6b67.boutiques",
+    name="3dTagalign",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dTagalignParameters = typing.TypedDict('V3dTagalignParameters', {
+    "__STYX_TYPE__": typing.Literal["3dTagalign"],
+    "input_dataset": InputPathType,
+    "master_dataset": InputPathType,
+    "tagset_file": typing.NotRequired[InputPathType | None],
+    "no_keep_tags": bool,
+    "matvec_file": typing.NotRequired[str | None],
+    "rotate": bool,
+    "affine": bool,
+    "rotscl": bool,
+    "prefix": typing.NotRequired[str | None],
+    "verbose": bool,
+    "dummy": bool,
+    "linear_interpolation": bool,
+    "cubic_interpolation": bool,
+    "nearest_neighbor_interpolation": bool,
+    "quintic_interpolation": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dTagalign": v_3d_tagalign_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 {
+        "3dTagalign": v_3d_tagalign_outputs,
+    }.get(t)
+
+
+class V3dTagalignOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_tagalign(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_dataset_head: OutputPathType | None
+    """Output dataset in AFNI format (.HEAD)"""
+    output_dataset_brick: OutputPathType | None
+    """Output dataset in AFNI format (.BRIK)"""
+    output_matvec_file: OutputPathType | None
+    """Output transformation matrix and vector file"""
+
+
+def v_3d_tagalign_params(
+    input_dataset: InputPathType,
+    master_dataset: InputPathType,
+    tagset_file: InputPathType | None = None,
+    no_keep_tags: bool = False,
+    matvec_file: str | None = None,
+    rotate: bool = False,
+    affine: bool = False,
+    rotscl: bool = False,
+    prefix: str | None = None,
+    verbose: bool = False,
+    dummy: bool = False,
+    linear_interpolation: bool = False,
+    cubic_interpolation: bool = False,
+    nearest_neighbor_interpolation: bool = False,
+    quintic_interpolation: bool = False,
+) -> V3dTagalignParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_dataset: Input dataset to align.
+        master_dataset: Use dataset 'mset' as the master dataset. This option\
+            is mandatory.
+        tagset_file: Use the tagset in the .tag file instead of dset.
+        no_keep_tags: Don't put transformed locations of dset's tags into the\
+            output dataset [default = keep tags].
+        matvec_file: Write the matrix+vector transformation to file 'mfile'.\
+            This can be used with 3dWarp's '-matvec_in2out' option to align other\
+            datasets in the same way (e.g., functional datasets).
+        rotate: Compute the transformation as a rotation + shift (default).
+        affine: Compute the transformation as a general affine map, where the\
+            matrix is a general 3x3 matrix.
+        rotscl: Compute transformation as a rotation times an isotropic\
+            scaling; where matrix is an orthogonal matrix times a scalar.
+        prefix: Specify the prefix for the output dataset.
+        verbose: Print progress reports.
+        dummy: Don't actually rotate the dataset, just compute the\
+            transformation matrix and vector. If '-matvec' is used, the mfile will\
+            be written.
+        linear_interpolation: Use linear interpolation method.
+        cubic_interpolation: Use cubic interpolation method (default).
+        nearest_neighbor_interpolation: Use nearest neighbour interpolation\
+            method.
+        quintic_interpolation: Use quintic interpolation method.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dTagalign",
+        "input_dataset": input_dataset,
+        "master_dataset": master_dataset,
+        "no_keep_tags": no_keep_tags,
+        "rotate": rotate,
+        "affine": affine,
+        "rotscl": rotscl,
+        "verbose": verbose,
+        "dummy": dummy,
+        "linear_interpolation": linear_interpolation,
+        "cubic_interpolation": cubic_interpolation,
+        "nearest_neighbor_interpolation": nearest_neighbor_interpolation,
+        "quintic_interpolation": quintic_interpolation,
+    }
+    if tagset_file is not None:
+        params["tagset_file"] = tagset_file
+    if matvec_file is not None:
+        params["matvec_file"] = matvec_file
+    if prefix is not None:
+        params["prefix"] = prefix
+    return params
+
+
+def v_3d_tagalign_cargs(
+    params: V3dTagalignParameters,
+    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("3dTagalign")
+    cargs.append(execution.input_file(params.get("input_dataset")))
+    cargs.extend([
+        "-master",
+        execution.input_file(params.get("master_dataset"))
+    ])
+    if params.get("tagset_file") is not None:
+        cargs.extend([
+            "-tagset",
+            execution.input_file(params.get("tagset_file"))
+        ])
+    if params.get("no_keep_tags"):
+        cargs.append("-nokeeptags")
+    if params.get("matvec_file") is not None:
+        cargs.extend([
+            "-matvec",
+            params.get("matvec_file")
+        ])
+    if params.get("rotate"):
+        cargs.append("-rotate")
+    if params.get("affine"):
+        cargs.append("-affine")
+    if params.get("rotscl"):
+        cargs.append("-rotscl")
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("verbose"):
+        cargs.append("-verb")
+    if params.get("dummy"):
+        cargs.append("-dummy")
+    if params.get("linear_interpolation"):
+        cargs.append("-linear")
+    if params.get("cubic_interpolation"):
+        cargs.append("-cubic")
+    if params.get("nearest_neighbor_interpolation"):
+        cargs.append("-NN")
+    if params.get("quintic_interpolation"):
+        cargs.append("-quintic")
+    return cargs
+
+
+def v_3d_tagalign_outputs(
+    params: V3dTagalignParameters,
+    execution: Execution,
+) -> V3dTagalignOutputs:
+    """
+    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 = V3dTagalignOutputs(
+        root=execution.output_file("."),
+        output_dataset_head=execution.output_file(params.get("prefix") + "+orig.HEAD") if (params.get("prefix") is not None) else None,
+        output_dataset_brick=execution.output_file(params.get("prefix") + "+orig.BRIK") if (params.get("prefix") is not None) else None,
+        output_matvec_file=execution.output_file(params.get("matvec_file")) if (params.get("matvec_file") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_tagalign_execute(
+    params: V3dTagalignParameters,
+    execution: Execution,
+) -> V3dTagalignOutputs:
+    """
+    Rotates/translates dataset 'dset' to be aligned with the master using the
+    tagsets embedded in their .HEAD files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dTagalignOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_tagalign_cargs(params, execution)
+    ret = v_3d_tagalign_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_tagalign(
+    input_dataset: InputPathType,
+    master_dataset: InputPathType,
+    tagset_file: InputPathType | None = None,
+    no_keep_tags: bool = False,
+    matvec_file: str | None = None,
+    rotate: bool = False,
+    affine: bool = False,
+    rotscl: bool = False,
+    prefix: str | None = None,
+    verbose: bool = False,
+    dummy: bool = False,
+    linear_interpolation: bool = False,
+    cubic_interpolation: bool = False,
+    nearest_neighbor_interpolation: bool = False,
+    quintic_interpolation: bool = False,
+    runner: Runner | None = None,
+) -> V3dTagalignOutputs:
+    """
+    Rotates/translates dataset 'dset' to be aligned with the master using the
+    tagsets embedded in their .HEAD files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_dataset: Input dataset to align.
+        master_dataset: Use dataset 'mset' as the master dataset. This option\
+            is mandatory.
+        tagset_file: Use the tagset in the .tag file instead of dset.
+        no_keep_tags: Don't put transformed locations of dset's tags into the\
+            output dataset [default = keep tags].
+        matvec_file: Write the matrix+vector transformation to file 'mfile'.\
+            This can be used with 3dWarp's '-matvec_in2out' option to align other\
+            datasets in the same way (e.g., functional datasets).
+        rotate: Compute the transformation as a rotation + shift (default).
+        affine: Compute the transformation as a general affine map, where the\
+            matrix is a general 3x3 matrix.
+        rotscl: Compute transformation as a rotation times an isotropic\
+            scaling; where matrix is an orthogonal matrix times a scalar.
+        prefix: Specify the prefix for the output dataset.
+        verbose: Print progress reports.
+        dummy: Don't actually rotate the dataset, just compute the\
+            transformation matrix and vector. If '-matvec' is used, the mfile will\
+            be written.
+        linear_interpolation: Use linear interpolation method.
+        cubic_interpolation: Use cubic interpolation method (default).
+        nearest_neighbor_interpolation: Use nearest neighbour interpolation\
+            method.
+        quintic_interpolation: Use quintic interpolation method.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dTagalignOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TAGALIGN_METADATA)
+    params = v_3d_tagalign_params(
+        input_dataset=input_dataset,
+        master_dataset=master_dataset,
+        tagset_file=tagset_file,
+        no_keep_tags=no_keep_tags,
+        matvec_file=matvec_file,
+        rotate=rotate,
+        affine=affine,
+        rotscl=rotscl,
+        prefix=prefix,
+        verbose=verbose,
+        dummy=dummy,
+        linear_interpolation=linear_interpolation,
+        cubic_interpolation=cubic_interpolation,
+        nearest_neighbor_interpolation=nearest_neighbor_interpolation,
+        quintic_interpolation=quintic_interpolation,
+    )
+    return v_3d_tagalign_execute(params, execution)
+
+
+__all__ = [
+    "V3dTagalignOutputs",
+    "V3dTagalignParameters",
+    "V_3D_TAGALIGN_METADATA",
+    "v_3d_tagalign",
+    "v_3d_tagalign_params",
+]

niwrap_afni/afni/v_3d_tcat.py

@@ -0,0 +1,223 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_TCAT_METADATA = Metadata(
+    id="857f0c4b1d6c6ff7212eb0f219b0756a253e1817.boutiques",
+    name="3dTcat",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dTcatParameters = typing.TypedDict('V3dTcatParameters', {
+    "__STYX_TYPE__": typing.Literal["3dTcat"],
+    "rlt": typing.NotRequired[typing.Literal["", "+", "++"] | None],
+    "in_files": InputPathType,
+    "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
+    "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 {
+        "3dTcat": v_3d_tcat_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 {
+        "3dTcat": v_3d_tcat_outputs,
+    }.get(t)
+
+
+class V3dTcatOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_tcat(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_file: OutputPathType
+    """Output image file name."""
+    out_file_: OutputPathType
+    """Output file."""
+
+
+def v_3d_tcat_params(
+    in_files: InputPathType,
+    rlt: typing.Literal["", "+", "++"] | None = None,
+    outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
+    verbose: bool = False,
+) -> V3dTcatParameters:
+    """
+    Build parameters.
+    
+    Args:
+        in_files: Input file to 3dtcat.
+        rlt: '' or '+' or '++'. Remove linear trends in each voxel time series\
+            loaded from each input dataset, separately. option -rlt removes the\
+            least squares fit of 'a+b*t' to each voxel time series. option -rlt+\
+            adds dataset mean back in. option -rlt++ adds overall mean of all\
+            dataset timeseries back in.
+        outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
+        verbose: Print out some verbose output as the program.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dTcat",
+        "in_files": in_files,
+        "verbose": verbose,
+    }
+    if rlt is not None:
+        params["rlt"] = rlt
+    if outputtype is not None:
+        params["outputtype"] = outputtype
+    return params
+
+
+def v_3d_tcat_cargs(
+    params: V3dTcatParameters,
+    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("3dTcat")
+    if params.get("rlt") is not None:
+        cargs.extend([
+            "-rlt",
+            params.get("rlt") + execution.input_file(params.get("in_files"))
+        ])
+    cargs.append("[OUT_FILE]")
+    if params.get("outputtype") is not None:
+        cargs.append(params.get("outputtype"))
+    if params.get("verbose"):
+        cargs.append("-verb")
+    return cargs
+
+
+def v_3d_tcat_outputs(
+    params: V3dTcatParameters,
+    execution: Execution,
+) -> V3dTcatOutputs:
+    """
+    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 = V3dTcatOutputs(
+        root=execution.output_file("."),
+        out_file=execution.output_file(pathlib.Path(params.get("in_files")).name + "_tcat"),
+        out_file_=execution.output_file("out_file"),
+    )
+    return ret
+
+
+def v_3d_tcat_execute(
+    params: V3dTcatParameters,
+    execution: Execution,
+) -> V3dTcatOutputs:
+    """
+    Concatenate sub-bricks from input datasets into one big 3D+time dataset.
+    TODO Replace InputMultiPath in_files with Traits.List, if possible. Current
+    version adds extra whitespace.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dTcatOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_tcat_cargs(params, execution)
+    ret = v_3d_tcat_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_tcat(
+    in_files: InputPathType,
+    rlt: typing.Literal["", "+", "++"] | None = None,
+    outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
+    verbose: bool = False,
+    runner: Runner | None = None,
+) -> V3dTcatOutputs:
+    """
+    Concatenate sub-bricks from input datasets into one big 3D+time dataset.
+    TODO Replace InputMultiPath in_files with Traits.List, if possible. Current
+    version adds extra whitespace.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        in_files: Input file to 3dtcat.
+        rlt: '' or '+' or '++'. Remove linear trends in each voxel time series\
+            loaded from each input dataset, separately. option -rlt removes the\
+            least squares fit of 'a+b*t' to each voxel time series. option -rlt+\
+            adds dataset mean back in. option -rlt++ adds overall mean of all\
+            dataset timeseries back in.
+        outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
+        verbose: Print out some verbose output as the program.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dTcatOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TCAT_METADATA)
+    params = v_3d_tcat_params(
+        rlt=rlt,
+        in_files=in_files,
+        outputtype=outputtype,
+        verbose=verbose,
+    )
+    return v_3d_tcat_execute(params, execution)
+
+
+__all__ = [
+    "V3dTcatOutputs",
+    "V3dTcatParameters",
+    "V_3D_TCAT_METADATA",
+    "v_3d_tcat",
+    "v_3d_tcat_params",
+]