niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__afni_run_me.py

@@ -0,0 +1,191 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__AFNI_RUN_ME_METADATA = Metadata(
+    id="aeac26149fa34d0c42e1c07c261b19ac0706d90b.boutiques",
+    name="@afni.run.me",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VAfniRunMeParameters = typing.TypedDict('VAfniRunMeParameters', {
+    "__STYX_TYPE__": typing.Literal["@afni.run.me"],
+    "go": bool,
+    "curl": bool,
+    "help": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@afni.run.me": v__afni_run_me_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 VAfniRunMeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__afni_run_me(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v__afni_run_me_params(
+    go: bool = False,
+    curl: bool = False,
+    help_: bool = False,
+) -> VAfniRunMeParameters:
+    """
+    Build parameters.
+    
+    Args:
+        go: Execute the work.
+        curl: Default to curl instead of wget.
+        help_: Show help message.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@afni.run.me",
+        "go": go,
+        "curl": curl,
+        "help": help_,
+    }
+    return params
+
+
+def v__afni_run_me_cargs(
+    params: VAfniRunMeParameters,
+    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("@afni.run.me")
+    if params.get("go"):
+        cargs.append("-go")
+    if params.get("curl"):
+        cargs.append("-curl")
+    if params.get("help"):
+        cargs.append("-help")
+    return cargs
+
+
+def v__afni_run_me_outputs(
+    params: VAfniRunMeParameters,
+    execution: Execution,
+) -> VAfniRunMeOutputs:
+    """
+    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 = VAfniRunMeOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v__afni_run_me_execute(
+    params: VAfniRunMeParameters,
+    execution: Execution,
+) -> VAfniRunMeOutputs:
+    """
+    A tool to execute a specific command.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VAfniRunMeOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__afni_run_me_cargs(params, execution)
+    ret = v__afni_run_me_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__afni_run_me(
+    go: bool = False,
+    curl: bool = False,
+    help_: bool = False,
+    runner: Runner | None = None,
+) -> VAfniRunMeOutputs:
+    """
+    A tool to execute a specific command.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        go: Execute the work.
+        curl: Default to curl instead of wget.
+        help_: Show help message.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VAfniRunMeOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__AFNI_RUN_ME_METADATA)
+    params = v__afni_run_me_params(
+        go=go,
+        curl=curl,
+        help_=help_,
+    )
+    return v__afni_run_me_execute(params, execution)
+
+
+__all__ = [
+    "VAfniRunMeOutputs",
+    "VAfniRunMeParameters",
+    "V__AFNI_RUN_ME_METADATA",
+    "v__afni_run_me",
+    "v__afni_run_me_params",
+]

niwrap_afni/afni/v__align_centers.py

@@ -0,0 +1,324 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__ALIGN_CENTERS_METADATA = Metadata(
+    id="f29fbec7d33b88a11144d9ab1edf49dc32ae31cf.boutiques",
+    name="@Align_Centers",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VAlignCentersParameters = typing.TypedDict('VAlignCentersParameters', {
+    "__STYX_TYPE__": typing.Literal["@Align_Centers"],
+    "base": InputPathType,
+    "dset": InputPathType,
+    "children": typing.NotRequired[list[InputPathType] | None],
+    "echo": bool,
+    "overwrite": bool,
+    "prefix": typing.NotRequired[str | None],
+    "matrix_only": bool,
+    "matrix_only_no_dset": bool,
+    "no_cp": bool,
+    "center_grid": bool,
+    "center_cm": bool,
+    "center_cm_no_amask": bool,
+    "shift_xform": typing.NotRequired[InputPathType | None],
+    "shift_xform_inv": typing.NotRequired[InputPathType | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@Align_Centers": v__align_centers_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 {
+        "@Align_Centers": v__align_centers_outputs,
+    }.get(t)
+
+
+class VAlignCentersOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__align_centers(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    transform_matrix: OutputPathType
+    """Transform matrix needed for the shift applied to DSET."""
+    shifted_dset: OutputPathType | None
+    """Shifted Dataset aligned with the base volume."""
+    shifted_child_dsets: OutputPathType | None
+    """Shifted child datasets aligned with the base volume."""
+
+
+def v__align_centers_params(
+    base: InputPathType,
+    dset: InputPathType,
+    children: list[InputPathType] | None = None,
+    echo: bool = False,
+    overwrite: bool = False,
+    prefix: str | None = None,
+    matrix_only: bool = False,
+    matrix_only_no_dset: bool = False,
+    no_cp: bool = False,
+    center_grid: bool = False,
+    center_cm: bool = False,
+    center_cm_no_amask: bool = False,
+    shift_xform: InputPathType | None = None,
+    shift_xform_inv: InputPathType | None = None,
+) -> VAlignCentersParameters:
+    """
+    Build parameters.
+    
+    Args:
+        base: Base volume, typically a template. Can also specify RAI\
+            coordinates for center alignment.
+        dset: Dataset to be aligned to BASE.
+        children: Additional datasets (originally in register with DSET) that\
+            should be shifted in the same way.
+        echo: Echo all commands to terminal for debugging.
+        overwrite: Overwrite existing output files.
+        prefix: Custom prefix for the result files.
+        matrix_only: Only output the transform needed to align the centers\
+            without shifting any child volumes.
+        matrix_only_no_dset: Like -1Dmat_only, but no datasets are created or\
+            changed.
+        no_cp: Do not create new data; shift existing ones. Use with caution.
+        center_grid: Center is that of the volume's grid (default).
+        center_cm: Center is the center of mass of the volume.
+        center_cm_no_amask: Like -cm, but with no automask.
+        shift_xform: Apply shift translation from a 1D file.
+        shift_xform_inv: Apply inverse of shift translation from a 1D file.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@Align_Centers",
+        "base": base,
+        "dset": dset,
+        "echo": echo,
+        "overwrite": overwrite,
+        "matrix_only": matrix_only,
+        "matrix_only_no_dset": matrix_only_no_dset,
+        "no_cp": no_cp,
+        "center_grid": center_grid,
+        "center_cm": center_cm,
+        "center_cm_no_amask": center_cm_no_amask,
+    }
+    if children is not None:
+        params["children"] = children
+    if prefix is not None:
+        params["prefix"] = prefix
+    if shift_xform is not None:
+        params["shift_xform"] = shift_xform
+    if shift_xform_inv is not None:
+        params["shift_xform_inv"] = shift_xform_inv
+    return params
+
+
+def v__align_centers_cargs(
+    params: VAlignCentersParameters,
+    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("@Align_Centers")
+    cargs.append(execution.input_file(params.get("base")))
+    cargs.append(execution.input_file(params.get("dset")))
+    if params.get("children") is not None:
+        cargs.extend([
+            "-child",
+            *[execution.input_file(f) for f in params.get("children")]
+        ])
+    if params.get("echo"):
+        cargs.append("-echo")
+    if params.get("overwrite"):
+        cargs.append("-overwrite")
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("matrix_only"):
+        cargs.append("-1Dmat_only")
+    if params.get("matrix_only_no_dset"):
+        cargs.append("-1Dmat_only_nodset")
+    if params.get("no_cp"):
+        cargs.append("-no_cp")
+    if params.get("center_grid"):
+        cargs.append("-grid")
+    if params.get("center_cm"):
+        cargs.append("-cm")
+    if params.get("center_cm_no_amask"):
+        cargs.append("-cm_no_amask")
+    if params.get("shift_xform") is not None:
+        cargs.extend([
+            "-shift_xform",
+            execution.input_file(params.get("shift_xform"))
+        ])
+    if params.get("shift_xform_inv") is not None:
+        cargs.extend([
+            "-shift_xform_inv",
+            execution.input_file(params.get("shift_xform_inv"))
+        ])
+    return cargs
+
+
+def v__align_centers_outputs(
+    params: VAlignCentersParameters,
+    execution: Execution,
+) -> VAlignCentersOutputs:
+    """
+    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 = VAlignCentersOutputs(
+        root=execution.output_file("."),
+        transform_matrix=execution.output_file(pathlib.Path(params.get("dset")).name + "_shft.1D"),
+        shifted_dset=execution.output_file(params.get("prefix") + "_shft+orig.BRIK") if (params.get("prefix") is not None) else None,
+        shifted_child_dsets=execution.output_file(params.get("prefix") + "_child_shft+orig.BRIK") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v__align_centers_execute(
+    params: VAlignCentersParameters,
+    execution: Execution,
+) -> VAlignCentersOutputs:
+    """
+    Moves the center of a dataset (DSET) to the center of a base volume (BASE) and
+    optionally creates a transform matrix.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VAlignCentersOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__align_centers_cargs(params, execution)
+    ret = v__align_centers_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__align_centers(
+    base: InputPathType,
+    dset: InputPathType,
+    children: list[InputPathType] | None = None,
+    echo: bool = False,
+    overwrite: bool = False,
+    prefix: str | None = None,
+    matrix_only: bool = False,
+    matrix_only_no_dset: bool = False,
+    no_cp: bool = False,
+    center_grid: bool = False,
+    center_cm: bool = False,
+    center_cm_no_amask: bool = False,
+    shift_xform: InputPathType | None = None,
+    shift_xform_inv: InputPathType | None = None,
+    runner: Runner | None = None,
+) -> VAlignCentersOutputs:
+    """
+    Moves the center of a dataset (DSET) to the center of a base volume (BASE) and
+    optionally creates a transform matrix.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        base: Base volume, typically a template. Can also specify RAI\
+            coordinates for center alignment.
+        dset: Dataset to be aligned to BASE.
+        children: Additional datasets (originally in register with DSET) that\
+            should be shifted in the same way.
+        echo: Echo all commands to terminal for debugging.
+        overwrite: Overwrite existing output files.
+        prefix: Custom prefix for the result files.
+        matrix_only: Only output the transform needed to align the centers\
+            without shifting any child volumes.
+        matrix_only_no_dset: Like -1Dmat_only, but no datasets are created or\
+            changed.
+        no_cp: Do not create new data; shift existing ones. Use with caution.
+        center_grid: Center is that of the volume's grid (default).
+        center_cm: Center is the center of mass of the volume.
+        center_cm_no_amask: Like -cm, but with no automask.
+        shift_xform: Apply shift translation from a 1D file.
+        shift_xform_inv: Apply inverse of shift translation from a 1D file.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VAlignCentersOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__ALIGN_CENTERS_METADATA)
+    params = v__align_centers_params(
+        base=base,
+        dset=dset,
+        children=children,
+        echo=echo,
+        overwrite=overwrite,
+        prefix=prefix,
+        matrix_only=matrix_only,
+        matrix_only_no_dset=matrix_only_no_dset,
+        no_cp=no_cp,
+        center_grid=center_grid,
+        center_cm=center_cm,
+        center_cm_no_amask=center_cm_no_amask,
+        shift_xform=shift_xform,
+        shift_xform_inv=shift_xform_inv,
+    )
+    return v__align_centers_execute(params, execution)
+
+
+__all__ = [
+    "VAlignCentersOutputs",
+    "VAlignCentersParameters",
+    "V__ALIGN_CENTERS_METADATA",
+    "v__align_centers",
+    "v__align_centers_params",
+]