niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/fat_proc_map_to_dti.py

@@ -0,0 +1,308 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FAT_PROC_MAP_TO_DTI_METADATA = Metadata(
+    id="2b3d016adec8a1c1a140ee39d2b30af25ebd671d.boutiques",
+    name="fat_proc_map_to_dti",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+FatProcMapToDtiParameters = typing.TypedDict('FatProcMapToDtiParameters', {
+    "__STYX_TYPE__": typing.Literal["fat_proc_map_to_dti"],
+    "source": InputPathType,
+    "base": InputPathType,
+    "prefix": str,
+    "followers_nn": typing.NotRequired[list[InputPathType] | None],
+    "followers_wsinc5": typing.NotRequired[list[InputPathType] | None],
+    "followers_surf": typing.NotRequired[list[InputPathType] | None],
+    "followers_ndset": typing.NotRequired[list[InputPathType] | None],
+    "followers_spec": typing.NotRequired[list[InputPathType] | None],
+    "matrix": typing.NotRequired[InputPathType | None],
+    "workdir": typing.NotRequired[str | None],
+    "no_cmd_out": bool,
+    "no_clean": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "fat_proc_map_to_dti": fat_proc_map_to_dti_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 FatProcMapToDtiOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `fat_proc_map_to_dti(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def fat_proc_map_to_dti_params(
+    source: InputPathType,
+    base: InputPathType,
+    prefix: str,
+    followers_nn: list[InputPathType] | None = None,
+    followers_wsinc5: list[InputPathType] | None = None,
+    followers_surf: list[InputPathType] | None = None,
+    followers_ndset: list[InputPathType] | None = None,
+    followers_spec: list[InputPathType] | None = None,
+    matrix: InputPathType | None = None,
+    workdir: str | None = None,
+    no_cmd_out: bool = False,
+    no_clean: bool = False,
+) -> FatProcMapToDtiParameters:
+    """
+    Build parameters.
+    
+    Args:
+        source: T1w volume file (source volume).
+        base: DWI reference volume file.
+        prefix: Output prefix for files and snapshots.
+        followers_nn: Follower data sets with NN interpolation.
+        followers_wsinc5: Follower data sets with wsinc5 interpolation.
+        followers_surf: Surface follower data sets.
+        followers_ndset: NIML follower data sets.
+        followers_spec: Spec follower data sets.
+        matrix: Pre-made matrix file for transformation.
+        workdir: Specify a working directory.
+        no_cmd_out: Don't save the command line call of this program.
+        no_clean: Do not delete temporary working directory.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "fat_proc_map_to_dti",
+        "source": source,
+        "base": base,
+        "prefix": prefix,
+        "no_cmd_out": no_cmd_out,
+        "no_clean": no_clean,
+    }
+    if followers_nn is not None:
+        params["followers_nn"] = followers_nn
+    if followers_wsinc5 is not None:
+        params["followers_wsinc5"] = followers_wsinc5
+    if followers_surf is not None:
+        params["followers_surf"] = followers_surf
+    if followers_ndset is not None:
+        params["followers_ndset"] = followers_ndset
+    if followers_spec is not None:
+        params["followers_spec"] = followers_spec
+    if matrix is not None:
+        params["matrix"] = matrix
+    if workdir is not None:
+        params["workdir"] = workdir
+    return params
+
+
+def fat_proc_map_to_dti_cargs(
+    params: FatProcMapToDtiParameters,
+    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("fat_proc_map_to_dti")
+    cargs.extend([
+        "-source",
+        execution.input_file(params.get("source"))
+    ])
+    cargs.extend([
+        "-base",
+        execution.input_file(params.get("base"))
+    ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("followers_nn") is not None:
+        cargs.extend([
+            "-followers_NN",
+            *[execution.input_file(f) for f in params.get("followers_nn")]
+        ])
+    if params.get("followers_wsinc5") is not None:
+        cargs.extend([
+            "-followers_wsinc5",
+            *[execution.input_file(f) for f in params.get("followers_wsinc5")]
+        ])
+    if params.get("followers_surf") is not None:
+        cargs.extend([
+            "-followers_surf",
+            *[execution.input_file(f) for f in params.get("followers_surf")]
+        ])
+    if params.get("followers_ndset") is not None:
+        cargs.extend([
+            "-followers_ndset",
+            *[execution.input_file(f) for f in params.get("followers_ndset")]
+        ])
+    if params.get("followers_spec") is not None:
+        cargs.extend([
+            "-followers_spec",
+            *[execution.input_file(f) for f in params.get("followers_spec")]
+        ])
+    if params.get("matrix") is not None:
+        cargs.extend([
+            "-matrix",
+            execution.input_file(params.get("matrix"))
+        ])
+    if params.get("workdir") is not None:
+        cargs.extend([
+            "-workdir",
+            params.get("workdir")
+        ])
+    if params.get("no_cmd_out"):
+        cargs.append("-no_cmd_out")
+    if params.get("no_clean"):
+        cargs.append("-no_clean")
+    return cargs
+
+
+def fat_proc_map_to_dti_outputs(
+    params: FatProcMapToDtiParameters,
+    execution: Execution,
+) -> FatProcMapToDtiOutputs:
+    """
+    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 = FatProcMapToDtiOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def fat_proc_map_to_dti_execute(
+    params: FatProcMapToDtiParameters,
+    execution: Execution,
+) -> FatProcMapToDtiOutputs:
+    """
+    A program for mapping data sets into DWI space, suitable for aligning anatomical
+    ROI maps or EPI data to a DWI reference volume.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `FatProcMapToDtiOutputs`).
+    """
+    params = execution.params(params)
+    cargs = fat_proc_map_to_dti_cargs(params, execution)
+    ret = fat_proc_map_to_dti_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def fat_proc_map_to_dti(
+    source: InputPathType,
+    base: InputPathType,
+    prefix: str,
+    followers_nn: list[InputPathType] | None = None,
+    followers_wsinc5: list[InputPathType] | None = None,
+    followers_surf: list[InputPathType] | None = None,
+    followers_ndset: list[InputPathType] | None = None,
+    followers_spec: list[InputPathType] | None = None,
+    matrix: InputPathType | None = None,
+    workdir: str | None = None,
+    no_cmd_out: bool = False,
+    no_clean: bool = False,
+    runner: Runner | None = None,
+) -> FatProcMapToDtiOutputs:
+    """
+    A program for mapping data sets into DWI space, suitable for aligning anatomical
+    ROI maps or EPI data to a DWI reference volume.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        source: T1w volume file (source volume).
+        base: DWI reference volume file.
+        prefix: Output prefix for files and snapshots.
+        followers_nn: Follower data sets with NN interpolation.
+        followers_wsinc5: Follower data sets with wsinc5 interpolation.
+        followers_surf: Surface follower data sets.
+        followers_ndset: NIML follower data sets.
+        followers_spec: Spec follower data sets.
+        matrix: Pre-made matrix file for transformation.
+        workdir: Specify a working directory.
+        no_cmd_out: Don't save the command line call of this program.
+        no_clean: Do not delete temporary working directory.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `FatProcMapToDtiOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FAT_PROC_MAP_TO_DTI_METADATA)
+    params = fat_proc_map_to_dti_params(
+        source=source,
+        base=base,
+        prefix=prefix,
+        followers_nn=followers_nn,
+        followers_wsinc5=followers_wsinc5,
+        followers_surf=followers_surf,
+        followers_ndset=followers_ndset,
+        followers_spec=followers_spec,
+        matrix=matrix,
+        workdir=workdir,
+        no_cmd_out=no_cmd_out,
+        no_clean=no_clean,
+    )
+    return fat_proc_map_to_dti_execute(params, execution)
+
+
+__all__ = [
+    "FAT_PROC_MAP_TO_DTI_METADATA",
+    "FatProcMapToDtiOutputs",
+    "FatProcMapToDtiParameters",
+    "fat_proc_map_to_dti",
+    "fat_proc_map_to_dti_params",
+]

niwrap_afni/afni/fat_proc_select_vols.py

@@ -0,0 +1,266 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FAT_PROC_SELECT_VOLS_METADATA = Metadata(
+    id="797c7f4cdd720c40e5ac1cdfb28e7156b1b6687a.boutiques",
+    name="fat_proc_select_vols",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+FatProcSelectVolsParameters = typing.TypedDict('FatProcSelectVolsParameters', {
+    "__STYX_TYPE__": typing.Literal["fat_proc_select_vols"],
+    "dwi_input": InputPathType,
+    "img_input": InputPathType,
+    "prefix": str,
+    "in_bads": typing.NotRequired[InputPathType | None],
+    "apply_to_vols": bool,
+    "do_movie": typing.NotRequired[str | None],
+    "workdir": typing.NotRequired[str | None],
+    "no_cmd_out": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "fat_proc_select_vols": fat_proc_select_vols_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 {
+        "fat_proc_select_vols": fat_proc_select_vols_outputs,
+    }.get(t)
+
+
+class FatProcSelectVolsOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `fat_proc_select_vols(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_selector_string: OutputPathType
+    """Text file with AFNI-usable selector string"""
+
+
+def fat_proc_select_vols_params(
+    dwi_input: InputPathType,
+    img_input: InputPathType,
+    prefix: str,
+    in_bads: InputPathType | None = None,
+    apply_to_vols: bool = False,
+    do_movie: str | None = None,
+    workdir: str | None = None,
+    no_cmd_out: bool = False,
+) -> FatProcSelectVolsParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dwi_input: Input DWI dataset.
+        img_input: 2D image of the DWI dataset.
+        prefix: Output prefix for files.
+        in_bads: A single column file of integers representing bad volumes\
+            indices (optional).
+        apply_to_vols: Apply the created selection of good volumes to the DWI\
+            dataset.
+        do_movie: Output a movie of the newly created dataset. Only 'AGIF' or\
+            'MPEG' arguments can be used.
+        workdir: Specify a working directory.
+        no_cmd_out: Don't save the command line call of this program and the\
+            location where it was run.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "fat_proc_select_vols",
+        "dwi_input": dwi_input,
+        "img_input": img_input,
+        "prefix": prefix,
+        "apply_to_vols": apply_to_vols,
+        "no_cmd_out": no_cmd_out,
+    }
+    if in_bads is not None:
+        params["in_bads"] = in_bads
+    if do_movie is not None:
+        params["do_movie"] = do_movie
+    if workdir is not None:
+        params["workdir"] = workdir
+    return params
+
+
+def fat_proc_select_vols_cargs(
+    params: FatProcSelectVolsParameters,
+    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("fat_proc_select_vols")
+    cargs.extend([
+        "-in_dwi",
+        execution.input_file(params.get("dwi_input"))
+    ])
+    cargs.extend([
+        "-in_img",
+        execution.input_file(params.get("img_input"))
+    ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("in_bads") is not None:
+        cargs.extend([
+            "-in_bads",
+            execution.input_file(params.get("in_bads"))
+        ])
+    if params.get("apply_to_vols"):
+        cargs.append("-apply_to_vols")
+    if params.get("do_movie") is not None:
+        cargs.extend([
+            "-do_movie",
+            params.get("do_movie")
+        ])
+    if params.get("workdir") is not None:
+        cargs.extend([
+            "-workdir",
+            params.get("workdir")
+        ])
+    if params.get("no_cmd_out"):
+        cargs.append("-no_cmd_out")
+    return cargs
+
+
+def fat_proc_select_vols_outputs(
+    params: FatProcSelectVolsParameters,
+    execution: Execution,
+) -> FatProcSelectVolsOutputs:
+    """
+    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 = FatProcSelectVolsOutputs(
+        root=execution.output_file("."),
+        output_selector_string=execution.output_file(params.get("prefix") + "_bads.txt"),
+    )
+    return ret
+
+
+def fat_proc_select_vols_execute(
+    params: FatProcSelectVolsParameters,
+    execution: Execution,
+) -> FatProcSelectVolsOutputs:
+    """
+    Tool for building a selector string for AFNI subbricks and/or 1D text files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `FatProcSelectVolsOutputs`).
+    """
+    params = execution.params(params)
+    cargs = fat_proc_select_vols_cargs(params, execution)
+    ret = fat_proc_select_vols_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def fat_proc_select_vols(
+    dwi_input: InputPathType,
+    img_input: InputPathType,
+    prefix: str,
+    in_bads: InputPathType | None = None,
+    apply_to_vols: bool = False,
+    do_movie: str | None = None,
+    workdir: str | None = None,
+    no_cmd_out: bool = False,
+    runner: Runner | None = None,
+) -> FatProcSelectVolsOutputs:
+    """
+    Tool for building a selector string for AFNI subbricks and/or 1D text files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dwi_input: Input DWI dataset.
+        img_input: 2D image of the DWI dataset.
+        prefix: Output prefix for files.
+        in_bads: A single column file of integers representing bad volumes\
+            indices (optional).
+        apply_to_vols: Apply the created selection of good volumes to the DWI\
+            dataset.
+        do_movie: Output a movie of the newly created dataset. Only 'AGIF' or\
+            'MPEG' arguments can be used.
+        workdir: Specify a working directory.
+        no_cmd_out: Don't save the command line call of this program and the\
+            location where it was run.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `FatProcSelectVolsOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FAT_PROC_SELECT_VOLS_METADATA)
+    params = fat_proc_select_vols_params(
+        dwi_input=dwi_input,
+        img_input=img_input,
+        prefix=prefix,
+        in_bads=in_bads,
+        apply_to_vols=apply_to_vols,
+        do_movie=do_movie,
+        workdir=workdir,
+        no_cmd_out=no_cmd_out,
+    )
+    return fat_proc_select_vols_execute(params, execution)
+
+
+__all__ = [
+    "FAT_PROC_SELECT_VOLS_METADATA",
+    "FatProcSelectVolsOutputs",
+    "FatProcSelectVolsParameters",
+    "fat_proc_select_vols",
+    "fat_proc_select_vols_params",
+]