niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__suma_make_spec_sf.py

@@ -0,0 +1,207 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__SUMA_MAKE_SPEC_SF_METADATA = Metadata(
+    id="e84849d3eeb33bb18d791b3e555fb699941d3809.boutiques",
+    name="@SUMA_Make_Spec_SF",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VSumaMakeSpecSfParameters = typing.TypedDict('VSumaMakeSpecSfParameters', {
+    "__STYX_TYPE__": typing.Literal["@SUMA_Make_Spec_SF"],
+    "debug_level": typing.NotRequired[int | None],
+    "surface_path": typing.NotRequired[str | None],
+    "subject_id": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@SUMA_Make_Spec_SF": v__suma_make_spec_sf_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 {
+        "@SUMA_Make_Spec_SF": v__suma_make_spec_sf_outputs,
+    }.get(t)
+
+
+class VSumaMakeSpecSfOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__suma_make_spec_sf(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_files: OutputPathType
+    """All created files are stored in SURFACES directory"""
+
+
+def v__suma_make_spec_sf_params(
+    subject_id: str,
+    debug_level: int | None = None,
+    surface_path: str | None = None,
+) -> VSumaMakeSpecSfParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subject_id: Required subject ID for file naming.
+        debug_level: Print debug information along the way.
+        surface_path: Path to directory containing 'SURFACES' and AFNI volume\
+            used in creating the surfaces.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@SUMA_Make_Spec_SF",
+        "subject_id": subject_id,
+    }
+    if debug_level is not None:
+        params["debug_level"] = debug_level
+    if surface_path is not None:
+        params["surface_path"] = surface_path
+    return params
+
+
+def v__suma_make_spec_sf_cargs(
+    params: VSumaMakeSpecSfParameters,
+    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("@SUMA_Make_Spec_SF")
+    if params.get("debug_level") is not None:
+        cargs.extend([
+            "-debug",
+            str(params.get("debug_level"))
+        ])
+    if params.get("surface_path") is not None:
+        cargs.extend([
+            "-sfpath",
+            params.get("surface_path")
+        ])
+    cargs.extend([
+        "-sid",
+        params.get("subject_id")
+    ])
+    return cargs
+
+
+def v__suma_make_spec_sf_outputs(
+    params: VSumaMakeSpecSfParameters,
+    execution: Execution,
+) -> VSumaMakeSpecSfOutputs:
+    """
+    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 = VSumaMakeSpecSfOutputs(
+        root=execution.output_file("."),
+        output_files=execution.output_file("SURFACES/*"),
+    )
+    return ret
+
+
+def v__suma_make_spec_sf_execute(
+    params: VSumaMakeSpecSfParameters,
+    execution: Execution,
+) -> VSumaMakeSpecSfOutputs:
+    """
+    Prepare for surface viewing in SUMA.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VSumaMakeSpecSfOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__suma_make_spec_sf_cargs(params, execution)
+    ret = v__suma_make_spec_sf_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__suma_make_spec_sf(
+    subject_id: str,
+    debug_level: int | None = None,
+    surface_path: str | None = None,
+    runner: Runner | None = None,
+) -> VSumaMakeSpecSfOutputs:
+    """
+    Prepare for surface viewing in SUMA.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        subject_id: Required subject ID for file naming.
+        debug_level: Print debug information along the way.
+        surface_path: Path to directory containing 'SURFACES' and AFNI volume\
+            used in creating the surfaces.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VSumaMakeSpecSfOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__SUMA_MAKE_SPEC_SF_METADATA)
+    params = v__suma_make_spec_sf_params(
+        debug_level=debug_level,
+        surface_path=surface_path,
+        subject_id=subject_id,
+    )
+    return v__suma_make_spec_sf_execute(params, execution)
+
+
+__all__ = [
+    "VSumaMakeSpecSfOutputs",
+    "VSumaMakeSpecSfParameters",
+    "V__SUMA_MAKE_SPEC_SF_METADATA",
+    "v__suma_make_spec_sf",
+    "v__suma_make_spec_sf_params",
+]

niwrap_afni/afni/v__suma_renumber_fs.py

@@ -0,0 +1,209 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__SUMA_RENUMBER_FS_METADATA = Metadata(
+    id="c19b88d98568eb300b3deddf6a92cffe231ec7b8.boutiques",
+    name="@SUMA_renumber_FS",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VSumaRenumberFsParameters = typing.TypedDict('VSumaRenumberFsParameters', {
+    "__STYX_TYPE__": typing.Literal["@SUMA_renumber_FS"],
+    "sumadir": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@SUMA_renumber_FS": v__suma_renumber_fs_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 {
+        "@SUMA_renumber_FS": v__suma_renumber_fs_outputs,
+    }.get(t)
+
+
+class VSumaRenumberFsOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__suma_renumber_fs(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    ren_all: OutputPathType
+    """Whole parcellation/segmentation file with renumbered ROIs."""
+    ren_gm: OutputPathType
+    """Gray matter tissue segmentation map."""
+    ren_wmat: OutputPathType
+    """White matter tissue segmentation map."""
+    ren_csf: OutputPathType
+    """Cerebrospinal fluid tissue segmentation map."""
+    ren_vent: OutputPathType
+    """Ventricles and choroid plexus tissue segmentation map."""
+    ren_othr: OutputPathType
+    """Other tissue segmentation map (optic chiasm, non-WM-hypointens, etc.)."""
+    ren_unkn: OutputPathType
+    """Unknown tissue segmentation map (FS-defined 'unknown', with voxel value
+    >0)."""
+    ren_gmrois: OutputPathType
+    """Gray matter ROIs without '*-Cerebral-Cortex' dots."""
+    fs_ap_wm: OutputPathType
+    """White matter mask (excluding the dotted part from FS)."""
+    fs_ap_latvent: OutputPathType
+    """Lateral ventricles mask ('*-Lateral-Ventricle')."""
+    ren_lbl_table: OutputPathType
+    """Labeltable of the new ROI values."""
+
+
+def v__suma_renumber_fs_params(
+    sumadir: str,
+) -> VSumaRenumberFsParameters:
+    """
+    Build parameters.
+    
+    Args:
+        sumadir: Path to the 'SUMA/' directory created by @SUMA_Make_Spec_FS.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@SUMA_renumber_FS",
+        "sumadir": sumadir,
+    }
+    return params
+
+
+def v__suma_renumber_fs_cargs(
+    params: VSumaRenumberFsParameters,
+    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("@SUMA_renumber_FS")
+    cargs.append(params.get("sumadir"))
+    return cargs
+
+
+def v__suma_renumber_fs_outputs(
+    params: VSumaRenumberFsParameters,
+    execution: Execution,
+) -> VSumaRenumberFsOutputs:
+    """
+    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 = VSumaRenumberFsOutputs(
+        root=execution.output_file("."),
+        ren_all=execution.output_file("*_REN_all.nii.gz"),
+        ren_gm=execution.output_file("*_REN_gm.nii.gz"),
+        ren_wmat=execution.output_file("*_REN_wmat.nii.gz"),
+        ren_csf=execution.output_file("*_REN_csf.nii.gz"),
+        ren_vent=execution.output_file("*_REN_vent.nii.gz"),
+        ren_othr=execution.output_file("*_REN_othr.nii.gz"),
+        ren_unkn=execution.output_file("*_REN_unkn.nii.gz"),
+        ren_gmrois=execution.output_file("*_REN_gmrois.nii.gz"),
+        fs_ap_wm=execution.output_file("fs_ap_wm.nii.gz"),
+        fs_ap_latvent=execution.output_file("fs_ap_latvent.nii.gz"),
+        ren_lbl_table=execution.output_file("*_REN_all.niml.lt"),
+    )
+    return ret
+
+
+def v__suma_renumber_fs_execute(
+    params: VSumaRenumberFsParameters,
+    execution: Execution,
+) -> VSumaRenumberFsOutputs:
+    """
+    This script processes FreeSurfer-generated parcellation files and produces
+    various derived datasets and segmentation maps.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VSumaRenumberFsOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__suma_renumber_fs_cargs(params, execution)
+    ret = v__suma_renumber_fs_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__suma_renumber_fs(
+    sumadir: str,
+    runner: Runner | None = None,
+) -> VSumaRenumberFsOutputs:
+    """
+    This script processes FreeSurfer-generated parcellation files and produces
+    various derived datasets and segmentation maps.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        sumadir: Path to the 'SUMA/' directory created by @SUMA_Make_Spec_FS.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VSumaRenumberFsOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__SUMA_RENUMBER_FS_METADATA)
+    params = v__suma_renumber_fs_params(
+        sumadir=sumadir,
+    )
+    return v__suma_renumber_fs_execute(params, execution)
+
+
+__all__ = [
+    "VSumaRenumberFsOutputs",
+    "VSumaRenumberFsParameters",
+    "V__SUMA_RENUMBER_FS_METADATA",
+    "v__suma_renumber_fs",
+    "v__suma_renumber_fs_params",
+]

niwrap_afni/afni/v__suma_reprefixize_spec.py

@@ -0,0 +1,221 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__SUMA_REPREFIXIZE_SPEC_METADATA = Metadata(
+    id="79a14c14207eea4a930de74235d137c817b02f37.boutiques",
+    name="@suma_reprefixize_spec",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VSumaReprefixizeSpecParameters = typing.TypedDict('VSumaReprefixizeSpecParameters', {
+    "__STYX_TYPE__": typing.Literal["@suma_reprefixize_spec"],
+    "input_file": InputPathType,
+    "prefix": str,
+    "output_dir": str,
+    "work_dir": str,
+    "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 {
+        "@suma_reprefixize_spec": v__suma_reprefixize_spec_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 {
+        "@suma_reprefixize_spec": v__suma_reprefixize_spec_outputs,
+    }.get(t)
+
+
+class VSumaReprefixizeSpecOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__suma_reprefixize_spec(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    prefixed_spec_files: OutputPathType
+    """Prefixed SUMA specification files"""
+
+
+def v__suma_reprefixize_spec_params(
+    input_file: InputPathType,
+    prefix: str,
+    output_dir: str,
+    work_dir: str,
+    no_clean: bool = False,
+) -> VSumaReprefixizeSpecParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Input SUMA specification file.
+        prefix: Prefix to be added to the file names.
+        output_dir: Output directory where the prefixed files will be saved.
+        work_dir: Working directory for temporary files.
+        no_clean: Flag to avoid cleaning temporary files.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@suma_reprefixize_spec",
+        "input_file": input_file,
+        "prefix": prefix,
+        "output_dir": output_dir,
+        "work_dir": work_dir,
+        "no_clean": no_clean,
+    }
+    return params
+
+
+def v__suma_reprefixize_spec_cargs(
+    params: VSumaReprefixizeSpecParameters,
+    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("@suma_reprefixize_spec")
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input_file"))
+    ])
+    cargs.extend([
+        "-preprefix",
+        params.get("prefix")
+    ])
+    cargs.extend([
+        "-odir",
+        params.get("output_dir")
+    ])
+    cargs.extend([
+        "-workdir",
+        params.get("work_dir")
+    ])
+    if params.get("no_clean"):
+        cargs.append("-no_clean")
+    return cargs
+
+
+def v__suma_reprefixize_spec_outputs(
+    params: VSumaReprefixizeSpecParameters,
+    execution: Execution,
+) -> VSumaReprefixizeSpecOutputs:
+    """
+    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 = VSumaReprefixizeSpecOutputs(
+        root=execution.output_file("."),
+        prefixed_spec_files=execution.output_file(params.get("output_dir") + "/*.spec"),
+    )
+    return ret
+
+
+def v__suma_reprefixize_spec_execute(
+    params: VSumaReprefixizeSpecParameters,
+    execution: Execution,
+) -> VSumaReprefixizeSpecOutputs:
+    """
+    A tool for prefixing and working with SUMA specification files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VSumaReprefixizeSpecOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__suma_reprefixize_spec_cargs(params, execution)
+    ret = v__suma_reprefixize_spec_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__suma_reprefixize_spec(
+    input_file: InputPathType,
+    prefix: str,
+    output_dir: str,
+    work_dir: str,
+    no_clean: bool = False,
+    runner: Runner | None = None,
+) -> VSumaReprefixizeSpecOutputs:
+    """
+    A tool for prefixing and working with SUMA specification files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: Input SUMA specification file.
+        prefix: Prefix to be added to the file names.
+        output_dir: Output directory where the prefixed files will be saved.
+        work_dir: Working directory for temporary files.
+        no_clean: Flag to avoid cleaning temporary files.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VSumaReprefixizeSpecOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__SUMA_REPREFIXIZE_SPEC_METADATA)
+    params = v__suma_reprefixize_spec_params(
+        input_file=input_file,
+        prefix=prefix,
+        output_dir=output_dir,
+        work_dir=work_dir,
+        no_clean=no_clean,
+    )
+    return v__suma_reprefixize_spec_execute(params, execution)
+
+
+__all__ = [
+    "VSumaReprefixizeSpecOutputs",
+    "VSumaReprefixizeSpecParameters",
+    "V__SUMA_REPREFIXIZE_SPEC_METADATA",
+    "v__suma_reprefixize_spec",
+    "v__suma_reprefixize_spec_params",
+]