niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__afni_orient2_raimap.py

@@ -0,0 +1,172 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__AFNI_ORIENT2_RAIMAP_METADATA = Metadata(
+    id="ade1258888a2ab4d7104b72e6f2921d74eaf281c.boutiques",
+    name="@AfniOrient2RAImap",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VAfniOrient2RaimapParameters = typing.TypedDict('VAfniOrient2RaimapParameters', {
+    "__STYX_TYPE__": typing.Literal["@AfniOrient2RAImap"],
+    "orientation_code": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@AfniOrient2RAImap": v__afni_orient2_raimap_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 VAfniOrient2RaimapOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__afni_orient2_raimap(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v__afni_orient2_raimap_params(
+    orientation_code: str,
+) -> VAfniOrient2RaimapParameters:
+    """
+    Build parameters.
+    
+    Args:
+        orientation_code: Orientation code (e.g., RAI, LSP).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@AfniOrient2RAImap",
+        "orientation_code": orientation_code,
+    }
+    return params
+
+
+def v__afni_orient2_raimap_cargs(
+    params: VAfniOrient2RaimapParameters,
+    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("@AfniOrient2RAImap")
+    cargs.append(params.get("orientation_code"))
+    return cargs
+
+
+def v__afni_orient2_raimap_outputs(
+    params: VAfniOrient2RaimapParameters,
+    execution: Execution,
+) -> VAfniOrient2RaimapOutputs:
+    """
+    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 = VAfniOrient2RaimapOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v__afni_orient2_raimap_execute(
+    params: VAfniOrient2RaimapParameters,
+    execution: Execution,
+) -> VAfniOrient2RaimapOutputs:
+    """
+    Returns the index map for the RAI directions.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VAfniOrient2RaimapOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__afni_orient2_raimap_cargs(params, execution)
+    ret = v__afni_orient2_raimap_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__afni_orient2_raimap(
+    orientation_code: str,
+    runner: Runner | None = None,
+) -> VAfniOrient2RaimapOutputs:
+    """
+    Returns the index map for the RAI directions.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        orientation_code: Orientation code (e.g., RAI, LSP).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VAfniOrient2RaimapOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__AFNI_ORIENT2_RAIMAP_METADATA)
+    params = v__afni_orient2_raimap_params(
+        orientation_code=orientation_code,
+    )
+    return v__afni_orient2_raimap_execute(params, execution)
+
+
+__all__ = [
+    "VAfniOrient2RaimapOutputs",
+    "VAfniOrient2RaimapParameters",
+    "V__AFNI_ORIENT2_RAIMAP_METADATA",
+    "v__afni_orient2_raimap",
+    "v__afni_orient2_raimap_params",
+]

niwrap_afni/afni/v__afni_orient_sign.py

@@ -0,0 +1,179 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__AFNI_ORIENT_SIGN_METADATA = Metadata(
+    id="15cd2787067ab0ba26eeeccbc4360543d4f091c5.boutiques",
+    name="@AfniOrientSign",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VAfniOrientSignParameters = typing.TypedDict('VAfniOrientSignParameters', {
+    "__STYX_TYPE__": typing.Literal["@AfniOrientSign"],
+    "infile": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@AfniOrientSign": v__afni_orient_sign_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 {
+        "@AfniOrientSign": v__afni_orient_sign_outputs,
+    }.get(t)
+
+
+class VAfniOrientSignOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__afni_orient_sign(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outfile: OutputPathType
+    """Output file containing the orientation signs of the dataset"""
+
+
+def v__afni_orient_sign_params(
+    infile: InputPathType,
+) -> VAfniOrientSignParameters:
+    """
+    Build parameters.
+    
+    Args:
+        infile: Input image file to determine orientation.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@AfniOrientSign",
+        "infile": infile,
+    }
+    return params
+
+
+def v__afni_orient_sign_cargs(
+    params: VAfniOrientSignParameters,
+    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("@AfniOrientSign")
+    cargs.extend([
+        "-orient",
+        execution.input_file(params.get("infile"))
+    ])
+    return cargs
+
+
+def v__afni_orient_sign_outputs(
+    params: VAfniOrientSignParameters,
+    execution: Execution,
+) -> VAfniOrientSignOutputs:
+    """
+    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 = VAfniOrientSignOutputs(
+        root=execution.output_file("."),
+        outfile=execution.output_file(pathlib.Path(params.get("infile")).name + "_orient.txt"),
+    )
+    return ret
+
+
+def v__afni_orient_sign_execute(
+    params: VAfniOrientSignParameters,
+    execution: Execution,
+) -> VAfniOrientSignOutputs:
+    """
+    A tool within the AFNI suite to determine the orientation signs of datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VAfniOrientSignOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__afni_orient_sign_cargs(params, execution)
+    ret = v__afni_orient_sign_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__afni_orient_sign(
+    infile: InputPathType,
+    runner: Runner | None = None,
+) -> VAfniOrientSignOutputs:
+    """
+    A tool within the AFNI suite to determine the orientation signs of datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        infile: Input image file to determine orientation.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VAfniOrientSignOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__AFNI_ORIENT_SIGN_METADATA)
+    params = v__afni_orient_sign_params(
+        infile=infile,
+    )
+    return v__afni_orient_sign_execute(params, execution)
+
+
+__all__ = [
+    "VAfniOrientSignOutputs",
+    "VAfniOrientSignParameters",
+    "V__AFNI_ORIENT_SIGN_METADATA",
+    "v__afni_orient_sign",
+    "v__afni_orient_sign_params",
+]

niwrap_afni/afni/v__afni_r_package_install.py

@@ -0,0 +1,241 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__AFNI_R_PACKAGE_INSTALL_METADATA = Metadata(
+    id="fbda411dd713485ac9f89d612bf7133847c9a67e.boutiques",
+    name="@afni_R_package_install",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VAfniRPackageInstallParameters = typing.TypedDict('VAfniRPackageInstallParameters', {
+    "__STYX_TYPE__": typing.Literal["@afni_R_package_install"],
+    "afni": bool,
+    "shiny": bool,
+    "bayes_view": bool,
+    "circos": bool,
+    "custom_packages": typing.NotRequired[str | None],
+    "mirror": typing.NotRequired[str | None],
+    "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_R_package_install": v__afni_r_package_install_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 {
+        "@afni_R_package_install": v__afni_r_package_install_outputs,
+    }.get(t)
+
+
+class VAfniRPackageInstallOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__afni_r_package_install(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    install_log: OutputPathType
+    """A log file listing all installed R packages."""
+
+
+def v__afni_r_package_install_params(
+    afni: bool = False,
+    shiny: bool = False,
+    bayes_view: bool = False,
+    circos: bool = False,
+    custom_packages: str | None = None,
+    mirror: str | None = None,
+    help_: bool = False,
+) -> VAfniRPackageInstallParameters:
+    """
+    Build parameters.
+    
+    Args:
+        afni: Install AFNI related R packages.
+        shiny: Install AFNI related shiny app packages.
+        bayes_view: Install R packages for bayes_view.
+        circos: Install OmicCircos for FATCAT_matplot.
+        custom_packages: Install custom R packages (space-separated list). Must\
+            start and end with double quotes.
+        mirror: Set the CRAN mirror to a custom URL.
+        help_: Show help message.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@afni_R_package_install",
+        "afni": afni,
+        "shiny": shiny,
+        "bayes_view": bayes_view,
+        "circos": circos,
+        "help": help_,
+    }
+    if custom_packages is not None:
+        params["custom_packages"] = custom_packages
+    if mirror is not None:
+        params["mirror"] = mirror
+    return params
+
+
+def v__afni_r_package_install_cargs(
+    params: VAfniRPackageInstallParameters,
+    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_R_package_install")
+    if params.get("afni"):
+        cargs.append("-afni")
+    if params.get("shiny"):
+        cargs.append("-shiny")
+    if params.get("bayes_view"):
+        cargs.append("-bayes_view")
+    if params.get("circos"):
+        cargs.append("-circos")
+    if params.get("custom_packages") is not None:
+        cargs.extend([
+            "-custom",
+            params.get("custom_packages")
+        ])
+    if params.get("mirror") is not None:
+        cargs.extend([
+            "-mirror",
+            params.get("mirror")
+        ])
+    if params.get("help"):
+        cargs.append("-help")
+    return cargs
+
+
+def v__afni_r_package_install_outputs(
+    params: VAfniRPackageInstallParameters,
+    execution: Execution,
+) -> VAfniRPackageInstallOutputs:
+    """
+    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 = VAfniRPackageInstallOutputs(
+        root=execution.output_file("."),
+        install_log=execution.output_file("R_packages_installed.txt"),
+    )
+    return ret
+
+
+def v__afni_r_package_install_execute(
+    params: VAfniRPackageInstallParameters,
+    execution: Execution,
+) -> VAfniRPackageInstallOutputs:
+    """
+    Helper script to install R packages for various afni-ish purposes.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VAfniRPackageInstallOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__afni_r_package_install_cargs(params, execution)
+    ret = v__afni_r_package_install_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__afni_r_package_install(
+    afni: bool = False,
+    shiny: bool = False,
+    bayes_view: bool = False,
+    circos: bool = False,
+    custom_packages: str | None = None,
+    mirror: str | None = None,
+    help_: bool = False,
+    runner: Runner | None = None,
+) -> VAfniRPackageInstallOutputs:
+    """
+    Helper script to install R packages for various afni-ish purposes.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        afni: Install AFNI related R packages.
+        shiny: Install AFNI related shiny app packages.
+        bayes_view: Install R packages for bayes_view.
+        circos: Install OmicCircos for FATCAT_matplot.
+        custom_packages: Install custom R packages (space-separated list). Must\
+            start and end with double quotes.
+        mirror: Set the CRAN mirror to a custom URL.
+        help_: Show help message.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VAfniRPackageInstallOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__AFNI_R_PACKAGE_INSTALL_METADATA)
+    params = v__afni_r_package_install_params(
+        afni=afni,
+        shiny=shiny,
+        bayes_view=bayes_view,
+        circos=circos,
+        custom_packages=custom_packages,
+        mirror=mirror,
+        help_=help_,
+    )
+    return v__afni_r_package_install_execute(params, execution)
+
+
+__all__ = [
+    "VAfniRPackageInstallOutputs",
+    "VAfniRPackageInstallParameters",
+    "V__AFNI_R_PACKAGE_INSTALL_METADATA",
+    "v__afni_r_package_install",
+    "v__afni_r_package_install_params",
+]