niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/build_afni_py.py

@@ -0,0 +1,330 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+BUILD_AFNI_PY_METADATA = Metadata(
+    id="8b01bbfc26acb4a73b16110f6849bc381629f972.boutiques",
+    name="build_afni.py",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+BuildAfniPyParameters = typing.TypedDict('BuildAfniPyParameters', {
+    "__STYX_TYPE__": typing.Literal["build_afni.py"],
+    "build_root": str,
+    "clean_root": typing.NotRequired[str | None],
+    "git_branch": typing.NotRequired[str | None],
+    "git_tag": typing.NotRequired[str | None],
+    "git_update": typing.NotRequired[str | None],
+    "make_target": typing.NotRequired[str | None],
+    "makefile": typing.NotRequired[str | None],
+    "package": typing.NotRequired[str | None],
+    "prep_only": bool,
+    "run_cmake": typing.NotRequired[str | None],
+    "run_make": typing.NotRequired[str | None],
+    "verbose_level": typing.NotRequired[float | None],
+    "version": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "build_afni.py": build_afni_py_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 {
+        "build_afni.py": build_afni_py_outputs,
+    }.get(t)
+
+
+class BuildAfniPyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `build_afni_py(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    command_history_file: OutputPathType
+    """Command history file"""
+    screen_output_history: OutputPathType
+    """Screen output history file"""
+
+
+def build_afni_py_params(
+    build_root: str,
+    clean_root: str | None = None,
+    git_branch: str | None = None,
+    git_tag: str | None = None,
+    git_update: str | None = None,
+    make_target: str | None = None,
+    makefile: str | None = None,
+    package: str | None = None,
+    prep_only: bool = False,
+    run_cmake: str | None = None,
+    run_make: str | None = None,
+    verbose_level: float | None = None,
+    version: bool = False,
+) -> BuildAfniPyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        build_root: Root directory to use for git and building.
+        clean_root: Specify whether to clean up the build_root. Default is yes.
+        git_branch: Specify a branch to checkout in git. Default is master.
+        git_tag: Specify a tag to checkout in git. Default is LAST_TAG.
+        git_update: Specify whether to update git repo. Default is yes.
+        make_target: Specify target for make command. Default is itall.
+        makefile: Specify an alternate Makefile to build from.
+        package: Specify the desired package to build.
+        prep_only: Prepare to but do not run (c)make.
+        run_cmake: Choose whether to run a cmake build. Default is no.
+        run_make: Choose whether to run a make build. Default is yes.
+        verbose_level: Set the verbosity level. Default is 1.
+        version: Show the current version.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "build_afni.py",
+        "build_root": build_root,
+        "prep_only": prep_only,
+        "version": version,
+    }
+    if clean_root is not None:
+        params["clean_root"] = clean_root
+    if git_branch is not None:
+        params["git_branch"] = git_branch
+    if git_tag is not None:
+        params["git_tag"] = git_tag
+    if git_update is not None:
+        params["git_update"] = git_update
+    if make_target is not None:
+        params["make_target"] = make_target
+    if makefile is not None:
+        params["makefile"] = makefile
+    if package is not None:
+        params["package"] = package
+    if run_cmake is not None:
+        params["run_cmake"] = run_cmake
+    if run_make is not None:
+        params["run_make"] = run_make
+    if verbose_level is not None:
+        params["verbose_level"] = verbose_level
+    return params
+
+
+def build_afni_py_cargs(
+    params: BuildAfniPyParameters,
+    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("build_afni.py")
+    cargs.extend([
+        "-build_root",
+        params.get("build_root")
+    ])
+    if params.get("clean_root") is not None:
+        cargs.extend([
+            "-clean_root",
+            params.get("clean_root")
+        ])
+    if params.get("git_branch") is not None:
+        cargs.extend([
+            "-git_branch",
+            params.get("git_branch")
+        ])
+    if params.get("git_tag") is not None:
+        cargs.extend([
+            "-git_tag",
+            params.get("git_tag")
+        ])
+    if params.get("git_update") is not None:
+        cargs.extend([
+            "-git_update",
+            params.get("git_update")
+        ])
+    if params.get("make_target") is not None:
+        cargs.extend([
+            "-make_target",
+            params.get("make_target")
+        ])
+    if params.get("makefile") is not None:
+        cargs.extend([
+            "-makefile",
+            params.get("makefile")
+        ])
+    if params.get("package") is not None:
+        cargs.extend([
+            "-package",
+            params.get("package")
+        ])
+    if params.get("prep_only"):
+        cargs.append("-prep_only")
+    if params.get("run_cmake") is not None:
+        cargs.extend([
+            "-run_cmake",
+            params.get("run_cmake")
+        ])
+    if params.get("run_make") is not None:
+        cargs.extend([
+            "-run_make",
+            params.get("run_make")
+        ])
+    if params.get("verbose_level") is not None:
+        cargs.extend([
+            "-verb",
+            str(params.get("verbose_level"))
+        ])
+    if params.get("version"):
+        cargs.append("-ver")
+    return cargs
+
+
+def build_afni_py_outputs(
+    params: BuildAfniPyParameters,
+    execution: Execution,
+) -> BuildAfniPyOutputs:
+    """
+    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 = BuildAfniPyOutputs(
+        root=execution.output_file("."),
+        command_history_file=execution.output_file(params.get("build_root") + "/hist_commands.txt"),
+        screen_output_history=execution.output_file(params.get("build_root") + "/screen_output_history.txt"),
+    )
+    return ret
+
+
+def build_afni_py_execute(
+    params: BuildAfniPyParameters,
+    execution: Execution,
+) -> BuildAfniPyOutputs:
+    """
+    Compile an AFNI package from the git repository.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `BuildAfniPyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = build_afni_py_cargs(params, execution)
+    ret = build_afni_py_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def build_afni_py(
+    build_root: str,
+    clean_root: str | None = None,
+    git_branch: str | None = None,
+    git_tag: str | None = None,
+    git_update: str | None = None,
+    make_target: str | None = None,
+    makefile: str | None = None,
+    package: str | None = None,
+    prep_only: bool = False,
+    run_cmake: str | None = None,
+    run_make: str | None = None,
+    verbose_level: float | None = None,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> BuildAfniPyOutputs:
+    """
+    Compile an AFNI package from the git repository.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        build_root: Root directory to use for git and building.
+        clean_root: Specify whether to clean up the build_root. Default is yes.
+        git_branch: Specify a branch to checkout in git. Default is master.
+        git_tag: Specify a tag to checkout in git. Default is LAST_TAG.
+        git_update: Specify whether to update git repo. Default is yes.
+        make_target: Specify target for make command. Default is itall.
+        makefile: Specify an alternate Makefile to build from.
+        package: Specify the desired package to build.
+        prep_only: Prepare to but do not run (c)make.
+        run_cmake: Choose whether to run a cmake build. Default is no.
+        run_make: Choose whether to run a make build. Default is yes.
+        verbose_level: Set the verbosity level. Default is 1.
+        version: Show the current version.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `BuildAfniPyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(BUILD_AFNI_PY_METADATA)
+    params = build_afni_py_params(
+        build_root=build_root,
+        clean_root=clean_root,
+        git_branch=git_branch,
+        git_tag=git_tag,
+        git_update=git_update,
+        make_target=make_target,
+        makefile=makefile,
+        package=package,
+        prep_only=prep_only,
+        run_cmake=run_cmake,
+        run_make=run_make,
+        verbose_level=verbose_level,
+        version=version,
+    )
+    return build_afni_py_execute(params, execution)
+
+
+__all__ = [
+    "BUILD_AFNI_PY_METADATA",
+    "BuildAfniPyOutputs",
+    "BuildAfniPyParameters",
+    "build_afni_py",
+    "build_afni_py_params",
+]

niwrap_afni/afni/cat_matvec.py

@@ -0,0 +1,185 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+CAT_MATVEC_METADATA = Metadata(
+    id="ea044673965ec2f3a89f325814e9677a680c6cec.boutiques",
+    name="cat_matvec",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+CatMatvecParameters = typing.TypedDict('CatMatvecParameters', {
+    "__STYX_TYPE__": typing.Literal["cat_matvec"],
+    "four_by_four_format": bool,
+    "matvec_spec": list[str],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "cat_matvec": cat_matvec_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 CatMatvecOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `cat_matvec(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def cat_matvec_params(
+    matvec_spec: list[str],
+    four_by_four_format: bool = False,
+) -> CatMatvecParameters:
+    """
+    Build parameters.
+    
+    Args:
+        matvec_spec: Specifies the matrix transformation. Can take forms\
+            described in the documentation.
+        four_by_four_format: Output matrix in augmented form (last row is 0 0 0\
+            1). This option does not work with -MATRIX or -ONELINE.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "cat_matvec",
+        "four_by_four_format": four_by_four_format,
+        "matvec_spec": matvec_spec,
+    }
+    return params
+
+
+def cat_matvec_cargs(
+    params: CatMatvecParameters,
+    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("cat_matvec")
+    if params.get("four_by_four_format"):
+        cargs.append("-4x4")
+    cargs.extend(params.get("matvec_spec"))
+    return cargs
+
+
+def cat_matvec_outputs(
+    params: CatMatvecParameters,
+    execution: Execution,
+) -> CatMatvecOutputs:
+    """
+    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 = CatMatvecOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def cat_matvec_execute(
+    params: CatMatvecParameters,
+    execution: Execution,
+) -> CatMatvecOutputs:
+    """
+    Catenates 3D rotation+shift matrix+vector transformations.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `CatMatvecOutputs`).
+    """
+    params = execution.params(params)
+    cargs = cat_matvec_cargs(params, execution)
+    ret = cat_matvec_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def cat_matvec(
+    matvec_spec: list[str],
+    four_by_four_format: bool = False,
+    runner: Runner | None = None,
+) -> CatMatvecOutputs:
+    """
+    Catenates 3D rotation+shift matrix+vector transformations.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        matvec_spec: Specifies the matrix transformation. Can take forms\
+            described in the documentation.
+        four_by_four_format: Output matrix in augmented form (last row is 0 0 0\
+            1). This option does not work with -MATRIX or -ONELINE.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `CatMatvecOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(CAT_MATVEC_METADATA)
+    params = cat_matvec_params(
+        four_by_four_format=four_by_four_format,
+        matvec_spec=matvec_spec,
+    )
+    return cat_matvec_execute(params, execution)
+
+
+__all__ = [
+    "CAT_MATVEC_METADATA",
+    "CatMatvecOutputs",
+    "CatMatvecParameters",
+    "cat_matvec",
+    "cat_matvec_params",
+]

niwrap_afni/afni/ccalc.py

@@ -0,0 +1,192 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+CCALC_METADATA = Metadata(
+    id="858c935b6b57b9962c3e64fe8202799fde8e6c22.boutiques",
+    name="ccalc",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+CcalcParameters = typing.TypedDict('CcalcParameters', {
+    "__STYX_TYPE__": typing.Literal["ccalc"],
+    "format": typing.NotRequired[str | None],
+    "expr": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "ccalc": ccalc_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 CcalcOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `ccalc(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def ccalc_params(
+    expr: str,
+    format_: str | None = None,
+) -> CcalcParameters:
+    """
+    Build parameters.
+    
+    Args:
+        expr: Evaluate an expression specified on command line, return answer\
+            and quit.
+        format_: Format output in a nice form. Choose from 'double', 'nice',\
+            'int', 'rint', 'cint', 'fint', or custom format string (e.g., %n.mf).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "ccalc",
+        "expr": expr,
+    }
+    if format_ is not None:
+        params["format"] = format_
+    return params
+
+
+def ccalc_cargs(
+    params: CcalcParameters,
+    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("ccalc")
+    if params.get("format") is not None:
+        cargs.extend([
+            "-form",
+            params.get("format")
+        ])
+    cargs.extend([
+        "-eval",
+        params.get("expr")
+    ])
+    return cargs
+
+
+def ccalc_outputs(
+    params: CcalcParameters,
+    execution: Execution,
+) -> CcalcOutputs:
+    """
+    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 = CcalcOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def ccalc_execute(
+    params: CcalcParameters,
+    execution: Execution,
+) -> CcalcOutputs:
+    """
+    Command line calculator with formatted output options.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `CcalcOutputs`).
+    """
+    params = execution.params(params)
+    cargs = ccalc_cargs(params, execution)
+    ret = ccalc_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def ccalc(
+    expr: str,
+    format_: str | None = None,
+    runner: Runner | None = None,
+) -> CcalcOutputs:
+    """
+    Command line calculator with formatted output options.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        expr: Evaluate an expression specified on command line, return answer\
+            and quit.
+        format_: Format output in a nice form. Choose from 'double', 'nice',\
+            'int', 'rint', 'cint', 'fint', or custom format string (e.g., %n.mf).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `CcalcOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(CCALC_METADATA)
+    params = ccalc_params(
+        format_=format_,
+        expr=expr,
+    )
+    return ccalc_execute(params, execution)
+
+
+__all__ = [
+    "CCALC_METADATA",
+    "CcalcOutputs",
+    "CcalcParameters",
+    "ccalc",
+    "ccalc_params",
+]