niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__move_to_series_dirs.py

@@ -0,0 +1,255 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__MOVE_TO_SERIES_DIRS_METADATA = Metadata(
+    id="43e65ff4ccb7c662ae1bcaef0b7fb14c99b76809.boutiques",
+    name="@move.to.series.dirs",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VMoveToSeriesDirsParameters = typing.TypedDict('VMoveToSeriesDirsParameters', {
+    "__STYX_TYPE__": typing.Literal["@move.to.series.dirs"],
+    "action": typing.NotRequired[typing.Literal["copy", "move"] | None],
+    "dprefix": typing.NotRequired[str | None],
+    "tag": typing.NotRequired[str | None],
+    "test": bool,
+    "help": bool,
+    "hist": bool,
+    "ver": bool,
+    "dicom_files": list[InputPathType],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@move.to.series.dirs": v__move_to_series_dirs_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 VMoveToSeriesDirsOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__move_to_series_dirs(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v__move_to_series_dirs_params(
+    dicom_files: list[InputPathType],
+    action: typing.Literal["copy", "move"] | None = None,
+    dprefix: str | None = None,
+    tag: str | None = None,
+    test: bool = False,
+    help_: bool = False,
+    hist: bool = False,
+    ver: bool = False,
+) -> VMoveToSeriesDirsParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dicom_files: Specify input DICOM files (e.g., IMG*).
+        action: Specify action to perform: copy or move. Default is copy.
+        dprefix: Specify directory root for output series directories. Default\
+            is current directory.
+        tag: Specify the DICOM tag to use for partitioning. Default is\
+            0020,0011 (REL Series Number).
+        test: Run in test mode, only show what would be done without actually\
+            moving any files.
+        help_: Show help information.
+        hist: Show modification history.
+        ver: Show version number.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@move.to.series.dirs",
+        "test": test,
+        "help": help_,
+        "hist": hist,
+        "ver": ver,
+        "dicom_files": dicom_files,
+    }
+    if action is not None:
+        params["action"] = action
+    if dprefix is not None:
+        params["dprefix"] = dprefix
+    if tag is not None:
+        params["tag"] = tag
+    return params
+
+
+def v__move_to_series_dirs_cargs(
+    params: VMoveToSeriesDirsParameters,
+    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("@move.to.series.dirs")
+    if params.get("action") is not None:
+        cargs.extend([
+            "-action",
+            params.get("action")
+        ])
+    if params.get("dprefix") is not None:
+        cargs.extend([
+            "-dprefix",
+            params.get("dprefix")
+        ])
+    if params.get("tag") is not None:
+        cargs.extend([
+            "-tag",
+            params.get("tag")
+        ])
+    if params.get("test"):
+        cargs.append("-test")
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("hist"):
+        cargs.append("-hist")
+    if params.get("ver"):
+        cargs.append("-ver")
+    cargs.extend([execution.input_file(f) for f in params.get("dicom_files")])
+    return cargs
+
+
+def v__move_to_series_dirs_outputs(
+    params: VMoveToSeriesDirsParameters,
+    execution: Execution,
+) -> VMoveToSeriesDirsOutputs:
+    """
+    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 = VMoveToSeriesDirsOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v__move_to_series_dirs_execute(
+    params: VMoveToSeriesDirsParameters,
+    execution: Execution,
+) -> VMoveToSeriesDirsOutputs:
+    """
+    Partition DICOM files into series directories by copying or moving them to new
+    series directories.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VMoveToSeriesDirsOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__move_to_series_dirs_cargs(params, execution)
+    ret = v__move_to_series_dirs_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__move_to_series_dirs(
+    dicom_files: list[InputPathType],
+    action: typing.Literal["copy", "move"] | None = None,
+    dprefix: str | None = None,
+    tag: str | None = None,
+    test: bool = False,
+    help_: bool = False,
+    hist: bool = False,
+    ver: bool = False,
+    runner: Runner | None = None,
+) -> VMoveToSeriesDirsOutputs:
+    """
+    Partition DICOM files into series directories by copying or moving them to new
+    series directories.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dicom_files: Specify input DICOM files (e.g., IMG*).
+        action: Specify action to perform: copy or move. Default is copy.
+        dprefix: Specify directory root for output series directories. Default\
+            is current directory.
+        tag: Specify the DICOM tag to use for partitioning. Default is\
+            0020,0011 (REL Series Number).
+        test: Run in test mode, only show what would be done without actually\
+            moving any files.
+        help_: Show help information.
+        hist: Show modification history.
+        ver: Show version number.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VMoveToSeriesDirsOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__MOVE_TO_SERIES_DIRS_METADATA)
+    params = v__move_to_series_dirs_params(
+        action=action,
+        dprefix=dprefix,
+        tag=tag,
+        test=test,
+        help_=help_,
+        hist=hist,
+        ver=ver,
+        dicom_files=dicom_files,
+    )
+    return v__move_to_series_dirs_execute(params, execution)
+
+
+__all__ = [
+    "VMoveToSeriesDirsOutputs",
+    "VMoveToSeriesDirsParameters",
+    "V__MOVE_TO_SERIES_DIRS_METADATA",
+    "v__move_to_series_dirs",
+    "v__move_to_series_dirs_params",
+]

niwrap_afni/afni/v__no_ext.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__NO_EXT_METADATA = Metadata(
+    id="e146bd1bed02e711ff41cccbd0a20832085fd087.boutiques",
+    name="@NoExt",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VNoExtParameters = typing.TypedDict('VNoExtParameters', {
+    "__STYX_TYPE__": typing.Literal["@NoExt"],
+    "extensions": typing.NotRequired[list[str] | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@NoExt": v__no_ext_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 {
+        "@NoExt": v__no_ext_outputs,
+    }.get(t)
+
+
+class VNoExtOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__no_ext(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outfile: OutputPathType
+    """File name with specified extensions removed"""
+
+
+def v__no_ext_params(
+    extensions: list[str] | None = None,
+) -> VNoExtParameters:
+    """
+    Build parameters.
+    
+    Args:
+        extensions: Extensions to be removed.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@NoExt",
+    }
+    if extensions is not None:
+        params["extensions"] = extensions
+    return params
+
+
+def v__no_ext_cargs(
+    params: VNoExtParameters,
+    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("@NoExt")
+    cargs.append("<inputfile>")
+    if params.get("extensions") is not None:
+        cargs.extend(params.get("extensions"))
+    return cargs
+
+
+def v__no_ext_outputs(
+    params: VNoExtParameters,
+    execution: Execution,
+) -> VNoExtOutputs:
+    """
+    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 = VNoExtOutputs(
+        root=execution.output_file("."),
+        outfile=execution.output_file("output"),
+    )
+    return ret
+
+
+def v__no_ext_execute(
+    params: VNoExtParameters,
+    execution: Execution,
+) -> VNoExtOutputs:
+    """
+    Tool for removing specified extensions from filenames.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VNoExtOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__no_ext_cargs(params, execution)
+    ret = v__no_ext_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__no_ext(
+    extensions: list[str] | None = None,
+    runner: Runner | None = None,
+) -> VNoExtOutputs:
+    """
+    Tool for removing specified extensions from filenames.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        extensions: Extensions to be removed.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VNoExtOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__NO_EXT_METADATA)
+    params = v__no_ext_params(
+        extensions=extensions,
+    )
+    return v__no_ext_execute(params, execution)
+
+
+__all__ = [
+    "VNoExtOutputs",
+    "VNoExtParameters",
+    "V__NO_EXT_METADATA",
+    "v__no_ext",
+    "v__no_ext_params",
+]

niwrap_afni/afni/v__no_pound.py

@@ -0,0 +1,174 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__NO_POUND_METADATA = Metadata(
+    id="27d35f86a77d04034e08074da72efd10ccb9fa51.boutiques",
+    name="@NoPound",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VNoPoundParameters = typing.TypedDict('VNoPoundParameters', {
+    "__STYX_TYPE__": typing.Literal["@NoPound"],
+    "afni_files": 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 {
+        "@NoPound": v__no_pound_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 VNoPoundOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__no_pound(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v__no_pound_params(
+    afni_files: list[str],
+) -> VNoPoundParameters:
+    """
+    Build parameters.
+    
+    Args:
+        afni_files: List of AFNI files where # characters should be replaced\
+            with -.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@NoPound",
+        "afni_files": afni_files,
+    }
+    return params
+
+
+def v__no_pound_cargs(
+    params: VNoPoundParameters,
+    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("@NoPound")
+    cargs.extend(params.get("afni_files"))
+    return cargs
+
+
+def v__no_pound_outputs(
+    params: VNoPoundParameters,
+    execution: Execution,
+) -> VNoPoundOutputs:
+    """
+    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 = VNoPoundOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v__no_pound_execute(
+    params: VNoPoundParameters,
+    execution: Execution,
+) -> VNoPoundOutputs:
+    """
+    Replaces all # characters in AFNI filenames with a -.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VNoPoundOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__no_pound_cargs(params, execution)
+    ret = v__no_pound_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__no_pound(
+    afni_files: list[str],
+    runner: Runner | None = None,
+) -> VNoPoundOutputs:
+    """
+    Replaces all # characters in AFNI filenames with a -.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        afni_files: List of AFNI files where # characters should be replaced\
+            with -.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VNoPoundOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__NO_POUND_METADATA)
+    params = v__no_pound_params(
+        afni_files=afni_files,
+    )
+    return v__no_pound_execute(params, execution)
+
+
+__all__ = [
+    "VNoPoundOutputs",
+    "VNoPoundParameters",
+    "V__NO_POUND_METADATA",
+    "v__no_pound",
+    "v__no_pound_params",
+]