niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/unpackimadir2.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 *
+
+UNPACKIMADIR2_METADATA = Metadata(
+    id="bdf6eb9c77635e9326080586e7654d60496c26b4.boutiques",
+    name="unpackimadir2",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+Unpackimadir2Parameters = typing.TypedDict('Unpackimadir2Parameters', {
+    "__STYX_TYPE__": typing.Literal["unpackimadir2"],
+    "directory": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "unpackimadir2": unpackimadir2_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 Unpackimadir2Outputs(typing.NamedTuple):
+    """
+    Output object returned when calling `unpackimadir2(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def unpackimadir2_params(
+    directory: InputPathType,
+) -> Unpackimadir2Parameters:
+    """
+    Build parameters.
+    
+    Args:
+        directory: Image directory to unpack.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "unpackimadir2",
+        "directory": directory,
+    }
+    return params
+
+
+def unpackimadir2_cargs(
+    params: Unpackimadir2Parameters,
+    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("unpackimadir2")
+    cargs.append(execution.input_file(params.get("directory")))
+    return cargs
+
+
+def unpackimadir2_outputs(
+    params: Unpackimadir2Parameters,
+    execution: Execution,
+) -> Unpackimadir2Outputs:
+    """
+    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 = Unpackimadir2Outputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def unpackimadir2_execute(
+    params: Unpackimadir2Parameters,
+    execution: Execution,
+) -> Unpackimadir2Outputs:
+    """
+    Tool to unpack image directories, from FreeSurfer suite.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `Unpackimadir2Outputs`).
+    """
+    params = execution.params(params)
+    cargs = unpackimadir2_cargs(params, execution)
+    ret = unpackimadir2_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def unpackimadir2(
+    directory: InputPathType,
+    runner: Runner | None = None,
+) -> Unpackimadir2Outputs:
+    """
+    Tool to unpack image directories, from FreeSurfer suite.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        directory: Image directory to unpack.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `Unpackimadir2Outputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(UNPACKIMADIR2_METADATA)
+    params = unpackimadir2_params(
+        directory=directory,
+    )
+    return unpackimadir2_execute(params, execution)
+
+
+__all__ = [
+    "UNPACKIMADIR2_METADATA",
+    "Unpackimadir2Outputs",
+    "Unpackimadir2Parameters",
+    "unpackimadir2",
+    "unpackimadir2_params",
+]

niwrap_freesurfer/freesurfer/unpackmincdir.py

@@ -0,0 +1,260 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+UNPACKMINCDIR_METADATA = Metadata(
+    id="665926cbe3f5b98854ac7511f567b75246bc682e.boutiques",
+    name="unpackmincdir",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+UnpackmincdirParameters = typing.TypedDict('UnpackmincdirParameters', {
+    "__STYX_TYPE__": typing.Literal["unpackmincdir"],
+    "source_directory": str,
+    "target_directory": str,
+    "scan_sequence_info": typing.NotRequired[str | None],
+    "functional_sequence": typing.NotRequired[str | None],
+    "functional_subdirectory": typing.NotRequired[str | None],
+    "minc_only": bool,
+    "no_copy": bool,
+    "umask": typing.NotRequired[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 {
+        "unpackmincdir": unpackmincdir_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 UnpackmincdirOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `unpackmincdir(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def unpackmincdir_params(
+    source_directory: str,
+    target_directory: str,
+    scan_sequence_info: str | None = None,
+    functional_sequence: str | None = None,
+    functional_subdirectory: str | None = None,
+    minc_only: bool = False,
+    no_copy: bool = False,
+    umask: str | None = None,
+) -> UnpackmincdirParameters:
+    """
+    Build parameters.
+    
+    Args:
+        source_directory: Source directory containing the MINC files.
+        target_directory: Target directory to unpack the contents to.
+        scan_sequence_info: Scan sequence directives file, e.g.,\
+            freesurfer_alpha/scanseq.info.
+        functional_sequence: Use seqname for functionals (example:\
+            ep2d_fid_ts_20b2604).
+        functional_subdirectory: Functional subdirectory, e.g., bold.
+        minc_only: Do not unpack into bshorts.
+        no_copy: Create directories but do not copy/convert data.
+        umask: Unix file permission mask (default: 22).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "unpackmincdir",
+        "source_directory": source_directory,
+        "target_directory": target_directory,
+        "minc_only": minc_only,
+        "no_copy": no_copy,
+    }
+    if scan_sequence_info is not None:
+        params["scan_sequence_info"] = scan_sequence_info
+    if functional_sequence is not None:
+        params["functional_sequence"] = functional_sequence
+    if functional_subdirectory is not None:
+        params["functional_subdirectory"] = functional_subdirectory
+    if umask is not None:
+        params["umask"] = umask
+    return params
+
+
+def unpackmincdir_cargs(
+    params: UnpackmincdirParameters,
+    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("unpackmincdir")
+    cargs.extend([
+        "-src",
+        params.get("source_directory")
+    ])
+    cargs.extend([
+        "-targ",
+        params.get("target_directory")
+    ])
+    if params.get("scan_sequence_info") is not None:
+        cargs.extend([
+            "-scanseqinfo",
+            params.get("scan_sequence_info")
+        ])
+    if params.get("functional_sequence") is not None:
+        cargs.extend([
+            "-funcseq",
+            params.get("functional_sequence")
+        ])
+    if params.get("functional_subdirectory") is not None:
+        cargs.extend([
+            "-fsd",
+            params.get("functional_subdirectory")
+        ])
+    if params.get("minc_only"):
+        cargs.append("-minconly")
+    if params.get("no_copy"):
+        cargs.append("-nocopy")
+    if params.get("umask") is not None:
+        cargs.extend([
+            "-umask",
+            params.get("umask")
+        ])
+    return cargs
+
+
+def unpackmincdir_outputs(
+    params: UnpackmincdirParameters,
+    execution: Execution,
+) -> UnpackmincdirOutputs:
+    """
+    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 = UnpackmincdirOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def unpackmincdir_execute(
+    params: UnpackmincdirParameters,
+    execution: Execution,
+) -> UnpackmincdirOutputs:
+    """
+    Tool for unpacking directories with MINC files.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `UnpackmincdirOutputs`).
+    """
+    params = execution.params(params)
+    cargs = unpackmincdir_cargs(params, execution)
+    ret = unpackmincdir_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def unpackmincdir(
+    source_directory: str,
+    target_directory: str,
+    scan_sequence_info: str | None = None,
+    functional_sequence: str | None = None,
+    functional_subdirectory: str | None = None,
+    minc_only: bool = False,
+    no_copy: bool = False,
+    umask: str | None = None,
+    runner: Runner | None = None,
+) -> UnpackmincdirOutputs:
+    """
+    Tool for unpacking directories with MINC files.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        source_directory: Source directory containing the MINC files.
+        target_directory: Target directory to unpack the contents to.
+        scan_sequence_info: Scan sequence directives file, e.g.,\
+            freesurfer_alpha/scanseq.info.
+        functional_sequence: Use seqname for functionals (example:\
+            ep2d_fid_ts_20b2604).
+        functional_subdirectory: Functional subdirectory, e.g., bold.
+        minc_only: Do not unpack into bshorts.
+        no_copy: Create directories but do not copy/convert data.
+        umask: Unix file permission mask (default: 22).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `UnpackmincdirOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(UNPACKMINCDIR_METADATA)
+    params = unpackmincdir_params(
+        source_directory=source_directory,
+        target_directory=target_directory,
+        scan_sequence_info=scan_sequence_info,
+        functional_sequence=functional_sequence,
+        functional_subdirectory=functional_subdirectory,
+        minc_only=minc_only,
+        no_copy=no_copy,
+        umask=umask,
+    )
+    return unpackmincdir_execute(params, execution)
+
+
+__all__ = [
+    "UNPACKMINCDIR_METADATA",
+    "UnpackmincdirOutputs",
+    "UnpackmincdirParameters",
+    "unpackmincdir",
+    "unpackmincdir_params",
+]

niwrap_freesurfer/freesurfer/unpacksdcmdir.py

@@ -0,0 +1,190 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+UNPACKSDCMDIR_METADATA = Metadata(
+    id="874ca0580e83acbaad099d815a81e39d50b1ac26.boutiques",
+    name="unpacksdcmdir",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+UnpacksdcmdirParameters = typing.TypedDict('UnpacksdcmdirParameters', {
+    "__STYX_TYPE__": typing.Literal["unpacksdcmdir"],
+    "input_directory": str,
+    "output_directory": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "unpacksdcmdir": unpacksdcmdir_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 {
+        "unpacksdcmdir": unpacksdcmdir_outputs,
+    }.get(t)
+
+
+class UnpacksdcmdirOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `unpacksdcmdir(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    unpacked_data: OutputPathType
+    """The directory that will contain the unpacked data."""
+
+
+def unpacksdcmdir_params(
+    input_directory: str,
+    output_directory: str,
+) -> UnpacksdcmdirParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_directory: The directory containing SD card data to be unpacked.
+        output_directory: The output directory where unpacked data will be\
+            stored.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "unpacksdcmdir",
+        "input_directory": input_directory,
+        "output_directory": output_directory,
+    }
+    return params
+
+
+def unpacksdcmdir_cargs(
+    params: UnpacksdcmdirParameters,
+    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("unpacksdcmdir")
+    cargs.append(params.get("input_directory"))
+    cargs.append(params.get("output_directory"))
+    return cargs
+
+
+def unpacksdcmdir_outputs(
+    params: UnpacksdcmdirParameters,
+    execution: Execution,
+) -> UnpacksdcmdirOutputs:
+    """
+    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 = UnpacksdcmdirOutputs(
+        root=execution.output_file("."),
+        unpacked_data=execution.output_file(params.get("output_directory") + "/unpacked_data"),
+    )
+    return ret
+
+
+def unpacksdcmdir_execute(
+    params: UnpacksdcmdirParameters,
+    execution: Execution,
+) -> UnpacksdcmdirOutputs:
+    """
+    A tool for unpacking SD card directories, typically used in neuroimaging
+    workflows. It seems to have a dependency on Tcl, as indicated by the error
+    messages.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `UnpacksdcmdirOutputs`).
+    """
+    params = execution.params(params)
+    cargs = unpacksdcmdir_cargs(params, execution)
+    ret = unpacksdcmdir_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def unpacksdcmdir(
+    input_directory: str,
+    output_directory: str,
+    runner: Runner | None = None,
+) -> UnpacksdcmdirOutputs:
+    """
+    A tool for unpacking SD card directories, typically used in neuroimaging
+    workflows. It seems to have a dependency on Tcl, as indicated by the error
+    messages.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input_directory: The directory containing SD card data to be unpacked.
+        output_directory: The output directory where unpacked data will be\
+            stored.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `UnpacksdcmdirOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(UNPACKSDCMDIR_METADATA)
+    params = unpacksdcmdir_params(
+        input_directory=input_directory,
+        output_directory=output_directory,
+    )
+    return unpacksdcmdir_execute(params, execution)
+
+
+__all__ = [
+    "UNPACKSDCMDIR_METADATA",
+    "UnpacksdcmdirOutputs",
+    "UnpacksdcmdirParameters",
+    "unpacksdcmdir",
+    "unpacksdcmdir_params",
+]