niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_afnito_nifti.py

@@ -0,0 +1,245 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_AFNITO_NIFTI_METADATA = Metadata(
+    id="c2219650fbe1d83f01eda91dff81cc7a82f46430.boutiques",
+    name="3dAFNItoNIFTI",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dAfnitoNiftiParameters = typing.TypedDict('V3dAfnitoNiftiParameters', {
+    "__STYX_TYPE__": typing.Literal["3dAFNItoNIFTI"],
+    "input_dataset": InputPathType,
+    "prefix": typing.NotRequired[str | None],
+    "verbose": bool,
+    "force_float": bool,
+    "pure": bool,
+    "denote": bool,
+    "oldid": bool,
+    "newid": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dAFNItoNIFTI": v_3d_afnito_nifti_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 {
+        "3dAFNItoNIFTI": v_3d_afnito_nifti_outputs,
+    }.get(t)
+
+
+class V3dAfnitoNiftiOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_afnito_nifti(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_nifti: OutputPathType | None
+    """Output NIfTI file."""
+
+
+def v_3d_afnito_nifti_params(
+    input_dataset: InputPathType,
+    prefix: str | None = None,
+    verbose: bool = False,
+    force_float: bool = False,
+    pure: bool = False,
+    denote: bool = False,
+    oldid: bool = False,
+    newid: bool = False,
+) -> V3dAfnitoNiftiParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_dataset: Input AFNI dataset.
+        prefix: Output NIfTI file prefix.
+        verbose: Print progress messages (increases verbosity if repeated).
+        force_float: Force the output dataset to be 32-bit floats.
+        pure: Do not write an AFNI extension field into the output file.
+        denote: Remove text notes from AFNI extension field that might contain\
+            identifying information.
+        oldid: Retain the input dataset's AFNI ID code.
+        newid: Assign a new AFNI ID code to the dataset (default action).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dAFNItoNIFTI",
+        "input_dataset": input_dataset,
+        "verbose": verbose,
+        "force_float": force_float,
+        "pure": pure,
+        "denote": denote,
+        "oldid": oldid,
+        "newid": newid,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    return params
+
+
+def v_3d_afnito_nifti_cargs(
+    params: V3dAfnitoNiftiParameters,
+    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("3dAFNItoNIFTI")
+    cargs.append(execution.input_file(params.get("input_dataset")))
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("verbose"):
+        cargs.append("-verb")
+    if params.get("force_float"):
+        cargs.append("-float")
+    if params.get("pure"):
+        cargs.append("-pure")
+    if params.get("denote"):
+        cargs.append("-denote")
+    if params.get("oldid"):
+        cargs.append("-oldid")
+    if params.get("newid"):
+        cargs.append("-newid")
+    return cargs
+
+
+def v_3d_afnito_nifti_outputs(
+    params: V3dAfnitoNiftiParameters,
+    execution: Execution,
+) -> V3dAfnitoNiftiOutputs:
+    """
+    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 = V3dAfnitoNiftiOutputs(
+        root=execution.output_file("."),
+        output_nifti=execution.output_file(params.get("prefix") + ".nii") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_afnito_nifti_execute(
+    params: V3dAfnitoNiftiParameters,
+    execution: Execution,
+) -> V3dAfnitoNiftiOutputs:
+    """
+    Converts an AFNI dataset to a NIfTI-1.1 file.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dAfnitoNiftiOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_afnito_nifti_cargs(params, execution)
+    ret = v_3d_afnito_nifti_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_afnito_nifti(
+    input_dataset: InputPathType,
+    prefix: str | None = None,
+    verbose: bool = False,
+    force_float: bool = False,
+    pure: bool = False,
+    denote: bool = False,
+    oldid: bool = False,
+    newid: bool = False,
+    runner: Runner | None = None,
+) -> V3dAfnitoNiftiOutputs:
+    """
+    Converts an AFNI dataset to a NIfTI-1.1 file.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_dataset: Input AFNI dataset.
+        prefix: Output NIfTI file prefix.
+        verbose: Print progress messages (increases verbosity if repeated).
+        force_float: Force the output dataset to be 32-bit floats.
+        pure: Do not write an AFNI extension field into the output file.
+        denote: Remove text notes from AFNI extension field that might contain\
+            identifying information.
+        oldid: Retain the input dataset's AFNI ID code.
+        newid: Assign a new AFNI ID code to the dataset (default action).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dAfnitoNiftiOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_AFNITO_NIFTI_METADATA)
+    params = v_3d_afnito_nifti_params(
+        input_dataset=input_dataset,
+        prefix=prefix,
+        verbose=verbose,
+        force_float=force_float,
+        pure=pure,
+        denote=denote,
+        oldid=oldid,
+        newid=newid,
+    )
+    return v_3d_afnito_nifti_execute(params, execution)
+
+
+__all__ = [
+    "V3dAfnitoNiftiOutputs",
+    "V3dAfnitoNiftiParameters",
+    "V_3D_AFNITO_NIFTI_METADATA",
+    "v_3d_afnito_nifti",
+    "v_3d_afnito_nifti_params",
+]

niwrap_afni/afni/v_3d_afnito_niml.py

@@ -0,0 +1,175 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_AFNITO_NIML_METADATA = Metadata(
+    id="98f63f2e946d67b9373a37700e5abbc719dca8ea.boutiques",
+    name="3dAFNItoNIML",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dAfnitoNimlParameters = typing.TypedDict('V3dAfnitoNimlParameters', {
+    "__STYX_TYPE__": typing.Literal["3dAFNItoNIML"],
+    "dset": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dAFNItoNIML": v_3d_afnito_niml_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 V3dAfnitoNimlOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_afnito_niml(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v_3d_afnito_niml_params(
+    dset: InputPathType,
+) -> V3dAfnitoNimlParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dset: AFNI dataset.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dAFNItoNIML",
+        "dset": dset,
+    }
+    return params
+
+
+def v_3d_afnito_niml_cargs(
+    params: V3dAfnitoNimlParameters,
+    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("3dAFNItoNIML")
+    cargs.append("[OPTIONS]")
+    cargs.append(execution.input_file(params.get("dset")))
+    return cargs
+
+
+def v_3d_afnito_niml_outputs(
+    params: V3dAfnitoNimlParameters,
+    execution: Execution,
+) -> V3dAfnitoNimlOutputs:
+    """
+    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 = V3dAfnitoNimlOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v_3d_afnito_niml_execute(
+    params: V3dAfnitoNimlParameters,
+    execution: Execution,
+) -> V3dAfnitoNimlOutputs:
+    """
+    Dumps AFNI dataset header information to stdout in NIML format. Mostly for
+    debugging and testing purposes!.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dAfnitoNimlOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_afnito_niml_cargs(params, execution)
+    ret = v_3d_afnito_niml_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_afnito_niml(
+    dset: InputPathType,
+    runner: Runner | None = None,
+) -> V3dAfnitoNimlOutputs:
+    """
+    Dumps AFNI dataset header information to stdout in NIML format. Mostly for
+    debugging and testing purposes!.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dset: AFNI dataset.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dAfnitoNimlOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_AFNITO_NIML_METADATA)
+    params = v_3d_afnito_niml_params(
+        dset=dset,
+    )
+    return v_3d_afnito_niml_execute(params, execution)
+
+
+__all__ = [
+    "V3dAfnitoNimlOutputs",
+    "V3dAfnitoNimlParameters",
+    "V_3D_AFNITO_NIML_METADATA",
+    "v_3d_afnito_niml",
+    "v_3d_afnito_niml_params",
+]

niwrap_afni/afni/v_3d_afnito_raw.py

@@ -0,0 +1,202 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_AFNITO_RAW_METADATA = Metadata(
+    id="67bff5ed68a691d8da5e7aa97ecf946e7772101e.boutiques",
+    name="3dAFNItoRaw",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dAfnitoRawParameters = typing.TypedDict('V3dAfnitoRawParameters', {
+    "__STYX_TYPE__": typing.Literal["3dAFNItoRaw"],
+    "output_file": typing.NotRequired[str | None],
+    "force_float": bool,
+    "dataset": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dAFNItoRaw": v_3d_afnito_raw_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 V3dAfnitoRawOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_afnito_raw(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v_3d_afnito_raw_params(
+    dataset: str,
+    output_file: str | None = None,
+    force_float: bool = False,
+) -> V3dAfnitoRawParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dataset: Input AFNI dataset with possible modifiers for sub-brick and\
+            sub-range selection.
+        output_file: Name of the output file (not an AFNI dataset prefix).\
+            Default is rawxyz.dat.
+        force_float: Force floating point output. Floating point forced if any\
+            sub-brik scale factors not equal to 1.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dAFNItoRaw",
+        "force_float": force_float,
+        "dataset": dataset,
+    }
+    if output_file is not None:
+        params["output_file"] = output_file
+    return params
+
+
+def v_3d_afnito_raw_cargs(
+    params: V3dAfnitoRawParameters,
+    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("3dAFNItoRaw")
+    if params.get("output_file") is not None:
+        cargs.extend([
+            "-output",
+            params.get("output_file")
+        ])
+    if params.get("force_float"):
+        cargs.append("-datum float")
+    cargs.append(params.get("dataset"))
+    return cargs
+
+
+def v_3d_afnito_raw_outputs(
+    params: V3dAfnitoRawParameters,
+    execution: Execution,
+) -> V3dAfnitoRawOutputs:
+    """
+    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 = V3dAfnitoRawOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v_3d_afnito_raw_execute(
+    params: V3dAfnitoRawParameters,
+    execution: Execution,
+) -> V3dAfnitoRawOutputs:
+    """
+    Convert an AFNI brik file with multiple sub-briks to a raw file with each
+    sub-brik voxel concatenated voxel-wise.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dAfnitoRawOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_afnito_raw_cargs(params, execution)
+    ret = v_3d_afnito_raw_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_afnito_raw(
+    dataset: str,
+    output_file: str | None = None,
+    force_float: bool = False,
+    runner: Runner | None = None,
+) -> V3dAfnitoRawOutputs:
+    """
+    Convert an AFNI brik file with multiple sub-briks to a raw file with each
+    sub-brik voxel concatenated voxel-wise.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dataset: Input AFNI dataset with possible modifiers for sub-brick and\
+            sub-range selection.
+        output_file: Name of the output file (not an AFNI dataset prefix).\
+            Default is rawxyz.dat.
+        force_float: Force floating point output. Floating point forced if any\
+            sub-brik scale factors not equal to 1.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dAfnitoRawOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_AFNITO_RAW_METADATA)
+    params = v_3d_afnito_raw_params(
+        output_file=output_file,
+        force_float=force_float,
+        dataset=dataset,
+    )
+    return v_3d_afnito_raw_execute(params, execution)
+
+
+__all__ = [
+    "V3dAfnitoRawOutputs",
+    "V3dAfnitoRawParameters",
+    "V_3D_AFNITO_RAW_METADATA",
+    "v_3d_afnito_raw",
+    "v_3d_afnito_raw_params",
+]