niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_acost.py

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+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_ACOST_METADATA = Metadata(
+    id="0ff6573e114cd6d142c6db98eac6125eecf4d8dc.boutiques",
+    name="3dAcost",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dAcostParameters = typing.TypedDict('V3dAcostParameters', {
+    "__STYX_TYPE__": typing.Literal["3dAcost"],
+    "infile": InputPathType,
+    "basefile": InputPathType,
+    "outfile": str,
+    "all_cost": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dAcost": v_3d_acost_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 {
+        "3dAcost": v_3d_acost_outputs,
+    }.get(t)
+
+
+class V3dAcostOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_acost(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_head: OutputPathType
+    """Output aligned dataset (HEAD file)"""
+    output_brik: OutputPathType
+    """Output aligned dataset (BRIK file)"""
+
+
+def v_3d_acost_params(
+    infile: InputPathType,
+    basefile: InputPathType,
+    outfile: str,
+    all_cost: bool = False,
+) -> V3dAcostParameters:
+    """
+    Build parameters.
+    
+    Args:
+        infile: Input dataset for allineation.
+        basefile: Base dataset for allineation.
+        outfile: Prefix for the output dataset.
+        all_cost: Prints all alignment cost metrics.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dAcost",
+        "infile": infile,
+        "basefile": basefile,
+        "outfile": outfile,
+        "all_cost": all_cost,
+    }
+    return params
+
+
+def v_3d_acost_cargs(
+    params: V3dAcostParameters,
+    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("3dAcost")
+    cargs.append(execution.input_file(params.get("infile")))
+    cargs.extend([
+        "-base",
+        execution.input_file(params.get("basefile"))
+    ])
+    cargs.extend([
+        "-prefix",
+        params.get("outfile")
+    ])
+    if params.get("all_cost"):
+        cargs.append("-allcostX")
+    return cargs
+
+
+def v_3d_acost_outputs(
+    params: V3dAcostParameters,
+    execution: Execution,
+) -> V3dAcostOutputs:
+    """
+    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 = V3dAcostOutputs(
+        root=execution.output_file("."),
+        output_head=execution.output_file(params.get("outfile") + "+orig.HEAD"),
+        output_brik=execution.output_file(params.get("outfile") + "+orig.BRIK"),
+    )
+    return ret
+
+
+def v_3d_acost_execute(
+    params: V3dAcostParameters,
+    execution: Execution,
+) -> V3dAcostOutputs:
+    """
+    Allineate dataset to a base dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dAcostOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_acost_cargs(params, execution)
+    ret = v_3d_acost_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_acost(
+    infile: InputPathType,
+    basefile: InputPathType,
+    outfile: str,
+    all_cost: bool = False,
+    runner: Runner | None = None,
+) -> V3dAcostOutputs:
+    """
+    Allineate dataset to a base dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        infile: Input dataset for allineation.
+        basefile: Base dataset for allineation.
+        outfile: Prefix for the output dataset.
+        all_cost: Prints all alignment cost metrics.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dAcostOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_ACOST_METADATA)
+    params = v_3d_acost_params(
+        infile=infile,
+        basefile=basefile,
+        outfile=outfile,
+        all_cost=all_cost,
+    )
+    return v_3d_acost_execute(params, execution)
+
+
+__all__ = [
+    "V3dAcostOutputs",
+    "V3dAcostParameters",
+    "V_3D_ACOST_METADATA",
+    "v_3d_acost",
+    "v_3d_acost_params",
+]

niwrap_afni/afni/v_3d_afnito3_d.py

@@ -0,0 +1,177 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_AFNITO3_D_METADATA = Metadata(
+    id="51230e7f67f1e0eb607573872e1507d7fe45f41a.boutiques",
+    name="3dAFNIto3D",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dAfnito3DParameters = typing.TypedDict('V3dAfnito3DParameters', {
+    "__STYX_TYPE__": typing.Literal["3dAFNIto3D"],
+    "dataset": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dAFNIto3D": v_3d_afnito3_d_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 {
+        "3dAFNIto3D": v_3d_afnito3_d_outputs,
+    }.get(t)
+
+
+class V3dAfnito3DOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_afnito3_d(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outfile: OutputPathType
+    """Output 3D file, either in binary or text format"""
+
+
+def v_3d_afnito3_d_params(
+    dataset: InputPathType,
+) -> V3dAfnito3DParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dataset: AFNI dataset to be converted.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dAFNIto3D",
+        "dataset": dataset,
+    }
+    return params
+
+
+def v_3d_afnito3_d_cargs(
+    params: V3dAfnito3DParameters,
+    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("3dAFNIto3D")
+    cargs.append("[OPTIONS]")
+    cargs.append(execution.input_file(params.get("dataset")))
+    return cargs
+
+
+def v_3d_afnito3_d_outputs(
+    params: V3dAfnito3DParameters,
+    execution: Execution,
+) -> V3dAfnito3DOutputs:
+    """
+    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 = V3dAfnito3DOutputs(
+        root=execution.output_file("."),
+        outfile=execution.output_file("[PREFIX].3D"),
+    )
+    return ret
+
+
+def v_3d_afnito3_d_execute(
+    params: V3dAfnito3DParameters,
+    execution: Execution,
+) -> V3dAfnito3DOutputs:
+    """
+    Reads in an AFNI dataset, and writes it out as a 3D file.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dAfnito3DOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_afnito3_d_cargs(params, execution)
+    ret = v_3d_afnito3_d_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_afnito3_d(
+    dataset: InputPathType,
+    runner: Runner | None = None,
+) -> V3dAfnito3DOutputs:
+    """
+    Reads in an AFNI dataset, and writes it out as a 3D file.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dataset: AFNI dataset to be converted.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dAfnito3DOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_AFNITO3_D_METADATA)
+    params = v_3d_afnito3_d_params(
+        dataset=dataset,
+    )
+    return v_3d_afnito3_d_execute(params, execution)
+
+
+__all__ = [
+    "V3dAfnito3DOutputs",
+    "V3dAfnito3DParameters",
+    "V_3D_AFNITO3_D_METADATA",
+    "v_3d_afnito3_d",
+    "v_3d_afnito3_d_params",
+]

niwrap_afni/afni/v_3d_afnito_analyze.py

@@ -0,0 +1,219 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_AFNITO_ANALYZE_METADATA = Metadata(
+    id="8e009ca0525a816d98d8d648c7fbae2324df58e2.boutiques",
+    name="3dAFNItoANALYZE",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dAfnitoAnalyzeParameters = typing.TypedDict('V3dAfnitoAnalyzeParameters', {
+    "__STYX_TYPE__": typing.Literal["3dAFNItoANALYZE"],
+    "4d_option": bool,
+    "orient_option": typing.NotRequired[str | None],
+    "output_name": str,
+    "afni_dataset": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dAFNItoANALYZE": v_3d_afnito_analyze_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 {
+        "3dAFNItoANALYZE": v_3d_afnito_analyze_outputs,
+    }.get(t)
+
+
+class V3dAfnitoAnalyzeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_afnito_analyze(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_hdr_file: OutputPathType
+    """ANALYZE header file for each sub-brick"""
+    output_img_file: OutputPathType
+    """ANALYZE image file for each sub-brick"""
+    output_4d_hdr_file: OutputPathType
+    """Single ANALYZE header file if using -4D option"""
+    output_4d_img_file: OutputPathType
+    """Single ANALYZE image file if using -4D option"""
+
+
+def v_3d_afnito_analyze_params(
+    output_name: str,
+    afni_dataset: InputPathType,
+    v_4d_option: bool = False,
+    orient_option: str | None = None,
+) -> V3dAfnitoAnalyzeParameters:
+    """
+    Build parameters.
+    
+    Args:
+        output_name: Output ANALYZE file base name (e.g., aname).
+        afni_dataset: Input AFNI dataset.
+        v_4d_option: Write all data to one big ANALYZE file pair named\
+            aname.hdr/aname.img.
+        orient_option: Flip the dataset to a different orientation when writing\
+            to ANALYZE files (e.g., LPI).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dAFNItoANALYZE",
+        "4d_option": v_4d_option,
+        "output_name": output_name,
+        "afni_dataset": afni_dataset,
+    }
+    if orient_option is not None:
+        params["orient_option"] = orient_option
+    return params
+
+
+def v_3d_afnito_analyze_cargs(
+    params: V3dAfnitoAnalyzeParameters,
+    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("3dAFNItoANALYZE")
+    if params.get("4d_option"):
+        cargs.append("-4D")
+    if params.get("orient_option") is not None:
+        cargs.extend([
+            "-orient",
+            params.get("orient_option")
+        ])
+    cargs.append(params.get("output_name"))
+    cargs.append(execution.input_file(params.get("afni_dataset")))
+    return cargs
+
+
+def v_3d_afnito_analyze_outputs(
+    params: V3dAfnitoAnalyzeParameters,
+    execution: Execution,
+) -> V3dAfnitoAnalyzeOutputs:
+    """
+    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 = V3dAfnitoAnalyzeOutputs(
+        root=execution.output_file("."),
+        output_hdr_file=execution.output_file(params.get("output_name") + "_[INDEX].hdr"),
+        output_img_file=execution.output_file(params.get("output_name") + "_[INDEX].img"),
+        output_4d_hdr_file=execution.output_file(params.get("output_name") + ".hdr"),
+        output_4d_img_file=execution.output_file(params.get("output_name") + ".img"),
+    )
+    return ret
+
+
+def v_3d_afnito_analyze_execute(
+    params: V3dAfnitoAnalyzeParameters,
+    execution: Execution,
+) -> V3dAfnitoAnalyzeOutputs:
+    """
+    Writes AFNI dataset to ANALYZE 7.5 format .hdr/.img file pairs.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dAfnitoAnalyzeOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_afnito_analyze_cargs(params, execution)
+    ret = v_3d_afnito_analyze_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_afnito_analyze(
+    output_name: str,
+    afni_dataset: InputPathType,
+    v_4d_option: bool = False,
+    orient_option: str | None = None,
+    runner: Runner | None = None,
+) -> V3dAfnitoAnalyzeOutputs:
+    """
+    Writes AFNI dataset to ANALYZE 7.5 format .hdr/.img file pairs.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        output_name: Output ANALYZE file base name (e.g., aname).
+        afni_dataset: Input AFNI dataset.
+        v_4d_option: Write all data to one big ANALYZE file pair named\
+            aname.hdr/aname.img.
+        orient_option: Flip the dataset to a different orientation when writing\
+            to ANALYZE files (e.g., LPI).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dAfnitoAnalyzeOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_AFNITO_ANALYZE_METADATA)
+    params = v_3d_afnito_analyze_params(
+        v_4d_option=v_4d_option,
+        orient_option=orient_option,
+        output_name=output_name,
+        afni_dataset=afni_dataset,
+    )
+    return v_3d_afnito_analyze_execute(params, execution)
+
+
+__all__ = [
+    "V3dAfnitoAnalyzeOutputs",
+    "V3dAfnitoAnalyzeParameters",
+    "V_3D_AFNITO_ANALYZE_METADATA",
+    "v_3d_afnito_analyze",
+    "v_3d_afnito_analyze_params",
+]