niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_allineate.py

@@ -0,0 +1,350 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_ALLINEATE_METADATA = Metadata(
+    id="9e9b34eca4cf79e9ab56b274a89a3cd8dc932bed.boutiques",
+    name="3dAllineate",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dAllineateParameters = typing.TypedDict('V3dAllineateParameters', {
+    "__STYX_TYPE__": typing.Literal["3dAllineate"],
+    "source": InputPathType,
+    "base": typing.NotRequired[InputPathType | None],
+    "prefix": str,
+    "param_save": typing.NotRequired[str | None],
+    "param_apply": typing.NotRequired[str | None],
+    "matrix_save": typing.NotRequired[str | None],
+    "matrix_apply": typing.NotRequired[str | None],
+    "cost": typing.NotRequired[str | None],
+    "interp": typing.NotRequired[str | None],
+    "final": typing.NotRequired[str | None],
+    "nmatch": typing.NotRequired[float | None],
+    "nopad": bool,
+    "verbose": bool,
+    "quiet": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dAllineate": v_3d_allineate_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 {
+        "3dAllineate": v_3d_allineate_outputs,
+    }.get(t)
+
+
+class V3dAllineateOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_allineate(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_brik: OutputPathType
+    """Output dataset brick file"""
+    out_head: OutputPathType
+    """Output dataset head file"""
+    out_param_save: OutputPathType | None
+    """File holding saved warp parameters"""
+    out_matrix_save: OutputPathType | None
+    """File holding saved matrix transformations"""
+
+
+def v_3d_allineate_params(
+    source: InputPathType,
+    prefix: str,
+    base: InputPathType | None = None,
+    param_save: str | None = None,
+    param_apply: str | None = None,
+    matrix_save: str | None = None,
+    matrix_apply: str | None = None,
+    cost: str | None = None,
+    interp: str | None = None,
+    final: str | None = None,
+    nmatch: float | None = None,
+    nopad: bool = False,
+    verbose: bool = False,
+    quiet: bool = False,
+) -> V3dAllineateParameters:
+    """
+    Build parameters.
+    
+    Args:
+        source: Source dataset file.
+        prefix: Output prefix.
+        base: Base dataset file.
+        param_save: Save the warp parameters in ASCII (.1D) format into file.
+        param_apply: Read warp parameters from file and apply them to the\
+            source dataset.
+        matrix_save: Save the transformation matrix for each sub-brick into\
+            file.
+        matrix_apply: Use the matrices in file to define the spatial\
+            transformations to be applied.
+        cost: Defines the 'cost' function that defines the matching between the\
+            source and the base.
+        interp: Defines interpolation method to use during matching process.
+        final: Defines the interpolation mode used to create the output dataset.
+        nmatch: Use at most 'nnn' scattered points to match the datasets.
+        nopad: Do not use zero-padding on the base image.
+        verbose: Print out verbose progress reports.
+        quiet: Don't print out verbose stuff.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dAllineate",
+        "source": source,
+        "prefix": prefix,
+        "nopad": nopad,
+        "verbose": verbose,
+        "quiet": quiet,
+    }
+    if base is not None:
+        params["base"] = base
+    if param_save is not None:
+        params["param_save"] = param_save
+    if param_apply is not None:
+        params["param_apply"] = param_apply
+    if matrix_save is not None:
+        params["matrix_save"] = matrix_save
+    if matrix_apply is not None:
+        params["matrix_apply"] = matrix_apply
+    if cost is not None:
+        params["cost"] = cost
+    if interp is not None:
+        params["interp"] = interp
+    if final is not None:
+        params["final"] = final
+    if nmatch is not None:
+        params["nmatch"] = nmatch
+    return params
+
+
+def v_3d_allineate_cargs(
+    params: V3dAllineateParameters,
+    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("3dAllineate")
+    cargs.append(execution.input_file(params.get("source")))
+    if params.get("base") is not None:
+        cargs.extend([
+            "-base",
+            execution.input_file(params.get("base"))
+        ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("param_save") is not None:
+        cargs.extend([
+            "-1Dparam_save",
+            params.get("param_save")
+        ])
+    if params.get("param_apply") is not None:
+        cargs.extend([
+            "-1Dparam_apply",
+            params.get("param_apply")
+        ])
+    if params.get("matrix_save") is not None:
+        cargs.extend([
+            "-1Dmatrix_save",
+            params.get("matrix_save")
+        ])
+    if params.get("matrix_apply") is not None:
+        cargs.extend([
+            "-1Dmatrix_apply",
+            params.get("matrix_apply")
+        ])
+    if params.get("cost") is not None:
+        cargs.extend([
+            "-cost",
+            params.get("cost")
+        ])
+    if params.get("interp") is not None:
+        cargs.extend([
+            "-interp",
+            params.get("interp")
+        ])
+    if params.get("final") is not None:
+        cargs.extend([
+            "-final",
+            params.get("final")
+        ])
+    if params.get("nmatch") is not None:
+        cargs.extend([
+            "-nmatch",
+            str(params.get("nmatch"))
+        ])
+    if params.get("nopad"):
+        cargs.append("-nopad")
+    if params.get("verbose"):
+        cargs.append("-verb")
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    return cargs
+
+
+def v_3d_allineate_outputs(
+    params: V3dAllineateParameters,
+    execution: Execution,
+) -> V3dAllineateOutputs:
+    """
+    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 = V3dAllineateOutputs(
+        root=execution.output_file("."),
+        out_brik=execution.output_file(params.get("prefix") + "+orig.BRIK"),
+        out_head=execution.output_file(params.get("prefix") + "+orig.HEAD"),
+        out_param_save=execution.output_file(params.get("param_save")) if (params.get("param_save") is not None) else None,
+        out_matrix_save=execution.output_file(params.get("matrix_save")) if (params.get("matrix_save") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_allineate_execute(
+    params: V3dAllineateParameters,
+    execution: Execution,
+) -> V3dAllineateOutputs:
+    """
+    Program to align one dataset (the 'source') to a 'base' dataset using an affine
+    (matrix) transformation of space.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dAllineateOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_allineate_cargs(params, execution)
+    ret = v_3d_allineate_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_allineate(
+    source: InputPathType,
+    prefix: str,
+    base: InputPathType | None = None,
+    param_save: str | None = None,
+    param_apply: str | None = None,
+    matrix_save: str | None = None,
+    matrix_apply: str | None = None,
+    cost: str | None = None,
+    interp: str | None = None,
+    final: str | None = None,
+    nmatch: float | None = None,
+    nopad: bool = False,
+    verbose: bool = False,
+    quiet: bool = False,
+    runner: Runner | None = None,
+) -> V3dAllineateOutputs:
+    """
+    Program to align one dataset (the 'source') to a 'base' dataset using an affine
+    (matrix) transformation of space.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        source: Source dataset file.
+        prefix: Output prefix.
+        base: Base dataset file.
+        param_save: Save the warp parameters in ASCII (.1D) format into file.
+        param_apply: Read warp parameters from file and apply them to the\
+            source dataset.
+        matrix_save: Save the transformation matrix for each sub-brick into\
+            file.
+        matrix_apply: Use the matrices in file to define the spatial\
+            transformations to be applied.
+        cost: Defines the 'cost' function that defines the matching between the\
+            source and the base.
+        interp: Defines interpolation method to use during matching process.
+        final: Defines the interpolation mode used to create the output dataset.
+        nmatch: Use at most 'nnn' scattered points to match the datasets.
+        nopad: Do not use zero-padding on the base image.
+        verbose: Print out verbose progress reports.
+        quiet: Don't print out verbose stuff.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dAllineateOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_ALLINEATE_METADATA)
+    params = v_3d_allineate_params(
+        source=source,
+        base=base,
+        prefix=prefix,
+        param_save=param_save,
+        param_apply=param_apply,
+        matrix_save=matrix_save,
+        matrix_apply=matrix_apply,
+        cost=cost,
+        interp=interp,
+        final=final,
+        nmatch=nmatch,
+        nopad=nopad,
+        verbose=verbose,
+        quiet=quiet,
+    )
+    return v_3d_allineate_execute(params, execution)
+
+
+__all__ = [
+    "V3dAllineateOutputs",
+    "V3dAllineateParameters",
+    "V_3D_ALLINEATE_METADATA",
+    "v_3d_allineate",
+    "v_3d_allineate_params",
+]

niwrap_afni/afni/v_3d_amp_to_rsfc.py

@@ -0,0 +1,262 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_AMP_TO_RSFC_METADATA = Metadata(
+    id="27e3a8435ad8a4458d62e5fc746c88a2665d19fa.boutiques",
+    name="3dAmpToRSFC",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dAmpToRsfcParameters = typing.TypedDict('V3dAmpToRsfcParameters', {
+    "__STYX_TYPE__": typing.Literal["3dAmpToRSFC"],
+    "in_amp": typing.NotRequired[InputPathType | None],
+    "in_pow": typing.NotRequired[InputPathType | None],
+    "prefix": str,
+    "band": list[float],
+    "mask": typing.NotRequired[InputPathType | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dAmpToRSFC": v_3d_amp_to_rsfc_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 {
+        "3dAmpToRSFC": v_3d_amp_to_rsfc_outputs,
+    }.get(t)
+
+
+class V3dAmpToRsfcOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_amp_to_rsfc(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_alff: OutputPathType
+    """Amplitude of low frequency fluctuations (L1 sum)."""
+    output_malff: OutputPathType
+    """ALFF divided by the mean value within the input/estimated whole brain
+    mask (mean-scaled ALFF)."""
+    output_falff: OutputPathType
+    """ALFF divided by sum of full amplitude spectrum (fractional ALFF)."""
+    output_rsfa: OutputPathType
+    """Square-root of summed square of low frequency fluctuations (L2 sum)."""
+    output_mrsfa: OutputPathType
+    """RSFA divided by the mean value within the input/estimated whole brain
+    mask (mean-scaled RSFA)."""
+    output_frsfa: OutputPathType
+    """ALFF divided by sum of full amplitude spectrum (fractional RSFA)."""
+
+
+def v_3d_amp_to_rsfc_params(
+    prefix: str,
+    band: list[float],
+    in_amp: InputPathType | None = None,
+    in_pow: InputPathType | None = None,
+    mask: InputPathType | None = None,
+) -> V3dAmpToRsfcParameters:
+    """
+    Build parameters.
+    
+    Args:
+        prefix: Output file prefix; file names will be: PREFIX_ALFF,\
+            PREFIX_FALFF, etc.
+        band: Lower and upper boundaries of the low frequency fluctuations\
+            (LFFs), within the interval [FBOT, FTOP].
+        in_amp: Input file of one-sided spectral amplitudes, such as output by\
+            3dLombScargle.
+        in_pow: Input file of a one-sided power spectrum, such as output by\
+            3dLombScargle.
+        mask: Volume mask of voxels to include for calculations.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dAmpToRSFC",
+        "prefix": prefix,
+        "band": band,
+    }
+    if in_amp is not None:
+        params["in_amp"] = in_amp
+    if in_pow is not None:
+        params["in_pow"] = in_pow
+    if mask is not None:
+        params["mask"] = mask
+    return params
+
+
+def v_3d_amp_to_rsfc_cargs(
+    params: V3dAmpToRsfcParameters,
+    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("3dAmpToRSFC")
+    cargs.append("{")
+    if params.get("in_amp") is not None:
+        cargs.extend([
+            "-in_amp",
+            execution.input_file(params.get("in_amp"))
+        ])
+    cargs.append("|")
+    if params.get("in_pow") is not None:
+        cargs.extend([
+            "-in_pow",
+            execution.input_file(params.get("in_pow"))
+        ])
+    cargs.append("}")
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    cargs.extend([
+        "-band",
+        *map(str, params.get("band"))
+    ])
+    cargs.append("{")
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    cargs.append("}")
+    cargs.append("{")
+    cargs.append("-nifti")
+    cargs.append("}")
+    return cargs
+
+
+def v_3d_amp_to_rsfc_outputs(
+    params: V3dAmpToRsfcParameters,
+    execution: Execution,
+) -> V3dAmpToRsfcOutputs:
+    """
+    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 = V3dAmpToRsfcOutputs(
+        root=execution.output_file("."),
+        output_alff=execution.output_file(params.get("prefix") + "_ALFF*"),
+        output_malff=execution.output_file(params.get("prefix") + "_MALFF*"),
+        output_falff=execution.output_file(params.get("prefix") + "_FALFF*"),
+        output_rsfa=execution.output_file(params.get("prefix") + "_RSFA*"),
+        output_mrsfa=execution.output_file(params.get("prefix") + "_MRSFA*"),
+        output_frsfa=execution.output_file(params.get("prefix") + "_FRSFA*"),
+    )
+    return ret
+
+
+def v_3d_amp_to_rsfc_execute(
+    params: V3dAmpToRsfcParameters,
+    execution: Execution,
+) -> V3dAmpToRsfcOutputs:
+    """
+    Convert spectral amplitudes into standard RSFC parameters.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dAmpToRsfcOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_amp_to_rsfc_cargs(params, execution)
+    ret = v_3d_amp_to_rsfc_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_amp_to_rsfc(
+    prefix: str,
+    band: list[float],
+    in_amp: InputPathType | None = None,
+    in_pow: InputPathType | None = None,
+    mask: InputPathType | None = None,
+    runner: Runner | None = None,
+) -> V3dAmpToRsfcOutputs:
+    """
+    Convert spectral amplitudes into standard RSFC parameters.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        prefix: Output file prefix; file names will be: PREFIX_ALFF,\
+            PREFIX_FALFF, etc.
+        band: Lower and upper boundaries of the low frequency fluctuations\
+            (LFFs), within the interval [FBOT, FTOP].
+        in_amp: Input file of one-sided spectral amplitudes, such as output by\
+            3dLombScargle.
+        in_pow: Input file of a one-sided power spectrum, such as output by\
+            3dLombScargle.
+        mask: Volume mask of voxels to include for calculations.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dAmpToRsfcOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_AMP_TO_RSFC_METADATA)
+    params = v_3d_amp_to_rsfc_params(
+        in_amp=in_amp,
+        in_pow=in_pow,
+        prefix=prefix,
+        band=band,
+        mask=mask,
+    )
+    return v_3d_amp_to_rsfc_execute(params, execution)
+
+
+__all__ = [
+    "V3dAmpToRsfcOutputs",
+    "V3dAmpToRsfcParameters",
+    "V_3D_AMP_TO_RSFC_METADATA",
+    "v_3d_amp_to_rsfc",
+    "v_3d_amp_to_rsfc_params",
+]