niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3ddot.py

@@ -0,0 +1,322 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3DDOT_METADATA = Metadata(
+    id="4d259267b87f75dc1b81e232092499e6d326d8fd.boutiques",
+    name="3ddot",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3ddotParameters = typing.TypedDict('V3ddotParameters', {
+    "__STYX_TYPE__": typing.Literal["3ddot"],
+    "input_datasets": list[InputPathType],
+    "mask": typing.NotRequired[InputPathType | None],
+    "mrange": typing.NotRequired[list[float] | None],
+    "demean": bool,
+    "docor": bool,
+    "dodot": bool,
+    "docoef": bool,
+    "dosums": bool,
+    "doeta2": bool,
+    "dodice": bool,
+    "show_labels": bool,
+    "upper": bool,
+    "full": bool,
+    "1D": bool,
+    "NIML": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3ddot": v_3ddot_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 {
+        "3ddot": v_3ddot_outputs,
+    }.get(t)
+
+
+class V3ddotOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3ddot(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    result: OutputPathType
+    """Resulting coefficient or statistical values printed to stdout"""
+
+
+def v_3ddot_params(
+    input_datasets: list[InputPathType],
+    mask: InputPathType | None = None,
+    mrange: list[float] | None = None,
+    demean: bool = False,
+    docor: bool = False,
+    dodot: bool = False,
+    docoef: bool = False,
+    dosums: bool = False,
+    doeta2: bool = False,
+    dodice: bool = False,
+    show_labels: bool = False,
+    upper: bool = False,
+    full: bool = False,
+    v_1_d: bool = False,
+    niml: bool = False,
+) -> V3ddotParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_datasets: List of input datasets to be used (e.g. img1+orig,\
+            img2+orig).
+        mask: Dataset to be used as a mask; only voxels with nonzero values\
+            will be averaged.
+        mrange: Restrict mask values to those between a and b (inclusive) for\
+            masking purposes.
+        demean: Remove the mean from each volume prior to computing the\
+            correlation.
+        docor: Return the correlation coefficient (default).
+        dodot: Return the dot product (unscaled).
+        docoef: Return the least square fit coefficients {a,b}.
+        dosums: Return xbar, ybar, variance, covariance, and correlation\
+            coefficient.
+        doeta2: Return eta-squared (Cohen, NeuroImage 2008).
+        dodice: Return the Dice coefficient (the Sorensen-Dice index).
+        show_labels: Print sub-brick labels to help identify what is being\
+            correlated.
+        upper: Compute upper triangular matrix.
+        full: Compute the whole matrix.
+        v_1_d: Add comment headings for the 1D format.
+        niml: Write output in NIML 1D format.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3ddot",
+        "input_datasets": input_datasets,
+        "demean": demean,
+        "docor": docor,
+        "dodot": dodot,
+        "docoef": docoef,
+        "dosums": dosums,
+        "doeta2": doeta2,
+        "dodice": dodice,
+        "show_labels": show_labels,
+        "upper": upper,
+        "full": full,
+        "1D": v_1_d,
+        "NIML": niml,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    if mrange is not None:
+        params["mrange"] = mrange
+    return params
+
+
+def v_3ddot_cargs(
+    params: V3ddotParameters,
+    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("3ddot")
+    cargs.extend([execution.input_file(f) for f in params.get("input_datasets")])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("mrange") is not None:
+        cargs.extend([
+            "-mrange",
+            *map(str, params.get("mrange"))
+        ])
+    if params.get("demean"):
+        cargs.append("-demean")
+    if params.get("docor"):
+        cargs.append("-docor")
+    if params.get("dodot"):
+        cargs.append("-dodot")
+    if params.get("docoef"):
+        cargs.append("-docoef")
+    if params.get("dosums"):
+        cargs.append("-dosums")
+    if params.get("doeta2"):
+        cargs.append("-doeta2")
+    if params.get("dodice"):
+        cargs.append("-dodice")
+    if params.get("show_labels"):
+        cargs.append("-show_labels")
+    if params.get("upper"):
+        cargs.append("-upper")
+    if params.get("full"):
+        cargs.append("-full")
+    if params.get("1D"):
+        cargs.append("-1D")
+    if params.get("NIML"):
+        cargs.append("-NIML")
+    return cargs
+
+
+def v_3ddot_outputs(
+    params: V3ddotParameters,
+    execution: Execution,
+) -> V3ddotOutputs:
+    """
+    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 = V3ddotOutputs(
+        root=execution.output_file("."),
+        result=execution.output_file("stdout"),
+    )
+    return ret
+
+
+def v_3ddot_execute(
+    params: V3ddotParameters,
+    execution: Execution,
+) -> V3ddotOutputs:
+    """
+    Computes correlation coefficients between sub-brick pairs.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3ddotOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3ddot_cargs(params, execution)
+    ret = v_3ddot_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3ddot(
+    input_datasets: list[InputPathType],
+    mask: InputPathType | None = None,
+    mrange: list[float] | None = None,
+    demean: bool = False,
+    docor: bool = False,
+    dodot: bool = False,
+    docoef: bool = False,
+    dosums: bool = False,
+    doeta2: bool = False,
+    dodice: bool = False,
+    show_labels: bool = False,
+    upper: bool = False,
+    full: bool = False,
+    v_1_d: bool = False,
+    niml: bool = False,
+    runner: Runner | None = None,
+) -> V3ddotOutputs:
+    """
+    Computes correlation coefficients between sub-brick pairs.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_datasets: List of input datasets to be used (e.g. img1+orig,\
+            img2+orig).
+        mask: Dataset to be used as a mask; only voxels with nonzero values\
+            will be averaged.
+        mrange: Restrict mask values to those between a and b (inclusive) for\
+            masking purposes.
+        demean: Remove the mean from each volume prior to computing the\
+            correlation.
+        docor: Return the correlation coefficient (default).
+        dodot: Return the dot product (unscaled).
+        docoef: Return the least square fit coefficients {a,b}.
+        dosums: Return xbar, ybar, variance, covariance, and correlation\
+            coefficient.
+        doeta2: Return eta-squared (Cohen, NeuroImage 2008).
+        dodice: Return the Dice coefficient (the Sorensen-Dice index).
+        show_labels: Print sub-brick labels to help identify what is being\
+            correlated.
+        upper: Compute upper triangular matrix.
+        full: Compute the whole matrix.
+        v_1_d: Add comment headings for the 1D format.
+        niml: Write output in NIML 1D format.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3ddotOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DDOT_METADATA)
+    params = v_3ddot_params(
+        input_datasets=input_datasets,
+        mask=mask,
+        mrange=mrange,
+        demean=demean,
+        docor=docor,
+        dodot=dodot,
+        docoef=docoef,
+        dosums=dosums,
+        doeta2=doeta2,
+        dodice=dodice,
+        show_labels=show_labels,
+        upper=upper,
+        full=full,
+        v_1_d=v_1_d,
+        niml=niml,
+    )
+    return v_3ddot_execute(params, execution)
+
+
+__all__ = [
+    "V3ddotOutputs",
+    "V3ddotParameters",
+    "V_3DDOT_METADATA",
+    "v_3ddot",
+    "v_3ddot_params",
+]

niwrap_afni/afni/v_3ddot_beta.py

@@ -0,0 +1,214 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3DDOT_BETA_METADATA = Metadata(
+    id="3ccc06408d9c3d573076ee49d8aa6d0e1e01b141.boutiques",
+    name="3ddot_beta",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3ddotBetaParameters = typing.TypedDict('V3ddotBetaParameters', {
+    "__STYX_TYPE__": typing.Literal["3ddot_beta"],
+    "input_file": InputPathType,
+    "prefix": str,
+    "doeta2": bool,
+    "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 {
+        "3ddot_beta": v_3ddot_beta_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 {
+        "3ddot_beta": v_3ddot_beta_outputs,
+    }.get(t)
+
+
+class V3ddotBetaOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3ddot_beta(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """Output text file containing the correlation-like matrix"""
+
+
+def v_3ddot_beta_params(
+    input_file: InputPathType,
+    prefix: str,
+    doeta2: bool = False,
+    mask: InputPathType | None = None,
+) -> V3ddotBetaParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Input file with N bricks.
+        prefix: Output prefix for the result file.
+        doeta2: Required flag for performing eta2 tests.
+        mask: Optional mask file within which to take values.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3ddot_beta",
+        "input_file": input_file,
+        "prefix": prefix,
+        "doeta2": doeta2,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    return params
+
+
+def v_3ddot_beta_cargs(
+    params: V3ddotBetaParameters,
+    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("3ddot_beta")
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input_file"))
+    ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("doeta2"):
+        cargs.append("-doeta2")
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    return cargs
+
+
+def v_3ddot_beta_outputs(
+    params: V3ddotBetaParameters,
+    execution: Execution,
+) -> V3ddotBetaOutputs:
+    """
+    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 = V3ddotBetaOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("prefix") + "_eta2.dat"),
+    )
+    return ret
+
+
+def v_3ddot_beta_execute(
+    params: V3ddotBetaParameters,
+    execution: Execution,
+) -> V3ddotBetaOutputs:
+    """
+    Beta version of updating 3ddot, currently only performing eta2 tests and
+    outputting a full matrix to a text file.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3ddotBetaOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3ddot_beta_cargs(params, execution)
+    ret = v_3ddot_beta_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3ddot_beta(
+    input_file: InputPathType,
+    prefix: str,
+    doeta2: bool = False,
+    mask: InputPathType | None = None,
+    runner: Runner | None = None,
+) -> V3ddotBetaOutputs:
+    """
+    Beta version of updating 3ddot, currently only performing eta2 tests and
+    outputting a full matrix to a text file.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: Input file with N bricks.
+        prefix: Output prefix for the result file.
+        doeta2: Required flag for performing eta2 tests.
+        mask: Optional mask file within which to take values.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3ddotBetaOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DDOT_BETA_METADATA)
+    params = v_3ddot_beta_params(
+        input_file=input_file,
+        prefix=prefix,
+        doeta2=doeta2,
+        mask=mask,
+    )
+    return v_3ddot_beta_execute(params, execution)
+
+
+__all__ = [
+    "V3ddotBetaOutputs",
+    "V3ddotBetaParameters",
+    "V_3DDOT_BETA_METADATA",
+    "v_3ddot_beta",
+    "v_3ddot_beta_params",
+]