niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__compute_gcor.py

@@ -0,0 +1,246 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__COMPUTE_GCOR_METADATA = Metadata(
+    id="7c21653eea6abdf613e32c0ba0461541cf95e2ae.boutiques",
+    name="@compute_gcor",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VComputeGcorParameters = typing.TypedDict('VComputeGcorParameters', {
+    "__STYX_TYPE__": typing.Literal["@compute_gcor"],
+    "input": InputPathType,
+    "mask": typing.NotRequired[InputPathType | None],
+    "corr_vol_prefix": typing.NotRequired[str | None],
+    "initial_trs": typing.NotRequired[float | None],
+    "no_demean": bool,
+    "save_tmp": bool,
+    "verbose": typing.NotRequired[float | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@compute_gcor": v__compute_gcor_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 {
+        "@compute_gcor": v__compute_gcor_outputs,
+    }.get(t)
+
+
+class VComputeGcorOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__compute_gcor(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    corr_vol_brik: OutputPathType | None
+    """Output correlation volume BRIK file"""
+    corr_vol_head: OutputPathType | None
+    """Output correlation volume HEAD file"""
+
+
+def v__compute_gcor_params(
+    input_: InputPathType,
+    mask: InputPathType | None = None,
+    corr_vol_prefix: str | None = None,
+    initial_trs: float | None = None,
+    no_demean: bool = False,
+    save_tmp: bool = False,
+    verbose: float | None = None,
+) -> VComputeGcorParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_: Specify input dataset to compute the GCOR over.
+        mask: Specify mask dataset, for restricting the computation.
+        corr_vol_prefix: Specify prefix for correlation volume output.
+        initial_trs: Specify number of initial TRs to ignore.
+        no_demean: Do not demean as the first step.
+        save_tmp: Save temporary files (do not remove at end).
+        verbose: Set verbose level (0=quiet, 3=max).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@compute_gcor",
+        "input": input_,
+        "no_demean": no_demean,
+        "save_tmp": save_tmp,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    if corr_vol_prefix is not None:
+        params["corr_vol_prefix"] = corr_vol_prefix
+    if initial_trs is not None:
+        params["initial_trs"] = initial_trs
+    if verbose is not None:
+        params["verbose"] = verbose
+    return params
+
+
+def v__compute_gcor_cargs(
+    params: VComputeGcorParameters,
+    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("@compute_gcor")
+    cargs.append(execution.input_file(params.get("input")))
+    if params.get("mask") is not None:
+        cargs.append(execution.input_file(params.get("mask")))
+    if params.get("corr_vol_prefix") is not None:
+        cargs.extend([
+            "-corr_vol",
+            params.get("corr_vol_prefix")
+        ])
+    if params.get("initial_trs") is not None:
+        cargs.extend([
+            "-nfirst",
+            str(params.get("initial_trs"))
+        ])
+    if params.get("no_demean"):
+        cargs.append("-no_demean")
+    if params.get("save_tmp"):
+        cargs.append("-savetmp")
+    if params.get("verbose") is not None:
+        cargs.extend([
+            "-verb",
+            str(params.get("verbose"))
+        ])
+    return cargs
+
+
+def v__compute_gcor_outputs(
+    params: VComputeGcorParameters,
+    execution: Execution,
+) -> VComputeGcorOutputs:
+    """
+    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 = VComputeGcorOutputs(
+        root=execution.output_file("."),
+        corr_vol_brik=execution.output_file(params.get("corr_vol_prefix") + "+tlrc.BRIK") if (params.get("corr_vol_prefix") is not None) else None,
+        corr_vol_head=execution.output_file(params.get("corr_vol_prefix") + "+tlrc.HEAD") if (params.get("corr_vol_prefix") is not None) else None,
+    )
+    return ret
+
+
+def v__compute_gcor_execute(
+    params: VComputeGcorParameters,
+    execution: Execution,
+) -> VComputeGcorOutputs:
+    """
+    Compute GCOR, the global correlation.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VComputeGcorOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__compute_gcor_cargs(params, execution)
+    ret = v__compute_gcor_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__compute_gcor(
+    input_: InputPathType,
+    mask: InputPathType | None = None,
+    corr_vol_prefix: str | None = None,
+    initial_trs: float | None = None,
+    no_demean: bool = False,
+    save_tmp: bool = False,
+    verbose: float | None = None,
+    runner: Runner | None = None,
+) -> VComputeGcorOutputs:
+    """
+    Compute GCOR, the global correlation.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_: Specify input dataset to compute the GCOR over.
+        mask: Specify mask dataset, for restricting the computation.
+        corr_vol_prefix: Specify prefix for correlation volume output.
+        initial_trs: Specify number of initial TRs to ignore.
+        no_demean: Do not demean as the first step.
+        save_tmp: Save temporary files (do not remove at end).
+        verbose: Set verbose level (0=quiet, 3=max).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VComputeGcorOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__COMPUTE_GCOR_METADATA)
+    params = v__compute_gcor_params(
+        input_=input_,
+        mask=mask,
+        corr_vol_prefix=corr_vol_prefix,
+        initial_trs=initial_trs,
+        no_demean=no_demean,
+        save_tmp=save_tmp,
+        verbose=verbose,
+    )
+    return v__compute_gcor_execute(params, execution)
+
+
+__all__ = [
+    "VComputeGcorOutputs",
+    "VComputeGcorParameters",
+    "V__COMPUTE_GCOR_METADATA",
+    "v__compute_gcor",
+    "v__compute_gcor_params",
+]

niwrap_afni/afni/v__compute_oc_weights.py

@@ -0,0 +1,287 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__COMPUTE_OC_WEIGHTS_METADATA = Metadata(
+    id="4427220e56bd9be0b0fb6b294b7d2992dca6669c.boutiques",
+    name="@compute_OC_weights",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VComputeOcWeightsParameters = typing.TypedDict('VComputeOcWeightsParameters', {
+    "__STYX_TYPE__": typing.Literal["@compute_OC_weights"],
+    "echo_times": typing.NotRequired[str | None],
+    "echo_dsets": list[str],
+    "prefix": typing.NotRequired[str | None],
+    "def_to_equal": typing.NotRequired[str | None],
+    "oc_method": typing.NotRequired[str | None],
+    "sum_weight_tolerance": typing.NotRequired[float | None],
+    "t2_star_limit": typing.NotRequired[float | None],
+    "work_dir": typing.NotRequired[str | None],
+    "verbosity": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@compute_OC_weights": v__compute_oc_weights_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 {
+        "@compute_OC_weights": v__compute_oc_weights_outputs,
+    }.get(t)
+
+
+class VComputeOcWeightsOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__compute_oc_weights(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_oc_weights: OutputPathType | None
+    """Resulting OC weights dataset"""
+
+
+def v__compute_oc_weights_params(
+    echo_dsets: list[str],
+    echo_times: str | None = None,
+    prefix: str | None = None,
+    def_to_equal: str | None = None,
+    oc_method: str | None = None,
+    sum_weight_tolerance: float | None = None,
+    t2_star_limit: float | None = None,
+    work_dir: str | None = None,
+    verbosity: bool = False,
+) -> VComputeOcWeightsParameters:
+    """
+    Build parameters.
+    
+    Args:
+        echo_dsets: Specify one run of multi-echo EPI data.
+        echo_times: Specify echo times as list (e.g., "15 30.5 41"). Use either\
+            -echo_times or -echo_times_files.
+        prefix: Specify prefix of resulting OC weights dataset (e.g.,\
+            OC.weights.SUBJ).
+        def_to_equal: Specify whether to default to equal weights (default =\
+            no).
+        oc_method: Specify which OC method to employ (default = OC_A).
+        sum_weight_tolerance: Tolerance for summed weight difference from 1.0\
+            (default = 0.001).
+        t2_star_limit: Specify limit for T2* values (default = 300).
+        work_dir: Specify directory to compute results in.
+        verbosity: Increase verbosity of output.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@compute_OC_weights",
+        "echo_dsets": echo_dsets,
+        "verbosity": verbosity,
+    }
+    if echo_times is not None:
+        params["echo_times"] = echo_times
+    if prefix is not None:
+        params["prefix"] = prefix
+    if def_to_equal is not None:
+        params["def_to_equal"] = def_to_equal
+    if oc_method is not None:
+        params["oc_method"] = oc_method
+    if sum_weight_tolerance is not None:
+        params["sum_weight_tolerance"] = sum_weight_tolerance
+    if t2_star_limit is not None:
+        params["t2_star_limit"] = t2_star_limit
+    if work_dir is not None:
+        params["work_dir"] = work_dir
+    return params
+
+
+def v__compute_oc_weights_cargs(
+    params: VComputeOcWeightsParameters,
+    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("@compute_OC_weights")
+    if params.get("echo_times") is not None:
+        cargs.extend([
+            "-echo_times",
+            params.get("echo_times")
+        ])
+    cargs.extend([
+        "-echo_dsets",
+        *params.get("echo_dsets")
+    ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("def_to_equal") is not None:
+        cargs.extend([
+            "-def_to_equal",
+            params.get("def_to_equal")
+        ])
+    if params.get("oc_method") is not None:
+        cargs.extend([
+            "-oc_method",
+            params.get("oc_method")
+        ])
+    if params.get("sum_weight_tolerance") is not None:
+        cargs.extend([
+            "-sum_weight_tolerance",
+            str(params.get("sum_weight_tolerance"))
+        ])
+    if params.get("t2_star_limit") is not None:
+        cargs.extend([
+            "-t2_star_limit",
+            str(params.get("t2_star_limit"))
+        ])
+    if params.get("work_dir") is not None:
+        cargs.extend([
+            "-work_dir",
+            params.get("work_dir")
+        ])
+    if params.get("verbosity"):
+        cargs.append("-verb")
+    return cargs
+
+
+def v__compute_oc_weights_outputs(
+    params: VComputeOcWeightsParameters,
+    execution: Execution,
+) -> VComputeOcWeightsOutputs:
+    """
+    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 = VComputeOcWeightsOutputs(
+        root=execution.output_file("."),
+        output_oc_weights=execution.output_file(params.get("prefix") + "+tlrc.HEAD") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v__compute_oc_weights_execute(
+    params: VComputeOcWeightsParameters,
+    execution: Execution,
+) -> VComputeOcWeightsOutputs:
+    """
+    Compute optimal combined weights dataset for multi-echo EPI data.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VComputeOcWeightsOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__compute_oc_weights_cargs(params, execution)
+    ret = v__compute_oc_weights_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__compute_oc_weights(
+    echo_dsets: list[str],
+    echo_times: str | None = None,
+    prefix: str | None = None,
+    def_to_equal: str | None = None,
+    oc_method: str | None = None,
+    sum_weight_tolerance: float | None = None,
+    t2_star_limit: float | None = None,
+    work_dir: str | None = None,
+    verbosity: bool = False,
+    runner: Runner | None = None,
+) -> VComputeOcWeightsOutputs:
+    """
+    Compute optimal combined weights dataset for multi-echo EPI data.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        echo_dsets: Specify one run of multi-echo EPI data.
+        echo_times: Specify echo times as list (e.g., "15 30.5 41"). Use either\
+            -echo_times or -echo_times_files.
+        prefix: Specify prefix of resulting OC weights dataset (e.g.,\
+            OC.weights.SUBJ).
+        def_to_equal: Specify whether to default to equal weights (default =\
+            no).
+        oc_method: Specify which OC method to employ (default = OC_A).
+        sum_weight_tolerance: Tolerance for summed weight difference from 1.0\
+            (default = 0.001).
+        t2_star_limit: Specify limit for T2* values (default = 300).
+        work_dir: Specify directory to compute results in.
+        verbosity: Increase verbosity of output.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VComputeOcWeightsOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__COMPUTE_OC_WEIGHTS_METADATA)
+    params = v__compute_oc_weights_params(
+        echo_times=echo_times,
+        echo_dsets=echo_dsets,
+        prefix=prefix,
+        def_to_equal=def_to_equal,
+        oc_method=oc_method,
+        sum_weight_tolerance=sum_weight_tolerance,
+        t2_star_limit=t2_star_limit,
+        work_dir=work_dir,
+        verbosity=verbosity,
+    )
+    return v__compute_oc_weights_execute(params, execution)
+
+
+__all__ = [
+    "VComputeOcWeightsOutputs",
+    "VComputeOcWeightsParameters",
+    "V__COMPUTE_OC_WEIGHTS_METADATA",
+    "v__compute_oc_weights",
+    "v__compute_oc_weights_params",
+]