niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_1ddot.py

@@ -0,0 +1,249 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_1DDOT_METADATA = Metadata(
+    id="89e3bea294b27fb22b4f6d2f28db83dbf8daea66.boutiques",
+    name="1ddot",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V1ddotParameters = typing.TypedDict('V1ddotParameters', {
+    "__STYX_TYPE__": typing.Literal["1ddot"],
+    "one_flag": bool,
+    "dem_flag": bool,
+    "cov_flag": bool,
+    "inn_flag": bool,
+    "rank_flag": bool,
+    "terse_flag": bool,
+    "okzero_flag": bool,
+    "input_files": list[InputPathType],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "1ddot": v_1ddot_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 {
+        "1ddot": v_1ddot_outputs,
+    }.get(t)
+
+
+class V1ddotOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_1ddot(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    stdout_output: OutputPathType
+    """Output correlation or covariance matrix printed to stdout."""
+
+
+def v_1ddot_params(
+    input_files: list[InputPathType],
+    one_flag: bool = False,
+    dem_flag: bool = False,
+    cov_flag: bool = False,
+    inn_flag: bool = False,
+    rank_flag: bool = False,
+    terse_flag: bool = False,
+    okzero_flag: bool = False,
+) -> V1ddotParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_files: Input 1D files.
+        one_flag: Make 1st vector be all 1's.
+        dem_flag: Remove mean from all vectors (conflicts with '-one').
+        cov_flag: Compute with covariance matrix instead of correlation.
+        inn_flag: Compute with inner product matrix instead.
+        rank_flag: Compute Spearman rank correlation instead (also implies\
+            '-terse').
+        terse_flag: Output only the correlation or covariance matrix without\
+            any garnish.
+        okzero_flag: Do not quit if a vector is all zeros. The correlation\
+            matrix will have 0 where NaNs ought to go.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "1ddot",
+        "one_flag": one_flag,
+        "dem_flag": dem_flag,
+        "cov_flag": cov_flag,
+        "inn_flag": inn_flag,
+        "rank_flag": rank_flag,
+        "terse_flag": terse_flag,
+        "okzero_flag": okzero_flag,
+        "input_files": input_files,
+    }
+    return params
+
+
+def v_1ddot_cargs(
+    params: V1ddotParameters,
+    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("1ddot")
+    if params.get("one_flag"):
+        cargs.append("-one")
+    if params.get("dem_flag"):
+        cargs.append("-dem")
+    if params.get("cov_flag"):
+        cargs.append("-cov")
+    if params.get("inn_flag"):
+        cargs.append("-inn")
+    if params.get("rank_flag"):
+        cargs.append("-rank")
+    if params.get("terse_flag"):
+        cargs.append("-terse")
+    if params.get("okzero_flag"):
+        cargs.append("-okzero")
+    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
+    cargs.append(">")
+    cargs.append("stdout.txt")
+    return cargs
+
+
+def v_1ddot_outputs(
+    params: V1ddotParameters,
+    execution: Execution,
+) -> V1ddotOutputs:
+    """
+    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 = V1ddotOutputs(
+        root=execution.output_file("."),
+        stdout_output=execution.output_file("stdout.txt"),
+    )
+    return ret
+
+
+def v_1ddot_execute(
+    params: V1ddotParameters,
+    execution: Execution,
+) -> V1ddotOutputs:
+    """
+    Computes the correlation matrix of the input 1D files and their inverse
+    correlation matrix.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V1ddotOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_1ddot_cargs(params, execution)
+    ret = v_1ddot_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_1ddot(
+    input_files: list[InputPathType],
+    one_flag: bool = False,
+    dem_flag: bool = False,
+    cov_flag: bool = False,
+    inn_flag: bool = False,
+    rank_flag: bool = False,
+    terse_flag: bool = False,
+    okzero_flag: bool = False,
+    runner: Runner | None = None,
+) -> V1ddotOutputs:
+    """
+    Computes the correlation matrix of the input 1D files and their inverse
+    correlation matrix.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_files: Input 1D files.
+        one_flag: Make 1st vector be all 1's.
+        dem_flag: Remove mean from all vectors (conflicts with '-one').
+        cov_flag: Compute with covariance matrix instead of correlation.
+        inn_flag: Compute with inner product matrix instead.
+        rank_flag: Compute Spearman rank correlation instead (also implies\
+            '-terse').
+        terse_flag: Output only the correlation or covariance matrix without\
+            any garnish.
+        okzero_flag: Do not quit if a vector is all zeros. The correlation\
+            matrix will have 0 where NaNs ought to go.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V1ddotOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_1DDOT_METADATA)
+    params = v_1ddot_params(
+        one_flag=one_flag,
+        dem_flag=dem_flag,
+        cov_flag=cov_flag,
+        inn_flag=inn_flag,
+        rank_flag=rank_flag,
+        terse_flag=terse_flag,
+        okzero_flag=okzero_flag,
+        input_files=input_files,
+    )
+    return v_1ddot_execute(params, execution)
+
+
+__all__ = [
+    "V1ddotOutputs",
+    "V1ddotParameters",
+    "V_1DDOT_METADATA",
+    "v_1ddot",
+    "v_1ddot_params",
+]

niwrap_afni/afni/v_1deval.py

@@ -0,0 +1,265 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_1DEVAL_METADATA = Metadata(
+    id="da64e5acb6bc6cd359ef137e00f938392ac2b5e3.boutiques",
+    name="1deval",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V1devalParameters = typing.TypedDict('V1devalParameters', {
+    "__STYX_TYPE__": typing.Literal["1deval"],
+    "del": typing.NotRequired[float | None],
+    "start": typing.NotRequired[float | None],
+    "num": typing.NotRequired[float | None],
+    "index": typing.NotRequired[InputPathType | None],
+    "1D": bool,
+    "symbols": typing.NotRequired[list[InputPathType] | None],
+    "expression": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "1deval": v_1deval_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 {
+        "1deval": v_1deval_outputs,
+    }.get(t)
+
+
+class V1devalOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_1deval(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_1_d: OutputPathType
+    """Output of evaluated expression."""
+
+
+def v_1deval_params(
+    expression: str,
+    del_: float | None = None,
+    start: float | None = None,
+    num: float | None = None,
+    index: InputPathType | None = None,
+    v_1_d: bool = False,
+    symbols: list[InputPathType] | None = None,
+) -> V1devalParameters:
+    """
+    Build parameters.
+    
+    Args:
+        expression: Expression to evaluate.
+        del_: Use 'd' as the step for a single undetermined variable in the\
+            expression.
+        start: Start at value 's' for a single undetermined variable in the\
+            expression.
+        num: Evaluate the expression 'n' times.
+        index: Read index column from file i.1D and write it out as 1st column\
+            of output.
+        v_1_d: Write output in the form of a single '1D:' string suitable for\
+            input on the command line of another program.
+        symbols: Read time series file and assign it to the symbol 'a'. Letters\
+            'a' to 'z' may be used as symbols.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "1deval",
+        "1D": v_1_d,
+        "expression": expression,
+    }
+    if del_ is not None:
+        params["del"] = del_
+    if start is not None:
+        params["start"] = start
+    if num is not None:
+        params["num"] = num
+    if index is not None:
+        params["index"] = index
+    if symbols is not None:
+        params["symbols"] = symbols
+    return params
+
+
+def v_1deval_cargs(
+    params: V1devalParameters,
+    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("1deval")
+    if params.get("del") is not None:
+        cargs.extend([
+            "-del",
+            str(params.get("del"))
+        ])
+    if params.get("start") is not None:
+        cargs.extend([
+            "-start",
+            str(params.get("start"))
+        ])
+    if params.get("num") is not None:
+        cargs.extend([
+            "-num",
+            str(params.get("num"))
+        ])
+    if params.get("index") is not None:
+        cargs.extend([
+            "-index",
+            execution.input_file(params.get("index"))
+        ])
+    if params.get("1D"):
+        cargs.append("-1D:")
+    if params.get("symbols") is not None:
+        cargs.extend([
+            "-a",
+            *[execution.input_file(f) for f in params.get("symbols")]
+        ])
+    cargs.extend([
+        "-expr",
+        params.get("expression")
+    ])
+    return cargs
+
+
+def v_1deval_outputs(
+    params: V1devalParameters,
+    execution: Execution,
+) -> V1devalOutputs:
+    """
+    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 = V1devalOutputs(
+        root=execution.output_file("."),
+        output_1_d=execution.output_file("output.1D"),
+    )
+    return ret
+
+
+def v_1deval_execute(
+    params: V1devalParameters,
+    execution: Execution,
+) -> V1devalOutputs:
+    """
+    Evaluates an expression that may include columns of data from one or more text
+    files and writes the result to stdout.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V1devalOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_1deval_cargs(params, execution)
+    ret = v_1deval_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_1deval(
+    expression: str,
+    del_: float | None = None,
+    start: float | None = None,
+    num: float | None = None,
+    index: InputPathType | None = None,
+    v_1_d: bool = False,
+    symbols: list[InputPathType] | None = None,
+    runner: Runner | None = None,
+) -> V1devalOutputs:
+    """
+    Evaluates an expression that may include columns of data from one or more text
+    files and writes the result to stdout.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        expression: Expression to evaluate.
+        del_: Use 'd' as the step for a single undetermined variable in the\
+            expression.
+        start: Start at value 's' for a single undetermined variable in the\
+            expression.
+        num: Evaluate the expression 'n' times.
+        index: Read index column from file i.1D and write it out as 1st column\
+            of output.
+        v_1_d: Write output in the form of a single '1D:' string suitable for\
+            input on the command line of another program.
+        symbols: Read time series file and assign it to the symbol 'a'. Letters\
+            'a' to 'z' may be used as symbols.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V1devalOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_1DEVAL_METADATA)
+    params = v_1deval_params(
+        del_=del_,
+        start=start,
+        num=num,
+        index=index,
+        v_1_d=v_1_d,
+        symbols=symbols,
+        expression=expression,
+    )
+    return v_1deval_execute(params, execution)
+
+
+__all__ = [
+    "V1devalOutputs",
+    "V1devalParameters",
+    "V_1DEVAL_METADATA",
+    "v_1deval",
+    "v_1deval_params",
+]