niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_1d_tsort.py

@@ -0,0 +1,216 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_1D_TSORT_METADATA = Metadata(
+    id="731309e5236007bd69df120b6a0494a5de798eeb.boutiques",
+    name="1dTsort",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V1dTsortParameters = typing.TypedDict('V1dTsortParameters', {
+    "__STYX_TYPE__": typing.Literal["1dTsort"],
+    "dec_order": bool,
+    "transpose": bool,
+    "column": typing.NotRequired[float | None],
+    "imode": bool,
+    "infile": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "1dTsort": v_1d_tsort_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 {
+    }.get(t)
+
+
+class V1dTsortOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_1d_tsort(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v_1d_tsort_params(
+    infile: InputPathType,
+    dec_order: bool = False,
+    transpose: bool = False,
+    column: float | None = None,
+    imode: bool = False,
+) -> V1dTsortParameters:
+    """
+    Build parameters.
+    
+    Args:
+        infile: Input 1D file to be sorted.
+        dec_order: Sort into decreasing order.
+        transpose: Transpose the file before output.
+        column: Sort only on column #j (counting starts at 0), and carry the\
+            rest of the columns with it.
+        imode: Typecast all values to integers, return the mode in the input\
+            then exit. No sorting results are returned.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "1dTsort",
+        "dec_order": dec_order,
+        "transpose": transpose,
+        "imode": imode,
+        "infile": infile,
+    }
+    if column is not None:
+        params["column"] = column
+    return params
+
+
+def v_1d_tsort_cargs(
+    params: V1dTsortParameters,
+    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("1dTsort")
+    if params.get("dec_order"):
+        cargs.append("-dec")
+    if params.get("transpose"):
+        cargs.append("-flip")
+    if params.get("column") is not None:
+        cargs.extend([
+            "-col",
+            str(params.get("column"))
+        ])
+    if params.get("imode"):
+        cargs.append("-imode")
+    cargs.append(execution.input_file(params.get("infile")))
+    return cargs
+
+
+def v_1d_tsort_outputs(
+    params: V1dTsortParameters,
+    execution: Execution,
+) -> V1dTsortOutputs:
+    """
+    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 = V1dTsortOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v_1d_tsort_execute(
+    params: V1dTsortParameters,
+    execution: Execution,
+) -> V1dTsortOutputs:
+    """
+    Sorts each column of the input 1D file and writes 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 `V1dTsortOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_1d_tsort_cargs(params, execution)
+    ret = v_1d_tsort_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_1d_tsort(
+    infile: InputPathType,
+    dec_order: bool = False,
+    transpose: bool = False,
+    column: float | None = None,
+    imode: bool = False,
+    runner: Runner | None = None,
+) -> V1dTsortOutputs:
+    """
+    Sorts each column of the input 1D file and writes result to stdout.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        infile: Input 1D file to be sorted.
+        dec_order: Sort into decreasing order.
+        transpose: Transpose the file before output.
+        column: Sort only on column #j (counting starts at 0), and carry the\
+            rest of the columns with it.
+        imode: Typecast all values to integers, return the mode in the input\
+            then exit. No sorting results are returned.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V1dTsortOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_1D_TSORT_METADATA)
+    params = v_1d_tsort_params(
+        dec_order=dec_order,
+        transpose=transpose,
+        column=column,
+        imode=imode,
+        infile=infile,
+    )
+    return v_1d_tsort_execute(params, execution)
+
+
+__all__ = [
+    "V1dTsortOutputs",
+    "V1dTsortParameters",
+    "V_1D_TSORT_METADATA",
+    "v_1d_tsort",
+    "v_1d_tsort_params",
+]

niwrap_afni/afni/v_1d_upsample.py

@@ -0,0 +1,195 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_1D_UPSAMPLE_METADATA = Metadata(
+    id="02884fd865c7324c68f35d9eccdb7a0f5cff9cb5.boutiques",
+    name="1dUpsample",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V1dUpsampleParameters = typing.TypedDict('V1dUpsampleParameters', {
+    "__STYX_TYPE__": typing.Literal["1dUpsample"],
+    "upsample_factor": float,
+    "input_file": InputPathType,
+    "linear_interpolation": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "1dUpsample": v_1d_upsample_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 {
+        "1dUpsample": v_1d_upsample_outputs,
+    }.get(t)
+
+
+class V1dUpsampleOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_1d_upsample(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """Upsampled 1D time series output"""
+
+
+def v_1d_upsample_params(
+    upsample_factor: float,
+    input_file: InputPathType,
+    linear_interpolation: bool = False,
+) -> V1dUpsampleParameters:
+    """
+    Build parameters.
+    
+    Args:
+        upsample_factor: Upsample factor (integer from 2..32).
+        input_file: Input 1D time series file.
+        linear_interpolation: Use 1st order polynomials (i.e., linear\
+            interpolation) instead of 7th order polynomials.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "1dUpsample",
+        "upsample_factor": upsample_factor,
+        "input_file": input_file,
+        "linear_interpolation": linear_interpolation,
+    }
+    return params
+
+
+def v_1d_upsample_cargs(
+    params: V1dUpsampleParameters,
+    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("1dUpsample")
+    cargs.append(str(params.get("upsample_factor")))
+    cargs.append(execution.input_file(params.get("input_file")))
+    if params.get("linear_interpolation"):
+        cargs.append("-one")
+    return cargs
+
+
+def v_1d_upsample_outputs(
+    params: V1dUpsampleParameters,
+    execution: Execution,
+) -> V1dUpsampleOutputs:
+    """
+    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 = V1dUpsampleOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file("ethel.1D"),
+    )
+    return ret
+
+
+def v_1d_upsample_execute(
+    params: V1dUpsampleParameters,
+    execution: Execution,
+) -> V1dUpsampleOutputs:
+    """
+    Upsamples a 1D time series to a finer time grid.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V1dUpsampleOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_1d_upsample_cargs(params, execution)
+    ret = v_1d_upsample_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_1d_upsample(
+    upsample_factor: float,
+    input_file: InputPathType,
+    linear_interpolation: bool = False,
+    runner: Runner | None = None,
+) -> V1dUpsampleOutputs:
+    """
+    Upsamples a 1D time series to a finer time grid.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        upsample_factor: Upsample factor (integer from 2..32).
+        input_file: Input 1D time series file.
+        linear_interpolation: Use 1st order polynomials (i.e., linear\
+            interpolation) instead of 7th order polynomials.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V1dUpsampleOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_1D_UPSAMPLE_METADATA)
+    params = v_1d_upsample_params(
+        upsample_factor=upsample_factor,
+        input_file=input_file,
+        linear_interpolation=linear_interpolation,
+    )
+    return v_1d_upsample_execute(params, execution)
+
+
+__all__ = [
+    "V1dUpsampleOutputs",
+    "V1dUpsampleParameters",
+    "V_1D_UPSAMPLE_METADATA",
+    "v_1d_upsample",
+    "v_1d_upsample_params",
+]

niwrap_afni/afni/v_1dcat.py

@@ -0,0 +1,266 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_1DCAT_METADATA = Metadata(
+    id="6497fba75068a5e9c7d3930e26c7a5f42390e7b0.boutiques",
+    name="1dcat",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V1dcatParameters = typing.TypedDict('V1dcatParameters', {
+    "__STYX_TYPE__": typing.Literal["1dcat"],
+    "input_files": list[InputPathType],
+    "tsv_output": bool,
+    "csv_output": bool,
+    "nonconst_output": bool,
+    "nonfixed_output": bool,
+    "number_format": typing.NotRequired[str | None],
+    "stack_output": bool,
+    "column_row_selection": typing.NotRequired[str | None],
+    "ok_empty": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "1dcat": v_1dcat_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 {
+        "1dcat": v_1dcat_outputs,
+    }.get(t)
+
+
+class V1dcatOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_1dcat(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    concatenated_output: OutputPathType
+    """Concatenated output in specified format"""
+
+
+def v_1dcat_params(
+    input_files: list[InputPathType],
+    tsv_output: bool = False,
+    csv_output: bool = False,
+    nonconst_output: bool = False,
+    nonfixed_output: bool = False,
+    number_format: str | None = None,
+    stack_output: bool = False,
+    column_row_selection: str | None = None,
+    ok_empty: bool = False,
+) -> V1dcatParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_files: Input 1D or TSV/CSV files to concatenate.
+        tsv_output: Output in TSV format with tabs as separators and a header\
+            line.
+        csv_output: Output in CSV format with commas as separators and a header\
+            line.
+        nonconst_output: Omit columns that are identically constant from the\
+            output.
+        nonfixed_output: Keep only columns marked as 'free' in the 3dAllineate\
+            header.
+        number_format: Specify the format of the numbers to be output.
+        stack_output: Stack the columns of the resulting matrix in the output.
+        column_row_selection: Apply the same column/row selection string to all\
+            filenames on the command line.
+        ok_empty: Exit quietly when encountering an empty file on disk.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "1dcat",
+        "input_files": input_files,
+        "tsv_output": tsv_output,
+        "csv_output": csv_output,
+        "nonconst_output": nonconst_output,
+        "nonfixed_output": nonfixed_output,
+        "stack_output": stack_output,
+        "ok_empty": ok_empty,
+    }
+    if number_format is not None:
+        params["number_format"] = number_format
+    if column_row_selection is not None:
+        params["column_row_selection"] = column_row_selection
+    return params
+
+
+def v_1dcat_cargs(
+    params: V1dcatParameters,
+    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("1dcat")
+    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
+    if params.get("tsv_output"):
+        cargs.append("-tsvout")
+    if params.get("csv_output"):
+        cargs.append("-csvout")
+    if params.get("nonconst_output"):
+        cargs.append("-nonconst")
+    if params.get("nonfixed_output"):
+        cargs.append("-nonfixed")
+    if params.get("number_format") is not None:
+        cargs.extend([
+            "-form",
+            params.get("number_format")
+        ])
+    if params.get("stack_output"):
+        cargs.append("-stack")
+    if params.get("column_row_selection") is not None:
+        cargs.extend([
+            "-sel",
+            params.get("column_row_selection")
+        ])
+    if params.get("ok_empty"):
+        cargs.append("-OKempty")
+    return cargs
+
+
+def v_1dcat_outputs(
+    params: V1dcatParameters,
+    execution: Execution,
+) -> V1dcatOutputs:
+    """
+    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 = V1dcatOutputs(
+        root=execution.output_file("."),
+        concatenated_output=execution.output_file("stdout"),
+    )
+    return ret
+
+
+def v_1dcat_execute(
+    params: V1dcatParameters,
+    execution: Execution,
+) -> V1dcatOutputs:
+    """
+    Concatenates columns of multiple 1D or TSV/CSV files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V1dcatOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_1dcat_cargs(params, execution)
+    ret = v_1dcat_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_1dcat(
+    input_files: list[InputPathType],
+    tsv_output: bool = False,
+    csv_output: bool = False,
+    nonconst_output: bool = False,
+    nonfixed_output: bool = False,
+    number_format: str | None = None,
+    stack_output: bool = False,
+    column_row_selection: str | None = None,
+    ok_empty: bool = False,
+    runner: Runner | None = None,
+) -> V1dcatOutputs:
+    """
+    Concatenates columns of multiple 1D or TSV/CSV files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_files: Input 1D or TSV/CSV files to concatenate.
+        tsv_output: Output in TSV format with tabs as separators and a header\
+            line.
+        csv_output: Output in CSV format with commas as separators and a header\
+            line.
+        nonconst_output: Omit columns that are identically constant from the\
+            output.
+        nonfixed_output: Keep only columns marked as 'free' in the 3dAllineate\
+            header.
+        number_format: Specify the format of the numbers to be output.
+        stack_output: Stack the columns of the resulting matrix in the output.
+        column_row_selection: Apply the same column/row selection string to all\
+            filenames on the command line.
+        ok_empty: Exit quietly when encountering an empty file on disk.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V1dcatOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_1DCAT_METADATA)
+    params = v_1dcat_params(
+        input_files=input_files,
+        tsv_output=tsv_output,
+        csv_output=csv_output,
+        nonconst_output=nonconst_output,
+        nonfixed_output=nonfixed_output,
+        number_format=number_format,
+        stack_output=stack_output,
+        column_row_selection=column_row_selection,
+        ok_empty=ok_empty,
+    )
+    return v_1dcat_execute(params, execution)
+
+
+__all__ = [
+    "V1dcatOutputs",
+    "V1dcatParameters",
+    "V_1DCAT_METADATA",
+    "v_1dcat",
+    "v_1dcat_params",
+]