niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/float_scan.py

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+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FLOAT_SCAN_METADATA = Metadata(
+    id="d795b3de53df65306720fe08c5de7896c3c07e43.boutiques",
+    name="float_scan",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+FloatScanParameters = typing.TypedDict('FloatScanParameters', {
+    "__STYX_TYPE__": typing.Literal["float_scan"],
+    "fix_illegal_values": bool,
+    "verbose_mode": bool,
+    "skip_count": typing.NotRequired[int | None],
+    "input_file": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "float_scan": float_scan_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 {
+        "float_scan": float_scan_outputs,
+    }.get(t)
+
+
+class FloatScanOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `float_scan(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    stdout_file: OutputPathType
+    """Output file with illegal values replaced by 0 when -fix flag is used"""
+
+
+def float_scan_params(
+    input_file: InputPathType,
+    fix_illegal_values: bool = False,
+    verbose_mode: bool = False,
+    skip_count: int | None = None,
+) -> FloatScanParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Input file containing IEEE floating point numbers.
+        fix_illegal_values: Writes a copy of the input file to stdout,\
+            replacing illegal values with 0.
+        verbose_mode: Verbose mode: print out index of each illegal value.
+        skip_count: Skip the first n floating point locations (i.e., the first\
+            4*n bytes) in the file.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "float_scan",
+        "fix_illegal_values": fix_illegal_values,
+        "verbose_mode": verbose_mode,
+        "input_file": input_file,
+    }
+    if skip_count is not None:
+        params["skip_count"] = skip_count
+    return params
+
+
+def float_scan_cargs(
+    params: FloatScanParameters,
+    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("float_scan")
+    if params.get("fix_illegal_values"):
+        cargs.append("-fix")
+    if params.get("verbose_mode"):
+        cargs.append("-v")
+    if params.get("skip_count") is not None:
+        cargs.extend([
+            "-skip",
+            str(params.get("skip_count"))
+        ])
+    cargs.append(execution.input_file(params.get("input_file")))
+    return cargs
+
+
+def float_scan_outputs(
+    params: FloatScanParameters,
+    execution: Execution,
+) -> FloatScanOutputs:
+    """
+    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 = FloatScanOutputs(
+        root=execution.output_file("."),
+        stdout_file=execution.output_file("stdout"),
+    )
+    return ret
+
+
+def float_scan_execute(
+    params: FloatScanParameters,
+    execution: Execution,
+) -> FloatScanOutputs:
+    """
+    Scans the input file of IEEE floating point numbers for illegal values:
+    infinities and not-a-number (NaN) values.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `FloatScanOutputs`).
+    """
+    params = execution.params(params)
+    cargs = float_scan_cargs(params, execution)
+    ret = float_scan_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def float_scan(
+    input_file: InputPathType,
+    fix_illegal_values: bool = False,
+    verbose_mode: bool = False,
+    skip_count: int | None = None,
+    runner: Runner | None = None,
+) -> FloatScanOutputs:
+    """
+    Scans the input file of IEEE floating point numbers for illegal values:
+    infinities and not-a-number (NaN) values.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: Input file containing IEEE floating point numbers.
+        fix_illegal_values: Writes a copy of the input file to stdout,\
+            replacing illegal values with 0.
+        verbose_mode: Verbose mode: print out index of each illegal value.
+        skip_count: Skip the first n floating point locations (i.e., the first\
+            4*n bytes) in the file.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `FloatScanOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FLOAT_SCAN_METADATA)
+    params = float_scan_params(
+        fix_illegal_values=fix_illegal_values,
+        verbose_mode=verbose_mode,
+        skip_count=skip_count,
+        input_file=input_file,
+    )
+    return float_scan_execute(params, execution)
+
+
+__all__ = [
+    "FLOAT_SCAN_METADATA",
+    "FloatScanOutputs",
+    "FloatScanParameters",
+    "float_scan",
+    "float_scan_params",
+]

niwrap_afni/afni/from3d.py

@@ -0,0 +1,292 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FROM3D_METADATA = Metadata(
+    id="d88853bc4909a884c5e078f5005fa8e795031713.boutiques",
+    name="from3d",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+From3dParameters = typing.TypedDict('From3dParameters', {
+    "__STYX_TYPE__": typing.Literal["from3d"],
+    "verbose": bool,
+    "nsize": bool,
+    "raw": bool,
+    "float": bool,
+    "zfirst": typing.NotRequired[float | None],
+    "zlast": typing.NotRequired[float | None],
+    "tfirst": typing.NotRequired[float | None],
+    "tlast": typing.NotRequired[float | None],
+    "input": InputPathType,
+    "prefix": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "from3d": from3d_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 {
+        "from3d": from3d_outputs,
+    }.get(t)
+
+
+class From3dOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `from3d(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    extracted_images: OutputPathType
+    """Extracted 2D images from the 3D dataset"""
+
+
+def from3d_params(
+    input_: InputPathType,
+    prefix: str,
+    verbose: bool = False,
+    nsize: bool = False,
+    raw: bool = False,
+    float_: bool = False,
+    zfirst: float | None = None,
+    zlast: float | None = None,
+    tfirst: float | None = None,
+    tlast: float | None = None,
+) -> From3dParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_: Read 3D dataset from file 'fname'.
+        prefix: Write 2D images using prefix 'rname'.
+        verbose: Print out verbose information during the run.
+        nsize: Adjust size of 2D data file to be NxN, by padding with zeros,\
+            where N is a power of 2.
+        raw: Write images in 'raw' format (just the data bytes). There will be\
+            no header information saying what the image dimensions are.
+        float_: Write images as floats, no matter what they are in the dataset\
+            itself.
+        zfirst: Set 'num' = number of first z slice to be extracted (default =\
+            1).
+        zlast: Set 'num' = number of last z slice to be extracted (default =\
+            largest).
+        tfirst: Set 'num' = number of first time slice to be extracted (default\
+            = 1).
+        tlast: Set 'num' = number of last time slice to be extracted (default =\
+            largest).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "from3d",
+        "verbose": verbose,
+        "nsize": nsize,
+        "raw": raw,
+        "float": float_,
+        "input": input_,
+        "prefix": prefix,
+    }
+    if zfirst is not None:
+        params["zfirst"] = zfirst
+    if zlast is not None:
+        params["zlast"] = zlast
+    if tfirst is not None:
+        params["tfirst"] = tfirst
+    if tlast is not None:
+        params["tlast"] = tlast
+    return params
+
+
+def from3d_cargs(
+    params: From3dParameters,
+    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("from3d")
+    if params.get("verbose"):
+        cargs.append("-v")
+    if params.get("nsize"):
+        cargs.append("-nsize")
+    if params.get("raw"):
+        cargs.append("-raw")
+    if params.get("float"):
+        cargs.append("-float")
+    if params.get("zfirst") is not None:
+        cargs.extend([
+            "-zfirst",
+            str(params.get("zfirst"))
+        ])
+    if params.get("zlast") is not None:
+        cargs.extend([
+            "-zlast",
+            str(params.get("zlast"))
+        ])
+    if params.get("tfirst") is not None:
+        cargs.extend([
+            "-tfirst",
+            str(params.get("tfirst"))
+        ])
+    if params.get("tlast") is not None:
+        cargs.extend([
+            "-tlast",
+            str(params.get("tlast"))
+        ])
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input"))
+    ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    return cargs
+
+
+def from3d_outputs(
+    params: From3dParameters,
+    execution: Execution,
+) -> From3dOutputs:
+    """
+    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 = From3dOutputs(
+        root=execution.output_file("."),
+        extracted_images=execution.output_file(params.get("prefix") + "*.img"),
+    )
+    return ret
+
+
+def from3d_execute(
+    params: From3dParameters,
+    execution: Execution,
+) -> From3dOutputs:
+    """
+    Extract 2D image files from a 3D AFNI dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `From3dOutputs`).
+    """
+    params = execution.params(params)
+    cargs = from3d_cargs(params, execution)
+    ret = from3d_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def from3d(
+    input_: InputPathType,
+    prefix: str,
+    verbose: bool = False,
+    nsize: bool = False,
+    raw: bool = False,
+    float_: bool = False,
+    zfirst: float | None = None,
+    zlast: float | None = None,
+    tfirst: float | None = None,
+    tlast: float | None = None,
+    runner: Runner | None = None,
+) -> From3dOutputs:
+    """
+    Extract 2D image files from a 3D AFNI dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_: Read 3D dataset from file 'fname'.
+        prefix: Write 2D images using prefix 'rname'.
+        verbose: Print out verbose information during the run.
+        nsize: Adjust size of 2D data file to be NxN, by padding with zeros,\
+            where N is a power of 2.
+        raw: Write images in 'raw' format (just the data bytes). There will be\
+            no header information saying what the image dimensions are.
+        float_: Write images as floats, no matter what they are in the dataset\
+            itself.
+        zfirst: Set 'num' = number of first z slice to be extracted (default =\
+            1).
+        zlast: Set 'num' = number of last z slice to be extracted (default =\
+            largest).
+        tfirst: Set 'num' = number of first time slice to be extracted (default\
+            = 1).
+        tlast: Set 'num' = number of last time slice to be extracted (default =\
+            largest).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `From3dOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FROM3D_METADATA)
+    params = from3d_params(
+        verbose=verbose,
+        nsize=nsize,
+        raw=raw,
+        float_=float_,
+        zfirst=zfirst,
+        zlast=zlast,
+        tfirst=tfirst,
+        tlast=tlast,
+        input_=input_,
+        prefix=prefix,
+    )
+    return from3d_execute(params, execution)
+
+
+__all__ = [
+    "FROM3D_METADATA",
+    "From3dOutputs",
+    "From3dParameters",
+    "from3d",
+    "from3d_params",
+]