niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/imstack.py

@@ -0,0 +1,209 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+IMSTACK_METADATA = Metadata(
+    id="4d6200fa2e1b9b6bfc0d03b2731f1be8201a7a22.boutiques",
+    name="imstack",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+ImstackParameters = typing.TypedDict('ImstackParameters', {
+    "__STYX_TYPE__": typing.Literal["imstack"],
+    "image_files": list[InputPathType],
+    "data_type": typing.NotRequired[typing.Literal["short", "float"] | None],
+    "output_prefix": typing.NotRequired[str | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "imstack": imstack_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 {
+        "imstack": imstack_outputs,
+    }.get(t)
+
+
+class ImstackOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `imstack(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_data_file: OutputPathType | None
+    """Output data file"""
+    output_header_file: OutputPathType | None
+    """Output header file"""
+
+
+def imstack_params(
+    image_files: list[InputPathType],
+    data_type: typing.Literal["short", "float"] | None = None,
+    output_prefix: str | None = None,
+) -> ImstackParameters:
+    """
+    Build parameters.
+    
+    Args:
+        image_files: Input image filenames.
+        data_type: Converts the output data file to be 'type', which is either\
+            'short' or 'float'. The default type is the type of the first image.
+        output_prefix: Names the output files to be 'name'.b'type' and\
+            'name'.hdr. The default name is 'obi-wan-kenobi'.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "imstack",
+        "image_files": image_files,
+    }
+    if data_type is not None:
+        params["data_type"] = data_type
+    if output_prefix is not None:
+        params["output_prefix"] = output_prefix
+    return params
+
+
+def imstack_cargs(
+    params: ImstackParameters,
+    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("imstack")
+    cargs.extend([execution.input_file(f) for f in params.get("image_files")])
+    if params.get("data_type") is not None:
+        cargs.extend([
+            "-datum",
+            params.get("data_type")
+        ])
+    if params.get("output_prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("output_prefix")
+        ])
+    return cargs
+
+
+def imstack_outputs(
+    params: ImstackParameters,
+    execution: Execution,
+) -> ImstackOutputs:
+    """
+    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 = ImstackOutputs(
+        root=execution.output_file("."),
+        output_data_file=execution.output_file(params.get("output_prefix") + ".b" + params.get("data_type")) if (params.get("output_prefix") is not None and params.get("data_type") is not None) else None,
+        output_header_file=execution.output_file(params.get("output_prefix") + ".hdr") if (params.get("output_prefix") is not None) else None,
+    )
+    return ret
+
+
+def imstack_execute(
+    params: ImstackParameters,
+    execution: Execution,
+) -> ImstackOutputs:
+    """
+    Stacks up a set of 2D images into one big file (a la MGH).
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `ImstackOutputs`).
+    """
+    params = execution.params(params)
+    cargs = imstack_cargs(params, execution)
+    ret = imstack_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def imstack(
+    image_files: list[InputPathType],
+    data_type: typing.Literal["short", "float"] | None = None,
+    output_prefix: str | None = None,
+    runner: Runner | None = None,
+) -> ImstackOutputs:
+    """
+    Stacks up a set of 2D images into one big file (a la MGH).
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        image_files: Input image filenames.
+        data_type: Converts the output data file to be 'type', which is either\
+            'short' or 'float'. The default type is the type of the first image.
+        output_prefix: Names the output files to be 'name'.b'type' and\
+            'name'.hdr. The default name is 'obi-wan-kenobi'.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `ImstackOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(IMSTACK_METADATA)
+    params = imstack_params(
+        image_files=image_files,
+        data_type=data_type,
+        output_prefix=output_prefix,
+    )
+    return imstack_execute(params, execution)
+
+
+__all__ = [
+    "IMSTACK_METADATA",
+    "ImstackOutputs",
+    "ImstackParameters",
+    "imstack",
+    "imstack_params",
+]

niwrap_afni/afni/imstat.py

@@ -0,0 +1,217 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+IMSTAT_METADATA = Metadata(
+    id="c59c01eb2a12e7d9a2066403a73878b709e55aa5.boutiques",
+    name="imstat",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+ImstatParameters = typing.TypedDict('ImstatParameters', {
+    "__STYX_TYPE__": typing.Literal["imstat"],
+    "no_label": bool,
+    "quiet": bool,
+    "pixstat_prefix": typing.NotRequired[str | None],
+    "image_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 {
+        "imstat": imstat_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 {
+        "imstat": imstat_outputs,
+    }.get(t)
+
+
+class ImstatOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `imstat(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    mean_output: OutputPathType | None
+    """Mean of pixel-wise statistics for the collection of 2D images"""
+    sdev_output: OutputPathType | None
+    """Standard deviation of pixel-wise statistics for the collection of 2D
+    images"""
+
+
+def imstat_params(
+    image_files: list[InputPathType],
+    no_label: bool = False,
+    quiet: bool = False,
+    pixstat_prefix: str | None = None,
+) -> ImstatParameters:
+    """
+    Build parameters.
+    
+    Args:
+        image_files: Input image file(s).
+        no_label: Don't write labels on each file's summary line.
+        quiet: Don't print statistics for each file.
+        pixstat_prefix: If more than one image file is given, then\
+            'prefix.mean' and 'prefix.sdev' will be written as the pixel-wise\
+            statistics images of the whole collection. These images will be in the\
+            'flim' floating point format. [This option only works on 2D images!].
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "imstat",
+        "no_label": no_label,
+        "quiet": quiet,
+        "image_files": image_files,
+    }
+    if pixstat_prefix is not None:
+        params["pixstat_prefix"] = pixstat_prefix
+    return params
+
+
+def imstat_cargs(
+    params: ImstatParameters,
+    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("imstat")
+    if params.get("no_label"):
+        cargs.append("-nolabel")
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    if params.get("pixstat_prefix") is not None:
+        cargs.extend([
+            "-pixstat",
+            params.get("pixstat_prefix")
+        ])
+    cargs.extend([execution.input_file(f) for f in params.get("image_files")])
+    return cargs
+
+
+def imstat_outputs(
+    params: ImstatParameters,
+    execution: Execution,
+) -> ImstatOutputs:
+    """
+    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 = ImstatOutputs(
+        root=execution.output_file("."),
+        mean_output=execution.output_file(params.get("pixstat_prefix") + ".mean") if (params.get("pixstat_prefix") is not None) else None,
+        sdev_output=execution.output_file(params.get("pixstat_prefix") + ".sdev") if (params.get("pixstat_prefix") is not None) else None,
+    )
+    return ret
+
+
+def imstat_execute(
+    params: ImstatParameters,
+    execution: Execution,
+) -> ImstatOutputs:
+    """
+    Calculation of statistics of one or more images.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `ImstatOutputs`).
+    """
+    params = execution.params(params)
+    cargs = imstat_cargs(params, execution)
+    ret = imstat_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def imstat(
+    image_files: list[InputPathType],
+    no_label: bool = False,
+    quiet: bool = False,
+    pixstat_prefix: str | None = None,
+    runner: Runner | None = None,
+) -> ImstatOutputs:
+    """
+    Calculation of statistics of one or more images.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        image_files: Input image file(s).
+        no_label: Don't write labels on each file's summary line.
+        quiet: Don't print statistics for each file.
+        pixstat_prefix: If more than one image file is given, then\
+            'prefix.mean' and 'prefix.sdev' will be written as the pixel-wise\
+            statistics images of the whole collection. These images will be in the\
+            'flim' floating point format. [This option only works on 2D images!].
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `ImstatOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(IMSTAT_METADATA)
+    params = imstat_params(
+        no_label=no_label,
+        quiet=quiet,
+        pixstat_prefix=pixstat_prefix,
+        image_files=image_files,
+    )
+    return imstat_execute(params, execution)
+
+
+__all__ = [
+    "IMSTAT_METADATA",
+    "ImstatOutputs",
+    "ImstatParameters",
+    "imstat",
+    "imstat_params",
+]

niwrap_afni/afni/imupsam.py

@@ -0,0 +1,205 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+IMUPSAM_METADATA = Metadata(
+    id="156965091ca5242419f26a19463380332f6a9731.boutiques",
+    name="imupsam",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+ImupsamParameters = typing.TypedDict('ImupsamParameters', {
+    "__STYX_TYPE__": typing.Literal["imupsam"],
+    "ascii_flag": bool,
+    "factor": int,
+    "input_image": InputPathType,
+    "output_image": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "imupsam": imupsam_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 {
+        "imupsam": imupsam_outputs,
+    }.get(t)
+
+
+class ImupsamOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `imupsam(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_image_file: OutputPathType
+    """Upsampled image output file"""
+
+
+def imupsam_params(
+    factor: int,
+    input_image: InputPathType,
+    output_image: str,
+    ascii_flag: bool = False,
+) -> ImupsamParameters:
+    """
+    Build parameters.
+    
+    Args:
+        factor: Upsampling factor; must be an integer in the range 2 to 30.
+        input_image: Path of the input 2D image file.
+        output_image: Path of the output upsampled image file. Use '-' to write\
+            to stdout.
+        ascii_flag: Write the result in ASCII format: all numbers for the file\
+            are output, with no header info.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "imupsam",
+        "ascii_flag": ascii_flag,
+        "factor": factor,
+        "input_image": input_image,
+        "output_image": output_image,
+    }
+    return params
+
+
+def imupsam_cargs(
+    params: ImupsamParameters,
+    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("imupsam")
+    if params.get("ascii_flag"):
+        cargs.append("-A")
+    cargs.append(str(params.get("factor")))
+    cargs.append(execution.input_file(params.get("input_image")))
+    cargs.append(params.get("output_image"))
+    return cargs
+
+
+def imupsam_outputs(
+    params: ImupsamParameters,
+    execution: Execution,
+) -> ImupsamOutputs:
+    """
+    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 = ImupsamOutputs(
+        root=execution.output_file("."),
+        output_image_file=execution.output_file(params.get("output_image")),
+    )
+    return ret
+
+
+def imupsam_execute(
+    params: ImupsamParameters,
+    execution: Execution,
+) -> ImupsamOutputs:
+    """
+    Upsamples a 2D image by a specified factor.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `ImupsamOutputs`).
+    """
+    params = execution.params(params)
+    cargs = imupsam_cargs(params, execution)
+    ret = imupsam_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def imupsam(
+    factor: int,
+    input_image: InputPathType,
+    output_image: str,
+    ascii_flag: bool = False,
+    runner: Runner | None = None,
+) -> ImupsamOutputs:
+    """
+    Upsamples a 2D image by a specified factor.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        factor: Upsampling factor; must be an integer in the range 2 to 30.
+        input_image: Path of the input 2D image file.
+        output_image: Path of the output upsampled image file. Use '-' to write\
+            to stdout.
+        ascii_flag: Write the result in ASCII format: all numbers for the file\
+            are output, with no header info.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `ImupsamOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(IMUPSAM_METADATA)
+    params = imupsam_params(
+        ascii_flag=ascii_flag,
+        factor=factor,
+        input_image=input_image,
+        output_image=output_image,
+    )
+    return imupsam_execute(params, execution)
+
+
+__all__ = [
+    "IMUPSAM_METADATA",
+    "ImupsamOutputs",
+    "ImupsamParameters",
+    "imupsam",
+    "imupsam_params",
+]