niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/abids_json_info_py.py

@@ -0,0 +1,247 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+ABIDS_JSON_INFO_PY_METADATA = Metadata(
+    id="29b15b0c3b3b92b7936e8e79bd8f79411f0e65a4.boutiques",
+    name="abids_json_info.py",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+AbidsJsonInfoPyParameters = typing.TypedDict('AbidsJsonInfoPyParameters', {
+    "__STYX_TYPE__": typing.Literal["abids_json_info.py"],
+    "json_files": list[InputPathType],
+    "tr_flag": bool,
+    "te_flag": bool,
+    "te_sec_flag": bool,
+    "match_nii_flag": bool,
+    "field_list": typing.NotRequired[list[str] | None],
+    "list_fields_flag": bool,
+    "help_flag": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "abids_json_info.py": abids_json_info_py_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 AbidsJsonInfoPyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `abids_json_info_py(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def abids_json_info_py_params(
+    json_files: list[InputPathType],
+    tr_flag: bool = False,
+    te_flag: bool = False,
+    te_sec_flag: bool = False,
+    match_nii_flag: bool = False,
+    field_list: list[str] | None = None,
+    list_fields_flag: bool = False,
+    help_flag: bool = False,
+) -> AbidsJsonInfoPyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        json_files: Specify .json file(s).
+        tr_flag: Print the TR from the json file in seconds, from the\
+            'RepetitionTime' field.
+        te_flag: Print out the 'EchoTime' field in milliseconds (the json file\
+            stores it in seconds).
+        te_sec_flag: Print the 'EchoTime' field in seconds.
+        match_nii_flag: Check if there is a .nii or .nii.gz file that matches\
+            the .json file (1 if the dataset is loadable).
+        field_list: Print any field or list of fields from the json file.
+        list_fields_flag: Print a list of the available fields from the .json\
+            file. This must be the only argument specified.
+        help_flag: Show this help message and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "abids_json_info.py",
+        "json_files": json_files,
+        "tr_flag": tr_flag,
+        "te_flag": te_flag,
+        "te_sec_flag": te_sec_flag,
+        "match_nii_flag": match_nii_flag,
+        "list_fields_flag": list_fields_flag,
+        "help_flag": help_flag,
+    }
+    if field_list is not None:
+        params["field_list"] = field_list
+    return params
+
+
+def abids_json_info_py_cargs(
+    params: AbidsJsonInfoPyParameters,
+    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("abids_json_info.py")
+    cargs.extend([execution.input_file(f) for f in params.get("json_files")])
+    if params.get("tr_flag"):
+        cargs.append("-TR")
+    if params.get("te_flag"):
+        cargs.append("-TE")
+    if params.get("te_sec_flag"):
+        cargs.append("-TE_sec")
+    if params.get("match_nii_flag"):
+        cargs.append("-match_nii")
+    if params.get("field_list") is not None:
+        cargs.extend([
+            "-field",
+            *params.get("field_list")
+        ])
+    if params.get("list_fields_flag"):
+        cargs.append("-list_fields")
+    if params.get("help_flag"):
+        cargs.append("-help")
+    return cargs
+
+
+def abids_json_info_py_outputs(
+    params: AbidsJsonInfoPyParameters,
+    execution: Execution,
+) -> AbidsJsonInfoPyOutputs:
+    """
+    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 = AbidsJsonInfoPyOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def abids_json_info_py_execute(
+    params: AbidsJsonInfoPyParameters,
+    execution: Execution,
+) -> AbidsJsonInfoPyOutputs:
+    """
+    A tool to extract information from BIDS formatted json files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `AbidsJsonInfoPyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = abids_json_info_py_cargs(params, execution)
+    ret = abids_json_info_py_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def abids_json_info_py(
+    json_files: list[InputPathType],
+    tr_flag: bool = False,
+    te_flag: bool = False,
+    te_sec_flag: bool = False,
+    match_nii_flag: bool = False,
+    field_list: list[str] | None = None,
+    list_fields_flag: bool = False,
+    help_flag: bool = False,
+    runner: Runner | None = None,
+) -> AbidsJsonInfoPyOutputs:
+    """
+    A tool to extract information from BIDS formatted json files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        json_files: Specify .json file(s).
+        tr_flag: Print the TR from the json file in seconds, from the\
+            'RepetitionTime' field.
+        te_flag: Print out the 'EchoTime' field in milliseconds (the json file\
+            stores it in seconds).
+        te_sec_flag: Print the 'EchoTime' field in seconds.
+        match_nii_flag: Check if there is a .nii or .nii.gz file that matches\
+            the .json file (1 if the dataset is loadable).
+        field_list: Print any field or list of fields from the json file.
+        list_fields_flag: Print a list of the available fields from the .json\
+            file. This must be the only argument specified.
+        help_flag: Show this help message and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `AbidsJsonInfoPyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ABIDS_JSON_INFO_PY_METADATA)
+    params = abids_json_info_py_params(
+        json_files=json_files,
+        tr_flag=tr_flag,
+        te_flag=te_flag,
+        te_sec_flag=te_sec_flag,
+        match_nii_flag=match_nii_flag,
+        field_list=field_list,
+        list_fields_flag=list_fields_flag,
+        help_flag=help_flag,
+    )
+    return abids_json_info_py_execute(params, execution)
+
+
+__all__ = [
+    "ABIDS_JSON_INFO_PY_METADATA",
+    "AbidsJsonInfoPyOutputs",
+    "AbidsJsonInfoPyParameters",
+    "abids_json_info_py",
+    "abids_json_info_py_params",
+]

niwrap_afni/afni/abids_json_tool_py.py

@@ -0,0 +1,212 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+ABIDS_JSON_TOOL_PY_METADATA = Metadata(
+    id="9cd5d1cbe0772f0f1c51d0bd811ef0336e43437f.boutiques",
+    name="abids_json_tool.py",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+AbidsJsonToolPyParameters = typing.TypedDict('AbidsJsonToolPyParameters', {
+    "__STYX_TYPE__": typing.Literal["abids_json_tool.py"],
+    "input_file": InputPathType,
+    "prefix": str,
+    "del_json": typing.NotRequired[str | None],
+    "values_stay_str": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "abids_json_tool.py": abids_json_tool_py_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 AbidsJsonToolPyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `abids_json_tool_py(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def abids_json_tool_py_params(
+    input_file: InputPathType,
+    prefix: str,
+    del_json: str | None = None,
+    values_stay_str: bool = False,
+) -> AbidsJsonToolPyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: One file to convert. Enter NULL with -add_json to create\
+            new json file.
+        prefix: Output file name.
+        del_json: Remove attribute (KEY) from the -input json file.
+        values_stay_str: Each numeric or str item gets saved as a str;\
+            otherwise, guess at int and float.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "abids_json_tool.py",
+        "input_file": input_file,
+        "prefix": prefix,
+        "values_stay_str": values_stay_str,
+    }
+    if del_json is not None:
+        params["del_json"] = del_json
+    return params
+
+
+def abids_json_tool_py_cargs(
+    params: AbidsJsonToolPyParameters,
+    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("abids_json_tool.py")
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input_file"))
+    ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("del_json") is not None:
+        cargs.extend([
+            "-del_json",
+            params.get("del_json")
+        ])
+    if params.get("values_stay_str"):
+        cargs.append("-values_stay_str")
+    return cargs
+
+
+def abids_json_tool_py_outputs(
+    params: AbidsJsonToolPyParameters,
+    execution: Execution,
+) -> AbidsJsonToolPyOutputs:
+    """
+    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 = AbidsJsonToolPyOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def abids_json_tool_py_execute(
+    params: AbidsJsonToolPyParameters,
+    execution: Execution,
+) -> AbidsJsonToolPyOutputs:
+    """
+    This script helps to manipulate json files in various ways.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `AbidsJsonToolPyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = abids_json_tool_py_cargs(params, execution)
+    ret = abids_json_tool_py_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def abids_json_tool_py(
+    input_file: InputPathType,
+    prefix: str,
+    del_json: str | None = None,
+    values_stay_str: bool = False,
+    runner: Runner | None = None,
+) -> AbidsJsonToolPyOutputs:
+    """
+    This script helps to manipulate json files in various ways.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: One file to convert. Enter NULL with -add_json to create\
+            new json file.
+        prefix: Output file name.
+        del_json: Remove attribute (KEY) from the -input json file.
+        values_stay_str: Each numeric or str item gets saved as a str;\
+            otherwise, guess at int and float.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `AbidsJsonToolPyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ABIDS_JSON_TOOL_PY_METADATA)
+    params = abids_json_tool_py_params(
+        input_file=input_file,
+        prefix=prefix,
+        del_json=del_json,
+        values_stay_str=values_stay_str,
+    )
+    return abids_json_tool_py_execute(params, execution)
+
+
+__all__ = [
+    "ABIDS_JSON_TOOL_PY_METADATA",
+    "AbidsJsonToolPyOutputs",
+    "AbidsJsonToolPyParameters",
+    "abids_json_tool_py",
+    "abids_json_tool_py_params",
+]

niwrap_afni/afni/abids_tool.py

@@ -0,0 +1,191 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+ABIDS_TOOL_METADATA = Metadata(
+    id="ecdd7e187a3a330cd02d094f809fb0b75a51fe76.boutiques",
+    name="abids_tool",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+AbidsToolParameters = typing.TypedDict('AbidsToolParameters', {
+    "__STYX_TYPE__": typing.Literal["abids_tool"],
+    "input_files": list[InputPathType],
+    "copy_prefix": typing.NotRequired[list[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 {
+        "abids_tool": abids_tool_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 AbidsToolOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `abids_tool(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def abids_tool_params(
+    input_files: list[InputPathType],
+    copy_prefix: list[str] | None = None,
+) -> AbidsToolParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_files: At least one 3d+time dataset in NIFTI format.
+        copy_prefix: Copy both the NIFTI dataset(s) and matching .json file(s)\
+            to PREFIX. Must have the same number of prefixes as datasets.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "abids_tool",
+        "input_files": input_files,
+    }
+    if copy_prefix is not None:
+        params["copy_prefix"] = copy_prefix
+    return params
+
+
+def abids_tool_cargs(
+    params: AbidsToolParameters,
+    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("abids_tool.py")
+    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
+    if params.get("copy_prefix") is not None:
+        cargs.extend([
+            "-copy",
+            *params.get("copy_prefix")
+        ])
+    return cargs
+
+
+def abids_tool_outputs(
+    params: AbidsToolParameters,
+    execution: Execution,
+) -> AbidsToolOutputs:
+    """
+    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 = AbidsToolOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def abids_tool_execute(
+    params: AbidsToolParameters,
+    execution: Execution,
+) -> AbidsToolOutputs:
+    """
+    A tool to work with BIDS formatted datasets created with dcm2niix_afni or
+    dcm2niix, mainly to pull information from the matching JSON file and refit the
+    input dataset using 3drefit.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `AbidsToolOutputs`).
+    """
+    params = execution.params(params)
+    cargs = abids_tool_cargs(params, execution)
+    ret = abids_tool_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def abids_tool(
+    input_files: list[InputPathType],
+    copy_prefix: list[str] | None = None,
+    runner: Runner | None = None,
+) -> AbidsToolOutputs:
+    """
+    A tool to work with BIDS formatted datasets created with dcm2niix_afni or
+    dcm2niix, mainly to pull information from the matching JSON file and refit the
+    input dataset using 3drefit.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_files: At least one 3d+time dataset in NIFTI format.
+        copy_prefix: Copy both the NIFTI dataset(s) and matching .json file(s)\
+            to PREFIX. Must have the same number of prefixes as datasets.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `AbidsToolOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ABIDS_TOOL_METADATA)
+    params = abids_tool_params(
+        input_files=input_files,
+        copy_prefix=copy_prefix,
+    )
+    return abids_tool_execute(params, execution)
+
+
+__all__ = [
+    "ABIDS_TOOL_METADATA",
+    "AbidsToolOutputs",
+    "AbidsToolParameters",
+    "abids_tool",
+    "abids_tool_params",
+]