niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/ap_run_simple_rest.py

@@ -0,0 +1,293 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+AP_RUN_SIMPLE_REST_METADATA = Metadata(
+    id="51acc3d2305cb727e55055aa552281969a79036d.boutiques",
+    name="ap_run_simple_rest",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+ApRunSimpleRestParameters = typing.TypedDict('ApRunSimpleRestParameters', {
+    "__STYX_TYPE__": typing.Literal["ap_run_simple_rest"],
+    "anat": typing.NotRequired[InputPathType | None],
+    "epi": list[InputPathType],
+    "nt_rm": typing.NotRequired[float | None],
+    "run_ap": bool,
+    "run_proc": bool,
+    "subjid": typing.NotRequired[str | None],
+    "template": typing.NotRequired[InputPathType | None],
+    "compressor": typing.NotRequired[str | None],
+    "verb": typing.NotRequired[float | None],
+    "echo": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "ap_run_simple_rest": ap_run_simple_rest_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 {
+        "ap_run_simple_rest": ap_run_simple_rest_outputs,
+    }.get(t)
+
+
+class ApRunSimpleRestOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `ap_run_simple_rest(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    run_ap_script: OutputPathType | None
+    """afni_proc.py command script"""
+    proc_script: OutputPathType | None
+    """proc script (if AP is run)"""
+    proc_results_dir: OutputPathType | None
+    """proc results directory (if run)"""
+    text_output_files: OutputPathType
+    """Text output files from AP and proc scripts"""
+
+
+def ap_run_simple_rest_params(
+    epi: list[InputPathType],
+    anat: InputPathType | None = None,
+    nt_rm: float | None = None,
+    run_ap: bool = False,
+    run_proc: bool = False,
+    subjid: str | None = None,
+    template: InputPathType | None = None,
+    compressor: str | None = None,
+    verb: float | None = None,
+    echo: bool = False,
+) -> ApRunSimpleRestParameters:
+    """
+    Build parameters.
+    
+    Args:
+        epi: EPI datasets.
+        anat: Single anatomical dataset.
+        nt_rm: Number of time points to remove from starts of runs.
+        run_ap: Run the afni_proc.py command.
+        run_proc: Run the proc script from afni_proc.py command.
+        subjid: Specify subject ID for file names.
+        template: Specify template for standard space.
+        compressor: Control automatic compression of *.BRIK files.
+        verb: Specify verbosity level.
+        echo: Same as verbosity level 3.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "ap_run_simple_rest",
+        "epi": epi,
+        "run_ap": run_ap,
+        "run_proc": run_proc,
+        "echo": echo,
+    }
+    if anat is not None:
+        params["anat"] = anat
+    if nt_rm is not None:
+        params["nt_rm"] = nt_rm
+    if subjid is not None:
+        params["subjid"] = subjid
+    if template is not None:
+        params["template"] = template
+    if compressor is not None:
+        params["compressor"] = compressor
+    if verb is not None:
+        params["verb"] = verb
+    return params
+
+
+def ap_run_simple_rest_cargs(
+    params: ApRunSimpleRestParameters,
+    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("ap_run_simple_rest.tcsh")
+    if params.get("anat") is not None:
+        cargs.extend([
+            "-anat",
+            execution.input_file(params.get("anat"))
+        ])
+    cargs.extend([
+        "-epi",
+        *[execution.input_file(f) for f in params.get("epi")]
+    ])
+    if params.get("nt_rm") is not None:
+        cargs.extend([
+            "-nt_rm",
+            str(params.get("nt_rm"))
+        ])
+    if params.get("run_ap"):
+        cargs.append("-run_ap")
+    if params.get("run_proc"):
+        cargs.append("-run_proc")
+    if params.get("subjid") is not None:
+        cargs.extend([
+            "-subjid",
+            params.get("subjid")
+        ])
+    if params.get("template") is not None:
+        cargs.extend([
+            "-template",
+            execution.input_file(params.get("template"))
+        ])
+    if params.get("compressor") is not None:
+        cargs.extend([
+            "-compressor",
+            params.get("compressor")
+        ])
+    if params.get("verb") is not None:
+        cargs.extend([
+            "-verb",
+            str(params.get("verb"))
+        ])
+    if params.get("echo"):
+        cargs.append("-echo")
+    return cargs
+
+
+def ap_run_simple_rest_outputs(
+    params: ApRunSimpleRestParameters,
+    execution: Execution,
+) -> ApRunSimpleRestOutputs:
+    """
+    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 = ApRunSimpleRestOutputs(
+        root=execution.output_file("."),
+        run_ap_script=execution.output_file("run_ap_" + params.get("subjid")) if (params.get("subjid") is not None) else None,
+        proc_script=execution.output_file("proc." + params.get("subjid")) if (params.get("subjid") is not None) else None,
+        proc_results_dir=execution.output_file(params.get("subjid") + ".results") if (params.get("subjid") is not None) else None,
+        text_output_files=execution.output_file("out.*"),
+    )
+    return ret
+
+
+def ap_run_simple_rest_execute(
+    params: ApRunSimpleRestParameters,
+    execution: Execution,
+) -> ApRunSimpleRestOutputs:
+    """
+    Run a quick afni_proc.py analysis for QC.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `ApRunSimpleRestOutputs`).
+    """
+    params = execution.params(params)
+    cargs = ap_run_simple_rest_cargs(params, execution)
+    ret = ap_run_simple_rest_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def ap_run_simple_rest(
+    epi: list[InputPathType],
+    anat: InputPathType | None = None,
+    nt_rm: float | None = None,
+    run_ap: bool = False,
+    run_proc: bool = False,
+    subjid: str | None = None,
+    template: InputPathType | None = None,
+    compressor: str | None = None,
+    verb: float | None = None,
+    echo: bool = False,
+    runner: Runner | None = None,
+) -> ApRunSimpleRestOutputs:
+    """
+    Run a quick afni_proc.py analysis for QC.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        epi: EPI datasets.
+        anat: Single anatomical dataset.
+        nt_rm: Number of time points to remove from starts of runs.
+        run_ap: Run the afni_proc.py command.
+        run_proc: Run the proc script from afni_proc.py command.
+        subjid: Specify subject ID for file names.
+        template: Specify template for standard space.
+        compressor: Control automatic compression of *.BRIK files.
+        verb: Specify verbosity level.
+        echo: Same as verbosity level 3.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `ApRunSimpleRestOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(AP_RUN_SIMPLE_REST_METADATA)
+    params = ap_run_simple_rest_params(
+        anat=anat,
+        epi=epi,
+        nt_rm=nt_rm,
+        run_ap=run_ap,
+        run_proc=run_proc,
+        subjid=subjid,
+        template=template,
+        compressor=compressor,
+        verb=verb,
+        echo=echo,
+    )
+    return ap_run_simple_rest_execute(params, execution)
+
+
+__all__ = [
+    "AP_RUN_SIMPLE_REST_METADATA",
+    "ApRunSimpleRestOutputs",
+    "ApRunSimpleRestParameters",
+    "ap_run_simple_rest",
+    "ap_run_simple_rest_params",
+]

niwrap_afni/afni/apqc_make_html.py

@@ -0,0 +1,175 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+APQC_MAKE_HTML_METADATA = Metadata(
+    id="a958dc9e454decaf99b430f63930ca86b1108a1f.boutiques",
+    name="apqc_make_html",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+ApqcMakeHtmlParameters = typing.TypedDict('ApqcMakeHtmlParameters', {
+    "__STYX_TYPE__": typing.Literal["apqc_make_html"],
+    "qc_dir": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "apqc_make_html": apqc_make_html_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 ApqcMakeHtmlOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `apqc_make_html(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def apqc_make_html_params(
+    qc_dir: str,
+) -> ApqcMakeHtmlParameters:
+    """
+    Build parameters.
+    
+    Args:
+        qc_dir: Directory where QC files will be saved.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "apqc_make_html",
+        "qc_dir": qc_dir,
+    }
+    return params
+
+
+def apqc_make_html_cargs(
+    params: ApqcMakeHtmlParameters,
+    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("apqc_make_html.py")
+    cargs.extend([
+        "-qc_dir",
+        params.get("qc_dir")
+    ])
+    return cargs
+
+
+def apqc_make_html_outputs(
+    params: ApqcMakeHtmlParameters,
+    execution: Execution,
+) -> ApqcMakeHtmlOutputs:
+    """
+    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 = ApqcMakeHtmlOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def apqc_make_html_execute(
+    params: ApqcMakeHtmlParameters,
+    execution: Execution,
+) -> ApqcMakeHtmlOutputs:
+    """
+    Tool to generate HTML reports.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `ApqcMakeHtmlOutputs`).
+    """
+    params = execution.params(params)
+    cargs = apqc_make_html_cargs(params, execution)
+    ret = apqc_make_html_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def apqc_make_html(
+    qc_dir: str,
+    runner: Runner | None = None,
+) -> ApqcMakeHtmlOutputs:
+    """
+    Tool to generate HTML reports.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        qc_dir: Directory where QC files will be saved.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `ApqcMakeHtmlOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(APQC_MAKE_HTML_METADATA)
+    params = apqc_make_html_params(
+        qc_dir=qc_dir,
+    )
+    return apqc_make_html_execute(params, execution)
+
+
+__all__ = [
+    "APQC_MAKE_HTML_METADATA",
+    "ApqcMakeHtmlOutputs",
+    "ApqcMakeHtmlParameters",
+    "apqc_make_html",
+    "apqc_make_html_params",
+]

niwrap_afni/afni/apqc_make_tcsh_py.py

@@ -0,0 +1,245 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+APQC_MAKE_TCSH_PY_METADATA = Metadata(
+    id="9963574d56b682af5542493c6e37b26eeae1361e.boutiques",
+    name="apqc_make_tcsh.py",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+ApqcMakeTcshPyParameters = typing.TypedDict('ApqcMakeTcshPyParameters', {
+    "__STYX_TYPE__": typing.Literal["apqc_make_tcsh.py"],
+    "uvar_json": InputPathType,
+    "subj_dir": str,
+    "review_style": typing.NotRequired[str | None],
+    "mot_grayplot_off": bool,
+    "vstat_list": 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 {
+        "apqc_make_tcsh.py": apqc_make_tcsh_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 {
+        "apqc_make_tcsh.py": apqc_make_tcsh_py_outputs,
+    }.get(t)
+
+
+class ApqcMakeTcshPyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `apqc_make_tcsh_py(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    qc_html: OutputPathType
+    """Quality Control HTML file generated by APQC."""
+
+
+def apqc_make_tcsh_py_params(
+    uvar_json: InputPathType,
+    subj_dir: str,
+    review_style: str | None = None,
+    mot_grayplot_off: bool = False,
+    vstat_list: list[str] | None = None,
+) -> ApqcMakeTcshPyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        uvar_json: Text file of user variables created by gen_ss_review.py that\
+            catalogs important files in the results directory for the APQC.
+        subj_dir: Location of AP results directory (often '.', as this program\
+            is often run from within the AP results directory).
+        review_style: The 'style' of the APQC HTML output HTML. Allowed\
+            keywords are: {none, basic, pythonic}. Using 'pythonic' is recommended.
+        mot_grayplot_off: Turn off the grayplot generation. This option was\
+            created for a specific case with a large dataset. Not recommended to\
+            use generally.
+        vstat_list: Provide a list of label items to specify which volume's\
+            images should appear in the vstat QC block. Each item should correspond\
+            to subbrick label basename in the stats_dset. 'Full_Fstat' is always\
+            included. If not used, default logic picks up to 5 items to show.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "apqc_make_tcsh.py",
+        "uvar_json": uvar_json,
+        "subj_dir": subj_dir,
+        "mot_grayplot_off": mot_grayplot_off,
+    }
+    if review_style is not None:
+        params["review_style"] = review_style
+    if vstat_list is not None:
+        params["vstat_list"] = vstat_list
+    return params
+
+
+def apqc_make_tcsh_py_cargs(
+    params: ApqcMakeTcshPyParameters,
+    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("apqc_make_tcsh.py")
+    cargs.extend([
+        "-uvar_json",
+        execution.input_file(params.get("uvar_json"))
+    ])
+    cargs.extend([
+        "-subj_dir",
+        params.get("subj_dir")
+    ])
+    if params.get("review_style") is not None:
+        cargs.extend([
+            "-review_style",
+            params.get("review_style")
+        ])
+    if params.get("mot_grayplot_off"):
+        cargs.append("-mot_grayplot_off")
+    if params.get("vstat_list") is not None:
+        cargs.extend([
+            "-vstat_list",
+            *params.get("vstat_list")
+        ])
+    return cargs
+
+
+def apqc_make_tcsh_py_outputs(
+    params: ApqcMakeTcshPyParameters,
+    execution: Execution,
+) -> ApqcMakeTcshPyOutputs:
+    """
+    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 = ApqcMakeTcshPyOutputs(
+        root=execution.output_file("."),
+        qc_html=execution.output_file("qc_*"),
+    )
+    return ret
+
+
+def apqc_make_tcsh_py_execute(
+    params: ApqcMakeTcshPyParameters,
+    execution: Execution,
+) -> ApqcMakeTcshPyOutputs:
+    """
+    This program creates the single subject (ss) HTML review script
+    '@ss_review_html' which generates images and text for the afni_proc.py quality
+    control (APQC) HTML.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `ApqcMakeTcshPyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = apqc_make_tcsh_py_cargs(params, execution)
+    ret = apqc_make_tcsh_py_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def apqc_make_tcsh_py(
+    uvar_json: InputPathType,
+    subj_dir: str,
+    review_style: str | None = None,
+    mot_grayplot_off: bool = False,
+    vstat_list: list[str] | None = None,
+    runner: Runner | None = None,
+) -> ApqcMakeTcshPyOutputs:
+    """
+    This program creates the single subject (ss) HTML review script
+    '@ss_review_html' which generates images and text for the afni_proc.py quality
+    control (APQC) HTML.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        uvar_json: Text file of user variables created by gen_ss_review.py that\
+            catalogs important files in the results directory for the APQC.
+        subj_dir: Location of AP results directory (often '.', as this program\
+            is often run from within the AP results directory).
+        review_style: The 'style' of the APQC HTML output HTML. Allowed\
+            keywords are: {none, basic, pythonic}. Using 'pythonic' is recommended.
+        mot_grayplot_off: Turn off the grayplot generation. This option was\
+            created for a specific case with a large dataset. Not recommended to\
+            use generally.
+        vstat_list: Provide a list of label items to specify which volume's\
+            images should appear in the vstat QC block. Each item should correspond\
+            to subbrick label basename in the stats_dset. 'Full_Fstat' is always\
+            included. If not used, default logic picks up to 5 items to show.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `ApqcMakeTcshPyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(APQC_MAKE_TCSH_PY_METADATA)
+    params = apqc_make_tcsh_py_params(
+        uvar_json=uvar_json,
+        subj_dir=subj_dir,
+        review_style=review_style,
+        mot_grayplot_off=mot_grayplot_off,
+        vstat_list=vstat_list,
+    )
+    return apqc_make_tcsh_py_execute(params, execution)
+
+
+__all__ = [
+    "APQC_MAKE_TCSH_PY_METADATA",
+    "ApqcMakeTcshPyOutputs",
+    "ApqcMakeTcshPyParameters",
+    "apqc_make_tcsh_py",
+    "apqc_make_tcsh_py_params",
+]