How to use the mriqc.config.loggers.cli function in mriqc

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github poldracklab / mriqc / mriqc / reports / individual.py View on Github external
def _get_details(in_iqms, modality):
        in_prov = in_iqms.pop("provenance", {})
        warn_dict = in_prov.pop("warnings", None)
        sett_dict = in_prov.pop("settings", None)

        wf_details = []
        if modality == "bold":
            bold_exclude_index = in_iqms.get("dumb_trs")
            if bold_exclude_index is None:
                config.loggers.cli.warning(
                    "Building bold report: no exclude index was found"
                )
            elif bold_exclude_index > 0:
                msg = """\
<span class="problematic">Non-steady state (strong T1 contrast) has been detected in the \
first {} volumes</span>. They were excluded before generating any QC measures and plots."""
                wf_details.append(msg.format(bold_exclude_index))

            wf_details.append(
                "Framewise Displacement was computed using <code>3dvolreg</code> (AFNI)")

            fd_thres = sett_dict.pop("fd_thres")
            if fd_thres is not None:
                wf_details.append(
                    "Framewise Displacement threshold was defined at %f mm" % fd_thres
                )
github poldracklab / mriqc / mriqc / cli / parser.py View on Github external
with open(opts.use_plugin) as f:
            plugin_settings = loadyml(f)
        _plugin = plugin_settings.get("plugin")
        if _plugin:
            config.nipype.plugin = _plugin
            config.nipype.plugin_args = plugin_settings.get("plugin_args", {})
            config.nipype.nprocs = config.nipype.plugin_args.get(
                "nprocs", config.nipype.nprocs
            )

    # Resource management options
    # Note that we're making strong assumptions about valid plugin args
    # This may need to be revisited if people try to use batch plugins
    if 1 &lt; config.nipype.nprocs &lt; config.nipype.omp_nthreads:
        config.loggers.cli.warning(
            "Per-process threads (--omp-nthreads=%d) exceed total "
            "threads (--nthreads/--n_cpus=%d)",
            config.nipype.omp_nthreads,
            config.nipype.nprocs,
        )

    bids_dir = config.execution.bids_dir
    output_dir = config.execution.output_dir
    work_dir = config.execution.work_dir
    version = config.environment.version

    # Ensure input and output folders are not the same
    if output_dir == bids_dir:
        parser.error(
            "The selected output folder is the same as the input BIDS folder. "
            "Please modify the output path (suggestion: %s)."
github poldracklab / mriqc / mriqc / reports / group.py View on Github external
id_labels = list(set(def_comps) & set(dataframe.columns.ravel().tolist()))
        dataframe["label"] = dataframe[id_labels].apply(
            _format_labels, args=(id_labels,), axis=1
        )
    else:
        dataframe = pd.read_csv(
            csv_file, index_col=False, sep="\t", dtype={"bids_name": object}
        )
        dataframe = dataframe.rename(index=str, columns={"bids_name": "label"})

    nPart = len(dataframe)

    failed = None
    if csv_failed is not None and op.isfile(csv_failed):
        config.loggers.cli.warning(f'Found failed-workflows table "{csv_failed}"')
        failed_df = pd.read_csv(csv_failed, index_col=False)
        cols = list(set(id_labels) & set(failed_df.columns.ravel().tolist()))

        try:
            failed_df = failed_df.sort_values(by=cols)
        except AttributeError:
            failed_df = failed_df.sort(columns=cols)

        # myfmt not defined
        # failed = failed_df[cols].apply(myfmt, args=(cols,), axis=1).ravel().tolist()

    csv_groups = []
    datacols = dataframe.columns.ravel().tolist()
    for group, units in QCGROUPS[mod]:
        dfdict = {"iqm": [], "value": [], "label": [], "units": []}
github poldracklab / mriqc / mriqc / cli / run.py View on Github external
mriqc_wf.write_graph(graph2use="colored", format="svg", simple_form=True)

        # Clean up master process before running workflow, which may create forks
        gc.collect()

        if not config.execution.dry_run:
            # Warn about submitting measures BEFORE
            if not config.execution.no_sub:
                config.loggers.cli.warning(config.DSA_MESSAGE)

            # run MRIQC
            mriqc_wf.run(**config.nipype.get_plugin())

            # Warn about submitting measures AFTER
            if not config.execution.no_sub:
                config.loggers.cli.warning(config.DSA_MESSAGE)
        config.loggers.cli.log(25, "Participant level finished successfully.")

    # Set up group level
    if "group" in config.workflow.analysis_level:
        from ..utils.bids import DEFAULT_TYPES
        from ..reports import group_html
        from ..utils.misc import generate_tsv  # , generate_pred

        config.loggers.cli.info("Group level started...")

        # Generate reports
        mod_group_reports = []
        for mod in config.execution.modalities or DEFAULT_TYPES:
            output_dir = config.execution.output_dir
            dataframe, out_tsv = generate_tsv(output_dir, mod)
            # If there are no iqm.json files, nothing to do.
github poldracklab / mriqc / mriqc / cli / run.py View on Github external
import gc
    from multiprocessing import Process, Manager
    from .parser import parse_args

    # Run parser
    parse_args()

    # CRITICAL Save the config to a file. This is necessary because the execution graph
    # is built as a separate process to keep the memory footprint low. The most
    # straightforward way to communicate with the child process is via the filesystem.
    config_file = config.execution.work_dir / ".mriqc.toml"
    config.to_filename(config_file)

    # Set up participant level
    if "participant" in config.workflow.analysis_level:
        config.loggers.cli.log(
            25,
            f"""
    Running MRIQC version {config.environment.version}:
      * BIDS dataset path: {config.execution.bids_dir}.
      * Output folder: {config.execution.output_dir}.
      * Analysis levels: {config.workflow.analysis_level}.
""",
        )
        # CRITICAL Call build_workflow(config_file, retval) in a subprocess.
        # Because Python on Linux does not ever free virtual memory (VM), running the
        # workflow construction jailed within a process preempts excessive VM buildup.
        with Manager() as mgr:
            from .workflow import build_workflow

            retval = mgr.dict()
            p = Process(target=build_workflow, args=(str(config_file), retval))