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

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github poldracklab / mriqc / mriqc / interfaces / common.py View on Github external
def _run_interface(self, runtime):
        nii = nb.load(self.inputs.in_file)
        zooms = nii.header.get_zooms()
        size_diff = np.array(zooms[:3]) - (self.inputs.pixel_size - 0.1)
        if np.all(size_diff >= -1e-3):
            config.loggers.interface.info("Voxel size is large enough")
            self._results["out_file"] = self.inputs.in_file
            if isdefined(self.inputs.in_mask):
                self._results["out_mask"] = self.inputs.in_mask
            return runtime

        config.loggers.interface.info(
            "One or more voxel dimensions (%f, %f, %f) are smaller than "
            "the requested voxel size (%f) - diff=(%f, %f, %f)",
            zooms[0],
            zooms[1],
            zooms[2],
            self.inputs.pixel_size,
            size_diff[0],
            size_diff[1],
            size_diff[2],
        )

        # Figure out new matrix
        # 1) Get base affine
        aff_base = nii.header.get_base_affine()
        aff_base_inv = np.linalg.inv(aff_base)
github poldracklab / mriqc / mriqc / qc / anatomical.py View on Github external
.. math::

        \text{SNR} = \frac{\mu_F}{\sqrt{\frac{2}{4-\pi}}\,\sigma_\text{air}}.


    :param float mu_fg: mean of foreground.
    :param float sigma_air: standard deviation of the air surrounding the head ("hat" mask).

    :return: the computed SNR for the foreground segmentation

    """
    if sigma_air < 1.0:
        from .. import config

        config.loggers.interface.warning(
            f"SNRd - background sigma is too small ({sigma_air})"
        )
        sigma_air += 1.0

    return float(DIETRICH_FACTOR * mu_fg / sigma_air)
github poldracklab / mriqc / mriqc / classifier / data.py View on Github external
)
        x_df = x_df.drop(nan_labels)

    # Print out some info
    nsamples = len(x_df)
    config.loggers.interface.info(
        f'Created dataset X="{feat_file}", Y="{label_file}" (N={nsamples} valid samples)'
    )

    # Inform about ratings distribution
    labels = sorted(list(set(x_df[rate_label].values.ravel().tolist())))
    ldist = []
    for l in labels:
        ldist.append(int(np.sum(x_df[rate_label] == l)))

    config.loggers.interface.info(
        "Ratings distribution: %s (%s, %s)",
        "/".join(["%d" % x for x in ldist]),
        "/".join(["%.2f%%" % (100 * x / nsamples) for x in ldist]),
        "accept/exclude" if len(ldist) == 2 else "exclude/doubtful/accept",
    )

    return x_df, feat_names
github poldracklab / mriqc / mriqc / interfaces / webapi.py View on Github external
url.netloc,
            path=path,
            scheme=url.scheme,
            port=port,
            email=email,
        )

        try:
            self._results["api_id"] = response.json()["_id"]
        except (AttributeError, KeyError, ValueError):
            # response did not give us an ID
            errmsg = (
                "QC metrics upload failed to create an ID for the record "
                "uplOADED. rEsponse from server follows: {}".format(response.text)
            )
            config.loggers.interface.warning(errmsg)

        if response.status_code == 201:
            config.loggers.interface.info("QC metrics successfully uploaded.")
            return runtime

        errmsg = "QC metrics failed to upload. Status %d: %s" % (
            response.status_code,
            response.text,
        )
        config.loggers.interface.warning(errmsg)
        if self.inputs.strict:
            raise RuntimeError(response.text)

        return runtime
github poldracklab / mriqc / mriqc / interfaces / bids.py View on Github external
if not isdefined(val) or key == "trait_added":
                continue

            if not self.expr.match(key) is None:
                root_adds.append(key)
                continue

            key, val = _process_name(key, val)
            self._out_dict[key] = val

        for root_key in root_adds:
            val = self.inputs._outputs.get(root_key, None)
            if isinstance(val, dict):
                self._out_dict.update(val)
            else:
                config.loggers.interface.warning(
                    'Output "%s" is not a dictionary (value="%s"), '
                    "discarding output.",
                    root_key,
                    str(val),
                )

        # Fill in the "bids_meta" key
        id_dict = {}
        for comp in list(BIDS_COMP.keys()):
            comp_val = getattr(self.inputs, comp, None)
            if isdefined(comp_val) and comp_val is not None:
                id_dict[comp] = comp_val
        id_dict["modality"] = self.inputs.modality

        if isdefined(self.inputs.metadata) and self.inputs.metadata:
            id_dict.update(self.inputs.metadata)
github poldracklab / mriqc / mriqc / interfaces / webapi.py View on Github external
# Hash fields that may contain personal information
    data["bids_meta"] = _hashfields(data["bids_meta"])

    if email:
        data["provenance"]["email"] = email

    if path and not path.endswith("/"):
        path += "/"
        if path.startswith("/"):
            path = path[1:]

    headers = {"Authorization": SECRET_KEY, "Content-Type": "application/json"}

    webapi_url = "{}://{}:{}/{}{}".format(scheme, loc, port, path, modality)
    config.loggers.interface.info("MRIQC Web API: submitting to <%s>", webapi_url)
    try:
        # if the modality is bold, call "bold" endpoint
        response = requests.post(webapi_url, headers=headers, data=dumps(data))
    except requests.ConnectionError as err:
        errmsg = (
            "QC metrics failed to upload due to connection error shown below:\n%s" % err
        )
        return Bunch(status_code=1, text=errmsg)

    return response
github poldracklab / mriqc / mriqc / classifier / data.py View on Github external
y_df = y_df[y_df["bids_ids"].isin(list(x_df.bids_ids.values.ravel()))]

    # Drop indexing column
    del x_df["bids_ids"]
    del y_df["bids_ids"]

    # Merge Y dataframe into X
    x_df = pd.merge(x_df, y_df, on=bids_comps_x, how="left")

    if merged_name is not None:
        x_df.to_csv(merged_name, index=False)

    # Drop samples with invalid rating
    nan_labels = x_df[x_df[rate_label].isnull()].index.ravel().tolist()
    if nan_labels:
        config.loggers.interface.info(
            f"Dropping {len(nan_labels)} samples for having non-numerical labels,"
        )
        x_df = x_df.drop(nan_labels)

    # Print out some info
    nsamples = len(x_df)
    config.loggers.interface.info(
        f'Created dataset X="{feat_file}", Y="{label_file}" (N={nsamples} valid samples)'
    )

    # Inform about ratings distribution
    labels = sorted(list(set(x_df[rate_label].values.ravel().tolist())))
    ldist = []
    for l in labels:
        ldist.append(int(np.sum(x_df[rate_label] == l)))
github poldracklab / mriqc / mriqc / qc / anatomical.py View on Github external
}

    if "bg" not in output:
        output["bg"] = {
            "mean": 0.0,
            "median": 0.0,
            "p95": 0.0,
            "p05": 0.0,
            "k": 0.0,
            "stdv": sqrt(sum(val["stdv"] ** 2 for _, val in list(output.items()))),
            "mad": sqrt(sum(val["mad"] ** 2 for _, val in list(output.items()))),
            "n": sum(val["n"] for _, val in list(output.items())),
        }

    if "bg" in output and output["bg"]["mad"] == 0.0 and output["bg"]["stdv"] > 1.0:
        config.loggers.interface.warning(
            "estimated MAD in the background was too small (MAD=%f)",
            output["bg"]["mad"],
        )
        output["bg"]["mad"] = output["bg"]["stdv"] / DIETRICH_FACTOR
    return output
github poldracklab / mriqc / mriqc / interfaces / common.py View on Github external
def _run_interface(self, runtime):
        # Squeeze 4th dimension if possible (#660)
        nii = nb.squeeze_image(nb.load(self.inputs.in_file))
        hdr = nii.header.copy()
        if self.inputs.check_ras:
            nii = nb.as_closest_canonical(nii)

        if self.inputs.check_dtype:
            changed = True
            datatype = int(hdr["datatype"])

            if datatype == 1:
                config.loggers.interface.warning(
                    'Input image %s has a suspicious data type "%s"',
                    self.inputs.in_file,
                    hdr.get_data_dtype(),
                )

            # signed char and bool to uint8
            if datatype == 1 or datatype == 2 or datatype == 256:
                dtype = np.uint8

            # int16 to uint16
            elif datatype == 4:
                dtype = np.uint16

            # Signed long, long long, etc to uint32
            elif datatype == 8 or datatype == 1024 or datatype == 1280:
                dtype = np.uint32