dclab 0.67.0__cp314-cp314-macosx_11_0_arm64.whl

dclab/rtdc_dataset/check.py

@@ -0,0 +1,902 @@
+"""Check RT-DC datasets for completeness"""
+import copy
+import functools
+import warnings
+
+import h5py
+import numpy as np
+
+from .copier import is_properly_compressed
+from .core import RTDCBase
+from .fmt_hdf5 import RTDC_HDF5
+from .fmt_hierarchy import RTDC_Hierarchy
+from .load import load_file
+
+from .. import definitions as dfn
+
+#: These sections should be fully present, except for the
+#: keys in :data:`OPTIONAL_KEYS`.
+DESIRABLE_SECTIONS = {
+    "experiment",
+    "imaging",
+    "setup",
+}
+
+#: log names that end with these strings are not checked
+IGNORED_LOG_NAMES = {
+    "_para.ini",
+    "_image.ini",
+    "FG_Config.mcf",
+    "parameters.txt",
+    "_SoftwareSettings.ini",
+    "dckit-history",
+}
+
+#: keys that must be present for every measurement
+IMPORTANT_KEYS = {
+    "experiment": [
+        "date",
+        "event count",
+        "run index",
+        "sample",
+        "time"],
+    "imaging": [
+        "flash device",
+        "flash duration",
+        "frame rate",
+        "pixel size",
+        "roi position x",
+        "roi position y",
+        "roi size x",
+        "roi size y"],
+    "setup": [
+        "channel width",
+        "chip region",
+        "flow rate",
+        "medium"],
+}
+
+#: keys that must be present for fluorescence measurements
+IMPORTANT_KEYS_FL = {
+    "fluorescence": [
+        "bit depth",
+        "channel count",
+        "channels installed",
+        "laser count",
+        "lasers installed",
+        "sample rate",
+        "samples per event",
+        "signal max",
+        "signal min",
+        "trace median"],
+}
+
+#: maximum line length in log files
+LOG_MAX_LINE_LENGTH = 100
+
+#: keys that are optional
+OPTIONAL_KEYS = {
+    "experiment": [
+        "run identifier",
+        "timestamp",
+    ],
+    "fluorescence": [
+        "baseline 1 offset",
+        "baseline 2 offset",
+        "baseline 3 offset",
+        # name, lambda, power have their own special tests
+        "channel 1 name",
+        "channel 2 name",
+        "channel 3 name",
+        "laser 1 lambda",
+        "laser 2 lambda",
+        "laser 3 lambda",
+        "laser 1 power",
+        "laser 2 power",
+        "laser 3 power",
+    ],
+    "setup": [
+        "temperature",
+        "chip identifier",
+    ],
+}
+
+#: valid metadata choices
+#: .. versionchanged:: 0.29.1
+#:    medium not restricted to certain set of choices anymore
+VALID_CHOICES = {}
+
+
+@functools.total_ordering
+class ICue(object):
+    def __init__(self, msg, level, category, data=None, identifier=None,
+                 cfg_section=None, cfg_key=None, cfg_choices=None):
+        """Integrity cue"""
+        #: human-readable message
+        self.msg = msg
+        #: severity level ("violation", "alert", or "info")
+        self.level = level
+        #: machine-readable data associated with the check
+        self.data = data
+        #: fail category
+        self.category = category
+        #: identifier e.g. for UI manipulation in DCKit
+        self.identifier = identifier
+        #: section (only for categories "missing metadata", "bad metadata")
+        self.cfg_section = cfg_section
+        #: key (only for categories "missing metadata", "bad metadata");
+        #: can be omitted e.g. to communicate that the entire section is
+        #: missing
+        self.cfg_key = cfg_key
+        #: allowed choices for the specific [section]: key combination
+        #: (only for categories "missing metadata", "bad metadata")
+        self.cfg_choices = cfg_choices
+        if self.cfg_choices is None:
+            if (cfg_section in VALID_CHOICES
+                    and cfg_key in VALID_CHOICES[cfg_section]):
+                self.cfg_choices = VALID_CHOICES[cfg_section][cfg_key]
+
+    def __eq__(self, other):
+        leveld = {"info": 0,
+                  "violation": 1,
+                  "alert": 2,
+                  }
+        return ((leveld[self.level], self.cfg_section or "",
+                 self.cfg_key or "", self.category, self.msg) ==
+                (leveld[other.level], other.cfg_section or "",
+                 other.cfg_key or "", other.category, other.msg))
+
+    def __lt__(self, other):
+        leveld = {"info": 0,
+                  "violation": 1,
+                  "alert": 2, }
+        return ((leveld[self.level], self.cfg_section or "",
+                 self.cfg_key or "", self.category, self.msg) <
+                (leveld[other.level], other.cfg_section or "",
+                 other.cfg_key or "", other.category, other.msg))
+
+    def __repr__(self):
+        return f"<ICue: '{self.msg}' at 0x{hex(id(self))}>"
+
+    @staticmethod
+    def get_level_summary(cues):
+        """For a list of ICue, return the abundance of all levels"""
+        levels = {"info": 0,
+                  "alert": 0,
+                  "violation": 0}
+        for cue in cues:
+            levels[cue.level] += 1
+        return levels
+
+
+class IntegrityChecker(object):
+    def __init__(self, path_or_ds):
+        """Check the integrity of a dataset
+
+        The argument must be either a path to an .rtdc or .tdms file
+        or an instance of `RTDCBase`. If a path is given, then all
+        warnings (e.g. UnknownConfigurationKeyWarning) are catched
+        and added to the cue list.
+
+        Usage:
+
+        .. code:: python
+
+            ic = IntegrityChecker("/path/to/data.rtdc")
+            cues = ic.check()
+
+        """
+        self.warn_cues = []
+        if isinstance(path_or_ds, RTDCBase):
+            self.ds = path_or_ds
+            self.finally_close = False
+        else:
+            with warnings.catch_warnings(record=True) as ws:
+                warnings.simplefilter("always")
+                self.ds = load_file(path_or_ds, enable_basins=False)
+                for ww in ws:
+                    self.warn_cues.append(ICue(
+                        msg=f"{ww.category.__name__}: {ww.message}",
+                        level="alert",
+                        category="warning"))
+            self.finally_close = True
+
+    def __enter__(self):
+        return self
+
+    def __exit__(self, *args):
+        # close the file
+        if self.finally_close and hasattr(self.ds, "__exit__"):
+            self.ds.__exit__(*args)
+
+    @property
+    def has_fluorescence(self):
+        if ("fluorescence" in self.ds
+                or "fl1_max" in self.ds
+                or "fl2_max" in self.ds
+                or "fl3_max" in self.ds):
+            fl = True
+        else:
+            fl = False
+        return fl
+
+    def check(self, **kwargs):
+        """Run all checks
+
+        This method calls all class methods that start with `check_`.
+        `kwargs` are passed to all methods. Possible options are:
+
+        - "expand_section" `bool`: add a cue for every missing
+          metadata key if a section is missing
+        """
+        cues = []
+        funcs = IntegrityChecker.__dict__
+        if not len(self.ds) == np.sum(self.ds.filter.all):
+            raise NotImplementedError(
+                "Integrity checks for datasets with active event filters "
+                "are not supported!")
+        elif self.ds.__class__ == RTDC_Hierarchy:
+            raise NotImplementedError(
+                "Integrity checks for 'RTDC_Hierarchy' instances are "
+                "not supported!")
+        for ff in sorted(funcs.keys()):
+            if ff.startswith("check_fl_") and not self.has_fluorescence:
+                # skip
+                continue
+            elif ff.startswith("check_"):
+                cues += funcs[ff](self, **kwargs)
+        return sorted(self.warn_cues + cues)
+
+    def check_basin_features_internal(self, **kwargs):
+        """Check whether internal basin features are properly defined"""
+        cues = []
+        basins = self.ds.basins_get_dicts()
+        for bn in basins:
+            if bn["type"] == "internal":
+                bpaths = bn["paths"]
+                if bpaths != ["basin_events"]:
+                    cues.append(
+                        ICue(msg=f"Uncommon internal basin path: {bpaths}",
+                             level="alert",
+                             category="basin data",
+                             ))
+                else:
+                    if "basin_events" not in self.ds.h5file:
+                        cues.append(
+                            ICue(msg="Missing internal basin group "
+                                     "'basin_events', although an internal "
+                                     "basin is defined",
+                                 level="violation",
+                                 category="basin data",
+                                 ))
+                    else:
+                        for feat in bn["features"]:
+                            if feat not in self.ds.h5file["basin_events"]:
+                                cues.append(
+                                    ICue(msg=f"Missing internal basin "
+                                             f"feature {feat}",
+                                         level="violation",
+                                         category="basin data",
+                                         ))
+        return cues
+
+    def check_compression(self, **kwargs):
+        cues = []
+        if self.ds.format == "tdms":
+            compression = "None"
+            data = {"compressed": 0,
+                    "total": 1,
+                    "uncompressed": 0,
+                    }
+        elif self.ds.format == "hdf5":
+            def iter_count_compression(h5):
+                comp_i = 0
+                noco_i = 0
+                for key in h5:
+                    obj = h5[key]
+                    if isinstance(obj, h5py.Dataset):
+                        if is_properly_compressed(obj):
+                            # data are compressed with at least level 5
+                            comp_i += 1
+                        else:
+                            # no compression
+                            noco_i += 1
+                    elif isinstance(obj, h5py.Group):
+                        coi, noi = iter_count_compression(obj)
+                        comp_i += coi
+                        noco_i += noi
+                    else:
+                        raise ValueError(f"Unknown object: {obj}")
+                return comp_i, noco_i
+
+            comp, noco = iter_count_compression(self.ds.h5file)
+            if noco == 0:
+                compression = "All"
+            elif comp == 0:
+                compression = "None"
+            else:
+                compression = f"Partial ({comp} of {noco+comp})"
+            data = {"compressed": comp,
+                    "total": noco + comp,
+                    "uncompressed": noco,
+                    }
+        else:
+            compression = "Unknown"
+            data = None
+        cues.append(ICue(
+            msg=f"Compression: {compression}",
+            level="info",
+            category="general",
+            data=data))
+        return cues
+
+    def check_empty(self, **kwargs):
+        """The dataset should contain events"""
+        cues = []
+        lends = len(self.ds)
+        if lends == 0:
+            cues.append(ICue(
+                msg="The dataset does not contain any events",
+                level="alert",
+                category="feature data"))
+        return cues
+
+    def check_external_links(self, **kwargs):
+        """An HDF5 dataset should not contain external links"""
+        cues = []
+        if isinstance(self.ds, RTDC_HDF5):
+            has_external, h5object = hdf5_has_external(self.ds.h5file)
+            if has_external:
+                cues.append(ICue(
+                    msg=f"The HDF5 file contains at least one external "
+                        f"link: '{h5object}'",
+                    level="violation",
+                    category="format HDF5"))
+        return cues
+
+    def check_feat_index(self, **kwargs):
+        """The index of the dataset should be monotonous"""
+        cues = []
+        lends = len(self.ds)
+        if "index" in self.ds:
+            if not np.all(self.ds["index"] == np.arange(1, lends + 1)):
+                cues.append(ICue(
+                    msg="The index feature is not enumerated correctly",
+                    level="violation",
+                    category="feature data"))
+        return cues
+
+    def check_feature_size(self, **kwargs):
+        cues = []
+        lends = len(self.ds)
+        for feat in self.ds.features_innate:
+            if feat == "trace":
+                for tr in list(self.ds["trace"].keys()):
+                    if len(self.ds["trace"][tr]) != lends:
+                        cues.append(ICue(
+                            msg=f"Features: wrong event count: 'trace/{tr}' "
+                                + f"({len(self.ds['trace'][tr])} of {lends})",
+                            level="violation",
+                            category="feature size"))
+            else:
+                if len(self.ds[feat]) != lends:
+                    cues.append(ICue(
+                        msg=f"Features: wrong event count: '{feat}' "
+                            + f"({len(self.ds[feat])} of {lends})",
+                        level="violation",
+                        category="feature size"))
+        return cues
+
+    def check_features_unknown_hdf5(self, **kwargs):
+        """Check for features that are not defined in dclab
+
+        The idea here is to make sure that third-party software is made
+        aware of the fact that it is storing unknown features in an HDF5
+        file. If this is the case, then this will e.g. raise an error in
+        DCOR-Aid, such that people don't lose new features upon upload.
+        """
+        # Ignored unknown features are features that are actually known
+        # but omitting them is not a big deal.
+        ignore_unknown_features = [
+            "def",  # An old Shape-In version stored "def" instead of "deform"
+            ]
+        cues = []
+        if self.ds.format == "hdf5":
+            for feat in self.ds.h5file["events"]:
+                if not dfn.feature_exists(feat):
+                    if feat in ignore_unknown_features:
+                        continue
+                    cues.append(ICue(
+                        msg=f"Features: Unknown key '{feat}'",
+                        level="violation",
+                        category="feature unknown"))
+        return cues
+
+    def check_fl_metadata_channel_names(self, **kwargs):
+        cues = []
+        for ii in range(1, 4):
+            chn = f"channel {ii} name"
+            fli = f"fl{ii}_max"
+            if (fli in self.ds
+                    and chn not in self.ds.config["fluorescence"]):
+                # Channel names must be defined when there is
+                # a corresponding fluorescence signal.
+                cues.append(ICue(
+                    msg=f"Metadata: Missing key [fluorescence] '{chn}'",
+                    level="alert",
+                    category="metadata missing",
+                    cfg_section="fluorescence",
+                    cfg_key=chn))
+            elif (fli not in self.ds
+                  and chn in self.ds.config["fluorescence"]):
+                # Channel names must not be defined when there is
+                # no corresponding fluorescence signal.
+                cues.append(ICue(
+                    msg=f"Metadata: Unused key defined [fluorescence] '{chn}'",
+                    level="alert",
+                    category="metadata invalid",
+                    cfg_section="fluorescence",
+                    cfg_key=chn))
+        return cues
+
+    def check_fl_num_channels(self, **kwargs):
+        cues = []
+        # check for number of channels
+        if "channel count" in self.ds.config["fluorescence"]:
+            chc1 = self.ds.config["fluorescence"]["channel count"]
+            chc2 = 0
+            for ii in range(1, 4):
+                chn = f"channel {ii} name"
+                ecn = f"fl{ii}_max"
+                if (chn in self.ds.config["fluorescence"] and
+                        ecn in self.ds._events):
+                    chc2 += 1
+            if chc1 != chc2:
+                cues.append(ICue(
+                    msg="Metadata: fluorescence channel count inconsistent",
+                    level="violation",
+                    category="metadata wrong",
+                    cfg_section="fluorescence",
+                    cfg_key="channel count"))
+        return cues
+
+    def check_fl_num_lasers(self, **kwargs):
+        cues = []
+        # check for number of lasers
+        if "laser count" in self.ds.config["fluorescence"]:
+            lsc1 = self.ds.config["fluorescence"]["laser count"]
+            lsc2 = 0
+            for ii in range(1, 4):
+                kl = f"laser {ii} lambda"
+                kp = f"laser {ii} power"
+                if (kl in self.ds.config["fluorescence"] and
+                        kp in self.ds.config["fluorescence"] and
+                        self.ds.config["fluorescence"][kp] != 0):
+                    lsc2 += 1
+            if lsc1 != lsc2:
+                cues.append(ICue(
+                    msg="Metadata: fluorescence laser count inconsistent",
+                    level="violation",
+                    category="metadata wrong",
+                    cfg_section="fluorescence",
+                    cfg_key="laser count"))
+        return cues
+
+    def check_fl_samples_per_event(self, **kwargs):
+        cues = []
+        # check for samples per event
+        if "samples per event" in self.ds.config["fluorescence"]:
+            spe = self.ds.config["fluorescence"]["samples per event"]
+            if "trace" in self.ds:
+                for key in self.ds["trace"].keys():
+                    spek = self.ds["trace"][key][0].size
+                    if spek != spe:
+                        cues.append(ICue(
+                            msg="Metadata: wrong number of samples per "
+                                + f"event: {key} (expected {spe}, got {spek})",
+                            level="violation",
+                            category="metadata wrong",
+                            cfg_section="fluorescence",
+                            cfg_key="samples per event"))
+        return cues
+
+    def check_fl_max_positive(self, **kwargs):
+        """Check if all fl?_max values are >0.1"""
+        cues = []
+        neg_feats = []
+        for fl in ['fl1_max', 'fl2_max', 'fl3_max']:
+            if fl in self.ds:
+                if min(self.ds[fl]) <= 0.1:
+                    neg_feats.append(fl)
+        if neg_feats:
+            cues.append(ICue(
+                msg=f"Negative value for feature(s): {', '.join(neg_feats)}",
+                level="alert",
+                category="feature data"))
+        return cues
+
+    def check_fl_max_ctc_positive(self, **kwargs):
+        """Check if all fl?_max_ctc values are > 0.1"""
+        cues = []
+        neg_feats = []
+        for fl in ['fl1_max_ctc', 'fl2_max_ctc', 'fl3_max_ctc']:
+            if fl in self.ds:
+                if min(self.ds[fl]) <= 0.1:
+                    neg_feats.append(fl)
+        if neg_feats:
+            cues.append(ICue(
+                msg=f"Negative value for feature(s): {', '.join(neg_feats)}",
+                level="alert",
+                category="feature data"))
+        return cues
+
+    def check_flow_rate(self, **kwargs):
+        """Make sure sheath and sample flow rates add up"""
+        cues = []
+        if ("setup" in self.ds.config
+                and "flow rate" in self.ds.config["setup"]
+                and "flow rate sample" in self.ds.config["setup"]
+                and "flow rate sheath" in self.ds.config["setup"]):
+            frsum = self.ds.config["setup"]["flow rate"]
+            frsam = self.ds.config["setup"]["flow rate sample"]
+            frshe = self.ds.config["setup"]["flow rate sheath"]
+            if not np.allclose(frsum, frsam + frshe):
+                for k in ["flow rate", "flow rate sheath", "flow rate sample"]:
+                    cues.append(ICue(
+                        msg="Metadata: Flow rates don't add up (sheath "
+                            + f"{frshe:g} + sample {frsam:g} "
+                            + f"!= channel {frsum:g})",
+                        level="alert",
+                        category="metadata wrong",
+                        cfg_section="setup",
+                        cfg_key=k))
+        return cues
+
+    def check_fmt_hdf5(self, **kwargs):
+        cues = []
+        # hdf5-based checks
+        if self.ds.format == "hdf5":
+            # check meta data of images
+            for feat in ["image", "image_bg", "mask"]:
+                if feat in self.ds._events:
+                    imdat = self.ds[feat]
+                    for key, val in [['CLASS', b'IMAGE'],
+                                     ['IMAGE_VERSION', b'1.2'],
+                                     ['IMAGE_SUBCLASS', b'IMAGE_GRAYSCALE']]:
+                        if key not in imdat.attrs:
+                            cues.append(ICue(
+                                msg=f"HDF5: '/{feat}': missing "
+                                    + f"attribute '{key}'",
+                                level="alert",
+                                category="format HDF5"))
+                        elif imdat.attrs.get_id(key).dtype.char != "S":
+                            cues.append(ICue(
+                                msg=f"HDF5: '/{feat}': attribute '{key}' "
+                                    + "should be fixed-length ASCII string",
+                                level="alert",
+                                category="format HDF5"))
+                        elif imdat.attrs[key] != val:
+                            cues.append(ICue(
+                                msg=f"HDF5: '/{feat}': attribute '{key}' "
+                                    + f"should have value '{val}'",
+                                level="alert",
+                                category="format HDF5"))
+            # check length of logs
+            with h5py.File(self.ds.path, mode="r") as h5:
+                if "logs" in h5:
+                    logs = h5["logs"]
+                    for logname in logs.keys():
+                        # ignore tmds meta data log files
+                        lign = [logname.endswith(n) for n in IGNORED_LOG_NAMES]
+                        if sum(lign):
+                            continue
+                        log = logs[logname]
+                        for ii in range(len(log)):
+                            if len(log[ii]) > LOG_MAX_LINE_LENGTH:
+                                cues.append(ICue(
+                                    msg=f"Logs: {logname} line {ii} "
+                                        + "exceeds maximum line length "
+                                        + f"{LOG_MAX_LINE_LENGTH}",
+                                    level="alert",
+                                    category="format HDF5"))
+        return cues
+
+    def check_info(self, **kwargs):
+        cues = [
+            ICue(
+                msg=f"Fluorescence: {self.has_fluorescence}",
+                level="info",
+                category="general"),
+            ICue(
+                msg=f"Data file format: {self.ds.format}",
+                level="info",
+                category="general")]
+        return cues
+
+    def check_metadata_bad(self, **kwargs):
+        cues = []
+        # check for ROI size
+        if ("imaging" in self.ds.config
+                and "roi size x" in self.ds.config["imaging"]
+                and "roi size y" in self.ds.config["imaging"]):
+            for ii, roi in enumerate(["roi size y", "roi size x"]):
+                for feat in ["image", "image_bg", "mask"]:
+                    if feat in self.ds:
+                        soll = self.ds[feat].shape[ii+1]
+                        ist = self.ds.config["imaging"][roi]
+                        if soll != ist:
+                            cues.append(ICue(
+                                msg="Metadata: Mismatch [imaging] "
+                                    + f"'{roi}' and feature {feat} "
+                                    + f"({ist} vs {soll})",
+                                level="violation",
+                                category="metadata wrong",
+                                cfg_section="imaging",
+                                cfg_key=roi))
+        return cues
+
+    def check_metadata_bad_greater_zero(self, **kwargs):
+        cues = []
+        # check for ROI size
+        for sec, key in [
+            ["imaging", "frame rate"],
+            ["imaging", "pixel size"],
+            ["setup", "channel width"],
+            ["setup", "flow rate"],
+        ]:
+            value = self.ds.config.get(sec, {}).get(key)
+            if value is not None and value <= 0:
+                cues.append(ICue(
+                    msg=f"Metadata: Invalid value for [{sec}] '{key}': "
+                        + f"'{value}'!",
+                    level="violation",
+                    category="metadata wrong",
+                    cfg_section=sec,
+                    cfg_key=key))
+        return cues
+
+    def check_metadata_choices(self, **kwargs):
+        cues = []
+        for sec in VALID_CHOICES:
+            for key in VALID_CHOICES[sec]:
+                if sec in self.ds.config and key in self.ds.config[sec]:
+                    val = self.ds.config[sec][key]
+                    if val not in VALID_CHOICES[sec][key]:
+                        cues.append(ICue(
+                            msg=f"Metadata: Invalid value [{sec}] {key}: "
+                                + f"'{val}'",
+                            level="violation",
+                            category="metadata wrong",
+                            cfg_section=sec,
+                            cfg_key=key,
+                            cfg_choices=VALID_CHOICES[sec][key]))
+        return cues
+
+    def check_metadata_hdf5_type(self, **kwargs):
+        """This is a low-level HDF5 check"""
+        cues = []
+        if self.ds.format == "hdf5":
+            for entry in self.ds.h5file.attrs:
+                if entry.count(":"):
+                    sec, key = entry.split(":")
+                    val_act = self.ds.h5file.attrs[entry]  # actual value
+                    if isinstance(val_act, bytes):
+                        val_act = val_act.decode("utf-8")
+                    # Check whether the config key exists
+                    if dfn.config_key_exists(sec, key):
+                        func = dfn.get_config_value_func(sec, key)
+                        val_exp = func(val_act)  # expected value
+                        if (isinstance(val_exp, (list, tuple, np.ndarray))
+                                and np.allclose(val_exp, val_act)):
+                            continue
+                        elif val_exp == val_act:
+                            continue
+                        else:
+                            cues.append(ICue(
+                                msg=f"Metadata: [{sec}]: '{key}' should be "
+                                    + f"'{val_exp}', but is '{val_act}'!",
+                                level="alert",
+                                category="metadata wrong",
+                                cfg_section=sec,
+                                cfg_key=key))
+        return cues
+
+    def check_metadata_online_filter_polygon_points_shape(self, **kwargs):
+        cues = []
+        if "online_filter" in self.ds.config:
+            for key in self.ds.config["online_filter"].keys():
+                if key.endswith("polygon points"):
+                    points = self.ds.config["online_filter"][key]
+                    if points.shape[1] != 2 or points.shape[0] < 3:
+                        cues.append(ICue(
+                            msg="Metadata: Wrong shape [online_filter] "
+                                + f"{key}: '{points.shape}'",
+                            level="violation",
+                            category="metadata wrong",
+                            cfg_section="online_filter",
+                            cfg_key=key))
+        return cues
+
+    def check_metadata_missing(self, expand_section=True, **kwargs):
+        cues = []
+        # These "must" be present:
+        important = copy.deepcopy(IMPORTANT_KEYS)
+        if self.has_fluorescence:
+            important.update(IMPORTANT_KEYS_FL)
+        # A list of sections we would like to investigate
+        secs_investiage = list(set(important.keys()) | set(DESIRABLE_SECTIONS))
+
+        for sec in secs_investiage:
+            if sec not in self.ds.config and not expand_section:
+                cues.append(ICue(
+                    msg=f"Metadata: Missing section '{sec}'",
+                    level="violation" if sec in important else "alert",
+                    category="metadata missing",
+                    cfg_section=sec))
+            else:
+                for key in dfn.config_keys[sec]:
+                    if key not in self.ds.config[sec]:
+                        if sec in OPTIONAL_KEYS and key in OPTIONAL_KEYS[sec]:
+                            # ignore this key
+                            continue
+                        elif sec in important and key in important[sec]:
+                            level = "violation"
+                        else:
+                            level = "alert"
+                        cues.append(ICue(
+                            msg=f"Metadata: Missing key [{sec}] '{key}'",
+                            level=level,
+                            category="metadata missing",
+                            cfg_section=sec,
+                            cfg_key=key))
+        # check for temperature
+        if "temp" in self.ds:
+            if "temperature" not in self.ds.config["setup"]:
+                cues.append(ICue(
+                    msg="Metadata: Missing key [setup] 'temperature', "
+                        + "because the 'temp' feature is given",
+                    level="alert",
+                    category="metadata missing",
+                    cfg_section="setup",
+                    cfg_key="temperature"))
+        return cues
+
+    def check_ml_class(self, **kwargs):
+        """Try to comput ml_class feature and display error message"""
+        cues = []
+        if "ml_class" in self.ds:
+            try:
+                self.ds["ml_class"]
+            except ValueError as e:
+                cues.append(ICue(
+                    msg=e.args[0],
+                    level="violation",
+                    category="feature data"))
+        return cues
+
+    def check_shapein_issue3_bad_medium(self, **kwargs):
+        """Some versions of Shape-In stored wrong [setup]: medium
+
+        The problem only affects selection of "CellCarrier" which had
+        index 0 and as a result "CellCarrierB" was written to the file.
+        This means we only have to check for the Shape-In version and
+        whether the medium is 'CellCarrierB'. In DCKit, the user can
+        then manually edit the medium.
+
+        Affected Shape-In versions: >=2.2.1.0,<2.2.2.3
+        Also affected if bad config file was used: 2.2.2.4, 2.3.0.0
+
+        https://github.com/ZELLMECHANIK-DRESDEN/ShapeIn_Issues/issues/3
+        """
+        cues = []
+        medium = self.ds.config["setup"].get("medium", "")
+        si_ver = self.ds.config["setup"].get("software version", "")
+        si_ver = si_ver.strip("dev")  # for e.g. "2.2.1.0dev"
+        if (medium == "CellCarrierB"
+                and si_ver in ["2.2.1.0", "2.2.2.0", "2.2.2.1", "2.2.2.2",
+                               "2.2.2.3",
+                               # The issue can still occur for these versions
+                               # of Shape-In if a bad configuration file
+                               # is used.
+                               "2.2.2.4", "2.3.0.0"]):
+            cues.append(ICue(
+                msg="Metadata: Please verify that 'medium' is really "
+                    + "'CellCarrierB' (Shape-In issue #3)",
+                level="alert",
+                category="metadata wrong",
+                identifier="Shape-In issue #3",
+                cfg_section="setup",
+                cfg_key="medium"))
+        return cues
+
+    def check_temperature_zero_zmd(self, **kwargs):
+        """If there is a loose cable, then temperature might be all-zero
+
+        https://github.com/DC-analysis/dclab/issues/183
+        """
+        cues = []
+        from_zmd = "ZMD" in self.ds.config["setup"].get("identifier", "")
+        if from_zmd and "temp" in self.ds:
+            temp = self.ds["temp"]
+            if np.allclose(temp[:10], 0) and np.allclose(temp, 0):
+                cues.append(ICue(
+                    msg="Feature: The 'temp' feature is all-zero, check "
+                        "the cables of the temperature sensor!",
+                    level="violation",
+                    category="feature data"))
+        return cues
+
+    def sanity_check(self):
+        """Sanity check that tests whether the data can be accessed"""
+        cues = []
+        cues += self.check_feature_size()
+        cues += self.check_metadata_bad()
+        for cue in cues:
+            cue.msg = "Sanity check failed: " + cue.msg
+        return [ci for ci in cues if ci.level == "violation"]
+
+
+def check_dataset(path_or_ds):
+    """Check whether a dataset is complete
+
+    Parameters
+    ----------
+    path_or_ds: str or pathlib.Path or RTDCBase
+        Full path to a dataset on disk or an instance of RTDCBase
+
+    Returns
+    -------
+    violations: list of str
+        Dataset format violations (hard)
+    alerts: list of str
+        Dataset format alerts (soft)
+    info: list of str
+        Dataset information
+    """
+    aler = []
+    info = []
+    viol = []
+    with IntegrityChecker(path_or_ds) as ic:
+        # perform all checks
+        icues = ic.check(expand_section=False)
+        for cue in icues:
+            if cue.level == "info":
+                info.append(cue.msg)
+            elif cue.level == "alert":
+                aler.append(cue.msg)
+            elif cue.level == "violation":
+                viol.append(cue.msg)
+    return sorted(viol), sorted(aler), sorted(info)
+
+
+def hdf5_has_external(h5):
+    """Check recursively, whether an h5py object contains external data
+
+    External data includes binary data in external files, virtual
+    datasets, and external links.
+
+    Returns a tuple of either
+
+    - `(True, path_ext)` if the object contains external data
+    - `(False, None)` if this is not the case
+
+    where `path_ext` is the path to the group or dataset in `h5`.
+
+    .. versionadded:: 0.62.0
+
+    """
+    for key in h5:
+        obj = h5[key]
+        if (obj.file != h5.file  # not in same file
+                or (isinstance(obj, h5py.Dataset)
+                    and (obj.is_virtual  # virtual dataset
+                         or obj.external))):  # external dataset
+            # These are external data
+            return True, f"{h5.name}/{key}".replace("//", "/")
+        elif isinstance(obj, h5py.Group):
+            # Perform recursive check for external data
+            has_ext, path_ext = hdf5_has_external(obj)
+            if has_ext:
+                return True, path_ext
+    else:
+        return False, None