dclab 0.67.0__cp314-cp314-macosx_10_13_x86_64.whl

dclab/rtdc_dataset/config.py

@@ -0,0 +1,533 @@
+"""RT-DC dataset configuration"""
+import copy
+from collections import UserDict
+import json
+import numbers
+import pathlib
+import sys
+import warnings
+
+import numpy as np
+
+from .. import definitions as dfn
+
+
+class WrongConfigurationTypeWarning(UserWarning):
+    pass
+
+
+class EmptyConfigurationKeyWarning(UserWarning):
+    pass
+
+
+class UnknownConfigurationKeyWarning(UserWarning):
+    pass
+
+
+class BadUserConfigurationKeyWarning(UserWarning):
+    pass
+
+
+class BadUserConfigurationValueWarning(UserWarning):
+    pass
+
+
+class ConfigurationDict(UserDict):
+    def __init__(self, section=None, *args, **kwargs):
+        """A case-insensitive dict that is section-aware
+
+        Instantiate this dictionary like any other dictionary.
+        All keys will be treated as lower-case keys. If `section`
+        is given, new entries will be checked using the function
+        :func:`verify_section_key`.
+        """
+        self.section = section
+        super(ConfigurationDict, self).__init__(*args, **kwargs)
+        self._convert_keys()
+
+    def __getitem__(self, key):
+        return super(ConfigurationDict,
+                     self).__getitem__(self.__class__._k(key))
+
+    def __setitem__(self, key, value):
+        key = self.__class__._k(key)
+        # make sure "section: key" exists
+        if self.section:
+            valid = verify_section_key(self.section, key)
+            # check for empty string values
+            if valid and isinstance(value, str) and len(value) == 0:
+                warnings.warn(
+                    "Empty value for [{}]: '{}'!".format(self.section, key),
+                    EmptyConfigurationKeyWarning,
+                )
+                valid = False
+        else:
+            valid = True
+        if value is None:
+            warnings.warn(
+                f"Bad value '{value}' for [{self.section}]: '{key}'!",
+                BadUserConfigurationValueWarning,
+            )
+            valid = False
+        if valid:
+            # only set valid keys
+            if self.section:
+                typ = dfn.get_config_value_type(self.section, key)
+                if typ is not None and not isinstance(value, typ):
+                    warnings.warn(
+                        f"Type of configuration key [{self.section}]: {key} "
+                        f"should be {typ}, got {type(value)}!",
+                        WrongConfigurationTypeWarning)
+                # convert value to its correct type (independent of case above)
+                convfunc = dfn.get_config_value_func(self.section, key)
+                value = convfunc(value)
+
+            super(ConfigurationDict, self).__setitem__(key, value)
+
+    def __delitem__(self, key):
+        return super(ConfigurationDict,
+                     self).__delitem__(self.__class__._k(key))
+
+    def __contains__(self, key):
+        return super(ConfigurationDict,
+                     self).__contains__(self.__class__._k(key))
+
+    @classmethod
+    def _k(cls, key):
+        """Convert a key to lower case"""
+        return key.lower() if isinstance(key, str) else key
+
+    def _convert_keys(self):
+        for k in list(self.keys()):
+            v = super(ConfigurationDict, self).pop(k)
+            self.__setitem__(k, v)
+
+    def get(self, key, *args, **kwargs):
+        return super(ConfigurationDict,
+                     self).get(self.__class__._k(key), *args, **kwargs)
+
+    def items(self):
+        keys = list(self.keys())
+        keys.sort()
+        out = [(k, self[k]) for k in keys]
+        return out
+
+    def pop(self, key, *args, **kwargs):
+        return super(ConfigurationDict,
+                     self).pop(self.__class__._k(key), *args, **kwargs)
+
+    def setdefault(self, key, *args, **kwargs):
+        return super(ConfigurationDict,
+                     self).setdefault(self.__class__._k(key), *args, **kwargs)
+
+    def update(self, E=None, **F):
+        if E is None:
+            E = {}
+        for key in E:
+            self.__setitem__(key, E[key])
+        for key in F:
+            self.__setitem__(key, F[key])
+
+
+class Configuration(object):
+    def __init__(self, files=None, cfg=None, disable_checks=False):
+        """Configuration class for RT-DC datasets
+
+        This class has a dictionary-like interface to access
+        and set configuration values, e.g.
+
+        .. code::
+
+            cfg = load_from_file("/path/to/config.txt")
+            # access the channel width
+            cfg["setup"]["channel width"]
+            # modify the channel width
+            cfg["setup"]["channel width"] = 30
+
+        Parameters
+        ----------
+        files: list of files
+            The config files with which to initialize the configuration
+        cfg: dict-like
+            The dictionary with which to initialize the configuration
+        disable_checks: bool
+            Set this to True if you want to avoid checking against
+            section and key names defined in `dclab.definitions`
+            using :func:`verify_section_key`. This avoids excess
+            warning messages when loading data from configuration
+            files not generated by dclab.
+        """
+        if cfg is None:
+            cfg = {}
+        if files is None:
+            files = []
+        self.disable_checks = disable_checks
+
+        self._cfg = ConfigurationDict()
+
+        # set initial default values
+        self._init_default_filter_values()
+
+        # Update with additional dictionary
+        self.update(cfg)
+
+        # Load configuration files
+        for f in files:
+            self.update(load_from_file(f))
+
+    def __contains__(self, key):
+        return self._cfg.__contains__(key)
+
+    def __getitem__(self, sec):
+        if sec not in self and (sec in dfn.config_keys or sec == "user"):
+            # create an empty section for user-convenience
+            section = None if self.disable_checks else sec
+            self._cfg[sec] = ConfigurationDict(section=section)
+        item = self._cfg.__getitem__(sec)
+        return item
+
+    def __iter__(self):
+        return self._cfg.__iter__()
+
+    def __len__(self):
+        return len(self._cfg)
+
+    def __repr__(self):
+        rep = ""
+        keys = sorted(list(self.keys()))
+        for key in keys:
+            rep += "- {}\n".format(key)
+            subkeys = sorted(list(self[key].keys()))
+            for subkey in subkeys:
+                rep += "   {}: {}\n".format(subkey, self[key][subkey])
+        return rep
+
+    def __setitem__(self, *args):
+        self._cfg.__setitem__(*args)
+
+    def _init_default_filter_values(self):
+        """Set default initial values
+
+        The default values are hard-coded for backwards compatibility
+        and for several functionalities in dclab.
+        """
+        # Do not filter out invalid event values
+        self["filtering"]["remove invalid events"] = False
+        # Enable filters switch is mandatory
+        self["filtering"]["enable filters"] = True
+        # Limit events integer to downsample output data
+        self["filtering"]["limit events"] = 0
+        # Polygon filter list
+        self["filtering"]["polygon filters"] = []
+        # Defaults to no hierarchy parent
+        self["filtering"]["hierarchy parent"] = "none"
+
+        # Make sure that all filtering values have a default value
+        # (otherwise we will get problems with resetting filters)
+        for item in dfn.CFG_ANALYSIS["filtering"]:
+            if item[0] not in self["filtering"]:
+                raise KeyError(
+                    "No default value set for [filtering]:{}".format(item[0]))
+
+    def as_dict(self, pop_filtering=False):
+        data = json.loads(self.tojson())
+        if pop_filtering:
+            data.pop("filtering", None)
+        return data
+
+    def copy(self):
+        """Return copy of current configuration"""
+        return Configuration(cfg=copy.deepcopy(self._cfg))
+
+    def get(self, key, other):
+        """Famous `dict.get` function
+
+        .. versionadded:: 0.29.1
+
+        """
+        if key in self:
+            return self[key]
+        else:
+            return other
+
+    def tojson(self):
+        """Convert the configuration to a JSON string
+
+        Note that the data type of some configuration options
+        will likely be lost.
+        """
+        # Dear future person,
+        # if you would like to implement `fromjson`, you will have
+        # to set the `section` properly in the ConfigurationDict.
+        # Besides the data types, there might be other things to
+        # look out for. ~paulmueller
+        return json.dumps(dict(self),
+                          cls=ConfigurationJSONEncode,
+                          sort_keys=True)
+
+    def keys(self):
+        """Return the configuration keys (sections)"""
+        return self._cfg.keys()
+
+    def save(self, filename):
+        """Save the configuration to a file"""
+        filename = pathlib.Path(filename)
+        out_str = self.tostring()
+        with filename.open("w") as f:
+            f.write(out_str)
+
+    def tostring(self, sections=None):
+        """Convert the configuration to its string representation
+
+        The optional argument `sections` allows to export only
+        specific sections of the configuration, i.e.
+        `sections=dclab.dfn.CFG_METADATA` will only export
+        configuration data from the original measurement and no
+        filtering data.
+        """
+        out = []
+        if sections is None:
+            keys = sorted(list(self.keys()))
+        else:
+            keys = sorted([k for k in sections if k in self.keys()])
+        for key in keys:
+            out.append("[{}]".format(key))
+            section = self[key]
+            ikeys = list(section.keys())
+            ikeys.sort()
+            for ikey in ikeys:
+                var, val = keyval_typ2str(ikey, section[ikey])
+                out.append("{} = {}".format(var, val))
+            out.append("")
+
+        out_str = ""
+        for i in range(len(out)):
+            # win-like line endings
+            out_str += out[i]+"\n"
+        return out_str
+
+    def update(self, newcfg):
+        """Update current config with a dictionary"""
+        for sec in newcfg.keys():
+            if sec not in self._cfg:
+                section = None if self.disable_checks else sec
+                self._cfg[sec] = ConfigurationDict(section=section)
+            self._cfg[sec].update(newcfg[sec])
+
+
+class CaseInsensitiveDict(ConfigurationDict):
+    def __init__(self, *args, **kwargs):
+        warnings.warn("CaseInsensitiveDict is deprecated, use "
+                      + "ConfigurationDict instead.",
+                      DeprecationWarning)
+        super(CaseInsensitiveDict, self).__init__(*args, **kwargs)
+
+
+class ConfigurationJSONEncode(json.JSONEncoder):
+    def default(self, obj):
+        if isinstance(obj, ConfigurationDict):
+            return dict(obj)
+        elif isinstance(obj, np.ndarray):
+            return obj.tolist()
+        elif isinstance(obj, numbers.Integral):
+            return int(obj)
+        elif isinstance(obj, numbers.Number):
+            return float(obj)
+        elif isinstance(obj, (bool, np.bool_)):
+            return bool(obj)
+        return json.JSONEncoder.default(self, obj)
+
+
+def verify_section_key(section, key):
+    """Return True if the section-key combination exists"""
+    wcount = 0
+    if dfn.config_key_exists(section, key):
+        pass
+    elif section in ["plotting", "analysis"]:
+        # hijacked by Shape-Out 1
+        warnings.warn("The '{}' configuration key is deprecated!".format(
+            section), UnknownConfigurationKeyWarning)
+        wcount += 1
+    elif section == "filtering":
+        if key.endswith(" min") or key.endswith(" max"):
+            feat = key[:-4]
+            if not dfn.scalar_feature_exists(feat):
+                warnings.warn(
+                    "A range has been specified for an unknown feature "
+                    + "'{}' in the 'filtering' section!".format(feat),
+                    UnknownConfigurationKeyWarning)
+                wcount += 1
+        elif key == "limit events auto":
+            # Shape-Out 1 used this to limit the number of events to
+            # a common minimum.
+            if sys.version_info[0] != 2:
+                warnings.warn("The 'limit events auto' configuration key "
+                              " in the 'filtering' section is deprecated!")
+                wcount += 1
+        else:
+            warnings.warn(
+                "Unknown key '{}' in the 'filtering' section!".format(key),
+                UnknownConfigurationKeyWarning)
+            wcount += 1
+    elif section == "user":
+        # the keys must be strings for clarity
+        if not isinstance(key, str):
+            warnings.warn("The 'user' section keys must be strings, "
+                          f"got '{key}' of type '{type(key)}'!",
+                          BadUserConfigurationKeyWarning)
+            wcount += 1
+        elif len(key.strip()) == 0:
+            warnings.warn("The 'user' section keys must not be empty strings "
+                          "or consist of whitespace characters only!",
+                          BadUserConfigurationKeyWarning)
+            wcount += 1
+    elif section not in dfn.config_keys:
+        warnings.warn("Unknown section '{}'!".format(section),
+                      UnknownConfigurationKeyWarning)
+        wcount += 1
+    else:
+        warnings.warn(
+            "Unknown key '{}' in the '{}' section!".format(key, section),
+            UnknownConfigurationKeyWarning)
+        wcount += 1
+
+    return wcount == 0
+
+
+def load_from_file(cfg_file):
+    """Load the configuration from a file
+
+    Parameters
+    ----------
+    cfg_file: str
+        Path to configuration file
+
+    Returns
+    -------
+    cfg : ConfigurationDict
+        Dictionary with configuration parameters
+    """
+    path = pathlib.Path(cfg_file).resolve()
+    with path.open("r", errors="replace") as f:
+        code = f.readlines()
+
+    cfg = ConfigurationDict()
+    for line in code:
+        # We deal with comments and empty lines
+        # We need to check line length first and then we look for
+        # a hash.
+        line = line.split("#")[0].strip()
+        if len(line) != 0:
+            if line.startswith("[") and line.endswith("]"):
+                sec = line[1:-1].lower()
+                if sec not in cfg:
+                    cfg[sec] = ConfigurationDict()
+                continue
+            elif not line.count("="):
+                # ignore invalid lines
+                continue
+            var, val = line.split("=", 1)
+            var = var.strip().lower()
+            val = val.strip("' ").strip('" ').strip()
+            if len(val) == 0:
+                # skip invalid values
+                continue
+            # convert parameter value to correct type
+            if dfn.config_key_exists(sec, var):
+                convfunc = dfn.get_config_value_func(sec, var)
+                val = convfunc(val)
+            else:
+                # unknown parameter (e.g. plotting in DCscope), guess type
+                var, val = keyval_str2typ(var, val)
+            if len(var) != 0 and len(str(val)) != 0:
+                cfg[sec][var] = val
+    return cfg
+
+
+def keyval_str2typ(var, val):
+    """Convert a variable from a string to its correct type
+
+    Parameters
+    ----------
+    var: str
+        The variable name
+    val: str
+        The value of the variable represented as a string
+
+    Returns
+    -------
+    varout: str
+        Stripped lowercase `var`
+    valout: any type
+        The value converted from string to its presumed type
+
+    Notes
+    -----
+    This method is heuristic and is only intended for usage in
+    dclab.
+
+    See Also
+    --------
+    keyval_typ2str: the opposite
+    """
+    if not (isinstance(val, str)):
+        # already a type:
+        return var.strip(), val
+    var = var.strip().lower()
+    val = val.strip()
+    # Find values
+    if len(var) != 0 and len(val) != 0:
+        # check for float
+        if val.startswith("[") and val.endswith("]"):
+            if len(val.strip("[],")) == 0:
+                # empty list
+                values = []
+            else:
+                values = val.strip("[],").split(",")
+                values = [float(v) for v in values]
+            return var, values
+        elif val.lower() in ["true", "y"]:
+            return var, True
+        elif val.lower() in ["false", "n"]:
+            return var, False
+        elif val[0] in ["'", '"'] and val[-1] in ["'", '"']:
+            return var, val.strip("'").strip('"').strip()
+        elif dfn.scalar_feature_exists(val):
+            return var, val
+        else:
+            try:
+                return var, float(val.replace(",", "."))
+            except ValueError:
+                return var, val
+
+
+def keyval_typ2str(var, val):
+    """Convert a variable to a string
+
+    Parameters
+    ----------
+    var: str
+        The variable name
+    val: any type
+        The value of the variable
+
+    Returns
+    -------
+    varout: str
+        Stripped lowercase `var`
+    valout: any type
+        The value converted to a useful string representation
+
+    See Also
+    --------
+    keyval_str2typ: the opposite
+    """
+    varout = var.strip()
+    if isinstance(val, list):
+        data = ", ".join([keyval_typ2str(var, it)[1] for it in val])
+        valout = "["+data+"]"
+    elif isinstance(val, float):
+        valout = "{:.12f}".format(val)
+    else:
+        valout = "{}".format(val)
+    return varout, valout