tonik 0.0.1__py3-none-any.whl → 0.0.2__py3-none-any.whl

tonik/__init__.py

@@ -1 +1 @@
-from .xarray2hdf5 import xarray2hdf5
+from .lockerroom import Locker, LockerRoom

tonik/lockerroom.py

@@ -0,0 +1,290 @@
+from datetime import datetime, timedelta
+import logging
+import logging.config
+import os
+import re
+import tempfile
+
+import pandas as pd
+import xarray as xr
+
+from .xarray2hdf5 import xarray2hdf5
+
+
+ERROR_LOG_FILENAME = "tonik.log"
+
+LOGGING_CONFIG = {
+    "version": 1,
+    "disable_existing_loggers": False,
+    "formatters": {      
+        "default": {  # The formatter name, it can be anything that I wish
+            "format": "%(asctime)s:%(name)s:%(process)d:%(lineno)d " "%(levelname)s %(message)s",  #  What to add in the message
+            "datefmt": "%Y-%m-%d %H:%M:%S",  # How to display dates
+        },
+        "json": {  # The formatter name
+         "()": "pythonjsonlogger.jsonlogger.JsonFormatter",  # The class to instantiate!
+            # Json is more complex, but easier to read, display all attributes!
+            "format": """
+                    asctime: %(asctime)s
+                    created: %(created)f
+                    filename: %(filename)s
+                    funcName: %(funcName)s
+                    levelname: %(levelname)s
+                    levelno: %(levelno)s
+                    lineno: %(lineno)d
+                    message: %(message)s
+                    module: %(module)s
+                    msec: %(msecs)d
+                    name: %(name)s
+                    pathname: %(pathname)s
+                    process: %(process)d
+                    processName: %(processName)s
+                    relativeCreated: %(relativeCreated)d
+                    thread: %(thread)d
+                    threadName: %(threadName)s
+                    exc_info: %(exc_info)s
+                """,
+            "datefmt": "%Y-%m-%d %H:%M:%S",  # How to display dates
+        },
+    }, 
+    "handlers": {
+        "logfile": {  # The handler name
+            "formatter": "json",  # Refer to the formatter defined above
+            "level": "ERROR",  # FILTER: Only ERROR and CRITICAL logs
+            "class": "logging.handlers.RotatingFileHandler",  # OUTPUT: Which class to use
+            "filename": ERROR_LOG_FILENAME,  # Param for class above. Defines filename to use, load it from constant
+            "backupCount": 2,  # Param for class above. Defines how many log files to keep as it grows
+        }, 
+        "simple": {  # The handler name
+            "formatter": "default",  # Refer to the formatter defined above
+            "class": "logging.StreamHandler",  # OUTPUT: Same as above, stream to console
+            "stream": "ext://sys.stdout",
+        },
+    },
+    "loggers": { 
+        "zizou": {  # The name of the logger, this SHOULD match your module!
+            "level": "DEBUG",  # FILTER: only INFO logs onwards from "tryceratops" logger
+            "handlers": [
+                "simple",  # Refer the handler defined above
+            ],
+        },
+    },
+    "root": {
+        "level": "ERROR",  # FILTER: only INFO logs onwards
+        "handlers": [
+            "logfile",  # Refer the handler defined above
+        ]
+    },
+}
+
+logging.config.dictConfig(LOGGING_CONFIG)
+logger = logging.getLogger("__name__")
+
+
+class LockerRoom:
+    """
+    Query computed features
+
+    :param rootdir: Path to parent directory.
+    :type rootdir: str
+    :param starttime: Begin of request
+    :type starttime: :class:`datetime.datetime`
+    :param endtime: Begin of request
+    :type endtime: :class:`datetime.datetime`
+
+    >>> import datetime
+    >>> fq = FeatureRequest()
+    >>> start = datetime.datetime(2012,1,1,0,0,0)
+    >>> end = datetime.datetime(2012,1,2,23,59,59)
+    >>> group = 'Whakaari'
+    >>> site = 'WIZ'
+    >>> chan = 'HHZ'
+    >>> fq.group = group
+    >>> fq.starttime = start
+    >>> fq.endtime = end
+    >>> fq.site = site
+    >>> fq.channel = chan
+    >>> rsam = fq("rsam")
+    """
+    def __init__(self, group, rootdir=tempfile.gettempdir(),
+                 starttime=None, endtime=None):
+        self.groupdir = os.path.join(rootdir, group)
+        self.lockers = {} 
+
+    def get_locker(self, site, location, channel):
+        key = (site, location, channel)
+        if key not in self.lockers:
+            self.lockers[key] = Locker(site, location, channel, rootdir=self.groupdir)
+        return self.lockers[key]
+
+    def __repr__(self):
+        rstr = f"LockerRoom: {self.groupdir}\n"
+        for site, location, channel in self.lockers.keys():
+            rstr += f"Site: {site}, Location: {location}, Channel: {channel}\n" 
+        return rstr
+
+    def get_starttime(self):
+        return self.__starttime
+
+    def set_starttime(self, time):
+        if time is None:
+            self.__starttime = None
+            self.__sdate = None
+            return
+        self.__starttime = time
+        self.__sdate = '{}{:02d}{:02d}'.format(time.year,
+                                               time.month,
+                                               time.day)
+        for key, locker in self.lockers.items():
+            locker.starttime = time
+
+    def get_endtime(self):
+        return self.__endtime
+
+    def set_endtime(self, time):
+        if time is None:
+            self.__endtime = None
+            self.__edate = None
+            return
+        self.__endtime = time
+        self.__edate = '{}{:02d}{:02d}'.format(time.year,
+                                               time.month,
+                                               time.day)
+        for key, locker in self.lockers.items():
+            locker.endtime = time
+
+    starttime = property(get_starttime, set_starttime)
+    endtime = property(get_endtime, set_endtime)
+
+
+class Locker:
+    def __init__(self, site=None, location=None, channel=None,
+                 rootdir=None, starttime=None, endtime=None,
+                 interval='10min'):
+
+        self.site = site
+        self.location = location
+        self.channel = channel
+        self.starttime = starttime
+        self.endtime = endtime
+        self.rootdir = rootdir
+        self.interval = interval
+
+    def __call__(self, feature, stack_length=None):
+        """
+        Request a particular feature
+
+        :param feature: Feature name
+        :type feature: str
+        :param stack_length: length of moving average in time
+        :type stack_length: str
+
+        """
+        if self.endtime <= self.starttime:
+            raise ValueError('Startime has to be smaller than endtime.')
+
+        feature = feature.lower()
+        filename = os.path.join(self.sitedir, '%s.nc' % feature)
+        if not os.path.isfile(filename):
+            raise ValueError('Feature {} does not exist.'.format(feature))
+
+        logger.debug(f"Reading feature {feature} between {self.starttime} and {self.endtime}")
+        num_periods = None
+        if stack_length is not None:
+            valid_stack_units = ['W', 'D', 'H', 'T', 'min', 'S']
+            if not re.match(r'\d*\s*(\w*)', stack_length).group(1)\
+                   in valid_stack_units:
+                raise ValueError(
+                    'Stack length should be one of: {}'.
+                        format(', '.join(valid_stack_units))
+                )
+
+            if pd.to_timedelta(stack_length) < pd.to_timedelta(self.interval):
+                raise ValueError('Stack length {} is less than interval {}'.
+                                 format(stack_length, self.interval))
+
+            # Rewind starttime to account for stack length
+            self.starttime -= pd.to_timedelta(stack_length)
+
+            num_periods = (pd.to_timedelta(stack_length)/
+                           pd.to_timedelta(self.interval))
+            if not num_periods.is_integer():
+                raise ValueError(
+                    'Stack length {} / interval {} = {}, but it needs'
+                    ' to be a whole number'.
+                        format(stack_length, self.interval, num_periods))
+
+        xd_index = dict(datetime=slice(self.starttime,
+                                       (self.endtime-
+                                        pd.to_timedelta(self.interval))))
+        with xr.open_dataset(filename, group='original', engine='h5netcdf') as ds:
+            ds.sortby("datetime")
+            rq = ds.loc[xd_index].load()
+
+        # Stack features
+        if stack_length is not None:
+            logger.debug("Stacking feature...")
+            try:
+                xdf = rq[feature].rolling(datetime=int(num_periods),
+                                        center=False,
+                                        min_periods=1).mean()
+                # Return requested timeframe to that defined in initialisation
+                self.starttime += pd.to_timedelta(stack_length)
+                xdf_new = xdf.loc[
+                        self.starttime:
+                        self.endtime-pd.to_timedelta(self.interval)]
+                xdf_new = xdf_new.rename(feature)
+            except ValueError as e:
+                logger.error(e)
+                logger.error('Stack length {} is not valid for feature {}'.
+                             format(stack_length, feature))
+            else:
+                return xdf_new
+
+        return rq[feature]
+
+    def get_site(self):
+        return self.__site
+
+    def set_site(self, value):
+        self.__site = value
+
+    def get_location(self):
+        return self.__location
+
+    def set_location(self, value):
+        self.__location = value
+
+    def get_channel(self):
+        return self.__channel
+
+    def set_channel(self, value):
+        self.__channel = value
+
+    @property
+    def sitedir(self):
+        try:
+            __sdir =  os.path.join(self.rootdir,
+                                   self.site,
+                                   self.location,
+                                   self.channel)
+            os.makedirs(__sdir, exist_ok=True)
+            return __sdir
+        except TypeError:
+            return None
+
+    site = property(get_site, set_site)
+    location = property(get_location, set_location)
+    channel = property(get_channel, set_channel)
+
+    def load(self, *args, **kwargs):
+        """
+        Load a feature from disk
+        """
+        self.__call__(*args, **kwargs)
+
+    def save(self, data):
+        """
+        Save a feature to disk
+        """
+        xarray2hdf5(data, self.sitedir)

tonik/xarray2hdf5.py

@@ -3,10 +3,9 @@ import logging
 import os
 from warnings import filterwarnings
 
-from cftime import num2date, date2num, date2index
+from cftime import num2date, date2num
 import h5netcdf
 import numpy as np
-import xarray as xr
 
 
 def xarray2hdf5(xArray, fdir, rootGroupName="original", timedim="datetime"):

{tonik-0.0.1.dist-info → tonik-0.0.2.dist-info}/METADATA

@@ -1,8 +1,8 @@
 Metadata-Version: 2.1
 Name: tonik
-Version: 0.0.1
+Version: 0.0.2
 Summary: A collection of tools to integrate with GNS Science's time series classification platform.
-Project-URL: Homepage, https://github.com/tsc-tools/tonik
+Project-URL: Homepage, https://tsc-tools.github.io/tonik.github.io
 Project-URL: Issues, https://github.com/tsc-tools/tonik/issues
 Author-email: Yannik Behr <y.behr@gns.cri.nz>, Christof Mueller <c.mueller@gns.cri.nz>
 License-File: LICENSE
@@ -15,6 +15,7 @@ Requires-Dist: h5py
 Requires-Dist: netcdf4
 Requires-Dist: pandas
 Requires-Dist: pytest
+Requires-Dist: python-json-logger
 Requires-Dist: xarray
 Description-Content-Type: text/markdown
 

tonik-0.0.2.dist-info/RECORD

@@ -0,0 +1,7 @@
+tonik/__init__.py,sha256=hv2lVOfFLABQo5KsLFoA439lSst0asGuQYiAK0tZvEw,42
+tonik/lockerroom.py,sha256=6OOkf68UNQZrGLfnOo9bJsaeb-5PPH0NDGwCAdDzlqg,10162
+tonik/xarray2hdf5.py,sha256=biQ3KVt0QrxJhOWm38FwglzYkLhPtO13G1B1vVF2c6o,4090
+tonik-0.0.2.dist-info/METADATA,sha256=OBRXcvVKJwc5_Qv5MpXdDg0tC8Sg4f4N90yxwud57oo,916
+tonik-0.0.2.dist-info/WHEEL,sha256=KGYbc1zXlYddvwxnNty23BeaKzh7YuoSIvIMO4jEhvw,87
+tonik-0.0.2.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+tonik-0.0.2.dist-info/RECORD,,

tonik-0.0.1.dist-info/RECORD

@@ -1,6 +0,0 @@
-tonik/__init__.py,sha256=d7gnshn92xGI-U7YTs7Q5cMWjvLW45m-EXJ5IcYaZrs,36
-tonik/xarray2hdf5.py,sha256=sImRJ80EQ3yI_7xJg34VfS8SSIzkDtRHda3Mg959xPs,4122
-tonik-0.0.1.dist-info/METADATA,sha256=KS91xVocqwwtwLKprecpfp0JU15s-1xERkMqKBSpPS4,873
-tonik-0.0.1.dist-info/WHEEL,sha256=KGYbc1zXlYddvwxnNty23BeaKzh7YuoSIvIMO4jEhvw,87
-tonik-0.0.1.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-tonik-0.0.1.dist-info/RECORD,,