timeseries.py

# -*- coding: utf-8 -*-
"""
/***************************************************************************
                              EO Time Series Viewer
                              -------------------
        begin                : 2015-08-20
        git sha              : $Format:%H$
        copyright            : (C) 2017 by HU-Berlin
        email                : benjamin.jakimow@geo.hu-berlin.de
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   This program is free software; you can redistribute it and/or modify  *
 *   it under the terms of the GNU General Public License as published by  *
 *   the Free Software Foundation; either version 2 of the License, or     *
 *   (at your option) any later version.                                   *
 *                                                                         *
 ***************************************************************************/
"""
# noinspection PyPep8Naming

import sys, re, collections, traceback, time, json, urllib, types, enum, typing


import bisect

from qgis import *
from qgis.core import *
from qgis.gui import *
from qgis.PyQt.QtGui import *
from qgis.PyQt.QtWidgets import *
from qgis.PyQt.QtCore import *


from osgeo import gdal
from eotimeseriesviewer.dateparser import DOYfromDatetime64
from eotimeseriesviewer.utils import SpatialExtent, loadUI, px2geo

gdal.SetConfigOption('VRT_SHARED_SOURCE', '0') #!important. really. do not change this.

import numpy as np

from eotimeseriesviewer import messageLog
from eotimeseriesviewer.dateparser import parseDateFromDataSet

def transformGeometry(geom, crsSrc, crsDst, trans=None):
    if trans is None:
        assert isinstance(crsSrc, QgsCoordinateReferenceSystem)
        assert isinstance(crsDst, QgsCoordinateReferenceSystem)
        return transformGeometry(geom, None, None, trans=QgsCoordinateTransform(crsSrc, crsDst))
    else:
        assert isinstance(trans, QgsCoordinateTransform)
        return trans.transform(geom)

GDAL_DATATYPES = {}
for var in vars(gdal):
    match = re.search(r'^GDT_(?P<type>.*)$', var)
    if match:
        number = getattr(gdal, var)
        GDAL_DATATYPES[match.group('type')] = number
        GDAL_DATATYPES[match.group()] = number


METRIC_EXPONENTS = {
    "nm": -9, "um": -6, "mm": -3, "cm": -2, "dm": -1, "m": 0, "hm": 2, "km": 3
}
#add synonyms
METRIC_EXPONENTS['nanometers'] = METRIC_EXPONENTS['nm']
METRIC_EXPONENTS['micrometers'] = METRIC_EXPONENTS['um']
METRIC_EXPONENTS['millimeters'] = METRIC_EXPONENTS['mm']
METRIC_EXPONENTS['centimeters'] = METRIC_EXPONENTS['cm']
METRIC_EXPONENTS['decimeters'] = METRIC_EXPONENTS['dm']
METRIC_EXPONENTS['meters'] = METRIC_EXPONENTS['m']
METRIC_EXPONENTS['hectometers'] = METRIC_EXPONENTS['hm']
METRIC_EXPONENTS['kilometers'] = METRIC_EXPONENTS['km']

def convertMetricUnit(value, u1, u2):
    assert u1 in METRIC_EXPONENTS.keys()
    assert u2 in METRIC_EXPONENTS.keys()

    e1 = METRIC_EXPONENTS[u1]
    e2 = METRIC_EXPONENTS[u2]

    return value * 10**(e1-e2)


def getDS(pathOrDataset)->gdal.Dataset:
    """
    Returns a gdal.Dataset
    :param pathOrDataset: str | gdal.Dataset | QgsRasterLayer
    :return:
    """
    if isinstance(pathOrDataset, QgsRasterLayer):
        return getDS(pathOrDataset.source())
    elif isinstance(pathOrDataset, gdal.Dataset):
        return pathOrDataset
    elif isinstance(pathOrDataset, str):
        ds = gdal.Open(pathOrDataset)
        assert isinstance(ds, gdal.Dataset)
        return ds



def sensorID(nb:int, px_size_x:float, px_size_y:float, dt:int, wl:list, wlu:str)->str:
    """
    Create a sensor ID
    :param nb: number of bands
    :param px_size_x: pixel size x
    :param px_size_y: pixel size y
    :param wl: list of wavelength
    :param wlu: str, wavelength unit
    :return: str
    """
    assert dt in GDAL_DATATYPES.values()
    assert isinstance(nb, int) and nb > 0
    assert isinstance(px_size_x, (int, float)) and px_size_x > 0
    assert isinstance(px_size_y, (int, float)) and px_size_y > 0

    if wl != None:
        assert isinstance(wl, list)
        assert len(wl) == nb

    if wlu != None:
        assert isinstance(wlu, str)

    return json.dumps((nb, px_size_x, px_size_y, dt, wl, wlu))

def sensorIDtoProperties(idString:str)->tuple:
    """
    Reads a sensor id string and returns the sensor properties. See sensorID().
    :param idString: str
    :return: (ns, px_size_x, px_size_y, [wl], wlu)
    """
    nb, px_size_x, px_size_y, dt, wl, wlu = json.loads(idString)
    assert isinstance(dt, int) and dt >= 0
    assert isinstance(nb, int)
    assert isinstance(px_size_x, (int,float)) and px_size_x > 0
    assert isinstance(px_size_y, (int, float)) and px_size_y > 0
    if wl != None:
        assert isinstance(wl, list)
    if wlu != None:
        assert isinstance(wlu, str)

    return nb, px_size_x, px_size_y, dt, wl, wlu


class SensorInstrument(QObject):
    """
    Describes a Sensor Configuration
    """
    SensorNameSettingsPrefix = 'SensorName.'
    sigNameChanged = pyqtSignal(str)

    LUT_Wavelengths = dict({'B': 480,
                            'G': 570,
                            'R': 660,
                            'nIR': 850,
                            'swIR': 1650,
                            'swIR1': 1650,
                            'swIR2': 2150
                            })

    def __init__(self, sid:str, sensor_name:str=None, band_names:list = None):
        super(SensorInstrument, self).__init__()

        self.mId = sid

        self.nb, self.px_size_x, self.px_size_y, self.dataType, self.wl, self.wlu = sensorIDtoProperties(self.mId)

        if not isinstance(band_names, list):
            band_names = ['Band {}'.format(b+1) for b in range(self.nb)]

        assert len(band_names) == self.nb
        self.bandNames = band_names
        self.wlu = self.wlu
        if self.wl is None:
            self.wl = None
        else:
            self.wl = np.asarray(self.wl)

        if sensor_name is None:
            sensor_name = '{}bands@{}m'.format(self.nb, self.px_size_x)
            import eotimeseriesviewer.settings
            sensor_name = eotimeseriesviewer.settings.value(self._sensorSettingsKey(), sensor_name)
        self.mName = ''
        self.setName(sensor_name)

        self.hashvalue = hash(self.mId)

        from eotimeseriesviewer.tests import TestObjects
        import uuid
        path = '/vsimem/mockupImage.{}.bsq'.format(uuid.uuid4())
        self.mMockupDS = TestObjects.inMemoryImage(path=path, nb=self.nb, eType=self.dataType, ns=2, nl=2)

    def proxyLayer(self)->QgsRasterLayer:
        """
        Creates an "empty" layer that can be used as proxy for band names, data types and render styles
        :return: QgsRasterLayer
        """
        lyr = SensorProxyLayer(self.mMockupDS.GetFileList()[0], name=self.name(), sensor=self)
        lyr.nameChanged.connect(lambda l=lyr: self.setName(l.name()))
        lyr.setCustomProperty('eotsv/sensorid', self.id())
        self.sigNameChanged.connect(lyr.setName)
        return lyr

    def id(self)->str:
        """
        Returns the Sensor id
        :return: str
        """
        return self.mId

    def _sensorSettingsKey(self):
        return SensorInstrument.SensorNameSettingsPrefix+self.mId

    def setName(self, name: str):
        """
        Sets the sensor/product name
        :param name: str
        """
        if name != self.mName:
            self.mName = name
            import eotimeseriesviewer.settings
            eotimeseriesviewer.settings.setValue(self._sensorSettingsKey(), name)
            self.sigNameChanged.emit(self.name())

    def name(self)->str:
        """
        Returns the sensor name
        :return: str
        """
        return self.mName

    def __eq__(self, other):
        if not isinstance(other, SensorInstrument):
            return False
        return self.mId == other.mId

    def __hash__(self):
        return hash(self.id())

    def __repr__(self):
        return str(self.__class__) +' ' + self.name()

    def description(self)->str:
        """
        Returns a human-readable description
        :return: str
        """
        info = []
        info.append(self.name())
        info.append('{} Bands'.format(self.nb))
        info.append('Band\tName\tWavelength')
        for b in range(self.nb):
            if self.wl is not None:
                wl = str(self.wl[b])
            else:
                wl = 'unknown'
            info.append('{}\t{}\t{}'.format(b + 1, self.bandNames[b], wl))

        return '\n'.join(info)



class SensorProxyLayer(QgsRasterLayer):

    def __init__(self, *args, sensor:SensorInstrument, **kwds):
        super(SensorProxyLayer, self).__init__(*args, **kwds)
        self.mSensor = sensor

    def sensor(self)->SensorInstrument:
        """
        Returns the SensorInstrument this layer relates to
        :return: SensorInstrument
        """
        return self.mSensor

def verifyInputImage(datasource):
    """
    Checks if an image source can be uses as TimeSeriesDatum, i.e. if it can be read by gdal.Open() and
    if we can extract an observation date as numpy.datetime64.
    :param datasource: str with data source uri or gdal.Dataset
    :return: bool
    """

    if datasource is None:
        return None
    if isinstance(datasource, str):
        datasource = gdal.Open(datasource)
    if not isinstance(datasource, gdal.Dataset):
        return False

    if datasource.RasterCount == 0 and len(datasource.GetSubDatasets()) > 0:
        #logger.error('Can not open container {}.\nPlease specify a subdataset'.format(path))
        return False

    if datasource.GetDriver().ShortName == 'VRT':
        files = datasource.GetFileList()
        if len(files) > 0:
            for f in files:
                subDS = gdal.Open(f)
                if not isinstance(subDS, gdal.Dataset):
                    return False

    from eotimeseriesviewer.dateparser import parseDateFromDataSet
    date = parseDateFromDataSet(datasource)
    if date is None:
        return False

    return True



class TimeSeriesSource(object):
    """Provides some information on source images"""

    @staticmethod
    def create(source):
        """
        Reads the argument and returns a TimeSeriesSource
        :param source: gdal.Dataset, str, QgsRasterLayer
        :return: TimeSeriesSource
        """
        ds = None
        if isinstance(source, QgsRasterLayer):
            lyr = source
            provider = lyr.providerType()

            if provider == 'gdal':
                ds = gdal.Open(lyr.source())
            elif provider == 'wcs':
                parts = urllib.parse.parse_qs(lyr.source())
                url = re.search(r'^[^?]+', parts['url'][0]).group()
                identifier = re.search(r'^[^?]+', parts['identifier'][0]).group()

                uri2 = 'WCS:{}?coverage={}'.format(url, identifier)
                ds = gdal.Open(uri2)

                if not isinstance(ds, gdal.Dataset) or ds.RasterCount == 0:
                    dsGetCoverage = gdal.Open('WCS:{}'.format(url))
                    for subdatasetUrl, id in dsGetCoverage.GetSubDatasets():
                        if id == identifier:
                            ds = gdal.Open(subdatasetUrl)
                            break

            else:
                raise Exception('Unsupported raster data provider: {}'.format(provider))

        elif isinstance(source, str):
            ds = gdal.Open(source)

        elif isinstance(source, gdal.Dataset):
            ds = source

        else:
            raise Exception('Unsupported source: {}'.format(source))

        return TimeSeriesSource(ds)

    def __init__(self, dataset:gdal.Dataset):

        assert isinstance(dataset, gdal.Dataset)
        assert dataset.RasterCount > 0
        assert dataset.RasterYSize > 0
        assert dataset.RasterXSize > 0
        self.mUri = dataset.GetFileList()[0]

        self.mDate = parseDateFromDataSet(dataset)
        assert self.mDate is not None, 'Unable to find acquisition date of {}'.format(self.mUri)

        self.mDrv = dataset.GetDriver().ShortName
        self.mGT = dataset.GetGeoTransform()
        self.mWKT = dataset.GetProjection()
        self.mCRS = QgsCoordinateReferenceSystem(self.mWKT)

        self.mWL, self.mWLU = extractWavelengths(dataset)


        self.nb, self.nl, self.ns = dataset.RasterCount, dataset.RasterYSize, dataset.RasterXSize
        self.mGeoTransform = dataset.GetGeoTransform()
        px_x = float(abs(self.mGeoTransform[1]))
        px_y = float(abs(self.mGeoTransform[5]))
        self.mGSD = (px_x, px_y)
        self.mDataType = dataset.GetRasterBand(1).DataType
        self.mSid = sensorID(self.nb, px_x, px_y, self.mDataType, self.mWL, self.mWLU)

        self.mMetaData = collections.OrderedDict()
        for domain in dataset.GetMetadataDomainList():
            self.mMetaData[domain] = dataset.GetMetadata_Dict(domain)

        self.mUL = QgsPointXY(*px2geo(QPoint(0, 0), self.mGeoTransform, pxCenter=False))
        self.mLR = QgsPointXY(*px2geo(QPoint(self.ns + 1, self.nl + 1), self.mGeoTransform, pxCenter=False))

        self.mTimeSeriesDatum = None

    def name(self)->str:
        """
        Returns a name for this data source
        :return:
        """
        bn = os.path.basename(self.uri())
        return '{} {}'.format(bn, self.date())


    def uri(self)->str:
        """
        URI that can be used with GDAL to open a dataset
        :return: str
        """
        return self.mUri

    def qgsMimeDataUtilsUri(self)->QgsMimeDataUtils.Uri:
        uri = QgsMimeDataUtils.Uri()
        uri.name = self.name()
        uri.providerKey = 'gdal'
        uri.uri = self.uri()
        uri.layerType = 'raster'
        return uri

    def sid(self)->str:
        """
        Returns the sensor id
        :return: str
        """
        return self.mSid

    def timeSeriesDatum(self):
        """
        Returns the parent TimeSeriesDatum (if set)
        :return: TimeSeriesDatum
        """
        return self.mTimeSeriesDatum

    def setTimeSeriesDatum(self, tsd):
        """
        Sets the parent TimeSeriesDatum
        :param tsd: TimeSeriesDatum
        """
        self.mTimeSeriesDatum = tsd

    def date(self)->np.datetime64:
        return self.mDate

    def crs(self)->QgsCoordinateReferenceSystem:
        return self.mCRS

    def spatialExtent(self)->SpatialExtent:
        return SpatialExtent(self.mCRS, self.mUL, self.mLR)

    def __eq__(self, other):
        if not isinstance(other, TimeSeriesSource):
            return False
        return self.mUri == other.mUri


class TimeSeriesDatum(QAbstractTableModel):
    """
    A containe to store all image source related to a single observation date and sensor.
    """
    sigVisibilityChanged = pyqtSignal(bool)
    sigSourcesAdded = pyqtSignal(list)
    sigSourcesRemoved = pyqtSignal(list)
    sigRemoveMe = pyqtSignal()
    
    
    cnUri = 'Source'
    cnNS = 'ns'
    cnNB = 'nb'
    cnNL = 'nl'
    cnCRS = 'crs'
    
    ColumnNames = [cnNB, cnNL, cnNS, cnCRS, cnUri]
    
    def __init__(self, timeSeries, date:np.datetime64, sensor:SensorInstrument):
        """
        Constructor
        :param timeSeries: TimeSeries, parent TimeSeries instance, optional
        :param date: np.datetime64,
        :param sensor: SensorInstrument
        """
        super(TimeSeriesDatum, self).__init__()
        
        assert isinstance(date, np.datetime64)
        assert isinstance(sensor, SensorInstrument)
        
        self.mSensor = sensor
        self.mDate = date
        self.mDOY = DOYfromDatetime64(self.mDate)
        self.mSources = []
        self.mMasks = []
        self.mVisibility = True
        self.mTimeSeries = timeSeries
    
    def removeSource(self, source:TimeSeriesSource):
        
        if source in self.mSources:
            i = self.mSources.index(source)
            self.beginRemoveRows(QModelIndex(), i, i)
            self.mSources.remove(source)
            self.endRemoveRows()
            self.sigSourcesRemoved.emit([source])
        
    def addSource(self, source):
        """
        Adds an time series source to this TimeSeriesDatum
        :param path: TimeSeriesSource or any argument accepted by TimeSeriesSource.create()
        :return: TimeSeriesSource, if added
        """

        if not isinstance(source, TimeSeriesSource):
            return self.addSource(TimeSeriesSource.create(source))
        else:
            assert isinstance(source, TimeSeriesSource)
            assert self.mDate == source.date()
            assert self.mSensor.id() == source.sid()

            source.setTimeSeriesDatum(self)

            if source not in self.mSources:
                i = len(self)
                self.beginInsertRows(QModelIndex(), i, i)
                self.mSources.append(source)
                self.endInsertRows()
                self.sigSourcesAdded.emit([source])
                return source
            else:
                return None

    def setVisibility(self, b:bool):
        """
        Sets the visibility of the TimeSeriesDatum, i.e. whether linked MapCanvases will be shown to the user
        :param b: bool
        """
        old = self.mVisibility
        self.mVisibility = b
        if old != self.mVisibility:
            self.sigVisibilityChanged.emit(b)

    def isVisible(self):
        """
        Returns whether the TimeSeriesDatum is visible as MapCanvas
        :return: bool
        """
        return self.mVisibility

    def sensor(self)->SensorInstrument:
        """
        Returns the SensorInstrument
        :return: SensorInsturment
        """
        return self.mSensor

    def sources(self)->list:
        """
        Returns the source images
        :return: [list-of-TimeSeriesSource]
        """
        return self.mSources


    def sourceUris(self)->list:
        """
        Returns all source URIs  as list of strings-
        :return: [list-of-str]
        """
        return [tss.uri() for tss in self.sources()]

    def qgsMimeDataUtilsUris(self)->list:
        """
        Returns all source URIs as list of QgsMimeDataUtils.Uri
        :return: [list-of-QgsMimedataUtils.Uris]
        """
        return [s.qgsMimeDataUtilsUri() for s in self.sources()]

    def date(self)->np.datetime64:
        """
        Returns the observation date
        :return: numpy.datetime64
        """
        return np.datetime64(self.mDate)

    def decimalYear(self)->float:
        """
        Returns the observation date as decimal year (year + doy / (366+1) )
        :return: float
        """

        return self.year() + self.doy() / (366+1)

    def year(self)->int:
        """
        Returns the observation year
        :return: int
        """
        return self.mDate.astype(object).year

    def doy(self)->int:
        """
        Returns the day of Year (DOY)
        :return: int
        """
        return int(self.mDOY)

    def spatialExtent(self):
        """
        Returns the SpatialExtent of all data sources
        :return: SpatialExtent
        """
        ext = None
        for i, tss in enumerate(self.sources()):
            assert isinstance(tss, TimeSeriesSource)
            if i == 0:
                ext = tss.spatialExtent()
            else:
                ext.combineExtentWith(tss.spatialExtent())
        return ext

    def imageBorders(self)->QgsGeometry:
        """
        Retunrs the exact border polygon
        :return: QgsGeometry
        """

        return None

    def __repr__(self)->str:
        """
        String representation
        :return:
        """
        return 'TimeSeriesDatum({},{})'.format(str(self.mDate), str(self.mSensor))

    def __eq__(self, other)->bool:
        """
        Tow TimeSeriesDatum instances are equal if they have the same date, sensor and sources.
        :param other: TimeSeriesDatum
        :return: bool
        """
        if not isinstance(other, TimeSeriesDatum):
            return False
        return self.id() == other.id() and self.mSources == other.mSources


    def __contains__(self, item):
        return item in self.mSources

    def __getitem__(self, slice):
        return self.mSources[slice]

    def __iter__(self):
        """
        Iterator over all sources
        """
        return iter(self.mSources)

    def __len__(self)->int:
        """
        Returns the number of source images.
        :return: int
        """
        return len(self.mSources)

    def __lt__(self, other)->bool:
        """
        :param other: TimeSeriesDatum
        :return: bool
        """
        assert isinstance(other, TimeSeriesDatum)
        if self.date() < other.date():
            return True
        elif self.date() > other.date():
            return False
        else:
            return self.sensor().id() < other.sensor().id()
    
    def rowCount(self, parent: QModelIndex = QModelIndex()):
        
        return len(self)
    
    def columnCount(self, parent: QModelIndex):
        return len(TimeSeriesDatum.ColumnNames)
    
    def flags(self, index: QModelIndex):
        return Qt.ItemIsEnabled | Qt.ItemIsSelectable

    def headerData(self, section, orientation, role):
        assert isinstance(section, int)
        if orientation == Qt.Horizontal and role == Qt.DisplayRole:
            return TimeSeriesDatum.ColumnNames[section]
        else:
            return None

    
    def data(self, index: QModelIndex, role: int ):
        
        if not index.isValid():
            return None
        
        tss = self.mSources[index.row()]
        assert isinstance(tss, TimeSeriesSource)
        
        cn = TimeSeriesDatum.ColumnNames[index.column()]
        if role == Qt.UserRole:
            return tss
        
        if role == Qt.DisplayRole:
            if cn == TimeSeriesDatum.cnNB:
                return tss.nb
            if cn == TimeSeriesDatum.cnNS:
                return tss.ns
            if cn == TimeSeriesDatum.cnNL:
                return tss.nl
            if cn == TimeSeriesDatum.cnCRS:
                return tss.crs().description()
            if cn == TimeSeriesDatum.cnUri:
                return tss.uri()
        
        return None   
            
        
    def id(self)->tuple:
        """
        :return: tuple
        """
        return (self.mDate, self.mSensor.id())


    def mimeDataUris(self)->list:
        """
        Returns the sources of this TSD as list of QgsMimeDataUtils.Uris
        :return: [list-of-QgsMimeDataUtils]
        """
        results = []
        for tss in self.sources():
            assert isinstance(tss, TimeSeriesSource)

        [tss.uri() for tss in self.sources()]

    def __hash__(self):
        return hash(self.id())


class TimeSeriesTreeView(QTreeView):

    sigMoveToDateRequest = pyqtSignal(TimeSeriesDatum)

    def __init__(self, parent=None):
        super(TimeSeriesTreeView, self).__init__(parent)



    def contextMenuEvent(self, event: QContextMenuEvent):
        """
        Creates and shows the QMenu
        :param event: QContextMenuEvent
        """

        idx = self.indexAt(event.pos())
        tsd = self.model().data(idx, role=Qt.UserRole)

        menu = QMenu(self)
        a = menu.addAction('Copy value(s)')
        a.triggered.connect(lambda: self.onCopyValues())
        a = menu.addAction('Check')
        a.triggered.connect(lambda: self.onSetCheckState(Qt.Checked))
        a = menu.addAction('Uncheck')
        a.triggered.connect(lambda: self.onSetCheckState(Qt.Unchecked))
        if isinstance(tsd, TimeSeriesDatum):
            a = menu.addAction('Show {}'.format(tsd.date()))
            a.triggered.connect(lambda _, tsd=tsd: self.sigMoveToDateRequest.emit(tsd))

        menu.popup(QCursor.pos())

    def onSetCheckState(self, checkState):
        """
        Sets a ChecState to all selected rows
        :param checkState: Qt.CheckState
        """
        indices = self.selectionModel().selectedIndexes()
        rows = sorted(list(set([i.row() for i in indices])))
        model = self.model()
        if isinstance(model, QSortFilterProxyModel):
            for r in rows:
                idx = model.index(r, 0)
                model.setData(idx, checkState, Qt.CheckStateRole)

    def onCopyValues(self, delimiter='\t'):
        """
        Copies selected cell values to the clipboard
        """
        indices = self.selectionModel().selectedIndexes()
        model = self.model()
        if isinstance(model, QSortFilterProxyModel):
            from collections import OrderedDict
            R = OrderedDict()
            for idx in indices:
                if not idx.row() in R.keys():
                    R[idx.row()] = []
                R[idx.row()].append(model.data(idx, Qt.DisplayRole))
            info = []
            for k, values in R.items():
                info.append(delimiter.join([str(v) for v in values]))
            info = '\n'.join(info)
            QApplication.clipboard().setText(info)
        s = ""


class TimeSeriesTableView(QTableView):

    sigMoveToDateRequest = pyqtSignal(TimeSeriesDatum)

    def __init__(self, parent=None):
        super(TimeSeriesTableView, self).__init__(parent)

    def contextMenuEvent(self, event):
        """
        Creates and shows an QMenu
        :param event:
        """

        idx = self.indexAt(event.pos())
        tsd = self.model().data(idx, role=Qt.UserRole)


        menu = QMenu(self)
        a = menu.addAction('Copy value(s)')
        a.triggered.connect(lambda: self.onCopyValues())
        a = menu.addAction('Check')
        a.triggered.connect(lambda: self.onSetCheckState(Qt.Checked))
        a = menu.addAction('Uncheck')
        a.triggered.connect(lambda: self.onSetCheckState(Qt.Unchecked))
        if isinstance(tsd, TimeSeriesDatum):
            a = menu.addAction('Show {}'.format(tsd.date()))
            a.triggered.connect(lambda _, tsd=tsd: self.sigMoveToDateRequest.emit(tsd))

        menu.popup(QCursor.pos())

    def onSetCheckState(self, checkState):
        """
        Sets a ChecState to all selected rows
        :param checkState: Qt.CheckState
        """
        indices = self.selectionModel().selectedIndexes()
        rows = sorted(list(set([i.row() for i in indices])))
        model = self.model()
        if isinstance(model, TimeSeriesTableModel):
            for r in rows:
                idx = model.index(r, 0)
                model.setData(idx, checkState, Qt.CheckStateRole)

    def onCopyValues(self, delimiter='\t'):
        """
        Copies selected cell values to the clipboard
        """
        indices = self.selectionModel().selectedIndexes()
        model = self.model()
        if isinstance(model, QSortFilterProxyModel):
            from collections import OrderedDict
            R = OrderedDict()
            for idx in indices:
                if not idx.row() in R.keys():
                    R[idx.row()] = []
                R[idx.row()].append(model.data(idx, Qt.DisplayRole))
            info = []
            for k, values in R.items():
                info.append(delimiter.join([str(v) for v in values]))
            info = '\n'.join(info)
            QApplication.clipboard().setText(info)
        s = ""



class DateTimePrecision(enum.Enum):
    """
    Describes the precision to pares DateTimeStamps.
    """

    Year = 'Y'
    Month = 'M'
    Week = 'W'
    Day = 'D'
    Hour = 'h'
    Minute = 'm'
    Second = 's'
    Milisecond = 'ms'
    Original = 0


class TimeSeries(QAbstractItemModel):
    """
    The sorted list of data sources that specify the time series
    """

    sigTimeSeriesDatesAdded = pyqtSignal(list)
    sigTimeSeriesDatesRemoved = pyqtSignal(list)
    sigLoadingProgress = pyqtSignal(int, int, str)


    sigSensorAdded = pyqtSignal(SensorInstrument)
    sigSensorRemoved = pyqtSignal(SensorInstrument)

    sigSourcesAdded = pyqtSignal(list)
    sigSourcesRemoved = pyqtSignal(list)



    _sep = ';'

    def __init__(self, imageFiles=None):
        super(TimeSeries, self).__init__()
        self.mTSDs = list()
        self.mSensors = []
        self.mShape = None
        self.mDateTimePrecision = DateTimePrecision.Original

        self.mCurrentDates = []

        self.cnDate = 'Date'
        self.cnSensor = 'Sensor'
        self.cnNS = 'ns'
        self.cnNL = 'nl'
        self.cnNB = 'nb'
        self.cnCRS = 'CRS'
        self.cnImages = 'Source Image(s)'
        self.mColumnNames = [self.cnDate, self.cnSensor,
                             self.cnNS, self.cnNL, self.cnNB,
                             self.cnCRS, self.cnImages]

        self.mRootIndex = QModelIndex()


        if imageFiles is not None:
            self.addSources(imageFiles)


    def setCurrentDates(self, tsds:list):


        self.mCurrentDates.clear()
        self.mCurrentDates.extend(tsds)
        for tsd in tsds:
            assert isinstance(tsd, TimeSeriesDatum)
            if tsd in self:
                idx = self.tsdToIdx(tsd)
                # force reset of background color
                idx2 = self.index(idx.row(), self.columnCount()-1)
                self.dataChanged.emit(idx, idx2, [Qt.BackgroundColorRole])

    def sensor(self, sensorID:str)->SensorInstrument:
        """
        Returns the sensor with sid = sid
        :param sensorID: str, sensor id
        :return: SensorInstrument
        """
        assert isinstance(sensorID, str)
        for sensor in self.mSensors:
            assert isinstance(sensor, SensorInstrument)
            if sensor.id() == sensorID:
                return sensor
        return None


    def sensors(self)->list:
        """
        Returns the list of sensors derived from the TimeSeries data sources
        :return: [list-of-SensorInstruments]
        """
        return self.mSensors[:]

    def loadFromFile(self, path, n_max=None, progressDialog:QProgressDialog=None):
        """
        Loads a CSV file with source images of a TimeSeries
        :param path: str, Path of CSV file
        :param n_max: optional, maximum number of files to load
        """

        images = []
        masks = []
        with open(path, 'r') as f:
            lines = f.readlines()
            for l in lines:
                if re.match('^[ ]*[;#&]', l):
                    continue

                parts = re.split('[\n'+TimeSeries._sep+']', l)
                parts = [p for p in parts if p != '']
                images.append(parts[0])
                if len(parts) > 1:
                    masks.append(parts[1])


        if n_max:
            n_max = min([len(images), n_max])
            self.addSources(images[0:n_max], progressDialog=progressDialog)
        else:
            self.addSources(images, progressDialog=progressDialog)
        #self.addMasks(masks)