PlotToSat.ipynb

{
 "cells": [
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This module manages brings together all the classes for extracting time-series at multiple plot locations\n",
    " \n",
    "author:  Dr Milto Miltiadou\n",
    "version: 1.0"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import sys\n",
    "\n",
    "# check if GEE is already imported to avoid requesting authenticatiation multiple times\n",
    "modulename = 'ee'\n",
    "if modulename not in sys.modules: \n",
    "   # import GEE and Authenticate, token or log in will be asked from web browser\n",
    "   import ee\n",
    "   ee.Authenticate()\n",
    "   ee.Initialize()\n",
    "   print (\"Importing GEE\")\n",
    "else:\n",
    "   print('GEE already imported')\n",
    "   # google earth engine already imported and authenticated\n",
    "\n",
    "\n",
    "modulename = 'ipynb_masks'\n",
    "if modulename not in sys.modules:\n",
    "    %run Masks.ipynb\n",
    "    sys.modules['ipynb_masks'] = None\n",
    "#else\n",
    "    # module already loaded\n",
    "\n",
    "modulename = 'ipynb_Utils'\n",
    "if modulename not in sys.modules:\n",
    "    import Utils\n",
    "    # adding an identifier to sys.modules to avoiding loading the same file multiple times\n",
    "    sys.modules['ipynb_Utils'] = None \n",
    "#else\n",
    "   # Utils modules has already been loaded somewhere else\n",
    "\n",
    "# check if GEE is already imported to avoid requesting authenticatiation multiple times\n",
    "modulename = 'ipynb_Sentinel1'\n",
    "if modulename not in sys.modules:\n",
    "    %run Sentinel1.ipynb\n",
    "    # adding an identifier to sys.modules to avoiding loading the same file multiple times\n",
    "    sys.modules['ipynb_Sentinel1'] = None \n",
    "#else\n",
    "   # Sentinel1 modules has already been loaded somewhere else\n",
    "\n",
    "modulename = 'ipynb_Sentinel2b'\n",
    "if modulename not in sys.modules:\n",
    "    %run Sentinel2b.ipynb\n",
    "    # adding an identifier to sys.modules to avoiding loading the same file multiple times\n",
    "    sys.modules['ipynb_Sentinel2b'] = None \n",
    "#else\n",
    "   # Utils modules has already been loaded somewhere else\n",
    "\n",
    "import sys\n",
    "modulename = 'ipynb_FieldData'\n",
    "if modulename not in sys.modules:\n",
    "    %run FieldData.ipynb\n",
    "    # adding an identifier to sys.modules to avoiding loading the same file multiple times\n",
    "    sys.modules['FieldData'] = None \n",
    "#else\n",
    "   # Utils modules has already been loaded somewhere else\n",
    "\n",
    "# check if GEE is already imported to avoid requesting authenticatiation multiple times\n",
    "modulename = 'Masks'\n",
    "if modulename not in sys.modules:\n",
    "    # import Masks Class\n",
    "    %run Masks.ipynb\n",
    "# else:\n",
    "    # Mask class already imported and authenticated\n",
    "    \n",
    "modulename = 'Polygons'\n",
    "if modulename not in sys.modules:\n",
    "    %run Polygons.ipynb\n",
    "    # adding an identifier to sys.modules to avoiding loading the same file multiple times\n",
    "    sys.modules['ipynb_Polygons'] = None \n",
    "#else\n",
    "   # Utils modules has already been loaded somewhere else\n",
    "\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import numbers\n",
    "from datetime import date\n",
    "\n",
    "class PlotToSat:\n",
    "## @brief method that sets the year of interest\n",
    "    def setYear(self,year):\n",
    "        # check each collection to see if year exist and set valid to false if year doesn't exist\n",
    "        self.year = year\n",
    "        startdate = str(self.year)+'-01-01'\n",
    "        enddate   = str(self.year)+'-12-31'\n",
    "        today = date.today()\n",
    "        cy = today.year\n",
    "        if (cy==year): \n",
    "            enddate = today.strftime(\"%Y-%m-%d\")\n",
    "        # S1\n",
    "        ly = int(self.sentinel1Info[\"launchDate\"   ][0:4])\n",
    "        ry = int(self.sentinel1Info[\"retirmentDate\"][0:4])\n",
    "        if (year<ly or year>ry):\n",
    "            print(\"WARNING: Sentinel-1 data will not be exported as the year requested is before launched date or after retirement date.\")\n",
    "            self.sentinel1Info[\"startDate\"]=\"\"\n",
    "            self.sentinel1Info[\"endDate\"  ]=\"\"\n",
    "        elif (year==ly):\n",
    "            self.sentinel1Info[\"startDate\"]=self.sentinel1Info[\"launchDate\"]\n",
    "            self.sentinel1Info[\"endDate\"]=enddate\n",
    "        elif (year==ry):\n",
    "           self.sentinel1Info[\"startDate\"]=startdate\n",
    "           self.sentinel1Info[\"endDate\"]=self.sentinel1Info[\"retirmentDate\"]\n",
    "        else :\n",
    "            self.sentinel1Info[\"startDate\"]=startdate\n",
    "            self.sentinel1Info[\"endDate\"]=enddate\n",
    "        # S2\n",
    "        ly = int(self.sentinel2Info[\"launchDate\"][0:4])\n",
    "        if (year<ly or year>ry):\n",
    "            print(\"WARNING: Sentinel-2 data will not be exported as the year requested is before launched date.\")\n",
    "            self.sentinel2Info[\"startDate\"]=\"\"\n",
    "            self.sentinel2Info[\"endDate\"  ]=\"\"\n",
    "        elif (year==ly):\n",
    "            self.sentinel2Info[\"startDate\"]=self.sentinel2Info[\"launchDate\"]\n",
    "            self.sentinel2Info[\"endDate\"]=enddate\n",
    "        elif (year==ry):\n",
    "           self.sentinel2Info[\"startDate\"]=startdate\n",
    "           self.sentinel2Info[\"endDate\"]=self.sentinel2Info[\"retirmentDate\"]\n",
    "        else :\n",
    "            self.sentinel2Info[\"startDate\"]=startdate\n",
    "            self.sentinel2Info[\"endDate\"]=enddate\n",
    "\n",
    "        print (\"Sentinel1: \",self.sentinel1Info[\"startDate\"] ,self.sentinel1Info[\"endDate\"])\n",
    "        print (\"Sentinel2: \",self.sentinel2Info[\"startDate\"] ,self.sentinel2Info[\"endDate\"])\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "    ## Method that adds the field data to the Manager\n",
    "    # \n",
    "    # @param[in] properties: a dictionary containing the name of the csv file containing the \n",
    "    #   plot iformation, the projection and \n",
    "    #   the name of the column that give the year that the field data were collected\n",
    "    #   e.g. {'csvfilename':csvFile,'proj':\"EPSG:3042\", labelOfyearCol':\"year\"}\n",
    "\n",
    "    def addFieldData(self,properties): # csvfile,proj,yearlabel):\n",
    "\n",
    "        self.csvDF = FieldData(properties)\n",
    "        self.maxSize = self.csvDF.getLen()\n",
    "\n",
    "\n",
    "\n",
    "    def __init__(self,geometry,fieldDataProperties,year):\n",
    "        self.samplingSize = 400\n",
    "        self.sampleCount  = 0\n",
    "        self.maxSize      = 0\n",
    "        self.csvDF        = None\n",
    "        self.year         = 2017\n",
    "        self.shp          = None\n",
    "        self.shpPolygons  = None\n",
    "        self.shpPolKeyCol = None\n",
    "        \n",
    "        \n",
    "       \n",
    "        # else already false and reading plot data from csv file\n",
    "        self.filedataFilewithIDs = \"fieldDataWithIdentifiers/FieldDataWithIdentifiers.csv\"\n",
    "        #----------------------------------------------------\n",
    "        # Initialise collection \n",
    "        #----------------------------------------------------\n",
    "        todayDate = date.today().strftime(\"%Y-%m-%d\")\n",
    "        #----------------------------------------------------\n",
    "        self.sentinel1Info = {\n",
    "            \"identifier\"     : 'sentinel-1',\n",
    "            \"collection\"     : \"COPERNICUS/S1_GRD\",\n",
    "            \"launchDate\"     : \"2014-04-01\",\n",
    "            \"retirmentDate\"  : todayDate, #not retired yet\n",
    "            \"startDate\"      : \"\",\n",
    "            \"endDate\"        : \"\",\n",
    "            \"added\"          : False,\n",
    "            \"aspects\"        : False,\n",
    "            \"selectedBand\"   : [],\n",
    "            \"selectedIndices\": [],\n",
    "        }       \n",
    "        #----------------------------------------------------\n",
    "        self.sentinel2Info = {\n",
    "            \"identifier\"     : 'sentinel-2',                                              \n",
    "            \"collection\"     : \"COPERNICUS/S2_SR_HARMONIZED\",\n",
    "            \"launchDate\"     : \"2015-05-23\",\n",
    "            \"retirmentDate\"  :todayDate, #not retired yet\n",
    "            \"startDate\"      : \"\",\n",
    "            \"endDate\"        : \"\",\n",
    "            \"added\"          : False,\n",
    "            \"clouds\"         : 50,\n",
    "            \"selectedBand\"   : ['B1', 'B2', 'B3', 'B4', 'B5', 'B6', 'B7', 'B8', 'B8A', 'B9', 'B11', 'B12'],\n",
    "            \"selectedIndices\": [],\n",
    "        } \n",
    "\n",
    "\n",
    "\n",
    "        self.numberOfAvailableCols = 2\n",
    "        # the labels of the available collections\n",
    "        self.listOfAvailableCollections = ['sentinel-1', 'sentinel-2']\n",
    "        self.listOfAvailCollections = [sentinel1Info,sentinel2Info]\n",
    "        # else list have the smae  size and it is correct\n",
    "        self.geometry  = geometry\n",
    "\n",
    "        self.fiedplotData = None\n",
    "        self.proj = \"EPSG:3042\"\n",
    "        self.masks = {}\n",
    "        self.year = 0\n",
    "        self.radius = 30\n",
    "        self.csvfile = None\n",
    "        self.bufferredPoints = None\n",
    "        self.colX = \"CX\"\n",
    "        self.colY = \"CY\"\n",
    "        \n",
    "        if (isinstance(fieldDataProperties, str)):\n",
    "            self.shp = fieldDataProperties\n",
    "            print (\"Shapefile Loaded!\")\n",
    "            return\n",
    "        # else get information about plot data\n",
    "        \n",
    "        print (\"Return didn't work\")\n",
    "        if not ('outPlotFileWithIDs' in fieldDataProperties):\n",
    "            fieldDataProperties['outPlotFileWithIDs'] = self.filedataFilewithIDs\n",
    "        # else:\n",
    "          # outFlotFileWithIDs has been defined by the user  \n",
    "        \n",
    "        \n",
    "       \n",
    "        self.setYear(year)\n",
    "       \n",
    "        if \"shpfilename\" in fieldDataProperties:\n",
    "            self.shp = fieldDataProperties[\"shpfilename\"]\n",
    "            if (\"polygonKeyColumn\" in fieldDataProperties):\n",
    "               self.shpPolygons = Polygons(self.shp, fieldDataProperties[\"polygonKeyColumn\"])\n",
    "            else :\n",
    "                raise Exception (\"PlotToSat: \\\"polygonKeyColumn\\\" not provided!\" )\n",
    "        else : \n",
    "            self.addFieldData(fieldDataProperties)\n",
    "            if(self.csvDF == None or self.maxSize==0):\n",
    "                raise Exception(\"Manager: Plot data loaded are not correct!\")\n",
    "    \n",
    "    \n",
    "    def availableIndices(collection): \n",
    "        if collection == \"sentinel-2\" : \n",
    "            Sentinel2.printAvailableIndices()\n",
    "            \n",
    "    ## method that enables and disables exportation of Std values\n",
    "    #  @param[in] Bool is a boolean value True for enable and False for disable\n",
    "    def exportStd(self,Bool):\n",
    "        if (self.csvDF != None):\n",
    "            self.csvDF.exportStd(Bool)\n",
    "        elif self.shpPolygons!=None:\n",
    "            self.shpPolygons.exportStd(Bool)\n",
    "        else:\n",
    "            print (\"WARNING: exportStd did nothing as neither a csv file or a shp file are loaded\")\n",
    "        \n",
    "    ## method that enables and disables exportation of Std values\n",
    "    #  @param[in] Bool is a boolean value True for enable and False for disable\n",
    "    def exportMean(self,Bool):\n",
    "        if (self.csvDF != None):\n",
    "            self.csvDF.exportMean(Bool)\n",
    "        elif self.shpPolygons!=None:\n",
    "            self.shpPolygons.exportMean(Bool)\n",
    "        else:\n",
    "            print (\"WARNING: exportMean did nothing as neither a csv file or a shp file are loaded\")\n",
    "        \n",
    "    \n",
    "    \n",
    "    ## @brief method that defines the bands of interest \n",
    "    #  @param[in] collection of interest\n",
    "    #  @param[in] bands of interest\n",
    "    #  @note Currently only supporting Sentinel-2\n",
    "    def selectBands(self, collection, selectedBands ): \n",
    "        if (collection == \"sentinel-1\"):\n",
    "            self.sentinel1Info[\"selectedBand\"] = selectedBands\n",
    "        elif (collection == \"sentinel-2\"):\n",
    "            self.sentinel2Info[\"selectedBand\"] = selectedBands\n",
    "    \n",
    "    ## @brief method that defines the indices of interest for Sentinel-2\n",
    "    def selectIndices(self, collection, selectedIndices ): \n",
    "        if (collection == \"sentinel-1\"):\n",
    "            self.sentinel1Info[\"selectedIndices\"] = selectedIndices\n",
    "        elif (collection == \"sentinel-2\"):\n",
    "            self.sentinel2Info[\"selectedIndices\"] = selectedIndices\n",
    "    \n",
    "    \n",
    "\n",
    "    ## @brief method that prints the collections that are available within the system\n",
    "    def printAvailableCollections(self):\n",
    "        # new approach\n",
    "        print(\"There are \", self.numberOfAvailableCols,\" collections available within the system:\")\n",
    "        \n",
    "        labels      = [self.sentinel1Info[\"identifier\"],\n",
    "                       self.sentinel2Info[\"identifier\"]]\n",
    "        \n",
    "        collections = [self.sentinel1Info[\"collection\"],\n",
    "                       self.sentinel2Info[\"collection\"]]\n",
    "        \n",
    "        data = {\"label\": labels, \"collection\":collections}\n",
    "        df = pd.DataFrame(data)\n",
    "        print(df)\n",
    "            \n",
    "            \n",
    "\n",
    "    \n",
    "    ## Method that adjust the sampling of the plot data to avoid processing all of them at once and crusing\n",
    "    #  newSampling the the sampling limit\n",
    "    def setSampling(self, newSampling):\n",
    "        self.samplingSize = newSampling\n",
    "        if self.shp is not None:\n",
    "            self.shpPolygons.setSampling(newSampling)\n",
    "        print(\"NEW SAMPLING: = \", self.samplingSize)\n",
    "\n",
    "\n",
    "    \n",
    "\n",
    "    ## @brief method that sets the masks that will be applied \n",
    "    #  @param[in] newMasks the masks to be used\n",
    "    def setMasks(self, newMasks):\n",
    "        self.masks = newMasks\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "    ## method that adds a collection to the manager\n",
    "    # @param[in] label the label of the collection to be added e.g., 'sentinel-1'\n",
    "    # @param[in] a variable that may be used if needed e.g., cloudpercentage in sentinel2\n",
    "    def addCollection(self,label, vari):\n",
    "        if(label=='sentinel-1'):\n",
    "            self.sentinel1Info[\"added\"]  = True\n",
    "            if(isinstance(vari,bool)):\n",
    "                self.sentinel1Info[\"aspects\"]  = vari\n",
    "            else :\n",
    "                print(\"WARNING: Variable imported along with sentinel-1 is not a Boolean (True or False) value - Aspect maps will not be applied\")\n",
    "            print(\"Sentinel 1 added\")\n",
    "        elif (label == 'sentinel-2'):\n",
    "            self.sentinel2Info[\"added\"]  = True\n",
    "            if(isinstance(vari,numbers.Number) and vari>0 and vari<100):\n",
    "                self.sentinel2Info[\"clouds\"] = vari\n",
    "            else :\n",
    "                print(\"WARNINGING: Cloud value should be a number between (0,100). A 50 cloud coverage will be used.\")\n",
    "                self.sentinel2Info[\"clouds\"] = 50\n",
    "            print(\"Sentinel 2 added\")\n",
    "            \n",
    "    #loop through each collection and export data \n",
    "\n",
    "    def exportCollections(self,startOffeaturesFilenamesWithSampling,gdrivefolder):\n",
    "        if(self.sentinel1Info[\"startDate\"]!=\"\" and \n",
    "        self.sentinel1Info[\"endDate\"]!=\"\" and \n",
    "        self.sentinel1Info[\"added\"]):\n",
    "            print(\"Sentinel 1 collection parameters loaded are valid and system is now intepreting data\")\n",
    "            s1 = Sentinel1(\n",
    "                self.geometry,\n",
    "                self.sentinel1Info[\"startDate\"],\n",
    "                self.sentinel1Info[\"endDate\"],\n",
    "                self.masks,\n",
    "                self.sentinel1Info[\"aspects\"]\n",
    "                )\n",
    "            lys = int(self.sentinel1Info[\"startDate\" ][0:4])\n",
    "            lye = int(self.sentinel1Info[\"endDate\"   ][0:4])\n",
    "            if (lys!=lye):\n",
    "                raise Exception(\"ERROR: start end end data should have been in the same year\")\n",
    "            else: \n",
    "                s1.byMonth(lys)\n",
    "                if(self.sentinel1Info[\"aspects\"]):\n",
    "                    s1bandsAsc = s1.getCollectionToBandsAsc()\n",
    "                    s1bandsDes = s1.getCollectionToBandsDes()\n",
    "                    if (self.shp is None):\n",
    "                        self.csvDF.exportFeaturesMeanStdCSV(s1bandsAsc,startOffeaturesFilenamesWithSampling+\"_S1Asc\",gdrivefolder)\n",
    "                        self.csvDF.exportFeaturesMeanStdCSV(s1bandsDes,startOffeaturesFilenamesWithSampling+\"_S1Des\",gdrivefolder)\n",
    "                    else:\n",
    "                        self.shpPolygons.exportFeaturesMeanStdCSV(s1bandsAsc,startOffeaturesFilenamesWithSampling+\"_S1Asc\",gdrivefolder)\n",
    "                        self.shpPolygons.exportFeaturesMeanStdCSV(s1bandsDes,startOffeaturesFilenamesWithSampling+\"_S1Des\",gdrivefolder)\n",
    "                else :\n",
    "                    s1bands = s1.getCollectionToBands()            \n",
    "                    if (self.shp is None):\n",
    "                        self.csvDF.exportFeaturesMeanStdCSV(s1bands,startOffeaturesFilenamesWithSampling+\"_S1\",gdrivefolder)\n",
    "                    else :\n",
    "                        self.shpPolygons.exportFeaturesMeanStdCSV(s1bands,startOffeaturesFilenamesWithSampling+\"_S1\",gdrivefolder)\n",
    "\n",
    "        else:\n",
    "            print(\"WARNING: Sentinel 1 collection parameters loaded are NOT valid and system is skipping this collection\")\n",
    "\n",
    "\n",
    "        if(self.sentinel2Info[\"added\"]):\n",
    "            print(\"Sentinel 2 collection parameters loaded are valid and system is now intepreting data\")\n",
    "            s2 = Sentinel2(\n",
    "                self.geometry,\n",
    "                self.sentinel2Info,\n",
    "                self.masks\n",
    "                )\n",
    "            \n",
    "            lys = int(self.sentinel2Info[\"startDate\" ][0:4])\n",
    "            lye = int(self.sentinel2Info[\"endDate\"   ][0:4])\n",
    "            if (lys!=lye):\n",
    "                raise Exception(\"ERROR: start end end data should have been in the same year\")\n",
    "            else: \n",
    "                s2.byMonth(lys)\n",
    "                s2bands = s2.getCollectionToBands()\n",
    "                if (self.shp is None):\n",
    "                   self.csvDF.exportFeaturesMeanStdCSV(s2bands,startOffeaturesFilenamesWithSampling+\"_S2\",gdrivefolder)\n",
    "                else:\n",
    "                   self.shpPolygons.exportFeaturesMeanStdCSV(s2bands,startOffeaturesFilenamesWithSampling+\"_S2\",gdrivefolder)\n",
    "        else:\n",
    "                print(\"WARNING: Sentinel 2 collection parameters loaded are NOT valid and system is skipping this collection\")\n",
    "\n",
    "    def exprtFeaturesMinMax(self,gdrivefolder,startOffeaturesFilename, min,max):\n",
    "        currentMin = min\n",
    "        currentMax = max\n",
    "        strCurrentMin = str(currentMin  ).rjust(10,'0')\n",
    "        strCurrentMax = str(currentMax-1).rjust(10,'0')\n",
    "        startOffeaturesFilenamesWithSampling = startOffeaturesFilename+\"_\"+strCurrentMin+\"_\"+strCurrentMax\n",
    "        if self.shp is None :\n",
    "           bufferredPoints = self.csvDF.createBufferedPoints(currentMin,currentMax)\n",
    "           if bufferredPoints == None :\n",
    "               print (\"WARNING: exprtFeaturesMinMax: No data exported because range provided does not exist.\")\n",
    "               return\n",
    "        else :\n",
    "            polygons = self.shpPolygons.createPolygons(currentMin,currentMax)\n",
    "        \n",
    "        if ((self.shp is not None and polygons is not None) or self.csvDF is not None):\n",
    "            print (\"exporting collections\")\n",
    "            self.exportCollections(startOffeaturesFilenamesWithSampling,gdrivefolder)\n",
    "        else :\n",
    "               print( \"WARNING: Skipping exportation as polygons from \", currentMin, \" to \", currentMax, \n",
    "                     \" haven't been created\")\n",
    "     \n",
    "    ## method that exports a set of files containing the feature vectors\n",
    "    def exportFeatures(self,gdrivefolder,startOffeaturesFilename):\n",
    "        if (self.sentinel1Info[\"added\"] == False and self.sentinel2Info[\"added\"] == False):\n",
    "            raise Exception(\"ERROR: No collections have been added!\")\n",
    "        # else at least one collection has been \n",
    "        lenOfFieldData = 0\n",
    "        if self.shp is not None:\n",
    "            lenOfFieldData = self.shpPolygons.getLen()\n",
    "        else :\n",
    "            lenOfFieldData = self.csvDF.getLen()\n",
    "        currentMin = 0\n",
    "        currentMax = self.samplingSize\n",
    "        print (\"Self.sampling size \" , self.samplingSize)\n",
    "        while currentMin<lenOfFieldData :\n",
    "            strCurrentMin = str(currentMin  ).rjust(10,'0')\n",
    "            strCurrentMax = str(currentMax-1).rjust(10,'0')\n",
    "            startOffeaturesFilenamesWithSampling = startOffeaturesFilename+\"_\"+strCurrentMin+\"_\"+strCurrentMax\n",
    "            polygons = None\n",
    "            if self.shp is not None:\n",
    "                polygons = self.shpPolygons.createPolygons(currentMin,currentMax)\n",
    "            else:\n",
    "                polygons = self.csvDF.createBufferedPoints(currentMin,currentMax)\n",
    "           \n",
    "            \n",
    "            if ((self.shp is not None or self.csvDF is not None) and polygons is not None):\n",
    "                print (\"exporting collections\")\n",
    "                self.exportCollections(startOffeaturesFilenamesWithSampling,gdrivefolder)\n",
    "            else :\n",
    "               print( \"WARNING: Skipping exportation as polygons from \", currentMin, \" to \", currentMax, \n",
    "                     \" haven't been created\")\n",
    "        \n",
    "            currentMin = currentMax\n",
    "            currentMax = currentMax + self.samplingSize\n",
    "        print(\"    *** End of exportation = Check progress on the Tasks tab at GEE ***\")\n",
    "            "
   ]
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