FieldData_test.ipynb

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   "attachments": {},
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   "source": [
    "This is a test file for the FieldData class\n",
    "It requires input parameters from the command line as follow\n"
   ]
  },
  {
   "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",
    "else:\n",
    "   print('GEE already imported')\n",
    "   # google earth engine already imported and authenticated\n",
    "\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",
    "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",
    "modulename = 'ipynb_MapVisualisation'\n",
    "if modulename not in sys.modules:\n",
    "   %run MapVisualisation.ipynb\n",
    "   # adding an identifier to sys.modules to avoiding loading the same file multiple times\n",
    "   sys.modules['ipynb_MapVisualisation'] = None \n",
    "#else\n",
    "   # Utils modules has already been loaded somewhere else\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# parsing command line inputs - Could not find a way to add the arguments in ipython\n",
    "\"\"\" parser = argparse.ArgumentParser()\n",
    "parser.add_argument(\"-in\",\n",
    "     required=True,\n",
    "     help=\"The input csv file with its directory containing field plot data\",\n",
    "     metavar='<string>')\n",
    "\n",
    "\n",
    "\n",
    "params       = vars(parser.parse_args())\n",
    "csvFile      = params[\"in\"   ]\n",
    "\n",
    "\n",
    "print (\"imported csv file     = \", csvFile ) \"\"\"\n",
    "\n",
    "# import a Sentinel 2 collection and crop Spain\n",
    "countries = ee.FeatureCollection('USDOS/LSIB_SIMPLE/2017')\n",
    "AOI = countries.filter(ee.Filter.eq('country_na', 'Spain'))\n",
    "\n",
    "geometry = ee.Geometry.Polygon(\n",
    "    [[[-5.586640856054208, 40.07176423657564],\n",
    "      [-5.391633531835458, 40.07176423657564],\n",
    "      [-5.391633531835458, 40.17257546939766],\n",
    "      [-5.6106734488276455, 40.170476760191924]]])\n",
    "\n",
    "\n",
    "START_DATE = '2021-01-01'\n",
    "END_DATE = '2021-01-28'\n",
    "masks = {}#'gsw': 30, 'lmask': 30, 'forestMask': {30,2021}}\n",
    "\n",
    "\n",
    "s2_col = ee.ImageCollection('COPERNICUS/S2_SR_HARMONIZED') \\\n",
    "            .filterBounds(geometry) \\\n",
    "            .filterDate('2021-01-01', '2021-12-31') \\\n",
    "            .median()\n",
    "\n",
    "bandNames = s2_col.bandNames()\n",
    "\n",
    "bandnames = s2_col.bandNames()\n",
    "bandnames = bandnames.getInfo()\n",
    "        \n",
    "print(type(bandnames))\n",
    "print('Band names s2_col: ', bandnames)\n",
    "\n",
    "\n",
    "\n",
    "sentinel2Info = {\n",
    "    \"identifier\": 'sentinel-2',                                              \n",
    "    \"collection\": \"COPERNICUS/S2_SR_HARMONIZED\",\n",
    "    #\"launchDate\" : \"2015-05-23\",\n",
    "    #\"retirmentDate\":todayDate, #not retired yet\n",
    "    \"startDate\"   : START_DATE,\n",
    "    \"endDate\"     : END_DATE,\n",
    "    #\"added\"     : False,\n",
    "    \"clouds\"    : 50,\n",
    "    \"selectedBand\": ['B8', 'B4'],\n",
    "    \"selectedIndices\": ['ndvi']\n",
    "} \n",
    "\n",
    "\n",
    "s2 = Sentinel2(AOI,sentinel2Info, masks)\n",
    "s2.byMonth(2021)\n",
    "\n",
    "\n",
    "\n",
    "# Create ee.Geometry.Point objects for the corners\n",
    "lower_left_point = ee.Geometry.Point(\n",
    "                        [292002.67, 4448723.55],\"EPSG:3042\"\n",
    "                        )\n",
    "upper_right_point =ee.Geometry.Point(\n",
    "                        [292402.67, 4449073.55],\"EPSG:3042\"\n",
    "                        )\n",
    "\n",
    "# Construct a rectangle from the list of ee.Geometry.Point objects\n",
    "polygon =  ee.Geometry.Rectangle([lower_left_point, upper_right_point])\n",
    "\n",
    "\n",
    "polygon = ee.FeatureCollection([ee.Feature(ee.Geometry.Polygon(polygon.coordinates()))])\n",
    "\n",
    "\n",
    "# Coordinates of the rectangle's lower-left and upper-right corners\n",
    "x_min, y_min = 292002.67, 4448723.55\n",
    "x_max, y_max = 292402.67, 4449073.55\n",
    "\n",
    "MinPoint = ee.Geometry.Point([292002.67, 4448723.55], \"EPSG:3042\")\n",
    "MaxPoint = ee.Geometry.Point([292402.67, 4449073.55], \"EPSG:3042\")\n",
    "\n",
    "# Transform the point to latitudes and longitudes (WGS84)\n",
    "MinPoint_latlon = MinPoint.transform(\"EPSG:3857\")\n",
    "MaxPoint_latlon = MaxPoint.transform(\"EPSG:3857\")\n",
    "\n",
    "# Get the coordinates as a list\n",
    "coordinatesMinPoint = MinPoint_latlon.getInfo()[\"coordinates\"]\n",
    "coordinatesMaxPoint = MaxPoint_latlon.getInfo()[\"coordinates\"]\n",
    "\n",
    "# Extract latitude and longitude\n",
    "latitudeMinPoint, longitudeMinPoint = coordinatesMinPoint[1], coordinatesMinPoint[0]\n",
    "latitudeMaxPoint, longitudeMaxPoint = coordinatesMaxPoint[1], coordinatesMaxPoint[0]\n",
    "\n",
    "csvFile = \"./samplePlots.csv\"\n",
    "\n",
    "\n",
    "# Create a dictionary that holds the relevant plot information\n",
    "fieldData = {\n",
    "              \"csvfilename\"   : csvFile,\n",
    "              \"proj\"          : \"EPSG:3042\",\n",
    "              \"radius\"        : 200,\n",
    "              \"xcol\"          : \"CX\",    \n",
    "              \"ycol\"          : \"CY\",\n",
    "              \"outPlotFileWithIDs\"  :\"fieldDataWithIdentifiers/FieldDataTest.csv\"\n",
    "       }\n",
    "\n",
    "csvDF = FieldData(fieldData)\n",
    "# csvDF.filterYearsOfInterest(2017,2018,\"year\")\n",
    "\n",
    "# create a list of polygons for the field data 1-100\n",
    "bufferredPoints = csvDF.createBufferedPoints(1, 100)\n",
    "#print(bufferredPoints)\n",
    "\n",
    "s2bands = s2.getCollectionToBands()\n",
    "\n",
    "csvDF.exportFeaturesMeanStdCSV(s2bands,\"ouutCsvFeatureVectors2021_200_B4\",\"GEE\")\n",
    "\n",
    "\n",
    "\n",
    "# THIS IS THE OTHER METHOD THAT EXPORTS FOR EACH PIXEL - DOES NOT HANDLES GAPS SO NEEDS EXTRA POST-PROCESSSING\n",
    "# csvDF.exportfeatureVectorsToDrive(col,\"TestIndClassSentinel2c.csv\",\"earth_engine_demos\",10)\n",
    "# csvDF.mergeFeatureVectorsToPlotData(\"/home/milto/Documents/FLFScripts/sampleData/mergedcsv.csv\")\n",
    "# csvDF.exportPlotDataWithAddedIdentifiers(\"/home/milto/Documents/FLFScripts/sampleData/fieldDatawithIds.csv\")\n",
    "\n",
    "print(\"NOTE: in the example, there are no plots within the study area!\")\n",
    "print(\"   ***   EXIT   ***\")\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#%run MapVisualisation.ipynb\n",
    "my_map = folium.Map(location=[40,-3], zoom_start=5, height=400)\n",
    "# Add custom basemaps\n",
    "basemaps['Google Maps'].add_to(my_map)\n",
    "basemaps['Google Satellite Hybrid'].add_to(my_map)\n",
    "# Add Land Mask to the map\n",
    "my_map.add_ee_layer(s2_col, {'bands': ['B4', 'B3', 'B2'], 'min': 0, 'max': 2500, 'gamma': 1.1}, 'median'      )\n",
    "my_map.add_ee_layer(bufferredPoints, {},'bufferredPoints')\n",
    "\n",
    "my_map.add_ee_layer(geometry,{},\"geometry\")\n",
    "\n",
    "my_map.add_ee_layer(lower_left_point,{},\"lower_left_point\")\n",
    "\n",
    "# Add a layer control panel to the map.\n",
    "my_map.add_child(folium.LayerControl())\n",
    "plugins.Fullscreen().add_to(my_map)\n",
    "\n",
    "# Add a layer control panel to the map.\n",
    "my_map.add_child(folium.LayerControl())\n",
    "\n",
    "# Add fullscreen button\n",
    "plugins.Fullscreen().add_to(my_map)\n",
    "\n",
    "# Display the map.\n",
    "display(my_map)"
   ]
  }
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