Source code for fmask.config

"""
Configuration classes that define the inputs and parameters
for the fmask function.
"""
# This file is part of 'python-fmask' - a cloud masking module
# Copyright (C) 2015  Neil Flood
#
# 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 3
# of the License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
from __future__ import print_function, division

import abc
import numpy
import scipy.constants

from osgeo import gdal
gdal.UseExceptions()
from rios import applier
from . import fmaskerrors

FMASK_LANDSAT47 = 0
"Landsat 4 to 7"
FMASK_LANDSAT8 = 1
"Landsat 8"
FMASK_SENTINEL2 = 2
"Sentinel 2"

"""
Some constants for the various reflective bands used in fmask.
"""
#: ~475nm
BAND_BLUE = 0
#: ~560nm
BAND_GREEN = 1
#: ~660nm
BAND_RED = 2
#: ~780nm
BAND_NIR = 3
#: ~1360nm
BAND_CIRRUS = 4 # Sentinel2 + Landsat8 only
#: ~1610nm
BAND_SWIR1 = 5
#: ~2200nm
BAND_SWIR2 = 6

# These bands are used only for the Sentinel-2 Cloud Displacement Index code. They
# are NIR bands, with slightly different look angles, and used as per Frantz et al 2017.
#: ~865nm
BAND_S2CDI_NIR8A = 7
#: ~783nm
BAND_S2CDI_NIR7 = 8

BAND_WATERVAPOUR = 9

[docs]class FmaskConfig(object): """ Class that contains the configuration parameters of the fmask run. """ # some parameters for fmask operation keepIntermediates = False cloudBufferSize = 5 shadowBufferSize = 10 verbose = False strictFmask = False tempDir = '.' TOARefScaling = 10000.0 # Minimum number of pixels in a single cloud (before buffering). A non-zero value # would allow filtering of very small clouds. minCloudSize_pixels = 0 # constants from the paper that could probably be tweaked # equation numbers are from the original paper. Eqn1Swir2Thresh = 0.03 Eqn1ThermThresh = 27 Eqn2WhitenessThresh = 0.7 cirrusBandTestThresh = 0.01 Eqn7Swir2Thresh = 0.03 Eqn20ThermThresh = 3.8 Eqn20NirSnowThresh = 0.11 Eqn20GreenSnowThresh = 0.1 cirrusProbRatio = 0.04 Eqn19NIRFillThresh = 0.02 # Constant term at the end of Equation 17. Zhu's MATLAB code now has this as a configurable # value, which they recommend as 22.5% (i.e. 0.225) Eqn17CloudProbThresh = 0.2 # GDAL driver for final output file gdalDriverName = applier.DEFAULTDRIVERNAME # Do we do the Sentinel-2 Cloud Displacement Test ? sen2displacementTest = False sen2cdiWindow = 7 def __init__(self, sensor): """ Pass in the sensor (one of: FMASK_LANDSAT47, FMASK_LANDSAT8 or FMASK_SENTINEL2) and default of parameters will be set. These can be overridden using the functions on this object. """ self.sensor = sensor # Some standard file configurations for different sensors. # Assumed that panchromatic + thermal bands stored in separate files. # zero based indexing if sensor == FMASK_LANDSAT47: self.bands = {BAND_BLUE:0, BAND_GREEN:1, BAND_RED:2, BAND_NIR:3, BAND_SWIR1:4, BAND_SWIR2:5} elif sensor == FMASK_LANDSAT8: self.bands = {BAND_BLUE:1, BAND_GREEN:2, BAND_RED:3, BAND_NIR:4, BAND_SWIR1:5, BAND_SWIR2:6, BAND_CIRRUS:7} elif sensor == FMASK_SENTINEL2: # Assumes the input stack has ALL bands, in their numeric order (with 8A after 8) self.bands = {BAND_BLUE:1, BAND_GREEN:2, BAND_RED:3, BAND_NIR:7, BAND_SWIR1:11, BAND_SWIR2:12, BAND_WATERVAPOUR:9, BAND_CIRRUS:10, BAND_S2CDI_NIR7:6, BAND_S2CDI_NIR8A:8} else: msg = 'unrecognised sensor' raise fmaskerrors.FmaskParameterError(msg) # we can't do anything with the thermal yet since # we need a .mtl file or equivalent to get the gains etc self.thermalInfo = None # same with angles self.anglesInfo = None # obtain the usual extension for the GDAL driver used by RIOS # so we can create temporary files with this extension. driver = gdal.GetDriverByName(applier.DEFAULTDRIVERNAME) if driver is None: msg = 'Cannot find GDAL driver %s used by RIOS' msg = msg % applier.DEFAULTDRIVERNAME raise fmaskerrors.FmaskParameterError(msg) ext = driver.GetMetadataItem('DMD_EXTENSION') if ext is None: self.defaultExtension = '.tmp' else: self.defaultExtension = '.' + ext
[docs] def setReflectiveBand(self, band, index): """ Tell fmask which band is in which index in the reflectance data stack file. band should be one of the BAND_* constants. index is zero based (ie 0 is first band in the file). These are set to default values for each sensor which are normally correct, but this function can be used to update. """ self.bands[band] = index
[docs] def setThermalInfo(self, info): """ Set an instance of ThermalFileInfo. By default this is None and fmask assumes there is no thermal data available. The :func:`fmask.config.readThermalInfoFromLandsatMTL` function can be used to obtain this from a Landsat .mtl file. """ self.thermalInfo = info
[docs] def setAnglesInfo(self, info): """ Set an instance of AnglesInfo. By default this is None and will need to be set before fmask will run. The :func:`fmask.config.readAnglesFromLandsatMTL` function can be used to obtain this from a Landsat .mtl file. """ self.anglesInfo = info
[docs] def setTOARefScaling(self, scaling): """ Set the scaling used in the Top of Atmosphere reflectance image. DN's are divided by this number to get reflectance. This defaults to 1000.0 """ self.TOARefScaling = scaling
[docs] def setKeepIntermediates(self, keepIntermediates): """ Set to True to keep the intermediate files created in processed. This is False by default. """ self.keepIntermediates = keepIntermediates
[docs] def setCloudBufferSize(self, bufferSize): """ Extra buffer of this many pixels on cloud layer. Defaults to 5. """ self.cloudBufferSize = bufferSize
[docs] def setShadowBufferSize(self, bufferSize): """ Extra buffer of this many pixels on cloud layer. Defaults to 10. """ self.shadowBufferSize = bufferSize
[docs] def setMinCloudSize(self, minCloudSize): """ Set the minimum cloud size retained. This minimum is applied before any buffering of clouds. Size is specified as an area, in pixels. """ self.minCloudSize_pixels = minCloudSize
[docs] def setVerbose(self, verbose): """ Print informative messages. Defaults to False. """ self.verbose = verbose
[docs] def setStrictFmask(self, strictFmask): """ Set whatever options are necessary to run strictly as per Fmask paper (Zhu & Woodcock). Setting this will override the settings of other parameters on this object. """ self.strictFmask = strictFmask
[docs] def setTempDir(self, tempDir): """ Temporary directory to use. Defaults to '.' (the current directory). """ self.tempDir = tempDir
[docs] def setDefaultExtension(self, extension): """ Sets the default extension used by temporary files created by fmask. Defaults to the extension of the driver that RIOS is configured to use. Note that this should include the '.' - ie '.img'. """ self.defaultExtension = extension
[docs] def setEqn1Swir2Thresh(self, thresh): """ Change the threshold used by Equation 1 for the SWIR2 band. This defaults to 0.03 """ self.Eqn1Swir2Thresh = thresh
[docs] def setEqn1ThermThresh(self, thresh): """ Change the threshold used by Equation one for BT. This defaults to 27. """ self.Eqn1ThermThresh = thresh
[docs] def setEqn2WhitenessThresh(self, thresh): """ Change the threshold used by Equation 2 to determine whiteness from visible bands. This defaults to 0.7. """ self.Eqn2WhitenessThresh = thresh
[docs] def setCirrusBandTestThresh(self, thresh): """ Change the threshold used by Zhu et al 2015, section 2.2.1 for the cirrus band test. Defaults to 0.01. """ self.cirrusBandTestThresh = thresh
[docs] def setEqn7Swir2Thresh(self, thresh): """ Change the threshold used by Equation 7 (water test) for the Swir2 band. This defaults to 0.03. """ self.Eqn7Swir2Thresh = thresh
[docs] def setEqn17CloudProbThresh(self, thresh): """ Change the threshold used by Equation 17. The threshold given here is the constant term added to the end of the equation for the land probability threshold. Original paper had this as 0.2, although Zhu et al's MATLAB code now defaults it to 0.225 (i.e. 22.5%) """ self.Eqn17CloudProbThresh = thresh
[docs] def setEqn20ThermThresh(self, thresh): """ Change the threshold used by Equation 20 (snow) for BT. This defaults to 3.8. """ self.Eqn20ThermThresh = thresh
[docs] def setEqn20NirSnowThresh(self, thresh): """ Change the threshold used by Equation 20 (snow) for NIR reflectance. This defaults to 0.11 """ self.Eqn20NirSnowThresh = thresh
[docs] def setEqn20GreenSnowThresh(self, thresh): """ Change the threshold used by Equation 20 (snow) for green reflectance. This defaults to 0.1 """ self.Eqn20GreenSnowThresh = thresh
[docs] def setCirrusProbRatio(self, ratio): """ Change the ratio used by Zhu et al 2015 Equation 1 to determine the cirrus cloud probability. Defaults to 0.04. """ self.cirrusProbRatio = ratio
[docs] def setEqn19NIRFillThresh(self, thresh): """ Change the threshold used by Equation 19 to determine potential cloud shadow from the difference between NIR and flood filled NIR. Defaults to 0.02. """ self.Eqn19NIRFillThresh = thresh
[docs] def setSen2displacementTest(self, useDisplacementTest): """ Set whether or not to use the Frantz (2018) parallax displacement test to remove false clouds. Pass True if the test is desired, False otherwise. """ self.sen2displacementTest = useDisplacementTest
[docs] def setGdalDriverName(self, driverName): """ Change the GDAL driver used for writing the final output file. Default value is taken from the default for the RIOS package, as per $RIOS_DFLT_DRIVER. """ self.gdalDriverName = driverName
[docs]class FmaskFilenames(object): """ Class that contains the filenames used in the fmask run. """ toaRef = None thermal = None saturationMask = None outputMask = None def __init__(self, toaRefFile=None, thermalFile=None, outputMask=None, saturationMask=None): self.toaRef = toaRefFile self.thermal = thermalFile self.saturationMask = saturationMask self.outputMask = outputMask
[docs] def setThermalFile(self, thermalFile): """ Set the path of the input thermal file. To make use of this, the :func:`fmask.config.FmaskConfig.setThermalInfo` function must also be called so that fmask knows how to use the file. This file should be in any GDAL readable format. """ self.thermal = thermalFile
[docs] def setTOAReflectanceFile(self, toaRefFile): """ Set the path of the input top of atmosphere (TOA) file. It pays to check that the default set of bands match what fmask expects in the :class:`fmask.config.FmaskConfig` class and update if necessary. This should have numbers which are reflectance * 1000 Use the :func:`fmask.landsatTOA.makeTOAReflectance` function to create this file from raw Landsat radiance (or the fmask_usgsLandsatTOA.py command line program supplied with fmask). It is assumed that any values that are nulls in the original radiance image are set to the ignore values in the toaRefFile. This file should be in any GDAL readable format. """ self.toaRef = toaRefFile
[docs] def setSaturationMask(self, mask): """ Set the mask to use for ignoring saturated pixels. By default no mask is used and all pixels are assumed to be unsaturated. This will cause problems for the whiteness test if some pixels are in fact saturated, but not masked out. Use the :func:`fmask.saturation.makeSaturationMask` function to create this from input radiance data. This mask should be 1 for pixels that are saturated, 0 otherwise. Note that this is not in the original paper so cannot be considered 'strict', but if provided is used no matter the strict setting in :class:`fmask.config.FmaskConfig`. This file should be in any GDAL readable format. """ self.saturationMask = mask
[docs] def setOutputCloudMaskFile(self, cloudMask): """ Set the output cloud mask path. Note that this file will be written in the format that RIOS is currently configured to use. See the `RIOS documentation <http://rioshome.org/rios_imagewriter.html#rios.imagewriter.setDefaultDriver>`_ for more details. Note that the default is HFA (.img) and can be overridden using environment variables. """ self.outputMask = cloudMask
[docs]class ThermalFileInfo(object): """ Contains parameters for interpreting thermal file. See :func:`fmask.config.readThermalInfoFromLandsatMTL`. """ thermalBand1040um = None thermalGain1040um = None thermalOffset1040um = None thermalK1_1040um = None thermalK2_1040um = None def __init__(self, thermalBand1040um, thermalGain1040um, thermalOffset1040um, thermalK1_1040um, thermalK2_1040um): self.thermalBand1040um = thermalBand1040um self.thermalGain1040um = thermalGain1040um self.thermalOffset1040um = thermalOffset1040um self.thermalK1_1040um = thermalK1_1040um self.thermalK2_1040um = thermalK2_1040um
[docs] def scaleThermalDNtoC(self, scaledBT): """ Use the given params to unscale the thermal, and then convert it from K to C. Return a single 2-d array of the temperature in deg C. """ KELVIN_ZERO_DEGC = scipy.constants.zero_Celsius rad = (scaledBT[self.thermalBand1040um].astype(float) * self.thermalGain1040um + self.thermalOffset1040um) # see http://www.yale.edu/ceo/Documentation/Landsat_DN_to_Kelvin.pdf # and https://landsat.usgs.gov/Landsat8_Using_Product.php rad[rad <= 0] = 0.00001 # to stop errors below temp = self.thermalK2_1040um / numpy.log(self.thermalK1_1040um / rad + 1.0) bt = temp - KELVIN_ZERO_DEGC return bt
# Keys within a .mtl file for each band LANDSAT_RADIANCE_MULT = 'RADIANCE_MULT_BAND_%s' LANDSAT_RADIANCE_ADD = 'RADIANCE_ADD_BAND_%s' LANDSAT_K1_CONST = 'K1_CONSTANT_BAND_%s' LANDSAT_K2_CONST = 'K2_CONSTANT_BAND_%s' # Oldest format of MTL file has only min/max values LANDSAT_LMAX_KEY = 'LMAX_BAND%s' LANDSAT_LMIN_KEY = 'LMIN_BAND%s' LANDSAT_QCALMAX_KEY = 'QCALMAX_BAND%s' LANDSAT_QCALMIN_KEY = 'QCALMIN_BAND%s' # band numbers in mtl file for gain and offset for thermal LANDSAT_TH_BAND_NUM_DICT = {'LANDSAT_4' : '6', 'LANDSAT_5' : '6', 'LANDSAT_7' : '6_VCID_1', 'LANDSAT_8' : '10'} # for some reason L4, 5, and 7 don't # have these numbers in the mtl file, but L8 does # from http://www.yale.edu/ceo/Documentation/Landsat_DN_to_Kelvin.pdf LANDSAT_K1_DICT = {'TM' : 607.76, 'ETM' : 666.09, 'ETM+':666.09} LANDSAT_K2_DICT = {'TM' : 1260.56, 'ETM' : 1282.71, 'ETM+':1282.71}
[docs]def readThermalInfoFromLandsatMTL(mtlfile, thermalBand1040um=0): """ Returns an instance of ThermalFileInfo given a path to the mtl file and the index of the thermal band. """ mtlData = readMTLFile(mtlfile) gain = None offset = None k1 = None k2 = None if 'SPACECRAFT_ID' in mtlData: # we can now grab the gain and offset spaceCraft = mtlData['SPACECRAFT_ID'] band = LANDSAT_TH_BAND_NUM_DICT[spaceCraft] s = LANDSAT_RADIANCE_MULT % band oldestMtlFormat = (s not in mtlData) if not oldestMtlFormat: gain = float(mtlData[s]) s = LANDSAT_RADIANCE_ADD % band offset = float(mtlData[s]) else: # Oldest format MTL file if spaceCraft == "LANDSAT_7": band = "61" lMax = float(mtlData[LANDSAT_LMAX_KEY % band]) lMin = float(mtlData[LANDSAT_LMIN_KEY % band]) qcalMax = float(mtlData[LANDSAT_QCALMAX_KEY % band]) qcalMin = float(mtlData[LANDSAT_QCALMIN_KEY % band]) gain = (lMax - lMin) / (qcalMax - qcalMin) offset = lMin - qcalMin * gain if 'SENSOR_ID' in mtlData: # look for k1 and k2 sensor = mtlData['SENSOR_ID'] s = LANDSAT_K1_CONST % band if s in mtlData: k1 = float(mtlData[s]) else: # drop back to our own values if not in file k1 = LANDSAT_K1_DICT[sensor] s = LANDSAT_K2_CONST % band if s in mtlData: k2 = float(mtlData[s]) else: # drop back to our own values if not in file k2 = LANDSAT_K2_DICT[sensor] if gain is not None and offset is not None and k1 is not None and k2 is not None: thermalInfo = ThermalFileInfo(thermalBand1040um, gain, offset, k1, k2) else: msg = 'Cannot find SPACECRAFT_ID/SENSOR_ID in MTL file' raise fmaskerrors.FmaskFileError(msg) return thermalInfo
[docs]class AnglesInfo(object): """ Abstract base class that Contains view and solar angle information for file (in radians). """ __metaclass__ = abc.ABCMeta
[docs] def prepareForQuerying(self): """ Called when fmask is about to query this object for angles. Derived class should do any reading of files into memory required here. """
[docs] def releaseMemory(self): """ Called when fmask has finished querying this object. Can release any allocated memory. """
[docs] @abc.abstractmethod def getSolarZenithAngle(self, indices): """ Return the average solar zenith angle for the given indices """
[docs] @abc.abstractmethod def getSolarAzimuthAngle(self, indices): """ Return the average solar azimuth angle for the given indices """
[docs] @abc.abstractmethod def getViewZenithAngle(self, indices): """ Return the average view zenith angle for the given indices """
[docs] @abc.abstractmethod def getViewAzimuthAngle(self, indices): """ Return the average view azimuth angle for the given indices """
[docs] @abc.abstractmethod def setScaleToRadians(self, scale): """ Set scaling factor to get radians from angles image values. """
[docs]class AnglesFileInfo(AnglesInfo): """ An implementation of AnglesInfo that reads the information from GDAL supported files. """ def __init__(self, solarZenithFilename, solarZenithBand, solarAzimuthFilename, solarAzimuthBand, viewZenithFilename, viewZenithBand, viewAzimuthFilename, viewAzimuthBand): """ Initialises the object with the names and band numbers of the angles. band numbers should be 0 based - ie first band is 0. """ self.solarZenithFilename = solarZenithFilename self.solarZenithBand = solarZenithBand self.solarAzimuthFilename = solarAzimuthFilename self.solarAzimuthBand = solarAzimuthBand self.viewZenithFilename = viewZenithFilename self.viewZenithBand = viewZenithBand self.viewAzimuthFilename = viewAzimuthFilename self.viewAzimuthBand = viewAzimuthBand # these will contain the actual image data once read # by prepareForQuerying() self.solarZenithData = None self.solarAzimuthData = None self.viewZenithData = None self.viewAzimuthData = None # This default value matches the file produced by fmask_usgsLandsatMakeAnglesImage.py self.scaleToRadians = 0.01
[docs] @staticmethod def readData(filename, bandNum): ds = gdal.Open(filename) band = ds.GetRasterBand(bandNum + 1) data = band.ReadAsArray() del ds return data
[docs] def prepareForQuerying(self): """ Called when fmask is about to query this object for angles. """ self.solarZenithData = self.readData(self.solarZenithFilename, self.solarZenithBand) self.solarAzimuthData = self.readData(self.solarAzimuthFilename, self.solarAzimuthBand) self.viewZenithData = self.readData(self.viewZenithFilename, self.viewZenithBand) self.viewAzimuthData = self.readData(self.viewAzimuthFilename, self.viewAzimuthBand)
[docs] def releaseMemory(self): """ Called when fmask has finished querying this object. """ del self.solarZenithData del self.solarAzimuthData del self.viewZenithData del self.viewAzimuthData
[docs] def getSolarZenithAngle(self, indices): """ Return the average solar zenith angle for the given indices """ return self.solarZenithData[indices].mean() * self.scaleToRadians
[docs] def getSolarAzimuthAngle(self, indices): """ Return the average solar azimuth angle for the given indices """ return self.solarAzimuthData[indices].mean() * self.scaleToRadians
[docs] def getViewZenithAngle(self, indices): """ Return the average view zenith angle for the given indices """ return self.viewZenithData[indices].mean() * self.scaleToRadians
[docs] def getViewAzimuthAngle(self, indices): """ Return the average view azimuth angle for the given indices """ return self.viewAzimuthData[indices].mean() * self.scaleToRadians
[docs] def setScaleToRadians(self, scale): """ Set scaling factor to get radians from angles image values. """ self.scaleToRadians = scale
[docs]class AngleConstantInfo(AnglesInfo): """ An implementation of AnglesInfo that uses constant angles accross the scene. """ def __init__(self, solarZenithAngle, solarAzimuthAngle, viewZenithAngle, viewAzimuthAngle): self.solarZenithAngle = solarZenithAngle self.solarAzimuthAngle = solarAzimuthAngle self.viewZenithAngle = viewZenithAngle self.viewAzimuthAngle = viewAzimuthAngle
[docs] def getSolarZenithAngle(self, indices): """ Return the solar zenith angle """ return self.solarZenithAngle
[docs] def getSolarAzimuthAngle(self, indices): """ Return the solar azimuth angle """ return self.solarAzimuthAngle
[docs] def getViewZenithAngle(self, indices): """ Return the view zenith angle """ return self.viewZenithAngle
[docs] def getViewAzimuthAngle(self, indices): """ Return the view azimuth angle """ return self.viewAzimuthAngle
[docs]def readMTLFile(mtl): """ Very simple .mtl file reader that just creates a dictionary of key and values and returns it """ dict = {} for line in open(mtl): arr = line.split('=') if len(arr) == 2: (key, value) = arr dict[key.strip()] = value.replace('"', '').strip() # For the older format of the MTL file, a few fields had different names. So, we fake the # new names, so that the rest of the code can just use those. if 'ACQUISITION_DATE' in dict: dict['DATE_ACQUIRED'] = dict['ACQUISITION_DATE'] if 'SCENE_CENTER_SCAN_TIME' in dict: dict['SCENE_CENTER_TIME'] = dict['SCENE_CENTER_SCAN_TIME'] # Oldest format has spacecraft ID string formatted differently, so reformat it. spaceCraft = dict['SPACECRAFT_ID'] if spaceCraft.startswith('Landsat') and '_' not in spaceCraft: satNum = spaceCraft[-1] dict['SPACECRAFT_ID'] = "LANDSAT_" + satNum return dict
[docs]def readAnglesFromLandsatMTL(mtlfile): """ Given the path to a Landsat USGS .MTL file, read the angles out and return an instance of AngleConstantInfo. This is no longer supported, and this routine now raises an exception. """ msg = ("The simplified option of assuming constant angles across the whole image is "+ "no longer supported. You must use per-pixel angles. ") raise fmaskerrors.FmaskNotSupportedError(msg)