Ejemplo n.º 1
0
def boreali_processing(obj,  final_path):
    wavelen = [412, 443, 469, 488, 531, 547, 555, 645, 667, 678]
    cpa_limits = [0.01, 2,
                  0.01, 1,
                  0.01, 1, 10]
    b = Boreali('michigan', wavelen)

    n = Nansat(obj)
    dom = Domain('+proj=latlong +datum=WGS84 +ellps=WGS84 +no_defs', '-lle -86.3 44.6 -85.2 45.3 -ts 300 200')
    n.reproject(dom)
    theta = numpy.zeros_like(n[2])
    custom_n = Nansat(domain=n)
    band_rrs_numbers = list(map(lambda x: n._get_band_number('Rrs_' + str(x)),
                                wavelen))

    for index in range(0, len(wavelen)):
        # Преобразуем в Rrsw
        rrsw = n[band_rrs_numbers[index]] / (0.52 + 1.7 * n[band_rrs_numbers[index]])
        custom_n.add_band(rrsw, parameters={'name': 'Rrsw_' + str(wavelen[index]),
                                            'units': 'sr-1',
                                            'wavelength': wavelen[index]})

    custom_n = create_mask(custom_n)
    cpa = b.process(custom_n, cpa_limits, mask=custom_n['mask'], theta=theta, threads=4)

    custom_n.add_band(array=cpa[0], parameters={'name': 'chl',
                                                'long_name': 'Chlorophyl-a',
                                                'units': 'mg m-3'})
    custom_n.add_band(array=cpa[1], parameters={'name': 'tsm',
                                                'long_name': 'Total suspended matter',
                                                'units': 'g m-3'})
    custom_n.add_band(array=cpa[2], parameters={'name': 'doc',
                                                'long_name': 'Dissolved organic carbon',
                                                'units': 'gC m-3'})
    custom_n.add_band(array=cpa[3], parameters={'name': 'mse',
                                                'long_name': 'Root Mean Square Error',
                                                'units': 'sr-1'})
    custom_n.add_band(array=cpa[4], parameters={'name': 'mask',
                                                'long_name': 'L2 Boreali mask',
                                                'units': '1'})

    custom_n.export(final_path + obj.split('/')[-1] + 'cpa_deep.nc')

    fig_params = {'legend': True,
                  'LEGEND_HEIGHT': 0.5,
                  'NAME_LOCATION_Y': 0,
                  'mask_array': cpa[4],
                  'mask_lut': {1: [255, 255, 255], 2: [128, 128, 128], 4: [200, 200, 255]}}
    custom_n.write_figure(final_path + obj.split('/')[-1] + 'chl_deep.png', 'chl', clim=[0, 1.], **fig_params)
    custom_n.write_figure(final_path + obj.split('/')[-1] + 'tsm_deep.png', 'tsm', clim=[0, 1.], **fig_params)
    custom_n.write_figure(final_path + obj.split('/')[-1] + 'doc_deep.png', 'doc', clim=[0, .2], **fig_params)
    custom_n.write_figure(final_path + obj.split('/')[-1] + 'mse_deep.png', 'mse', clim=[1e-5, 1e-2], logarithm=True, **fig_params)
    n.write_figure(final_path + obj.split('/')[-1] + 'rgb_deep.png',
                   [16, 14, 6],
                   clim=[[0, 0, 0], [0.006, 0.04, 0.024]],
                   mask_array=cpa[4],
                   mask_lut={2: [128, 128, 128]})
Ejemplo n.º 2
0
    def _get_masked_windspeed(self, landmask=True, icemask=True):
        try:
            sar_windspeed = self['windspeed']
        except:
            raise ValueError('SAR wind has not been calculated, ' \
                'execute calculate_wind(winddir) first.')

        sar_windspeed[sar_windspeed<0] = 0
        palette = jet

        if landmask:
            try: # Land mask
                sar_windspeed = np.ma.masked_where(
                                    self.watermask()[1]==2, sar_windspeed)
                palette.set_bad([.3, .3, .3], 1.0) # Land is masked (bad)
            except:
                print 'Land mask not available'
        
        if icemask:
            try: # Ice mask
                try: # first try local file 
                    ice = Nansat('metno_local_hires_seaice_' + 
                            self.SAR_image_time.strftime('%Y%m%d'), 
                            mapperName='metno_local_hires_seaice')
                except: # otherwise Thredds
                    ice = Nansat('metno_hires_seaice:' + 
                            self.SAR_image_time.strftime('%Y%m%d'))
                ice.reproject(self)
                iceBandNo = ice._get_band_number(
                    {'standard_name': 'sea_ice_area_fraction'})
                sar_windspeed[ice[iceBandNo]>0] = -1
                palette.set_under('w', 1.0) # Ice is 'under' (-1)
            except:
                print 'Ice mask not available'

        return sar_windspeed, palette
Ejemplo n.º 3
0
    def _get_masked_windspeed(self, landmask=True, icemask=True):
        try:
            sar_windspeed = self['windspeed']
        except:
            raise ValueError('SAR wind has not been calculated, ' \
                'execute calculate_wind(winddir) first.')

        sar_windspeed[sar_windspeed < 0] = 0
        palette = jet

        if landmask:
            try:  # Land mask
                sar_windspeed = np.ma.masked_where(self.watermask()[1] == 2,
                                                   sar_windspeed)
                palette.set_bad([.3, .3, .3], 1.0)  # Land is masked (bad)
            except:
                print 'Land mask not available'

        if icemask:
            try:  # Ice mask
                try:  # first try local file
                    ice = Nansat('metno_local_hires_seaice_' +
                                 self.SAR_image_time.strftime('%Y%m%d'),
                                 mapperName='metno_local_hires_seaice')
                except:  # otherwise Thredds
                    ice = Nansat('metno_hires_seaice:' +
                                 self.SAR_image_time.strftime('%Y%m%d'))
                ice.reproject(self)
                iceBandNo = ice._get_band_number(
                    {'standard_name': 'sea_ice_area_fraction'})
                sar_windspeed[ice[iceBandNo] > 0] = -1
                palette.set_under('w', 1.0)  # Ice is 'under' (-1)
            except:
                print 'Ice mask not available'

        return sar_windspeed, palette
Ejemplo n.º 4
0
class SARWind(Nansat, object):
    '''
    A class for calculating wind speed from SAR images using CMOD
    '''

    def __init__(self, sar_image, winddir=None, pixelsize=500):
        '''
            Parameters
            -----------
            sar_image : string or Nansat object
                SAR image filename (original, raw file)
            winddir : int, string, Nansat, None
                Auxiliary wind field information needed to calculate
                SAR wind (must be or have wind direction)
        '''
        if isinstance(sar_image, str) or isinstance(sar_image, unicode):
            super(SARWind, self).__init__(sar_image)
        elif isinstance(sar_image, Nansat):
            super(SARWind, self).__init__(domain=sar_image)
            self.vrt = sar_image.vrt

        # Check that this is a SAR image with VV pol NRCS
        try:
            self.sigma0_bandNo = self._get_band_number(
                            {'standard_name': 
            'surface_backwards_scattering_coefficient_of_radar_wave', 
                            'polarization': 'VV'})
        except:
            raise TypeError(self.fileName + 
                ' does not have SAR NRCS in VV polarization')

        self.SAR_image_time = self.get_time(
                self.sigma0_bandNo).replace(tzinfo=None)

        if pixelsize != 'fullres':
            print 'Resizing SAR image to ' + str(pixelsize) + ' m pixel size'
            self.resize(pixelsize=pixelsize)

        self.winddir = winddir
        if winddir is not None:
            self.calculate_wind()


    def calculate_wind(self, winddir=None, storeModelSpeed=True):
        # Calculate wind speed from SAR sigma0 in VV polarization

        if winddir:
            self.winddir = winddir
        if self.winddir is None or self.winddir == 'online':
            self.winddir = 'ncep_wind_online' # default source

        if isinstance(self.winddir, int):
            # Constant wind direction is input
            print 'Using constant wind (from) direction: ' + str(self.winddir) + \
                    ' degrees clockwise from North'
            winddirArray = np.ones(self.shape())*self.winddir
            winddir_time = None
            storeModelSpeed = False # Not relevant if direction given as number
        else:
            # Nansat readable file
            if isinstance(self.winddir, str):
                try:
                    self.winddir = Nansat(self.winddir)
                except:
                    try:
                        self.winddir = Nansat(self.winddir + 
                                            datetime.strftime(
                                            self.SAR_image_time, ':%Y%m%d%H%M'))
                    except:
                        pass

            if not isinstance(self.winddir, Nansat):
                raise ValueError('Wind direction not available')

            winddir_time = self.winddir.get_time()[0]

            # Bi-linear interpolation onto SAR image
            self.winddir.reproject(self, eResampleAlg=1)

            # Check time difference between SAR image and wind direction object
            timediff = self.SAR_image_time - winddir_time
            hoursDiff = np.abs(timediff.total_seconds()/3600.)
            print 'Time difference between SAR image and wind direction: ' \
                    + '%.2f' % hoursDiff + ' hours'
            print 'SAR image time: ' + str(self.SAR_image_time)
            print 'Wind dir time: ' + str(winddir_time)
            if hoursDiff > 3:
                print '#########################################'
                print 'WARNING: time difference exceeds 3 hours!'
                print '#########################################'

            wind_u_bandNo = self.winddir._get_band_number({
                                'standard_name': 'eastward_wind',
                            })
            wind_v_bandNo = self.winddir._get_band_number({
                                'standard_name': 'northward_wind',
                            })
            # Get wind direction
            u_array = self.winddir[wind_u_bandNo]
            v_array = self.winddir[wind_v_bandNo]
            winddirArray = np.degrees(
                    np.arctan2(-u_array, -v_array)) # 0 from North, 90 from East


        # Calculate SAR wind with CMOD
        # TODO: 
        # - add other CMOD versions than CMOD5
        print 'Calculating SAR wind with CMOD...'
        startTime = datetime.now()

        windspeed = cmod5n_inverse(self[self.sigma0_bandNo], 
                        np.mod(winddirArray - self['SAR_look_direction'], 360), 
                        self['incidence_angle'])
        print 'Calculation time: ' + str(datetime.now() - startTime)

        windspeed[np.where(np.isnan(windspeed))] = np.nan
        windspeed[np.where(np.isinf(windspeed))] = np.nan

        # Add wind speed and direction as bands
        # TODO: make it possible to update existing bands... See
        # https://github.com/nansencenter/nansat/issues/58
        self.add_band(array=windspeed, parameters={
                        'wkv': 'wind_speed',
                        'name': 'windspeed',
                        'time': self.get_time(self.sigma0_bandNo),
                        'winddir_time': winddir_time
                })
        self.add_band(array=winddirArray, parameters={
                            'wkv': 'wind_from_direction',
                            'name': 'winddirection',
                            'time': winddir_time
                })

        if storeModelSpeed:
            self.add_band(array=self.winddir['windspeed'], parameters={
                            'wkv': 'wind_speed',
                            'name': 'model_windspeed',
                            'time': winddir_time,
            })

        # TODO: Replace U and V bands with pixelfunctions
        u = -windspeed*np.sin((180.0 - winddirArray)*np.pi/180.0)
        v = windspeed*np.cos((180.0 - winddirArray)*np.pi/180.0)
        self.add_band(array=u, parameters={
                            'wkv': 'eastward_wind',
        })
        self.add_band(array=v, parameters={
                            'wkv': 'northward_wind',
        })


    def _get_masked_windspeed(self, landmask=True, icemask=True):
        try:
            sar_windspeed = self['windspeed']
        except:
            raise ValueError('SAR wind has not been calculated, ' \
                'execute calculate_wind(winddir) first.')

        sar_windspeed[sar_windspeed<0] = 0
        palette = jet

        if landmask:
            try: # Land mask
                sar_windspeed = np.ma.masked_where(
                                    self.watermask()[1]==2, sar_windspeed)
                palette.set_bad([.3, .3, .3], 1.0) # Land is masked (bad)
            except:
                print 'Land mask not available'
        
        if icemask:
            try: # Ice mask
                try: # first try local file 
                    ice = Nansat('metno_local_hires_seaice_' + 
                            self.SAR_image_time.strftime('%Y%m%d'), 
                            mapperName='metno_local_hires_seaice')
                except: # otherwise Thredds
                    ice = Nansat('metno_hires_seaice:' + 
                            self.SAR_image_time.strftime('%Y%m%d'))
                ice.reproject(self)
                iceBandNo = ice._get_band_number(
                    {'standard_name': 'sea_ice_area_fraction'})
                sar_windspeed[ice[iceBandNo]>0] = -1
                palette.set_under('w', 1.0) # Ice is 'under' (-1)
            except:
                print 'Ice mask not available'

        return sar_windspeed, palette

    def write_geotiff(self, filename, landmask=True, icemask=True):

        sar_windspeed, palette = self._get_masked_windspeed(landmask, icemask)

        nansat_geotiff = Nansat(array=sar_windspeed, domain=self,
                                parameters = {'name': 'masked_windspeed',
                                              'minmax': '0 20'})
                        
        nansat_geotiff.write_geotiffimage(filename)


    def plot(self, filename=None, numVectorsX = 16, show=True,
                landmask=True, icemask=True, flip=True, maskWindAbove=35):
        ''' Basic plotting function showing CMOD wind speed
        overlaid vectors in SAR image projection'''

        try:
            sar_windspeed, palette = self._get_masked_windspeed(landmask, icemask)
        except:
            raise ValueError('SAR wind has not been calculated, ' \
                'execute calculate_wind(winddir) before plotting.')
        sar_windspeed[sar_windspeed>maskWindAbove] = np.nan

        winddirReductionFactor = np.round(
                self.vrt.dataset.RasterXSize/numVectorsX)
        # model_winddir is direction from which wind is blowing
        winddir_relative_up = 360 - self['winddirection'] + \
                                    self.azimuth_up()
        indX = range(0, self.vrt.dataset.RasterXSize, winddirReductionFactor)
        indY = range(0, self.vrt.dataset.RasterYSize, winddirReductionFactor)
        X, Y = np.meshgrid(indX, indY)
        try: # scaling of wind vector length, if model wind is available
            model_windspeed = self['model_windspeed']
            model_windspeed = model_windspeed[Y, X]
        except:
            model_windspeed = 8*np.ones(X.shape)

        Ux = np.sin(np.radians(winddir_relative_up[Y, X]))*model_windspeed
        Vx = np.cos(np.radians(winddir_relative_up[Y, X]))*model_windspeed

        # Make sure North is up, and east is right
        if flip == True:
            lon, lat = self.get_corners()
            if lat[0] < lat[1]:
                sar_windspeed = np.flipud(sar_windspeed)
                Ux = -np.flipud(Ux)
                Vx = -np.flipud(Vx)

            if lon[0] > lon[2]:
                sar_windspeed = np.fliplr(sar_windspeed)
                Ux = np.fliplr(Ux)
                Vx = np.fliplr(Vx)

        # Plotting
        figSize = sar_windspeed.shape
        legendPixels = 60.0
        legendPadPixels = 5.0
        legendFraction = legendPixels/figSize[0]
        legendPadFraction = legendPadPixels/figSize[0]
        dpi=100.0

        fig = plt.figure()
        fig.set_size_inches((figSize[1]/dpi, (figSize[0]/dpi)*
                                (1+legendFraction+legendPadFraction)))
        ax = fig.add_axes([0,0,1,1+legendFraction])
        ax.set_axis_off()
        plt.imshow(sar_windspeed, cmap=palette, interpolation='nearest')
        plt.clim([0, 20])
        cbar = plt.colorbar(orientation='horizontal', shrink=.80,
                     aspect=40,
                     fraction=legendFraction, pad=legendPadFraction)
        cbar.ax.set_ylabel('[m/s]', rotation=0)
        cbar.ax.yaxis.set_label_position('right')
        ax.quiver(X, Y, Ux, Vx, angles='xy', width=0.004,
                    scale=200, scale_units='width',
                    color=[.0, .0, .0], headaxislength=4)
        if filename is not None:
            fig.savefig(filename, pad_inches=0, dpi=dpi)
        if show:
            plt.show()
        return fig
Ejemplo n.º 5
0
def boreali_osw_processing(obj, final_path):
    """
    Мой код в данной функции основан на tutorial.py который я нашел в репозитории boreali.
    :param obj: путь до изображения
    :param final_path: Путь для сохранения файлов
    :return:
    """
    wavelen = [412, 443, 469, 488, 531, 547, 555, 645, 667, 678]

    cpa_limits = [0.01, 2,
                  0.01, 1,
                  0.01, 1, 10]

    h = get_deph()  # Глубина исследуемого района по батиметрии

    b = Boreali('michigan', wavelen)
    n = Nansat(obj)
    dom = Domain('+proj=latlong +datum=WGS84 +ellps=WGS84 +no_defs', '-lle -86.3 44.6 -85.2 45.3 -ts 300 200')
    n.reproject(dom)
    theta = numpy.zeros_like(n[2])

    custom_n = Nansat(domain=n)
    band_rrs_numbers = list(map(lambda x: n._get_band_number('Rrs_' + str(x)),
                                wavelen))   # Получаем список номеров бандов в которых лежат значения Rrs

    # для корректной работы складываем в custom_n значения и Rrs и Rrsw
    for index in range(0, len(wavelen)):
        rrsw = n[band_rrs_numbers[index]] / (0.52 + 1.7 * n[band_rrs_numbers[index]])   # Пересчитываем Rrs в Rrsw
        custom_n.add_band(rrsw, parameters={'name': 'Rrsw_' + str(wavelen[index]),  # Складываем в новый объект Rrsw
                                            'units': 'sr-1',
                                            'wavelength': wavelen[index]})
        # Складываем в новый объект значения Rrs
        custom_n.add_band(n[band_rrs_numbers[index]], parameters={'name': 'Rrs_' + str(wavelen[index]),
                                                                  'units': 'sr-1',
                                                                  'wavelength': wavelen[index]})

    custom_n = create_mask(custom_n)
    cpa = b.process(custom_n, cpa_limits,  mask=custom_n['mask'], depth=h, theta=theta, threads=4)

    custom_n.add_band(array=cpa[0], parameters={'name': 'chl',
                                                'long_name': 'Chlorophyl-a',
                                                'units': 'mg m-3'})
    custom_n.add_band(array=cpa[1], parameters={'name': 'tsm',
                                                'long_name': 'Total suspended matter',
                                                'units': 'g m-3'})
    custom_n.add_band(array=cpa[2], parameters={'name': 'doc',
                                                'long_name': 'Dissolved organic carbon',
                                                'units': 'gC m-3'})
    custom_n.add_band(array=cpa[3], parameters={'name': 'mse',
                                                'long_name': 'Root Mean Square Error',
                                                'units': 'sr-1'})
    custom_n.add_band(array=cpa[4], parameters={'name': 'mask',
                                                'long_name': 'L2 Boreali mask',
                                                'units': '1'})

    custom_n.export(final_path + obj.split('/')[-1] + 'cpa_OSW.nc')

    fig_params = {'legend': True,
                  'LEGEND_HEIGHT': 0.5,
                  'NAME_LOCATION_Y': 0,
                  'mask_array': cpa[4],
                  'mask_lut': {1: [255, 255, 255],
                               2: [128, 128, 128],
                               4: [200, 200, 255]}}
    custom_n.write_figure(final_path + obj.split('/')[-1] + 'chl_OSW.png', 'chl', clim=[0, 1.], **fig_params)
    custom_n.write_figure(final_path + obj.split('/')[-1] + 'tsm_OSW.png', 'tsm', clim=[0, 1.], **fig_params)
    custom_n.write_figure(final_path + obj.split('/')[-1] + 'doc_OSW.png', 'doc', clim=[0, .2], **fig_params)
    custom_n.write_figure(final_path + obj.split('/')[-1] + 'mse_OSW.png', 'mse', clim=[1e-5, 1e-2],
                          logarithm=True, **fig_params)
    n.write_figure(final_path + obj.split('/')[-1] + 'rgb_OSW.png',
                   [16, 14, 6],
                   clim=[[0, 0, 0], [0.006, 0.04, 0.024]],
                   mask_array=cpa[4],
                   mask_lut={2: [128, 128, 128]})