Mosaic Sentinel-2 images

A mosaic is a combination or merge of two or more images. With rasterio, you can create a single raster from multiple raster by mosaicking them together.

import glob, os
import numpy as np
import geopandas as gpd
import rasterio
import rasterio.plot
from rasterio.merge import merge
import matplotlib.pyplot as plt
from pathlib import Path

Set parameters

tile_list = ['31UFS','31UFR']
tile_list = ['31UFS','31UFR','31UGS','31UGR']


tile_list_str = '_'.join(tile_list)

nodata_val = -10000

Set directory

computer_path = '/export/miro/ndeffense/LBRAT2104/'
grp_nb        = '99'

# Directory for all work files
work_path = f'{computer_path}STUDENTS/GROUP_{grp_nb}/TP/'


masked_path = f'{work_path}3_L2A_MASKED_4tiles/'
mosaic_path = f'{work_path}5_L2A_MOSAIC_{tile_list_str}/'

print(mosaic_path)

Path(mosaic_path).mkdir(parents=True, exist_ok=True)

/export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/5_L2A_MOSAIC_31UFS_31UFR_31UGS_31UGR/

list_im_masked_one_tile = glob.glob(f'{masked_path}*{tile_list[0]}*_ROI_SCL.tif')
list_im_masked_all_tile = glob.glob(f'{masked_path}*_ROI_SCL.tif')

print(f'There are {len(list_im_masked_one_tile)} images')

There are 51 images

for im_file_1 in list_im_masked_one_tile:

    im_to_mosaic_list = [im_file_1]

    # Get date of image
    date_1 = os.path.basename(im_file_1)[7:7+8]

    # Get tile of image
    tile_1 = os.path.basename(im_file_1)[0:6]

    # Get spectral band
    band_1 = os.path.basename(im_file_1)[23:26]


    for im_file_2 in list_im_masked_all_tile:

        # Get date of image
        date_2 = os.path.basename(im_file_2)[7:7+8]

        # Get tile of image
        tile_2 = os.path.basename(im_file_2)[0:6]

        # Get spectral band
        band_2 = os.path.basename(im_file_2)[23:26]

        if date_1 == date_2:
            if band_1 == band_2:
                if tile_1 != tile_2:
                    print(f'Date : {date_1} - Band : {band_1}')
                    print('There are at least 2 images to mosaic')

                    im_to_mosaic_list.append(im_file_2)


    if len(im_to_mosaic_list) > 1:

        print(im_to_mosaic_list)

        mosaic_file = f'{mosaic_path}{os.path.basename(im_file_1)[:-4]}_mosaic_{tile_list_str}.tif'

        print(mosaic_file)

        src_files_to_mosaic = []
        for file in im_to_mosaic_list:
            src = rasterio.open(file)
            src_files_to_mosaic.append(src)

        src_files_to_mosaic[0].meta

        mosaic, out_trans = merge(src_files_to_mosaic)

        out_meta = src_files_to_mosaic[0].meta.copy()
        out_meta.update({"driver": "GTiff",
                         "height": mosaic.shape[1],
                         "width": mosaic.shape[2],
                         "transform": out_trans})

        with rasterio.open(mosaic_file, "w", **out_meta) as dst:
            dst.write(mosaic)

        for src in src_files_to_mosaic:
            src.close()

Date : 20200805 - Band : B11
There are at least 2 images to mosaic
Date : 20200805 - Band : B11
There are at least 2 images to mosaic
Date : 20200805 - Band : B11
There are at least 2 images to mosaic
['/export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/3_L2A_MASKED_4tiles/T31UFS_20200805T104031_B11_10m_ROI_SCL.tif', '/export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/3_L2A_MASKED_4tiles/T31UFR_20200805T104031_B11_10m_ROI_SCL.tif', '/export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/3_L2A_MASKED_4tiles/T31UGS_20200805T104031_B11_10m_ROI_SCL.tif', '/export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/3_L2A_MASKED_4tiles/T31UGR_20200805T104031_B11_10m_ROI_SCL.tif']
/export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/5_L2A_MOSAIC_31UFS_31UFR_31UGS_31UGR/T31UFS_20200805T104031_B11_10m_ROI_SCL_mosaic_31UFS_31UFR_31UGS_31UGR.tif
Date : 20200805 - Band : B04
There are at least 2 images to mosaic
Date : 20200805 - Band : B04
There are at least 2 images to mosaic
Date : 20200805 - Band : B04
There are at least 2 images to mosaic
['/export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/3_L2A_MASKED_4tiles/T31UFS_20200805T104031_B04_10m_ROI_SCL.tif', '/export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/3_L2A_MASKED_4tiles/T31UFR_20200805T104031_B04_10m_ROI_SCL.tif', '/export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/3_L2A_MASKED_4tiles/T31UGS_20200805T104031_B04_10m_ROI_SCL.tif', '/export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/3_L2A_MASKED_4tiles/T31UGR_20200805T104031_B04_10m_ROI_SCL.tif']
/export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/5_L2A_MOSAIC_31UFS_31UFR_31UGS_31UGR/T31UFS_20200805T104031_B04_10m_ROI_SCL_mosaic_31UFS_31UFR_31UGS_31UGR.tif
Date : 20200805 - Band : B08
There are at least 2 images to mosaic
Date : 20200805 - Band : B08
There are at least 2 images to mosaic
Date : 20200805 - Band : B08
There are at least 2 images to mosaic
['/export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/3_L2A_MASKED_4tiles/T31UFS_20200805T104031_B08_10m_ROI_SCL.tif', '/export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/3_L2A_MASKED_4tiles/T31UFR_20200805T104031_B08_10m_ROI_SCL.tif', '/export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/3_L2A_MASKED_4tiles/T31UGS_20200805T104031_B08_10m_ROI_SCL.tif', '/export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/3_L2A_MASKED_4tiles/T31UGR_20200805T104031_B08_10m_ROI_SCL.tif']
/export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/5_L2A_MOSAIC_31UFS_31UFR_31UGS_31UGR/T31UFS_20200805T104031_B08_10m_ROI_SCL_mosaic_31UFS_31UFR_31UGS_31UGR.tif