diff --git a/pysegcnn/core/cli.py b/pysegcnn/core/cli.py
new file mode 100644
index 0000000000000000000000000000000000000000..5d734df9a425ca2f78858e747a56a85a218bb4e0
--- /dev/null
+++ b/pysegcnn/core/cli.py
@@ -0,0 +1,65 @@
+"""Command line interface parsers.
+
+License
+-------
+
+ Copyright (c) 2020 Daniel Frisinghelli
+
+ This source code is licensed under the GNU General Public License v3.
+
+ See the LICENSE file in the repository's root directory.
+
+"""
+
+# !/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+# builtins
+import pathlib
+import argparse
+
+
+# epilogue to display at the end of each parser
+EPILOGUE = 'Author: Daniel Frisinghelli, daniel.frisinghelli@gmail.com'
+
+
+def structure_parser():
+ """Command line argument parser to standardize dataset structure.
+
+ Returns
+ -------
+ None.
+
+ """
+ parser = argparse.ArgumentParser(
+ description='Standardize the dataset directory structure.',
+ epilog=EPILOGUE,
+ formatter_class=lambda prog: argparse.RawDescriptionHelpFormatter(
+ prog, max_help_position=50, indent_increment=2))
+
+ # positional arguments
+
+ # positional argument: path to the archive
+ parser.add_argument('archive', type=pathlib.Path,
+ help='Path to the dataset archive.')
+
+ # positional argument: path to extract and restructure the dataset
+ parser.add_argument('target', type=pathlib.Path,
+ help='Path to save standardized dataset structure.')
+
+ # optional arguments
+
+ # default values
+ default = '(default: %(default)s)'
+
+ # optional argument: whether to overwrite existing files
+ parser.add_argument('-o', '--overwrite', type=bool,
+ help='Overwrite files {}'.format(default),
+ default=False, nargs='?', const=True, metavar='')
+
+ # optional argument: whether to copy or move extracted files
+ parser.add_argument('-r', '--remove', type=bool,
+ help='Remove original dataset {}'.format(default),
+ default=False, nargs='?', const=True, metavar='')
+
+ return parser
diff --git a/pysegcnn/preprocessing/sparcs.py b/pysegcnn/preprocessing/sparcs.py
index a8096f6f17a411a717b1ca95a224901475b60727..e8fc8d64856c3ad552478cd782feaf660d3a4628 100644
--- a/pysegcnn/preprocessing/sparcs.py
+++ b/pysegcnn/preprocessing/sparcs.py
@@ -15,192 +15,46 @@ License
# coding: utf-8
# builtins
-import os
-import glob
-import shutil
-
-# externals
-import gdal
-import numpy as np
+import sys
+from logging.config import dictConfig
# locals
-from pylandsat.core.untar import extract_data
-from pylandsat.core.calibration import landsat_radiometric_calibration
-
-
-def sparcs2pylandsat(source_path, target_path, overwrite=True):
- """Convert the Sparcs dataset structure to standard EO structure.
-
- Parameters
- ----------
- source_path : `str`
- Path to the Sparcs archive downloaded `here`_.
- target_path : `str`
- Path to save the preprocessed sparcs dataset.
- overwrite : `bool`
- Whether to overwrite existing files.
-
- Returns
- -------
- None.
-
- .. _here:
- https://www.usgs.gov/land-resources/nli/landsat/spatial-procedures-automated-removal-cloud-and-shadow-sparcs-validation
-
- """
- # create a directory for each scene
- for dirpath, dirnames, filenames in os.walk(source_path):
-
- # check if there are files in the current folder
- if not filenames:
- continue
-
- # iterate over the files to modify
- for file in filenames:
-
- # get the path to the file
- old_path = os.path.join(dirpath, file)
-
- # get name of the scene
- fname = file.split('_')[0]
-
- # define the new path to the file
- new_path = os.path.join(target_path, fname)
-
- # check if file is the metadata file
- if file.endswith('_mtl.txt'):
-
- # add the collection number to the metadata file
- with open(old_path, 'a') as mfile:
- mfile.write('COLLECTION_NUMBER = 1')
-
- # replace file ending
- file = file.replace('mtl', 'MTL')
-
- # move files to new directory
- if os.path.isfile(new_path + os.sep + file) and not overwrite:
- print('{} already exists.'.format(new_path + os.sep + file))
- continue
- else:
- os.makedirs(new_path, exist_ok=True)
- shutil.move(old_path, new_path + os.sep + file)
-
- # remove old file location
- shutil.rmtree(source_path)
-
-
-def destack_sparcs_raster(inpath, outpath=None, suffix='*_toa.tif'):
- """Destack a TIFF with more than one band into a TIFF file for each band.
-
- Parameters
- ----------
- inpath : `str`
- Path to a directory containing the TIFF file to destack.
- outpath : `str`, optional
- Path to save the output TIFF files. The default is None. If None,
- ``outpath`` = ``inpath``.
-
- Returns
- -------
- None.
-
- """
- # default: output directory is equal to the input directory
- if outpath is None:
- outpath = inpath
-
- # check if output directory exists
- if not os.path.exists(outpath):
- os.makedirs(outpath)
-
- # get the TIFF to destack
- tif = glob.glob(inpath + os.sep + '*data.tif').pop()
-
- # open the raster
- img = gdal.Open(tif)
-
- # check whether the current scene was already processed
- processed = glob.glob(inpath + os.sep + suffix)
- if len(processed) == img.RasterCount:
- print('Scene: {} already processed.'.format(os.path.basename(inpath)))
- img = None
- os.unlink(tif)
- return
-
- # image driver
- driver = gdal.GetDriverByName('GTiff')
- driver.Register()
-
- # output image type: digital numbers unsigned integer 16bit
- codage = gdal.GDT_UInt16
- nptype = np.uint16
-
- # image size and tiles
- cols = img.RasterXSize
- rows = img.RasterYSize
- bands = img.RasterCount
-
- # print progress
- imgname = os.path.basename(tif)
- print('Processing: {}'.format(imgname))
-
- # iterate the bands of the raster
- for b in range(1, bands + 1):
- # output file: replace for band name
- fname = os.path.join(outpath, imgname.replace('data', 'B' + str(b)))
- outDs = driver.Create(fname, cols, rows, 1, codage)
-
- # read the data of band b
- band = img.GetRasterBand(b)
- data = band.ReadAsArray().astype(nptype)
-
- # define output band
- outband = outDs.GetRasterBand(1)
-
- # write array to output band
- outband.WriteArray(data)
- outband.FlushCache()
-
- # Set the geographic information
- outDs.SetProjection(img.GetProjection())
- outDs.SetGeoTransform(img.GetGeoTransform())
-
- # clear memory
- del outband, band, data, outDs
-
- # remove old stacked GeoTIFF
- img = None
- os.unlink(tif)
+from pysegcnn.core.utils import (destack_tiff, standard_eo_structure,
+ extract_archive)
+from pysegcnn.core.logging import log_conf
+from pysegcnn.core.cli import structure_parser
if __name__ == '__main__':
- # define path to working directory
- # wd = 'C:/Eurac/2020/'
- wd = '/mnt/CEPH_PROJECTS/cci_snow/dfrisinghelli/'
-
- # path to the downloaded sparcs archive
- sparcs_archive = os.path.join(wd, '_Datasets/Archives/l8cloudmasks.zip')
-
- # path to save preprocessed sparcs dataset
- sparcs_path = os.path.join(wd, '_Datasets/Sparcs')
-
- # extract the raw archive to the output path
- location = extract_data(sparcs_archive, sparcs_path)
-
- # transform SPARCS directory structure to pylandsat standard
- sparcs2pylandsat(source_path=location, target_path=sparcs_path,
- overwrite=False)
-
- # destack the TIFF rasterstack to a single TIFF for each band and perform
- # radiometric calibration
- for scene in os.listdir(sparcs_path):
- # path to the current scene
- scene_path = os.path.join(sparcs_path, scene)
-
- # build the GeoTIFFs for each band
- destack_sparcs_raster(scene_path, suffix='*_toa.tif')
+ # configure logging
+ dictConfig(log_conf(__file__.replace('.py', '.log')))
+
+ # the argument parser
+ parser = structure_parser()
+
+ # parse the command line arguments
+ args = sys.argv[1:]
+ if not args:
+ parser.print_help()
+ sys.exit()
+ else:
+ args = parser.parse_args(args)
+
+ # extract the archive
+ extracted = extract_archive(args.archive, args.target, args.overwrite)
+
+ # transform SPARCS directory structure to standard structure
+ standard_eo_structure(source_path=extracted, target_path=args.target,
+ overwrite=args.overwrite, move=args.remove)
+
+ # destack the TIFF raster to a single TIFF for each band
+ for scene in args.target.iterdir():
+ # the TIFF file containing the bands
+ try:
+ data = next(scene.glob('*data.tif'))
+ except StopIteration:
+ continue
- # convert the digital number format to top of atmosphere reflectance
- landsat_radiometric_calibration(scene_path, exclude=[], suffix='_toa',
- overwrite=False, remove_raw=True)
+ # build the TIFFs for each band
+ destack_tiff(data, overwrite=args.overwrite, remove=args.remove)