Merge branch 'master' into enhancement/separate_sensorspecs

Conflicts:
	gms_preprocessing/misc/path_generator.py
	setup.py
	tests/CI_docker/context/environment_gms_preprocessing.yml

.gitlab-ci.yml

@@ -35,6 +35,8 @@ test_gms_preprocessing:
     # - cd ../../
     # make tests
 
+    - pip install git+https://gitext.gfz-potsdam.de/geomultisens/spechomo.git  # TODO remove as soon as this is included in the CI container
+
     # run tests
     - make nosetests
     - make docs

LICENSE

-GNU GENERAL PUBLIC LICENSE
-                      Version 3, 29 June 2007
+`gms_preprocessing` is distributed under the GNU General Public License, version 3 (GPLv3).
+
+Exceptions are listed in the following:
+
+* `gms_preprocessing` depends on tqdm, which is distributed under the Mozilla
+  Public Licence (MPL) v2.0 except for the files "tqdm/_tqdm.py", "setup.py",
+  "README.rst", "MANIFEST.in" and ".gitignore". Details can be found here:
+  https://github.com/tqdm/tqdm/blob/master/LICENCE.
+
+
+GNU GENERAL PUBLIC LICENSE, Version 3, 29 June 2007
+---------------------------------------------------
 
     gms_preprocessing - Spatial and spectral homogenization of satellite remote sensing data.
-    
-    Copyright 2018 Helmholtz Centre Potsdam GFZ German Research Centre for Geosciences, Potsdam, Germany
+
+    Copyright 2020 Helmholtz Centre Potsdam GFZ German Research Centre for Geosciences, Potsdam, Germany
 
     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
@@ -31,5 +41,3 @@ may consider it more useful to permit linking proprietary applications with
 the library.  If this is what you want to do, use the GNU Lesser General
 Public License instead of this License.  But first, please read
 <http://www.gnu.org/philosophy/why-not-lgpl.html>.
-
-

README.rst

@@ -27,7 +27,7 @@ Status
      :target: https://pyup.io/repos/github/geomultisens/gms_preprocessing/
      :alt: Updates
 
-.. image:: https://gitext.gfz-potsdam.de/geomultisens/gms_preprocessing/badges/master/build.svg
+.. image:: https://gitext.gfz-potsdam.de/geomultisens/gms_preprocessing/badges/master/pipeline.svg
         :target: https://gitext.gfz-potsdam.de/geomultisens/gms_preprocessing/commits/master
 .. image:: https://gitext.gfz-potsdam.de/geomultisens/gms_preprocessing/badges/master/coverage.svg
         :target: http://geomultisens.gitext.gfz-potsdam.de/gms_preprocessing/coverage/
@@ -55,7 +55,7 @@ Level-2 processing:
 ^^^^^^^^^^^^^^^^^^^
 
 * spatial homogenization
-* spectral homogenization
+* spectral homogenization (using `SpecHomo <https://gitext.gfz-potsdam.de/geomultisens/spechomo>`_
 * estimation of accuracy layers
 
 => application oriented analysis dataset
@@ -173,7 +173,7 @@ License
 
 gms_preprocessing - Spatial and spectral homogenization of satellite remote sensing data.
 
-Copyright 2018 Helmholtz Centre Potsdam GFZ German Research Centre for Geosciences, Potsdam, Germany
+Copyright 2020 Helmholtz Centre Potsdam GFZ German Research Centre for Geosciences, Potsdam, Germany
 
 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
@@ -204,7 +204,10 @@ Contact
 Credits
 -------
 
-The development of the gms_preprocessing package was funded by the German Federal Ministry of Education and Research (BMBF). The package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
+The development of the gms_preprocessing package was funded by the German Federal Ministry of Education and Research
+(BMBF, project grant code: 01 IS 14 010 A-C).
+
+The package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
 
 Landsat-5/7/8 satellite data and SRTM/ASTER digital elevation models have been have been provided by the US Geological
 Survey. Sentinel-2 data have been provided by ESA.

bin/run_gms.py

 # -*- coding: utf-8 -*-
+
+# gms_preprocessing, spatial and spectral homogenization of satellite remote sensing data
+#
+# Copyright (C) 2020  Daniel Scheffler (GFZ Potsdam, daniel.scheffler@gfz-potsdam.de)
+#
+# This software was developed within the context of the GeoMultiSens project funded
+# by the German Federal Ministry of Education and Research
+# (project grant code: 01 IS 14 010 A-C).
+#
+# 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. Please note the following exception: `spechomo` depends on tqdm, which
+# is distributed under the Mozilla Public Licence (MPL) v2.0 except for the files
+# "tqdm/_tqdm.py", "setup.py", "README.rst", "MANIFEST.in" and ".gitignore".
+# Details can be found here: https://github.com/tqdm/tqdm/blob/master/LICENCE.
+#
+# 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 Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 __author__ = 'Daniel Scheffler'
 
 import argparse

bin/run_gms.sh

 #!/usr/bin/env bash
 
+# gms_preprocessing, spatial and spectral homogenization of satellite remote sensing data
+#
+# Copyright (C) 2020  Daniel Scheffler (GFZ Potsdam, daniel.scheffler@gfz-potsdam.de)
+#
+# This software was developed within the context of the GeoMultiSens project funded
+# by the German Federal Ministry of Education and Research
+# (project grant code: 01 IS 14 010 A-C).
+#
+# 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. Please note the following exception: `spechomo` depends on tqdm, which
+# is distributed under the Mozilla Public Licence (MPL) v2.0 except for the files
+# "tqdm/_tqdm.py", "setup.py", "README.rst", "MANIFEST.in" and ".gitignore".
+# Details can be found here: https://github.com/tqdm/tqdm/blob/master/LICENCE.
+#
+# 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 Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+
 # execute python script
 # NOTE: This asserts that the gms_preprocessing has been installed via 'pip install...' and that the PATH environment
 #       variable points to the correct Python interpreter.

gms_preprocessing/__init__.py

 # -*- coding: utf-8 -*-
 
+# gms_preprocessing, spatial and spectral homogenization of satellite remote sensing data
+#
+# Copyright (C) 2020  Daniel Scheffler (GFZ Potsdam, daniel.scheffler@gfz-potsdam.de)
+#
+# This software was developed within the context of the GeoMultiSens project funded
+# by the German Federal Ministry of Education and Research
+# (project grant code: 01 IS 14 010 A-C).
+#
+# 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. Please note the following exception: `spechomo` depends on tqdm, which
+# is distributed under the Mozilla Public Licence (MPL) v2.0 except for the files
+# "tqdm/_tqdm.py", "setup.py", "README.rst", "MANIFEST.in" and ".gitignore".
+# Details can be found here: https://github.com/tqdm/tqdm/blob/master/LICENCE.
+#
+# 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 Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 import os
 if 'MPLBACKEND' not in os.environ:
     os.environ['MPLBACKEND'] = 'Agg'

gms_preprocessing/algorithms/L1A_P.py

 # -*- coding: utf-8 -*-
+
+# gms_preprocessing, spatial and spectral homogenization of satellite remote sensing data
+#
+# Copyright (C) 2020  Daniel Scheffler (GFZ Potsdam, daniel.scheffler@gfz-potsdam.de)
+#
+# This software was developed within the context of the GeoMultiSens project funded
+# by the German Federal Ministry of Education and Research
+# (project grant code: 01 IS 14 010 A-C).
+#
+# 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. Please note the following exception: `spechomo` depends on tqdm, which
+# is distributed under the Mozilla Public Licence (MPL) v2.0 except for the files
+# "tqdm/_tqdm.py", "setup.py", "README.rst", "MANIFEST.in" and ".gitignore".
+# Details can be found here: https://github.com/tqdm/tqdm/blob/master/LICENCE.
+#
+# 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 Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 import datetime
 import os
 import re
@@ -75,13 +100,13 @@ class L1A_object(GMS_object):
         self.proc_status = proc_status or 'initialized'  # if proc_status = 'running' is given by L1A_map
 
     def import_rasterdata(self):
-        if re.search("ALOS", self.satellite, re.I):
+        if re.search(r"ALOS", self.satellite, re.I):
             '''First 22 lines are nodata: = maybe due to an issue of the GDAL CEOS driver.
             But: UL of metadata refers to [row =0, col=21]! So the imported GeoTransform is correct when
             the first 21 columns are deleted.'''
             self.archive_to_rasObj(self.path_archive, self.path_InFilePreprocessor,
                                    subset=['block', [[None, None], [21, None]]])
-        elif re.search("Terra", self.satellite, re.I):
+        elif re.search(r"Terra", self.satellite, re.I):
             self.ASTER_HDF_to_rasObj(self.path_archive, path_output=self.path_InFilePreprocessor)
         else:
             self.archive_to_rasObj(self.path_archive, path_output=self.path_InFilePreprocessor)
@@ -113,23 +138,23 @@ class L1A_object(GMS_object):
 
         image_files = []
         is_ALOS_Landsat_S2 = \
-            re.search('ALOS', self.satellite) or re.search('Landsat', self.satellite) or \
-            re.search('Sentinel-2', self.satellite)
+            re.search(r'ALOS', self.satellite) or re.search(r'Landsat', self.satellite) or \
+            re.search(r'Sentinel-2', self.satellite)
         n_files2search = len(full_LayerBandsAssignment) if is_ALOS_Landsat_S2 else 1
 
         for File in HLP_F.sorted_nicely(files_in_archive):
             search_res = \
-                re.search("IMG-0[0-9]-[\s\S]*", File) if re.search('ALOS', self.satellite) else \
-                re.search("[\S]*_B[1-9][0-9]?[\S]*.TIF", File) if re.search('Landsat', self.satellite) else \
-                re.search("[0-9]*.tif", File) if re.search('RapidEye', self.satellite) else \
-                re.search("imagery.tif", File) if re.search('SPOT', self.satellite) else \
-                re.search("[\S]*.SAFE/GRANULE/%s/IMG_DATA/[\S]*_B[0-9][\S]*.jp2"
-                          % self.entity_ID, File) if re.search('Sentinel-2', self.satellite) else None
+                re.search(r"IMG-0[0-9]-[\s\S]*", File) if re.search(r'ALOS', self.satellite) else \
+                re.search(r"[\S]*_B[1-9][0-9]?[\S]*.TIF", File) if re.search(r'Landsat', self.satellite) else \
+                re.search(r"[0-9]*.tif", File) if re.search(r'RapidEye', self.satellite) else \
+                re.search(r"imagery.tif", File) if re.search(r'SPOT', self.satellite) else \
+                re.search(r"[\S]*.SAFE/GRANULE/%s/IMG_DATA/[\S]*_B[0-9][\S]*.jp2"
+                          % self.entity_ID, File) if re.search(r'Sentinel-2', self.satellite) else None
 
             if search_res:
-                if re.search('Sentinel-2', self.satellite):
+                if re.search(r'Sentinel-2', self.satellite):
                     # add only those files that are corresponding to subsystem (e.g. S2A10: fullLBA = ['2','3','4','8'])
-                    if 1 in [1 if re.search("[\S]*_B[0]?%s.jp2" % LBAn, os.path.basename(File)) else 0
+                    if 1 in [1 if re.search(r"[\S]*_B[0]?%s.jp2" % LBAn, os.path.basename(File)) else 0
                              for LBAn in full_LayerBandsAssignment]:
                         image_files.append(File)
                 else:
@@ -141,7 +166,7 @@ class L1A_object(GMS_object):
             # validate number of expected files #
             #####################################
 
-            if re.search('ETM+', self.sensor) and self.acq_datetime > datetime.datetime(year=2003, month=5, day=31):
+            if re.search(r'ETM+', self.sensor) and self.acq_datetime > datetime.datetime(year=2003, month=5, day=31):
                 expected_files_count = 2 * len(full_LayerBandsAssignment)
             else:
                 expected_files_count = len(full_LayerBandsAssignment)
@@ -299,9 +324,9 @@ class L1A_object(GMS_object):
         self.arr_desc = \
             'DN' if self.MetaObj.PhysUnit == 'DN' else \
             'Rad' if self.MetaObj.PhysUnit == "W * m-2 * sr-1 * micrometer-1" else \
-            'TOA_Ref' if re.search('TOA_Reflectance', self.MetaObj.PhysUnit, re.I) else \
-            'BOA_Ref' if re.search('BOA_Reflectance', self.MetaObj.PhysUnit, re.I) else \
-            'Temp' if re.search('Degrees Celsius', self.MetaObj.PhysUnit, re.I) else None
+            'TOA_Ref' if re.search(r'TOA_Reflectance', self.MetaObj.PhysUnit, re.I) else \
+            'BOA_Ref' if re.search(r'BOA_Reflectance', self.MetaObj.PhysUnit, re.I) else \
+            'Temp' if re.search(r'Degrees Celsius', self.MetaObj.PhysUnit, re.I) else None
 
         assert self.arr_desc, 'GMS_obj contains an unexpected physical unit: %s' % self.MetaObj.PhysUnit
 
@@ -391,7 +416,7 @@ class L1A_object(GMS_object):
                         (PI * U__earth_sun_distance_correction_factor);
                     L = (U__earth_sun_distance_correction_factor * rToa * e0__SOLAR_IRRADIANCE_For_band * cos(
                         Z__Sun_Angles_Grid_Zenith_Values)) / PI;"""
-                    if re.search('Sentinel-2', self.satellite, re.I):
+                    if re.search(r'Sentinel-2', self.satellite, re.I):
                         warnings.warn('Physical gain values unclear for Sentinel-2! This may cause errors when '
                                       'calculating radiance from TOA Reflectance. ESA provides only 12 gain values for '
                                       '13 bands and it not clear for which bands the gains are provided.')
@@ -456,7 +481,7 @@ class L1A_object(GMS_object):
             os.chdir(os.path.dirname(self.path_archive))
         rasObj = GEOP.GEOPROCESSING(self.MetaObj.Dataname, self.logger)
         if rasObj.geotransform == (0.0, 1.0, 0.0, 0.0, 0.0, 1.0) and rasObj.projection == '':
-            if re.search('ALOS', self.satellite) and self.MetaObj.ProcLCode == '1B2':
+            if re.search(r'ALOS', self.satellite) and self.MetaObj.ProcLCode == '1B2':
                 self.GeoTransProj_ok, self.GeoAlign_ok = False, True
             else:
                 self.GeoTransProj_ok, self.GeoAlign_ok = False, False
@@ -547,7 +572,7 @@ class L1A_object(GMS_object):
                        'mask_nodata') and self.mask_nodata is not None, "The L1A object needs to have a nodata mask."
         self.logger.info('Calculating true data corner positions (image and world coordinates)...')
 
-        # if re.search('ETM+', self.sensor) and self.acq_datetime > datetime.datetime(year=2003, month=5, day=31,
+        # if re.search(r'ETM+', self.sensor) and self.acq_datetime > datetime.datetime(year=2003, month=5, day=31,
         #                                                                             tzinfo=datetime.timezone.utc):
         if is_dataset_provided_as_fullScene(self.GMS_identifier):
             self.trueDataCornerPos = calc_FullDataset_corner_positions(self.mask_nodata, algorithm='numpy',
@@ -577,7 +602,7 @@ class L1A_object(GMS_object):
 
         else:
 
-            if re.search('AVNIR', self.sensor):
+            if re.search(r'AVNIR', self.sensor):
                 self.fullSceneCornerPos = calc_FullDataset_corner_positions(self.mask_nodata, algorithm='numpy',
                                                                             assert_four_corners=False)
                 # set true data corner positions (lon/lat coordinates)
@@ -588,7 +613,7 @@ class L1A_object(GMS_object):
             else:
                 # RapidEye or Sentinel-2 data
 
-                if re.search('Sentinel-2', self.satellite):
+                if re.search(r'Sentinel-2', self.satellite):
                     # get fullScene corner coordinates by database query
                     # -> calculate footprints for all granules of the same S2 datatake
                     # -> merge them and calculate overall corner positions

gms_preprocessing/algorithms/L1B_P.py

 # -*- coding: utf-8 -*-
+
+# gms_preprocessing, spatial and spectral homogenization of satellite remote sensing data
+#
+# Copyright (C) 2020  Daniel Scheffler (GFZ Potsdam, daniel.scheffler@gfz-potsdam.de)
+#
+# This software was developed within the context of the GeoMultiSens project funded
+# by the German Federal Ministry of Education and Research
+# (project grant code: 01 IS 14 010 A-C).
+#
+# 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. Please note the following exception: `spechomo` depends on tqdm, which
+# is distributed under the Mozilla Public Licence (MPL) v2.0 except for the files
+# "tqdm/_tqdm.py", "setup.py", "README.rst", "MANIFEST.in" and ".gitignore".
+# Details can be found here: https://github.com/tqdm/tqdm/blob/master/LICENCE.
+#
+# 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 Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 """
 Level 1B Processor:
 

gms_preprocessing/algorithms/L1C_P.py

 # -*- coding: utf-8 -*-
+
+# gms_preprocessing, spatial and spectral homogenization of satellite remote sensing data
+#
+# Copyright (C) 2020  Daniel Scheffler (GFZ Potsdam, daniel.scheffler@gfz-potsdam.de)
+#
+# This software was developed within the context of the GeoMultiSens project funded
+# by the German Federal Ministry of Education and Research
+# (project grant code: 01 IS 14 010 A-C).
+#
+# 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. Please note the following exception: `spechomo` depends on tqdm, which
+# is distributed under the Mozilla Public Licence (MPL) v2.0 except for the files
+# "tqdm/_tqdm.py", "setup.py", "README.rst", "MANIFEST.in" and ".gitignore".
+# Details can be found here: https://github.com/tqdm/tqdm/blob/master/LICENCE.
+#
+# 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 Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 """Level 1C Processor:   Atmospheric correction of TOA-reflectance data."""
 
 import warnings
@@ -269,7 +294,7 @@ class AtmCorr(object):
         # append AtmCorr object to input L1C objects
         # [setattr(L1C_obj, 'AtmCorr', self) for L1C_obj in self.inObjs] # too big for serialization
 
-        if not re.search('Sentinel-2', self.inObjs[0].satellite, re.I):
+        if not re.search(r'Sentinel-2', self.inObjs[0].satellite, re.I):
             self.logger.debug('Calculation of acquisition geometry arrays is currently only validated for Sentinel-2!')
             # validation possible by comparing S2 angles provided by ESA with own angles  # TODO
 
@@ -649,7 +674,7 @@ class AtmCorr(object):
         :return: <np.ndarray> 2D array (with 20m resolution in case of Sentinel-2)
         """
         # determine which input GMS object is used to generate DEM
-        if re.search('Sentinel-2', self.inObjs[0].satellite):
+        if re.search(r'Sentinel-2', self.inObjs[0].satellite):
             # in case of Sentinel-2 the 20m DEM must be passed
             inObj4dem = [obj for obj in self.inObjs if obj.arr.xgsd == 20]
             if not inObj4dem:

gms_preprocessing/algorithms/L2A_P.py

 # -*- coding: utf-8 -*-
+
+# gms_preprocessing, spatial and spectral homogenization of satellite remote sensing data
+#
+# Copyright (C) 2020  Daniel Scheffler (GFZ Potsdam, daniel.scheffler@gfz-potsdam.de)
+#
+# This software was developed within the context of the GeoMultiSens project funded
+# by the German Federal Ministry of Education and Research
+# (project grant code: 01 IS 14 010 A-C).
+#
+# 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. Please note the following exception: `spechomo` depends on tqdm, which
+# is distributed under the Mozilla Public Licence (MPL) v2.0 except for the files
+# "tqdm/_tqdm.py", "setup.py", "README.rst", "MANIFEST.in" and ".gitignore".
+# Details can be found here: https://github.com/tqdm/tqdm/blob/master/LICENCE.
+#
+# 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 Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 """Level 2A Processor: Spatial homogenization"""
 
 from .L1C_P import L1C_object

gms_preprocessing/algorithms/L2B_P.py

 # -*- coding: utf-8 -*-
+
+# gms_preprocessing, spatial and spectral homogenization of satellite remote sensing data
+#
+# Copyright (C) 2020  Daniel Scheffler (GFZ Potsdam, daniel.scheffler@gfz-potsdam.de)
+#
+# This software was developed within the context of the GeoMultiSens project funded
+# by the German Federal Ministry of Education and Research
+# (project grant code: 01 IS 14 010 A-C).
+#
+# 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. Please note the following exception: `spechomo` depends on tqdm, which
+# is distributed under the Mozilla Public Licence (MPL) v2.0 except for the files
+# "tqdm/_tqdm.py", "setup.py", "README.rst", "MANIFEST.in" and ".gitignore".
+# Details can be found here: https://github.com/tqdm/tqdm/blob/master/LICENCE.
+#
+# 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 Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 """
 Level 2B Processor: Spectral homogenization
 """
@@ -77,7 +102,10 @@ class L2B_object(L2A_object):
         # perform spectral homogenization of image data #
         #################################################
 
-        SpH = SpectralHomogenizer(classifier_rootDir=CFG.path_spechomo_classif, logger=self.logger, CPUs=CFG.CPUs)
+        from ..processing.multiproc import is_mainprocess
+        SpH = SpectralHomogenizer(classifier_rootDir=CFG.path_spechomo_classif,
+                                  logger=self.logger,
+                                  CPUs=CFG.CPUs if is_mainprocess() else 1)
 
         if method == 'LI' or CFG.datasetid_spectral_ref is None:
             # linear interpolation (if intended by user or in case of custom spectral characteristics of target sensor)

gms_preprocessing/algorithms/L2C_P.py

 # -*- coding: utf-8 -*-
+
+# gms_preprocessing, spatial and spectral homogenization of satellite remote sensing data
+#
+# Copyright (C) 2020  Daniel Scheffler (GFZ Potsdam, daniel.scheffler@gfz-potsdam.de)
+#
+# This software was developed within the context of the GeoMultiSens project funded
+# by the German Federal Ministry of Education and Research
+# (project grant code: 01 IS 14 010 A-C).
+#
+# 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. Please note the following exception: `spechomo` depends on tqdm, which
+# is distributed under the Mozilla Public Licence (MPL) v2.0 except for the files
+# "tqdm/_tqdm.py", "setup.py", "README.rst", "MANIFEST.in" and ".gitignore".
+# Details can be found here: https://github.com/tqdm/tqdm/blob/master/LICENCE.
+#
+# 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 Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 """Level 2C Processor:  Quality layers"""
 
 import numpy as np

gms_preprocessing/algorithms/__init__.py

-###############################################################################
+# -*- coding: utf-8 -*-
+
+# gms_preprocessing, spatial and spectral homogenization of satellite remote sensing data
+#
+# Copyright (C) 2020  Daniel Scheffler (GFZ Potsdam, daniel.scheffler@gfz-potsdam.de)
 #
-#   algorithms/__init__.py - This file is part of the gms_preprocessing package.
+# This software was developed within the context of the GeoMultiSens project funded
+# by the German Federal Ministry of Education and Research
+# (project grant code: 01 IS 14 010 A-C).
 #
-#   Written by Daniel Scheffler
-#   GFZ Potsdam, Section 1.4
+# 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. Please note the following exception: `spechomo` depends on tqdm, which
+# is distributed under the Mozilla Public Licence (MPL) v2.0 except for the files
+# "tqdm/_tqdm.py", "setup.py", "README.rst", "MANIFEST.in" and ".gitignore".
+# Details can be found here: https://github.com/tqdm/tqdm/blob/master/LICENCE.
 #
-###############################################################################
+# 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 Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 
 from . import geoprocessing
 from . import L1A_P

gms_preprocessing/algorithms/cloud_masking.py

 # -*- coding: utf-8 -*-
 
+# gms_preprocessing, spatial and spectral homogenization of satellite remote sensing data
+#
+# Copyright (C) 2020  Daniel Scheffler (GFZ Potsdam, daniel.scheffler@gfz-potsdam.de)
+#
+# This software was developed within the context of the GeoMultiSens project funded
+# by the German Federal Ministry of Education and Research
+# (project grant code: 01 IS 14 010 A-C).
+#
+# 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. Please note the following exception: `spechomo` depends on tqdm, which
+# is distributed under the Mozilla Public Licence (MPL) v2.0 except for the files
+# "tqdm/_tqdm.py", "setup.py", "README.rst", "MANIFEST.in" and ".gitignore".
+# Details can be found here: https://github.com/tqdm/tqdm/blob/master/LICENCE.
+#
+# 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 Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 import os
 import fnmatch
 import tempfile
@@ -481,7 +505,7 @@ class Cloud_Mask_Creator(object):
         self.GMS_obj.logger.info("Calculating cloud mask based on '%s' algorithm..." % self.algorithm)
 
         if self.algorithm == 'FMASK':
-            if re.search('Landsat', self.GMS_obj.satellite, re.I):
+            if re.search(r'Landsat', self.GMS_obj.satellite, re.I):
                 FMR = FMASK_Runner_Landsat(self.GMS_obj.path_archive, self.GMS_obj.satellite)
 
             else:

gms_preprocessing/algorithms/geoprocessing.py

 # -*- coding: utf-8 -*-
+
+# gms_preprocessing, spatial and spectral homogenization of satellite remote sensing data
+#
+# Copyright (C) 2020  Daniel Scheffler (GFZ Potsdam, daniel.scheffler@gfz-potsdam.de)
+#
+# This software was developed within the context of the GeoMultiSens project funded
+# by the German Federal Ministry of Education and Research
+# (project grant code: 01 IS 14 010 A-C).
+#
+# 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. Please note the following exception: `spechomo` depends on tqdm, which
+# is distributed under the Mozilla Public Licence (MPL) v2.0 except for the files
+# "tqdm/_tqdm.py", "setup.py", "README.rst", "MANIFEST.in" and ".gitignore".
+# Details can be found here: https://github.com/tqdm/tqdm/blob/master/LICENCE.
+#
+# 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 Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 """
 GEOPROCESSING OBJECT
 "GIS operations to manipulate spatial data.
@@ -90,7 +115,7 @@ class GEOPROCESSING(object):
                 #                     '/vsitar' '.gz': '/vsigzip'}
                 p1 = [geodata.split(i)[0] + i for i in ['.zip', '.tar', '.tar.gz', '.gz', '.tgz']
                       if len(geodata.split(i)) > 1 and geodata.split(i)[1].startswith('/')][0]
-                path2check = os.path.abspath('.' + re.search('/vsi[\s\S]*(/[\s\S,.]*)', p1, re.I).group(1))
+                path2check = os.path.abspath('.' + re.search(r'/vsi[\s\S]*(/[\s\S,.]*)', p1, re.I).group(1))
             assert os.path.exists(path2check), "ERROR: data %s does not exist!" % path2check
             assert self.inDs is not None, "ERROR: Could not open %s!" % self.filename