gms_object.py 87 KB
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# -*- coding: utf-8 -*-

import collections
import copy
import datetime
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import functools
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import glob
import json
import os
import re
import shutil
import sys
import warnings
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import logging
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from collections import OrderedDict
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from itertools import chain
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from typing import Iterable, List, Union, TYPE_CHECKING  # noqa F401  # flake8 issue
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import numpy as np
import spectral
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from spectral.io import envi
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from numba import jit
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from pandas import DataFrame, read_csv
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from nested_dict import nested_dict
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try:
    from osgeo import gdalnumeric
except ImportError:
    import gdalnumeric
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from geoarray import GeoArray
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from py_tools_ds.geo.coord_grid import is_coord_grid_equal
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from py_tools_ds.geo.projection import EPSG2WKT
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from py_tools_ds.geo.map_info import geotransform2mapinfo, mapinfo2geotransform
from py_tools_ds.geo.coord_calc import calc_FullDataset_corner_positions
from py_tools_ds.geo.coord_trafo import pixelToLatLon, pixelToMapYX
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from sicor.options import get_options as get_ac_options
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from ..misc.logging import GMS_logger as DatasetLogger
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from ..model.mgrs_tile import MGRS_tile
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from ..model.metadata import METADATA, get_dict_LayerOptTherm, metaDict_to_metaODict
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from ..model.dataset import Dataset
from ..misc import path_generator as PG
from ..misc import database_tools as DB_T
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from ..options.config import GMS_config as CFG
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from ..algorithms import geoprocessing as GEOP
from ..io import input_reader as INP_R
from ..io import output_writer as OUT_W
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from ..misc import helper_functions as HLP_F
from ..misc import definition_dicts as DEF_D
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if TYPE_CHECKING:
    from ..algorithms.L1C_P import L1C_object  # noqa F401  # flake8 issue

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__author__ = 'Daniel Scheffler'
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class GMS_object(Dataset):
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    # class attributes
    # NOTE: these attributes can be modified and seen by ALL GMS_object instances
    proc_status_all_GMSobjs = nested_dict()

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    def __init__(self, pathImage=''):
        # get all attributes of base class "Dataset"
        super(GMS_object, self).__init__()

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        # add private attributes
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        self._dict_LayerOptTherm = None
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        self._cloud_masking_algorithm = None
        self._meta_odict = None
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        self._coreg_info = None
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        self.job_ID = CFG.ID
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        # FIXME not needed anymore?:
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        # self.dataset_ID = int(DB_T.get_info_from_postgreSQLdb(CFG.conn_database, 'scenes', ['datasetid'],
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        #                                {'id': self.scene_ID})[0][0]) if self.scene_ID !=-9999 else -9999
        self.scenes_proc_ID = None  # set by Output writer after creation/update of db record in table scenes_proc
        self.mgrs_tiles_proc_ID = None  # set by Output writer after creation/update of db rec in table mgrs_tiles_proc
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        self.MGRS_info = None
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        # set pathes
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        self.path_cloud_class_obj = ''

        # handle initialization arguments
        if pathImage:
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            # run the setter for 'arr' of the base class 'Dataset' which creates an Instance of GeoArray
            self.arr = pathImage
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    def __getstate__(self):
        """Defines how the attributes of GMS object are pickled."""

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        self.close_loggers()
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        del self.pathGen  # path generator can only be used for the current processing level
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        # delete arrays if their in-mem size is to big to be pickled
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        # => (avoids MaybeEncodingError: Error sending result: '[<gms_preprocessing.algorithms.L2C_P.L2C_object
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        #    object at 0x7fc44f6399e8>]'. Reason: 'error("'i' format requires -2147483648 <= number <= 2147483647",)')
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        if self.proc_level == 'L2C' and CFG.inmem_serialization:
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            # FIXME check by bandname
            if self.mask_nodata is not None and self.masks.bands > 1 and self.mask_clouds is not None:
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                del self.masks
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        return self.__dict__

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    def set_pathes(self):
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        self.baseN = self.pathGen.get_baseN()
        self.path_procdata = self.pathGen.get_path_procdata()
        self.ExtractedFolder = self.pathGen.get_path_tempdir()
        self.path_logfile = self.pathGen.get_path_logfile()
        self.pathGen = PG.path_generator(self.__dict__)  # passes a logger in addition to previous attributes
        self.path_archive = self.pathGen.get_local_archive_path_baseN()
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        if not CFG.inmem_serialization:
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            self.path_InFilePreprocessor = os.path.join(self.ExtractedFolder, '%s%s_DN.bsq'
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                                                        % (self.entity_ID,
                                                           ('_%s' % self.subsystem if self.subsystem else '')))
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        else:  # keep data in memory
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            self.path_InFilePreprocessor = None  # None: keeps all produced data in memory (numpy array attributes)
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        self.path_MetaPreprocessor = self.path_archive

    def validate_pathes(self):
        if not os.path.isfile(self.path_archive) and not os.path.isdir(self.path_archive):
            self.logger.info("The %s dataset '%s' has not been processed earlier and no corresponding raw data archive"
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                             "has been found at %s." % (self.sensor, self.entity_ID, self.path_archive))
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            self.logger.info('Trying to download the dataset...')
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            self.path_archive_valid = self._data_downloader(self.sensor, self.entity_ID)
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        else:
            self.path_archive_valid = True

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        if not CFG.inmem_serialization and self.ExtractedFolder and not os.path.isdir(self.ExtractedFolder):
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            os.makedirs(self.ExtractedFolder)

        assert os.path.exists(self.path_archive), 'Invalid path to RAW data. File %s does not exist at %s.' \
                                                  % (os.path.basename(self.path_archive),
                                                     os.path.dirname(self.path_archive))
        assert isinstance(self.path_archive, str), 'Invalid path to RAW data. Got %s instead of string or unicode.' \
                                                   % type(self.path_archive)
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        if not CFG.inmem_serialization and self.ExtractedFolder:
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            assert os.path.exists(self.path_archive), \
                'Invalid path for temporary files. Directory %s does not exist.' % self.ExtractedFolder
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    @property
    def logger(self):
        if self._loggers_disabled:
            return None
        if self._logger and self._logger.handlers[:]:
            return self._logger
        else:
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            self._logger = DatasetLogger('log__' + self.baseN, fmt_suffix=self.scene_ID, path_logfile=self.path_logfile,
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                                         log_level=CFG.log_level, append=True)
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            return self._logger

    @logger.setter
    def logger(self, logger):
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        assert isinstance(logger, logging.Logger) or logger in ['not set', None], \
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            "GMS_obj.logger can not be set to %s." % logger
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        # save prior logs
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        # if logger is None and self._logger is not None:
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        #    self.log += self.logger.captured_stream
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        self._logger = logger

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    @property
    def proc_status(self):
        # type: () -> str
        """
        Get the processing status of the current GMS_object (subclass) instance for the current processing level.

        Possible values: 'initialized', 'running', 'finished', 'failed'
        """
        # NOTE: self.proc_status_all_GMSobjs is a class attribute (visible and modifyable from any other subsystem)
        return self.proc_status_all_GMSobjs[self.scene_ID][self.subsystem][self.proc_level]

    @proc_status.setter
    def proc_status(self, new_status):
        # type: (str) -> None
        self.proc_status_all_GMSobjs[self.scene_ID][self.subsystem][self.proc_level] = new_status

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    @property
    def GMS_identifier(self):
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        return collections.OrderedDict(zip(
            ['image_type', 'Satellite', 'Sensor', 'Subsystem', 'proc_level', 'dataset_ID', 'logger'],
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            [self.image_type, self.satellite, self.sensor, self.subsystem, self.proc_level, self.dataset_ID,
             self.logger]))
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    @property
    def MetaObj(self):
        if self._meta_odict:
            # if there is already a meta_odict -> create a new MetaObj from it (ensures synchronization!)
            self._MetaObj = METADATA(self.GMS_identifier).from_odict(self._meta_odict)
            del self.meta_odict
        elif not self._MetaObj:
            # if there is no meta_odict and no MetaObj -> create MetaObj by reading metadata from disk
            pass  # reading from disk should use L1A_P.L1A_object.import_metadata -> so just return None

        return self._MetaObj

    @MetaObj.setter
    def MetaObj(self, MetaObj):
        assert isinstance(MetaObj, METADATA), "'MetaObj' can only be set to an instance of METADATA class. " \
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                                              "Got %s." % type(MetaObj)
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        self._MetaObj = MetaObj

        # update meta_odict
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        del self.meta_odict  # it is recreated if getter is used the next time
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    @MetaObj.deleter
    def MetaObj(self):
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        if hasattr(self, '_MetaObj') and self._MetaObj and hasattr(self._MetaObj, 'logger') and \
                self._MetaObj.logger not in [None, 'not set']:
            self._MetaObj.logger.close()
            self._MetaObj.logger = None

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        self._MetaObj = None

    @property
    def meta_odict(self):
        if self._MetaObj:
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            # if there is already a MetaObj -> create new meta_odict from it (ensures synchronization!)
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            self._meta_odict = self._MetaObj.to_odict()
            del self.MetaObj
        elif not self._meta_odict:
            # if there is no MetaObj and no meta_odict -> use MetaObj getter to read metadata from disk
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            pass  # reading from disk should use L1A_P.L1A_object.import_metadata -> so just return None
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            self._meta_odict = None

        return self._meta_odict

    @meta_odict.setter
    def meta_odict(self, odict):
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        assert isinstance(odict, (collections.OrderedDict, dict)), "'meta_odict' can only be set to an instance of " \
                                                                   "collections.OrderedDict. Got %s." % type(odict)
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        self._meta_odict = odict

        # update MetaObj
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        del self.MetaObj  # it is recreated if getter is used the next time
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    @meta_odict.deleter
    def meta_odict(self):
        self._meta_odict = None

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    @property
    def dict_LayerOptTherm(self):
        if self._dict_LayerOptTherm:
            return self._dict_LayerOptTherm
        elif self.LayerBandsAssignment:
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            self._dict_LayerOptTherm = get_dict_LayerOptTherm(self.identifier, self.LayerBandsAssignment)
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            return self._dict_LayerOptTherm
        else:
            return None

    @property
    def georef(self):
        """Returns True if the current dataset can serve as spatial reference."""
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        return True if self.image_type == 'RSD' and re.search('OLI', self.sensor, re.I) else False

    @property
    def coreg_needed(self):
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        if self._coreg_needed is None:
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            self._coreg_needed = not (self.dataset_ID == CFG.datasetid_spatial_ref)
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        return self._coreg_needed
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    @coreg_needed.setter
    def coreg_needed(self, value):
        self._coreg_needed = value

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    @property
    def coreg_info(self):
        if not self._coreg_info:
            self._coreg_info = {
                'corrected_shifts_px': {'x': 0, 'y': 0},
                'corrected_shifts_map': {'x': 0, 'y': 0},
                'original map info': self.meta_odict['map info'],
                'updated map info': None,
                'reference scene ID': None,
                'reference entity ID': None,
                'reference geotransform': None,
                # reference projection must be the own projection in order to avoid overwriting with a wrong EPSG
                'reference projection': self.meta_odict['coordinate system string'],
                'reference extent': {'rows': None, 'cols': None},
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                'reference grid': [list(CFG.spatial_ref_gridx),
                                   list(CFG.spatial_ref_gridy)],
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                'success': False
            }

        return self._coreg_info

    @coreg_info.setter
    def coreg_info(self, val):
        self._coreg_info = val

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    @property
    def resamp_needed(self):
        if self._resamp_needed is None:
            gt = mapinfo2geotransform(self.meta_odict['map info'])
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            self._resamp_needed = not is_coord_grid_equal(gt, CFG.spatial_ref_gridx,
                                                          CFG.spatial_ref_gridy)
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        return self._resamp_needed

    @resamp_needed.setter
    def resamp_needed(self, value):
        self._resamp_needed = value

    @property
    def masks(self):
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        # if self.mask_nodata is not None and self.mask_clouds is not None and \
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        #     self._masks is not None and self._masks.bands==1:

        #     self.build_combined_masks_array()

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        return self._masks

    @masks.setter
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    def masks(self, *geoArr_initArgs):
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        """
        NOTE: This does not automatically update mask_nodata and mask_clouds BUT if mask_nodata and mask_clouds are
        None their getters will automatically synchronize!
        """
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        if geoArr_initArgs[0] is not None:
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            self._masks = GeoArray(*geoArr_initArgs)
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            self._masks.nodata = 0
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            self._masks.gt = self.arr.gt
            self._masks.prj = self.arr.prj
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        else:
            del self.masks
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    @masks.deleter
    def masks(self):
        self._masks = None

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    @property
    def mask_clouds_confidence(self):
        return self._mask_clouds_confidence

    @mask_clouds_confidence.setter
    def mask_clouds_confidence(self, *geoArr_initArgs):
        if geoArr_initArgs[0] is not None:
            cnfArr = GeoArray(*geoArr_initArgs)

            assert cnfArr.shape == self.arr.shape[:2], \
                "The 'mask_clouds_confidence' GeoArray can only be instanced with an array of the same dimensions " \
                "like GMS_obj.arr. Got %s." % str(cnfArr.shape)

            if cnfArr._nodata is None:
                cnfArr.nodata = DEF_D.get_outFillZeroSaturated(cnfArr.dtype)[0]
            cnfArr.gt = self.arr.gt
            cnfArr.prj = self.arr.prj
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            cnfArr.bandnames = ['confidence']
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            self._mask_clouds_confidence = cnfArr
        else:
            del self._mask_clouds_confidence

    @mask_clouds_confidence.deleter
    def mask_clouds_confidence(self):
        self._mask_clouds_confidence = None

    @property
    def ac_errors(self):
        """Returns an instance of GeoArray containing error information calculated by the atmospheric correction.

        :return:
        """

        return self._ac_errors  # FIXME should give a warning if None

    @ac_errors.setter
    def ac_errors(self, *geoArr_initArgs):
        if geoArr_initArgs[0] is not None:
            errArr = GeoArray(*geoArr_initArgs)

            if CFG.ac_bandwise_accuracy:
                assert errArr.shape == self.arr.shape, \
                    "The 'ac_errors' GeoArray can only be instanced with an array of the same dimensions like " \
                    "GMS_obj.arr. Got %s." % str(errArr.shape)
            else:
                assert errArr.shape[:2] == self.arr.shape[:2], \
                    "The 'ac_errors' GeoArray can only be instanced with an array of the same X/Y dimensions like " \
                    "GMS_obj.arr. Got %s." % str(errArr.shape)

            if errArr._nodata is None:
                errArr.nodata = DEF_D.get_outFillZeroSaturated(errArr.dtype)[0]
            errArr.gt = self.arr.gt
            errArr.prj = self.arr.prj
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            errArr.bandnames = self.LBA2bandnames(self.LayerBandsAssignment) if errArr.ndim == 3 else ['median']
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            self._ac_errors = errArr
        else:
            del self.ac_errors

    @ac_errors.deleter
    def ac_errors(self):
        self._ac_errors = None

    @property
    def spec_homo_errors(self):
        """Returns an instance of GeoArray containing error information calculated during spectral homogenization.

        :return:
        """

        return self._spec_homo_errors  # FIXME should give a warning if None

    @spec_homo_errors.setter
    def spec_homo_errors(self, *geoArr_initArgs):
        if geoArr_initArgs[0] is not None:
            errArr = GeoArray(*geoArr_initArgs)

            if CFG.spechomo_bandwise_accuracy:
                assert errArr.shape == self.arr.shape, \
                    "The 'spec_homo_errors' GeoArray can only be instanced with an array of the same dimensions like " \
                    "GMS_obj.arr. Got %s." % str(errArr.shape)
            else:
                assert errArr.shape[:2] == self.arr.shape[:2], \
                    "The 'spec_homo_errors' GeoArray can only be instanced with an array of the same X/Y dimensions " \
                    "like GMS_obj.arr. Got %s." % str(errArr.shape)

            if errArr._nodata is None:
                errArr.nodata = DEF_D.get_outFillZeroSaturated(errArr.dtype)[0]
            errArr.gt = self.arr.gt
            errArr.prj = self.arr.prj
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            errArr.bandnames = self.LBA2bandnames(self.LayerBandsAssignment) if errArr.ndim == 3 else ['median']
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            self._spec_homo_errors = errArr
        else:
            del self.spec_homo_errors

    @spec_homo_errors.deleter
    def spec_homo_errors(self):
        self._spec_homo_errors = None

    @property
    def accuracy_layers(self):
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        if not self._accuracy_layers:
            if not self.proc_level.startswith('L2'):
                self.logger.warning('Attempt to get %s accuracy layers failed - they are a Level 2 feature only.'
                                    % self.proc_level)
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            self.logger.info('Generating combined accuracy layers array..')
            try:
                from ..algorithms.L2C_P import AccuracyCube
                self._accuracy_layers = AccuracyCube(self)
            except Exception as e:
                raise RuntimeError('Failed to generate AccuracyCube!', e)
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        return self._accuracy_layers
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    @accuracy_layers.setter
    def accuracy_layers(self, geoArr_initArgs):
        if geoArr_initArgs[0] is not None:
            acc_lay = GeoArray(geoArr_initArgs)
            assert acc_lay.shape[:2] == self.arr.shape[:2],\
                "The 'accuracy_layers' GeoArray can only be instanced with an array of the same dimensions like " \
                "GMS_obj.arr. Got %s." % str(acc_lay.shape)

            if acc_lay._nodata is None:
                acc_lay.nodata = DEF_D.get_outFillZeroSaturated(acc_lay.dtype)[0]
            acc_lay.gt = self.arr.gt
            acc_lay.prj = self.arr.prj

            if not acc_lay.bandnames:
                raise ValueError

            self._accuracy_layers = acc_lay
        else:
            del self._accuracy_layers

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    @accuracy_layers.deleter
    def accuracy_layers(self):
        self._accuracy_layers = None

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    @property
    def accuracy_layers_meta(self):
        if self._accuracy_layers is not None:
            return {'map info': geotransform2mapinfo(self._accuracy_layers.gt, self._accuracy_layers.projection),
                    'coordinate system string': self._accuracy_layers.projection,
                    'bands': self._accuracy_layers.bands,
                    'band names': list(self._accuracy_layers.bandnames),
                    'data ignore value': self._accuracy_layers.nodata}
        else:
            return None

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    @property
    def cloud_masking_algorithm(self):
        if not self._cloud_masking_algorithm:
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            self._cloud_masking_algorithm = CFG.cloud_masking_algorithm[self.satellite]
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        return self._cloud_masking_algorithm

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    @property
    def ac_options(self):
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        # type: () -> dict
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        """
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        Returns the options dictionary needed as input for atmospheric correction. If an empty dictionary is returned,
        atmospheric correction is not yet available for the current sensor and will later be skipped.
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        """
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        if not self._ac_options:
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            path_ac_options = CFG.path_custom_sicor_options or PG.get_path_ac_options(self.GMS_identifier)
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            if path_ac_options and os.path.exists(path_ac_options):
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                # don't validate because options contain pathes that do not exist on another server:
                opt_dict = get_ac_options(path_ac_options, validation=False)
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                # update some file paths depending on the current environment
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                opt_dict['DEM']['fn'] = CFG.path_dem_proc_srtm_90m
                opt_dict['ECMWF']['path_db'] = CFG.path_ECMWF_db
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                opt_dict['S2Image'][
                    'S2_MSI_granule_path'] = None  # only a placeholder -> will always be None for GMS usage
                opt_dict['output'] = []  # outputs are not needed for GMS -> so
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                opt_dict['report']['report_path'] = os.path.join(self.pathGen.get_path_procdata(), '[TYPE]')
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                if 'uncertainties' in opt_dict:
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                    if CFG.ac_estimate_accuracy:
                        opt_dict['uncertainties']['snr_model'] = PG.get_path_snr_model(self.GMS_identifier)
                    else:
                        del opt_dict['uncertainties']  # SICOR will not compute uncertainties if that key is missing
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                # apply custom configuration
                opt_dict["logger"]['level'] = CFG.log_level
                opt_dict["ram"]['upper_limit'] = CFG.ac_max_ram_gb
                opt_dict["ram"]['unit'] = 'GB'
                opt_dict["AC"]['fill_nonclear_areas'] = CFG.ac_fillnonclear_areas
                opt_dict["AC"]['clear_area_labels'] = CFG.ac_clear_area_labels
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                # opt_dict['AC']['n_cores'] = CFG.CPUs if CFG.allow_subMultiprocessing else 1
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                self._ac_options = opt_dict
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            else:
                self.logger.warning('There is no options file available for atmospheric correction. '
                                    'Atmospheric correction must be skipped.')
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        return self._ac_options

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    def get_copied_dict_and_props(self, remove_privates=False):
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        # type: (bool) -> dict
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        """Returns a copy of the current object dictionary including the current values of all object properties."""
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        # loggers must be closed
        self.close_GMS_loggers()
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        # this disables automatic recreation of loggers (otherwise loggers are created by using getattr()):
        self._loggers_disabled = True
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        out_dict = self.__dict__.copy()

        # add properties
        property_names = [p for p in dir(self.__class__) if isinstance(getattr(self.__class__, p), property)]
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        [out_dict.update({propK: copy.copy(getattr(self, propK))}) for propK in property_names]
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        # remove private attributes
        if remove_privates:
            out_dict = {k: v for k, v in out_dict.items() if not k.startswith('_')}

        self._loggers_disabled = False  # enables automatic recreation of loggers

        return out_dict

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    def attributes2dict(self, remove_privates=False):
        # type: (bool) -> dict
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        """Returns a copy of the current object dictionary including the current values of all object properties."""
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        # loggers must be closed
        self.close_GMS_loggers()
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        # this disables automatic recreation of loggers (otherwise loggers are created by using getattr()):
        self._loggers_disabled = True
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        out_dict = self.__dict__.copy()

        # add some selected property values
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        for i in ['GMS_identifier', 'LayerBandsAssignment', 'coreg_needed', 'coreg_info', 'resamp_needed',
                  'dict_LayerOptTherm', 'georef', 'meta_odict']:
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            out_dict[i] = getattr(self, i)
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        # remove private attributes
        if remove_privates:
            out_dict = {k: v for k, v in out_dict.items() if not k.startswith('_')}

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        self._loggers_disabled = False  # enables automatic recreation of loggers
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        return out_dict

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    def _data_downloader(self, sensor, entity_ID):
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        self.logger.info('Data downloader started.')
        success = False
        " > download source code for Landsat here < "
        if not success:
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            self.logger.critical(
                "Download for %s dataset '%s' failed. No further processing possible." % (sensor, entity_ID))
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            raise RuntimeError('Archive download failed.')
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        return success

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    def from_disk(self, tuple_GMS_subset):
        """Fills an already instanced GMS object with data from disk. Excludes array attributes in Python mode.

        :param tuple_GMS_subset:    <tuple> e.g. ('/path/gms_file.gms', ['cube', None])
        """
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        path_GMS_file = tuple_GMS_subset[0]
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        GMSfileDict = INP_R.GMSfile2dict(path_GMS_file)
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        # copy all attributes from GMS file (private attributes are not touched since they are not included in GMS file)
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        self.meta_odict = GMSfileDict['meta_odict']  # set that first in order to make some getters and setters work
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        for key, value in GMSfileDict.items():
            if key in ['GMS_identifier', 'georef', 'dict_LayerOptTherm']:
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                continue  # properties that should better be created on the fly
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            try:
                setattr(self, key, value)
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            except Exception:
                raise AttributeError("Can't set attribute %s." % key)
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        self.acq_datetime = datetime.datetime.strptime(self.acq_datetime, '%Y-%m-%d %H:%M:%S.%f%z')
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        self.arr_shape, self.arr_pos = tuple_GMS_subset[1]

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        self.arr = self.pathGen.get_path_imagedata()
        # self.mask_nodata and self.mask_clouds are auto-synchronized via self.masks (see their getters):
        self.masks = self.pathGen.get_path_maskdata()
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        return copy.copy(self)

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    def from_sensor_subsystems(self, list_GMS_objs):
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        # type: (List[GMS_object]) -> GMS_object
        # TODO convert to classmethod
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        """Merge separate GMS objects belonging to the same scene-ID into ONE GMS object.

        :param list_GMS_objs:   <list> of GMS objects covering the same geographic area but representing different
                                sensor subsystems (e.g. 3 GMS_objects for Sentinel-2 10m/20m/60m bands)
        """

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        # assertions
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        assert len(list_GMS_objs) > 1, "'GMS_object.from_sensor_subsystems()' expects multiple input GMS objects. " \
                                       "Got %d." % len(list_GMS_objs)
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        assert all([is_coord_grid_equal(list_GMS_objs[0].arr.gt, *obj.arr.xygrid_specs) for obj in list_GMS_objs[1:]]),\
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            "The input GMS objects must have the same pixel grid. Received: %s" \
            % np.array([obj.arr.xygrid_specs for obj in list_GMS_objs])
        assert len(list(set([GMS_obj.proc_level for GMS_obj in list_GMS_objs]))) == 1, \
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            "The input GMS objects for GMS_object.from_sensor_subsystems() must have the same processing level."
        subsystems = [GMS_obj.subsystem for GMS_obj in list_GMS_objs]
        assert len(subsystems) == len(list(set(subsystems))), \
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            "The input 'list_GMS_objs' contains duplicates: %s" % subsystems
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        ##################
        # merge logfiles #
        ##################

        # read all logs into DataFrame, sort it by the first column
        [GMS_obj.close_GMS_loggers() for GMS_obj in list_GMS_objs]  # close the loggers of the input objects
        paths_inLogs = [GMS_obj.pathGen.get_path_logfile() for GMS_obj in list_GMS_objs]
        allLogs_df = DataFrame()
        for log in paths_inLogs:
            df = read_csv(log, sep='\n', delimiter=':   ', header=None,
                          engine='python')  # engine suppresses a pandas warning
            allLogs_df = allLogs_df.append(
                df)  # FIXME this will log e.g. atm. corr 3 times for S2A -> use captured streams instead?

        allLogs_df = allLogs_df.sort_values(0)

        # set common metadata, needed for logfile
        self.baseN = list_GMS_objs[0].pathGen.get_baseN(merged_subsystems=True)
        self.path_logfile = list_GMS_objs[0].pathGen.get_path_logfile(merged_subsystems=True)
        self.scene_ID = list_GMS_objs[0].scene_ID

        # write the merged logfile and flush previous logger
        np.savetxt(self.path_logfile, np.array(allLogs_df), delimiter=':   ', fmt="%s")
        self.close_GMS_loggers()

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        # log
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        self.logger.info('Merging the subsystems %s to a single GMS object...'
                         % ', '.join([GMS_obj.subsystem for GMS_obj in list_GMS_objs]))
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        # find the common extent. NOTE: boundsMap is expected in the order [xmin,xmax,ymin,ymax]
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        geoExtents = np.array([GMS_obj.arr.box.boundsMap for GMS_obj in list_GMS_objs])
        common_extent = (min(geoExtents[:, 0]), max(geoExtents[:, 1]), min(geoExtents[:, 2]), max(geoExtents[:, 3]))
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        ##################
        # MERGE METADATA #
        ##################

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        # copy all attributes from the first input GMS file (private attributes are not touched)
        for key, value in list_GMS_objs[0].__dict__.copy().items():
            if key in ['GMS_identifier', 'georef', 'dict_LayerOptTherm']:
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                continue  # properties that should better be created on the fly
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            elif key in ['baseN', 'path_logfile', 'scene_ID', 'subsystem']:
                continue  # either previously set with common values or not needed for merged GMS_object
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            try:
                setattr(self, key, value)
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            except Exception:
                raise AttributeError("Can't set attribute %s." % key)
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        # update LayerBandsAssignment and get full list of output bandnames
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        from .metadata import get_LayerBandsAssignment
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        # use identifier of first input GMS object for getting LBA (respects current proc_level):
        gms_idf = list_GMS_objs[0].GMS_identifier
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        self.LayerBandsAssignment = get_LayerBandsAssignment(gms_idf, return_fullLBA=True)
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        bandnames = ['B%s' % i if len(i) == 2 else 'B0%s' % i for i in self.LayerBandsAssignment]
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        # update layer-dependent metadata with respect to remaining input GMS objects
        self.meta_odict.update({
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            'band names': [('Band %s' % i) for i in self.LayerBandsAssignment],
            'LayerBandsAssignment': self.LayerBandsAssignment,
            'Subsystem': '',
            'PhysUnit': self.meta_odict['PhysUnit'],  # TODO can contain val_optical / val_thermal
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        })
        self.subsystem = ''
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        del self.pathGen  # must be refreshed because subsystem is now ''
        self.close_GMS_loggers()  # must also be refreshed because it depends on pathGen
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        for attrN in ['SolIrradiance', 'CWL', 'FWHM', 'Offsets', 'OffsetsRef', 'Gains', 'GainsRef',
                      'ThermalConstK1', 'ThermalConstK2', 'ViewingAngle_arrProv', 'IncidenceAngle_arrProv']:
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            # combine values from separate subsystems to a single value
            attrDic_fullLBA = {}
            for GMS_obj in list_GMS_objs:
                attr_val = getattr(GMS_obj.MetaObj, attrN)
                if isinstance(attr_val, list):
                    attrDic_fullLBA.update(dict(zip(GMS_obj.LayerBandsAssignment, attr_val)))
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                elif isinstance(attr_val, (dict, collections.OrderedDict)):
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                    attrDic_fullLBA.update(attr_val)
                else:
                    raise ValueError(attrN)

            # update the attribute in self.MetaObj
            if attrDic_fullLBA:
                val2set = [attrDic_fullLBA[bN] for bN in self.LayerBandsAssignment] \
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                    if isinstance(getattr(list_GMS_objs[0].MetaObj, attrN), list) else attrDic_fullLBA
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                setattr(self.MetaObj, attrN, val2set)

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        ####################
        # MERGE ARRAY DATA #
        ####################
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        # overwrite array data with merged arrays, clipped to common_extent and reordered according to FullLayerBandsAss
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        for attrname in ['arr', 'ac_errors', 'dem', 'mask_nodata', 'mask_clouds', 'mask_clouds_confidence', 'masks']:

            # get current attribute of each subsystem without running property getters
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            all_arrays = [getattr(GMS_obj, '_%s' % attrname) for GMS_obj in list_GMS_objs]
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            # get the same geographical extent for each input GMS object
            if len(set(tuple(ext) for ext in geoExtents.tolist())) > 1:
                # in case of different extents
                geoArrs_same_extent = []

                for geoArr in all_arrays:

                    if geoArr is not None:
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                        # FIXME mask_clouds_confidence is no GeoArray until here
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                        # FIXME -> has no nodata value -> calculation throughs warning
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                        geoArr_same_extent = \
                            GeoArray(*geoArr.get_mapPos(
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                                mapBounds=np.array(common_extent)[[0, 2, 1, 3]],  # pass (xmin, ymin, xmax, ymax)
                                mapBounds_prj=geoArr.prj),
                                     bandnames=list(geoArr.bandnames.keys()),
                                     nodata=geoArr.nodata)
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                        geoArrs_same_extent.append(geoArr_same_extent)
                    else:
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                        # e.g. in case of cloud mask that is only appended to the GMS object with the same
                        # spatial resolution)
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                        geoArrs_same_extent.append(None)

            else:
                # skip get_mapPos() if all input GMS objects have the same extent
                geoArrs_same_extent = all_arrays

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            # validate output GeoArrays #
            #############################
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            if len([gA for gA in geoArrs_same_extent if gA is not None]) > 1:
                equal_bounds = all([geoArrs_same_extent[0].box.boundsMap == gA.box.boundsMap
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                                    for gA in geoArrs_same_extent[1:]])
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                equal_epsg = all([geoArrs_same_extent[0].epsg == gA.epsg for gA in geoArrs_same_extent[1:]])
                equal_xydims = all([geoArrs_same_extent[0].shape[:2] == gA.shape[:2] for gA in geoArrs_same_extent[1:]])
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                if not all([equal_bounds, equal_epsg, equal_xydims]):
                    raise RuntimeError('Something went wrong during getting the same geographical extent for all the '
                                       'input GMS objects. The extents, projections or pixel dimensions of the '
                                       'calculated input GMS objects are not equal.')

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            # set output arrays #
            #####################
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            # handle those arrays where bands have to be reordered according to FullLayerBandsAssignment
            if attrname in ['arr', 'ac_errors'] and list(set(geoArrs_same_extent)) != [None]:
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                # check that each desired band name for the current attribute is provided by one of the input
                # GMS objects
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                available_bandNs = list(chain.from_iterable([list(gA.bandnames) for gA in geoArrs_same_extent]))
                for bN in bandnames:
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                    if bN not in available_bandNs:
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                        raise ValueError("The given input GMS objects (subsystems) do not provide a bandname '%s' for "
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                                         "the attribute '%s'. Available band names amongst all input GMS objects are: "
                                         "%s" % (bN, attrname, str(available_bandNs)))
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                # merge arrays
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                def get_band(bandN):
                    return [gA[bandN] for gA in geoArrs_same_extent if gA and bandN in gA.bandnames][0]
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                full_geoArr = GeoArray(np.dstack((get_band(bandN) for bandN in bandnames)),
                                       geoArrs_same_extent[0].gt, geoArrs_same_extent[0].prj,
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                                       bandnames=bandnames,
                                       nodata=geoArrs_same_extent[0].nodata)
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                setattr(self, attrname, full_geoArr)

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            # handle the remaining arrays
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            else:
                # masks, dem, mask_nodata, mask_clouds, mask_clouds_confidence
                if attrname == 'dem':
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                    # use the DEM of the first input object
                    # (if the grid is the same, the DEMs should be the same anyway)
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                    self.dem = geoArrs_same_extent[0]
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                elif attrname == 'mask_nodata':
                    # must not be merged -> self.arr is already merged, so just recalculate it (np.all)
                    self.mask_nodata = self.calc_mask_nodata(overwrite=True)
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                elif attrname == 'mask_clouds':
                    # possibly only present in ONE subsystem (set by atm. Corr.)
                    mask_clouds = [msk for msk in geoArrs_same_extent if msk is not None]
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                    if len(mask_clouds) > 1:
                        raise ValueError('Expected mask clouds in only one subsystem. Got %s.' % len(mask_clouds))
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                    self.mask_clouds = mask_clouds[0] if mask_clouds else None
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                elif attrname == 'mask_clouds_confidence':
                    # possibly only present in ONE subsystem (set by atm. Corr.)
                    mask_clouds_conf = [msk for msk in geoArrs_same_extent if msk is not None]
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                    if len(mask_clouds_conf) > 1:
                        raise ValueError(
                            'Expected mask_clouds_conf in only one subsystem. Got %s.' % len(mask_clouds_conf))
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                    self.mask_clouds_confidence = mask_clouds_conf[0] if mask_clouds_conf else None
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                elif attrname == 'masks':
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                    # self.mask_nodata and self.mask_clouds will already be set here -> so just recreate it from there
                    self.masks = None

        # recreate self.masks
        self.build_combined_masks_array()

        # update array-dependent metadata
        self.meta_odict.update({
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            'samples': self.arr.cols, 'lines': self.arr.rows, 'bands': self.arr.bands,
            'map info': geotransform2mapinfo(self.arr.gt, self.arr.prj), 'coordinate system string': self.arr.prj, })
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        # set shape of full array
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        self.shape_fullArr = self.arr.shape
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        return copy.copy(self)

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    def from_tiles(self, list_GMS_tiles):
        # type: (list) -> self
        """Merge separate GMS objects with different spatial coverage but belonging to the same scene-ID to ONE GMS object.

        :param list_GMS_tiles: <list> of GMS objects that have been created by cut_GMS_obj_into_blocks()
        """
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        if 'IMapUnorderedIterator' in str(type(list_GMS_tiles)):
            list_GMS_tiles = list(list_GMS_tiles)

        # copy all attributes except of array attributes
        tile1 = list_GMS_tiles[0]
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        [setattr(self, i, getattr(tile1, i)) for i in tile1.__dict__
         if not callable(getattr(tile1, i)) and not isinstance(getattr(tile1, i), (np.ndarray, GeoArray))]
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        # MERGE ARRAY-ATTRIBUTES
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        list_arraynames = [i for i in tile1.__dict__ if not callable(getattr(tile1, i)) and
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                           isinstance(getattr(tile1, i), (np.ndarray, GeoArray))]
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        list_arraynames = ['_arr'] + [i for i in list_arraynames if
                                      i != '_arr']  # list must start with _arr, otherwise setters will not work
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        for arrname in list_arraynames:
            samplearray = getattr(tile1, arrname)
            assert isinstance(samplearray, (np.ndarray, GeoArray)), \
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                'Received a %s object for attribute %s. Expected a numpy array or an instance of GeoArray.' \
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                % (type(samplearray), arrname)
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            is_3d = samplearray.ndim == 3
            bands = (samplearray.shape[2],) if is_3d else ()  # dynamic -> works for arr, cld_arr,...
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            target_shape = tuple(self.shape_fullArr[:2]) + bands
            target_dtype = samplearray.dtype
            merged_array = self._numba_array_merger(list_GMS_tiles, arrname, target_shape, target_dtype)

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            setattr(self, arrname if not arrname.startswith('_') else arrname[1:],
                    merged_array)  # use setters if possible
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            # NOTE: this asserts that each attribute starting with '_' has also a property with a setter!

        # UPDATE ARRAY-DEPENDENT ATTRIBUTES
        self.arr_shape = 'cube'
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        self.arr_pos = None
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        # update MetaObj attributes
        self.meta_odict.update({
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            'samples': self.arr.cols, 'lines': self.arr.rows, 'bands': self.arr.bands,
            'map info': geotransform2mapinfo(self.arr.gt, self.arr.prj), 'coordinate system string': self.arr.prj, })
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        # calculate data_corners_imXY (mask_nodata is always an array here because get_mapPos always returns an array)
        corners_imYX = calc_FullDataset_corner_positions(
            self.mask_nodata, assert_four_corners=False, algorithm='shapely')
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        self.trueDataCornerPos = [(YX[1], YX[0]) for YX in corners_imYX]  # [UL, UR, LL, LR]
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        # calculate trueDataCornerLonLat
        data_corners_LatLon = pixelToLatLon(self.trueDataCornerPos, geotransform=self.arr.gt, projection=self.arr.prj)
        self.trueDataCornerLonLat = [(YX[1], YX[0]) for YX in data_corners_LatLon]

        # calculate trueDataCornerUTM
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        data_corners_utmYX = pixelToMapYX(self.trueDataCornerPos, geotransform=self.arr.gt,
                                          projection=self.arr.prj)  # FIXME asserts gt in UTM coordinates
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        self.trueDataCornerUTM = [(YX[1], YX[0]) for YX in data_corners_utmYX]

        return copy.copy(self)

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    @staticmethod
    @jit
    def _numba_array_merger(list_GMS_tiles, arrname2merge, target_shape, target_dtype):
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        # type: (list, str, tuple, np.dtype) -> np.ndarray
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        """
        private function, e.g. called by merge_GMS_tiles_to_GMS_obj() in order to fasten array merging

        :param list_GMS_tiles:
        :param arrname2merge:
        :param target_shape:
        :param target_dtype:
        :return:
        """
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        out_arr = np.empty(target_shape, dtype=target_dtype)
        for idx, tile in enumerate(list_GMS_tiles):
            rowStart, rowEnd = tile.arr_pos[0]
            colStart, colEnd = tile.arr_pos[1]
            out_arr[rowStart:rowEnd + 1, colStart:colEnd + 1] = getattr(tile, arrname2merge)
        return out_arr

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    def log_for_fullArr_or_firstTile(self, log_msg, subset=None):
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        """Send a message to the logger only if full array or the first tile is currently processed.
        This function can be called when processing any tile but log message will only be sent from first tile.

        :param log_msg:  the log message to be logged
        :param subset:   subset argument as sent to e.g. DN2TOARadRefTemp that indicates which tile is to be processed.
                         Not needed if self.arr_pos is not None.
        """
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        if subset is None and \
            (self.arr_shape == 'cube' or self.arr_pos is None or [self.arr_pos[0][0], self.arr_pos[1][0]] == [0, 0]) or\
                subset == ['cube', None] or (subset and [subset[1][0][0], subset[1][1][0]] == [0, 0]) or \
                hasattr(self, 'logAtThisTile') and getattr(self, 'logAtThisTile'):  # cube or 1st tile
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            self.logger.info(log_msg)
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        else:
            pass

    def apply_nodata_mask_to_ObjAttr(self, attrname, out_nodata_val=None):
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        # type: (str,int) -> None
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        """Applies self.mask_nodata to the specified array attribute by setting all values where mask_nodata is 0 to the
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        given nodata value.

        :param attrname:         The attribute to apply the nodata mask to. Must be an array attribute or
                                 a string path to a previously saved ENVI-file.
        :param out_nodata_val:   set the values of the given attribute to this value.
        """

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        assert hasattr(self, attrname)
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        if getattr(self, attrname) is not None:
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            if isinstance(getattr(self, attrname), str):
                update_spec_vals = True if attrname == 'arr' else False
                self.apply_nodata_mask_to_saved_ENVIfile(getattr(self, attrname), out_nodata_val, update_spec_vals)
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            else:
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                assert isinstance(getattr(self, attrname), (np.ndarray, GeoArray)), \
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                    'L1A_obj.%s must be a numpy array or an instance of GeoArray. Got type %s.' \
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                    % (attrname, type(getattr(self, attrname)))
                assert hasattr(self, 'mask_nodata') and self.mask_nodata is not None
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                self.log_for_fullArr_or_firstTile('Applying nodata mask to L1A_object.%s...' % attrname)
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                nodata_val = out_nodata_val if out_nodata_val else \
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                    DEF_D.get_outFillZeroSaturated(getattr(self, attrname).dtype)[0]
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                getattr(self, attrname)[self.mask_nodata.astype(np.int8) == 0] = nodata_val
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                if attrname == 'arr':
                    self.MetaObj.spec_vals['fill'] = nodata_val
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    def build_combined_masks_array(self):
        # type: () -> dict
        """Generates self.masks attribute (unsigned integer 8bit) from by concatenating all masks included in GMS obj.
        The corresponding metadata is assigned to L1A_obj.masks_meta. Empty mask attributes are skipped."""

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        arrays2combine = [aN for aN in ['mask_nodata', 'mask_clouds']
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                          if hasattr(self, aN) and isinstance(getattr(self, aN), (GeoArray, np.ndarray))]
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        if arrays2combine:
            self.log_for_fullArr_or_firstTile('Combining masks...')
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            def get_data(arrName): return getattr(self, arrName).astype(np.uint8)[:, :, None]
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            for aN in arrays2combine:
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                if False in np.equal(getattr(self, aN), getattr(self, aN).astype(np.uint8)):
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                    warnings.warn('Some pixel values of attribute %s changed during data type '
                                  'conversion within build_combined_masks_array().')

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            # set self.masks
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            self.masks = get_data(arrays2combine[0]) if len(arrays2combine) == 1 else \
                np.concatenate([get_data(aN) for aN in arrays2combine], axis=2)
            self.masks.bandnames = arrays2combine  # set band names of GeoArray (allows later indexing by band name)
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            # set self.masks_meta
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            nodataVal = DEF_D.get_outFillZeroSaturated(self.masks.dtype)[0]
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            self.masks_meta = {'map info': self.MetaObj.map_info, 'coordinate system string': self.MetaObj.projection,
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                               'bands': len(arrays2combine), 'band names': arrays2combine,
                               'data ignore value': nodataVal}
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            return {'desc': 'masks', 'row_start': 0, 'row_end': self.shape_fullArr[0],
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                    'col_start': 0, 'col_end': self.shape_fullArr[1], 'data': self.masks}  # usually not needed
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    def apply_nodata_mask_to_saved_ENVIfile(self, path_saved_ENVIhdr, custom_nodata_val=None, update_spec_vals=False):
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        # type: (str,int,bool) -> None
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        """Applies self.mask_nodata to a saved ENVI file with the same X/Y dimensions like self.mask_nodata by setting all
         values where mask_nodata is 0 to the given nodata value.
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        :param path_saved_ENVIhdr:  <str> The path of the ENVI file to apply the nodata mask to.
        :param custom_nodata_val:   <int> set the values of the given attribute to this value.
        :param update_spec_vals:    <bool> whether to update self.MetaObj.spec_vals['fill']
        """

        self.log_for_fullArr_or_firstTile('Applying nodata mask to saved ENVI file...')
        assert os.path.isfile(path_saved_ENVIhdr)
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        assert hasattr(self, 'mask_nodata') and self.mask_nodata is not None
        if not path_saved_ENVIhdr.endswith('.hdr') and os.path.isfile(os.path.splitext(path_saved_ENVIhdr)[0] + '.hdr'):
            path_saved_ENVIhdr = os.path.splitext(path_saved_ENVIhdr)[0] + '.hdr'
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        if custom_nodata_val is None:
1020
            dtype_IDL = int(INP_R.read_ENVIhdr_to_dict(path_saved_ENVIhdr)['data type'])
1021
            nodata_val = DEF_D.get_outFillZeroSaturated(DEF_D.dtype_lib_IDL_Python[dtype_IDL])[0]
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        else:
            nodata_val = custom_nodata_val
1024
        FileObj = spectral.open_image(path_saved_ENVIhdr)
1025
        File_memmap = FileObj.open_memmap(writable=True)
1026
        File_memmap[self.mask_nodata == 0] = nodata_val
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        if update_spec_vals:
            self.MetaObj.spec_vals['fill'] = nodata_val