CoReg.py 77.5 KB
Newer Older
1
2
# -*- coding: utf-8 -*-

3
4
# AROSICS - Automated and Robust Open-Source Image Co-Registration Software
#
5
# Copyright (C) 2017-2020  Daniel Scheffler (GFZ Potsdam, daniel.scheffler@gfz-potsdam.de)
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
#
# 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 Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
#
# 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/>.

24
25
26
import os
import time
import warnings
27
from copy import copy
28
from typing import Iterable, Union, Tuple  # noqa F401
29
30

# custom
31
32
33
34
try:
    import gdal
except ImportError:
    from osgeo import gdal
35
import numpy as np
36

37
38
39
try:
    import pyfftw
except ImportError:
40
    pyfftw = None
41
from shapely.geometry import Point, Polygon
42
from skimage.exposure import rescale_intensity
43
44

# internal modules
45
from .DeShifter import DESHIFTER, _dict_rspAlg_rsp_Int
46
47
from . import geometry as GEO
from . import plotting as PLT
48

49
from geoarray import GeoArray
50
from py_tools_ds.convenience.object_oriented import alias_property
51
from py_tools_ds.geo.coord_calc import get_corner_coordinates
52
53
54
from py_tools_ds.geo.vector.topology import get_overlap_polygon, get_smallest_boxImYX_that_contains_boxMapYX
from py_tools_ds.geo.projection import prj_equal, get_proj4info
from py_tools_ds.geo.vector.geometry import boxObj, round_shapelyPoly_coords
55
from py_tools_ds.geo.coord_grid import move_shapelyPoly_to_image_grid, is_coord_grid_equal
56
from py_tools_ds.geo.coord_trafo import reproject_shapelyGeometry, mapXY2imXY, imXY2mapXY
57
58
59
from py_tools_ds.geo.raster.reproject import warp_ndarray
from py_tools_ds.geo.map_info import geotransform2mapinfo
from py_tools_ds.similarity.raster import calc_ssim
60
from py_tools_ds.io.vector.writer import write_shp
61

62
__author__ = 'Daniel Scheffler'
63
64


65
class GeoArray_CoReg(GeoArray):
66
    def __init__(self, CoReg_params, imID):
67
68
        # type: (dict, str) -> None

69
        assert imID in ['ref', 'shift']
Daniel Scheffler's avatar
CoReg:    
Daniel Scheffler committed
70

71
72
        # run GeoArray init
        path_or_geoArr = CoReg_params['im_ref'] if imID == 'ref' else CoReg_params['im_tgt']
73
74
75
        nodata = CoReg_params['nodata'][0 if imID == 'ref' else 1]
        progress = CoReg_params['progress']
        q = CoReg_params['q'] if not CoReg_params['v'] else False
76

77
        super(GeoArray_CoReg, self).__init__(path_or_geoArr, nodata=nodata, progress=progress, q=q)
78

79
        self.imID = imID
80
        self.imName = 'reference image' if imID == 'ref' else 'image to be shifted'
81
        self.v = CoReg_params['v']
82
83

        assert isinstance(self, GeoArray), \
84
            'Something went wrong with the creation of GeoArray instance for the %s. The created ' \
85
            'instance does not seem to belong to the GeoArray class. If you are working in Jupyter Notebook, reset ' \
86
            'the kernel and try again.' % self.imName
87

88
        # set title to be used in plots
89
        self.title = os.path.basename(self.filePath) if self.filePath else self.imName
90
91

        # validate params
92
93
        # assert self.prj, 'The %s has no projection.' % self.imName # TODO
        # assert not re.search('LOCAL_CS', self.prj), 'The %s is not georeferenced.' % self.imName # TODO
94
95
96
        assert self.gt, 'The %s has no map information.' % self.imName

        # set band4match
97
98
99
100
101
        self.band4match = (CoReg_params['r_b4match'] if imID == 'ref' else CoReg_params['s_b4match']) - 1
        assert self.bands >= self.band4match + 1 >= 1, \
            "The %s has %s %s. So its band number to match must be %s%s. Got %s." \
            % (self.imName, self.bands, 'bands' if self.bands > 1 else
               'band', 'between 1 and ' if self.bands > 1 else '', self.bands, self.band4match)
102

103
104
        # set footprint_poly
        given_footprint_poly = CoReg_params['footprint_poly_%s' % ('ref' if imID == 'ref' else 'tgt')]
105
        given_corner_coord = CoReg_params['data_corners_%s' % ('ref' if imID == 'ref' else 'tgt')]
106
107

        if given_footprint_poly:
108
            self.footprint_poly = given_footprint_poly
109
        elif given_corner_coord is not None:
110
            self.footprint_poly = Polygon(given_corner_coord)
111
112
        elif not CoReg_params['calc_corners']:
            # use the image extent
113
            self.footprint_poly = Polygon(get_corner_coordinates(gt=self.gt, cols=self.cols, rows=self.rows))
114
        else:
115
116
117
            # footprint_poly is calculated automatically by GeoArray
            if not CoReg_params['q']:
                print('Calculating actual data corner coordinates for %s...' % self.imName)
118

119
            self.calc_mask_nodata(fromBand=self.band4match)  # this avoids that all bands have to be read
120

121
122
123
124
        # validate footprint poly
        if not self.footprint_poly.is_valid:
            self.footprint_poly = self.footprint_poly.buffer(0)

125
        if not self.q:
Daniel Scheffler's avatar
Daniel Scheffler committed
126
            print('Bounding box of calculated footprint for %s:\n\t%s' % (self.imName, self.footprint_poly.bounds))
127

128
129
130
        # add bad data mask
        given_mask = CoReg_params['mask_baddata_%s' % ('ref' if imID == 'ref' else 'tgt')]
        if given_mask:
131
            self.mask_baddata = given_mask  # runs GeoArray.mask_baddata.setter -> sets it to BadDataMask()
Daniel Scheffler's avatar
Daniel Scheffler committed
132

133
    poly = alias_property('footprint_poly')  # ensures that self.poly is updated if self.footprint_poly is updated
Daniel Scheffler's avatar
Daniel Scheffler committed
134
135


136
class COREG(object):
Daniel Scheffler's avatar
Daniel Scheffler committed
137
138
139
140
141
142
143
    """The COREG class detects and corrects global X/Y shifts between a target and refernce image.

    Geometric shifts are calculated at a specific (adjustable) image position. Correction performs a global shifting
    in X- or Y direction.

    See help(COREG) for documentation!
    """
144

145
    def __init__(self, im_ref, im_tgt, path_out=None, fmt_out='ENVI', out_crea_options=None, r_b4match=1, s_b4match=1,
146
                 wp=(None, None), ws=(256, 256), max_iter=5, max_shift=5, align_grids=False, match_gsd=False,
147
148
                 out_gsd=None, target_xyGrid=None, resamp_alg_deshift='cubic', resamp_alg_calc='cubic',
                 footprint_poly_ref=None, footprint_poly_tgt=None, data_corners_ref=None, data_corners_tgt=None,
149
                 nodata=(None, None), calc_corners=True, binary_ws=True, mask_baddata_ref=None, mask_baddata_tgt=None,
Daniel Scheffler's avatar
Daniel Scheffler committed
150
                 CPUs=None, force_quadratic_win=True, progress=True, v=False, path_verbose_out=None, q=False,
151
                 ignore_errors=False):
Daniel Scheffler's avatar
Daniel Scheffler committed
152
        """Get an instance of the COREG class.
153

154
155
156
157
        :param im_ref(str, GeoArray):   source path (any GDAL compatible image format is supported) or GeoArray instance
                                        of reference image
        :param im_tgt(str, GeoArray):   source path (any GDAL compatible image format is supported) or GeoArray instance
                                        of image to be shifted
158
        :param path_out(str):           target path of the coregistered image
159
160
161
                                            - if None (default), the method correct_shifts() does not write to disk
                                            - if 'auto': /dir/of/im1/<im1>__shifted_to__<im0>.bsq
        :param fmt_out(str):            raster file format for output file. ignored if path_out is None. can be any GDAL
162
                                        compatible raster file format (e.g. 'ENVI', 'GTIFF'; default: ENVI). Refer to
163
                                        http://www.gdal.org/formats_list.html to get a full list of supported formats.
164
165
        :param out_crea_options(list):  GDAL creation options for the output image,
                                        e.g. ["QUALITY=80", "REVERSIBLE=YES", "WRITE_METADATA=YES"]
166
167
168
169
        :param r_b4match(int):          band of reference image to be used for matching (starts with 1; default: 1)
        :param s_b4match(int):          band of shift image to be used for matching (starts with 1; default: 1)
        :param wp(tuple):               custom matching window position as map values in the same projection like the
                                        reference image (default: central position of image overlap)
Daniel Scheffler's avatar
Daniel Scheffler committed
170
        :param ws(tuple):               custom matching window size [pixels] (default: (256,256))
171
172
        :param max_iter(int):           maximum number of iterations for matching (default: 5)
        :param max_shift(int):          maximum shift distance in reference image pixel units (default: 5 px)
173
174
        :param align_grids(bool):       align the coordinate grids of the image to be and the reference image
                                        (default: 0)
175
176
177
        :param match_gsd(bool):         match the output pixel size to pixel size of the reference image (default: 0)
        :param out_gsd(tuple):          xgsd ygsd: set the output pixel size in map units
                                        (default: original pixel size of the image to be shifted)
178
179
        :param target_xyGrid(list):     a list with a target x-grid and a target y-grid like [[15,45], [15,45]]
                                        This overrides 'out_gsd', 'align_grids' and 'match_gsd'.
180
        :param resamp_alg_deshift(str)  the resampling algorithm to be used for shift correction (if neccessary)
181
182
                                        valid algorithms: nearest, bilinear, cubic, cubic_spline, lanczos, average,
                                                          mode, max, min, med, q1, q3
183
184
185
                                        default: cubic
        :param resamp_alg_calc(str)     the resampling algorithm to be used for all warping processes during calculation
                                        of spatial shifts
186
187
                                        (valid algorithms: nearest, bilinear, cubic, cubic_spline, lanczos, average,
                                                           mode, max, min, med, q1, q3)
188
                                        default: cubic (highly recommended)
189
190
        :param footprint_poly_ref(str): footprint polygon of the reference image (WKT string or
                                        shapely.geometry.Polygon),
191
192
                                        e.g. 'POLYGON ((299999 6000000, 299999 5890200, 409799 5890200, 409799 6000000,
                                                        299999 6000000))'
193
194
        :param footprint_poly_tgt(str): footprint polygon of the image to be shifted (WKT string or
                                        shapely.geometry.Polygon)
195
196
197
198
199
200
                                        e.g. 'POLYGON ((299999 6000000, 299999 5890200, 409799 5890200, 409799 6000000,
                                                        299999 6000000))'
        :param data_corners_ref(list):  map coordinates of data corners within reference image.
                                        ignored if footprint_poly_ref is given.
        :param data_corners_tgt(list):  map coordinates of data corners within image to be shifted.
                                        ignored if footprint_poly_tgt is given.
201
202
203
204
205
        :param nodata(tuple):           no data values for reference image and image to be shifted
        :param calc_corners(bool):      calculate true positions of the dataset corners in order to get a useful
                                        matching window position within the actual image overlap
                                        (default: 1; deactivated if '-cor0' and '-cor1' are given
        :param binary_ws(bool):         use binary X/Y dimensions for the matching window (default: 1)
206
207
208
209
210
211
212
213
214
215
216
217
        :param mask_baddata_ref(str, GeoArray): path to a 2D boolean mask file (or an instance of GeoArray) for the
                                                reference image where all bad data pixels (e.g. clouds) are marked with
                                                True and the remaining pixels with False. Must have the same geographic
                                                extent and projection like 'im_ref'. The mask is used to check if the
                                                chosen matching window position is valid in the sense of useful data.
                                                Otherwise this window position is rejected.
        :param mask_baddata_tgt(str, GeoArray): path to a 2D boolean mask file (or an instance of GeoArray) for the
                                                image to be shifted where all bad data pixels (e.g. clouds) are marked
                                                with True and the remaining pixels with False. Must have the same
                                                geographic extent and projection like 'im_ref'. The mask is used to
                                                check if the chosen matching window position is valid in the sense of
                                                useful data. Otherwise this window position is rejected.
Daniel Scheffler's avatar
Daniel Scheffler committed
218
219
        :param CPUs(int):               number of CPUs to use during pixel grid equalization
                                        (default: None, which means 'all CPUs available')
220
        :param force_quadratic_win(bool):   force a quadratic matching window (default: 1)
221
        :param progress(bool):          show progress bars (default: True)
222
        :param v(bool):                 verbose mode (default: False)
223
224
        :param path_verbose_out(str):   an optional output directory for intermediate results
                                        (if not given, no intermediate results are written to disk)
225
226
        :param q(bool):                 quiet mode (default: False)
        :param ignore_errors(bool):     Useful for batch processing. (default: False)
227
228
229
                                        In case of error COREG.success == False and COREG.x_shift_px/COREG.y_shift_px
                                        is None
        """
230
        self.params = dict([x for x in locals().items() if x[0] != "self"])
231

232
        # assertions
233
        assert gdal.GetDriverByName(fmt_out), "'%s' is not a supported GDAL driver." % fmt_out
234
235
236
237
238
239
        if match_gsd and out_gsd:
            warnings.warn("'-out_gsd' is ignored because '-match_gsd' is set.\n")
        if out_gsd:
            assert isinstance(out_gsd, list) and len(out_gsd) == 2, 'out_gsd must be a list with two values.'
        if data_corners_ref and not isinstance(data_corners_ref[0],
                                               list):  # group if not [[x,y],[x,y]..] but [x,y,x,y,]
240
            data_corners_ref = [data_corners_ref[i:i + 2] for i in range(0, len(data_corners_ref), 2)]
241
        if data_corners_tgt and not isinstance(data_corners_tgt[0], list):  # group if not [[x,y],[x,y]..]
242
            data_corners_tgt = [data_corners_tgt[i:i + 2] for i in range(0, len(data_corners_tgt), 2)]
243
        if nodata:
244
245
            assert isinstance(nodata, Iterable) and len(nodata) == 2, \
                "'nodata' must be an iterable with two values. Got %s with length %s." % (type(nodata), len(nodata))
246
        for rspAlg in [resamp_alg_deshift, resamp_alg_calc]:
247
            assert rspAlg in _dict_rspAlg_rsp_Int.keys(), "'%s' is not a supported resampling algorithm." % rspAlg
248
        if resamp_alg_calc in ['average', 5] and (v or not q):
249
            warnings.warn("The resampling algorithm 'average' causes sinus-shaped patterns in fft images that will "
250
251
                          "affect the precision of the calculated spatial shifts! It is highly recommended to "
                          "choose another resampling algorithm.")
252

253
254
255
256
257
258
259
260
261
262
263
264
        self.path_out = path_out  # updated by self.set_outpathes
        self.fmt_out = fmt_out
        self.out_creaOpt = out_crea_options
        self.win_pos_XY = wp  # updated by self.get_opt_winpos_winsize()
        self.win_size_XY = ws  # updated by self.get_opt_winpos_winsize()
        self.max_iter = max_iter
        self.max_shift = max_shift
        self.align_grids = align_grids
        self.match_gsd = match_gsd
        self.out_gsd = out_gsd
        self.target_xyGrid = target_xyGrid
        self.rspAlg_DS = resamp_alg_deshift \
265
            if isinstance(resamp_alg_deshift, str) else _dict_rspAlg_rsp_Int[resamp_alg_deshift]
266
        self.rspAlg_calc = resamp_alg_calc \
267
            if isinstance(resamp_alg_calc, str) else _dict_rspAlg_rsp_Int[resamp_alg_calc]
268
269
270
        self.calc_corners = calc_corners
        self.CPUs = CPUs
        self.bin_ws = binary_ws
271
        self.force_quadratic_win = force_quadratic_win
272
273
274
275
276
277
278
        self.v = v
        self.path_verbose_out = path_verbose_out
        self.q = q if not v else False  # overridden by v
        self.progress = progress if not q else False  # overridden by q

        self.ignErr = ignore_errors
        self.max_win_sz_changes = 3  # TODO: änderung der window size, falls nach max_iter kein valider match gefunden
279
280
281
282
283
284
        self.ref = None  # type: GeoArray_CoReg # set by self.get_image_params
        self.shift = None  # type: GeoArray_CoReg # set by self.get_image_params
        self.matchBox = None  # type: boxObj # set by self.get_clip_window_properties()
        self.otherBox = None  # type: boxObj # set by self.get_clip_window_properties()
        self.matchWin = None  # type: GeoArray # set by self._get_image_windows_to_match()
        self.otherWin = None  # type: GeoArray # set by self._get_image_windows_to_match()
285
286
287
        self.overlap_poly = None  # set by self._get_overlap_properties()
        self.overlap_percentage = None  # set by self._get_overlap_properties()
        self.overlap_area = None  # set by self._get_overlap_properties()
288
289
        self.imfft_xgsd = None  # set by self.get_clip_window_properties()
        self.imfft_ygsd = None  # set by self.get_clip_window_properties()
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
        self.fftw_works = None  # set by self._calc_shifted_cross_power_spectrum()
        self.fftw_win_size_YX = None  # set by calc_shifted_cross_power_spectrum()

        self.x_shift_px = None  # always in shift image units (image coords) # set by calculate_spatial_shifts()
        self.y_shift_px = None  # always in shift image units (image coords) # set by calculate_spatial_shifts()
        self.x_shift_map = None  # set by self.get_updated_map_info()
        self.y_shift_map = None  # set by self.get_updated_map_info()
        self.vec_length_map = None
        self.vec_angle_deg = None
        self.updated_map_info = None  # set by self.get_updated_map_info()
        self.ssim_orig = None  # set by self._validate_ssim_improvement()
        self.ssim_deshifted = None  # set by self._validate_ssim_improvement()
        self._ssim_improved = None  # private attribute to be filled by self.ssim_improved
        self.shift_reliability = None  # set by self.calculate_spatial_shifts()

        self.tracked_errors = []  # expanded each time an error occurs
        self.success = None  # default
        self.deshift_results = None  # set by self.correct_shifts()
308
309
310
311

        gdal.AllRegister()
        self._get_image_params()
        self._set_outpathes(im_ref, im_tgt)
312
        self.grid2use = 'ref' if self.shift.xgsd <= self.ref.xgsd else 'shift'
313
314
        if self.v:
            print('resolutions: ', self.ref.xgsd, self.shift.xgsd)
315

316
        self._get_overlap_properties()
317
318

        if self.v and self.path_verbose_out:
319
320
321
            write_shp(os.path.join(self.path_verbose_out, 'poly_imref.shp'), self.ref.poly, self.ref.prj)
            write_shp(os.path.join(self.path_verbose_out, 'poly_im2shift.shp'), self.shift.poly, self.shift.prj)
            write_shp(os.path.join(self.path_verbose_out, 'overlap_poly.shp'), self.overlap_poly, self.ref.prj)
322

323
324
        # FIXME: transform_mapPt1_to_mapPt2(im2shift_center_map, ds_imref.GetProjection(), ds_im2shift.GetProjection())
        # FIXME später basteln für den fall, dass projektionen nicht gleich sind
325
326
327

        # get_clip_window_properties
        self._get_opt_winpos_winsize()
328
329
330
        if not self.q:
            print('Matching window position (X,Y): %s/%s' % (self.win_pos_XY[0], self.win_pos_XY[1]))
        self._get_clip_window_properties()  # sets self.matchBox, self.otherBox and much more
331

332
        if self.v and self.path_verbose_out and self.matchBox.mapPoly and self.success is not False:
333
334
            write_shp(os.path.join(self.path_verbose_out, 'poly_matchWin.shp'),
                      self.matchBox.mapPoly, self.matchBox.prj)
335

336
337
        self.success = False if self.success is False or not self.matchBox.boxMapYX else None
        self._coreg_info = None  # private attribute to be filled by self.coreg_info property
338

339
    def _handle_error(self, error, warn=False, warnMsg=None):
Daniel Scheffler's avatar
Daniel Scheffler committed
340
341
342
        """Append the given error to self.tracked_errors.

        This sets self.success to False and raises the error in case self.ignore_errors = True.
343
344
345
346
347
348
349
350
351
352
353
354
355

        :param error:   instance of an error
        :param warn:    whether to give a warning in case error would be ignored otherwise
        :param warnMsg: a custom message for the warning
        :return:
        """
        warn = warn or warnMsg is not None or self.v

        self.tracked_errors.append(error)
        self.success = False

        if self.ignErr and warn:
            warnMsg = repr(error) if not warnMsg else warnMsg
356
            print('\nWARNING: ' + warnMsg)
357
358
359
360

        if not self.ignErr:
            raise error

361
    def _set_outpathes(self, im_ref, im_tgt):
362
        assert isinstance(im_ref, (GeoArray, str)) and isinstance(im_tgt, (GeoArray, str)), \
363
            'COREG._set_outpathes() expects two file pathes (string) or two instances of the ' \
364
            'GeoArray class. Received %s and %s.' % (type(im_ref), type(im_tgt))
365

366
367
368
369
370
        def get_baseN(path):
            return os.path.splitext(os.path.basename(path))[0]

        # get input paths
        def get_input_path(im):
Daniel Scheffler's avatar
Daniel Scheffler committed
371
372
373
374
375
376
377
378
            path = im.filePath if isinstance(im, GeoArray) else im

            if isinstance(im, GeoArray) and im.filePath is None and self.path_out == 'auto':
                raise ValueError(self.path_out, "The output path must be explicitly set in case the input "
                                                "reference or target image is in-memory (without a reference to a "
                                                "physical file on disk). Received path_out='%s'." % self.path_out)

            return path
379

Daniel Scheffler's avatar
Daniel Scheffler committed
380
381
        path_im_ref = get_input_path(im_ref)
        path_im_tgt = get_input_path(im_tgt)
382

383
        if self.path_out:  # this also applies to self.path_out='auto'
384
385
386
387

            if self.path_out == 'auto':
                dir_out, fName_out = os.path.dirname(path_im_tgt), ''
            else:
388
                dir_out, fName_out = os.path.split(self.path_out)
389
390
391
392
393
394
395
396
397
398
399
400
401
402

            if dir_out and fName_out:
                # a valid output path is given => do nothing
                pass

            else:
                # automatically create an output directory and filename if not given
                if not dir_out:
                    if not path_im_ref:
                        dir_out = os.path.abspath(os.path.curdir)
                    else:
                        dir_out = os.path.dirname(path_im_ref)

                if not fName_out:
403
404
405
406
407
                    ext = 'bsq' if self.fmt_out == 'ENVI' else \
                        gdal.GetDriverByName(self.fmt_out).GetMetadataItem(gdal.DMD_EXTENSION)
                    fName_out = fName_out if fName_out not in ['.', ''] else \
                        '%s__shifted_to__%s' % (get_baseN(path_im_tgt), get_baseN(path_im_ref))
                    fName_out = fName_out + '.%s' % ext if ext else fName_out
408

409
                self.path_out = os.path.abspath(os.path.join(dir_out, fName_out))
410
411
412
413

                assert ' ' not in self.path_out, \
                    "The path of the output image contains whitespaces. This is not supported by GDAL."
        else:
414
            # this only happens if COREG is not instanced from within Python and self.path_out is explicitly set to None
415
416
417
418
419
420
421
422
423
424
425
            # => DESHIFTER will return an array
            pass

        if self.v:
            if self.path_verbose_out:
                dir_out, dirname_out = os.path.split(self.path_verbose_out)

                if not dir_out:
                    if self.path_out:
                        self.path_verbose_out = os.path.dirname(self.path_out)
                    else:
426
427
428
                        self.path_verbose_out = \
                            os.path.abspath(os.path.join(os.path.curdir, 'CoReg_verboseOut__%s__shifted_to__%s'
                                                         % (get_baseN(path_im_tgt), get_baseN(path_im_ref))))
429
430
431
432
433
434
435
436
437
                elif dirname_out and not dir_out:
                    self.path_verbose_out = os.path.abspath(os.path.join(os.path.curdir, dirname_out))

                assert ' ' not in self.path_verbose_out, \
                    "'path_verbose_out' contains whitespaces. This is not supported by GDAL."

        else:
            self.path_verbose_out = None

438
439
        if self.path_verbose_out and not os.path.isdir(self.path_verbose_out):
            os.makedirs(self.path_verbose_out)
440
441

    def _get_image_params(self):
442
443
        self.ref = GeoArray_CoReg(self.params, 'ref')
        self.shift = GeoArray_CoReg(self.params, 'shift')
444
445
446
447
448

        if not prj_equal(self.ref.prj, self.shift.prj):
            raise RuntimeError(
                'Input projections are not equal. Different projections are currently not supported. Got %s / %s.'
                % (get_proj4info(proj=self.ref.prj), get_proj4info(proj=self.shift.prj)))
449

450
    def _get_overlap_properties(self):
451
452
453
454
        overlap_tmp = get_overlap_polygon(self.ref.poly, self.shift.poly, self.v)
        self.overlap_poly = overlap_tmp['overlap poly']  # has to be in reference projection
        self.overlap_percentage = overlap_tmp['overlap percentage']
        self.overlap_area = overlap_tmp['overlap area']
455
456
457
458

        assert self.overlap_poly, 'The input images have no spatial overlap.'

        # overlap are must at least cover 16*16 pixels
459
460
461
462
        px_area = self.ref.xgsd * self.ref.ygsd if self.grid2use == 'ref' else self.shift.xgsd * self.shift.ygsd
        px_covered = self.overlap_area / px_area
        assert px_covered > 16 * 16, \
            'Overlap area covers only %s pixels. At least 16*16 pixels are needed.' % px_covered
463

464
    def equalize_pixGrids(self):
Daniel Scheffler's avatar
Daniel Scheffler committed
465
        """Equalize image grids and projections of reference and target image (align target to reference)."""
466
467
        if not (prj_equal(self.ref.prj, self.shift.prj) and
                is_coord_grid_equal(self.ref.gt, *self.shift.xygrid_specs)):
468
469
            if not self.q:
                print("Equalizing pixel grids and projections of reference and target image...")
Daniel Scheffler's avatar
Daniel Scheffler committed
470

471
            if self.grid2use == 'ref':
472
                # resample target image to reference image
Daniel Scheffler's avatar
Bugfix.    
Daniel Scheffler committed
473
474
                if self.shift.bands > 1:
                    self.shift = self.shift.get_subset(zslice=slice(self.shift.band4match, self.shift.band4match + 1))
475
                self.shift.reproject_to_new_grid(prototype=self.ref, CPUs=self.CPUs)
476
                self.shift.band4match = 0  # after resampling there is only one band in the GeoArray
477

478
479
            else:
                # resample reference image to target image
Daniel Scheffler's avatar
Bugfix.    
Daniel Scheffler committed
480
481
                if self.ref.bands > 1:
                    self.ref = self.ref.get_subset(zslice=slice(self.ref.band4match, self.ref.band4match + 1))
482
                self.ref.reproject_to_new_grid(prototype=self.shift, CPUs=self.CPUs)
Daniel Scheffler's avatar
Daniel Scheffler committed
483
                self.ref.band4match = 0  # after resampling there is only one band in the GeoArray
484

485
486
487
            # self.ref.gt = (self.ref.gt[0], 1, self.ref.gt[2], self.ref.gt[3], self.ref.gt[4], -1)
            # self.shift.gt = (self.shift.gt[0], 1, self.shift.gt[2], self.shift.gt[3], self.shift.gt[4], -1)

488
    def show_image_footprints(self):
Daniel Scheffler's avatar
Daniel Scheffler committed
489
490
491
492
        """Show a web map containing the calculated footprints and overlap area of the input images.

        NOTE: This method is intended to be called from Jupyter Notebook.
        """
493
494
495
        # TODO different colors for polygons
        assert self.overlap_poly, 'Please calculate the overlap polygon first.'

496
497
        import folium
        import geojson
498

499
500
501
        refPoly = reproject_shapelyGeometry(self.ref.poly, self.ref.epsg, 4326)
        shiftPoly = reproject_shapelyGeometry(self.shift.poly, self.shift.epsg, 4326)
        overlapPoly = reproject_shapelyGeometry(self.overlap_poly, self.shift.epsg, 4326)
502
        matchBoxPoly = reproject_shapelyGeometry(self.matchBox.mapPoly, self.shift.epsg, 4326)
503
504

        m = folium.Map(location=tuple(np.array(overlapPoly.centroid.coords.xy).flatten())[::-1])
505
        for poly in [refPoly, shiftPoly, overlapPoly, matchBoxPoly]:
506
507
508
509
            gjs = geojson.Feature(geometry=poly, properties={})
            folium.GeoJson(gjs).add_to(m)
        return m

510
    def show_matchWin(self, figsize=(15, 15), interactive=True, after_correction=None, pmin=2, pmax=98):
511
        """Show the image content within the matching window.
512

513
514
        :param figsize:             <tuple> figure size
        :param interactive:         <bool> whether to return an interactive figure based on 'holoviews' library
515
516
517
518
519
        :param after_correction:    True/False: show the image content AFTER shift correction or before
                                    None: show both states - before and after correction (default)
        :param pmin:                percentage to be used for excluding the darkest pixels from stretching (default: 2)
        :param pmax:                percentage to be used for excluding the brightest pixels from stretching
                                    (default: 98)
520
521
        :return:
        """
522
523
524
525
526
        if interactive:
            # use Holoviews
            try:
                import holoviews as hv
            except ImportError:
527
                hv = None
528
529
530
531
            if not hv:
                raise ImportError(
                    "This method requires the library 'holoviews'. It can be installed for Anaconda with "
                    "the shell command 'conda install -c ioam holoviews bokeh'.")
532

533
            hv.notebook_extension('matplotlib')
534
535
536
537
538
539
540
541
542
543
            hv.Store.add_style_opts(hv.Image, ['vmin', 'vmax'])

            # hv.Store.option_setters.options().Image = hv.Options('style', cmap='gnuplot2')
            # hv.Store.add_style_opts(hv.Image, ['cmap'])
            # renderer = hv.Store.renderers['matplotlib'].instance(fig='svg', holomap='gif')
            # RasterPlot = renderer.plotting_class(hv.Image)
            # RasterPlot.cmap = 'gray'
            otherWin_corr = self._get_deshifted_otherWin()
            xmin, xmax, ymin, ymax = self.matchBox.boundsMap

544
            def get_hv_image(geoArr):
545
546
547
548
549
                arr_masked = np.ma.masked_equal(geoArr[:], geoArr.nodata)
                vmin = np.nanpercentile(arr_masked.compressed(), pmin)
                vmax = np.nanpercentile(arr_masked.compressed(), pmax)
                arr2plot = rescale_intensity(arr_masked, in_range=(vmin, vmax), out_range='int8')

550
551
552
553
554
555
556
557
                return hv.Image(arr2plot, bounds=(xmin, ymin, xmax, ymax))\
                    .opts(style={'cmap': 'gray',
                                 'vmin': vmin,
                                 'vmax': vmax,
                                 'interpolation': 'none'},
                          plot={'fig_inches': figsize,
                                # 'fig_size': 100,
                                'show_grid': True})
558

559
560
561
            hvIm_matchWin = get_hv_image(self.matchWin)
            hvIm_otherWin_orig = get_hv_image(self.otherWin)
            hvIm_otherWin_corr = get_hv_image(otherWin_corr)
562

563
564
565
            if after_correction is None:
                # view both states
                print('Matching window before and after correction (above and below): ')
566

567
                # get layouts (docs on options: http://build.holoviews.org/Tutorials/Options.html)
568
569
                layout_before = (hvIm_matchWin + hvIm_matchWin).opts(plot=dict(fig_inches=figsize))
                layout_after = (hvIm_otherWin_orig + hvIm_otherWin_corr).opts(plot=dict(fig_inches=figsize))
570

571
572
573
574
575
576
577
578
579
580
                # plot!
                imgs = {1: layout_before, 2: layout_after}
                hmap = hv.HoloMap(imgs, kdims=['image']).collate().cols(1)

            else:
                # view state before or after correction
                imgs = {1: hvIm_matchWin, 2: hvIm_otherWin_corr if after_correction else hvIm_otherWin_orig}
                hmap = hv.HoloMap(imgs, kdims=['image'])

            # Construct a HoloMap by evaluating the function over all the keys
581
            # hmap = hv.HoloMap(imgs_corr, kdims=['image']) +  hv.HoloMap(imgs_corr, kdims=['image'])
582

583
584
            # Construct a HoloMap by defining the sampling on the Dimension
            # dmap = hv.DynamicMap(image_slice, kdims=[hv.Dimension('z_axis', values=keys)])
585

586
            return hmap
587

588
589
        else:
            # TODO add titles
Daniel Scheffler's avatar
Daniel Scheffler committed
590
            # TODO handle after_correction=None here
591
            self.matchWin.show(figsize=figsize)
592
            if after_correction:
593
                self._get_deshifted_otherWin().show(figsize=figsize, pmin=pmin, pmax=pmax)
594
            else:
595
                self.otherWin.show(figsize=figsize, pmin=pmin, pmax=pmax)
596
597

    def show_cross_power_spectrum(self, interactive=False):
Daniel Scheffler's avatar
Daniel Scheffler committed
598
599
600
601
        """Show a 3D surface of the cross power spectrum.

        NOTE: The cross power spectrum is the result from phase correlating the reference and target
              image within the matching window.
602
603
604
605
606
607
608

        :param interactive:  whether to return an interactice 3D surface plot based on 'plotly' library
        :return:
        """
        if interactive:
            # create plotly 3D surface

609
            # import plotly.plotly as py # online mode -> every plot is uploaded into online plotly account
610
611
612
613
614
615
            from plotly.offline import iplot, init_notebook_mode
            import plotly.graph_objs as go

            init_notebook_mode(connected=True)

            z_data = self._calc_shifted_cross_power_spectrum()
616
            data = [go.Surface(z=z_data)]
617
618
619
620
621
            layout = go.Layout(
                title='cross power spectrum',
                autosize=False,
                width=1000,
                height=1000,
622
                margin={'l': 65, 'r': 50, 'b': 65, 't': 90})
623
            fig = go.Figure(data=data, layout=layout)
624
625
626
627
628
629
630
631

            return iplot(fig, filename='SCPS')

        else:
            # use matplotlib
            scps = self._calc_shifted_cross_power_spectrum()
            PLT.subplot_3dsurface(scps.astype(np.float32))

632
    def _get_opt_winpos_winsize(self):
Daniel Scheffler's avatar
Daniel Scheffler committed
633
634
635
        """Calculate optimal window position and size in reference image units.

        NOTE: The returned values are computed according to DGM, cloud_mask and trueCornerLonLat.
636
        """
637
638
639
640
        # dummy algorithm: get center position of overlap instead of searching ideal window position in whole overlap
        # TODO automatischer Algorithmus zur Bestimmung der optimalen Window Position

        wp = tuple(self.win_pos_XY)
641
642
        assert type(self.win_pos_XY) in [tuple, list, np.ndarray], \
            'The window position must be a tuple of two elements. Got %s with %s elements.' % (type(wp), len(wp))
643
644
645
        wp = tuple(wp)

        if None in wp:
646
            # use centroid point if possible
647
648
649
            overlap_center_pos_x, overlap_center_pos_y = self.overlap_poly.centroid.coords.xy
            wp = (wp[0] if wp[0] else overlap_center_pos_x[0]), (wp[1] if wp[1] else overlap_center_pos_y[0])

650
            # validate window position
651
            if not self.overlap_poly.buffer(1e-5).contains(Point(wp)):
652
653
654
655
656
657
658
659
660
661
662
                # in case the centroid point is not within overlap area
                if not self.q:
                    warnings.warn("The centroid point of the two input images could not be used as matching window "
                                  "position since it is outside of the overlap area. Instead the so called "
                                  "'representative point' is used. Alternatively you can provide your own window "
                                  "position as input parameter.")

                # -> use representative point: a point that is garanteed to be within overlap polygon
                overlap_center_pos_x, overlap_center_pos_y = self.overlap_poly.representative_point().coords.xy
                wp = overlap_center_pos_x[0], overlap_center_pos_y[0]

663
            assert self.overlap_poly.buffer(1e-5).contains(Point(wp))
664
665
666

        else:
            # validate window position
667
            if not self.overlap_poly.buffer(1e-5).contains(Point(wp)):
668
                self._handle_error(ValueError('The provided window position %s/%s is outside of the overlap '
669
                                              'area of the two input images. Check the coordinates.' % wp))
670
671
672
673
674
675

        # check if window position is within bad data area if a respective mask has been provided
        for im in [self.ref, self.shift]:
            if im.mask_baddata is not None:
                imX, imY = mapXY2imXY(wp, im.mask_baddata.gt)

676
                if im.mask_baddata[int(imY), int(imX)] is True:
677
                    self._handle_error(
678
                        RuntimeError('According to the provided bad data mask for the %s the chosen window position '
679
680
681
                                     '%s / %s is within a bad data area. Using this window position for coregistration '
                                     'is not reasonable. Please provide a better window position!'
                                     % (im.imName, wp[0], wp[1])))
682

683
684
        self.win_pos_XY = wp
        self.win_size_XY = (int(self.win_size_XY[0]), int(self.win_size_XY[1])) if self.win_size_XY else (512, 512)
685
686

    def _get_clip_window_properties(self):
Daniel Scheffler's avatar
Daniel Scheffler committed
687
688
689
690
691
        """Calculate all properties of the matching window and the other window.

        These windows are used to read the corresponding image positions in the reference and the target image.

        NOTE: Even if X- and Y-dimension of the target window is equal, the output window can be NON-quadratic!
692
693
694
        """
        # FIXME image sizes like 10000*256 are still possible

695
696
697
698
699
700
701
702
703
        wpX, wpY = self.win_pos_XY
        wsX, wsY = self.win_size_XY
        ref_wsX, ref_wsY = (wsX * self.ref.xgsd, wsY * self.ref.ygsd)  # image units -> map units
        shift_wsX, shift_wsY = (wsX * self.shift.xgsd, wsY * self.shift.ygsd)  # image units -> map units
        ref_box_kwargs = {'wp': (wpX, wpY), 'ws': (ref_wsX, ref_wsY), 'gt': self.ref.gt}
        shift_box_kwargs = {'wp': (wpX, wpY), 'ws': (shift_wsX, shift_wsY), 'gt': self.shift.gt}
        matchBox = boxObj(**ref_box_kwargs) if self.grid2use == 'ref' else boxObj(**shift_box_kwargs)
        otherBox = boxObj(**shift_box_kwargs) if self.grid2use == 'ref' else boxObj(**ref_box_kwargs)
        overlapWin = boxObj(mapPoly=self.overlap_poly, gt=self.ref.gt)
704
705

        # clip matching window to overlap area
706
707
        matchBox.mapPoly = matchBox.mapPoly.intersection(overlapWin.mapPoly)

708
        # check if matchBox extent touches no data area of the image -> if yes: shrink it
709
710
        overlapPoly_within_matchWin = matchBox.mapPoly.intersection(self.overlap_poly)
        if overlapPoly_within_matchWin.area < matchBox.mapPoly.area:
711
712
            wsX_start, wsY_start = 1 if wsX >= wsY else wsX / wsY, 1 if wsY >= wsX else wsY / wsX
            box = boxObj(**dict(wp=(wpX, wpY), ws=(wsX_start, wsY_start), gt=matchBox.gt))
713
            while True:
714
                box.buffer_imXY(1, 1)
715
716
717
718
                if not box.mapPoly.within(overlapPoly_within_matchWin):
                    box.buffer_imXY(-1, -1)
                    matchBox = box
                    break
719
720

        # move matching window to imref grid or im2shift grid
721
722
        mW_rows, mW_cols = (self.ref.rows, self.ref.cols) if self.grid2use == 'ref' else \
            (self.shift.rows, self.shift.cols)
723
        matchBox.mapPoly = move_shapelyPoly_to_image_grid(matchBox.mapPoly, matchBox.gt, mW_rows, mW_cols, 'NW')
724

725
726
        # check, ob durch Verschiebung auf Grid die matchBox außerhalb von overlap_poly geschoben wurde
        if not matchBox.mapPoly.within(overlapWin.mapPoly):
727
            # matchPoly weiter verkleinern # 1 px buffer reicht, weil window nur auf das Grid verschoben wurde
728
            xLarger, yLarger = matchBox.is_larger_DimXY(overlapWin.boundsIm)
729
            matchBox.buffer_imXY(-1 if xLarger else 0, -1 if yLarger else 0)
730
731

        # matching_win direkt auf grid2use (Rundungsfehler bei Koordinatentrafo beseitigen)
732
        matchBox.imPoly = round_shapelyPoly_coords(matchBox.imPoly, precision=0)
733
734

        # Check, ob match Fenster größer als anderes Fenster
735
        if not (matchBox.mapPoly.within(otherBox.mapPoly) or matchBox.mapPoly == otherBox.mapPoly):
736
            # dann für anderes Fenster kleinstes Fenster finden, das match-Fenster umgibt
737
738
            otherBox.boxImYX = get_smallest_boxImYX_that_contains_boxMapYX(
                matchBox.boxMapYX, otherBox.gt, tolerance_ndigits=5)  # avoids float coordinate rounding issues
739
740

        # evtl. kann es sein, dass bei Shift-Fenster-Vergrößerung das shift-Fenster zu groß für den overlap wird
Daniel Scheffler's avatar
Daniel Scheffler committed
741
        t_start = time.time()
742
        while not otherBox.mapPoly.within(overlapWin.mapPoly):
Daniel Scheffler's avatar
Daniel Scheffler committed
743
            # -> match Fenster verkleinern und neues otherBox berechnen
744
745
            xLarger, yLarger = otherBox.is_larger_DimXY(overlapWin.boundsIm)
            matchBox.buffer_imXY(-1 if xLarger else 0, -1 if yLarger else 0)
746
            previous_area = otherBox.mapPoly.area
747
748
            otherBox.boxImYX = get_smallest_boxImYX_that_contains_boxMapYX(
                matchBox.boxMapYX, otherBox.gt, tolerance_ndigits=5)  # avoids float coordinate rounding issues)
749

750
            if previous_area == otherBox.mapPoly.area or time.time() - t_start > 1.5:
Daniel Scheffler's avatar
Daniel Scheffler committed
751
752
                # happens e.g in case of a triangular footprint
                # NOTE: first condition is not always fulfilled -> therefore added timeout of 1.5 sec
753
                self._handle_error(
754
755
                    RuntimeError('Matching window in target image is larger than overlap area but further shrinking '
                                 'the matching window is not possible. Check if the footprints of the input data have '
756
                                 'been computed correctly.' +
757
758
                                 (' Matching window shrinking timed out.' if time.time() - t_start > 5 else '')))
                break  # break out of while loop in order to avoid that code gets stuck here
759

Daniel Scheffler's avatar
Daniel Scheffler committed
760
761
762
763
764
765
766
        # output validation
        for winBox in [matchBox, otherBox]:
            if winBox.imDimsYX[0] < 16 or winBox.imDimsYX[1] < 16:
                self._handle_error(
                    RuntimeError("One of the input images does not have sufficient gray value information "
                                 "(non-no-data values) for placing a matching window at the position %s. "
                                 "Matching failed." % str((wpX, wpY))))
Daniel Scheffler's avatar
Daniel Scheffler committed
767

768
        if self.success is not False:
Daniel Scheffler's avatar
Daniel Scheffler committed
769
            # check result -> ProgrammingError if not fulfilled
770
771
772
            def within_equal(inner, outer):
                return inner.within(outer.buffer(1e-5)) or inner.equals(outer)

Daniel Scheffler's avatar
Daniel Scheffler committed
773
774
            assert within_equal(matchBox.mapPoly, otherBox.mapPoly)
            assert within_equal(otherBox.mapPoly, overlapWin.mapPoly)
775

776
777
            self.imfft_xgsd = self.ref.xgsd if self.grid2use == 'ref' else self.shift.xgsd
            self.imfft_ygsd = self.ref.ygsd if self.grid2use == 'ref' else self.shift.ygsd
778
779
780
781
782
            self.ref.win, self.shift.win = (matchBox, otherBox) if self.grid2use == 'ref' else (otherBox, matchBox)
            self.matchBox, self.otherBox = matchBox, otherBox
            self.ref.win.size_YX = tuple([int(i) for i in self.ref.win.imDimsYX])
            self.shift.win.size_YX = tuple([int(i) for i in self.shift.win.imDimsYX])
            match_win_size_XY = tuple(reversed([int(i) for i in matchBox.imDimsYX]))
783

784
785
            if not self.q and match_win_size_XY != self.win_size_XY:
                print('Target window size %s not possible due to too small overlap area or window position too close '
786
                      'to an image edge. New matching window size: %s.' % (self.win_size_XY, match_win_size_XY))
787

788
789
                # write_shp('/misc/hy5/scheffler/Temp/matchMapPoly.shp', matchBox.mapPoly,matchBox.prj)
                # write_shp('/misc/hy5/scheffler/Temp/otherMapPoly.shp', otherBox.mapPoly,otherBox.prj)
790
791

    def _get_image_windows_to_match(self):
Daniel Scheffler's avatar
Daniel Scheffler committed
792
        """Read the matching window and the other window as subsets.
793

Daniel Scheffler's avatar
Daniel Scheffler committed
794
795
796
        Th other window is resampled to the resolution and the pixel grid of the matching window.
        The result consists of two images with the same dimensions and exactly the same corner coordinates.
        """
797
798
        match_fullGeoArr = self.ref if self.grid2use == 'ref' else self.shift
        other_fullGeoArr = self.shift if self.grid2use == 'ref' else self.ref
799
800

        # matchWin per subset-read einlesen -> self.matchWin.data
801
        rS, rE, cS, cE = GEO.get_GeoArrayPosition_from_boxImYX(self.matchBox.boxImYX)
802
        assert np.array_equal(np.abs(np.array([rS, rE, cS, cE])), np.array([rS, rE, cS, cE])) and \
Daniel Scheffler's avatar
Daniel Scheffler committed
803
            rE <= match_fullGeoArr.rows and cE <= match_fullGeoArr.cols, \
804
805
806
807
808
            'Requested area is not completely within the input array for %s.' % match_fullGeoArr.imName
        self.matchWin = GeoArray(match_fullGeoArr[rS:rE + 1, cS:cE + 1, match_fullGeoArr.band4match],
                                 geotransform=GEO.get_subset_GeoTransform(match_fullGeoArr.gt, self.matchBox.boxImYX),
                                 projection=copy(match_fullGeoArr.prj),
                                 nodata=copy(match_fullGeoArr.nodata))
809
        self.matchWin.imID = match_fullGeoArr.imID
810
811

        # otherWin per subset-read einlesen
812
        rS, rE, cS, cE = GEO.get_GeoArrayPosition_from_boxImYX(self.otherBox.boxImYX)
813
        assert np.array_equal(np.abs(np.array([rS, rE, cS, cE])), np.array([rS, rE, cS, cE])) and \
Daniel Scheffler's avatar
Daniel Scheffler committed
814
            rE <= other_fullGeoArr.rows and cE <= other_fullGeoArr.cols, \
815
816
817
818
819
            'Requested area is not completely within the input array for %s.' % other_fullGeoArr.imName
        self.otherWin = GeoArray(other_fullGeoArr[rS:rE + 1, cS:cE + 1, other_fullGeoArr.band4match],
                                 geotransform=GEO.get_subset_GeoTransform(other_fullGeoArr.gt, self.otherBox.boxImYX),
                                 projection=copy(other_fullGeoArr.prj),
                                 nodata=copy(other_fullGeoArr.nodata))
820
        self.otherWin.imID = other_fullGeoArr.imID
821

822
823
        # self.matchWin.deepcopy_array()
        # self.otherWin.deepcopy_array()
824
825
826

        if self.v:
            print('Original matching windows:')
827
828
829
            ref_data, shift_data = (self.matchWin[:], self.otherWin[:]) if self.grid2use == 'ref' else \
                (self.otherWin[:], self.matchWin[:])
            PLT.subplot_imshow([ref_data, shift_data], [self.ref.title, self.shift.title], grid=True)
830

831
        # resample otherWin.arr to the resolution of matchWin AND make sure the pixel edges are identical
832
        # (in order to make each image show the same window with the same coordinates)
833
834
835
836
        # TODO replace cubic resampling by PSF resampling - average resampling leads to sinus like distortions in the
        # TODO fft image that make a precise coregistration impossible. Thats why there is currently no way around
        # TODO cubic resampling.
        tgt_xmin, tgt_xmax, tgt_ymin, tgt_ymax = self.matchBox.boundsMap
837
838

        # equalize pixel grids and projection of matchWin and otherWin (ONLY if grids are really different)
839
840
        if not (self.matchWin.xygrid_specs == self.otherWin.xygrid_specs and
                prj_equal(self.matchWin.prj, self.otherWin.prj)):
841
842
843
844
            self.otherWin.arr, self.otherWin.gt = warp_ndarray(self.otherWin.arr,
                                                               self.otherWin.gt,
                                                               self.otherWin.prj,
                                                               self.matchWin.prj,
845
                                                               out_gsd=(self.imfft_xgsd, abs(self.imfft_ygsd)),
846
847
848
849
850
                                                               out_bounds=([tgt_xmin, tgt_ymin, tgt_xmax, tgt_ymax]),
                                                               rspAlg=_dict_rspAlg_rsp_Int[self.rspAlg_calc],
                                                               in_nodata=self.otherWin.nodata,
                                                               CPUs=self.CPUs,
                                                               progress=False)[:2]
851
852

        if self.matchWin.shape != self.otherWin.shape:
853
            self._handle_error(
854
                RuntimeError('Caught a possible ProgrammingError at window position %s: Bad output of '
855
                             'get_image_windows_to_match. Reference image shape is %s whereas shift '
856
                             'image shape is %s.' % (str(self.matchBox.wp), self.matchWin.shape, self.otherWin.shape)),
857
858
                warn=True)

Daniel Scheffler's avatar
Daniel Scheffler committed
859
        # check of odd dimensions of output images
860
861
        rows, cols = [i if i % 2 == 0 else i - 1 for i in self.matchWin.shape]
        self.matchWin.arr, self.otherWin.arr = self.matchWin.arr[:rows, :cols], self.otherWin.arr[:rows, :cols]
Daniel Scheffler's avatar
Daniel Scheffler committed
862
        if self.matchWin.box.imDimsYX != self.matchBox.imDimsYX:
863
864
            self.matchBox = self.matchWin.box  # update matchBox
            self.otherBox = self.otherWin.box  # update otherBox
865

866
        assert self.matchWin.arr is not None and self.otherWin.arr is not None, 'Creation of matching windows failed.'
867
868
869

    @staticmethod
    def _shrink_winsize_to_binarySize(win_shape_YX, target_size=None):
870
        # type: (tuple, tuple) -> Union[Tuple[int, int], None]
Daniel Scheffler's avatar
Daniel Scheffler committed
871
872
873
        """Shrink a given window size to the closest binary window size (a power of 2).

        NOTE: X- and Y-dimension are handled separately.
874
875
876
877

        :param win_shape_YX:    <tuple> source window shape as pixel units (rows,colums)
        :param target_size:     <tuple> source window shape as pixel units (rows,colums)
        """
878
        binarySizes = [2 ** i for i in range(3, 14)]  # [8, 16, 32, 64, 128, 256, 512, 1024, 2048, 4096, 8192]
879
880
881
        possibSizes_X = [i for i in binarySizes if i <= win_shape_YX[1]]
        possibSizes_Y = [i for i in binarySizes if i <= win_shape_YX[0]]
        if possibSizes_X and possibSizes_Y:
882
883
884
885
            tgt_size_X, tgt_size_Y = target_size if target_size else (max(possibSizes_X), max(possibSizes_Y))
            closest_to_target_X = int(min(possibSizes_X, key=lambda x: abs(x - tgt_size_X)))
            closest_to_target_Y = int(min(possibSizes_Y, key=lambda y: abs(y - tgt_size_Y)))
            return closest_to_target_Y, closest_to_target_X
886
887
888
889
        else:
            return None

    def _calc_shifted_cross_power_spectrum(self, im0=None, im1=None, precision=np.complex64):
Daniel Scheffler's avatar
Daniel Scheffler committed
890
        """Calculate the shifted cross power spectrum for quantifying X/Y-shifts.
891

892
893
894
895
        :param im0:         reference image
        :param im1:         subject image to shift
        :param precision:   to be quantified as a datatype
        :return:            2D-numpy-array of the shifted cross power spectrum
896
        """
897
898
        im0 = im0 if im0 is not None else self.matchWin[:] if self.matchWin.imID == 'ref' else self.otherWin[:]
        im1 = im1 if im1 is not None else self.otherWin[:] if self.otherWin.imID == 'shift' else self.matchWin[:]
899

900
        assert im0.shape == im1.shape, 'The reference and the target image must have the same dimensions.'
901
902
903
904
        if im0.shape[0] % 2 != 0:
            warnings.warn('Odd row count in one of the match images!')
        if im1.shape[1] % 2 != 0:
            warnings.warn('Odd column count in one of the match images!')
905

906
907
        wsYX = self._shrink_winsize_to_binarySize(im0.shape) if self.bin_ws else im0.shape
        wsYX = ((min(wsYX),) * 2 if self.force_quadratic_win else wsYX) if wsYX else None
908

909
        if wsYX not in [None, (0, 0)]:
910
            time0 = time.time()
911
912
913
914
915
            if self.v:
                print('final window size: %s/%s (X/Y)' % (wsYX[1], wsYX[0]))
                # FIXME size of self.matchWin is not updated
                # FIXME CoRegPoints_grid.WIN_SZ is taken from self.matchBox.imDimsYX but this is not updated

916
            center_YX =