Merge branch 'main' into installation-pip-note

.editorconfig

@@ -1,4 +1,4 @@
-# http://editorconfig.org
+# https://editorconfig.org
 
 root = true
 

.gitlab-ci.yml

@@ -16,7 +16,7 @@ test_arosics:
 
     # update py_tools_ds and geoarray
     - mamba update py-tools-ds geoarray
-    - mamba install "scikit-image>=0.21.0"  # TODO: remove as soon as CI runner is rebuilt
+    - mamba install joblib>=1.3.0  # TODO remove is CI runner is rebuilt
 
     # run tests
     - make pytest

HISTORY.rst

@@ -2,6 +2,52 @@
 History
 =======
 
+1.10.3 (coming soon)
+--------------------
+
+* !52: Added minimal version for joblib to fix https://github.com/GFZ/arosics/issues/39.
+
+
+1.10.2 (2024-02-13)
+-------------------
+
+* !49: Updated copyright.
+* !50: Replaced deprecated http links.
+* !51: Replaced the multiprocessing implementation with parallelization based on joblib including mem-mapping. This
+  reduces the memory load and should fix potential deadlocks on Windows (https://github.com/GFZ/arosics/issues/36).
+
+
+1.10.1 (2023-12-22)
+-------------------
+
+* !47: Fixed some code style and language issues.
+* !48: Resolved #91 (RuntimeWarning: invalid value encountered in true_divide).
+
+
+1.10.0 (2023-12-15)
+-------------------
+
+* !43: Added parameter 'skip_outliers' to Tie_Point_Grid.to_PointShapefile() (closes #90) and improved test.
+* !44: Removed deprecated Tie_Point_Grid.Tie_Point_Grid._to_PointShapefile() method
+  which was replaced by to_PointShapefile().
+* !45: Replaced unittest assertions with pytest plain assertions.
+* !46: Removed deprecated Tie_Point_Grid.to_Raster_using_Kriging().
+
+
+1.9.4 (2023-11-23)
+------------------
+
+* !42: Fixed https://github.com/GFZ/arosics/issues/33
+  ('TypeError: ufunc 'invert' not supported for the input types' when using input mask).
+
+
+1.9.3 (2023-10-16)
+------------------
+
+* !41: Fixed #86 (ValueError when calling CoReg.show_matchWin(interactive=True))
+  and improved interactive output of CoReg.show_matchWin.
+
+
 1.9.2 (2023-08-11)
 ------------------
 

LICENSE

@@ -1,6 +1,6 @@
 Apache License
                            Version 2.0, January 2004
-                        http://www.apache.org/licenses/
+                        https://www.apache.org/licenses/
 
    TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
 

arosics/CoReg.py

@@ -2,7 +2,7 @@
 
 # AROSICS - Automated and Robust Open-Source Image Co-Registration Software
 #
-# Copyright (C) 2017-2023
+# Copyright (C) 2017-2024
 # - Daniel Scheffler (GFZ Potsdam, daniel.scheffler@gfz-potsdam.de)
 # - Helmholtz Centre Potsdam - GFZ German Research Centre for Geosciences Potsdam,
 #   Germany (https://www.gfz-potsdam.de/)
@@ -15,7 +15,7 @@
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
 #
-#   http://www.apache.org/licenses/LICENSE-2.0
+#   https://www.apache.org/licenses/LICENSE-2.0
 #
 # Unless required by applicable law or agreed to in writing, software
 # distributed under the License is distributed on an "AS IS" BASIS,
@@ -28,9 +28,10 @@
 import warnings
 from copy import copy
 from typing import Iterable, Union, Tuple, List, Optional  # noqa F401
+from multiprocessing import cpu_count
 
 # custom
-from osgeo import gdal
+from osgeo import gdal  # noqa
 import numpy as np
 
 from packaging.version import parse as parse_version
@@ -141,7 +142,7 @@ def __init__(self,
 
         # add bad data mask
         given_mask = CoReg_params['mask_baddata_%s' % ('ref' if imID == 'ref' else 'tgt')]
-        if given_mask:
+        if given_mask is not None:
             self.mask_baddata = given_mask  # runs GeoArray.mask_baddata.setter -> sets it to BadDataMask()
 
     poly = alias_property('footprint_poly')  # ensures that self.poly is updated if self.footprint_poly is updated
@@ -221,7 +222,7 @@ def __init__(self,
             band of shift image to be used for matching (starts with 1; default: 1)
 
         :param wp:
-            custom matching window position as (X, Y) map coordinate in the same projection like the reference image
+            custom matching window position as (X, Y) map coordinate in the same projection as the reference image
             (default: central position of image overlap)
 
         :param ws:
@@ -235,7 +236,7 @@ def __init__(self,
 
         :param align_grids:
             True: align the input coordinate grid to the reference (does not affect the output pixel size as long as
-            input and output pixel sizes are compatible (5:30 or 10:30 but not 4:30), default = False
+            input and output pixel sizes are compatible (5:30 or 10:30 but not 4:30)), default = False
 
             - NOTE: If this is set to False, the mis-registration in the target image is corrected by updating its
               geocoding information only, i.e., without performing any resampling which preserves the original
@@ -284,7 +285,7 @@ def __init__(self,
 
         :param calc_corners:
              calculate true positions of the dataset corners in order to get a useful matching window position within
-             the actual image overlap (default: True; deactivated if '-cor0' and '-cor1' are given
+             the actual image overlap (default: True; deactivated if '-cor0' and '-cor1' are given)
 
         :param binary_ws:
             use binary X/Y dimensions for the matching window (default: True)
@@ -293,13 +294,13 @@ def __init__(self,
             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.
+            position is valid in the sense of useful data. Otherwise, this window position is rejected.
 
         :param mask_baddata_tgt:
             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.
+            position is valid in the sense of useful data. Otherwise, this window position is rejected.
 
         :param CPUs:
             number of CPUs to use during pixel grid equalization (default: None, which means 'all CPUs available')
@@ -375,7 +376,7 @@ def __init__(self,
         self.rspAlg_calc = resamp_alg_calc \
             if isinstance(resamp_alg_calc, str) else _dict_rspAlg_rsp_Int[resamp_alg_calc]
         self.calc_corners = calc_corners
-        self.CPUs = CPUs
+        self.CPUs = CPUs if CPUs and CPUs <= cpu_count() else cpu_count()
         self.bin_ws = binary_ws
         self.force_quadratic_win = force_quadratic_win
         self.v = v
@@ -692,7 +693,7 @@ def show_matchWin(self,
                 hv = None
             if not hv:
                 raise ImportError(
-                    "This method requires the library 'holoviews'. It can be installed for Anaconda with "
+                    "This method requires the library 'holoviews'. It can be installed for Conda with "
                     "the shell command 'conda install -c conda-forge holoviews bokeh'.")
 
             hv.notebook_extension('matplotlib')
@@ -706,38 +707,53 @@ def show_matchWin(self,
             otherWin_corr = self._get_deshifted_otherWin() if after_correction in [True, None] else None
             xmin, xmax, ymin, ymax = self.matchBox.boundsMap
 
-            def get_hv_image(geoArr):
+            def get_hv_image(geoArr: GeoArray):
                 from skimage.exposure import rescale_intensity  # import here to avoid static TLS ImportError
 
                 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')
 
-                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})
+                return (
+                    hv.Image(
+                        arr2plot,
+                        bounds=(xmin, ymin, xmax, ymax)
+                    ).options(
+                        cmap='gray',
+                        vmin=vmin,
+                        vmax=vmax,
+                        interpolation='none',
+                        fig_inches=figsize,
+                        show_grid=True
+                    )
+                )
 
             hvIm_matchWin = get_hv_image(self.matchWin)
             hvIm_otherWin_orig = get_hv_image(self.otherWin)
             hvIm_otherWin_corr = get_hv_image(otherWin_corr) if after_correction in [True, None] else None
 
             if after_correction is None:
                 # view both states
-                print('Matching window before and after correction (above and below): ')
+                print('Matching window before and after correction (left and right): ')
 
                 # get layouts (docs on options: https://holoviews.org/user_guide)
-                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))
+                layout_before = (
+                    hvIm_matchWin.options(title='BEFORE co-registration') +
+                    hvIm_matchWin.options(title='AFTER co-registration')
+                ).options(
+                    fig_inches=figsize
+                )
+                layout_after = (
+                    hvIm_otherWin_orig.options(title='BEFORE co-registration') +
+                    hvIm_otherWin_corr.options(title='AFTER co-registration')
+                ).options(
+                    fig_inches=figsize
+                )
 
                 # plot!
                 imgs = {1: layout_before, 2: layout_after}
-                hmap = hv.HoloMap(imgs, kdims=['image']).collate().cols(1)
+                hmap = hv.HoloMap(imgs, kdims=['image']).collate().cols(2)
 
             else:
                 # view state before or after correction
@@ -953,7 +969,7 @@ def _get_clip_window_properties(self) -> None:
 
             if previous_area == otherBox.mapPoly.area or \
                time.time() - t_start > 1.5:
-                # happens e.g in case of a triangular footprint
+                # happens, e.g, in case of a triangular footprint
                 # NOTE: first condition is not always fulfilled -> therefore added timeout of 1.5 sec
                 self._handle_error(
                     RuntimeError('Matching window in target image is larger than overlap area but further shrinking '
@@ -1155,8 +1171,8 @@ def _calc_shifted_cross_power_spectrum(self,
                     fft_arr0 = pyfftw.FFTW(in_arr0, np.empty_like(in_arr0), axes=(0, 1))()
                     fft_arr1 = pyfftw.FFTW(in_arr1, np.empty_like(in_arr1), axes=(0, 1))()
 
-                    # catch empty output arrays (for some reason this happens sometimes..) -> use numpy fft
-                    # => this is caused by the call of pyfftw.FFTW. Exactly in that moment the input array
+                    # catch empty output arrays (for some reason this happens sometimes) -> use numpy fft
+                    # => this is caused by the call of pyfftw.FFTW. Exactly at that moment the input array
                     #    in_arr0 is overwritten with zeros (maybe this is a bug in pyFFTW?)
                     if np.std(fft_arr0) == 0 or np.std(fft_arr1) == 0:
                         raise RuntimeError('FFTW result is unexpectedly empty.')
@@ -1183,7 +1199,8 @@ def _calc_shifted_cross_power_spectrum(self,
             eps = np.abs(fft_arr1).max() * 1e-15
             # cps == cross-power spectrum of im0 and im2
 
-            temp = np.array(fft_arr0 * fft_arr1.conjugate()) / (np.abs(fft_arr0) * np.abs(fft_arr1) + eps)
+            with np.errstate(invalid='ignore'):  # ignore RuntimeWarning: invalid value encountered in true_divide
+                temp = np.array(fft_arr0 * fft_arr1.conjugate()) / (np.abs(fft_arr0) * np.abs(fft_arr1) + eps)
 
             time0 = time.time()
             if 'pyfft' in globals():
@@ -1231,11 +1248,13 @@ def _get_shifts_from_peakpos(peakpos: np.array,
     @staticmethod
     def _clip_image(im, center_YX, winSzYX):  # TODO this is also implemented in GeoArray
 
-        def get_bounds(YX, wsY, wsX):
-            return int(YX[1] - (wsX / 2)),\
-                   int(YX[1] + (wsX / 2)),\
-                   int(YX[0] - (wsY / 2)),\
-                   int(YX[0] + (wsY / 2))
+        def get_bounds(YX: tuple, wsY: float, wsX: float):
+            return (
+                int(YX[1] - (wsX / 2)),
+                int(YX[1] + (wsX / 2)),
+                int(YX[0] - (wsY / 2)),
+                int(YX[0] + (wsY / 2))
+            )
 
         wsY, wsX = winSzYX
         xmin, xmax, ymin, ymax = get_bounds(center_YX, wsY, wsX)
@@ -1447,7 +1466,9 @@ def normalize(array: np.ndarray) -> np.ndarray:
         # check if shapes of two images are unequal (due to bug (?), in some cases otherWin_deshift_geoArr does not have
         # the exact same dimensions as self.matchWin -> maybe bounds are handled differently by gdal.Warp)
         if not self.matchWin.shape == otherWin_deshift_geoArr.shape:  # FIXME this seems to be already fixed
-            warnings.warn('SSIM input array shapes are not equal! This issue seemed to be already fixed.. ')
+            warnings.warn('SSIM input array shapes are not equal. This should not happen. '
+                          'If it happens with your data, please report it here so that the issue can be fixed: '
+                          'https://git.gfz-potsdam.de/danschef/arosics/-/issues/85')
             matchFull = \
                 self.ref if self.matchWin.imID == 'ref' else\
                 self.shift

arosics/CoReg_local.py

@@ -2,7 +2,7 @@
 
 # AROSICS - Automated and Robust Open-Source Image Co-Registration Software
 #
-# Copyright (C) 2017-2023
+# Copyright (C) 2017-2024
 # - Daniel Scheffler (GFZ Potsdam, daniel.scheffler@gfz-potsdam.de)
 # - Helmholtz Centre Potsdam - GFZ German Research Centre for Geosciences Potsdam,
 #   Germany (https://www.gfz-potsdam.de/)
@@ -15,7 +15,7 @@
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
 #
-#   http://www.apache.org/licenses/LICENSE-2.0
+#   https://www.apache.org/licenses/LICENSE-2.0
 #
 # Unless required by applicable law or agreed to in writing, software
 # distributed under the License is distributed on an "AS IS" BASIS,
@@ -28,9 +28,10 @@
 from copy import copy
 from typing import Tuple, Union, Optional
 from collections import OrderedDict
+from multiprocessing import cpu_count
 
 # custom
-from osgeo import gdal
+from osgeo import gdal  # noqa
 from packaging.version import parse as parse_version
 try:
     import pyfftw
@@ -61,7 +62,7 @@ class COREG_LOCAL(object):
 
     Spatial shifts are calculated for each point in grid of which the parameters can be adjusted using keyword
     arguments. Shift correction performs a polynomial transformation using the calculated shifts of each point in the
-    grid as GCPs. Thus this class can be used to correct for locally varying geometric distortions of the target image.
+    grid as GCPs. Thus, this class can be used to correct for locally varying geometric distortions of the target image.
 
     See help(COREG_LOCAL) for documentation.
     """
@@ -187,7 +188,7 @@ def __init__(self,
 
         :param align_grids:
             True: align the input coordinate grid to the reference (does not affect the output pixel size as long as
-            input and output pixel sizes are compatible (5:30 or 10:30 but not 4:30), default = True
+            input and output pixel sizes are compatible (5:30 or 10:30 but not 4:30)), default = True
 
         :param match_gsd:
             True: match the input pixel size to the reference pixel size,
@@ -247,13 +248,13 @@ def __init__(self,
             path to a 2D boolean mask file (or an instance of BadDataMask) 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.
+            position is valid in the sense of useful data. Otherwise, this window position is rejected.
 
         :param mask_baddata_tgt:
             path to a 2D boolean mask file (or an instance of BadDataMask) 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.
+            position is valid in the sense of useful data. Otherwise, this window position is rejected.
 
         :param CPUs:
             number of CPUs to use during calculation of tie point grid (default: None, which means 'all CPUs available')
@@ -309,7 +310,7 @@ def __init__(self,
         self.outFillVal = outFillVal
         self.bin_ws = binary_ws
         self.force_quadratic_win = force_quadratic_win
-        self.CPUs = CPUs
+        self.CPUs = CPUs if CPUs and CPUs <= cpu_count() else cpu_count()
         self.path_verbose_out = ''  # TODO
         self.v = v
         self.q = q if not v else False  # overridden by v