Moved arosics_cli.py from bin to arosics folder to avoid entry point issues at...

Moved arosics_cli.py from bin to arosics folder to avoid entry point issues at conda-forge. Replaced some http links with https.

Signed-off-by: Daniel Scheffler <danschef@gfz-potsdam.de>

.zenodo.json

@@ -35,7 +35,7 @@
         },
         {
             "scheme": "url",
-            "identifier": "http://www.mdpi.com/2072-4292/9/7/676",
+            "identifier": "https://www.mdpi.com/2072-4292/9/7/676",
             "relation": "isCitedBy",
             "resource_type": "publication-article"
         }

CITATION

@@ -23,7 +23,7 @@ A BibTeX entry for LaTeX users should look like this
   month        = jul,
   year         = 2017,
   note         = {{This is the version as used in Scheffler et al.
-                   (2017): http://www.mdpi.com/2072-4292/9/7/676.}},
+                   (2017): https://www.mdpi.com/2072-4292/9/7/676.}},
   publisher    = {Zenodo},
   version      = {0.2.1},
   doi          = {10.5281/zenodo.3743085},

README.rst

@@ -9,7 +9,7 @@ An Automated and Robust Open-Source Image Co-Registration Software for Multi-Sen
 * Free software: GNU General Public License v3 or later (GPLv3+)
 * **Documentation:** https://danschef.git-pages.gfz-potsdam.de/arosics/doc/
 * The (open-access) **paper** corresponding to this software repository can be found here:
-  `Scheffler et al. 2017 <http://www.mdpi.com/2072-4292/9/7/676>`__
+  `Scheffler et al. 2017 <https://www.mdpi.com/2072-4292/9/7/676>`__
   (cite as: Scheffler D, Hollstein A, Diedrich H, Segl K, Hostert P. AROSICS: An Automated and Robust Open-Source
   Image Co-Registration Software for Multi-Sensor Satellite Data. Remote Sensing. 2017; 9(7):676).
 * Information on how to **cite the AROSICS Python package** can be found in the

arosics/CoReg.py

@@ -196,8 +196,8 @@ class COREG(object):
 
         :param fmt_out:
             raster file format for output file. ignored if path_out is None. can be any GDAL compatible raster file
-            format (e.g. 'ENVI', 'GTIFF'; default: ENVI). Refer to http://www.gdal.org/formats_list.html to get a full
-            list of supported formats.
+            format (e.g. 'ENVI', 'GTIFF'; default: ENVI). Refer to https://gdal.org/drivers/raster/index.html to get a
+            full list of supported formats.
 
         :param out_crea_options:
           GDAL creation options for the output image, e.g. ["QUALITY=80", "REVERSIBLE=YES", "WRITE_METADATA=YES"]
@@ -260,7 +260,8 @@ class COREG(object):
             map coordinates of data corners within image to be shifted. ignored if footprint_poly_tgt is given.
 
         :param nodata:
-            no data values for reference image and image to be shifted
+            no-data values for reference image and image to be shifted. The default is (None, None) which indicates
+            that there is no specific no-data value for both of the input images.
 
         :param calc_corners:
              calculate true positions of the dataset corners in order to get a useful matching window position within
@@ -1367,7 +1368,7 @@ class COREG(object):
         # compute SSIM BEFORE shift correction #
         ########################################
 
-        # using gaussian weights could lead to value errors in case of small images when the automatically calulated
+        # using gaussian weights could lead to value errors in case of small images when the automatically calculated
         # window size exceeds the image size
         self.ssim_orig = ssim(normalize(np.ma.masked_equal(self.matchWin[:],
                                                            self.matchWin.nodata)),

arosics/CoReg_local.py

@@ -128,8 +128,8 @@ class COREG_LOCAL(object):
 
         :param fmt_out:
             raster file format for output file. ignored if path_out is None. Can be any GDAL compatible raster file
-            format (e.g. 'ENVI', 'GTIFF'; default: ENVI). Refer to http://www.gdal.org/formats_list.html to get a full
-            list of supported formats.
+            format (e.g. 'ENVI', 'GTIFF'; default: ENVI). Refer to https://gdal.org/drivers/raster/index.html to get a
+            full list of supported formats.
 
         :param out_crea_options:
             GDAL creation options for the output image, e.g. ["QUALITY=80", "REVERSIBLE=YES", "WRITE_METADATA=YES"]

bin/arosics_cli.py → arosics/arosics_cli.py

@@ -117,12 +117,12 @@ def get_arosics_argparser():
                     '(daniel.scheffler [at] gfz-potsdam [dot] de). The scientific background is described in the paper '
                     'Scheffler D, Hollstein A, Diedrich H, Segl K, Hostert P. AROSICS: An Automated and Robust '
                     'Open-Source Image Co-Registration Software for Multi-Sensor Satellite Data. Remote Sensing. 2017;'
-                    ' 9(7):676." (http://www.mdpi.com/2072-4292/9/7/676)',
+                    ' 9(7):676." (https://www.mdpi.com/2072-4292/9/7/676)',
 
         epilog="DETAILED DESCRIPTION: AROSICS detects and corrects global as well as local misregistrations between "
                "two input images in the subpixel scale, that are often present in satellite imagery. The input images "
-               "can have any GDAL compatible image format (http://www.gdal.org/formats_list.html). Both of them must "
-               "be approximately geocoded. In case of ENVI files, this means they must have a 'map info' and a "
+               "can have any GDAL compatible image format (https://gdal.org/drivers/raster/index.html). Both of them "
+               "must be approximately geocoded. In case of ENVI files, this means they must have a 'map info' and a "
                "'coordinate system string' as attributes of their header file. The input images must have a geographic "
                "overlap but clipping them to same geographical extent is NOT neccessary. Please do not perform any "
                "spatial resampling of the input images before applying this algorithm. Any needed resampling of the "

docs/about.rst

@@ -19,7 +19,7 @@ is automatically calculated.
 For detailed algorithm description and use cases refer to the corresponding (open-access) paper that can be found here:
 `Scheffler D, Hollstein A, Diedrich H, Segl K, Hostert P. AROSICS: An Automated and Robust Open-Source Image
 Co-Registration Software for Multi-Sensor Satellite Data. Remote Sensing. 2017; 9(7):676
-<http://www.mdpi.com/2072-4292/9/7/676>`__.
+<https://www.mdpi.com/2072-4292/9/7/676>`__.
 
 
 * GitLab Repository: https://git.gfz-potsdam.de/danschef/arosics/

docs/cli_reference.rst

@@ -7,7 +7,7 @@ arosics
 At the command line, arosics provides the **arosics** command:
 
 .. argparse::
-   :filename: ./../bin/arosics_cli.py
+   :filename: ./../arosics/arosics_cli.py
    :func: get_arosics_argparser
    :prog: arosics
 

docs/conf.py

@@ -31,7 +31,7 @@ project_root = os.path.dirname(cwd)
 # version is used.
 sys.path.insert(0, project_root)
 
-import arosics
+import arosics  # noqa E402
 
 # -- General configuration ---------------------------------------------
 

docs/usage/global_coreg.rst

@@ -144,7 +144,7 @@ numpy array and its corresponding geoinformation.
 
 To write the coregistered image to disk, the :class:`arosics.COREG` class needs to be instanced with a filepath given to
 keyword 'path_out'. The output raster format can be any format supported by GDAL.
-Find a list of supported formats here: http://www.gdal.org/formats_list.html
+Find a list of supported formats here: https://gdal.org/drivers/raster/index.html
 
 
 apply detected shifts to multiple images

docs/usage/input_data_requirements.rst

@@ -5,7 +5,7 @@ Compatible image formats
 ~~~~~~~~~~~~~~~~~~~~~~~~
 
 The input images can have any GDAL compatible image format. You can find a list here:
-http://www.gdal.org/formats_list.html
+https://gdal.org/drivers/raster/index.html
 
 
 Geocoding

setup.py

@@ -90,7 +90,7 @@ setup(
     description="An Automated and Robust Open-Source Image Co-Registration Software for Multi-Sensor Satellite Data",
     entry_points={
         'console_scripts': [
-            'arosics=bin.arosics_cli:main',
+            'arosics=arosics.arosics_cli:main',
         ],
     },
     extras_require={
@@ -107,7 +107,7 @@ setup(
     long_description=readme + '\n\n' + history,
     name='arosics',
     packages=find_packages(exclude=['tests*']),
-    scripts=["bin/arosics_cli.py"],  # TODO Deprecated in 1.4.1. Remove in future.
+    scripts=["arosics/arosics_cli.py"],  # TODO Deprecated in 1.4.1. Remove in future.
     setup_requires=req_setup,
     test_suite='tests',
     tests_require=req + req_test,

tests/test_COREG.py

@@ -308,6 +308,78 @@ class CompleteWorkflow_INTER1_S2A_S2A(unittest.TestCase):
             CR.show_image_footprints()
 
 
+class Test_Bug_SSIM_unequal_dims(unittest.TestCase):
+    def test_coreg(self):
+        # ref = '/home/gfz-fe/scheffler/temp/coreg_bug_ssim_unequal_dims/rgb.tif'
+        ref = '/home/gfz-fe/scheffler/temp/coreg_bug_ssim_unequal_dims/rgb_BSQ.bsq'
+        tgt = '/home/gfz-fe/scheffler/temp/coreg_bug_ssim_unequal_dims/red.tif'
+
+        cr = COREG(ref, tgt, wp=(392820.125995486, 5178269.142020599), ws=(2056, 2056), progress=False, nodata=(0, 0))
+        cr.calculate_spatial_shifts()
+
+    def test_coreg_local(self):
+        from arosics import COREG_LOCAL
+        # ref = '/home/gfz-fe/scheffler/temp/coreg_bug_ssim_unequal_dims/rgb.tif'
+        ref = '/home/gfz-fe/scheffler/temp/coreg_bug_ssim_unequal_dims/rgb_BSQ.bsq'
+        tgt = '/home/gfz-fe/scheffler/temp/coreg_bug_ssim_unequal_dims/red.tif'
+
+        kwargs = dict(
+            grid_res=512,
+            window_size=(2056, 2056),
+            path_out='/home/gfz-fe/scheffler/temp/coreg_bug_ssim_unequal_dims/output.tif',
+            projectDir=None,
+            q=False,
+            v=True,
+            fmt_out='GTIFF',
+            min_reliability=60,
+            max_shift=128,
+            max_iter=3,
+            match_gsd=False,
+            out_crea_options=[
+                'PHOTOMETRIC=MINISBLACK',
+                'COMPRESS=LZW',
+                'ALPHA=NO'],
+            CPUs=1)
+        # kwargs['nodata'] = (-10000, -10000)
+        kwargs['nodata'] = (0, -10000)
+        CRL = COREG_LOCAL(ref, tgt, **kwargs)
+        CRL.correct_shifts()
+
+    def test_from_dump(self):
+        import dill
+        with open('/home/gfz-fe/scheffler/temp/coreg_bug_ssim_unequal_dims/dump.dill', 'rb') as inF:
+            cr = dill.load(inF)
+
+        cr.ref.nodata = 0
+        cr.ignErr = False
+        cr.calculate_spatial_shifts()
+        cr._validate_ssim_improvement()
+
+
+class Test_Bug_SSIM_outOfRange(unittest.TestCase):
+    def test_coreg(self):
+        ref = '/home/gfz-fe/scheffler/temp/coreg_raul_alonso/reference.tif'
+        tgt = '/home/gfz-fe/scheffler/temp/coreg_raul_alonso/target.tif'
+        crl = COREG(ref, tgt,
+                    # window_size=(512,512),
+                    max_shift=10,
+                    nodata=(0, 0))
+        crl.calculate_spatial_shifts()
+        crl = None
+
+    def test_coreg_local(self):
+        from arosics import COREG_LOCAL
+        ref = '/home/gfz-fe/scheffler/temp/coreg_raul_alonso/reference.tif'
+        tgt = '/home/gfz-fe/scheffler/temp/coreg_raul_alonso/target.tif'
+        crl = COREG_LOCAL(ref, tgt, 50,
+                          # window_size=(512,512),
+                          max_shift=10,
+                          min_reliability=40,
+                          calc_corners=False,
+                          nodata=(0, 0))
+        crl.calculate_spatial_shifts()
+
+
 if __name__ == '__main__':
     import nose2
     nose2.main()