Merge branch 'master' into dev

Conflicts:
	tests/test_COREG.py

.gitlab-ci.yml

@@ -12,18 +12,16 @@ variables:
 
 stages:
   - test
-  - deploy_pages
-  - deploy_to_pypi
+  - deploy
   - cleanup
 
 
 test_arosics:
   stage: test
   script:
-    - source /root/anaconda3/bin/activate
-    - export GDAL_DATA=/root/anaconda3/share/gdal
+    - source /root/miniconda3/bin/activate
+    - export GDAL_DATA=/root/miniconda3/share/gdal
     - export PYTHONPATH=$PYTHONPATH:/root  # /root <- directory needed later
-    - pip install rednose # remove as soon as it is included in test runner
     - make nosetests
     - make docs
   artifacts:
@@ -32,35 +30,69 @@ test_arosics:
     - docs/_build/html/
     - nosetests.html
     - nosetests.xml
+    when: always
+
+
+test_styles:
+  stage: test
+  script:
+    - source /root/miniconda3/bin/activate
+    - export GDAL_DATA=/root/miniconda3/share/gdal
+    - export PYTHONPATH=$PYTHONPATH:/root  # /root <- directory needed later
+    - make lint
+  artifacts:
+    paths:
+    - tests/linting/flake8.log
+    - tests/linting/pycodestyle.log
+    - tests/linting/pydocstyle.log
+    when: always
 
 
 test_arosics_install:
   stage: test
   script:
-    - source /root/anaconda3/bin/activate
-    - conda create -y -q --name arosics python=3.5
+    - source /root/miniconda3/bin/activate
+    - export GDAL_DATA=/root/miniconda3/share/gdal
+    - conda create -y -q --name arosics python=3
     - source activate arosics
-    - conda install --yes -q -c conda-forge numpy gdal scikit-image matplotlib # resolve these requirements with conda
+     # resolve some requirements with conda
+    - conda install --yes -q -c conda-forge numpy gdal scikit-image matplotlib pyproj rasterio shapely geopandas
+    # run installer
     - python setup.py install
+    # test if its importable
     - cd ..
     - pwd
     - ls
     - python -c "import arosics; print(arosics)"
     - python -c "from arosics import COREG, COREG_LOCAL"
+  only:
+    - master
 
 
-pages:
-  stage: deploy_pages
+pages:  # this job must be called 'pages' to advise GitLab to upload content to GitLab Pages
+  stage: deploy
   dependencies:
     - test_arosics
   script:
+    # Create the public directory
+    - rm -rf public
+    - mkdir public
+    - mkdir -p public/doc
+    - mkdir -p public/images/
     - mkdir -p public/coverage
-    - cp -r htmlcov/* public/coverage/
     - mkdir -p public/nosetests_reports
-    - cp nosetests.* public/nosetests_reports/
-    - mkdir -p public/doc
+    # Copy over the docs
     - cp -r docs/_build/html/* public/doc/
-
+    - cp -r docs/images/* public/images/
+    # Copy over the coverage reports
+    - cp -r htmlcov/* public/coverage/
+    # Copy over the nosetests reports
+    - cp nosetests.* public/nosetests_reports/
+    # Check if everything is working great
+    - ls -al public
+    - ls -al public/doc
+    - ls -al public/coverage
+    - ls -al public/nosetests_reports
   artifacts:
     paths:
       - public
@@ -70,11 +102,11 @@ pages:
 
 
 deploy_pypi:
-  stage: deploy_to_pypi
+  stage: deploy
   dependencies:
     - test_arosics
   script:   # Configure the PyPI credentials, then push the package, and cleanup the creds.
-    - source /root/anaconda3/bin/activate
+    - source /root/miniconda3/bin/activate
     - mkdir -p public/images/
     - cp -r docs/images/* public/images/
     - printf "[distutils]\nindex-servers =\n    pypi\n\n" >> ~/.pypirc

HISTORY.rst

@@ -28,11 +28,49 @@ Fixes and improvements:
 
 * fixed warping issues in case only very few tie points could be identified
 
-0.5.0 (coming soon)
--------------------
+0.5.0 (2017-09-19)
+------------------
+
+New features:
+
+* Added two test cases for local co-registration and the respective test data.
+
+* Added test cases for global co-registration
+
+* Added test of output writer and tie point grid visualization.
+
+* Added nosetests. Resolved some setup requirements by conda during test_arosics_install.
+
+* PEP8 code style now checked with automatic style checkers
 
 Fixes and improvements:
 
 * Coverage now also working in multiprocessing.
 
 * Replaced test data of test case INTER1 with LZW compressed GeoTIFFs to speed up testing.
+
+* Revised docker container builder.
+
+* Bugfix for unexpected FFTW return value that caused the matching to fail
+
+* Added some docstrings.
+
+* Refactored command line interface 'arosics.py' to 'arosics_cli.py' to fix import issues.
+
+* Added usage documentation for command line interface.
+
+* Removed pykrige from automatically installed libraries during setup. It is now optional (Fixes issue #12)
+
+* Bugfix in connection with optional library pyfftw.
+
+* Revised installation guidelines within README.rst, README.md and installation.rst. Added link for nosetests HTML report.
+
+* Fixed exception in case no arguments are provided to command line interface.
+
+* Revised error handling and added additional check for projection.
+
+* GDAL_DATA environment variable is now handled within py_tools_ds. Updated minimal version of py_tools_ds in setup.py.
+
+* Fixed pickling error when running COREG_LOCAL in multiprocessing under a Windows environment.
+
+* Replaced all occurrences of "quality grid" with "tie point grid". Updated version info.

Makefile

@@ -52,7 +52,9 @@ clean-test: ## remove test and coverage artifacts
 	rm -fr nosetests.xml
 
 lint: ## check style with flake8
-	flake8 arosics tests
+	flake8 --max-line-length=120 arosics tests > ./tests/linting/flake8.log
+	pycodestyle arosics --exclude="*.ipynb,*.ipynb*" --max-line-length=120 > ./tests/linting/pycodestyle.log
+	-pydocstyle arosics > ./tests/linting/pydocstyle.log
 
 test: ## run tests quickly with the default Python
 	python setup.py test

README.md

 
 [![logo](docs/images/arosics_logo.png)](https://gitext.gfz-potsdam.de/danschef/arosics/)
-  
+
 ### An Automated and Robust Open-Source Image Co-Registration Software for Multi-Sensor Satellite Data
 
 
 * Free software: GNU General Public License v3
 * Documentation: http://danschef.gitext.gfz-potsdam.de/arosics/doc/
-* The (open-access) paper corresponding to this software repository can be found here:  
+* The (open-access) paper corresponding to this software repository 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)
 
 
@@ -16,6 +16,9 @@
 [![build status](https://gitext.gfz-potsdam.de/danschef/arosics/badges/master/build.svg)](https://gitext.gfz-potsdam.de/danschef/arosics/commits/master)
 [![coverage report](https://gitext.gfz-potsdam.de/danschef/arosics/badges/master/coverage.svg)](http://danschef.gitext.gfz-potsdam.de/arosics/coverage/)
 [![pypi_status](https://img.shields.io/pypi/v/arosics.svg)](https://pypi.python.org/pypi/arosics)
+[![license](https://img.shields.io/pypi/l/arosics.svg)](https://gitext.gfz-potsdam.de/danschef/arosics/blob/master/LICENSE)
+[![python versions](https://img.shields.io/pypi/pyversions/arosics.svg)](https://img.shields.io/pypi/pyversions/arosics.svg)
+
 
 See also the latest [coverage](http://danschef.gitext.gfz-potsdam.de/arosics/coverage/) and the [nosetests](http://danschef.gitext.gfz-potsdam.de/arosics/nosetests_reports/nosetests.html) HTML report.
 
@@ -28,23 +31,23 @@ Perform automatic subpixel co-registration of two satellite image datasets based
 AROSICS detects and corrects local as well as global misregistrations between two input images in the subpixel scale, that are often present in satellite imagery.
 
 Prerequisites and hints:
-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 '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 data is done automatically. Thus, the input images may have different spatial resolutions. The current algorithm will not perform any ortho-rectification. So please use ortho-rectified input data in order to minimize local shifts in the input images.  
-  
-AROSICS supports local and global co-registration.  
-  
-* Local co-registration:  
-A dense grid of tie points is automatically computed, whereas tie points are subsequently validated using a multistage workflow. Only those tie points not marked as false-positives are used to compute the parameters of an affine transformation. Warping of the target image is done using an appropriate resampling technique (cubic by default).  
+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 '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 data is done automatically. Thus, the input images may have different spatial resolutions. The current algorithm will not perform any ortho-rectification. So please use ortho-rectified input data in order to minimize local shifts in the input images.
+
+AROSICS supports local and global co-registration.
 
-* Global co-registration:  
-Only a global X/Y translation is computed within a small subset of the input images (window position is adjustable). This allows very fast co-registration but only corrects for translational (global) X/Y shifts. The calculated subpixel-shifts are (by default) applied to the geocoding information of the output image. No spatial resampling is done automatically as long as both input images have the same projection. If you need the output image to be aligned to the reference image coordinate grid (by using an appropriate resampling algorithm), use the '-align_grids' option.  
+* Local co-registration:
+A dense grid of tie points is automatically computed, whereas tie points are subsequently validated using a multistage workflow. Only those tie points not marked as false-positives are used to compute the parameters of an affine transformation. Warping of the target image is done using an appropriate resampling technique (cubic by default).
 
+* Global co-registration:
+Only a global X/Y translation is computed within a small subset of the input images (window position is adjustable). This allows very fast co-registration but only corrects for translational (global) X/Y shifts. The calculated subpixel-shifts are (by default) applied to the geocoding information of the output image. No spatial resampling is done automatically as long as both input images have the same projection. If you need the output image to be aligned to the reference image coordinate grid (by using an appropriate resampling algorithm), use the '-align_grids' option.
+
+
+AROSICS is designed to robustly handle the typical difficulties of multi-sensoral/multi-temporal images. Clouds are automatically handled by the implemented outlier detection algorithms. The user may provide user-defined masks to exclude certain image areas from tie point creation. The image overlap area is automatically calculated. Thereby, no-data regions within the images are automatically respected. Providing the map coordinates of the actual data corners lets you save some calculation time, because in this case the automatic algorithm can be skipped. The no-data value of each image is automatically derived from the image corners. The verbose program mode gives some more output about the interim results, shows some figures and writes the used footprint and overlap polygons to disk. Note, that maybe the figures must be manually closed in in order to continue the processing (depending on your Python configuration).
 
-AROSICS is designed to robustly handle the typical difficulties of multi-sensoral/multi-temporal images. Clouds are automatically handled by the implemented outlier detection algorithms. The user may provide user-defined masks to exclude certain image areas from tie point creation. The image overlap area is automatically calculated. Thereby, no-data regions within the images are automatically respected. Providing the map coordinates of the actual data corners lets you save some calculation time, because in this case the automatic algorithm can be skipped. The no-data value of each image is automatically derived from the image corners. The verbose program mode gives some more output about the interim results, shows some figures and writes the used footprint and overlap polygons to disk. Note, that maybe the figures must be manually closed in in order to continue the processing (depending on your Python configuration).  
-  
 For further details regarding the implemented algorithm, example use cases, quality assessment and benchmarks refer to the above mentioned paper ([Scheffler et al. 2017](http://www.mdpi.com/2072-4292/9/7/676)).
 
 
- 
+
 
 Installation
 ------------
@@ -55,11 +58,15 @@ is run. This approach avoids problems with conflicting versions of the same soft
 Using [conda](https://conda.io/docs/), the recommended approach is:
 
 ```bash
-# create virtual environment for arosics, this is optional 
+# create virtual environment for arosics, this is optional
 conda create -y -q --name arosics python=3
 source activate arosics
-conda install -y -q -c conda-forge numpy gdal scikit-image matplotlib pyproj rasterio
-conda install -y -q -c conda-forge pyfftw basemap pykrige  # these libraries are optional
+conda install -y -q -c conda-forge numpy gdal scikit-image matplotlib pyproj rasterio shapely geopandas
+
+# optional libraries:
+conda install -y -q -c conda-forge basemap pykrige
+conda install -y -q -c conda-forge pyfftw  # Linux and MacOS
+conda install -y -q -c jesserobertson pyfftw  # Windows
 ```
 
 To install AROSICS, use the pip installer:
@@ -81,10 +88,7 @@ PATH=$PATH:/path/to/your/installation/folder/arosics:/path/to/your/installation/
 
 
 AROSICS has been tested with Python 3.4+ and Python 2.7. It should be fully compatible to all Python versions above 2.7.
-    
-
 
- 
 
 # Modules
 
@@ -215,7 +219,7 @@ CR.correct_shifts()
                  ('arr_shifted', array([[   0,    0,    0, ...,  953,  972, 1044],
                          [   0,    0,    0, ..., 1001,  973, 1019],
                          [   0,    0,    0, ...,  953,  985, 1020],
-                         ..., 
+                         ...,
                          [   0,    0,    0, ...,  755,  763,  773],
                          [   0,    0,    0, ...,  760,  763,  749],
                          [9999, 9999, 9999, ..., 9999, 9999, 9999]], dtype=uint16)),
@@ -265,7 +269,7 @@ DESHIFTER(im_target2, CR.coreg_info).correct_shifts()
                  ('arr_shifted', array([[   0,    0,    0, ...,  953,  972, 1044],
                          [   0,    0,    0, ..., 1001,  973, 1019],
                          [   0,    0,    0, ...,  953,  985, 1020],
-                         ..., 
+                         ...,
                          [   0,    0,    0, ...,  755,  763,  773],
                          [   0,    0,    0, ...,  760,  763,  749],
                          [9999, 9999, 9999, ..., 9999, 9999, 9999]], dtype=uint16)),
@@ -274,7 +278,7 @@ DESHIFTER(im_target2, CR.coreg_info).correct_shifts()
 
 
 
- 
+
 
 ### Shell console interface
 
@@ -285,7 +289,7 @@ The help instructions of the console interface can be accessed like this:
 python arosics_cli.py -h
 ```
 
-Follow these instructions to run AROSICS from a shell console. For example, the most simple call for a global 
+Follow these instructions to run AROSICS from a shell console. For example, the most simple call for a global
 co-registration would be like this:
 
 
@@ -293,9 +297,9 @@ co-registration would be like this:
 python arosics_cli.py global /path/to/your/ref_image.bsq /path/to/your/tgt_image.bsq
 ```
 
- 
 
- 
+
+
 
 ## CoReg_local
 
@@ -330,7 +334,7 @@ CRL.correct_shifts()
     Corner coordinates of image to be shifted:
     	[[319460.0, 5790510.0], [352270.0, 5900040.0], [409790.0, 5900040.0], [409790.0, 5790250.0], [319460.0, 5790250.0]]
     Matching window position (X,Y): 372220.10753674706/5841066.947109019
-    Calculating geometric quality grid (1977 points) in mode 'multiprocessing'...
+    Calculating tie point grid (1977 points) in mode 'multiprocessing'...
     	progress: |==================================================| 100.0% [1977/1977] Complete 9.75 sek
     Found 1144 valid GCPs.
     Correcting geometric shifts...
@@ -363,7 +367,7 @@ CRL.correct_shifts()
                  ('arr_shifted', array([[   0,    0,    0, ..., 1034,  996, 1001],
                          [   0,    0,    0, ..., 1046, 1114, 1124],
                          [   0,    0,    0, ..., 1021, 1126, 1148],
-                         ..., 
+                         ...,
                          [   0,    0,    0, ...,  760,  769,  805],
                          [   0,    0,    0, ...,  762,  755,  765],
                          [   0,    0,    0, ...,    0,    0,    0]], dtype=uint16)),
@@ -382,9 +386,9 @@ CRL = COREG_LOCAL(GeoArray(ref_ndarray, ref_gt, ref_prj),GeoArray(tgt_ndarray, t
 CRL.correct_shifts()
 ```
 
-#### visualize geometric quality grid with INITIAL shifts present in your input target image
+#### visualize tie point grid with INITIAL shifts present in your input target image
 
-Use the function COREG_LOCAL.view_CoRegPoints() to visualize the geometric quality grid with the calculated absolute lenghts of the shift vectors (the unit corresponds to the input projection - UTM in the shown example, thus the unit is 'meters'.).
+Use the function COREG_LOCAL.view_CoRegPoints() to visualize the tie point grid with the calculated absolute lenghts of the shift vectors (the unit corresponds to the input projection - UTM in the shown example, thus the unit is 'meters'.).
 
 NOTE: a calculation of reliable shifts above cloud covered areas is not possible. In the current version of AROSICS these areas are not masked. A proper masking is planned.
 
@@ -404,7 +408,7 @@ CRL.view_CoRegPoints(figsize=(15,15),backgroundIm='ref')
 
 The output figure shows the calculated absolute lenghts of the shift vectors - in this case with shifts up to ~25 meters.
 
-#### visualize geometric quality grid with shifts present AFTER shift correction
+#### visualize tie point grid with shifts present AFTER shift correction
 
 The remaining shifts after local correction can be calculated and visualized by instanciating COREG_LOCAL with the output path of the above instance of COREG_LOCAL.
 
@@ -422,7 +426,7 @@ CRL_after_corr.view_CoRegPoints(figsize=(15,15),backgroundIm='ref')
     	[[319460.0, 5790540.0], [352270.0, 5900030.0], [409780.0, 5900030.0], [409780.0, 5790260.0], [322970.0, 5790250.0], [319460.0, 5790280.0]]
     Matching window position (X,Y): 372216.38593955856/5841068.390957352
     Note: array has been downsampled to 1000 x 1000 for faster visualization.
-    Calculating geometric quality grid (1977 points) in mode 'multiprocessing'...
+    Calculating tie point grid (1977 points) in mode 'multiprocessing'...
     	progress: |==================================================| 100.0% [1977/1977] Complete 10.78 sek
 
 
@@ -432,7 +436,7 @@ CRL_after_corr.view_CoRegPoints(figsize=(15,15),backgroundIm='ref')
 
 The output figure shows a significant reduction of geometric shifts.
 
-#### show the points table of the calculated geometric quality grid
+#### show the points table of the calculated tie point grid
 
 NOTE: Point records where no valid match has been found are filled with -9999.
 
@@ -1510,18 +1514,18 @@ CRL.CoRegPoints_table
 
 
 
-#### export geometric quality grid to an ESRI point shapefile
+#### export tie point grid to an ESRI point shapefile
 
 
 ```python
-CRL.quality_grid.to_PointShapefile(path_out='/path/to/your/output_shapefile.shp')
+CRL.tiepoint_grid.to_PointShapefile(path_out='/path/to/your/output_shapefile.shp')
 ```
 
- 
+
 
 ### Shell console interface
 
-Follow these instructions to run AROSICS from a shell console. For example, the most simple call for a local 
+Follow these instructions to run AROSICS from a shell console. For example, the most simple call for a local
 co-registration would be like this:
 
 
@@ -1532,7 +1536,7 @@ python arosics_cli.py local /path/to/your/ref_image.bsq /path/to/your/tgt_image.
 
 # Credits
 
-This package was created with [Cookiecutter](https://github.com/audreyr/cookiecutter) and the 
-[audreyr/cookiecutter-pypackage](https://github.com/audreyr/cookiecutter-pypackage) project template. 
+This package was created with [Cookiecutter](https://github.com/audreyr/cookiecutter) and the
+[audreyr/cookiecutter-pypackage](https://github.com/audreyr/cookiecutter-pypackage) project template.
 The test data represent modified Copernicus Sentinel data (2016).
 

README.rst

@@ -29,6 +29,10 @@ Status
         :target: http://danschef.gitext.gfz-potsdam.de/arosics/coverage/
 .. image:: https://img.shields.io/pypi/v/arosics.svg
         :target: https://pypi.python.org/pypi/arosics
+.. image:: https://img.shields.io/pypi/l/arosics.svg
+        :target: https://gitext.gfz-potsdam.de/danschef/arosics/blob/master/LICENSE
+.. image:: https://img.shields.io/pypi/pyversions/arosics.svg
+        :target: https://img.shields.io/pypi/pyversions/arosics.svg
 
 See also the latest coverage_ report and the nosetests_ HTML report.
 
@@ -52,8 +56,12 @@ Using conda_, the recommended approach is:
     # create virtual environment for arosics, this is optional
     conda create -y -q --name arosics python=3
     source activate arosics
-    conda install -y -q -c conda-forge numpy gdal scikit-image matplotlib pyproj rasterio
-    conda install -y -q -c conda-forge pyfftw basemap pykrige  # these libraries are optional
+    conda install -y -q -c conda-forge numpy gdal scikit-image matplotlib pyproj rasterio shapely geopandas
+
+    # optional libraries:
+    conda install -y -q -c conda-forge basemap pykrige
+    conda install -y -q -c conda-forge pyfftw  # Linux and MacOS
+    conda install -y -q -c jesserobertson pyfftw  # Windows
 
 
 To install AROSICS, use the pip installer:
@@ -73,7 +81,6 @@ Or clone the repository via GIT and update the PATH environment variable:
     git clone https://gitext.gfz-potsdam.de/danschef/py_tools_ds.git
     PATH=$PATH:/path/to/your/installation/folder/arosics:/path/to/your/installation/folder/geoarray:/path/to/your/installation/folder/py_tools_ds
 
-
 Credits
 -------
 

arosics/__init__.py

@@ -2,24 +2,26 @@
 
 """Top-level package for arosics."""
 
-__author__ = """Daniel Scheffler"""
-__email__ = 'daniel.scheffler@gfz-potsdam.de'
-__version__ = '0.4.22'
-__versionalias__ = '2017-09-05_02'
-
 import warnings
+from importlib import util
 
 from arosics.CoReg import COREG
 from arosics.CoReg_local import COREG_LOCAL
 from arosics.DeShifter import DESHIFTER
 from arosics.Tie_Point_Grid import Tie_Point_Grid
 
+__author__ = """Daniel Scheffler"""
+__email__ = 'daniel.scheffler@gfz-potsdam.de'
+__version__ = '0.8.4'
+__versionalias__ = '2018-03-08_01'
+__all__ = ['COREG',
+           'COREG_LOCAL',
+           'DESHIFTER',
+           'Tie_Point_Grid']
+
 
 # check optional dependencies
-try:
-    import pyfftw
-except ImportError:
-    pyfftw = None
+if not util.find_spec('pyfftw'):
     warnings.warn('PYFFTW library is missing. However, coregistration works. But in some cases it can be much slower.')
 
-del warnings, pyfftw
+del util, warnings

arosics/geometry.py

 # -*- coding: utf-8 -*-
-__author__='Daniel Scheffler'
-
 import warnings
 import sys
 
 # custom
-import numpy  as np
+import numpy as np
 from geopandas import GeoDataFrame
 
-try:
-    import gdal
-    import osr
-    import ogr
-except ImportError:
-    from osgeo import gdal
-    from osgeo import osr
-    from osgeo import ogr
-
 # internal modules
 from py_tools_ds.geo.coord_calc import calc_FullDataset_corner_positions
 from py_tools_ds.geo.coord_trafo import pixelToMapYX, imYX2mapYX
 from geoarray import GeoArray
 
-
-
+__author__ = 'Daniel Scheffler'
 
 
 def angle_to_north(XY):
     """Calculates the angle between the lines [origin:[0,0],north:[0,1]] and
      [origin:[0,0],pointXY:[X,Y]] in clockwise direction. Returns values between 0 and 360 degrees.
      """
-    XY    = np.array(XY)
-    XYarr = XY if len(XY.shape)==2 else XY.reshape((1,2))
-    return np.abs(np.degrees(np.array(np.arctan2(XYarr[:,1],XYarr[:,0])-np.pi/2))%360)
+    XY = np.array(XY)
+    XYarr = XY if len(XY.shape) == 2 else XY.reshape((1, 2))
+    return np.abs(np.degrees(np.array(np.arctan2(XYarr[:, 1], XYarr[:, 0]) - np.pi / 2)) % 360)
 
 
-def get_true_corner_mapXY(fPath_or_geoarray, band=0, noDataVal=None, mp=1, v=0, q=0):
+def get_true_corner_mapXY(fPath_or_geoarray, band=0, noDataVal=None, mp=1, v=0, q=0):  # pragma: no cover
     # FIXME this function is not used anymore
     """
 
@@ -48,71 +36,77 @@ def get_true_corner_mapXY(fPath_or_geoarray, band=0, noDataVal=None, mp=1, v=0,
     :return:
     """
     warnings.warn('This function is not in use anymore. Use it on your own risk!', DeprecationWarning)
-    geoArr    = GeoArray(fPath_or_geoarray) if not isinstance(fPath_or_geoarray,GeoArray) else fPath_or_geoarray
+    geoArr = GeoArray(fPath_or_geoarray) if not isinstance(fPath_or_geoarray, GeoArray) else fPath_or_geoarray
 
-    rows,cols = geoArr.shape[:2]
-    gt, prj   = geoArr.geotransform, geoArr.projection
+    rows, cols = geoArr.shape[:2]
+    gt, prj = geoArr.geotransform, geoArr.projection
 
     assert gt and prj, 'GeoTransform an projection must be given for calculation of LonLat corner coordinates.'
 
-    mask_1bit = np.zeros((rows,cols),dtype='uint8') # zeros -> image area later overwritten by ones
+    mask_1bit = np.zeros((rows, cols), dtype='uint8')  # zeros -> image area later overwritten by ones
 
     if noDataVal is None:
-        mask_1bit[:,:] = 1
-    elif noDataVal=='ambiguous':
+        mask_1bit[:, :] = 1
+    elif noDataVal == 'ambiguous':
         warnings.warn("No data value could not be automatically detected. Thus the matching window used for shift "
-              "calculation had to be centered in the middle of the overlap area without respecting no data values. "
-              "To avoid this provide the correct no data values for reference and shift image via '-nodata'")
-        mask_1bit[:,:] = 1
+                      "calculation had to be centered in the middle of the overlap area without respecting no data "
+                      "values. To avoid this provide the correct no data values for reference and shift image via "
+                      "'-nodata'")
+        mask_1bit[:, :] = 1
     else:
-        band_data = geoArr[band] # TODO implement gdal_ReadAsArray_mp (reading in multiprocessing)
-        mask_1bit[band_data!=noDataVal] = 1
+        band_data = geoArr[band]  # TODO implement gdal_ReadAsArray_mp (reading in multiprocessing)
+        mask_1bit[band_data != noDataVal] = 1
 
-    if v: print('detected no data value',noDataVal)
+    if v:
+        print('detected no data value', noDataVal)
 
     try:
         corner_coords_YX = calc_FullDataset_corner_positions(mask_1bit, assert_four_corners=False, algorithm='shapely')
     except Exception:
         if v:
             warnings.warn("\nCalculation of corner coordinates failed within algorithm 'shapely' (Exception: %s)."
-                          " Using algorithm 'numpy' instead." %sys.exc_info()[1])
-        corner_coords_YX = calc_FullDataset_corner_positions(mask_1bit, assert_four_corners=False, algorithm='numpy') # FIXME numpy algorithm returns wrong values for S2A_OPER_MSI_L1C_TL_SGS__20160608T153121_A005024_T33UUU_B03.jp2 (Hannes)
+                          " Using algorithm 'numpy' instead." % sys.exc_info()[1])
+        # FIXME numpy algorithm returns wrong values for S2A_OPER_MSI_L1C_TL_SGS__20160608T153121_A005024_T33UUU_B03.jp2
+        # FIXME (Hannes)
+        corner_coords_YX = \
+            calc_FullDataset_corner_positions(mask_1bit, assert_four_corners=False, algorithm='numpy')
 
-    if len(corner_coords_YX)==4: # this avoids shapely self intersection
-        corner_coords_YX = list(np.array(corner_coords_YX)[[0,1,3,2]]) # UL, UR, LL, LR => UL, UR, LR, LL
+    if len(corner_coords_YX) == 4:  # this avoids shapely self intersection
+        corner_coords_YX = list(np.array(corner_coords_YX)[[0, 1, 3, 2]])  # UL, UR, LL, LR => UL, UR, LR, LL
 
     # check if enough unique coordinates have been found
-    if not len(GeoDataFrame(corner_coords_YX).drop_duplicates().values)>=3:
+    if not len(GeoDataFrame(corner_coords_YX).drop_duplicates().values) >= 3:
         if not q:
             warnings.warn('\nThe algorithm for automatically detecting the actual image coordinates did not find '
                           'enough unique corners. Using outer image corner coordinates instead.')
-        corner_coords_YX = ((0, 0), (0, cols-1), (rows-1, 0), (rows-1, cols-1))
+        corner_coords_YX = ((0, 0), (0, cols - 1), (rows - 1, 0), (rows - 1, cols - 1))
 
     # check if all points are unique
-    #all_coords_are_unique = len([UL, UR, LL, LR]) == len(GeoDataFrame([UL, UR, LL, LR]).drop_duplicates().values)
-    #UL, UR, LL, LR = (UL, UR, LL, LR) if all_coords_are_unique else ((0, 0), (0, cols-1), (rows-1, 0), (rows-1, cols-1))
+    # all_coords_are_unique = len([UL, UR, LL, LR]) == len(GeoDataFrame([UL, UR, LL, LR]).drop_duplicates().values)
+    # UL, UR, LL, LR = \
+    #   (UL, UR, LL, LR) if all_coords_are_unique else ((0, 0), (0, cols-1), (rows-1, 0), (rows-1, cols-1))
 
-    get_mapYX     = lambda YX: pixelToMapYX(list(reversed(YX)),geotransform=gt,projection=prj)[0]
+    def get_mapYX(YX): return pixelToMapYX(list(reversed(YX)), geotransform=gt, projection=prj)[0]
     corner_pos_XY = [list(reversed(i)) for i in [get_mapYX(YX) for YX in corner_coords_YX]]
     return corner_pos_XY
 
 
-def get_subset_GeoTransform(gt_fullArr,subset_box_imYX):
-    gt_subset = list(gt_fullArr[:]) # copy
-    gt_subset[3],gt_subset[0] = imYX2mapYX(subset_box_imYX[0],gt_fullArr)
+def get_subset_GeoTransform(gt_fullArr, subset_box_imYX):
+    gt_subset = list(gt_fullArr[:])  # copy
+    gt_subset[3], gt_subset[0] = imYX2mapYX(subset_box_imYX[0], gt_fullArr)
     return gt_subset
 
 
 def get_gdalReadInputs_from_boxImYX(boxImYX):
     """Returns row_start,col_start,rows_count,cols_count and assumes boxImYX as [UL_YX,UR_YX,LR_YX,LL_YX)"""
     rS, cS = boxImYX[0]
-    clip_sz_x = abs(boxImYX[1][1]-boxImYX[0][1]) # URx-ULx
-    clip_sz_y = abs(boxImYX[0][0]-boxImYX[3][0]) # ULy-LLy
-    return cS, rS, clip_sz_x,clip_sz_y
+    clip_sz_x = abs(boxImYX[1][1] - boxImYX[0][1])  # URx-ULx
+    clip_sz_y = abs(boxImYX[0][0] - boxImYX[3][0])  # ULy-LLy
+    return cS, rS, clip_sz_x, clip_sz_y
 
 
 def get_GeoArrayPosition_from_boxImYX(boxImYX):
     """Returns row_start,row_end,col_start,col_end and assumes boxImYX as [UL_YX,UR_YX,LR_YX,LL_YX)"""
-    rS, cS = boxImYX[0] # UL
-    rE, cE = boxImYX[2] # LR
-    return rS, rE-1, cS, cE-1 # -1 because boxImYX represents outer box and includes the LR corner of LR pixel
\ No newline at end of file
+    rS, cS = boxImYX[0]  # UL
+    rE, cE = boxImYX[2]  # LR
+    return rS, rE - 1, cS, cE - 1  # -1 because boxImYX represents outer box and includes the LR corner of LR pixel

arosics/io.py

-import ctypes