Added test and test data for geo.raster.conversion.raster2polygon(). Replaced...

Added test and test data for geo.raster.conversion.raster2polygon(). Replaced skimage downsampling by GDAL variant. Removed scikit-learn dependency.
Signed-off-by: Daniel Scheffler <danschef@gfz-potsdam.de>

.gitattributes

+*.tif filter=lfs diff=lfs merge=lfs -text
+*.bsq filter=lfs diff=lfs merge=lfs -text

HISTORY.rst

@@ -2,6 +2,14 @@
 History
 =======
 
+0.16.10 (2021-05-07)
+--------------------
+
+* Added test and test data for geo.raster.conversion.raster2polygon().
+* Replaced skimage downsampling by GDAL variant.
+* Removed scikit-learn dependency.
+
+
 0.16.9 (2021-05-07)
 -------------------
 

docs/installation.rst

@@ -42,7 +42,6 @@ to resolve the following dependencies before the pip installer is run:
     * geopandas
     * numpy
     * pyproj >=2.1.0
-    * scikit-image
     * shapely
 
 

py_tools_ds/geo/raster/conversion.py

@@ -31,6 +31,7 @@ from osgeo import gdal, osr, ogr
 from ...io.raster.gdal import get_GDAL_ds_inmem
 from ...processing.progress_mon import ProgressBar, Timer
 from ...compatibility.python.exceptions import TimeoutError as TimeoutError_comp
+from ..raster.reproject import warp_ndarray
 
 
 def raster2polygon(array, gt, prj, DN2extract=1, exact=True, maxfeatCount=None,
@@ -53,16 +54,12 @@ def raster2polygon(array, gt, prj, DN2extract=1, exact=True, maxfeatCount=None,
 
     # downsample input array in case is has more than 1e8 pixels to prevent crash
     if not exact and array.size > 1e8:  # 10000 x 10000 px
-        zoom_factor = 1e8 / array.size
-
         # downsample with nearest neighbour
-        from skimage.transform import rescale  # import here to avoid static TLS import error
-        array = rescale(array, zoom_factor, order=0, preserve_range=True, mode='edge').astype(bool)
-
-        # update pixel sizes within gt
-        gt = list(gt)
-        gt[1] /= zoom_factor
-        gt[5] /= zoom_factor
+        zoom_factor = (8000 * 8000 / array.size) ** 0.5
+        array, gt, prj = warp_ndarray(array, gt, prj,
+                                      out_gsd=(gt[1] / zoom_factor, gt[5] / zoom_factor),
+                                      rspAlg='near',
+                                      q=True)
 
     src_ds = get_GDAL_ds_inmem(array, gt, prj)
     src_band = src_ds.GetRasterBand(1)

requirements.txt

@@ -6,5 +6,4 @@ pandas
 pyproj>=2.1.0
 shapely
 six
-scikit-image
 spectral

setup.py

@@ -43,13 +43,13 @@ requirements = [
     'packaging',  # remove when dropping Python 2.7 support
     'pandas',
     'pyproj>=2.2.0',
-    'scikit-image',
     'shapely',
     'six',
     'spectral'
 ]
 setup_requirements = ['setuptools']
-test_requirements = requirements + ["coverage", "nose", "nose2", "nose-htmloutput", "rednose", "shapely", "urlchecker"]
+test_requirements = requirements + ["coverage", "gdal", "nose", "nose2", "nose-htmloutput", "rednose", "shapely",
+                                    "urlchecker"]
 
 setup(
     name='py_tools_ds',

tests/CI_docker/context/environment_py_tools_ds.yml

 name: py_tools_ds
 
 channels: &id1
-  - http://conda.anaconda.org/conda-forge
+  - conda-forge
 
 dependencies:
   - python=3.*.*

tests/test_geo/test_raster/test_conversion.py

+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+# py_tools_ds
+#
+# Copyright (C) 2019  Daniel Scheffler (GFZ Potsdam, daniel.scheffler@gfz-potsdam.de)
+#
+# 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/>.
+
+"""
+test_conversion
+---------------
+
+Tests for `py_tools_ds.geo.raster.conversion` module.
+"""
+
+import os
+from unittest import TestCase
+
+from osgeo import gdal
+
+from py_tools_ds.geo.raster.conversion import raster2polygon
+import py_tools_ds
+
+tests_path = os.path.abspath(os.path.join(py_tools_ds.__file__, "..", "..", "tests"))
+
+
+class Test_raster2polygon(TestCase):
+    def setUp(self) -> None:
+        try:
+            # load a large mask containing an irregular binary shape with a complex footprint (27408x17604)
+            ds = gdal.Open(os.path.join(tests_path, 'data', 'mask_large.tif'))
+            self.mask = ds.ReadAsArray().astype(bool)
+            self.gt = ds.GetGeoTransform()
+            self.prj = ds.GetProjection()
+
+        finally:
+            del ds
+
+    def test_raster2polygon(self):
+        raster2polygon(self.mask, self.gt, self.prj, exact=False)