.travis.yml

@@ -2,10 +2,6 @@ dist: trusty
 
 language: python
 
-python:
-  - "2.7"
-  - "3.6"
-
 env:
   global:
     - PIP_WHEEL_DIR=$HOME/.cache/pip/wheels
@@ -14,17 +10,33 @@ env:
     - GDALBUILD=$HOME/gdalbuild
     - PROJINST=$HOME/gdalinstall
     - PROJBUILD=$HOME/projbuild
-  matrix:
-    - GDALVERSION="1.11.5" PROJVERSION="4.8.0"
-    - GDALVERSION="2.0.3" PROJVERSION="4.9.3"
-    - GDALVERSION="2.1.4" PROJVERSION="4.9.3"
-    - GDALVERSION="2.2.4" PROJVERSION="4.9.3"
-    - GDALVERSION="2.3.3" PROJVERSION="4.9.3"
-    - GDALVERSION="2.4.2" PROJVERSION="4.9.3"
-    - GDALVERSION="3.0.1" PROJVERSION="6.1.1"
-    - GDALVERSION="master" PROJVERSION="6.1.1"
 
-matrix:
+jobs:
+  include:
+    - python: "2.7"
+      env: GDALVERSION="1.11.5" PROJVERSION="4.8.0"
+    - python: "2.7"
+      env: GDALVERSION="2.2.4" PROJVERSION="4.9.3"
+    - python: "3.6"
+      env: GDALVERSION="2.2.4" PROJVERSION="4.9.3"
+    - python: "3.6"
+      env: GDALVERSION="2.3.3" PROJVERSION="4.9.3"
+    - python: "2.7"
+      env: GDALVERSION="2.4.3" PROJVERSION="4.9.3"
+    - python: "3.6"
+      env: GDALVERSION="2.4.3" PROJVERSION="4.9.3"
+    - python: "3.7"
+      env: GDALVERSION="2.4.3" PROJVERSION="4.9.3"
+    - python: "3.8"
+      env: GDALVERSION="2.4.3" PROJVERSION="4.9.3"
+    - python: "3.6"
+      env: GDALVERSION="3.0.1" PROJVERSION="6.1.1"
+    - python: "3.7"
+      env: GDALVERSION="3.0.1" PROJVERSION="6.1.1"
+    - python: "3.8"
+      env: GDALVERSION="3.0.1" PROJVERSION="6.1.1"
+    - python: "3.8"
+      env: GDALVERSION="master" PROJVERSION="6.1.1"
  allow_failures:
     - env: GDALVERSION="master" PROJVERSION="6.1.1"
 

CHANGES.txt

 Changes
 =======
 
+1.1.1 (2019-11-13)
+------------------
+
+Bug fixes:
+
+- Calling a dataset's sample method with coordinates outside the extent of a
+  dataset with a nodata value of None has raised a TypeError (#1822). Now, it
+  gives the values we would get from a boundless read of the dataset's values.
+- Use new set_proj_search_path() function to set the PROJ data search path. For
+  GDAL versions before 3.0 this sets the PROJ_LIB environment variable. For
+  GDAL version 3.0 this calls OSRSetPROJSearchPaths(), which overrides
+  PROJ_LIB (#1823).
+- Check for header.dxf file instead of pcs.csv when looking for installed GDAL
+  data. The latter is gone with GDAL 3.0 but the former remains (#1823).
+- RGB rasters are now properly displayed by rasterio.plot.show (#1650).
+
+Notes:
+
+- The wheels on PyPI include GDAL 2.4.3 with a patch that addresses the
+  multithreading issue reported in #1828.
+
 1.1.0 (2019-10-07)
 ------------------
 

debian/changelog

+rasterio (1.1.1-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream release.
+
+ -- Bas Couwenberg <sebastic@debian.org>  Thu, 14 Nov 2019 05:29:17 +0100
+
 rasterio (1.1.0-1) unstable; urgency=medium
 
   * Team upload.

rasterio/__init__.py

@@ -42,7 +42,7 @@ import rasterio.path
 
 
 __all__ = ['band', 'open', 'pad', 'Env']
-__version__ = "1.1.0"
+__version__ = "1.1.1"
 __gdal_version__ = gdal_version()
 
 # Rasterio attaches NullHandler to the 'rasterio' logger and its

rasterio/_env.pyx

@@ -20,6 +20,7 @@ import threading
 from rasterio._base cimport _safe_osr_release
 from rasterio._err import CPLE_BaseError
 from rasterio._err cimport exc_wrap_ogrerr, exc_wrap_int
+from rasterio._shim cimport set_proj_search_path
 
 from libc.stdio cimport stderr
 
@@ -243,18 +244,18 @@ class GDALDataFinder(object):
         if prefix is None:
             prefix = __file__
         datadir = os.path.abspath(os.path.join(os.path.dirname(prefix), "gdal_data"))
-        return datadir if os.path.exists(os.path.join(datadir, 'pcs.csv')) else None
+        return datadir if os.path.exists(os.path.join(datadir, 'header.dxf')) else None
 
     def search_prefix(self, prefix=sys.prefix):
         """Check sys.prefix location"""
         datadir = os.path.join(prefix, 'share', 'gdal')
-        return datadir if os.path.exists(os.path.join(datadir, 'pcs.csv')) else None
+        return datadir if os.path.exists(os.path.join(datadir, 'header.dxf')) else None
 
     def search_debian(self, prefix=sys.prefix):
         """Check Debian locations"""
         gdal_release_name = GDALVersionInfo("RELEASE_NAME")
         datadir = os.path.join(prefix, 'share', 'gdal', '{}.{}'.format(*gdal_release_name.split('.')[:2]))
-        return datadir if os.path.exists(os.path.join(datadir, 'pcs.csv')) else None
+        return datadir if os.path.exists(os.path.join(datadir, 'header.dxf')) else None
 
 
 @contextmanager
@@ -359,6 +360,8 @@ cdef class GDALEnv(ConfigEnv):
 
                     if 'PROJ_LIB' in os.environ:
                         log.debug("PROJ_LIB found in environment: %r.", os.environ['PROJ_LIB'])
+                        path = os.environ["PROJ_LIB"]
+                        set_proj_data_search_path(path)
 
                     elif PROJDataFinder().has_data():
                         log.debug("PROJ data files are available at built-in paths")
@@ -367,8 +370,8 @@ cdef class GDALEnv(ConfigEnv):
                         path = PROJDataFinder().search()
 
                         if path:
-                            os.environ['PROJ_LIB'] = path
-                            log.debug("PROJ data not found in environment, set to %r.", path)
+                            log.debug("PROJ data not found in environment, setting to %r.", path)
+                            set_proj_data_search_path(path)
 
                     if driver_count() == 0:
                         CPLPopErrorHandler()
@@ -404,3 +407,8 @@ cdef class GDALEnv(ConfigEnv):
 
     def _dump_open_datasets(self):
         GDALDumpOpenDatasets(stderr)
+
+
+def set_proj_data_search_path(path):
+    """Set PROJ data search path"""
+    set_proj_search_path(path)

rasterio/_io.pyx

@@ -762,30 +762,35 @@ cdef class DatasetReaderBase(DatasetBase):
                 mask = mask | self.read_masks(i, **kwargs)
             return mask
 
-    def sample(self, xy, indexes=None):
+    def sample(self, xy, indexes=None, masked=False):
         """Get the values of a dataset at certain positions
 
         Values are from the nearest pixel. They are not interpolated.
 
         Parameters
         ----------
-        xy : iterable, pairs of floats
-            A sequence or generator of (x, y) pairs.
-
-        indexes : list of ints or a single int, optional
-            If `indexes` is a list, the result is a 3D array, but is
-            a 2D array if it is a band index number.
+        xy : iterable
+            Pairs of x, y coordinates (floats) in the dataset's
+            reference system.
+        indexes : int or list of int
+            Indexes of dataset bands to sample.
+        masked : bool, default: False
+            Whether to mask samples that fall outside the extent of the
+            dataset.
 
         Returns
-        -------
-        Iterable, yielding dataset values for the specified `indexes`
-        as an ndarray.
+        ------
+        iterable
+            Arrays of length equal to the number of specified indexes
+            containing the dataset values for the bands corresponding to
+            those indexes.
+
         """
         # In https://github.com/mapbox/rasterio/issues/378 a user has
         # found what looks to be a Cython generator bug. Until that can
         # be confirmed and fixed, the workaround is a pure Python
         # generator implemented in sample.py.
-        return sample_gen(self, xy, indexes)
+        return sample_gen(self, xy, indexes=indexes, masked=masked)
 
 
 @contextmanager

rasterio/_shim.pxd

@@ -7,3 +7,4 @@ cdef int io_multi_band(GDALDatasetH hds, int mode, float xoff, float yoff, float
 cdef int io_multi_mask(GDALDatasetH hds, int mode, float xoff, float yoff, float width, float height, object data, Py_ssize_t[:] indexes, int resampling=*) except -1
 cdef const char* osr_get_name(OGRSpatialReferenceH hSrs)
 cdef void osr_set_traditional_axis_mapping_strategy(OGRSpatialReferenceH hSrs)
+cdef void set_proj_search_path(object path)

rasterio/_shim1.pyx

@@ -5,6 +5,8 @@ include "directives.pxi"
 # The baseline GDAL API.
 include "gdal.pxi"
 
+import os
+
 # Implementation specific to GDAL<2.0
 from rasterio import dtypes
 from rasterio.enums import Resampling
@@ -185,3 +187,7 @@ cdef const char* osr_get_name(OGRSpatialReferenceH hSrs):
 
 cdef void osr_set_traditional_axis_mapping_strategy(OGRSpatialReferenceH hSrs):
     pass
+
+
+cdef void set_proj_search_path(object path):
+    os.environ["PROJ_LIB"] = path

rasterio/_shim20.pyx

@@ -8,6 +8,7 @@ include "gdal.pxi"
 # Shim API for GDAL >= 2.0
 include "shim_rasterioex.pxi"
 
+import os
 
 # Declarations and implementations specific for GDAL = 2.0
 cdef extern from "gdal.h" nogil:
@@ -77,3 +78,7 @@ cdef const char* osr_get_name(OGRSpatialReferenceH hSrs):
 
 cdef void osr_set_traditional_axis_mapping_strategy(OGRSpatialReferenceH hSrs):
     pass
+
+
+cdef void set_proj_search_path(object path):
+    os.environ["PROJ_LIB"] = path

rasterio/_shim21.pyx

@@ -10,6 +10,7 @@ include "gdal.pxi"
 # Shim API for GDAL >= 2.0
 include "shim_rasterioex.pxi"
 
+import os
 
 # Declarations and implementations specific for GDAL >= 2.1
 cdef extern from "gdal.h" nogil:
@@ -78,3 +79,7 @@ cdef const char* osr_get_name(OGRSpatialReferenceH hSrs):
 
 cdef void osr_set_traditional_axis_mapping_strategy(OGRSpatialReferenceH hSrs):
     pass
+
+
+cdef void set_proj_search_path(object path):
+    os.environ["PROJ_LIB"] = path

rasterio/_shim30.pyx

@@ -25,6 +25,7 @@ cdef extern from "ogr_srs_api.h" nogil:
 
     const char* OSRGetName(OGRSpatialReferenceH hSRS)
     void OSRSetAxisMappingStrategy(OGRSpatialReferenceH hSRS, OSRAxisMappingStrategy)
+    void OSRSetPROJSearchPaths(const char *const *papszPaths)
 
 
 from rasterio._err cimport exc_wrap_pointer
@@ -90,3 +91,12 @@ cdef const char* osr_get_name(OGRSpatialReferenceH hSrs):
 
 cdef void osr_set_traditional_axis_mapping_strategy(OGRSpatialReferenceH hSrs):
     OSRSetAxisMappingStrategy(hSrs, OAMS_TRADITIONAL_GIS_ORDER)
+
+
+cdef void set_proj_search_path(object path):
+    cdef char **paths = NULL
+    cdef const char *path_c = NULL
+    path_b = path.encode("utf-8")
+    path_c = path_b
+    paths = CSLAddString(paths, path_c)
+    OSRSetPROJSearchPaths(paths)

rasterio/env.py

@@ -10,7 +10,7 @@ import warnings
 
 from rasterio._env import (
         GDALEnv, get_gdal_config, set_gdal_config,
-        GDALDataFinder, PROJDataFinder)
+        GDALDataFinder, PROJDataFinder, set_proj_data_search_path)
 from rasterio.compat import string_types, getargspec
 from rasterio.errors import (
     EnvError, GDALVersionError, RasterioDeprecationWarning)
@@ -645,13 +645,9 @@ if 'GDAL_DATA' not in os.environ:
             os.environ['GDAL_DATA'] = path
             log.debug("GDAL_DATA not found in environment, set to %r.", path)
 
-if 'PROJ_LIB' not in os.environ:
-
-    path = PROJDataFinder().search_wheel()
-
-    if path:
-        os.environ['PROJ_LIB'] = path
-        log.debug("PROJ data found in package, PROJ_LIB set to %r.", path)
+if "PROJ_LIB" in os.environ:
+    path = os.environ["PROJ_LIB"]
+    set_proj_data_search_path(path)
 
 # See https://github.com/mapbox/rasterio/issues/1631.
 elif PROJDataFinder().has_data():
@@ -661,5 +657,5 @@ if 'PROJ_LIB' not in os.environ:
     path = PROJDataFinder().search()
 
     if path:
-            os.environ['PROJ_LIB'] = path
-            log.debug("PROJ data not found in environment, set to %r.", path)
+        log.debug("PROJ data not found in environment, setting to %r.", path)
+        set_proj_data_search_path(path)

rasterio/plot.py

@@ -93,10 +93,19 @@ def show(source, with_bounds=True, contour=False, contour_label_kws=None,
             arr = source.read(1, masked=True)
         else:
             try:
-                source_colorinterp = OrderedDict(zip(source.indexes, source.colorinterp))
+
+                # Lookup table for the color space in the source file. This will allow us to re-order it
+                # to RGB if needed
+                source_colorinterp = OrderedDict(zip(source.colorinterp, source.indexes))
+
                 colorinterp = rasterio.enums.ColorInterp
+
+                # Gather the indexes of the RGB channels in that order
                 rgb_indexes = [source_colorinterp[ci] for ci in
                                (colorinterp.red, colorinterp.green, colorinterp.blue)]
+
+                # Read the image in the proper order so the numpy array will have the colors in the
+                # order expected by matplotlib (RGB)
                 arr = source.read(rgb_indexes, masked=True)
                 arr = reshape_as_image(arr)
 

rasterio/sample.py

@@ -5,8 +5,29 @@ import numpy
 from rasterio.windows import Window
 
 
-def sample_gen(dataset, xy, indexes=None):
-    """Generator for sampled pixels"""
+def sample_gen(dataset, xy, indexes=None, masked=False):
+    """Sample pixels from a dataset
+
+    Parameters
+    ----------
+    dataset : rasterio Dataset
+        Opened in "r" mode.
+    xy : iterable
+        Pairs of x, y coordinates in the dataset's reference system.
+    indexes : int or list of int
+        Indexes of dataset bands to sample.
+    masked : bool, default: False
+        Whether to mask samples that fall outside the extent of the
+        dataset.
+
+    Yields
+    ------
+    array
+        A array of length equal to the number of specified indexes
+        containing the dataset values for the bands corresponding to
+        those indexes.
+
+    """
     index = dataset.index
     read = dataset.read
 
@@ -15,9 +36,9 @@ def sample_gen(dataset, xy, indexes=None):
 
     for x, y in xy:
         row_off, col_off = index(x, y)
-        if row_off < 0 or col_off < 0:
-            yield numpy.ones((dataset.count,), dtype=dataset.dtypes[0]) * dataset.nodata
-        else:
+#        if row_off < 0 or col_off < 0:
+#            yield numpy.ones((dataset.count,), dtype=dataset.dtypes[0]) * dataset.nodata
+#        else:
         window = Window(col_off, row_off, 1, 1)
-            data = read(indexes, window=window, masked=False)
+        data = read(indexes, window=window, masked=masked, boundless=True)
         yield data[:, 0, 0]

tests/test__env.py

@@ -13,7 +13,7 @@ def mock_wheel(tmpdir):
     moduledir = tmpdir.mkdir("rasterio")
     moduledir.ensure("__init__.py")
     moduledir.ensure("_env.py")
-    moduledir.ensure("gdal_data/pcs.csv")
+    moduledir.ensure("gdal_data/header.dxf")
     moduledir.ensure("proj_data/epsg")
     return moduledir
 
@@ -21,7 +21,7 @@ def mock_wheel(tmpdir):
 @pytest.fixture
 def mock_fhs(tmpdir):
     """A fake FHS system"""
-    tmpdir.ensure("share/gdal/pcs.csv")
+    tmpdir.ensure("share/gdal/header.dxf")
     tmpdir.ensure("share/proj/epsg")
     return tmpdir
 
@@ -29,13 +29,13 @@ def mock_fhs(tmpdir):
 @pytest.fixture
 def mock_debian(tmpdir):
     """A fake Debian multi-install system"""
-    tmpdir.ensure("share/gdal/1.11/pcs.csv")
-    tmpdir.ensure("share/gdal/2.0/pcs.csv")
-    tmpdir.ensure("share/gdal/2.1/pcs.csv")
-    tmpdir.ensure("share/gdal/2.2/pcs.csv")
-    tmpdir.ensure("share/gdal/2.3/pcs.csv")
-    tmpdir.ensure("share/gdal/2.4/pcs.csv")
-    tmpdir.ensure("share/gdal/3.0/pcs.csv")
+    tmpdir.ensure("share/gdal/1.11/header.dxf")
+    tmpdir.ensure("share/gdal/2.0/header.dxf")
+    tmpdir.ensure("share/gdal/2.1/header.dxf")
+    tmpdir.ensure("share/gdal/2.2/header.dxf")
+    tmpdir.ensure("share/gdal/2.3/header.dxf")
+    tmpdir.ensure("share/gdal/2.4/header.dxf")
+    tmpdir.ensure("share/gdal/3.0/header.dxf")
     tmpdir.ensure("share/proj/epsg")
     return tmpdir
 

tests/test_env.py

@@ -138,7 +138,7 @@ def test_ensure_env_decorator_sets_gdal_data_prefix(find_file, gdalenv, monkeypa
 
     find_file.return_value = None
 
-    tmpdir.ensure("share/gdal/pcs.csv")
+    tmpdir.ensure("share/gdal/header.dxf")
     monkeypatch.delenv('GDAL_DATA', raising=False)
     monkeypatch.setattr(sys, 'prefix', str(tmpdir))
 
@@ -154,7 +154,7 @@ def test_ensure_env_decorator_sets_gdal_data_wheel(find_file, gdalenv, monkeypat
 
     find_file.return_value = None
 
-    tmpdir.ensure("gdal_data/pcs.csv")
+    tmpdir.ensure("gdal_data/header.dxf")
     monkeypatch.delenv('GDAL_DATA', raising=False)
     monkeypatch.setattr(_env, '__file__', str(tmpdir.join(os.path.basename(_env.__file__))))
 

tests/test_sampling.py

+import numpy
+
 import rasterio
 
 
@@ -13,6 +15,24 @@ def test_sampling_beyond_bounds():
         assert list(data) == [0, 0, 0]
 
 
+def test_sampling_beyond_bounds_no_nodata():
+    with rasterio.open('tests/data/RGB2.byte.tif') as src:
+        data = next(src.sample([(-10, 2719200.0)]))
+        assert list(data) == [0, 0, 0]
+
+
+def test_sampling_beyond_bounds_masked():
+    with rasterio.open('tests/data/RGBA.byte.tif') as src:
+        data = next(src.sample([(-10, 2719200.0)], masked=True))
+        assert list(data.mask) == [True, True, True, False]
+
+
+def test_sampling_beyond_bounds_nan():
+    with rasterio.open('tests/data/float_nan.tif') as src:
+        data = next(src.sample([(-10, 0.0)]))
+        assert numpy.isnan(data)
+
+
 def test_sampling_indexes():
     with rasterio.open('tests/data/RGB.byte.tif') as src:
         data = next(src.sample([(220650.0, 2719200.0)], indexes=[2]))