From fdc9ed0d0e67945c476d6684af00bea7f21796a9 Mon Sep 17 00:00:00 2001
From: jlaura <jlaura@usgs.gov>
Date: Wed, 22 Aug 2018 20:48:58 -0700
Subject: [PATCH] Adds tests for GDAL not installed (#71)
* Adds tests for GDAL not installed
* typo in travis else
* proper matrix build
* semicolons...I write python
* updates test with conditional osr
* Proper pytest skipping enabled for conditional imports
* missed pytest import
* Typos
* Mixing pytest and unittest
* typos and imports
* typos city
* removes hasosr
* fixes wrapper for conditional gdal
* Removes test for non-available gdal
---
.travis.yml | 14 ++-
plio/camera/__init__.py | 20 ++++
plio/camera/csm.py | 13 +--
plio/camera/tests/test_csm.py | 10 +-
plio/io/__init__.py | 23 ++++
plio/io/extract_metadata.py | 21 ++--
plio/io/io_gdal.py | 25 ++---
plio/io/io_spectral_profiler.py | 3 +-
plio/io/tests/test_io_gdal.py | 15 +--
plio/io/tests/test_io_spectral_profiler.py | 6 +-
plio/io/tests/test_metadata.py | 121 +++++++++++----------
11 files changed, 155 insertions(+), 116 deletions(-)
diff --git a/.travis.yml b/.travis.yml
index f4d6990..618e0fa 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -10,8 +10,10 @@ os:
- osx
env:
- - PYTHON_VERSION=3.5
- - PYTHON_VERSION=3.6
+ - PYTHON_VERSION=3.5 HAS_GDAL=true
+ - PYTHON_VERSION=3.6 HAS_GDAL=true
+ - PYTHON_VERSION=3.5 HAS_GDAL=false
+ - PYTHON_VERSION=3.6 HAS_GDAL=false
before_install:
# We do this conditionally because it saves us some downloading if the
@@ -36,8 +38,12 @@ before_install:
install:
- conda config --add channels usgs-astrogeology
- - conda config --add channels conda-forge
- - conda install libgdal gdal numpy pyproj h5py pvl scipy protobuf affine jinja2 networkx pandas sqlalchemy pyyaml ncurses usgscam pytest pytest-cov sh coveralls nbsphinx
+ - conda config --add channels conda-forge
+ - if $HAS_GDAL; then
+ conda install libgdal gdal numpy pyproj h5py pvl scipy protobuf affine jinja2 networkx pandas sqlalchemy pyyaml ncurses pytest pytest-cov sh coveralls nbsphinx;
+ else
+ conda install numpy pyproj h5py pvl scipy protobuf affine jinja2 networkx pandas sqlalchemy pyyaml ncurses pytest pytest-cov sh coveralls nbsphinx;
+ fi
script:
- pytest --cov=plio
diff --git a/plio/camera/__init__.py b/plio/camera/__init__.py
index e69de29..3f4336c 100644
--- a/plio/camera/__init__.py
+++ b/plio/camera/__init__.py
@@ -0,0 +1,20 @@
+import importlib
+import warnings
+
+cam = importlib.find_loader('usgscam')
+cycsm_isd = importlib.find_loader('cycsm.isd')
+
+if cam:
+ cam = cam.load_module()
+
+if cycsm_isd:
+ cycsm_isd = cycsm_isd.load_module()
+
+def conditional_cameras(func):
+ def cam_check(*args, **kwargs):
+ if cam:
+ return func(*args, **kwargs)
+ else:
+ warning.warn('Trying to call a camera method, but usgscam is not installed.')
+ return None
+ return cam_check
\ No newline at end of file
diff --git a/plio/camera/csm.py b/plio/camera/csm.py
index b555efc..6e20e79 100644
--- a/plio/camera/csm.py
+++ b/plio/camera/csm.py
@@ -1,17 +1,11 @@
import datetime
import json
-try:
- import usgscam as cam
- from cycsm.isd import Isd
- camera_support = True
-except:
- camera_support = False
import requests
from plio.utils.utils import find_in_dict
from plio.io.io_json import NumpyEncoder
-
+from plio.camera import conditional_cameras, cam, cycsm_isd
def data_from_cube(header):
data = {}
@@ -28,16 +22,15 @@ def data_from_cube(header):
data['SPACECRAFT_CLOCK_START_COUNT'] = find_in_dict(header, 'SpacecraftClockCount')
return data
+@conditional_cameras
def create_camera(obj, url='http://smalls:8002/api/1.0/missions/mars_reconnaissance_orbiter/csm_isd'):
- if not camera_support:
- print("Usgscam library not installed. Camera capabilities are disabled")
data = json.dumps(data_from_cube(obj.metadata), cls=NumpyEncoder)
r = requests.post(url, data=data)
# Get the ISD back and instantiate a local ISD for the image
isd = r.json()['data']['isd']
- i = Isd.loads(isd)
+ i = cycsm_isd.Isd.loads(isd)
# Create the plugin and camera as usual
plugin = cam.genericls.Plugin()
diff --git a/plio/camera/tests/test_csm.py b/plio/camera/tests/test_csm.py
index ce6cf12..7f2cd90 100644
--- a/plio/camera/tests/test_csm.py
+++ b/plio/camera/tests/test_csm.py
@@ -5,9 +5,7 @@ from unittest import mock
import pytest
import pvl
-import usgscam
-
-from plio.camera import csm
+from plio.camera import csm, cam, conditional_cameras
from plio.examples import get_path
def mock_requests_post(*args, **kwargs):
@@ -35,11 +33,13 @@ def header():
def req_obj():
return
+@pytest.mark.skipif(cam is None, reason="Cameras not installed")
def test_data_from_cube(header):
data = csm.data_from_cube(header)
assert data['START_TIME'] == datetime.datetime(2008, 9, 17, 5, 8, 10, 820000)
+@pytest.mark.skipif(cam is None, reason="Cameras not installed")
@mock.patch('requests.post', side_effect=mock_requests_post)
def test_create_camera(header):
- cam = csm.create_camera(header)
- assert isinstance(cam, usgscam.genericls.SensorModel)
+ created_camera = csm.create_camera(header)
+ assert isinstance(create_camera, cam.genericls.SensorModel)
diff --git a/plio/io/__init__.py b/plio/io/__init__.py
index f040a7c..ce170f1 100644
--- a/plio/io/__init__.py
+++ b/plio/io/__init__.py
@@ -1,3 +1,26 @@
+# Conditional imports for GDAL
+import importlib
+import warnings
+
+gdal = importlib.find_loader('gdal')
+ogr = importlib.find_loader('osgeo.ogr')
+osr = importlib.find_loader('osr')
+
+if gdal:
+ gdal = gdal.load_module()
+ ogr = ogr.load_module()
+ osr = osr.load_module()
+ gdal.UseExceptions()
+
+def conditional_gdal(func):
+ def has_gdal(*args, **kwargs):
+ if gdal:
+ return func(*args, **kwargs)
+ else:
+ warning.warn('Trying to call a GDAL method, but GDAL is not installed.')
+ return None
+ return has_gdal
+
from . import io_autocnetgraph
from . import io_controlnetwork
from . import io_db
diff --git a/plio/io/extract_metadata.py b/plio/io/extract_metadata.py
index 547b578..6d94c2a 100644
--- a/plio/io/extract_metadata.py
+++ b/plio/io/extract_metadata.py
@@ -1,14 +1,10 @@
-try:
- from osgeo import osr
- hasosr = True
-except:
- hasosr = False
-
+from plio.io import osr, conditional_gdal
import_options = ['ImportFromWkt', 'ImportFromProj4',
'ImportFromEPSG', 'ImportFromUSGS',
'ImportFromXML']
+@conditional_gdal
def extract_projstring(proj_string):
"""
Import an OSR supported projection string into
@@ -25,10 +21,7 @@ def extract_projstring(proj_string):
OSR spatial reference object
"""
- if hasosr:
- srs = osr.SpatialReference()
- else:
- return
+ srs = osr.SpatialReference()
for import_option in import_options:
try:
func = getattr(srs, import_option)
@@ -42,6 +35,7 @@ def extract_projstring(proj_string):
srs.MorphFromESRI()
return srs
+@conditional_gdal
def get_standard_parallels(srs):
"""
Get all standard parallels for a given map projection
@@ -62,6 +56,7 @@ def get_standard_parallels(srs):
parallels[i] = srs.GetProjParm('Standard_Parallel_{}'.format(i+1), 0.0)
return parallels
+@conditional_gdal
def get_central_meridian(srs):
"""
Get the central meridian of the projection
@@ -79,6 +74,7 @@ def get_central_meridian(srs):
return srs.GetProjParm('central_meridian', 0.0)
+@conditional_gdal
def get_spheroid(srs):
"""
Get the semi-major, semi-minor, and inverse flattening
@@ -100,6 +96,7 @@ def get_spheroid(srs):
invflattening = srs.GetInvFlattening()
return semimajor, semiminor, invflattening
+@conditional_gdal
def get_projection_name(srs):
"""
Extract the projection name from a
@@ -118,6 +115,7 @@ def get_projection_name(srs):
proj_name = srs.GetAttrValue("PROJECTION", 0)
return proj_name
+@conditional_gdal
def get_false_easting(srs):
"""
Extract the false easting parameter from a
@@ -136,6 +134,7 @@ def get_false_easting(srs):
return srs.GetProjParm('False_Easting', 0)
+@conditional_gdal
def get_false_northing(srs):
"""
Extract the false northing parameter from a
@@ -154,6 +153,7 @@ def get_false_northing(srs):
return srs.GetProjParm('False_Northing', 0)
+@conditional_gdal
def get_scale_factor(srs):
"""
Extract the scale factor, k, from a spatial reference system (if present)
@@ -171,6 +171,7 @@ def get_scale_factor(srs):
return srs.GetProjParm('scale_factor', 1.0)
+@conditional_gdal
def get_latitude_of_origin(srs):
"""
Extract the latitude of origin from
diff --git a/plio/io/io_gdal.py b/plio/io/io_gdal.py
index 249511d..a890015 100644
--- a/plio/io/io_gdal.py
+++ b/plio/io/io_gdal.py
@@ -6,20 +6,12 @@ import warnings
import affine
import numpy as np
import pvl
-try:
- # Try the full GDAL stack
- import gdal
- from osgeo import ogr
- import osr
- gdal.UseExceptions()
- has_gdal = True
-except:
- has_gdal = False
-
-from plio.io import extract_metadata
+
+
+from plio.io import extract_metadata, conditional_gdal
from plio.geofuncs import geofuncs
from plio.utils.utils import find_in_dict
-
+from plio.io import gdal, ogr, osr
NP2GDAL_CONVERSION = {
"uint8": 1,
@@ -158,7 +150,7 @@ class GeoDataset(object):
"""
self.file_name = file_name
- if not has_gdal:
+ if not gdal:
raise ImportError('No module name gdal.')
self.dataset = gdal.Open(file_name)
if self.dataset is None:
@@ -581,7 +573,7 @@ def array_to_raster(array, file_name, projection=None,
A GDAL supported bittype, e.g. GDT_Int32
Default: GDT_Float64
"""
- if not has_gdal:
+ if not gdal:
raise ImportError('No module named gdal.')
driver = gdal.GetDriverByName(outformat)
try:
@@ -617,7 +609,7 @@ def array_to_raster(array, file_name, projection=None,
bnd.WriteArray(array[:,:,i - 1])
dataset.FlushCache()
-
+@conditional_gdal
def match_rasters(match_to, match_from, destination,
resampling_method='GRA_Bilinear', ndv=0):
"""
@@ -658,9 +650,6 @@ def match_rasters(match_to, match_from, destination,
match_from__srs = match_from.dataset.GetProjection()
match_from__gt = match_from.geotransform
- if not has_gdal:
- raise ImportError('No module named gdal.')
-
dst = gdal.GetDriverByName('GTiff').Create(destination, width, height, 1,
gdalconst.GDT_Float64)
diff --git a/plio/io/io_spectral_profiler.py b/plio/io/io_spectral_profiler.py
index a82db13..dc31aa0 100755
--- a/plio/io/io_spectral_profiler.py
+++ b/plio/io/io_spectral_profiler.py
@@ -4,7 +4,6 @@ import pvl
import numpy as np
from plio.utils.utils import find_in_dict
-from plio.io.io_gdal import GeoDataset
class Spectral_Profiler(object):
@@ -169,5 +168,7 @@ class Spectral_Profiler(object):
-------
"""
+
+ from plio.io.io_gdal import GeoDataset
path, ext = os.path.splitext(self.input_data)
self.browse = GeoDataset(path + extension)
diff --git a/plio/io/tests/test_io_gdal.py b/plio/io/tests/test_io_gdal.py
index f3d5255..38ef04f 100644
--- a/plio/io/tests/test_io_gdal.py
+++ b/plio/io/tests/test_io_gdal.py
@@ -3,14 +3,17 @@ import sys
import unittest
import numpy as np
+import pytest
from plio.examples import get_path
sys.path.insert(0, os.path.abspath('..'))
from plio.io import io_gdal
+from plio.io import gdal
+@pytest.mark.skipif(gdal is None, reason="GDAL not installed")
class TestMercator(unittest.TestCase):
def setUp(self):
self.dataset = io_gdal.GeoDataset(get_path('Mars_MGS_MOLA_ClrShade_MAP2_0.0N0.0_MERC.tif'))
@@ -101,7 +104,7 @@ class TestMercator(unittest.TestCase):
self.assertEqual(arr.dtype, np.int8)
self.assertAlmostEqual(np.mean(arr), 10.10353227, 6)
-
+@pytest.mark.skipif(gdal is None, reason="GDAL not installed")
class TestLambert(unittest.TestCase):
def setUp(self):
self.dataset = io_gdal.GeoDataset(get_path('Lunar_LRO_LOLA_Shade_MAP2_90.0N20.0_LAMB.tif'))
@@ -143,6 +146,7 @@ class TestLambert(unittest.TestCase):
self.assertEqual(sp, [73.0, 42.0])
+@pytest.mark.skipif(gdal is None, reason="GDAL not installed")
class TestPolar(unittest.TestCase):
def setUp(self):
self.dataset = io_gdal.GeoDataset(get_path('Mars_MGS_MOLA_ClrShade_MAP2_90.0N0.0_POLA.tif'))
@@ -171,6 +175,7 @@ class TestPolar(unittest.TestCase):
self.assertAlmostEqual(pixel[0], 0.0, 6)
self.assertAlmostEqual(pixel[1], 0.0, 6)
+@pytest.mark.skipif(gdal is None, reason="GDAL not installed")
class TestWriter(unittest.TestCase):
def setUp(self):
self.arr = np.random.random((100,100))
@@ -240,11 +245,3 @@ class TestWriter(unittest.TestCase):
except:
pass
-class TestWithoutGdal(unittest.TestCase):
- def test_without_gdal(self):
- io_gdal.has_gdal = False
- with self.assertRaises(ImportError):
- io_gdal.GeoDataset('foo')
-
- def tearDown(self):
- io_gdal.has_gdal = True
diff --git a/plio/io/tests/test_io_spectral_profiler.py b/plio/io/tests/test_io_spectral_profiler.py
index 0446607..6b5b390 100644
--- a/plio/io/tests/test_io_spectral_profiler.py
+++ b/plio/io/tests/test_io_spectral_profiler.py
@@ -3,12 +3,15 @@ import sys
import unittest
import pandas as pd
+import pytest
sys.path.insert(0, os.path.abspath('..'))
from plio.examples import get_path
from plio.io import io_spectral_profiler
from plio.io.io_gdal import GeoDataset
+from plio.io import gdal
+
class Test_Spectral_Profiler_IO(unittest.TestCase):
@@ -19,7 +22,8 @@ class Test_Spectral_Profiler_IO(unittest.TestCase):
ds = io_spectral_profiler.Spectral_Profiler(self.examplefile)
self.assertEqual(ds.nspectra, 38)
self.assertEqual(ds.spectra[0].columns.tolist(), ['RAW', 'REF1', 'REF2', 'QA', 'RAD'])
-
+
+ @pytest.mark.skipif(gdal is None, reason="GDAL not installed")
def test_read_browse(self):
ds = io_spectral_profiler.Spectral_Profiler(self.examplefile)
ds.open_browse()
diff --git a/plio/io/tests/test_metadata.py b/plio/io/tests/test_metadata.py
index 5b28ff5..df63a00 100644
--- a/plio/io/tests/test_metadata.py
+++ b/plio/io/tests/test_metadata.py
@@ -1,60 +1,65 @@
-import unittest
-
-from osgeo import osr
-
-osr.UseExceptions()
+import pytest
from plio.io import extract_metadata as em
-
-
-class TestSRSProjectionExtraction(unittest.TestCase):
-
- def setUp(self):
- self.wktsrs = 'PROJCS["Moon2000_Mercator180",GEOGCS["GCS_Moon_2000",DATUM["D_Moon_2000",SPHEROID["Moon_2000_IAU_IAG",1737400.0,0.0]],PRIMEM["Reference_Meridian",0.0],UNIT["Degree",0.0174532925199433]],PROJECTION["Mercator"],PARAMETER["False_Easting",0.0],PARAMETER["False_Northing",0.0],PARAMETER["Central_Meridian",180.0],PARAMETER["Standard_Parallel_1",0.0],UNIT["Meter",1.0]]'
- self.wktsrs = 'PROJCS["Mercator",GEOGCS["GCS_Moon_2000",DATUM["D_Moon_2000",SPHEROID["Moon_2000_IAU_IAG",1737400.0,0.0]],PRIMEM["Reference_Meridian",0.0],UNIT["Degree",0.0174532925199433]],PROJECTION["Mercator"],PARAMETER["False_Easting",0.0],PARAMETER["False_Northing",0.0],PARAMETER["Central_Meridian",180.0],PARAMETER["Standard_Parallel_1",0.0],UNIT["Meter",1.0]]'
- self.srs = em.extract_projstring(self.wktsrs)
-
- def test_generate_srs(self):
- self.srs = em.extract_projstring(self.wktsrs)
-
- def test_false_easting(self):
- e = em.get_false_easting(self.srs)
- self.assertEqual(e, 0.0)
-
- def test_false_northing(self):
- n = em.get_false_northing(self.srs)
- self.assertEqual(n, 0.0)
-
- def test_projection_name(self):
- name = em.get_projection_name(self.srs)
- self.assertEqual(name, 'Mercator_2SP')
-
- def test_axes_extract(self):
- smajor, sminor, invflattening = em.get_spheroid(self.srs)
- self.assertEqual(smajor, 1737400.0)
- self.assertEqual(sminor, 1737400.0)
- self.assertEqual(invflattening, 0.0)
-
- def test_get_standard_parallels(self):
- parallels = em.get_standard_parallels(self.srs)
- self.assertEqual(parallels[0], 0.0)
- self.assertEqual(parallels[1], 0.0)
-
- def test_get_central_meridian(self):
- clon = em.get_central_meridian(self.srs)
- self.assertEqual(clon, 180.0)
-
- def test_export_to_proj4(self):
- """
- Check that proj4 is not supporting Moon2000_Mercator
- """
- proj4 = self.srs.ExportToProj4()
- self.assertEqual(proj4, '+proj=merc +lon_0=180 +lat_ts=0 +x_0=0 +y_0=0 +a=1737400 +b=1737400 +units=m +no_defs ')
-
- def test_scale_factor(self):
- k = em.get_scale_factor(self.srs)
- self.assertEqual(k, 1.0)
-
- def test_latitude_of_origin(self):
- lo = em.get_latitude_of_origin(self.srs)
- self.assertEqual(lo, 90.0)
+from plio.io import gdal
+
+@pytest.fixture
+def wkt_moon():
+ wktsrs = 'PROJCS["Moon2000_Mercator180",GEOGCS["GCS_Moon_2000",DATUM["D_Moon_2000",SPHEROID["Moon_2000_IAU_IAG",1737400.0,0.0]],PRIMEM["Reference_Meridian",0.0],UNIT["Degree",0.0174532925199433]],PROJECTION["Mercator"],PARAMETER["False_Easting",0.0],PARAMETER["False_Northing",0.0],PARAMETER["Central_Meridian",180.0],PARAMETER["Standard_Parallel_1",0.0],UNIT["Meter",1.0]]'
+ return em.extract_projstring(wktsrs)
+
+@pytest.fixture
+def srs_mars():
+ wktsrs = 'PROJCS["Mercator",GEOGCS["GCS_Moon_2000",DATUM["D_Moon_2000",SPHEROID["Moon_2000_IAU_IAG",1737400.0,0.0]],PRIMEM["Reference_Meridian",0.0],UNIT["Degree",0.0174532925199433]],PROJECTION["Mercator"],PARAMETER["False_Easting",0.0],PARAMETER["False_Northing",0.0],PARAMETER["Central_Meridian",180.0],PARAMETER["Standard_Parallel_1",0.0],UNIT["Meter",1.0]]'
+ return em.extract_projstring(wktsrs)
+
+@pytest.mark.skipif(gdal is None, reason="GDAL not installed")
+def test_false_easting(srs_mars):
+ e = em.get_false_easting(srs_mars)
+ assert e == 0.0
+
+@pytest.mark.skipif(gdal is None, reason="GDAL not installed")
+def test_false_northing(srs_mars):
+ n = em.get_false_northing(srs_mars)
+ assert n == 0.0
+
+@pytest.mark.skipif(gdal is None, reason="GDAL not installed")
+def test_projection_name(srs_mars):
+ name = em.get_projection_name(srs_mars)
+ assert name == 'Mercator_2SP'
+
+@pytest.mark.skipif(gdal is None, reason="GDAL not installed")
+def test_axes_extract(srs_mars):
+ smajor, sminor, invflattening = em.get_spheroid(srs_mars)
+ assert smajor == 1737400.0
+ assert sminor == 1737400.0
+ assert invflattening == 0.0
+
+@pytest.mark.skipif(gdal is None, reason="GDAL not installed")
+def test_get_standard_parallels(srs_mars):
+ parallels = em.get_standard_parallels(srs_mars)
+ assert parallels[0] == 0.0
+ assert parallels[1] == 0.0
+
+@pytest.mark.skipif(gdal is None, reason="GDAL not installed")
+def test_get_central_meridian(srs_mars):
+ clon = em.get_central_meridian(srs_mars)
+ assert clon == 180.0
+
+@pytest.mark.skipif(gdal is None, reason="GDAL not installed")
+def test_export_to_proj4(srs_mars):
+ """
+ Check that proj4 is not supporting Moon2000_Mercator
+ """
+ proj4 = srs_mars.ExportToProj4()
+ assert proj4 == '+proj=merc +lon_0=180 +lat_ts=0 +x_0=0 +y_0=0 +a=1737400 +b=1737400 +units=m +no_defs '
+
+@pytest.mark.skipif(gdal is None, reason="GDAL not installed")
+def test_scale_factor(srs_mars):
+ k = em.get_scale_factor(srs_mars)
+ assert k == 1.0
+
+@pytest.mark.skipif(gdal is None, reason="GDAL not installed")
+def test_latitude_of_origin(srs_mars):
+ lo = em.get_latitude_of_origin(srs_mars)
+ assert lo == 90.0
--
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