Merge pull request #181 from alexlib/python3

Python 3 compatibility

.gitignore

@@ -12,6 +12,7 @@ py_bind/optv/*.c
 py_bind/dist
 py_bind/build
 py_bind/liboptv
+py_bind/optv.egg-info/
 
 liboptv/config.h.in~
 liboptv/tests/check_fb.trs

.travis.yml

@@ -8,7 +8,7 @@ before_install:
 
 install:
   - conda update --yes conda
-  - conda create -n testenv --yes $DEPS numpy cython pyyaml nose python=$TRAVIS_PYTHON_VERSION
+  - conda create -n testenv --yes $DEPS numpy cython pyyaml nose six python=$TRAVIS_PYTHON_VERSION
   - source activate testenv
 
   # for debugging...

docker/Dockerfile.python3

@@ -0,0 +1,11 @@
+# A Dockerfile for an Ubuntu machine that can compile liboptv and the Cython extensions
+
+FROM python:3.7-stretch
+
+RUN apt-get update
+RUN apt-get --assume-yes install cmake
+RUN apt-get --assume-yes install g++
+# RUN apt-get --assume-yes install python-pip
+# RUN apt-get --assume-yes install python3
+# RUN pip install virtualenv
+RUN python3 -m venv /env

docker/docker-compose.yml

@@ -1,9 +1,11 @@
 # Set up the Ubuntu container so we can develop the Cython code on it
 version: '3'
 services:
-  optv-dev:
-    image: ptv-ubuntu:1
-    build: ./
+  optv-dev-python3:
+    image: ptv-ubuntu:python3
+    build: 
+      context: ./
+      dockerfile: Dockerfile.python3
     volumes:
       - ../:/src
     command: tail -f /dev/null

py_bind/README.txt

@@ -44,7 +44,7 @@ Testing the installation
 Regardless of the system you installed on, the shell commands are the same:
 
   cd tests/
-  nosetests .
+  nosetests *
 
 Usage example
 -------------

py_bind/optv/calibration.pyx

@@ -9,7 +9,6 @@ import numpy
 cimport numpy as cnp
 
 from optv.calibration import Calibration
-from mhlib import isnumeric
 
 cdef extern from "optv/calibration.h":
     calibration *read_calibration(char *ori_file, char *add_file,
@@ -160,7 +159,7 @@ cdef class Calibration:
             of point from sensor middle and sensor-point distance, in this 
             order.
         """
-        if (object>prim_point_pos).shape != (3,):
+        if (<object>prim_point_pos).shape != (3,):
             raise ValueError("Expected a 3-element array")
 
         self._calibration[0].int_par.xh = prim_point_pos[0]

py_bind/optv/image_processing.pyx

@@ -1,6 +1,7 @@
 from optv.parameters cimport ControlParams, control_par
 import numpy as np
 cimport numpy as np
+from six import string_types
 
 def preprocess_image(np.ndarray[ndim=2, dtype=np.uint8_t] input_img,
                    int filter_hp,
@@ -41,10 +42,10 @@ def preprocess_image(np.ndarray[ndim=2, dtype=np.uint8_t] input_img,
         output_img = np.empty_like(input_img)
 
     if filter_hp == 2:
-        if filter_file == None or not isinstance(filter_file, basestring):
+        if filter_file == None or not isinstance(filter_file, string_types):
             raise ValueError("Expecting a filter file name, received None or non-string.")
     else:
-        filter_file=""
+        filter_file=b""
 
     for arr in (input_img, output_img):
         if not arr.flags['C_CONTIGUOUS']:

py_bind/optv/tracker.pyx

@@ -14,9 +14,9 @@ from optv.orientation cimport cal_list2arr
 from optv.tracking_framebuf cimport fb_free
 
 default_naming = {
-    'corres': 'res/rt_is',
-    'linkage': 'res/ptv_is',
-    'prio': 'res/added'
+    'corres': b'res/rt_is',
+    'linkage': b'res/ptv_is',
+    'prio': b'res/added'
 }
 
 cdef class Tracker:

py_bind/requirements.txt

@@ -1,4 +1,5 @@
-Cython==0.29.5
+Cython==0.29.6
 nose==1.3.7
-numpy==1.16.1
-PyYAML>=4.2b1
+numpy==1.16.2
+PyYAML==5.1
+six

py_bind/setup.py

@@ -150,10 +150,10 @@ def mk_ext(name, files):
     package_data={
         'optv': ['*.pxd', '*.c', '*.h'],
     },
-    version='0.2.4',
+    version='0.2.5',
     install_requires=[
-        'numpy==1.16.1',
+        'numpy>=1.16.1',
         'pyyaml',
     ],
-    setup_requires=['numpy==1.16.1'],
+    setup_requires=['numpy>=1.16.1'],
 )

py_bind/test/test_calibration_binding.py

@@ -4,9 +4,9 @@
 
 class Test_Calibration(unittest.TestCase):
     def setUp(self):        
-        self.input_ori_file_name = "testing_fodder/calibration/cam1.tif.ori"
-        self.input_add_file_name = "testing_fodder/calibration/cam2.tif.addpar"
-        self.output_directory = "testing_fodder/calibration/testing_output/"
+        self.input_ori_file_name = b"testing_fodder/calibration/cam1.tif.ori"
+        self.input_add_file_name = b"testing_fodder/calibration/cam2.tif.addpar"
+        self.output_directory = b"testing_fodder/calibration/testing_output/"
 
         # create a temporary output directory (will be deleted by the end of test)
         if not os.path.exists(self.output_directory):
@@ -37,8 +37,8 @@ def test_full_instantiate(self):
 
     def test_Calibration_instantiation(self):
         """Filling a calibration object by reading ori files"""
-        self.output_ori_file_name = self.output_directory + "output_ori"
-        self.output_add_file_name = self.output_directory + "output_add"
+        self.output_ori_file_name = self.output_directory + b"output_ori"
+        self.output_add_file_name = self.output_directory + b"output_add"
 
         # Using a round-trip test.
         self.cal.from_file(self.input_ori_file_name, self.input_add_file_name)

py_bind/test/test_corresp.py

@@ -18,11 +18,11 @@ def test_instantiate(self):
         """Creating a MatchedCoords object"""
         cal = Calibration()
         cpar = ControlParams(4)
-        
+
         cal.from_file(
-            "testing_fodder/calibration/cam1.tif.ori",
-            "testing_fodder/calibration/cam2.tif.addpar")
-        cpar.read_control_par("testing_fodder/corresp/control.par")
+            b"testing_fodder/calibration/cam1.tif.ori",
+            b"testing_fodder/calibration/cam2.tif.addpar")
+        cpar.read_control_par(b"testing_fodder/corresp/control.par")
         targs = read_targets("testing_fodder/frame/cam1.", 333)
 
         mc = MatchedCoords(targs, cpar, cal)
@@ -39,9 +39,9 @@ class TestCorresp(unittest.TestCase):
     def test_full_corresp(self):
         """Full scene correspondences"""
         cpar = ControlParams(4)
-        cpar.read_control_par(r"testing_fodder/corresp/control.par")
+        cpar.read_control_par(b"testing_fodder/corresp/control.par")
         vpar = VolumeParams()
-        vpar.read_volume_par(r"testing_fodder/corresp/criteria.par")
+        vpar.read_volume_par(b"testing_fodder/corresp/criteria.par")
 
         # Cameras are at so high angles that opposing cameras don't see each 
         # other in the normal air-glass-water setting.
@@ -54,8 +54,8 @@ def test_full_corresp(self):
         for c in range(4):
             cal = Calibration()
             cal.from_file(
-                "testing_fodder/calibration/sym_cam%d.tif.ori" % (c + 1),
-                "testing_fodder/calibration/cam1.tif.addpar")
+                b"testing_fodder/calibration/sym_cam%d.tif.ori" % (c + 1),
+                b"testing_fodder/calibration/cam1.tif.addpar")
             cals.append(cal)
 
             # Generate test targets.
@@ -87,9 +87,9 @@ def test_full_corresp(self):
     def test_single_cam_corresp(self):
         """Single camera correspondence"""
         cpar = ControlParams(1)
-        cpar.read_control_par("testing_fodder/single_cam/parameters/ptv.par")
+        cpar.read_control_par(b"testing_fodder/single_cam/parameters/ptv.par")
         vpar = VolumeParams()
-        vpar.read_volume_par("testing_fodder/single_cam/parameters/criteria.par")
+        vpar.read_volume_par(b"testing_fodder/single_cam/parameters/criteria.par")
 
         # Cameras are at so high angles that opposing cameras don't see each 
         # other in the normal air-glass-water setting.
@@ -101,8 +101,8 @@ def test_single_cam_corresp(self):
         corrected = []
         cal = Calibration()
         cal.from_file(
-            "testing_fodder/single_cam/calibration/cam_1.tif.ori",
-            "testing_fodder/single_cam/calibration/cam_1.tif.addpar")
+            b"testing_fodder/single_cam/calibration/cam_1.tif.ori",
+            b"testing_fodder/single_cam/calibration/cam_1.tif.addpar")
         cals.append(cal)
 
         # Generate test targets.
@@ -127,4 +127,11 @@ def test_single_cam_corresp(self):
         _, _, num_targs = correspondences(
             img_pts, corrected, cals, vpar, cpar)
 
-        self.failUnlessEqual(num_targs, 9)
+        self.failUnlessEqual(num_targs, 9)
+
+
+
+if __name__ == "__main__":
+    import sys, os
+    print(os.path.abspath(os.curdir))
+    unittest.main()

py_bind/test/test_epipolar.py

@@ -17,24 +17,24 @@
 
 class TestEpipolarCurve(unittest.TestCase):
     def test_two_cameras(self):
-        ori_tmpl = r'testing_fodder/calibration/sym_cam{cam_num}.tif.ori'
-        add_file = r'testing_fodder/calibration/cam1.tif.addpar'
+        ori_tmpl = "testing_fodder/calibration/sym_cam{cam_num}.tif.ori"
+        add_file = "testing_fodder/calibration/cam1.tif.addpar"
 
         orig_cal = Calibration()
-        orig_cal.from_file(ori_tmpl.format(cam_num=1), add_file)
+        orig_cal.from_file(ori_tmpl.format(cam_num=1).encode(), add_file.encode())
         proj_cal = Calibration()
-        proj_cal.from_file(ori_tmpl.format(cam_num=3), add_file)
+        proj_cal.from_file(ori_tmpl.format(cam_num=3).encode(), add_file.encode())
 
         # reorient cams:
         orig_cal.set_angles(np.r_[0., -np.pi/4., 0.])
         proj_cal.set_angles(np.r_[0., 3*np.pi/4., 0.])
 
         cpar = ControlParams(4)
-        cpar.read_control_par("testing_fodder/corresp/control.par")
+        cpar.read_control_par(b"testing_fodder/corresp/control.par")
         sens_size = cpar.get_image_size()
 
         vpar = VolumeParams()
-        vpar.read_volume_par("testing_fodder/corresp/criteria.par")
+        vpar.read_volume_par(b"testing_fodder/corresp/criteria.par")
         vpar.set_Zmin_lay([-10, -10])
         vpar.set_Zmax_lay([10, 10])
 

py_bind/test/test_framebuf.py

@@ -48,7 +48,7 @@ def test_sort_y(self):
     def test_write_targets(self):
         """Round-trip test of writing targets."""
         targs = read_targets("../../liboptv/tests/testing_fodder/sample_", 42)
-        targs.write("testing_fodder/round_trip.", 1)
+        targs.write(b"testing_fodder/round_trip.", 1)
         tback = read_targets("testing_fodder/round_trip.", 1)
 
         self.failUnlessEqual(len(targs), len(tback))
@@ -67,9 +67,9 @@ def tearDown(self):
 class TestFrame(unittest.TestCase):
     def test_read_frame(self):
         """reading a frame"""
-        targ_files = ["testing_fodder/frame/cam%d." % c for c in xrange(1, 5)]
-        frm = Frame(4, corres_file_base="testing_fodder/frame/rt_is",
-            linkage_file_base="testing_fodder/frame/ptv_is", 
+        targ_files = ["testing_fodder/frame/cam%d.".encode() % c for c in range(1, 5)]
+        frm = Frame(4, corres_file_base=b"testing_fodder/frame/rt_is",
+            linkage_file_base=b"testing_fodder/frame/ptv_is", 
             target_file_base=targ_files, frame_num=333)
 
         pos = frm.positions()