adds basic APR and IO tests

Author: joeljonsson

pyapr/converter/converter_methods.py

@@ -21,17 +21,17 @@ def get_apr(image, rel_error=0.1, gradient_smoothing=2, verbose=True, params=Non
     else:
         par = params
 
-    if image.dtype in ('float', 'float32'):
+    if image.dtype == np.float32:
         parts = pyapr.FloatParticles()
         converter = pyapr.converter.FloatConverter()
-    elif image.dtype in ('short', 'uint16'):
+    elif image.dtype == np.uint16:
         parts = pyapr.ShortParticles()
         converter = pyapr.converter.ShortConverter()
     # elif image.dtype in {'byte', 'uint8'}:  # currently not working
     #     parts = pyapr.ByteParticles()
     #     converter = pyapr.converter.ByteConverter()
     else:
-        errstr = 'get_apr_interactive image dtype must be one of (float, float32, short, uint16), ' \
+        errstr = 'pyapr.converter.get_apr: input image dtype must be numpy.uint16 or numpy.float32, ' \
                  'but {} was given'.format(image.dtype)
         raise TypeError(errstr)
 
@@ -68,17 +68,17 @@ def get_apr_interactive(image, rel_error=0.1, gradient_smoothing=2, verbose=True
     else:
         par = params
 
-    if image.dtype in ('float', 'float32'):
+    if image.dtype == np.float32:
         parts = pyapr.FloatParticles()
         converter = pyapr.converter.FloatConverter()
-    elif image.dtype in ('short', 'uint16'):
+    elif image.dtype == np.uint16:
         parts = pyapr.ShortParticles()
         converter = pyapr.converter.ShortConverter()
     # elif image.dtype in {'byte', 'uint8'}:  # currently not working
     #     parts = pyapr.ByteParticles()
     #     converter = pyapr.converter.ByteConverter()
     else:
-        errstr = 'pyapr.converter.get_apr_interactive: image dtype must be one of (float, float32, short, uint16), ' \
+        errstr = 'pyapr.converter.get_apr_interactive: input image dtype must be numpy.uint16 or numpy.float32, ' \
                  'but {} was given'.format(image.dtype)
         raise TypeError(errstr)
 
@@ -122,14 +122,14 @@ def find_parameters_interactive(image, rel_error=0.1, gradient_smoothing=0, verb
     else:
         par = params
 
-    if image.dtype in ('float', 'float32'):
+    if image.dtype == np.float32:
         converter = pyapr.converter.FloatConverter()
-    elif image.dtype in ('short', 'uint16'):
+    elif image.dtype == np.uint16:
         converter = pyapr.converter.ShortConverter()
     # elif image.dtype in {'byte', 'uint8'}:  # currently not working
     #     converter = pyapr.converter.ByteConverter()
     else:
-        errstr = 'find_parameters_interactive image.dtype must be one of (float, float32, short, uint16), ' \
+        errstr = 'pyapr.converter.find_parameters_interactive: input image dtype must be numpy.uint16 or numpy.float32, ' \
                  'but {} was given'.format(image.dtype)
         raise TypeError(errstr)
 

pyapr/tests/testAPR.py

@@ -0,0 +1,77 @@
+import unittest
+import pyapr
+from skimage import io as skio
+import numpy as np
+import os
+
+
+class BasicTests(unittest.TestCase):
+
+    def setUp(self):
+        self.this_dir = os.path.dirname(os.path.abspath(__file__))
+        self.impath_3D = os.path.abspath(os.path.join(self.this_dir, '../../LibAPR/test/files/Apr/sphere_120/sphere_original.tif'))
+        self.impath_2D = os.path.abspath(os.path.join(self.this_dir, '../../LibAPR/test/files/Apr/sphere_2D/original.tif'))
+        self.impath_1D = os.path.abspath(os.path.join(self.this_dir, '../../LibAPR/test/files/Apr/sphere_1D/original.tif'))
+
+        self.apr_parameters = pyapr.APRParameters()
+        self.apr_parameters.sigma_th = 30
+        self.apr_parameters.grad_th = 15
+
+    def __convert_image(self, impath, dtype):
+        img = skio.imread(impath).astype(dtype)
+        apr, parts = pyapr.converter.get_apr(img, verbose=False, params=self.apr_parameters)
+
+        # TODO: use output_steps flag and check reconstruction condition
+
+        self.assertGreater(apr.computational_ratio(), 1)
+        self.assertGreater(len(parts), 1)
+
+    def test_get_apr(self):
+        self.__convert_image(self.impath_1D, np.uint16)
+        self.__convert_image(self.impath_2D, np.uint16)
+        self.__convert_image(self.impath_3D, np.uint16)
+
+        self.__convert_image(self.impath_1D, np.float32)
+        self.__convert_image(self.impath_2D, np.float32)
+        self.__convert_image(self.impath_3D, np.float32)
+
+        with self.assertRaises(TypeError):
+            self.__convert_image(self.impath_1D, np.float64)
+
+        with self.assertRaises(TypeError):
+            self.__convert_image(self.impath_1D, np.uint8)
+
+        with self.assertRaises(TypeError):
+            self.__convert_image(self.impath_1D, int)
+
+    def test_io(self):
+
+        # writes files to this path, later removes the file # TODO: find a better way to do this
+        fpath = os.path.join(self.this_dir, 'temporary_apr_file.apr')
+
+        for impath in (self.impath_1D, self.impath_2D, self.impath_3D):
+            img = skio.imread(impath)
+            apr, parts = pyapr.converter.get_apr(img, verbose=False, params=self.apr_parameters)
+
+            pyapr.io.write(fpath, apr, parts)
+
+            apr2 = pyapr.APR()
+            parts2 = pyapr.ShortParticles()
+
+            pyapr.io.read(fpath, apr2, parts2)
+
+            self.assertEqual(apr.org_dims(), apr2.org_dims())
+            self.assertEqual(apr.total_number_particles(), apr2.total_number_particles())
+            self.assertEqual(apr.total_number_particles(), len(parts2))
+
+            self.assertTrue(
+                np.alltrue(
+                    np.array(parts, copy=False) == np.array(parts2, copy=False)
+                )
+            )
+
+        os.remove(fpath)    # remove temporary file
+
+
+if __name__ == '__main__':
+    unittest.main()