Add unit tests

33 files changed, 141 insertions, 0 deletions

diff --git a/tests/data/sinogram-00000.tif b/tests/data/sinogram-00000.tif
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+++ b/tests/data/sinogram-00000.tif
diff --git a/tests/data/sinogram-00001.tif b/tests/data/sinogram-00001.tif
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+++ b/tests/data/sinogram-00001.tif
diff --git a/tests/data/sinogram-00002.tif b/tests/data/sinogram-00002.tif
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+++ b/tests/data/sinogram-00002.tif
diff --git a/tests/data/sinogram-00003.tif b/tests/data/sinogram-00003.tif
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+++ b/tests/data/sinogram-00003.tif
diff --git a/tests/data/sinogram-00004.tif b/tests/data/sinogram-00004.tif
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+++ b/tests/data/sinogram-00004.tif
diff --git a/tests/data/sinogram-00005.tif b/tests/data/sinogram-00005.tif
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+++ b/tests/data/sinogram-00005.tif
diff --git a/tests/data/sinogram-00006.tif b/tests/data/sinogram-00006.tif
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+++ b/tests/data/sinogram-00006.tif
diff --git a/tests/data/sinogram-00007.tif b/tests/data/sinogram-00007.tif
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+++ b/tests/data/sinogram-00007.tif
diff --git a/tests/data/sinogram-00008.tif b/tests/data/sinogram-00008.tif
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+++ b/tests/data/sinogram-00008.tif
diff --git a/tests/data/sinogram-00009.tif b/tests/data/sinogram-00009.tif
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+++ b/tests/data/sinogram-00009.tif
diff --git a/tests/data/sinogram-00010.tif b/tests/data/sinogram-00010.tif
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--- /dev/null
+++ b/tests/data/sinogram-00010.tif
diff --git a/tests/data/sinogram-00011.tif b/tests/data/sinogram-00011.tif
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index 0000000..f3288ce
--- /dev/null
+++ b/tests/data/sinogram-00011.tif
diff --git a/tests/data/sinogram-00012.tif b/tests/data/sinogram-00012.tif
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index 0000000..a507b54
--- /dev/null
+++ b/tests/data/sinogram-00012.tif
diff --git a/tests/data/sinogram-00013.tif b/tests/data/sinogram-00013.tif
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index 0000000..fe3de7d
--- /dev/null
+++ b/tests/data/sinogram-00013.tif
diff --git a/tests/data/sinogram-00014.tif b/tests/data/sinogram-00014.tif
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index 0000000..01facb6
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+++ b/tests/data/sinogram-00014.tif
diff --git a/tests/data/sinogram-00015.tif b/tests/data/sinogram-00015.tif
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index 0000000..a628731
--- /dev/null
+++ b/tests/data/sinogram-00015.tif
diff --git a/tests/expected/phantom-00000.tif b/tests/expected/phantom-00000.tif
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index 0000000..c669db2
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+++ b/tests/expected/phantom-00000.tif
diff --git a/tests/expected/phantom-00001.tif b/tests/expected/phantom-00001.tif
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index 0000000..37a4394
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+++ b/tests/expected/phantom-00001.tif
diff --git a/tests/expected/phantom-00002.tif b/tests/expected/phantom-00002.tif
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+++ b/tests/expected/phantom-00002.tif
diff --git a/tests/expected/phantom-00003.tif b/tests/expected/phantom-00003.tif
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+++ b/tests/expected/phantom-00003.tif
diff --git a/tests/expected/phantom-00004.tif b/tests/expected/phantom-00004.tif
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index 0000000..5ea52dd
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+++ b/tests/expected/phantom-00004.tif
diff --git a/tests/expected/phantom-00005.tif b/tests/expected/phantom-00005.tif
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index 0000000..038461f
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+++ b/tests/expected/phantom-00005.tif
diff --git a/tests/expected/phantom-00006.tif b/tests/expected/phantom-00006.tif
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index 0000000..5a89f04
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+++ b/tests/expected/phantom-00006.tif
diff --git a/tests/expected/phantom-00007.tif b/tests/expected/phantom-00007.tif
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index 0000000..2099005
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+++ b/tests/expected/phantom-00007.tif
diff --git a/tests/expected/phantom-00008.tif b/tests/expected/phantom-00008.tif
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index 0000000..892bc75
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+++ b/tests/expected/phantom-00008.tif
diff --git a/tests/expected/phantom-00009.tif b/tests/expected/phantom-00009.tif
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+++ b/tests/expected/phantom-00009.tif
diff --git a/tests/expected/phantom-00010.tif b/tests/expected/phantom-00010.tif
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index 0000000..35f7133
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+++ b/tests/expected/phantom-00010.tif
diff --git a/tests/expected/phantom-00011.tif b/tests/expected/phantom-00011.tif
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index 0000000..d530658
--- /dev/null
+++ b/tests/expected/phantom-00011.tif
diff --git a/tests/expected/phantom-00012.tif b/tests/expected/phantom-00012.tif
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index 0000000..c72dff9
--- /dev/null
+++ b/tests/expected/phantom-00012.tif
diff --git a/tests/expected/phantom-00013.tif b/tests/expected/phantom-00013.tif
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index 0000000..b65b6f1
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+++ b/tests/expected/phantom-00013.tif
diff --git a/tests/expected/phantom-00014.tif b/tests/expected/phantom-00014.tif
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+++ b/tests/expected/phantom-00014.tif
diff --git a/tests/expected/phantom-00015.tif b/tests/expected/phantom-00015.tif
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--- /dev/null
+++ b/tests/expected/phantom-00015.tif
diff --git a/tests/tests.py b/tests/tests.py
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index 0000000..a2fce52
--- /dev/null
+++ b/tests/tests.py
@@ -0,0 +1,141 @@
+import os
+import shutil
+import tempfile
+
+try:
+    import unittest2 as unittest
+except ImportError:
+    import unittest
+
+import numpy as np
+from nose_parameterized import parameterized
+from gi.repository import Ufo, GLib
+from libtiff import TIFF
+
+
+def data_path(suffix=''):
+    return os.path.join(os.path.abspath('./data'), suffix)
+
+def ref_path(suffix=''):
+    return os.path.join(os.path.abspath('./expected'), suffix)
+
+def ignore_message(domain, level, message, user):
+    pass
+
+GLib.log_set_handler('Ufo', GLib.LogLevelFlags.LEVEL_DEBUG, ignore_message, None)
+
+class BasicTests(unittest.TestCase):
+    def setUp(self):
+        self.pm = Ufo.PluginManager()
+        self.graph = Ufo.TaskGraph()
+        self.sched = Ufo.Scheduler()
+        self.tmpdir = tempfile.mkdtemp()
+
+    def tearDown(self):
+        shutil.rmtree(self.tmpdir)
+
+    def tmp_path(self, suffix=''):
+        return os.path.join(self.tmpdir, suffix)
+
+    def get_task(self, name, **kwargs):
+        plugin = self.pm.get_task(name)
+        plugin.set_properties(**kwargs)
+        return plugin
+
+    def test_read_write(self):
+        reader = self.get_task('reader', path=data_path('sinogram-*.tif'), count=5)
+        writer = self.get_task('writer', filename=self.tmp_path('b-%05i.tif'))
+
+        self.graph.connect_nodes(reader, writer)
+        self.sched.run(self.graph)
+
+        expected = ['b-%05i.tif' % i for i in xrange(5)]
+        found = os.listdir(self.tmpdir)
+
+        for fname in expected:
+            self.assertIn(fname, found)
+
+    def test_roi(self):
+        R = {'x': 2, 'y': 13, 'width': 256, 'height': 128}
+        input_name = data_path('sinogram-00005.tif')
+        output_name = self.tmp_path('roi-00000.tif')
+
+        reader = self.get_task('reader', path=input_name)
+        writer = self.get_task('writer', filename=self.tmp_path('roi-%05i.tif'))
+        roi = self.get_task('region-of-interest', **R)
+
+        self.graph.connect_nodes(reader, roi)
+        self.graph.connect_nodes(roi, writer)
+        self.sched.run(self.graph)
+
+        ref_img = TIFF.open(input_name, mode='r').read_image()
+        res_img = TIFF.open(output_name, mode='r').read_image()
+
+        # Cut it manually
+        ref_img = ref_img[R['y']:R['y']+R['height'], R['x']:R['x']+R['width']]
+
+        self.assertEqual(res_img.shape, ref_img.shape)
+        self.assertTrue((res_img == ref_img).all())
+
+    @parameterized.expand([(1, 0.5), (2, 0.5)])
+    def test_fft(self, dimension, expected):
+        input_name = data_path('sinogram-00005.tif')
+        output_name = self.tmp_path('r-00000.tif')
+
+        reader = self.get_task('reader', path=input_name)
+        writer = self.get_task('writer', filename=self.tmp_path('r-%05i.tif'))
+        fft = self.get_task('fft', dimensions=dimension)
+        ifft = self.get_task('ifft', dimensions=dimension)
+
+        self.graph.connect_nodes(reader, fft)
+        self.graph.connect_nodes(fft, ifft)
+        self.graph.connect_nodes(ifft, writer)
+        self.sched.run(self.graph)
+
+        ref_img = TIFF.open(input_name, mode='r').read_image()
+        res_img = TIFF.open(output_name, mode='r').read_image()
+        diff = np.sum(np.abs(ref_img - res_img))
+        self.assertLess(diff, expected)
+
+    def test_flatfield_correction(self):
+        input_name = data_path('sinogram-*.tif')
+        output_name = self.tmp_path('r-%i.tif')
+        flat = self.get_task('reader', path=input_name, count=2)
+        dark = self.get_task('reader', path=input_name, count=2)
+        proj = self.get_task('reader', path=input_name, count=10)
+        writer = self.get_task('writer', filename=output_name)
+
+        flat_avg = self.get_task('averager', num_generate=10)
+        dark_avg = self.get_task('averager', num_generate=10)
+        ffc = self.get_task('flat-field-correction')
+
+        self.graph.connect_nodes(dark, dark_avg)
+        self.graph.connect_nodes(flat, flat_avg)
+        self.graph.connect_nodes_full(proj, ffc, 0)
+        self.graph.connect_nodes_full(dark_avg, ffc, 1)
+        self.graph.connect_nodes_full(flat_avg, ffc, 2)
+        self.graph.connect_nodes(ffc, writer)
+        self.sched.run(self.graph)
+
+    # def test_filtered_backprojection(self):
+    #     reader = self.get_task('reader', path=data_path('sinogram*.tif'))
+    #     fft = self.get_task('fft')
+    #     ifft = self.get_task('ifft')
+    #     fltr = self.get_task('filter')
+    #     bp = self.get_task('backproject')
+    #     writer = self.get_task('writer', filename=self.tmp_path('r-%05i.tif'))
+
+    #     self.graph.connect_nodes(reader, fft)
+    #     self.graph.connect_nodes(fft, fltr)
+    #     self.graph.connect_nodes(fltr, ifft)
+    #     self.graph.connect_nodes(ifft, bp)
+    #     self.graph.connect_nodes(bp, writer)
+    #     self.sched.run(self.graph)
+
+    #     refs = sorted((ref_path(d) for d in os.listdir(ref_path())))
+    #     results = sorted((os.path.join(self.tmpdir, d) for d in os.listdir(self.tmpdir)))
+
+    #     for ref, res in zip(refs, results):
+    #         ref_img = TIFF.open(ref, mode='r').read_image()
+    #         res_img = TIFF.open(res, mode='r').read_image()
+    #         self.assertLess(np.sum(np.abs(res_img - ref_img)), 0.01)