Ejemplo n.º 1
0
    def testIteratorAccess2(self):
        reader = FeatureReader([self.trajfile, self.trajfile], self.topfile)
        reader.chunksize = 100

        frames = 0
        data = []
        for i, X in reader:
            frames += X.shape[0]
            data.append(X)
        self.assertEqual(frames, reader.trajectory_lengths()[0] * 2)
        # restore shape of input
        data = np.array(
            data[0:reader.trajectory_lengths()[0] / reader.chunksize]).reshape(self.xyz.shape)

        self.assertTrue(np.allclose(data, self.xyz))
Ejemplo n.º 2
0
    def testIteratorAccess2(self):
        reader = FeatureReader([self.trajfile, self.trajfile], self.topfile)
        reader.chunksize = 100

        frames = 0
        data = []
        for i, X in reader:
            frames += X.shape[0]
            data.append(X)
        self.assertEqual(frames, reader.trajectory_lengths()[0] * 2)
        # restore shape of input
        data = np.array(data[0:reader.trajectory_lengths()[0] /
                             reader.chunksize]).reshape(self.xyz.shape)

        self.assertTrue(np.allclose(data, self.xyz))
Ejemplo n.º 3
0
    def testTimeLaggedIterator(self):
        lag = 10
        reader = FeatureReader(self.trajfile, self.topfile)
        frames = 0
        data = []
        lagged = []
        for _, X, Y in reader.iterator(lag=lag):
            frames += X.shape[0]
            data.append(X)
            lagged.append(Y)

        assert len(data) == len(lagged)
        # .reshape(self.xyz.shape)
        merged_lagged = np.concatenate(lagged, axis=0)

        # reproduce outcome
        xyz_s = self.xyz.shape
        fake_lagged = self.xyz.reshape((xyz_s[0], -1))[lag:]

        self.assertTrue(np.allclose(merged_lagged, fake_lagged))

        # restore shape of input
        data = np.vstack(data).reshape(self.xyz[lag:].shape)

        self.assertEqual(frames, reader.trajectory_lengths()[0] - lag)
        self.assertTrue(np.allclose(data, self.xyz[:len(self.xyz) - lag]))
Ejemplo n.º 4
0
    def testTimeLaggedIterator(self):
        lag = 10
        reader = FeatureReader(self.trajfile, self.topfile)
        frames = 0
        data = []
        lagged = []
        for _, X, Y in reader.iterator(lag=lag):
            frames += X.shape[0]
            data.append(X)
            lagged.append(Y)

        assert len(data) == len(lagged)
        merged_lagged = np.concatenate(lagged, axis=0)  # .reshape(self.xyz.shape)

        # reproduce outcome
        xyz_s = self.xyz.shape
        fake_lagged = np.empty((xyz_s[0]-lag, xyz_s[1]*xyz_s[2]))
        fake_lagged = self.xyz.reshape((xyz_s[0], -1))[lag:]

        self.assertTrue(np.allclose(merged_lagged, fake_lagged))

        # restore shape of input
        data = np.array(data).reshape(self.xyz.shape)

        self.assertEqual(frames, reader.trajectory_lengths()[0])
        self.assertTrue(np.allclose(data, self.xyz))