test_tiffio.py

import unittest
import os
from PIL import Image
import numpy as np
import shutil
from neo.io.tiffio import TiffIO
import quantities as pq


class TestTiffIO(unittest.TestCase):

    def test_read_group_of_tiff_grayscale(self):
        directory = "test_tiff"
        if not os.path.exists(directory):
            os.makedirs(directory)
        # directory is live
        img = []
        for picture in range(10):
            img.append([])
            for y in range(50):
                img[picture].append([])
                for x in range(50):
                    img[picture][y].append(x)
        img = np.array(img, dtype=float)
        for image in range(10):
            # rotate image by 90 deg so that shifting the origin is meaningful in later test
            Image.fromarray(np.rot90(img[image])).save(directory + "/tiff_exemple" + str(image) + ".tif")

        ioclass = TiffIO(
            directory_path=directory, units="V", sampling_rate=1.0 * pq.Hz, spatial_scale=1.0 * pq.micrometer
        )
        blck = ioclass.read_block()
        self.assertEqual(len(blck.segments), 1)
        self.assertEqual(len(blck.segments[0].imagesequences), 1)
        self.assertEqual(blck.segments[0].imagesequences[0].any(), img.any())
        self.assertEqual(blck.segments[0].imagesequences[0].sampling_rate, 1.0 * pq.Hz)
        self.assertEqual(blck.segments[0].imagesequences[0].spatial_scale, 1.0 * pq.micrometer)

        ioclass_bl_origin = TiffIO(
            directory_path=directory,
            units="V",
            sampling_rate=1.0 * pq.Hz,
            spatial_scale=1.0 * pq.micrometer,
            origin='bottom-left',
        )
        blck_bl_origin = ioclass_bl_origin.read_block()

        self.assertAlmostEqual(
            blck.segments[0].imagesequences[0][0][0,0].magnitude,
            blck_bl_origin.segments[0].imagesequences[0][0][0,49].magnitude, # since flipped over y, [0,0] == [0,49]
            places=3, 
        )

        # end of directory
        shutil.rmtree(directory)


if __name__ == "__main__":
    unittest.main()