Source code for tests.test_formats_nifti_zip

#!/usr/bin/env python3

"""Test zip archive
"""

import unittest
import os.path
import tempfile
import numpy as np
import argparse

# from .context import imagedata
import src.imagedata.cmdline as cmdline
import src.imagedata.formats as formats
from src.imagedata.series import Series



[docs]
class TestNiftiZipRead(unittest.TestCase):

[docs]
    def setUp(self):
        parser = argparse.ArgumentParser()
        cmdline.add_argparse_options(parser)

        self.opts = parser.parse_args([])
        if len(self.opts.output_format) < 1:
            self.opts.output_format = ['nifti']


    # @unittest.skip("skipping test_read_single_file")

[docs]
    def test_read_single_file(self):
        si1 = Series(
            os.path.join(
                'data',
                'nifti',
                'time_all.zip?time/time_all_fl3d_dynamic_20190207140517_14.nii.gz'),
            'none',
            self.opts)
        self.assertEqual(si1.dtype, np.int16)
        self.assertEqual(si1.shape, (3, 3, 192, 152))


    # @unittest.skip("skipping test_read_single_file_wildcard")

[docs]
    def test_read_single_file_wildcard(self):
        si1 = Series(
            os.path.join('data', 'nifti', 'time_all.zip?*/*_14.nii.gz'),
            'none',
            self.opts)
        self.assertEqual(si1.dtype, np.int16)
        self.assertEqual(si1.shape, (3, 3, 192, 152))


    # @unittest.skip("skipping test_read_single_file_relative")

[docs]
    def test_read_single_file_relative(self):
        si1 = Series(
            os.path.join('data', 'nifti', 'time_all.zip?time/time_all_fl3d_dynamic_20190207140517_14.nii.gz'),
            'none',
            self.opts)
        self.assertEqual(si1.dtype, np.int16)
        self.assertEqual(si1.shape, (3, 3, 192, 152))


    # @unittest.skip("skipping test_read_single_directory")

[docs]
    def test_read_single_directory(self):
        si1 = Series(
            os.path.join('data', 'nifti', 'time_all.zip?time'),
            formats.INPUT_ORDER_TIME,
            self.opts)
        self.assertEqual(si1.dtype, np.int16)
        self.assertEqual(si1.shape, (3, 3, 192, 152))


    # @unittest.skip("skipping test_read_all_files")

[docs]
    def test_read_all_files(self):
        si1 = Series(
            os.path.join('data', 'nifti', 'time_all.zip'),
            formats.INPUT_ORDER_TIME,
            self.opts)
        self.assertEqual(si1.dtype, np.int16)
        self.assertEqual(si1.shape, (3, 3, 192, 152))





[docs]
class TestNiftiZipWrite(unittest.TestCase):

[docs]
    def setUp(self):
        parser = argparse.ArgumentParser()
        cmdline.add_argparse_options(parser)

        self.opts = parser.parse_args([])
        if len(self.opts.output_format) < 1:
            self.opts.output_format = ['nifti']


    # @unittest.skip("skipping test_write_single_file")

[docs]
    def test_write_single_file(self):
        si1 = Series(os.path.join(
            'data',
            'dicom',
            'cor_hf.zip'))
        with tempfile.TemporaryDirectory() as d:
            si1.write(os.path.join(d, 'nifti.zip'), formats=['nifti'])
            si2 = Series(os.path.join(d, 'nifti.zip?Image.nii.gz'))
        self.assertEqual(si1.dtype, si2.dtype)
        self.assertEqual(si1.shape, si2.shape)




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