#!/usr/bin/env python3
import unittest
import os.path
import tempfile
import numpy as np
import logging
import argparse
from .context import imagedata
import imagedata.cmdline
import imagedata.readdata
import imagedata.formats
from imagedata.series import Series
[docs]class Test3DNIfTIPlugin(unittest.TestCase):
[docs] def setUp(self):
parser = argparse.ArgumentParser()
imagedata.cmdline.add_argparse_options(parser)
self.opts = parser.parse_args(['--of', 'nifti', '--serdes', '1'])
plugins = imagedata.formats.get_plugins_list()
self.nifti_plugin = None
for pname, ptype, pclass in plugins:
if ptype == 'nifti':
self.nifti_plugin = pclass
self.assertIsNotNone(self.nifti_plugin)
# @unittest.skip("skipping test_read_single_file")
[docs] def test_read_single_file(self):
si1 = Series(
os.path.join('data', 'nifti', 'time_all', 'time_all_fl3d_dynamic_20190207140517_14.nii.gz'),
'none',
self.opts)
self.assertEqual(si1.input_format, 'nifti')
self.assertEqual(si1.dtype, np.int16)
self.assertEqual(si1.shape, (10, 40, 192, 152))
# @unittest.skip("skipping test_read_2D")
[docs] def test_read_2D(self):
dcm = Series(os.path.join('data', 'dicom', 'time', 'time00'))
si2 = dcm[0, ...]
with tempfile.TemporaryDirectory() as d:
si2.write(d, formats=['nifti'])
si3 = Series(d, template=si2)
with tempfile.TemporaryDirectory() as d:
si3.write(d, formats=['dicom'])
self.assertEqual(si2.dtype, si3.dtype)
self.assertEqual(si2.shape, si3.shape)
np.testing.assert_array_equal(si2, si3)
# @unittest.skip("skipping test_read_3D")
[docs] def test_read_3D(self):
dcm = Series(os.path.join('data', 'dicom', 'time', 'time00'))
with tempfile.TemporaryDirectory() as d:
dcm.write(d, formats=['nifti'])
si3 = Series(d, template=dcm)
with tempfile.TemporaryDirectory() as d:
si3.write(d, formats=['dicom'])
self.assertEqual(dcm.dtype, si3.dtype)
self.assertEqual(dcm.shape, si3.shape)
np.testing.assert_array_equal(dcm, si3)
# @unittest.skip("skipping test_qform_3D")
# @unittest.skip("skipping test_read_two_files")
[docs] def test_read_two_files(self):
si1 = Series(
[
os.path.join('data',
'nifti',
'time_all',
'time_all_fl3d_dynamic_20190207140517_14.nii.gz'),
os.path.join('data',
'nifti',
'time_all',
'time_all_fl3d_dynamic_20190207140517_14.nii.gz')
],
imagedata.formats.INPUT_ORDER_TIME,
self.opts)
self.assertEqual(si1.dtype, np.int16)
self.assertEqual(si1.shape, (2, 10, 40, 192, 152))
# @unittest.skip("skipping test_zipread_single_file")
[docs] def test_zipread_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, (10, 40, 192, 152))
# @unittest.skip("skipping test_zipread_single_directory")
[docs] def test_zipread_single_directory(self):
si1 = Series(
os.path.join('data', 'nifti', 'time_all.zip?time'),
imagedata.formats.INPUT_ORDER_TIME,
self.opts)
self.assertEqual(si1.dtype, np.int16)
self.assertEqual(si1.shape, (10, 40, 192, 152))
# @unittest.skip("skipping test_zipread_all_files")
[docs] def test_zipread_all_files(self):
si1 = Series(
os.path.join('data', 'nifti', 'time_all.zip'),
imagedata.formats.INPUT_ORDER_TIME,
self.opts)
self.assertEqual(si1.dtype, np.int16)
self.assertEqual(si1.shape, (10, 40, 192, 152))
# @unittest.skip("skipping test_write_single_file")
[docs] def test_write_single_file(self):
si1 = Series(
os.path.join(
'data',
'nifti',
'time_all',
'time_all_fl3d_dynamic_20190207140517_14.nii.gz'),
'none',
self.opts)
with tempfile.TemporaryDirectory() as d:
si1.write(d + '?Image%1d.nii.gz', formats=['nifti'])
si2 = Series(os.path.join(d, 'Image0.nii.gz'))
self.assertEqual(si1.dtype, si2.dtype)
self.assertEqual(si1.shape, si2.shape)
# @unittest.skip("skipping test_read_3d_nifti")
[docs] def test_read_3d_nifti(self):
si1 = Series(
os.path.join(
'data',
'nifti',
'time_all',
'time_all_fl3d_dynamic_20190207140517_14.nii.gz'),
imagedata.formats.INPUT_ORDER_TIME,
self.opts)
si1 = si1[0]
logging.debug('test_read_3d_nifti: si1 {} {} {} {}'.format(type(si1), si1.dtype, si1.min(), si1.max()))
logging.debug('test_read_3d_nifti: si1.slices {}'.format(si1.slices))
si1.spacing = (5, 0.41015625, 0.41015625)
for slice in range(si1.shape[0]):
si1.imagePositions = {
slice:
np.array([slice, 1, 0])
}
si1.orientation = np.array([1, 0, 0, 0, 1, 0])
logging.debug('test_read_3d_nifti: si1.tags {}'.format(si1.tags))
with tempfile.TemporaryDirectory() as d:
si1.write(os.path.join(d, 'nifti?Image_%05d'), formats=['nifti'], opts=self.opts)
logging.debug('test_read_3d_nifti: si1 {} {} {}'.format(si1.dtype, si1.min(), si1.max()))
si2 = Series(
os.path.join(d, 'nifti', 'Image_00000.nii.gz'),
'none',
self.opts)
# noinspection PyArgumentList
logging.debug('test_read_3d_nifti: si2 {} {} {}'.format(si2.dtype, si2.min(), si2.max()))
self.assertEqual(si1.shape, si2.shape)
np.testing.assert_array_equal(si1, si2)
logging.debug('test_read_3d_nifti: Get si1.slices {}'.format(si1.slices))
logging.debug('test_read_3d_nifti: Set s3')
s3 = si1.astype(np.float64)
logging.debug('test_read_3d_nifti: s3 {} {} {} {}'.format(type(s3),
issubclass(type(s3), Series), s3.dtype, s3.shape))
logging.debug('test_read_3d_nifti: s3 {} {} {}'.format(s3.dtype,
s3.min(), s3.max()))
logging.debug('test_read_3d_nifti: s3.slices {}'.format(s3.slices))
si3 = Series(s3)
np.testing.assert_array_almost_equal(si1, si3, decimal=4)
logging.debug('test_read_3d_nifti: si3.slices {}'.format(si3.slices))
logging.debug('test_read_3d_nifti: si3 {} {} {}'.format(type(si3), si3.dtype, si3.shape))
with tempfile.TemporaryDirectory() as d:
si3.write(os.path.join(d, 'n?Image_%05d'), formats=['nifti'], opts=self.opts)
s3 = si1 - si2
with tempfile.TemporaryDirectory() as d:
s3.write(os.path.join(d, 'diff?Image_%05d'), formats=['nifti'], opts=self.opts)
# @unittest.skip("skipping test_read_3d_nifti_no_opt")
# noinspection PyArgumentList
[docs] def test_read_3d_nifti_no_opt(self):
si1 = Series(os.path.join(
'data', 'nifti', 'time_all', 'time_all_fl3d_dynamic_20190207140517_14.nii.gz'))
logging.debug('test_read_3d_nifti_no_opt: si1 {} {} {} {}'.format(type(si1), si1.dtype, si1.min(), si1.max()))
logging.debug('test_read_3d_nifti_no_opt: si1.slices {}'.format(si1.slices))
# @unittest.skip("skipping test_write_3d_nifti_no_opt")
# noinspection PyArgumentList
[docs] def test_write_3d_nifti_no_opt(self):
si1 = Series(os.path.join('data', 'dicom', 'time', 'time00'))
logging.debug('test_write_3d_nifti_no_opt: si1 {} {} {} {}'.format(type(si1), si1.dtype, si1.min(), si1.max()))
logging.debug('test_write_3d_nifti_no_opt: si1.slices {}'.format(si1.slices))
with tempfile.TemporaryDirectory() as d:
si1.write(d, formats=['nifti'])
[docs]class Test4DNIfTIPlugin(unittest.TestCase):
[docs] def setUp(self):
parser = argparse.ArgumentParser()
imagedata.cmdline.add_argparse_options(parser)
self.opts = parser.parse_args(['--of', 'nifti', '--input_shape', '8x30'])
plugins = imagedata.formats.get_plugins_list()
self.nifti_plugin = None
for pname, ptype, pclass in plugins:
if ptype == 'nifti':
self.nifti_plugin = pclass
self.assertIsNotNone(self.nifti_plugin)
# @unittest.skip("skipping test_write_4d_nifti")
[docs] def test_write_4d_nifti(self):
si1 = Series(
os.path.join('data', 'dicom', 'time'),
imagedata.formats.INPUT_ORDER_TIME,
self.opts)
self.assertEqual(si1.dtype, np.uint16)
self.assertEqual(si1.shape, (10, 40, 192, 152))
si1.sort_on = imagedata.formats.SORT_ON_SLICE
logging.debug("test_write_4d_nifti: si1.sort_on {}".format(
imagedata.formats.sort_on_to_str(si1.sort_on)))
si1.output_dir = 'single'
# si1.output_dir = 'multi'
with tempfile.TemporaryDirectory() as d:
si1.write(d, formats=['nifti'], opts=self.opts)
# Read back the NIfTI data and verify that the header was modified
si2 = Series(
d,
imagedata.formats.INPUT_ORDER_TIME,
self.opts)
self.assertEqual(si1.shape, si2.shape)
np.testing.assert_array_equal(si1, si2)
if __name__ == '__main__':
unittest.main()