import unittest
import os.path
import tempfile
import numpy as np
import logging
import argparse
import imagedata.cmdline as cmdline
import imagedata.formats as formats
from imagedata.series import Series
from imagedata.collection import Cohort
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def list_files(startpath):
import os
for root, dirs, files in os.walk(startpath):
level = root.replace(startpath, '').count(os.sep)
indent = ' ' * 4 * level
print('{}{}/'.format(indent, os.path.basename(root)))
subindent = ' ' * 4 * (level + 1)
for f in files:
print('{}{}'.format(subindent, f))
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class Test3DMatPlugin(unittest.TestCase):
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def setUp(self):
parser = argparse.ArgumentParser()
cmdline.add_argparse_options(parser)
self.opts = parser.parse_args(['--of', 'mat', '--serdes', '1'])
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def test_mat_plugin(self):
plugins = formats.get_plugins_list()
self.mat_plugin = None
for pname, ptype, pclass in plugins:
if ptype == 'mat':
self.mat_plugin = pclass
self.assertIsNotNone(self.mat_plugin)
# @unittest.skip("skipping test_read_single_file")
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def test_read_single_file(self):
si1 = Series(
os.path.join('data', 'mat', 'time', 'Image_00000.mat'),
formats.INPUT_ORDER_TIME,
input_format='mat')
self.assertEqual(si1.dtype, np.uint16)
self.assertEqual(si1.shape, (3, 3, 192, 152))
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def test_dtype_int64(self):
si1 = Series(
os.path.join('data', 'mat', 'time', 'Image_00000.mat'),
'none',
dtype=int,
input_format='mat')
self.assertEqual(si1.dtype, np.int64)
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def test_dtype_float(self):
si1 = Series(
os.path.join('data', 'mat', 'time', 'Image_00000.mat'),
'none',
dtype=float,
input_format='mat')
self.assertEqual(si1.dtype, np.float64)
# @unittest.skip("skipping test_read_2D")
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def test_read_2D(self):
si1 = Series(
os.path.join('data', 'mat', 'time', 'Image_00000.mat'),
formats.INPUT_ORDER_TIME,
input_format='mat')
self.assertEqual(si1.dtype, np.uint16)
self.assertEqual(si1.shape, (3, 3, 192, 152))
si2 = si1[0, 0, ...]
with tempfile.TemporaryDirectory() as d:
si2.write(d, formats=['mat'])
si3 = Series(d, input_format='mat')
self.assertEqual(si2.dtype, si3.dtype)
self.assertEqual(si2.shape, si3.shape)
np.testing.assert_array_equal(si2, si3)
# @unittest.skip("skipping test_read_two_files")
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def test_read_two_files(self):
si1 = Series(
[os.path.join('data', 'mat', 'time', 'Image_00000.mat'),
os.path.join('data', 'mat', 'time', 'Image_00000.mat')],
formats.INPUT_ORDER_TIME,
input_format='mat')
self.assertEqual(si1.dtype, np.uint16)
self.assertEqual(si1.shape, (3, 3, 192, 152))
# @unittest.skip("skipping test_read_single_directory")
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def test_read_single_directory(self):
si1 = Series(
os.path.join('data', 'mat', 'time'),
formats.INPUT_ORDER_TIME,
input_format='mat')
self.assertEqual(si1.dtype, np.uint16)
self.assertEqual(si1.shape, (3, 3, 192, 152))
# @unittest.skip("skipping test_zipread_single_file")
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def test_zipread_single_file(self):
si1 = Series(
os.path.join('data', 'mat', 'time.zip?time/Image_00000.mat'),
'none',
input_format='mat')
self.assertEqual(si1.dtype, np.uint16)
self.assertEqual(si1.shape, (3, 3, 192, 152))
# @unittest.skip("skipping test_zipread_single_file_wildcard")
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def test_zipread_single_file_wildcard(self):
si1 = Series(
os.path.join('data', 'mat', 'time.zip?*Image_00000.mat'),
'none',
input_format='mat')
self.assertEqual(si1.dtype, np.uint16)
self.assertEqual(si1.shape, (3, 3, 192, 152))
# @unittest.skip("skipping test_zipread_single_file_relative")
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def test_zipread_single_file_relative(self):
si1 = Series(
os.path.join('data', 'mat', 'time.zip?time/Image_00000.mat'),
'none',
input_format='mat')
self.assertEqual(si1.dtype, np.uint16)
self.assertEqual(si1.shape, (3, 3, 192, 152))
# @unittest.skip("skipping test_zipread_single_directory")
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def test_zipread_single_directory(self):
si1 = Series(
os.path.join('data', 'mat', 'time.zip?time'),
formats.INPUT_ORDER_TIME,
input_format='mat')
self.assertEqual(si1.dtype, np.uint16)
self.assertEqual(si1.shape, (3, 3, 192, 152))
# @unittest.skip("skipping test_zipread_all_files")
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def test_zipread_all_files(self):
si1 = Series(
os.path.join('data', 'mat', 'time.zip'),
formats.INPUT_ORDER_TIME,
input_format='mat')
self.assertEqual(si1.dtype, np.uint16)
self.assertEqual(si1.shape, (3, 3, 192, 152))
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def test_write_ndarray(self):
with tempfile.TemporaryDirectory() as d:
Series(np.eye(128)).write(d, formats=['mat'])
# @unittest.skip("skipping test_write_single_file")
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def test_write_single_file(self):
si1 = Series(
os.path.join('data', 'mat', 'time', 'Image_00000.mat'),
'none',
input_format='mat')
with tempfile.TemporaryDirectory() as d:
si1.write(os.path.join(d, 'Image00000.mat'), formats=['mat'])
si2 = Series(os.path.join(d, 'Image00000.mat'), input_format='mat')
self.assertEqual(si1.dtype, si2.dtype)
self.assertEqual(si1.shape, si2.shape)
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def test_write_single_file_not_directory(self):
a = Series(np.eye(128))
with tempfile.TemporaryDirectory() as d:
filename = os.path.join(d, 'test.mat')
a.write(
filename,
formats=['mat']
)
if not os.path.isfile(filename):
raise AssertionError('File does not exist: {}'.format(filename))
# @unittest.skip("skipping test_write_single_directory")
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def test_write_single_directory(self):
si1 = Series(
os.path.join('data', 'mat', 'time'),
'none',
input_format='mat')
with tempfile.TemporaryDirectory() as d:
si1.write(d, formats=['mat'])
si2 = Series(d, input_format='mat')
self.assertEqual(si1.dtype, si2.dtype)
self.assertEqual(si1.shape, si2.shape)
# @unittest.skip("skipping test_read_3d_mat_no_opt")
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def test_read_3d_mat_no_opt(self):
si1 = Series(
os.path.join('data', 'mat', 'time', 'Image_00000.mat'),
'none',
input_format='mat')
with tempfile.TemporaryDirectory() as d:
si1.write(os.path.join(d, 'mat', 'Image_00000.mat'), formats=['mat'], opts=self.opts)
si2 = Series(os.path.join(d, 'mat', 'Image_00000.mat'), input_format='mat')
# @unittest.skip("skipping test_write_3d_mat_no_opt")
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def test_write_3d_mat_no_opt(self):
si1 = Series(
os.path.join('data', 'mat', 'time', 'Image_00000.mat'),
'none',
input_format='mat')
with tempfile.TemporaryDirectory() as d:
si1.write(os.path.join(d, 'mat', 'Image_{:05d}.mat'), formats=['mat'])
# @unittest.skip("skipping test_read_3d_mat")
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def test_write_3d_mat(self):
si1 = Series(
os.path.join('data', 'mat', 'time', 'Image_00000.mat'),
'none',
input_format='mat')
logging.debug('test_write_3d_mat: si1 {} {} {} {}'.format(type(si1), si1.dtype, si1.min(), si1.max()))
logging.debug('test_write_3d_mat: si1.shape {}, si1.slices {}'.format(si1.shape, si1.slices))
logging.debug('test_write_3d_mat: si1.tags {}'.format(si1.tags))
with tempfile.TemporaryDirectory() as d:
si1.write(os.path.join(d, 'mat', 'Image_00000.mat'), formats=['mat'], opts=self.opts)
logging.debug('test_write_3d_mat: si1 {} {} {}'.format(si1.dtype, si1.min(), si1.max()))
logging.debug('test_write_3d_mat: si1.shape {}, si1.slices {}'.format(si1.shape, si1.slices))
si2 = Series(
os.path.join(d, 'mat', 'Image_00000.mat'),
'none',
input_format='mat')
logging.debug('test_write_3d_mat: si2 {} {} {}'.format(si2.dtype, si2.min(), si2.max()))
self.assertEqual(si1.shape, si2.shape)
np.testing.assert_array_equal(si1, si2)
logging.debug('test_write_3d_mat: Get si1.slices {}'.format(si1.slices))
logging.debug('test_write_3d_mat: Set s3')
s3 = si1.astype(np.float64)
logging.debug('test_write_3d_mat: s3 {} {} {} {}'.format(type(s3),
issubclass(type(s3), Series), s3.dtype, s3.shape))
logging.debug('test_write_3d_mat: s3 {} {} {}'.format(s3.dtype,
s3.min(), s3.max()))
logging.debug('test_write_3d_mat: s3.slices {}'.format(s3.slices))
si3 = Series(s3)
np.testing.assert_array_almost_equal(si1, si3, decimal=4)
logging.debug('test_write_3d_mat: si3.slices {}'.format(si3.slices))
logging.debug('test_write_3d_mat: si3 {} {} {}'.format(type(si3), si3.dtype, si3.shape))
s3 = si1 - si2
with tempfile.TemporaryDirectory() as d:
s3.write(os.path.join(d, 'diff', 'Image_{:05d}.mat'), formats=['mat'], opts=self.opts)
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class Test4DMatPlugin(unittest.TestCase):
[docs]
def setUp(self):
parser = argparse.ArgumentParser()
cmdline.add_argparse_options(parser)
self.opts = parser.parse_args(['--of', 'mat'])
plugins = formats.get_plugins_list()
self.mat_plugin = None
for pname, ptype, pclass in plugins:
if ptype == 'mat':
self.mat_plugin = pclass
self.assertIsNotNone(self.mat_plugin)
# @unittest.skip("skipping test_write_4d_mat")
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def test_write_4d_mat(self):
si1 = Series(
os.path.join('data', 'mat', 'time', 'Image_00000.mat'),
formats.INPUT_ORDER_TIME,
input_format='mat')
self.assertEqual(si1.dtype, np.uint16)
self.assertEqual(si1.shape, (3, 3, 192, 152))
with tempfile.TemporaryDirectory() as d:
si1.write(os.path.join(d, 'mat', 'Image_00000.mat'), formats=['mat'], opts=self.opts)
# Read back the MAT data and compare to original si1
si2 = Series(
os.path.join(d, 'mat', 'Image_00000.mat'),
formats.INPUT_ORDER_TIME,
input_format='mat')
self.assertEqual(si1.shape, si2.shape)
np.testing.assert_array_equal(si1, si2)
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def test_write_cohort(self):
cohort = Cohort('data/dicom/cohort.zip', input_format='dicom')
with tempfile.TemporaryDirectory() as d:
cohort.write(d, formats=['mat'])
if __name__ == '__main__':
unittest.main()