def test_no_frame_specification_default(self):
testargs = 'foo.py -filename 1_a_#.mrc -output_dir /tmp'.split()
with patch('sys.argv', testargs):
obj = m()
self.assertTrue(obj.check)
self.assertEqual(0, obj.first_frame)
self.assertEqual(6, obj.last_frame)
def test_jpg_dir_creation(self):
testargs = 'foo.py -filename 1_a_#.mrc -output_dir /tmp -jpg_dir nonexist'.split()
with patch('sys.argv', testargs):
with patch('os.mkdir') as mock:
obj = m()
self.assertTrue(obj.check)
self.assertTrue(mock.called)
def test_default_frame_suffix(self):
testargs = 'foo.py -filename 1_a_#.mrc -output_dir /tmp'.split()
with patch('sys.argv', testargs):
obj = m()
exp = 'frames_n{}'
self.assertTrue(obj.check)
self.assertEqual(exp, obj.frames_suffix)
def test_default_frame_suffix(self):
testargs = 'foo.py -filename 1_a_#.mrc -output_dir /tmp'.split()
with patch('sys.argv', testargs):
obj = m()
exp = 'frames_n{}'
self.assertTrue(obj.check)
self.assertEqual(exp, obj.frames_suffix)
def test_non_frames_suffix_starting_underscore(self):
testargs = 'foo.py -filename 1_a_#.mrc -output_dir /tmp -frames_suffix _n#'.split()
with patch('sys.argv', testargs):
obj = m()
exp = '_n{}'
self.assertTrue(obj.check)
self.assertEqual(exp, obj.frames_suffix)
def test_output_dir_creation(self):
testargs = 'foo.py -filename 1_a_#.mrc -output_dir /tmp/tmp'.split()
with patch('sys.argv', testargs):
with patch('os.mkdir') as mock:
obj = m()
self.assertTrue(obj.check)
self.assertTrue(mock.called)
def test_no_frame_specification_default(self):
testargs = 'foo.py -filename 1_a_#.mrc -output_dir /tmp'.split()
with patch('sys.argv', testargs):
obj = m()
self.assertTrue(obj.check)
self.assertEqual(0, obj.first_frame)
self.assertEqual(6, obj.last_frame)
def test_n_frames(self):
testargs = 'foo.py -filename 1_a_#.mrc -n_frames 12 -output_dir /tmp'.split()
with patch('sys.argv', testargs):
obj = m()
self.assertTrue(obj.check)
self.assertEqual(0, obj.first_frame)
self.assertEqual(11, obj.last_frame)
def test_missing_frames(self):
'''
removing one frame for image 1
the remaining frame should end up in missing frames;
the corresponding image in orphan images
'''
os.remove(os.path.join(self.tempdir, ('badname_1_frame0.mrc')))
# adding one orphan frame (no parent image)
with open(os.path.join(self.tempdir, 'badname_5_frame0.mrc'), 'w'):
pass
testargs = ('foo.py -input_dir {temp} -output_dir {temp} -filename new_#.mrc'
' -frames_suffix {frame} -EPU_image_pattern * -n_frames 2')
testargs = testargs.format(temp = self.tempdir, frame = self.frame_suffix)
with patch('sys.argv', testargs.split()):
obj = m()
frames, integrated = obj.find_mrc_files(obj.input_dir, obj.EPU_image_pattern,
obj.frames_suffix)
obj.rename_files(frames, integrated)
missing_frames = len(glob.glob(os.path.join(self.tempdir, 'missing_frames', '*.mrc')))
orphan_frames = len(glob.glob(os.path.join(self.tempdir, 'orphan_frames', '*.mrc')))
orphan_images = len(glob.glob(os.path.join(self.tempdir, 'orphan_integrated', '*.mrc')))
frames = len(glob.glob(os.path.join(self.tempdir, 'frames', '*.mrc')))
integrated = len(glob.glob(os.path.join(self.tempdir, 'integrated', '*.mrc')))
self.assertEqual(missing_frames, 1)
self.assertEqual(orphan_frames, 1)
self.assertEqual(orphan_images, 1)
self.assertEqual(frames, 4)
self.assertEqual(integrated, 2)
def test_non_frames_suffix_starting_underscore(self):
testargs = 'foo.py -filename 1_a_#.mrc -output_dir /tmp -frames_suffix _n#'.split(
)
with patch('sys.argv', testargs):
obj = m()
exp = '_n{}'
self.assertTrue(obj.check)
self.assertEqual(exp, obj.frames_suffix)
def test_n_frames(self):
testargs = 'foo.py -filename 1_a_#.mrc -n_frames 12 -output_dir /tmp'.split(
)
with patch('sys.argv', testargs):
obj = m()
self.assertTrue(obj.check)
self.assertEqual(0, obj.first_frame)
self.assertEqual(11, obj.last_frame)
def test_find_files(self):
testargs = ('foo.py -input_dir {temp} -output_dir {temp} -filename #.mrc'
' -frames_suffix {frame} -EPU_image_pattern *')
testargs = testargs.format(temp = self.tempdir, frame = self.frame_suffix)
with patch('sys.argv', testargs.split()):
obj = m()
frames, integrated = obj.find_mrc_files(obj.input_dir, obj.EPU_image_pattern,
obj.frames_suffix)
self.assertEqual(integrated.sort(), self.exp_integrated.sort())
self.assertEqual(frames.sort(), self.exp_frames.sort())
def test_find_files(self):
testargs = (
'foo.py -input_dir {temp} -output_dir {temp} -filename #.mrc'
' -frames_suffix {frame} -EPU_image_pattern *')
testargs = testargs.format(temp=self.tempdir, frame=self.frame_suffix)
with patch('sys.argv', testargs.split()):
obj = m()
frames, integrated = obj.find_mrc_files(obj.input_dir,
obj.EPU_image_pattern,
obj.frames_suffix)
self.assertEqual(integrated.sort(), self.exp_integrated.sort())
self.assertEqual(frames.sort(), self.exp_frames.sort())
def test_find_files_scans_subfolders(self):
#creating an extra file in a subfolder
os.makedirs(os.path.join(self.tempdir, 'subfolder'))
with open(os.path.join(self.tempdir, 'subfolder/4.mrc'),'w') as f:
self.exp_integrated += [f.name]
testargs = ('foo.py -input_dir {temp} -output_dir {temp} -filename #.mrc'
' -frames_suffix {frame} -EPU_image_pattern *')
testargs = testargs.format(temp = self.tempdir, frame = self.frame_suffix)
with patch('sys.argv', testargs.split()):
obj = m()
frames, integrated = obj.find_mrc_files(obj.input_dir, obj.EPU_image_pattern,
obj.frames_suffix)
self.assertEqual(integrated.sort(), self.exp_integrated.sort())
self.assertEqual(frames.sort(), self.exp_frames.sort())
def test_find_files_scans_subfolders(self):
#creating an extra file in a subfolder
os.makedirs(os.path.join(self.tempdir, 'subfolder'))
with open(os.path.join(self.tempdir, 'subfolder/4.mrc'), 'w') as f:
self.exp_integrated += [f.name]
testargs = (
'foo.py -input_dir {temp} -output_dir {temp} -filename #.mrc'
' -frames_suffix {frame} -EPU_image_pattern *')
testargs = testargs.format(temp=self.tempdir, frame=self.frame_suffix)
with patch('sys.argv', testargs.split()):
obj = m()
frames, integrated = obj.find_mrc_files(obj.input_dir,
obj.EPU_image_pattern,
obj.frames_suffix)
self.assertEqual(integrated.sort(), self.exp_integrated.sort())
self.assertEqual(frames.sort(), self.exp_frames.sort())
def test_find_files_non_EPU_discarded(self):
#only the newly created file matches the EPU pattern
os.makedirs(os.path.join(self.tempdir, 'subfolder'))
with open(os.path.join(self.tempdir, 'subfolder/4.mrc'),'w') as f:
self.exp_integrated = [f.name]
self.exp_frames = []
EPU_image_pattern = '/subfolder/'
testargs = ('foo.py -input_dir {temp} -output_dir {temp} -filename #.mrc'
' -frames_suffix {frame} -EPU_image_pattern {EPU}')
testargs = testargs.format(temp = self.tempdir, frame = self.frame_suffix,
EPU = EPU_image_pattern)
with patch('sys.argv', testargs.split()):
obj = m()
frames, integrated = obj.find_mrc_files(obj.input_dir, obj.EPU_image_pattern,
obj.frames_suffix)
self.assertEqual(integrated.sort(), self.exp_integrated.sort())
self.assertEqual(frames.sort(), self.exp_frames.sort())
def test_find_files_non_EPU_discarded(self):
#only the newly created file matches the EPU pattern
os.makedirs(os.path.join(self.tempdir, 'subfolder'))
with open(os.path.join(self.tempdir, 'subfolder/4.mrc'), 'w') as f:
self.exp_integrated = [f.name]
self.exp_frames = []
EPU_image_pattern = '/subfolder/'
testargs = (
'foo.py -input_dir {temp} -output_dir {temp} -filename #.mrc'
' -frames_suffix {frame} -EPU_image_pattern {EPU}')
testargs = testargs.format(temp=self.tempdir,
frame=self.frame_suffix,
EPU=EPU_image_pattern)
with patch('sys.argv', testargs.split()):
obj = m()
frames, integrated = obj.find_mrc_files(obj.input_dir,
obj.EPU_image_pattern,
obj.frames_suffix)
self.assertEqual(integrated.sort(), self.exp_integrated.sort())
self.assertEqual(frames.sort(), self.exp_frames.sort())
def test_missing_frames(self):
'''
removing one frame for image 1
the remaining frame should end up in missing frames;
the corresponding image in orphan images
'''
os.remove(os.path.join(self.tempdir, ('badname_1_frame0.mrc')))
# adding one orphan frame (no parent image)
with open(os.path.join(self.tempdir, 'badname_5_frame0.mrc'), 'w'):
pass
testargs = (
'foo.py -input_dir {temp} -output_dir {temp} -filename new_#.mrc'
' -frames_suffix {frame} -EPU_image_pattern * -n_frames 2')
testargs = testargs.format(temp=self.tempdir, frame=self.frame_suffix)
with patch('sys.argv', testargs.split()):
obj = m()
frames, integrated = obj.find_mrc_files(obj.input_dir,
obj.EPU_image_pattern,
obj.frames_suffix)
obj.rename_files(frames, integrated)
missing_frames = len(
glob.glob(os.path.join(self.tempdir, 'missing_frames', '*.mrc')))
orphan_frames = len(
glob.glob(os.path.join(self.tempdir, 'orphan_frames', '*.mrc')))
orphan_images = len(
glob.glob(os.path.join(self.tempdir, 'orphan_integrated',
'*.mrc')))
frames = len(glob.glob(os.path.join(self.tempdir, 'frames', '*.mrc')))
integrated = len(
glob.glob(os.path.join(self.tempdir, 'integrated', '*.mrc')))
self.assertEqual(missing_frames, 1)
self.assertEqual(orphan_frames, 1)
self.assertEqual(orphan_images, 1)
self.assertEqual(frames, 4)
self.assertEqual(integrated, 2)
def test_existing_input_dir(self):
testargs = 'foo.py -filename 1_a_#.mrc -input_dir /tmp -output_dir /tmp'
with patch('sys.argv', testargs.split()):
obj = m()
self.assertTrue(obj.check)
self.assertEqual('/tmp', obj.input_dir)
def test_no_hash_in_frame_suffix(self):
testargs = 'foo.py -filename 1_a_#.mrc -output_dir /tmp -frames_suffix _n'.split()
with patch('sys.argv', testargs):
with self.assertRaises(SystemExit):
obj = m()
def test_digits_count(self):
testargs = 'foo.py -output_dir /tmp -filename 1_a_###.mrc'.split()
with patch('sys.argv', testargs):
obj = m()
self.assertTrue(obj.check)
self.assertEqual(3, obj.digits)
def test_first_last_not_a_number(self):
testargs = 'foo.py -filename 1_a_#.mrc -first_last a,b -output_dir /tmp'.split(
)
with patch('sys.argv', testargs):
with self.assertRaises(ValueError):
obj = m()
def test_no_EPU_pattern(self):
testargs = 'foo.py -filename 1_a_#.mrc -output_dir /tmp'.split()
with patch('sys.argv', testargs):
obj = m()
self.assertEqual(obj.EPU_image_pattern, '/Data/FoilHole')
def test_default_data_dir(self):
testargs = 'foo.py -output_dir /tmp -filename 1_a_#.mrc'.split()
with patch('sys.argv', testargs):
obj = m()
self.assertTrue(obj.check)
self.assertEqual(os.getcwd(), obj.input_dir)
def test_default_data_dir(self):
testargs = 'foo.py -output_dir /tmp -filename 1_a_#.mrc'.split()
with patch('sys.argv', testargs):
obj = m()
self.assertTrue(obj.check)
self.assertEqual(os.getcwd(), obj.input_dir)
def test_EPU_pattern_is_asterisk(self):
testargs = 'foo.py -filename 1_a_#.mrc -output_dir /tmp -EPU_image_pattern *'.split(
)
with patch('sys.argv', testargs):
obj = m()
self.assertEqual(obj.EPU_image_pattern, '')
def test_no_EPU_pattern(self):
testargs = 'foo.py -filename 1_a_#.mrc -output_dir /tmp'.split()
with patch('sys.argv', testargs):
obj = m()
self.assertEqual(obj.EPU_image_pattern, '/Data/FoilHole')
def test_nonexisting_input_dir(self):
testargs = 'foo.py -filename 1_a_#.mrc -input_dir /not/exists ' + \
'-output_dir /tmp'
with patch('sys.argv', testargs.split()):
with self.assertRaises(SystemExit):
obj = m()
def test_first_last_frame_number_no_comma(self):
testargs = 'foo.py -filename 1_a_#.mrc -first_last 1-2 -output_dir /tmp'.split()
with patch('sys.argv', testargs):
with self.assertRaises(SystemExit):
obj = m()
def test_nonexisting_input_dir(self):
testargs = 'foo.py -filename 1_a_#.mrc -input_dir /not/exists ' + \
'-output_dir /tmp'
with patch('sys.argv', testargs.split()):
with self.assertRaises(SystemExit):
obj = m()
def test_first_last_not_a_number(self):
testargs = 'foo.py -filename 1_a_#.mrc -first_last a,b -output_dir /tmp'.split()
with patch('sys.argv', testargs):
with self.assertRaises(ValueError):
obj = m()
def test_existing_input_dir(self):
testargs = 'foo.py -filename 1_a_#.mrc -input_dir /tmp -output_dir /tmp'
with patch('sys.argv', testargs.split()):
obj = m()
self.assertTrue(obj.check)
self.assertEqual('/tmp', obj.input_dir)
def test_EPU_pattern_is_asterisk(self):
testargs = 'foo.py -filename 1_a_#.mrc -output_dir /tmp -EPU_image_pattern *'.split()
with patch('sys.argv', testargs):
obj = m()
self.assertEqual(obj.EPU_image_pattern, '')
def test_digits_count(self):
testargs = 'foo.py -output_dir /tmp -filename 1_a_###.mrc'.split()
with patch('sys.argv', testargs):
obj = m()
self.assertTrue(obj.check)
self.assertEqual(3, obj.digits)
def test_no_hash_in_frame_suffix(self):
testargs = 'foo.py -filename 1_a_#.mrc -output_dir /tmp -frames_suffix _n'.split(
)
with patch('sys.argv', testargs):
with self.assertRaises(SystemExit):
obj = m()
def test_first_last_frame_number_no_comma(self):
testargs = 'foo.py -filename 1_a_#.mrc -first_last 1-2 -output_dir /tmp'.split(
)
with patch('sys.argv', testargs):
with self.assertRaises(SystemExit):
obj = m()
