def test_convert_mod_mrc_files_labels_not_file(self):
temp_dir = tempfile.mkdtemp()
try:
images_file = os.path.join(temp_dir, 'images.mrc')
labels_file = os.path.join(temp_dir, 'labels.mod')
os.makedirs(os.path.join(temp_dir, 'tmp'), mode=0o755)
open(images_file, 'a').close()
mrc2tif = os.path.join(temp_dir, 'mrc2tif')
f = open(mrc2tif, 'w')
f.write('#!/usr/bin/env python\nimport sys;sys.exit(0)\n')
f.flush()
f.close()
os.chmod(mrc2tif, stat.S_IRWXU | stat.S_IRGRP | stat.S_IROTH)
params = createchmtrainjob._parse_arguments(
'hi', [
images_file, labels_file, temp_dir, '--cluster', 'rocce',
'--imodbindir', temp_dir
])
createchmtrainjob._convert_mod_mrc_files(params)
self.fail('Expected IMODConversionError')
except IMODConversionError as e:
self.assertTrue(labels_file + ' is not a file, '
'cannot convert' in str(e))
finally:
shutil.rmtree(temp_dir)
def test_create_submit_script_rocce_cluster(self):
temp_dir = tempfile.mkdtemp()
try:
params = createchmtrainjob._parse_arguments(
'hi', ['./images', './labels', temp_dir, '--cluster', 'rocce'])
script = os.path.join(temp_dir,
createchmtrainjob.RUNTRAIN + 'rocce')
ucmd = createchmtrainjob._create_submit_script(params)
self.assertEqual(
ucmd, 'To submit run: cd ' + temp_dir + '; qsub ' + script)
f = open(script, 'r')
data = f.read()
f.close()
self.assertTrue('-N chmtrainjob' in data)
cwd = os.getcwd()
labelsdir = os.path.abspath(os.path.join(cwd, 'labels'))
imgdir = os.path.abspath(os.path.join(cwd, 'images'))
tmpdir = os.path.abspath(os.path.join(temp_dir, 'tmp'))
mystr = ('.img train ' + imgdir + ' ' + labelsdir +
' -S 2 -L 4 -m ' + tmpdir)
self.assertTrue(mystr in data)
# check the submit command got appended to end of readme file
f = open(os.path.join(temp_dir, createchmtrainjob.README_FILE),
'r')
data = f.read()
self.assertTrue('To submit run: cd ' + temp_dir in data)
f.close()
finally:
shutil.rmtree(temp_dir)
def test_parse_arguments(self):
params = createchmtrainjob._parse_arguments(
'hi', ['images', 'labels', 'outdir'])
self.assertEqual(params.images, 'images')
self.assertEqual(params.labels, 'labels')
self.assertEqual(params.outdir, 'outdir')
self.assertEqual(params.chmbin, './chm-0.1.0.img')
self.assertEqual(params.stage, 2)
self.assertEqual(params.level, 4)
self.assertEqual(params.cluster, 'rocce')
self.assertEqual(params.account, '')
self.assertEqual(params.jobname, 'chmtrainjob')
self.assertEqual(params.walltime, '24:00:00')
self.assertEqual(params.maxmem, 90)
self.assertEqual(params.cluster, 'rocce')
self.assertEqual(params.loglevel, 'WARNING')
self.assertEqual(params.imodbindir, '')
def test_convert_mod_mrc_files_images_is_not_a_dir_or_file(self):
temp_dir = tempfile.mkdtemp()
try:
images_file = os.path.join(temp_dir, 'images.mrc')
labels_file = os.path.join(temp_dir, 'labels.mod')
params = createchmtrainjob._parse_arguments(
'hi', [
images_file, labels_file, temp_dir, '--cluster', 'rocce',
'--imodbindir', temp_dir
])
createchmtrainjob._convert_mod_mrc_files(params)
self.fail('Expected InvalidInputDataError')
except InvalidInputDataError as e:
self.assertTrue(images_file + ' does not exist' in str(e))
finally:
shutil.rmtree(temp_dir)
def test_convert_mod_mrc_files_second_mrc2tif_fails(self):
temp_dir = tempfile.mkdtemp()
try:
images_file = os.path.join(temp_dir, 'images.mrc')
labels_file = os.path.join(temp_dir, 'labels.mod')
os.makedirs(os.path.join(temp_dir, createchmtrainjob.TMP_DIR),
mode=0o755)
open(images_file, 'a').close()
open(labels_file, 'a').close()
mrc2tif = os.path.join(temp_dir, 'mrc2tif')
f = open(mrc2tif, 'w')
f.write('#!/usr/bin/env python\nimport sys\n')
f.write('if "tmp.mrc" in sys.argv[2]:\n sys.exit(2)\n'
'sys.exit(0)\n')
f.flush()
f.close()
os.chmod(mrc2tif, stat.S_IRWXU | stat.S_IRGRP | stat.S_IROTH)
imodmop = os.path.join(temp_dir, 'imodmop')
f = open(imodmop, 'w')
f.write('#!/usr/bin/env python\nimport sys;sys.exit(0)\n')
f.flush()
f.close()
os.chmod(imodmop, stat.S_IRWXU | stat.S_IRGRP | stat.S_IROTH)
params = createchmtrainjob._parse_arguments(
'hi', [
images_file, labels_file, temp_dir, '--cluster', 'rocce',
'--imodbindir', temp_dir
])
createchmtrainjob._convert_mod_mrc_files(params)
self.fail('Expected IMODConversionError')
except IMODConversionError as e:
self.assertTrue('Non zero exit code from '
'mrc2tif: 2 : :' in str(e))
finally:
shutil.rmtree(temp_dir)
def test_convert_mod_mrc_files_success(self):
temp_dir = tempfile.mkdtemp()
try:
images_file = os.path.join(temp_dir, 'images.mrc')
labels_file = os.path.join(temp_dir, 'labels.mod')
os.makedirs(os.path.join(temp_dir, createchmtrainjob.TMP_DIR),
mode=0o755)
open(images_file, 'a').close()
open(labels_file, 'a').close()
mrc2tif = os.path.join(temp_dir, 'mrc2tif')
f = open(mrc2tif, 'w')
f.write('#!/usr/bin/env python\nimport sys\n')
f.write('sys.exit(0)\n')
f.flush()
f.close()
os.chmod(mrc2tif, stat.S_IRWXU | stat.S_IRGRP | stat.S_IROTH)
imodmop = os.path.join(temp_dir, 'imodmop')
f = open(imodmop, 'w')
f.write('#!/usr/bin/env python\nimport sys;sys.exit(0)\n')
f.flush()
f.close()
os.chmod(imodmop, stat.S_IRWXU | stat.S_IRGRP | stat.S_IROTH)
params = createchmtrainjob._parse_arguments(
'hi', [
images_file, labels_file, temp_dir, '--cluster', 'rocce',
'--imodbindir', temp_dir
])
img, lbl = createchmtrainjob._convert_mod_mrc_files(params)
self.assertEqual(
img, os.path.join(temp_dir, createchmtrainjob.IMAGES_DIR))
self.assertEqual(
lbl, os.path.join(temp_dir, createchmtrainjob.LABELS_DIR))
finally:
shutil.rmtree(temp_dir)