def test_region_by_identifier(self):
from jicbioimage.segment import SegmentedImage
input_array = np.array([[0, 0, 0],
[1, 1, 1],
[2, 2, 2]])
segmented_image = SegmentedImage.from_array(input_array)
with self.assertRaises(ValueError):
segmented_image.region_by_identifier(0)
with self.assertRaises(ValueError):
segmented_image.region_by_identifier(0.5)
with self.assertRaises(ValueError):
segmented_image.region_by_identifier(-1)
from jicbioimage.segment import Region
selected_region = segmented_image.region_by_identifier(1)
self.assertTrue(isinstance(selected_region, Region))
expected_output = Region.select_from_array(input_array, 1)
self.assertTrue(np.array_equal(selected_region,
expected_output))
def test_dilate(self):
from jicbioimage.segment import Region
test_array = np.array([[0, 0, 0, 0, 0],
[0, 0, 1, 1, 0],
[0, 1, 1, 0, 0],
[0, 1, 0, 0, 0],
[0, 0, 0, 0, 0]])
region = Region(test_array)
dilate_array = np.array([[0, 0, 1, 1, 0],
[0, 1, 1, 1, 1],
[1, 1, 1, 1, 0],
[1, 1, 1, 0, 0],
[0, 1, 0, 0, 0]], dtype=bool)
self.assertTrue(np.array_equal(region.dilate(),
dilate_array))
def test_region_select_from_array(self):
from jicbioimage.segment import Region
id_array = np.array([[0, 0, 0],
[1, 1, 1],
[2, 2, 2]])
region_1 = Region.select_from_array(id_array, 1)
self.assertFalse(region_1[0, 0])
self.assertTrue(region_1[1, 0])
self.assertFalse(region_1[2, 0])
self.assertEqual(region_1.area, 3)
def main():
# Parse the command line arguments.
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument("input_file", help="Input file")
parser.add_argument("mask_file", help="Mask file")
parser.add_argument("parameters_file", help="Parameters file")
parser.add_argument("output_dir", help="Output directory")
parser.add_argument("--debug", default=False, action="store_true",
help="Write out intermediate images")
args = parser.parse_args()
# Check that the input file exists.
if not os.path.isfile(args.input_file):
parser.error("{} not a file".format(args.input_file))
if not os.path.isfile(args.parameters_file):
parser.error("{} not a file".format(args.parameters_file))
# Read in the parameters.
params = Parameters.from_file(args.parameters_file)
# Create the output directory if it does not exist.
if not os.path.isdir(args.output_dir):
os.mkdir(args.output_dir)
AutoName.directory = args.output_dir
# Only write out intermediate images in debug mode.
if not args.debug:
AutoWrite.on = False
# Setup a logger for the script.
log_fname = "audit.log"
log_fpath = os.path.join(args.output_dir, log_fname)
logging_level = logging.INFO
if args.debug:
logging_level = logging.DEBUG
logging.basicConfig(filename=log_fpath, level=logging_level)
# Log some basic information about the script that is running.
logging.info("Script name: {}".format(__file__))
logging.info("Script version: {}".format(__version__))
logging.info("Parameters: {}".format(params))
# Run the analysis.
mask_im = Image.from_file(args.mask_file)
mask = Region.select_from_array(mask_im, 0)
identity(mask)
analyse_file(args.input_file, mask, args.output_dir, **params)
def test_background(self):
from jicbioimage.segment import SegmentedImage
input_array = np.array([[0, 0, 0],
[1, 1, 1],
[2, 2, 2]])
segmented_image = SegmentedImage.from_array(input_array)
from jicbioimage.segment import Region
background = segmented_image.background
expected_output = Region.select_from_array(input_array, 0)
self.assertTrue(np.array_equal(background,
expected_output))