def test_clean_removes_thumbnails():
"""parserix.clean removes thumbnail images"""
cleaned_up = clean.clean(test_paths)
for line in cleaned_up:
assert "thumb" not in line
cleaned_up_new = clean.clean(new_test_paths)
for line in cleaned_up_new:
assert "thumb" not in line
from parserix import clean
from parserix import parse
import datetime
import pytest
import os
test_list_path = os.path.join(os.path.abspath("tests"), "images.txt")
new_test_list_path = os.path.join(os.path.abspath("tests"), "new_images.txt")
test_paths = [line.strip() for line in open(test_list_path)]
new_test_paths = [line.strip() for line in open(new_test_list_path)]
# remove rubbish mixed in with file paths
clean_paths = clean.clean(test_paths)
new_clean_paths = clean.clean(new_test_paths)
EXAMPLE_PATH = "/mnt/ImageXpress/2015-07-31 val screen/val screen/HCC15691/2015-07-31/4014/val screen_B02_s1_w1_thumb62D4A363-7C7E-40D0-8A9E-55EC6681574D.tif"
NEW_EXAMPLE_PATH = "/mnt/Datastore/IGMM/ImageXpress2020/drug-discovery/GCGR-FDA/E13FDAa1/2021-04-03/490/TimePoint_1/val screen_B02_s1_w1_thumb62D4A363-7C7E-40D0-8A9E-55EC6681574D.tif"
def test_img_filename():
expected = "val screen_B02_s1_w1_thumb62D4A363-7C7E-40D0-8A9E-55EC6681574D.tif"
assert parse.img_filename(EXAMPLE_PATH) == expected
assert parse.img_filename(NEW_EXAMPLE_PATH) == expected
def test_path():
assert parse.path(
EXAMPLE_PATH
) == "/mnt/ImageXpress/2015-07-31 val screen/val screen/HCC15691/2015-07-31/4014"
assert parse.path(
"""
tests for nncell.image_prep
"""
import os
from nncell import image_prep
from parserix import parse
from parserix import clean
import numpy as np
import pytest
# sort out data for tests
TEST_DIR = os.path.abspath("tests")
PATH_TO_IMG_URLS = os.path.join(TEST_DIR, "test_images/images.txt")
IMG_URLS = clean.clean([i.strip() for i in open(PATH_TO_IMG_URLS).readlines()])
#####################################
# ImageDict tests
#####################################
def test_ImageDict_remove_channels():
channels_to_remove = [4, 5]
ImgDict = image_prep.ImageDict()
ans = ImgDict.remove_channels(IMG_URLS, channels_to_remove)
# parse channel numbers out of ans
img_names = [parse.img_filename(f) for f in ans]
img_channels = [parse.img_channel(name) for name in img_names]
for channel in img_channels:
assert channel not in channels_to_remove
def test_clean_removes_db_files():
"""parserix.clean removes Thumbs.db file left by windows"""
cleaned_up = clean.clean(test_paths)
assert "Thumbs.db" not in cleaned_up
cleaned_up_new = clean.clean(new_test_paths)
assert "Thumbs.db" not in cleaned_up_new
def test_clean_removes_something():
"""clean actually removes something"""
assert len(test_paths) > len(clean.clean(test_paths))
assert len(new_test_paths) > len(clean.clean(new_test_paths))