def add_plate(self, plates, exp_dir):
"""
add plate(s) from an experiment to the plate_store
plates being a string or list of strings of the plate names.
can only add plates from a single experiment directory
if adding plates from multiple experiments, then use multiple add_plate
methods
Parameters:
-----------
plates : string or list of strings
plate names of plates to be added
exp_dir : string
path to experiment directory that contains the plates
"""
if isinstance(plates, str):
full_path = exp_dir + plates
img_files = filelist.files_from_plate(full_path)
self.plate_store[plates] = [full_path, img_files]
elif isinstance(plates, list):
full_path = [exp_dir + i for i in plates]
img_files = [
filelist.files_from_plate(plate) for plate in full_path
]
for idx, plate in enumerate(plates):
self.plate_store[plate] = [full_path[idx], img_files[idx]]
else:
raise ValueError("plates has to be a string of a list of strings")
def test_files_from_plate_truncate():
"""files_from_plate with truncated file-paths"""
plate_path = os.path.join(TEST_PATH, "test-plate-1")
output = filelist.files_from_plate(plate_path,
clean=True, truncate=True)
for f in output:
assert len(f.split(os.sep)) == 4
def test_files_from_plate():
"""see if we get image files from a plate directory"""
plate_path = os.path.join(TEST_PATH, "test-plate-1")
output = filelist.files_from_plate(plate_path,
clean=True, truncate=False)
assert len(output) > 0
for f in output:
assert f.endswith(".tif")
def add_experiment(self, exp_dir):
"""
add all plates in an experiment to the platestore
Parameters:
-----------
exp_dir : string
path to imageXpress experiment that contains plate sub-directories
"""
self.exp_dir = exp_dir
plate_names = os.listdir(exp_dir)
plate_paths = filelist.paths_to_plates(exp_dir)
img_files = [filelist.files_from_plate(p) for p in plate_paths]
for idx, plate in enumerate(plate_names):
self.plate_store[plate] = [plate_paths[idx], img_files[idx]]
def test_files_from_plate_clean_false():
"""files_from_plate with clean as false"""
plate_path = os.path.join(TEST_PATH, "test-plate-1")
output = filelist.files_from_plate(plate_path,
clean=False, truncate=False)
assert len(output) > 0
import os
import pandas as pd
from cptools2 import splitter
from cptools2 import filelist
# need to have an image list
CURRENT_PATH = os.path.dirname(__file__)
TEST_PATH = os.path.join(CURRENT_PATH, "example_dir")
TEST_PATH_PLATE_1 = os.path.join(TEST_PATH, "test-plate-1")
# just use a single plate
IMG_LIST = filelist.files_from_plate(TEST_PATH_PLATE_1)
def test_well_site_table():
"""job_splitter._well_site_table(img_list)"""
output = splitter._well_site_table(IMG_LIST)
assert isinstance(output, pd.DataFrame)
# check the dataframe is the right size
# should have a row per image in image list and 3 columns
assert output.shape == (len(IMG_LIST), 3)
# need to short as for some unknown reason the order is being mixed up
# though doesn't matter as always use column names rather than index
assert sorted(output.columns.tolist()) == sorted(
["img_paths", "Metadata_well", "Metadata_site"])
def test_group_images():
"""job_splitter._group_images(df_img)"""
# create dataframe for _group_images
df_img = splitter._well_site_table(IMG_LIST)
output = splitter._group_images(df_img)