We are trying to track down exposure times information for experiments where we tested low vs high exposure times - there are some weirdnesses I don't fully understand. But to avoid it getting lost, this is the code used to extract them and confirm that the files are being read correctly.
import os
dirlist = os.listdir(os.curdir)
dirlist.sort()
for sub_dir in dirlist:
if '__' in sub_dir:
exposure_dict = {'Alexa 647':[],'Alexa 568':[], '488 long':[],'Alexa 488':[],'HOECHST 33342':[],'Brightfield CP':[]}
print("subdir", sub_dir)
with open(sub_dir + "/Images/Index.idx.xml", "r") as xmlfile:
lines = xmlfile.readlines()
name = False
exp = False
for line in lines:
if 'Oreintation' in line:
name = False
exp = False
if "<ChannelName>" in line:
name = line[line.find("<ChannelName>") + 13: line.rfind("<")]
if '<ExposureTime Unit="s">' in line:
exp = line[line.find('Unit') + 9 : line.rfind("<")]
if name:
exposure_dict[name].append(exp)
for k,v in exposure_dict.items():
exp_list = list(set(v))
exp_count_list = []
for exp in exp_list:
exp_count_list.append(len([x for x in v if x==exp]))
print(k,exp_list)
We are trying to track down exposure times information for experiments where we tested low vs high exposure times - there are some weirdnesses I don't fully understand. But to avoid it getting lost, this is the code used to extract them and confirm that the files are being read correctly.
Results for plates currently in figure
``` subdir 200921_193743-V__2020-09-21T13_34_13-Measurement1 Alexa 647 ['0.01'] Alexa 568 ['0.01'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] subdir 200921_193743-V__2020-09-21T14_50_14-Measurement2 Alexa 647 ['0.02'] Alexa 568 ['0.01'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] subdir 200922_015124-V__2020-09-21T19_47_54-Measurement1 Alexa 647 ['0.01'] Alexa 568 ['0.01'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] subdir 200922_015124-V__2020-09-21T21_04_16-Measurement2 Alexa 647 ['0.02'] Alexa 568 ['0.01'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] subdir BR00115125__2020-08-14T14_17_57-Measurement1 Alexa 647 ['0.01'] Alexa 568 ['0.01'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] subdir BR00115125__2020-08-15T07_02_34-Measurement2 Alexa 647 ['0.01'] Alexa 568 ['0.01'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] subdir BR00115126__2020-08-14T12_49_23-Measurement1 Alexa 647 ['0.01'] Alexa 568 ['0.01'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] subdir BR00115126__2020-08-15T05_34_05-Measurement2 Alexa 647 ['0.01'] Alexa 568 ['0.01'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] subdir BR00115128__2020-08-14T08_22_51-Measurement1 Alexa 647 ['0.01'] Alexa 568 ['0.01'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] subdir BR00115128__2020-08-15T03_38_52-Measurement2 Alexa 647 ['0.01'] Alexa 568 ['0.02'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] subdir BR00115132__2020-08-14T03_56_58-Measurement1 Alexa 647 ['0.01'] Alexa 568 ['0.01'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] subdir BR00115132__2020-08-15T01_25_14-Measurement2 Alexa 647 ['0.04'] Alexa 568 ['0.02'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] subdir BR00115133__2020-08-14T02_28_12-Measurement1 Alexa 647 ['0.01'] Alexa 568 ['0.01'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] subdir BR00115133__2020-08-15T08_31_19-Measurement2 Alexa 647 ['0.02'] Alexa 568 ['0.01'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] subdir BR00116620__2020-09-21T23_47_59-Measurement1 Alexa 647 ['0.01'] Alexa 568 ['0.01'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] subdir BR00116620__2020-09-22T19_45_41-Measurement2 Alexa 647 ['0.01'] Alexa 568 ['0.01'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] subdir BR00116621__2020-09-22T01_15_42-Measurement1 Alexa 647 ['0.01'] Alexa 568 ['0.01'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] subdir BR00116621__2020-09-22T21_13_32-Measurement2 Alexa 647 ['0.01'] Alexa 568 ['0.01'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] subdir BR00116622__2020-09-18T15_18_26-Measurement1 Alexa 647 ['0.01'] Alexa 568 ['0.01'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] subdir BR00116622__2020-09-21T16_25_19-Measurement1 Alexa 647 ['0.02'] Alexa 568 ['0.01'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] subdir BR00116624__2020-09-21T22_19_49-Measurement1 Alexa 647 ['0.01'] Alexa 568 ['0.01'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] subdir BR00116624__2020-09-22T18_17_35-Measurement2 Alexa 647 ['0.01'] Alexa 568 ['0.01'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] subdir BR00116625__2020-09-21T20_51_34-Measurement1 Alexa 647 ['0.01'] Alexa 568 ['0.01'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] subdir BR00116625__2020-09-22T10_04_13-Measurement2 Alexa 647 ['0.01'] Alexa 568 ['0.01'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] subdir BR00116627__2020-09-21T19_23_21-Measurement1 Alexa 647 ['0.01'] Alexa 568 ['0.01'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] subdir BR00116627__2020-09-22T08_35_56-Measurement2 Alexa 647 ['0.01'] Alexa 568 ['0.01'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] subdir BR00116628__2020-09-21T17_55_03-Measurement1 Alexa 647 ['0.01'] Alexa 568 ['0.01'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] subdir BR00116628__2020-09-22T07_07_34-Measurement2 Alexa 647 ['0.01'] Alexa 568 ['0.01'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] subdir BR00116629__2020-09-21T16_27_12-Measurement1 Alexa 647 ['0.01'] Alexa 568 ['0.01'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] subdir BR00116629__2020-09-22T05_39_49-Measurement2 Alexa 647 ['0.01'] Alexa 568 ['0.01'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] subdir BR00116630__2020-09-21T14_59_00-Measurement1 Alexa 647 ['0.01'] Alexa 568 ['0.01'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] subdir BR00116630__2020-09-22T04_11_32-Measurement2 Alexa 647 ['0.01'] Alexa 568 ['0.01'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] subdir BR00116631__2020-09-22T02_43_29-Measurement1 Alexa 647 ['0.01'] Alexa 568 ['0.01'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] subdir BR00116631__2020-09-22T22_41_32-Measurement2 Alexa 647 ['0.01'] Alexa 568 ['0.01'] 488 long ['0.01'] Alexa 488 ['0.01'] HOECHST 33342 ['0.01'] Brightfield CP ['0.01'] ```