sbesson
commented
1 year ago Looks like I had made some progress on this conversion in the same way as https://github.com/IDR/idr-metadata/issues/649 using the following script
import os
sourcedir="/uod/idr/filesets/idr0035-caie-drugresponse/images"
targetdir='/data/idr0035/sources/'
zarrdir="/data/idr0035/zarr/"
bf2raw_exec = "/opt/bioformats2raw/bioformats2raw-0.6.1/bin/bioformats2raw"
aws_exec = "~/venv/bin/aws"
with open('idr0035.HTD', 'r') as f:
htd_template = f.read()
plates = os.listdir(sourcedir)
commands = []
for plate in plates:
source_plate = os.path.join(sourcedir, plate)
target_plate = os.path.join(targetdir, plate)
os.makedirs(target_plate)
tiffs = os.listdir(source_plate)
for tiff in tiffs:
os.symlink(os.path.join(source_plate, tiff), os.path.join(target_plate, tiff))
htd_file = os.path.join(target_plate, "_".join(tiffs[0].split('_')[:2]) + ".HTD")
with open(htd_file,'w') as f:
f.write(htd_template.format(plate=plate))
zarr_plate = os.path.join(zarrdir, plate + ".zarr")
s3_zarr_plate = f"s3://idr0035/zarr/{plate}.zarr"
bf2raw_cmd = " ".join([bf2raw_exec, htd_file, zarr_plate, "-p"])
aws_cmd = " ".join(
[aws_exec, "--profile ebi", "--endpoint-url https://uk1s3.embassy.ebi.ac.uk" ,"s3 cp --recursive",
zarr_plate, s3_zarr_plate])
rm_cmd = " ".join(["rm", "-r", zarr_plate])
commands.append(" && ".join([bf2raw_cmd, aws_cmd, rm_cmd]))
with open("idr0035_commands", 'w') as f:
for command in commands:
f.write(command)
f.write('\n')and the following MetaXpress file
"HTSInfoFile", Version 1.0
"Description", "BBBC021 {plate}"
"PlateType", 1
"TimePoints", 1
"ZSeries", FALSE
"ZSteps", 1
"ZProjection", FALSE
"XWells", 12
"YWells", 8
"WellsSelection1", FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE
"WellsSelection2", FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE
"WellsSelection3", FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE
"WellsSelection4", FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE
"WellsSelection5", FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE
"WellsSelection6", FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE
"WellsSelection7", FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE
"WellsSelection8", FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE
"Sites", TRUE
"XSites", 2
"YSites", 2
"SiteSelection1", TRUE, TRUE
"SiteSelection2", TRUE, TRUE
"Waves", TRUE
"NWavelengths", 3
"WaveName1", "DAPI"
"WaveName2", "Tubulin"
"WaveName3", "Actin"
"WaveCollect1", 1
"WaveCollect2", 1
"WaveCollect3", 1
"WaveCollect4", 1
"WaveCollect5", 1
"UniquePlateIdentifier", "abc123"
"EndFile"A first plate has been uploaded to the idr0035 bucket and is ready for validation
(conversion) [sbesson@pilot-zarr2-dev idr0035]$ ~/venv/bin/aws --endpoint-url https://uk1s3.embassy.ebi.ac.uk --profile ebi s3 ls s3://idr0035/zarr/
PRE Week1_22123.zarr/
will-moore
idr0035-caie-drugresponse
Sample plate conversion failed with:
That looks unrelated to https://github.com/IDR/bioformats/issues/29 , doesn't it @sbesson ?