Delete excluded micrographs

Hi @AndreGraca,

You can do this by first downloading the movie_blob .cs file output from the exposures_rejected output result group of the Manually Curate Exposures job.
Screen Shot 2020-09-15 at 3.58.21 PM
You can also just get the path to the .cs file on the master node by navigating to the Outputs tab and pressing the “copy path” button on the movie_blob output:

Once you have the .cs file, you can then open it up using the instructions from our guide on manipulating .cs files here:

https://guide.cryosparc.com/processing-data/manipulating-.cs-files-created-by-cryosparc

You can then find the filenames, and either delete the files manually, or use python to do this for you.

For example, open a shell on the master node and run cryosparcm icli to start an interactive python session, then run the following:

from cryosparc2_compute import dataset
exposure_dset = dataset.Dataset() #initialize the dataset object
dataset_path = "<path_to_cs_file_here>"
exposure_dset.from_file(dataset_path) #load the .cs file
exposure_dset.data['movie_blob/path'] #will print out a sample of all the values in this field

# the following will write all the filenames to a text file that 
# can be piped to a unix delete command
with open("exposures_to_delete.txt", 'w') as openfile:
    for file_to_delete in exposure_dset.data['movie_blob/path']:
        openfile.write(file_to_delete + '\n')

#the following will delete the files sequentially
import os
for file_to_delete in exposure_dset.data['movie_blob/path']:
    try:
        os.remove(file_to_delete)
    except:
        print("Unable to delete {}".format(file_to_delete))
        continue
2 Likes