Commit 214d1be5 authored by Jonathan Juhl's avatar Jonathan Juhl
Browse files

Delete mic_extractor_sortem.py

parent 9fdd7808
import tensorflow as tf
import numpy as np
import mrcfile
output_path = '/emcc/misser11/out_optics_dub_stack.star'
output_dir =
input_star = '/emcc/misser11/out_optics_dub.star'
def open_star_file():
def make_star_file():
def load_big_micrograph(image_path):
def extract_particles(image,x_min,y_min,box_size):
zeros = tf.zeros(tf.shape(x_min)[0])
image_stack = tf.image.crop_and_resize(image,[y_min,x_min,y_min+box_size,x_min+box_size],zeros,[box_size,box_size])
with mrcfile.new('pa', compression='bzip2') as mrc:
for i in range(mrc_paths)
star_file = 'out_optics_dub.star'
def get_star_file_parameters(star_files):
with open(star_files, newline='') as csvfile:
reader = list(csvfile)
header = list(filter(lambda x: ('_rln' == x[0:4] or 'loop_' == x.strip()) and '_rlnMicrographName' not in x,reader))
header = [i.split()[0] for i in header]
header = ['_rlnImageName'] + header[1:]
index = 1
with open('out_star.star', 'w') as cv:
out = []
for i in reader:
if len(header) == len(i.split()):
i = i.split(' ')
new_i = [str("%06d@emcc/misser11/New_Project/Assets/ParticleStacks/particle_stack_1.mrc") % (index,)] +i[1:]
out.append(new_i)
index +=1
cv.write('data_images\n')
cv.write('\n')
cv.write('loop_\n')
for i in header:
cv.write(i+'\n')
cv.write('\n')
for i in out:
cv.write(' '.join(i))
get_star_file_parameters(star_f
\ No newline at end of file
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