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import json
import os
import numpy as np
from utils import fileIO,imgproc
import reports
import makereports
from pathlib import Path
import time
import re
coord_file = "config.json"
a_file = open(coord_file, "r")
config = json.load(a_file)
fov = '001'
z='02'
def download_azure():
if config["isRemote"]=="N" or os.path.exists(os.path.join(config['results_path'],'data')):
return None
os.system(config["azure_command"].format(config["raw_data_path"],os.path.join(config['results_path'],'data')))
return None
def check_params():
# Check to see if there are any params that need to be found
b_findz = len(config['z'])==0
b_findfov = len(config['fov'])==0
b_findir = len(config['ir'])==0
b_findwv = len(config['channel'])==0
# get all the images
if config["isRemote"] == "Y":
files = Path(os.path.join(config['results_path'],'data')).rglob('*.TIFF')
else:
files = Path(config['raw_data_path']).rglob('*.TIFF')
files = list(map(str,files))
# Find all channel, ir, fov, and z from the file names
re_filter = r"(.*)(\d{3})(?=nm).*(\B\d{2})\D(\B\d{3})\D(\B\d{2}\b)"
param_filter = re.compile(re_filter)
results = list(map(param_filter.search,files))
results =list(filter(lambda x: isinstance(x,re.Match), results))
# Get the list of parameters if they are needed
# Group 0 is the full match, so each capture group is 1 indexed
if b_findz:
zs = list(map(lambda x: x.group(5),results))
else:
zs = config['z']
if b_findir:
irs = list(map(lambda x: x.group(3),results))
else:
irs = config['ir']
if b_findfov:
fovs = list(map(lambda x: x.group(4),results))
else:
fovs = config['fov']
if b_findwv:
wvs = list(map(lambda x: x.group(2),results))
else:
wvs = config['channel']
if isinstance(results,list) and len(results)>0:
full_raw_path = results[0].group(1)
else:
full_raw_path=''
return sorted(list(set(zs)),key=int),sorted(list(set(fovs)),key=int),sorted(list(set(irs)),key=int),sorted(list(set(wvs)),key=int),full_raw_path
def check_dirs(files):
"""Checks to see if the directories for the files in the list exist. If they dont, then make those directories
Args:
files (list[str]): the list of files whose directory paths to create. Needs to be the full, not relative paths
"""
if not type(files) == list:
d = os.path.dirname(files)
if not os.path.isdir(d):
# print(files+'files' + d +'Does not exist')
os.makedirs(d)
else:
for f in files:
d = os.path.dirname(f)
if d != "" and not os.path.isdir(d):
# print(f+'files' + d +'Does not exist')
os.makedirs(d)
download_azure()
zs,fovs,irs,wvs,full_raw_path = check_params()
def create_image_stack():
out_file = os.path.join(config['results_path'],f'imgstack_{fov}_{z}.npy')
coord_file = os.path.join(config['results_path'],f'coord_{fov}_{z}.json')
check_dirs(out_file)
fileIO.create_image_stack(os.path.join(full_raw_path,config['raw_image_format']),fov,z,irs,wvs,out_file,coord_file)
def create_deconvolved_images():
in_file = os.path.join(config['results_path'],f'imgstack_{fov}_{z}.npy')
out_file = os.path.join(config['results_path'],'deconvolved',f'deconvolved_{fov}_{z}.npy')
check_dirs(out_file)
imgproc._deconvolute(in_file,out_file)
def create_brightness_report():
img_stack = os.path.join(config['results_path'],f'imgstack_{fov}_{z}.npy')
coord_file = os.path.join(config['results_path'],f'coord_{fov}_{z}.json')
out=os.path.join(config['results_path'],f'brightness_report_{fov}_{z}.pdf')
check_dirs(out)
makereports.brightness_worker(img_stack,coord_file,out,fov,z)
def create_focus_report():
img_stack = [os.path.join(config['results_path'],f'imgstack_{fov}_{z}.npy')]
coord_file = [os.path.join(config['results_path'],f'coord_{fov}_{z}.json')]
out=os.path.join(config['results_path'],f'focus_report_{fov}.pdf')
out_csv = os.path.join(config['results_path'],f'focus_report_{fov}.csv')
check_dirs(out)
makereports.focus_worker(img_stack,coord_file,out,out_csv,fov)
def compile_focus_reports():
in_files = [os.path.join(config['results_path'],f'focus_report_{fov}.csv')]
output = 'full_report_debug.csv'
makereports.compile_focus_report(in_files,output=output,irs=irs,wvs=wvs)
if __name__=='__main__':
start_time = time.time()
sub_start_time = time.time()
create_image_stack()
sub_end_time = time.time()
print(f'Image Stack: {sub_end_time-sub_start_time}')
sub_start_time = time.time()
create_deconvolved_images()
sub_end_time = time.time()
print(f'Deconvolved Stack: {sub_end_time-sub_start_time}')
sub_start_time = time.time()
create_brightness_report()
sub_end_time = time.time()
print(f'Brightness Report: {sub_end_time-sub_start_time}')
sub_start_time = time.time()
create_focus_report()
sub_end_time = time.time()
print(f'Focus Report: {sub_end_time-sub_start_time}')
sub_start_time = time.time()
compile_focus_reports()
sub_end_time = time.time()
print(f'Compiled Focus Report: {sub_end_time-sub_start_time}')
end_time = time.time()
print(f'Total Time: {end_time-start_time}') |