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from pathlib import Path
import re
import os
import makereports as reports
from utils import fileIO,imgproc
configfile: "config.json"
def download_azure():
if config["isRemote"]=="N" or os.path.exists(os.path.join(config['results_path'],'data')):
return None
shell(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
download_azure()
zs,fovs,irs,wvs,full_raw_path = check_params()
default_message= "rule {rule}, {wildcards}, threads: {threads}"
rule all_done:
input:
os.path.join(config['results_path'],'brightness_report.t'),
os.path.join(config['results_path'],'focus_report.t'),
os.path.join(config['results_path'],'deconvolved_brightness_report.t'),
os.path.join(config['results_path'],'masked_brightness_report.t'),
os.path.join(config['results_path'],'decodability_report.t')
output:
os.path.join(config['results_path'],'all_done.t')
run:
if config["isRemote"]=="Y":
shell("rm -rf \"{}\"".format(os.path.join(config['results_path'],'data')))
if config["delete_stack"]=="Y":
shell("rm -f \"{}\"".format(os.path.join(config['results_path'],'img*')))
shell("touch \"{output[0]}\"")
rule all:
threads:1
input:
os.path.join(config['results_path'],'all_done.t')
def isRemote(wildcards):
if config["isRemote"]=="N":
return config["raw_data_path"]
else:
return directory(os.path.join(config['results_path'],'data'))
rule create_image_stack:
threads:1
message: default_message
input:
isRemote
output:
out_file = os.path.join(config['results_path'],'imgstack_{fov}_{z}.npy'),
coord_file = os.path.join(config['results_path'],'coord_{fov}_{z}.json')
run:
fileIO.create_image_stack(os.path.join(full_raw_path,config['raw_image_format']),
wildcards.fov,wildcards.z,irs,wvs,output.out_file,output.coord_file)
rule deconvolve_images:
threads:1
message: default_message
input:
in_file = os.path.join(config['results_path'],'imgstack_{fov}_{z}.npy'),
output:
out_file = os.path.join(config['results_path'],'deconvolved','deconvolved_{fov}_{z}.npy')
run:
imgproc._deconvolute(input.in_file,output.out_file)
rule deconvolved_brightness_report:
threads:1
message: default_message
input:
img_stack = os.path.join(config['results_path'],'deconvolved','deconvolved_{fov}_{z}.npy'),
coord_file = os.path.join(config['results_path'],'coord_{fov}_{z}.json')
output:
out=os.path.join(config['results_path'],'deconvolved_brightness_report_{fov}_{z}.pdf')
run:
reports.generate_brightness_reports(input.img_stack,input.coord_file,output.out,wildcards.fov,wildcards.z)
rule compile_deconvolved_brightness_report:
threads:1
message: default_message
input:
expand(os.path.join(config['results_path'],'deconvolved_brightness_report_{fov}_{z}.pdf'),fov=fovs,z=zs)
output:
os.path.join(config['results_path'],'deconvolved_brightness_report.t')
shell:
"touch \"{output}\""
rule create_mask_images:
threads:1
message: default_message
input:
img_stack = os.path.join(config['results_path'],'deconvolved','deconvolved_{fov}_{z}.npy'),
output:
out_mask=os.path.join(config['results_path'],'masked','mask_{fov}_{z}.npy')
run:
imgproc.maskImages(input.img_stack,output.out_mask)
rule masked_brightness_report:
threads:1
message: default_message
input:
img_stack = os.path.join(config['results_path'],'imgstack_{fov}_{z}.npy'),
masks = os.path.join(config['results_path'],'masked','mask_{fov}_{z}.npy'),
coord_file = os.path.join(config['results_path'],'coord_{fov}_{z}.json')
output:
out=os.path.join(config['results_path'],'masked_brightness_report_{fov}_{z}.pdf')
run:
reports.generate_masked_brightness_reports(input.img_stack,input.coord_file,output.out,wildcards.fov,wildcards.z,input.masks)
rule compile_masked_brightness_report:
threads:1
message: default_message
input:
expand(os.path.join(config['results_path'],'masked_brightness_report_{fov}_{z}.pdf'),fov=fovs,z=zs)
output:
os.path.join(config['results_path'],'masked_brightness_report.t')
shell:
"touch \"{output}\""
rule brightness_report:
threads:1
message: default_message
input:
img_stack = os.path.join(config['results_path'],'imgstack_{fov}_{z}.npy'),
coord_file = os.path.join(config['results_path'],'coord_{fov}_{z}.json')
output:
out=os.path.join(config['results_path'],'brightness_report_{fov}_{z}.pdf')
run:
reports.generate_brightness_reports(input.img_stack,input.coord_file,output.out,wildcards.fov,wildcards.z)
rule compile_brightness_report:
threads:1
message: default_message
input:
expand(os.path.join(config['results_path'],'brightness_report_{fov}_{z}.pdf'),fov=fovs,z=zs)
output:
os.path.join(config['results_path'],'brightness_report.t')
shell:
"touch \"{output}\""
rule focus_report:
threads:1
message: default_message
input:
img_stack = expand(os.path.join(config['results_path'],'imgstack_{{fov}}_{z}.npy'),z=zs),
coord_file = expand(os.path.join(config['results_path'],'coord_{{fov}}_{z}.json'),z=zs)
output:
out=os.path.join(config['results_path'],'focus_report_{fov}.pdf'),
out_csvs = os.path.join(config['results_path'],'focus_report_{fov}.csv')
run:
reports.generate_focus_reports(input.img_stack,input.coord_file,output.out,output.out_csvs,wildcards.fov)
rule compile_focus_report:
threads:1
message: default_message
input:
files = expand(os.path.join(config['results_path'],'focus_report_{fov}.pdf'),fov=fovs),
csvs = expand(os.path.join(config['results_path'],'focus_report_{fov}.csv'),fov=fovs)
output:
combined = os.path.join(config['results_path'],'focus_report_all_fov.pdf'),
out = os.path.join(config['results_path'],'focus_report.t')
run:
reports.compile_focus_report(input.csvs,output.combined,irs,wvs)
shell("touch \"{output.out}\"")
rule decodability_report:
threads:1
message: default_message
input:
img_stack = os.path.join(config['results_path'],'deconvolved','deconvolved_{fov}_{z}.npy'),
coord_file = os.path.join(config['results_path'],'coord_{fov}_{z}.json'),
codebook_file = config["codebook_file"],
data_organization_file = config["data_org_file"]
output:
out=os.path.join(config['results_path'],'decodability_report_{fov}_{z}.pdf'),
out_stats = os.path.join(config['results_path'],'decodability_stats_{fov}_{z}.txt')
run:
reports.generate_decodability_reports(input.img_stack,input.coord_file,output.out,input.codebook_file,input.data_organization_file,wildcards.fov,wildcards.z,output.out_stats)
rule compile_decodability_report:
threads:1
message: default_message
input:
expand(os.path.join(config['results_path'],'decodability_report_{fov}_{z}.pdf'),fov=fovs,z=zs)
output:
os.path.join(config['results_path'],'decodability_report.t')
shell:
"touch \"{output}\"" |