import pypeliner.workflow
import pypeliner.app
import pypeliner.managed
import sys
import os
import shutil
from interface.tenxanalysis import TenxAnalysis
from utils.isabl import TenxDataStorage
from interface.qualitycontrol import QualityControl
from utils.config import Configuration, write_config
config = Configuration()
def Run(sampleid, species, umi_plot, mito_plot, ribo_plot, counts_plot,
raw_sce):
print("Running QC.")
tenx = TenxDataStorage(sampleid)
tenx_analysis = TenxAnalysis(tenx.tenx_path)
tenx_analysis.load()
tenx_analysis.extract()
qc = QualityControl(tenx_analysis, sampleid)
qc.run(mito=config.mito)
plots = qc.plots
umi = os.path.join(plots, "umi.png")
mito = os.path.join(plots, "mito.png")
ribo = os.path.join(plots, "ribo.png")
counts = os.path.join(plots, "counts.png")
pred = torch.clamp(complex_abs(pred), min=0.0, max=1.0)
target = torch.clamp(complex_abs(target), min=0.0, max=1.0)
return pred, target
return transform
if __name__ == '__main__':
# Run from main directory with python -m data.reconstruction.rec_transforms
import matplotlib.pyplot as plt
from torch.utils.data import DataLoader
from data.reconstruction.scar_seg import (get_train_set, get_val_set)
from utils.config import Configuration
conf = Configuration()
conf.input_mode = '2d'
conf.dataset_mode = 'reconstruction'
conf.downscale = 1
conf.undersampling = {
'sampling_scheme': "varden",
'acceleration_factor': 8,
'variable_acceleration': False
}
conf.augmentation = {
#'elastic_transform_sigma': 30,
#'elastic_transform_alpha': 1000,
'shift': (0, 10),
'rotate': 10,
'scale': (0.9, 1.1)
}
configuration_markup = {
'config': {
'ready': False,
},
'runtime': {
'secret_key': None,
'debug': False,
'allowed_hosts': 'localhost, 127.0.0.1',
},
'application': {
'api_delay': 0,
}
}
conf_path = 'conf/project.conf'
conf = Configuration(conf_path, configuration_markup)
BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
PROJECT_ROOT = os.path.dirname(os.path.abspath(__file__))
CONF_READY = conf.get_bool('config', 'ready')
if not CONF_READY:
print(
'[INFO] Configuration file has been generated but seems to be not yet edited.'
)
print('[INFO] Check: {}'.format(os.path.join(PROJECT_ROOT, conf_path)))
print('[INFO] Set option \'ready\' to \'True\' when you\'ll finish setup.')
print('[INFO] Aborting server startup.')
exit(0)
from utils.config import Configuration
conf = Configuration('app.conf', markdown='main')
PROJECT_NAME = conf.get('GENERIC', 'project_name')
VERSION = conf.get('GENERIC', 'version') or 'Aftermath'
TELEGRAM_BOT_TOKEN = conf.get('TELEGRAM', 'token')
AUTHOR_FULLNAME = conf.get('ABOUT', 'author_fullname')
AUTHOR_TELEGRAM = conf.get('ABOUT', 'author_telegram')
import os
from utils.config import Configuration
conf = Configuration('project.conf', markdown='main')
BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
PROJECT_ROOT = os.path.dirname(os.path.abspath(__file__))
SECRET_KEY = conf.get('PREDEFINED', 'secret_key')
DEBUG = conf.get('PREDEFINED', 'debug', 'bool')
ALLOWED_HOSTS = conf.get('DEPLOY', 'allowed_hosts', 'csv')
EMAIL_ENABLED = conf.get('EMAIL', 'enabled', 'bool')
if EMAIL_ENABLED:
EMAIL_USE_TLS = conf.get('EMAIL', 'use_tls', 'bool')
EMAIL_HOST = conf.get('EMAIL', 'host')
EMAIL_HOST_USER = conf.get('EMAIL', 'host_user')
EMAIL_HOST_PASSWORD = conf.get('EMAIL', 'host_password')
EMAIL_PORT = conf.get('EMAIL', 'port')
DEFAULT_FROM_EMAIL = conf.get('EMAIL', 'default_from')
INSTALLED_APPS = [
'django.contrib.admin',
'django.contrib.auth',
'django.contrib.contenttypes',
'django.contrib.sessions',
