#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
@author: kushal
Chatzigeorgiou Group
Sars International Centre for Marine Molecular Biology
GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007
A module that is globally accessible from all modules.
"""
import numpy as np
import os
from psutil import cpu_count
import json
from configparser import RawConfigParser
from warnings import warn
#################################################################
# System Configuration
#################################################################
if os.name == 'nt':
IS_WINDOWS = True
HOME = 'USERPROFILE'
else:
IS_WINDOWS = False
HOME = 'HOME'
try:
import caiman
except ImportError:
warn(
"Caiman package not found. "
"Caiman features will be disabled."
)
HAS_CAIMAN = False
else:
HAS_CAIMAN = True
# try:
# print("Importing ISX")
# import isx
# print("Imported ISX")
# except ImportError:
# warn("Inscopix API not found, Inscopix importer will be disabled")
# HAS_ISX = False
# else:
# HAS_ISX = True
try:
import tensorflow
except ImportError:
warn(
"tensorflow not found. Nuset segmentation will be disabled"
)
HAS_TENSORFLOW = False
else:
HAS_TENSORFLOW = True
try:
import tslearn
except ImportError:
warn(
"tslearn package not found. "
"tslearn features will be disabled."
)
HAS_TSLEARN = False
else:
HAS_TSLEARN = True
sys_cfg = {}
num_types = [int, float, np.int64, np.float64]
sys_cfg_dir: str = os.path.join(os.environ[HOME], '.mesmerize')
sys_cfg_file: str = os.path.join(sys_cfg_dir, 'config.json')
console_history_path = os.path.join(sys_cfg_dir, 'console_history')
if not os.path.isdir(console_history_path):
os.makedirs(console_history_path)
_prefix_comments = \
[
'# For example if you are running in an anaconda environment',
'# export PATH="/home/<user>/anaconda3:$PATH"',
'# source activate my_environment',
'# Or if you are using a python virtual environment',
'# source /<path_to_env>/activate',
'# Adjust these according to your hardware'
]
if IS_WINDOWS:
_prefix_commands = \
[
"# If using anaconda, you may need a command to activate the conda environment.",
"# If this is the case, uncomment the following line.",
"# conda activate mesmerize",
"\n"
]
else:
_prefix_commands = _prefix_comments + ["export MKL_NUM_THREADS=1",
"export OPENBLAS_NUM_THREADS=1", '\n']
default_sys_config = {'_MESMERIZE_N_THREADS': cpu_count() - 1,
'_MESMERIZE_USE_CUDA': False,
'_MESMERIZE_PYTHON_CALL': 'python3',
'_MESMERIZE_PREFIX_COMMANDS': '\n'.join(_prefix_commands),
'_MESMERIZE_CUSTOM_MODULES_DIR': os.environ[HOME] + '/mesmerize_custom_modules',
'_MESMERIZE_WORKDIR': '',
'recent_projects': []
}
if IS_WINDOWS:
default_sys_config.update({'_MESMERIZE_PYTHON_CALL': 'python'})
# patching in something that will probably be used in mesmerize v1.0 to simplify sys config things
class ENVIRONMENT:
def __init__(self):
self.LRU_CACHE_MAXSIZE: int = 64 # `maxsize` argument for @lru_cache
# update the default env vars with any that are specified in the env
def get_environment() -> ENVIRONMENT:
e = ENVIRONMENT()
for opt, val in e.__dict__.items():
# user can prefix the env vars with "MESMERIZE" if they want, but not necessary
if (opt in os.environ.keys()) or (f'MESMERIZE_{opt}' in os.environ.keys()):
setattr(e, opt, type(val)(os.environ[opt])) # to convert str to other types, like str -> int/float
return e
class SysConfig:
def __init__(self, n_threads: int,
use_cuda: bool,
python_call: str,
prefix_commands: str,
custom_modules_dir: str,
workdir: str,
recent_projects: list):
self.n_threads = n_threads
self.use_cuda = use_cuda
self.python_call = python_call
self.prefix_commands = prefix_commands
self.custom_modules_dir = custom_modules_dir
self.workdir = workdir
self.recent_projects = recent_projects
def create_new_sys_config() -> dict:
if not os.path.isdir(sys_cfg_dir):
os.makedirs(sys_cfg_dir)
save_sys_config(default_sys_config)
return default_sys_config
[docs]def get_sys_config() -> dict:
"""Get the user-set system configuration"""
if not os.path.isfile(sys_cfg_file):
return create_new_sys_config()
with open(sys_cfg_file, 'r') as f:
sys_cfg = json.load(f)
return sys_cfg
def save_sys_config(cfg: dict):
if not set(cfg.keys()).issubset(default_sys_config.keys()):
raise KeyError('Required config fields are missing. The following fields must be present:\n' + str(cfg.keys()))
if not cfg['_MESMERIZE_PREFIX_COMMANDS'].endswith('\n'):
cfg['_MESMERIZE_PREFIX_COMMANDS'] += '\n'
with open(sys_cfg_file, 'w') as f:
json.dump(cfg, f, indent=4)
#################################################################
# Project Configuration
#################################################################
proj_path = None
proj_cfg = RawConfigParser(allow_no_value=True)
proj_cfg['ROI_DEFS'] = {}
proj_cfg['STIM_DEFS'] = {}
proj_cfg.optionxform = str
special = {}
df_refs = {}
def save_proj_config():
set_proj_special()
with open(proj_path + '/config.cfg', 'w') as configfile:
proj_cfg.write(configfile)
def create_new_proj_config():
defaultInclude = ['SampleID', 'date', 'comments']
proj_cfg['INCLUDE'] = dict.fromkeys(defaultInclude)
defaultExclude = ['ImgInfoPath', 'ImgPath', 'ImgUUID', 'ROI_State', 'uuid_curve', 'misc', 'AnimalID']
proj_cfg['EXCLUDE'] = dict.fromkeys(defaultExclude)
proj_cfg['ROI_DEFS'] = {}
proj_cfg['STIM_DEFS'] = {}
proj_cfg['ALL_STIMS'] = {}
proj_cfg['CUSTOM_COLUMNS'] = {}
proj_cfg['CHILD_DFS'] = {}
set_proj_special()
save_proj_config()
def open_proj_config():
proj_cfg.read(proj_path + '/config.cfg')
set_proj_special()
def set_proj_special():
special['Timings'] = proj_cfg.options('STIM_DEFS')