def main():
from instamatic.utils import high_precision_timers
high_precision_timers.enable() # sleep timers with 1 ms resolution
# enable faster switching between threads
sys.setswitchinterval(0.001) # seconds
import psutil
p = psutil.Process(os.getpid())
p.nice(
psutil.REALTIME_PRIORITY_CLASS) # set python process as high priority
from instamatic import config
date = datetime.datetime.now().strftime("%Y-%m-%d")
logfile = config.logs_drc / f"instamatic_{date}.log"
logging.basicConfig(
format=
"%(asctime)s | %(module)s:%(lineno)s | %(levelname)s | %(message)s",
filename=logfile,
level=logging.DEBUG)
logging.captureWarnings(True)
log = logging.getLogger(__name__)
log.info("Instamatic-stem.gui started")
# Work-around for race condition (errors) that occurs when
# DataCollectionController tries to access them
from instamatic.gui.gui import MainFrame, DataCollectionController
from instamatic.camera import camera
cam = camera.Camera(config.cfg.camera, as_stream=True)
root = Tk()
gui = MainFrame(root, cam=cam, modules=MODULES)
from ..settings import default as settings
from ..beam_control import BeamCtrl
beam_ctrl = BeamCtrl(**settings)
experiment_ctrl = DataCollectionController(ctrl=None,
stream=cam,
beam_ctrl=beam_ctrl,
app=gui.app,
log=log)
experiment_ctrl.start()
root.mainloop()
def main():
import argparse
description = """Start instamatic with various functions (see below). If no arguments are given, start the instamatic GUI. The GUI is modular and can be defined using the config system. The GUI can be used to control the microscope and run the experiments. The GUI itself is further described on the GUI page."""
parser = argparse.ArgumentParser(description=description,
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('-s', '--script',
action='store', type=str, dest='script',
help='Run the script given')
parser.add_argument('-n', '--nav',
action='store', type=str, dest='nav_file',
help='Load the given .nav file')
parser.add_argument('-a', '--acquire_at_items',
action='store_true', dest='acquire_at_items',
help='Run the script file `--script` at every point marked with `Acquire` in the nav file `--nav`.')
parser.add_argument('-l', '--locate',
action='store', type=str, dest='locate',
help="Locate a requested directory and exit, i.e. `config`, `data`, `scripts`, `base`, 'work`, `logs`")
parser.add_argument('-o', '--open',
action='store', type=str, dest='show',
help='Open the requested directory and exit, see `--locate`.')
parser.add_argument('-i', '--info',
action='store_true', dest='info',
help='Show info about the current instamatic installation.')
parser.set_defaults(script=None,
acquire_at_items=False,
nav_file=None,
start_gui=True,
locate=None,
show=False,
info=False,
)
options = parser.parse_args()
if options.locate:
locate(options.locate)
exit()
if options.show:
locate(options.show, show=True)
exit()
if options.info:
show_info()
exit()
from instamatic.utils import high_precision_timers
high_precision_timers.enable() # sleep timers with 1 ms resolution
# enable faster switching between threads
sys.setswitchinterval(0.001) # seconds
from instamatic import banner
banner.register_thank_you_message()
from instamatic import config
date = datetime.datetime.now().strftime('%Y-%m-%d')
logfile = config.locations['logs'] / f'instamatic_{date}.log'
logging.basicConfig(format='%(asctime)s | %(module)s:%(lineno)s | %(levelname)s | %(message)s',
filename=logfile,
level=logging.DEBUG)
logging.captureWarnings(True)
log = logging.getLogger(__name__)
log.info(f'Instamatic started: {repr(options.__dict__)}')
from instamatic import TEMController
ctrl = TEMController.initialize(stream=True)
if options.nav_file:
from pyserialem import read_nav_file
nav_items = read_nav_file(options.nav_file, acquire_only=True)
if options.acquire_at_items:
ctrl.run_script_at_items(nav_items=nav_items, script=options.script)
elif options.script:
ctrl.run_script(options.script)
elif options.start_gui:
from instamatic.gui import start_gui
start_gui(ctrl, log=log)
def main():
import argparse
description = ""
parser = argparse.ArgumentParser(
description=description,
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument("-s",
"--script",
action="store",
type=str,
dest="script",
help="Run the script given")
parser.add_argument("-n",
"--nav",
action="store",
type=str,
dest="nav_file",
help="Load the given .nav file")
parser.add_argument(
"-a",
"--acquire_at_items",
action="store_true",
dest="acquire_at_items",
help=
"Run the script file `--script` at every point marked with `Acquire` in the nav file `--nav`."
)
parser.add_argument(
"-l",
"--locate",
action="store",
type=str,
dest="locate",
help=
"Locate a requested directory and exit, i.e. `config`, `data`, `scripts`, `base`, 'work`, `logs`"
)
parser.add_argument(
"-o",
"--open",
action="store",
type=str,
dest="open",
help="Open the requested directory and exit, see `--locate`.")
parser.set_defaults(
script=None,
acquire_at_items=False,
nav_file=None,
start_gui=True,
locate=None,
open=False,
)
options = parser.parse_args()
if options.locate:
locate(options.locate)
exit()
if options.open:
locate(options.open, open=True)
exit()
from instamatic.utils import high_precision_timers
high_precision_timers.enable() # sleep timers with 1 ms resolution
# enable faster switching between threads
sys.setswitchinterval(0.001) # seconds
from instamatic import version
version.register_thank_you_message()
from instamatic import config
date = datetime.datetime.now().strftime("%Y-%m-%d")
logfile = config.logs_drc / f"instamatic_{date}.log"
logging.basicConfig(
format=
"%(asctime)s | %(module)s:%(lineno)s | %(levelname)s | %(message)s",
filename=logfile,
level=logging.DEBUG)
logging.captureWarnings(True)
log = logging.getLogger(__name__)
log.info(f"Instamatic started: {repr(options.__dict__)}")
from instamatic import TEMController
ctrl = TEMController.initialize(stream=True)
if options.nav_file:
from instamatic.serialem import read_nav_file
nav_items = read_nav_file(options.nav_file, acquire_only=True)
if options.acquire_at_items:
ctrl.run_script_at_items(nav_items=nav_items, script=options.script)
elif options.script:
ctrl.run_script(options.script)
elif options.start_gui:
from instamatic.gui import start_gui
start_gui(ctrl, log=log)
import sounddevice as sd
import numpy as np
from math import ceil
from collections import defaultdict
from pprint import pprint
from instamatic.utils import high_precision_timers
high_precision_timers.enable()
def get_device_id(device, hostapi, kind="output"):
if kind == "output":
key = "max_output_channels"
elif key == "input":
key = "max_input_channels"
else:
raise ValueError(
"Invalid value for 'kind', must be 'input' or 'output'")
dct = defaultdict(dict)
for i, api in enumerate(sd.query_hostapis()):
for dev in api["devices"]:
dev_name = sd.query_devices(dev)["name"]
if sd.query_devices(dev)["max_output_channels"]:
dct[dev_name][i] = dev
return dct[device][hostapi]