def _init_dict(self):
"""Get list of functions and their doc strings from the uninitialized class"""
from instamatic.camera.camera import get_cam
cam = get_cam(self.name)
self._dct = {key:value for key, value in cam.__dict__.items() if not key.startswith("_")}
self._dct["get_attrs"] = None
def main():
"""
This tool will help to set up the configuration files for `instamatic`
It establishes a connection to the microscope and reads out the camera lengths
and magnification ranges
"""
### Connect to microscope
tem_name = choice_prompt(choices="jeol fei simulate".split(),
default="simulate",
question="Which microscope can I connect to?")
### Connect to camera
cam_name = choice_prompt(choices="None gatan tvips simulate".split(),
default="simulate",
question="Which camera can I connect to?")
## Fetch camera config
drc = Path(__file__).parent
choices = list(drc.glob("camera/*.yaml"))
choices.append(None)
cam_config = choice_prompt(choices=choices,
default=None,
question="Which camera type do you want to use (select closest one and modify if needed)?")
### Instantiate microscope / camera connection
from instamatic.TEMController.microscope import get_tem
from instamatic.camera.camera import get_cam
from instamatic.TEMController.TEMController import TEMController
cam = get_cam(cam_name)() if cam_name else None
tem = get_tem(tem_name)()
ctrl = TEMController(tem=tem, cam=cam)
ranges = ctrl.magnification.get_ranges()
ht = ctrl.high_tension # in V
wavelength = relativistic_wavelength(ht)
tem_config = {}
tem_config["name"] = tem_name
tem_config["wavelength"] = wavelength
for mode, rng in ranges.items():
tem_config["range_"+mode] = rng
calib_config = {}
calib_config["name"] = tem_name
### Find magnification ranges
for mode, rng in ranges.items():
if cam_name == "tvips":
pixelsizes = get_tvips_calibs(ctrl=ctrl, rng=rng, mode=mode, wavelength=wavelength)
else:
pixelsizes = {r: 1.0 for r in rng}
calib_config["pixelsize_"+mode] = pixelsizes
stagematrices = {r: [1, 0, 0, 1] for r in rng}
calib_config["stagematrix_"+mode] = stagematrices
### Write/copy configs
tem_config_fn = f"{tem_name}_tem.yaml"
calib_config_fn = f"{tem_name}_calib.yaml"
if cam_config:
cam_config_fn = f"{cam_name}_cam.yaml"
shutil.copyfile(cam_config, cam_config_fn)
yaml.dump(tem_config, open(tem_config_fn, "w"), sort_keys=False)
yaml.dump(calib_config, open(calib_config_fn, "w"), sort_keys=False)
print()
print(f"Wrote files config files:")
print(f" Copy {tem_config_fn} -> `{config.config_drc / tem_config_fn}`")
print(f" Copy {calib_config_fn} -> `{config.config_drc / calib_config_fn}`")
if cam_config:
print(f" Copy {cam_config_fn} -> `{config.config_drc / cam_config_fn}`")
print()
print(f"In `{config.config_drc / 'global.yaml'}`:")
print(f" microscope: {tem_name}_tem")
print(f" calibration: {tem_name}_calib")
if cam_config:
print(f" camera: {cam_name}_cam")
print()
print(f"Todo: Check and update the pixelsizes in `{calib_config_fn}`")
print( " In real space, pixelsize in nm")
print( " In reciprocal space, pixelsize in px/Angstrom")
def main():
import argparse
description = """
This tool will help to set up the configuration files for `instamatic`.
It establishes a connection to the microscope and reads out the camera lengths and magnification ranges.
"""
parser = argparse.ArgumentParser(
description=description,
formatter_class=argparse.RawDescriptionHelpFormatter)
options = parser.parse_args()
# Connect to microscope
tem_name = choice_prompt(choices='jeol fei simulate'.split(),
default='simulate',
question='Which microscope can I connect to?')
# Connect to camera
cam_name = choice_prompt(choices=[None, 'gatan', 'tvips', 'simulate'],
default='simulate',
question='Which camera can I connect to?')
# Fetch camera config
drc = Path(__file__).parent
choices = list(drc.glob('camera/*.yaml'))
choices.append(None)
cam_config = choice_prompt(choices=choices,
default=None,
question='Which camera type do you want to use (select closest one and modify if needed)?')
# Instantiate microscope / camera connection
from instamatic.TEMController.microscope import get_tem
from instamatic.camera.camera import get_cam
from instamatic.TEMController.TEMController import TEMController
cam = get_cam(cam_name)() if cam_name else None
tem = get_tem(tem_name)()
ctrl = TEMController(tem=tem, cam=cam)
try:
ranges = ctrl.magnification.get_ranges()
except BaseException:
print('Warning: Cannot access magnification ranges')
ranges = {}
ht = ctrl.high_tension # in V
wavelength = relativistic_wavelength(ht)
tem_config = {}
tem_config['name'] = tem_name
tem_config['wavelength'] = wavelength
for mode, rng in ranges.items():
tem_config['ranges'] = {mode: rng}
calib_config = {}
calib_config['name'] = tem_name
# Find magnification ranges
for mode, rng in ranges.items():
calib_config[mode] = {}
if cam_name == 'tvips':
pixelsizes = get_tvips_calibs(ctrl=ctrl, rng=rng, mode=mode, wavelength=wavelength)
else:
pixelsizes = {r: 1.0 for r in rng}
calib_config[mode]['pixelsize'] = pixelsizes
stagematrices = {r: [1, 0, 0, 1] for r in rng}
calib_config[mode]['stagematrix'] = stagematrices
# Write/copy configs
tem_config_fn = f'{tem_name}_tem.yaml'
calib_config_fn = f'{tem_name}_calib.yaml'
if cam_config:
cam_config_fn = f'{cam_name}_cam.yaml'
shutil.copyfile(cam_config, cam_config_fn)
yaml.dump(tem_config, open(tem_config_fn, 'w'), sort_keys=False)
yaml.dump(calib_config, open(calib_config_fn, 'w'), sort_keys=False)
microscope_drc = config.locations['microscope']
camera_drc = config.locations['camera']
calibration_drc = config.locations['calibration']
settings_yaml = config.locations['settings']
print()
print(f'Wrote files config files:')
print(f' Copy {tem_config_fn} -> `{microscope_drc / tem_config_fn}`')
print(f' Copy {calib_config_fn} -> `{calibration_drc / calib_config_fn}`')
if cam_config:
print(f' Copy {cam_config_fn} -> `{camera_drc / cam_config_fn}`')
print()
print(f'In `{settings_yaml}`:')
print(f' microscope: {tem_name}_tem')
print(f' calibration: {tem_name}_calib')
if cam_config:
print(f' camera: {cam_name}_cam')
print()
print(f'Todo: Check and update the pixelsizes in `{calib_config_fn}`')
print(' In real space, pixelsize in nm')
print(' In reciprocal space, pixelsize in px/Angstrom')