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film.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
The purpose of this object is to record a film (a series of images)
of a rotating sample on the goniometer as a function of goniometer axis (axes) position(s).
'''
from experiment import experiment
from camera import camera
from goniometer import goniometer
from fast_shutter import fast_shutter
import os
import pickle
import gevent
import time
class film(experiment):
specific_parameter_fields = [{'name': 'position', 'type': 'dict', 'description': 'dictionary with motor names as keys and their positions in mm as values'},
{'name': 'zoom', 'type': 'int', 'description': 'zoom value'},
{'name': 'calibration', 'type': 'array', 'description': 'camera pixel calibration mm per pixels (vertical, horizontal)'},
{'name': 'frontlightlevel', 'type': 'float', 'description': 'front light level'},
{'name': 'backlightlevel', 'type': 'float', 'description': 'back light level'},
{'name': 'scan_exposure_time', 'type': 'float', 'description': 'scan exposure time in s'},
{'name': 'scan_start_angle', 'type': 'float', 'description': 'scan start angle in degrees'},
{'name': 'scan_speed', 'type': 'float', 'description': 'scan speed in degrees per second'},
{'name': 'scan_range', 'type': 'float', 'description': 'scan range in degrees'},
{'name': 'kappa_position', 'type': 'float', 'description': 'kappa position in degrees'},
{'name': 'phi_position', 'type': 'float', 'description': 'phi position in degrees'},
{'name': 'md2_task_info', 'type': 'array', 'description': 'scan diagnostic information'},
{'name': 'frontlight', 'type': 'bool', 'description': 'use frontlight to illuminate sample'}]
def __init__(self,
name_pattern,
directory,
scan_range=360,
scan_exposure_time=3.6,
scan_start_angle=0,
position=None,
kappa_position=None,
phi_position=None,
zoom=None,
frontlight=False):
if hasattr(self, 'parameter_fields'):
self.parameter_fields += film.specific_parameter_fields
else:
self.parameter_fields = film.specific_parameter_fields[:]
experiment.__init__(self,
name_pattern=name_pattern,
directory=directory)
self.description = 'Optical scan, Proxima 2A, SOLEIL, %s' % time.ctime(self.timestamp)
self.scan_range = scan_range
self.scan_exposure_time = scan_exposure_time
self.scan_start_angle = scan_start_angle
self.position = position
self.kappa_position = kappa_position
self.phi_position = phi_position
self.zoom = zoom
self.frontlight = frontlight
self.camera = camera()
self.goniometer = goniometer()
self.fastshutter = fast_shutter()
self.md2_task_info = []
self.images = []
if position is None:
self.position = self.get_position()
else:
self.position = self.goniometer.check_position(position)
self._abort = None
def get_position(self):
self.goniometer.get_aligned_position()
def set_zoom(self, zoom):
self.camera.set_zoom(zoom)
def get_zoom(self):
return self.camera.get_zoom()
def get_calibration(self):
return self.camera.get_calibration()
def get_frontlightlevel(self):
return self.camera.get_frontlightlevel()
def get_backlightlevel(self):
return self.camera.get_backlightlevel()
def insert_backlight(self):
return self.goniometer.insert_backlight()
def insert_frontlight(self):
return self.goniometer.insert_frontlight()
def extract_frontlight(self):
return self.goniometer.extract_frontlight()
def get_omega_position(self):
return self.goniometer.get_omega_position()
def set_omega_position(self, omega_position, wait=True):
return self.goniometer.set_position({'Omega': omega_position}, wait=wait)
def get_kappa_position(self):
return self.goniometer.get_kappa_position()
def set_kappa_position(self, kappa_position, wait=True):
return self.goniometer.set_position({'Kappa': kappa_position}, wait=wait)
def get_phi_position(self):
return self.goniometer.get_kappa_position()
def set_phi_position(self, phi_position, wait=True):
return self.goniometer.set_position({'Phi': phi_position}, wait=wait)
def prepare(self):
self.check_directory(self.directory)
if self.scan_start_angle != None:
self.set_omega_position(self.scan_start_angle)
else:
self.scan_start_angle = self.goniometer.get_omega_position()
if self.kappa_position != None:
self.set_kappa_position(self.kappa_position)
else:
self.kappa_position= self.goniometer.get_kappa_position()
if self.phi_position != None:
self.set_phi_position(self.phi_position)
else:
self.phi_position= self.goniometer.get_phi_position()
if self.zoom != None:
self.camera.set_zoom(self.zoom)
else:
self.zoom = self.camera.get_zoom()
self.insert_backlight()
if self.frontlight != True:
self.extract_frontlight()
#def run(self, task_id=None):
#last_image = None
#if task_id is None:
#task_id = self.goniometer.start_scan()
#while self.goniometer.is_task_running(task_id):
#new_image_id = self.camera.get_image_id()
#if new_image_id != last_image:
#last_image = new_image_id
#self.images.append([new_image_id,
#self.goniometer.get_omega_position(),
#self.camera.get_rgbimage()])
#self.md2_task_info = self.goniometer.get_task_info(task_id)
#new_image_id = self.camera.get_image_id()
#if new_image_id != last_image_id:
#last_image_id = new_image_id
#self.images.append([new_image_id,
#self.get_omega_position(),
#self.camera.get_rgbimage()])
def run(self, task_id=None, step=-120, delta=0.25):
last_image_id = None
engaged_debt = 0.
engaged_range = 0.
k = 0
_start = time.time()
while task_id is None or self.goniometer.is_task_running(task_id) or engaged_range < self.scan_range - 1 and self._abort != True:
if task_id is None or self.goniometer.is_task_running(task_id) == False:
if task_id != None:
self.md2_task_info.append(self.goniometer.get_task_info(task_id))
if engaged_range < self.scan_range - 1:
task_id = self.set_omega_position(self.get_omega_position() + step + delta, wait=True)
k+=1
self.logger.info('%d task_id %s' % (k, task_id))
engaged_range += abs(step)
engaged_debt += delta
self.logger.info('engaged_range %.2f' % engaged_range)
task_id = self.set_omega_position(self.get_omega_position() + engaged_debt, wait=True)
_end = time.time()
self.md2_task_info.append(self.goniometer.get_task_info(task_id))
self.logger.info('nimages %d' % len(self.images))
self.logger.info('acquisition took %.2f' % (_end-_start))
return _start, _end
def cancel(self):
self._abort = True
self.goniometer.abort()
def clean(self):
self.collect_parameters()
self.save_parameters()
self.save_log()
self.save_results()
def get_results(self):
return self.images
def save_results(self):
f = open('%s.pickle' % self.get_templatge(), 'w')
pickle.dump(self.get_results(), f)
f.close()
def main():
import optparse
parser = optparse.OptionParser()
parser.add_option('-r', '--scan_range', default=360, type=float, help='Scan range (default: %default)')
parser.add_option('-e', '--scan_exposure_time', default=6, type=float, help='Exposure time (default: %default)')
parser.add_option('-n', '--name_pattern', default='sample', type=str, help='Distinguishing name of files to acquire')
parser.add_option('-d', '--directory', default='/tmp', type=str, help='Destination directory')
parser.add_option('-z', '--zoom', default=None, help='Camera zoom to use, current zoom is used by default')
parser.add_option('-f', '--frontlight', action='store_true', help='Insert frontlight.')
options, args = parser.parse_args()
acquisition = film(**vars(options))
acquisition.execute()
self.logger.info('nimages', len(acquisition.images))
if __name__ == '__main__':
main()