from scipy import misc
import numpy as np
import time
import yaml
import itertools as it
from pyfpm import web
from pyfpm.reconstruct import fpm_reconstruct
from pyfpm.fpmmath import set_iterator
from pyfpm.data import save_yaml_metadata
import pyfpm.data as dt
from pyfpm.coordinates import PlatformCoordinates
# Simulation parameters
cfg = dt.load_config()
samples, comp_cfg = dt.open_sampled('2017-05-26_152307.npy')
background, comp_cfg = dt.open_sampled('2017-05-26_145449_blank.npy')
# Connect to a web client running serve_microscope.py
pc = PlatformCoordinates(theta=0, phi=0, height=cfg.sample_height, cfg=cfg)
pc.generate_model(cfg.plat_model)
iterator = set_iterator(cfg)
# reconstruction
dx = cfg.patch_size[0]
x_range = range(0, cfg.video_size[1], dx)[:-1]
y_range = range(0, cfg.video_size[0], dx)[:-1]
# for i, point in enumerate(it.product(x_range, y_range)):
# init_point = [point[0], point[1]]
# rec, phase = fpm_reconstruct(samples, background, iterator, init_point,
# cfg=cfg, debug=False)
from numpy import abs, angle
import pyfpm.local as local
from pyfpm.reconstruct import fpm_reconstruct_epry, fpm_reconstruct
import pyfpm.coordtrans as ct
import pyfpm.data as dt
import pyfpm.inspector as ins
# Simulation parameters
cfg = dt.load_config()
mode = cfg.task
itertype = cfg.sweep
server_ip = cfg.server_ip
client = local.SimClient(cfg=cfg)
# samples, sample_cfg = dt.open_sampled('20181107_183532.npy', mode='sampling')
samples, sample_cfg = dt.open_sampled('simtest.npy', mode='simulation')
iterator = ct.set_iterator(cfg)
# total_time = 0
# for it in iterator:
# nx, ny = it['nx'], it['ny']
# iso, ss, power = it['acqpars']
# total_time += ss/1E6
# print(nx, ny, ss, total_time)
# First inspection
# iterator = ins.inspect_iterator(iterator, sample_cfg)
# iterator = ins.inspect_samples(iterator, samples, sample_cfg)
# ins.inspect_pupil(sample_cfg)
# Reconstruction
Last update: 28/10/2016
Use to locally simulate FPM.
Usage:
"""
import time
import matplotlib.pyplot as plt
import numpy as np
import pyfpm.local as local
from pyfpm.reconstruct import fpm_reconstruct_wrapper
import pyfpm.coordtrans as ct
import pyfpm.data as dt
import pyfpm.inspector as ins
# Simulation parameters
cfg = dt.load_config()
mode = cfg.task
itertype = cfg.sweep
server_ip = cfg.server_ip
client = local.SimClient(cfg=cfg)
samples, sample_cfg = dt.open_sampled('20180628_175813.npy', mode='sampling')
iterator = ct.set_iterator(cfg)
# Reconstruction
fpm_reconstruct_wrapper(samples=samples,
it=iterator,
cfg=sample_cfg,
debug=cfg.debug)
plt.show()
import itertools as it
import pygame
import matplotlib.pyplot as plt
import matplotlib.cm as cm
from scipy import misc
from skimage import measure
import h5py
import pyfpm.fpmmath as fpm
from pyfpm import web
from pyfpm.fpmmath import set_iterator
import pyfpm.data as dt
from pyfpm.coordinates import PlatformCoordinates
# Simulation parameters
comp_images, comp_cfg = dt.open_sampled('2017-05-22_172249.npy')
cfg = dt.load_config()
out_file = dt.generate_out_file(cfg.output_sample)
# Connect to a web client running serve_microscope.py
client = web.Client(cfg.server_ip)
pc = PlatformCoordinates(cfg=cfg)
pc.generate_model(cfg.plat_model)
iterator = set_iterator(cfg)
def acquire_image(pc, client, theta, phi, shift, power):
pc.set_coordinates(theta=theta, phi=phi, shift=shift, units='deg_shift')
[theta_plat, phi_plat, shift_plat,
power_plat] = pc.parameters_to_platform()
# ss = fpm.adjust_shutter_speed(tpsp[0], tpsp[1])
img = client.acquire(theta_plat,
import pyfpm.data as dt
# Simulation parameters
cfg = dt.load_config()
mode = cfg.task
itertype = cfg.sweep
server_ip = cfg.server_ip
iterator = ct.set_iterator(cfg)
client = local.SimClient(cfg=cfg)
#20180615_190312
#20180615_190312
# 20180618_163559
# 20180618_142136
# 20180622_141301
samples, sim_cfg = dt.open_sampled('20180622_175208.npy', mode='sampling')
# Reconstruction
start_time = time.time()
hr = int(client.lhscale) * int(cfg.patch_size[0])
rec, phase = fpm_reconstruct_epry(samples=samples,
hrshape=[hr, hr],
it=iterator,
cfg=sim_cfg,
debug=cfg.debug,
pupil_radius=client.pupil_radius,
kdsc=client.kdsc)
print('--- %s seconds ---' % (time.time() - start_time))
plt.show()
if not cfg.debug:
import matplotlib.pylab as plt
import matplotlib.pyplot as plt
import matplotlib.cm as cm
from scipy import misc
from skimage import measure
# import h5py
import pyfpm.fpmmath as fpm
from pyfpm import web
import pyfpm.coordtrans as ct
import pyfpm.data as dt
# from pyfpm.coordinates import PlatformCoordinates
# Simulation parameters
# samples, comp_cfg = dt.open_sampled('2017-05-26_145449.npy')
# background, comp_cfg = dt.open_sampled('2017-05-26_145449_blank.npy')
samples, comp_cfg = dt.open_sampled('outest.npy', mode='simulation')
# 150543
cfg = dt.load_config()
out_file = dt.generate_out_file(cfg.output_sample)
# Connect to a web client running serve_microscope.py
client = web.Client(cfg.server_ip)
iterator = ct.set_iterator(cfg)
# Start analysis
fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(25, 15))
plt.grid(False)
fig.show()
image_dict = dict()
iterator = ct.set_iterator(cfg)
corr_ims = list()