def verify_globals(config):
logger.debug('Verifying globals...')
# Get the current runmanager globals
logger.debug('Getting values of globals from runmanager.')
rm_globals = rm.get_globals()
current_values = [rm_globals[name] for name in config['mloop_params']]
# Retrieve the parameter values requested by M-LOOP on this iteration
logger.debug('Getting requested globals values from lyse.routine_storage.')
requested_values = lyse.routine_storage.params
requested_dict = dict(zip(config['mloop_params'], requested_values))
# Get the parameter values for the shot we just computed the cost for
logger.debug('Getting lyse dataframe.')
df = lyse.data()
shot_values = [df[name].iloc[-1] for name in config['mloop_params']]
# Verify integrity by cross-checking against what was requested
if not np.array_equal(current_values, requested_values):
message = (
'Cost requested for values different to those in runmanager.\n'
'Please add an executed shot to lyse with: {requested_dict}'
).format(requested_dict=requested_dict)
logger.error(message)
return False
if not np.array_equal(shot_values, requested_values):
message = (
'Cost requested for different values to those used to compute cost.\n'
'Please add an executed shot to lyse with: {requested_dict}'
).format(requested_dict=requested_dict)
logger.error(message)
return False
logger.debug('Globals verified.')
return True
def cost_analysis(cost_key=(None, ), maximize=True, x=None):
"""Return a cost dictionary to M-LOOP with at least:
{'bad': True} or {'cost': float}.
- Look for the latest cost in the cost_key column of the lyse
- DataFrame and an uncertainty ('u_' prefix at the lowest level).
- Report bad shot to M-LOOP if cost is nan or inf.
- Negate value in DataFrame if maximize = True.
- Fallback to reporting a constant or fake cost (from x).
"""
logger.debug('Getting cost...')
cost_dict = {'bad': False}
# Retrieve current lyse DataFrame
logger.debug('Getting lyse dataframe.')
df = lyse.data()
# Use the most recent shot
ix = -1
# Retrieve cost from specified column
if len(df) and cost_key in df:
cost = (df[cost_key].astype(float).values)[ix]
if np.isnan(cost) or np.isinf(cost):
cost_dict['bad'] = True
logger.info('Got bad cost: {cost}'.format(cost=cost))
else:
cost_dict['cost'] = (1 - 2 * maximize) * cost
logger.info('Got cost: {cost}'.format(cost=cost_dict['cost']))
u_cost_key = cost_key[:-1] + ('u_' + cost_key[-1], )
if u_cost_key in df:
cost_dict['uncer'] = df[u_cost_key].iloc[ix]
logger.info(
'Got uncertainty: {uncer}'.format(uncer=cost_dict['uncer']))
# If it doesn't exist, generate a fake cost
elif x is not None:
from fake_result import fake_result
cost_dict['cost'] = (1 - 2 * maximize) * fake_result(x)
logger.info('Faked cost: {cost}'.format(cost=cost_dict['cost']))
# Or just use a constant cost (for debugging)
else:
cost_dict['cost'] = 1.2
logger.info(
'Faked constant cost: {cost}'.format(cost=cost_dict['cost']))
return cost_dict
def __init__(self, h5_paths, n_rows=3, **kwargs):
self.h5_paths = h5_paths
super().__init__(**kwargs)
pg.mkQApp()
self.n_rows = n_rows
self.setWindowFlag(QtCore.Qt.WindowCloseButtonHint, False)
self.area = DockArea()
self.setCentralWidget(self.area)
self.resize(1000, 500)
self.dshotselector = Dock("Shot selector")
self.shotselector = ShotSelector()
self.dshotselector.addWidget(self.shotselector)
self.area.addDock(self.dshotselector, 'bottom')
self.qpg_dock = Dock("Quick Plot Generator")
self.qpg_dock.addWidget(QuickPlotGenerator(self))
self.qpg_dock.setMinimumSize(self.qpg_dock.minimumSizeHint())
self.area.addDock(self.qpg_dock)
self.show()
self.plots = {}
self.data_extractor_manager = DataExtractorManager()
self.shotselector.valueChanged.connect(self.refresh)
self.shotselector.selectionChanged.connect(self.refresh)
self.df = lyse.data()
# -*- coding: utf-8 -*-
"""
Created on Fri Jan 28 15:23:09 2022
@author: rubidium
"""
import lyse
import numpy as np
import matplotlib.pyplot as plt
import lmfit
df = lyse.data(n_sequences=1)
FIT = False
X_LABEL = 'cMOT time'
scan = df['scan']
# Let's obtain the dataframe for all of lyse's currently loaded shots:
# mot load rate was saved by a routine called calculate_load_rate:
Counts = df['MOT_Basic_Image_Process', 'Counts']
xWidth = df['MOT_Basic_Image_Process', 'xWidth']
yWidth = df['MOT_Basic_Image_Process', 'yWidth']
x0 = df['MOT_Basic_Image_Process', 'x0']
y0 = df['MOT_Basic_Image_Process', 'y0']
if FIT:
# Now fit to an exponential
model = lmfit.models.ExpressionModel("amp * (1 - exp(-x / tau))")
import lyse
import numpy as np
import matplotlib.pyplot as plt
import mloop_config
from fake_result import fake_result
try:
df = lyse.data()
config = mloop_config.get()
x = list(config['mloop_params'])[0]
y = config['cost_key']
try:
# Try to use the most recent mloop_session ID
gb = df.groupby('mloop_session')
mloop_session = list(gb.groups.keys())[-1]
subdf = gb.get_group(mloop_session)
except Exception:
# Fallback to the entire lyse DataFrame
subdf = df
mloop_session = None
subdf.plot(x=x, y=y, kind='scatter')
x_p = np.linspace(df[x].min(), df[x].max(), 200)
plt.plot(x_p, fake_result(x_p, s=0))
plt.axis(ymin=0, ymax=1.1)
plt.title('M-LOOP session: {:}'.format(mloop_session))
plt.show()
except Exception:
pass
P = np.dot(BW, B.T)
# The RHS of the least squares equation:
orig_projs = np.dot(BW, a.T)
# Solve for x:
x = np.linalg.solve(P, orig_projs)
# Reconstruct the target image
recon = np.dot(x.T, B)
return recon.reshape(ny, nx)
run = lyse.Run(lyse.path)
dataset = lyse.data(lyse.path)
try:
lyse.routine_storage.refs
except:
lyse.routine_storage.refs = None
lyse.routine_storage.dark_frames = None
with h5py.File(lyse.path) as h5file:
for orientation, images in h5file["images"].iteritems():
if orientation == "bottom":
for image_type, frameset in images.iteritems():
if image_type.startswith("absorption"):
element = image_type.split("_")[1]
isat_name = "_".join(
[orientation, element, "saturation_intensity"])
@author: dng5
"""
from __future__ import division, print_function
import numpy as np
import matplotlib.pyplot as plt
import lyse
from fancy_cost_functions import *
import pandas as pd
try:
lyse.path
except NameError:
import sys
path = sys.argv[1]
series = lyse.data(lyse.path)
param1 = series['dummy1']
param2 = series['dummy2']
run_instance = lyse.Run(lyse.path)
print(lyse.path)
sigma0 = (3 / 2 / np.pi) * 780e-9**2
# atom_number = np.nansum(naive_OD*(5.6e-6/6.0)**2/sigma0)
params = np.array([param1, param2])
fitness = sphere(params)
# run_instance.save_result('average_counts', atom_avg)
run_instance.save_result('fitness', fitness)
worksheet_early.write(1, head_i, heading, bold)
worksheet_late.write(1, head_i, heading, bold)
early_late_worksheets = [worksheet_early, worksheet_late]
worksheet_spectra.write(0, 0,
'Early times average energy spectra for each grid',
bold)
worksheet_spectra.write(1, 0, 'Grid radius (micron):', boldshaded)
worksheet_spectra.write(2, 0, 'k vector', bold)
## We'll plot everything in units of microns, so convert units here
pixel_conversion = dmd_pixel_size * 1e6
xi = xi * 1e6
## Get the dataframe from lyse
df = lyse.data(timeout=30)
## Throw out the bad shots
df = df[df['review_vortex_locations', 'Good'] == True]
## Segregate the dataframe into "early times" and "late times" (df_l and df_h for low and high hold times)
df_l = df[df['vortex_spoon_wait_time'] < 2]
df_h = df[df['vortex_spoon_wait_time'] > 3.9]
### Set up the figure windows and axes for this grid ###
### Fig. 2:
fig = figure("Grid size", figsize=(2.25, 3.45), facecolor=(1, 1, 1, 0))
## We use gridspec to arrange the subfigures
gs = GridSpec(6, 1, height_ratios=[0.6, 0.8, 0.8, 0.8, 0.8, 0.8])
from analysislib.johnstone_vortices_2018.parameters import *
## Check where to save output:
exp_config = LabConfig()
results_path = exp_config.get('paths', 'analysis_output_folder')
sequence_list = [
'20171004T093812', #4.2
'20171004T121555', #6.0
'20171005T090729', #7.9
'20171004T144649', #9.7
'20171006T101525' #11.5
]
## Get the dataframe from lyse
full_df = lyse.data(timeout=10)
## Setup a spreadsheet for saving data to
workbook = xlsxwriter.Workbook(os.path.join(results_path, 'time_data.xlsx'))
bold = workbook.add_format({'bold': True})
bold_center = workbook.add_format({'bold': True, 'align': 'center'})
boldshaded = workbook.add_format({'bold': True, 'bg_color': '#CCCCCC'})
shaded = workbook.add_format({
'bg_color': '#CCCCCC',
'align': 'center',
'left': 1,
'right': 1
})
leftborder = workbook.add_format({'left': 1})
rightborder = workbook.add_format({'right': 1})
boldleftborder = workbook.add_format({'bold': True, 'left': 1})