def proc_dir(d):
dv = ddict[d]
dir_obj = cu.Data_dir(dv[0], [0, 0, dv[-1]], dv[1])
dir_obj.load_dir(cu.simple_loader, maxfiles=maxfiles)
amps = []
for fil_obj in dir_obj.fobjs:
fil_obj.psd()
stagestuff = fil_obj.get_stage_settings(axis=straighten_axis)
amp = stagestuff[2] * cant_volts_to_um
amps.append(amp)
uamps = np.unique(amps)
if len(uamps) > 1:
print('STUPIDITYERROR: Multiple dirve amplitudes in directory')
newlist = []
for i in [0, 1, 2]:
if i == straighten_axis:
newlist.append(uamps[0])
else:
newlist.append(0.0)
dir_obj.drive_amplitude = newlist
return dir_obj
def proc_dir(d):
dv = ddict[d]
init_data = [dv[0], [0,0,dv[-1]], dv[1]]
dir_obj = cu.Data_dir(dv[0], [0,0,dv[-1]], dv[1])
dir_obj.load_dir(cu.simple_loader)
return dir_obj
def proc_dir(d):
# simple directory processing function to load data and find
# different cantilever positions
dv = ddict[d]
init_data = [dv[0], [0, 0, dv[-1]], dv[1]]
dir_obj = cu.Data_dir(dv[0], [0, 0, dv[-1]], dv[1])
dir_obj.load_dir(cu.simple_loader)
return dir_obj
def proc_dir(d):
dv = ddict[d]
init_data = [dv[0], [0, 0, dv[-1]], dv[1]]
dir_obj = cu.Data_dir(dv[0], [0, 0, dv[-1]], dv[1])
dir_obj.load_dir(cu.simple_loader, maxfiles=maxfiles)
#dir_obj.diagonalize_files
return dir_obj
def proc_dir(d):
dv = ddict[d]
dir_obj = cu.Data_dir(dv[0], [0, 0, dv[-1]], dv[1])
dir_obj.load_dir(cu.diag_loader, maxfiles=maxfiles)
dir_obj.load_H(tf_path)
if load_charge_cal:
dir_obj.load_step_cal(step_cal_path)
else:
dir_obj.charge_step_calibration = step_calibration
dir_obj.gravity_signals = force_curve_dic
dir_obj.calibrate_H()
dir_obj.diagonalize_files(
reconstruct_lowf=True,
lowf_thresh=200., #plot_Happ=True, \
build_conv_facs=True,
drive_freq=18.)
amps = []
for fil_obj in dir_obj.fobjs:
stagestuff = fil_obj.get_stage_settings(axis=straighten_axis)
amp = stagestuff[2] * cant_volts_to_um
amps.append(amp)
uamps = np.unique(amps)
if len(uamps) > 1:
print('STUPIDITYERROR: Multiple dirve amplitudes in directory')
newlist = []
for i in [0, 1, 2]:
if i == straighten_axis:
newlist.append(uamps[0])
else:
newlist.append(0.0)
dir_obj.drive_amplitude = newlist
return dir_obj
def proc_dir(d):
dv = ddict[d]
dir_obj = cu.Data_dir(dv[0], [0, 0, dv[-1]], dv[1])
dir_obj.load_dir(cu.diag_loader, maxfiles=maxfiles)
dir_obj.load_H("./trans_funcs/Hout_20160630.p")
dir_obj.load_step_cal('./calibrations/step_cal_20160701.p')
dir_obj.thermal_cal_file_path = '/data/20160627/bead1/1_5mbar_nocool_withap.h5'
dir_obj.thermal_calibration()
#dir_obj.thermal_cal_fobj.plt_thermal_fit()
#dir_obj.build_Hfuncs(fpeaks=[245, 255, 50], weight_peak=False, weight_above_thresh=True,\
# plot_fits=False, weight_phase=True)
dir_obj.diagonalize_files(simpleDCmat=False)
dir_obj.get_conv_facs()
#dir_obj.plot_H(cal=True)
return dir_obj
def proc_dir(d):
dv = ddict[d]
dir_obj = cu.Data_dir(dv[0], [0,-40,dv[-1]], dv[1])
dir_obj.load_dir(cu.diag_loader, maxfiles = maxfiles)
dir_obj.load_H(tf_path)
if load_charge_cal:
dir_obj.load_step_cal(step_cal_path)
else:
dir_obj.charge_step_calibration = step_calibration
dir_obj.gravity_signals = force_curve_dic
dir_obj.calibrate_H()
dir_obj.diagonalize_files(reconstruct_lowf=True, lowf_thresh=lpf_freq, #plot_Happ=True, \
build_conv_facs=True, drive_freq=step_cal_drive_freq)
return dir_obj
def proc_dir(d):
dv = ddict[d]
init_data = [dv[0], [0, 0, dv[-1]], dv[1]]
dir_obj = cu.Data_dir(dv[0], [0, 0, dv[-1]], dv[1])
files = []
# initially sort by time
for path in dir_obj.paths:
entries = [os.path.join(path, fn) for fn in os.listdir(path)]
entries = [(os.stat(path), path) for path in entries]
entries = [(stat.st_ctime, path) for stat, path in entries]
entries.sort(key=lambda x: (x[0]))
for thing in entries[-10:]:
print(thing)
for thing in entries:
if '.npy' in thing[1]:
continue
files.append(thing[1])
dir_obj.files = files[:]
dir_obj.load_dir(cu.simple_loader, maxfiles=maxfiles)
#dir_obj.diagonalize_files
return dir_obj
def proc_dir(d):
dv = ddict[d]
dir_obj = cu.Data_dir(dv[0], [0, 0, dv[-1]], dv[1])
dir_obj.load_dir(cu.diag_loader, maxfiles=maxfiles)
dir_obj.load_H(tf_path)
if load_charge_cal:
dir_obj.load_step_cal(step_cal_path)
#dir_obj.load_step_cal('./calibrations/step_cal_TEST.p')
else:
dir_obj.charge_step_calibration = step_calibration
dir_obj.calibrate_H()
dir_obj.diagonalize_files(
reconstruct_lowf=True,
lowf_thresh=200., #, plot_Happ=True) \
build_conv_facs=True,
cal_drive_freq=41.)
#dir_obj.plot_H(cal=True)
return dir_obj
time = fobj.Time
if time not in time_dict:
time_dict[time] = []
time_dict[time].append(fobj.fname)
else:
time_dict[time].append(fobj.fname)
times = list(time_dict.keys())
colors_yeay = bu.get_color_map( len(times) )
f, axarr = plt.subplots(len(axes_to_plot),2,sharey='row',sharex='all',figsize=(10,12),dpi=100)
for i, time in enumerate(times):
newobj = cu.Data_dir(0, init_data, time)
newobj.files = time_dict[time]
newobj.load_dir(cu.diag_loader, maxfiles=maxfiles)
newobj.load_H(tf_path)
newobj.load_step_cal(step_cal_path)
newobj.calibrate_H()
newobj.diagonalize_files(reconstruct_lowf=True,lowf_thresh=200.,# plot_Happ=True, \
build_conv_facs=True, drive_freq=cal_drive_freq, close_dat=False)
fobj = newobj.fobjs[0]
#print fobj.pos_data
#raw_input()
sharex='all',
sharey='all',
figsize=(7, 8),
dpi=100)
if subtract_background:
f2, axarr2 = plt.subplots(3,
2,
sharex='all',
sharey='all',
figsize=(10, 12),
dpi=100)
# Loop over files by cantilever position, make a new directory object for each
# position then bin all of the files at that position
for i, pos in enumerate(pos_keys):
newobj = cu.Data_dir(0, init_data, pos)
newobj.files = pos_dict[pos]
newobj.load_dir(cu.diag_loader, maxfiles=maxfiles)
newobj.get_avg_force_v_pos(cant_axis=cant_axis, bin_size=bin_size)
# Load the calibrations
newobj.load_H(tf_path)
if load_charge_cal:
newobj.load_step_cal(step_cal_path)
else:
newobj.charge_step_calibration = step_calibration
newobj.calibrate_H()
newobj.diagonalize_files(
reconstruct_lowf=True,
lowf_thresh=lpf, #plot_Happ=True, \
ylim = [6e-19, 1.5e-15]
maxfiles = 100
calibrate = True
tf_path = '/calibrations/transfer_funcs/Hout_20170903.p'
step_cal_path = '/calibrations/step_cals/step_cal_20170903.p'
res_freqs = np.array([223.9, 223.6, 46.6])
mass = (4. / 3) * np.pi * (2.4e-6)**3 * 2000
force_pos_cal = mass * (2 * np.pi * res_freqs)**2
use_force_pos_cal = True
charge_cal = [[''], 'Cal', 0]
charge_cal_dir_obj = cu.Data_dir(charge_cal[0], [0, 0, charge_cal[2]],
charge_cal[1])
charge_cal_dir_obj.load_step_cal(step_cal_path)
charge_cal_dir_obj.load_H(tf_path)
charge_cal_dir_obj.calibrate_H()
charge_cal_dir_obj.get_conv_facs()
charge_step_facs = charge_cal_dir_obj.conv_facs
pressures = []
def proc_dir(d):
dv = ddict[d]
init_data = [dv[0], [0, 0, dv[-1]], dv[1]]
dir_obj = cu.Data_dir(dv[0], [0, 0, dv[-1]], dv[1])
import tkinter
import tkinter.filedialog
import os, sys
from scipy.optimize import curve_fit
import bead_util as bu
from scipy.optimize import minimize_scalar as minimize
dirs = [13, 14, 15, 16]
cal = 5.0e-14
ddict = bu.load_dir_file(
"/home/charles/opt_lev_analysis/scripts/dirfiles/dir_file_june2017.txt")
load_from_file = False
new_obj = cu.Data_dir('shit_path', [0, 0, 0], "wheeeee")
new_obj.load_H("optphase2_Hout.p")
#new_obj.plot_H(phase=True, label=True)
Hmat = new_obj.build_avgH(fthresh=60)
plt.imshow(np.abs(Hmat))
plt.show()
Hmat_diag = np.linalg.inv(Hmat)
plt.imshow(np.abs(Hmat_diag))
plt.show()
print(np.abs(Hmat))
import numpy as np
import matplotlib.pyplot as plt
import cant_utils as cu
dat_dir = "/data/20160429/nobead/ysweepoverz_75_65"
load = True
dobj = cu.Data_dir(dat_dir, [0, 0, 0])
lfun = lambda fname, sep: cu.pos_loader(fname, sep, cant_axis=1)
if load == True:
dobj.load_dir(lfun)
dobj.save_dir()
else:
dobj.load_from_file()
labeler = lambda fobj: str(80 - np.mean(fobj.binned_cant_data[1, 2]))
def plt_sweeps(dobj, axis=1, ecal=5e-14):
#plots all of the binned data for axis.
for fobj in dobj.fobjs:
plt.errorbar(fobj.binned_cant_data[1, 1],
fobj.binned_pos_data[1, 1] * ecal,
fobj.binned_data_errors[1, 1] * ecal,
fmt='o-',
label=labeler(fobj))
plt.xlabel("Cantilever x position")
plt.ylabel("Apparent z background force")
#files = np.arange(0,40,1)
files = np.array([1, 2, 3, 4, 5, 6, 7, 8, 9, 10])
maxfiles = 1000
bin_size = 5
resp_axis = 1
tf_path = './trans_funcs/Hout_20160803.p'
step_cal_path = './calibrations/step_cal_20160803.p'
#################
if not load_charge_cal:
cal = [['/data/20160627/bead1/chargelp_withap_2nd_cal2'], 'Cal', 20]
cal_dir_obj = cu.Data_dir(cal[0], [0, 0, cal[2]], cal[1])
cal_dir_obj.load_dir(cu.simple_loader)
cal_dir_obj.build_step_cal_vec()
cal_dir_obj.step_cal()
cal_dir_obj.save_step_cal('./calibrations/step_cal_20160701.p')
for fobj in cal_dir_obj.fobjs:
fobj.close_dat()
step_calibration = cal_dir_obj.charge_step_calibration
#################
def proc_dir(d):
dv = ddict[d]
