"This notebook corresponds to version {{ version }} of the pipeline tool: https://github.com/NSLS-II/pipelines"
This notebook begins with a raw time-series of images and ends with $g_2(t)$ for a range of $q$, fit to an exponential or stretched exponential, and a two-time correlation functoin.
CHX Olog (https://logbook.nsls2.bnl.gov/11-ID/)
Import packages for I/O, visualization, and analysis.
In [2]:
from chxanalys.chx_packages import *
%matplotlib notebook
plt.rcParams.update({'figure.max_open_warning': 0})
plt.rcParams.update({ 'image.origin': 'lower' })
plt.rcParams.update({ 'image.interpolation': 'none' })
import pickle as cpk
from chxanalys.chx_xpcs_xsvs_jupyter_V1 import *
In [3]:
Javascript( '''
var nb = IPython.notebook;
var kernel = IPython.notebook.kernel;
var command = "NFP = '" + nb.base_url + nb.notebook_path + "'";
kernel.execute(command);
''' )
Out[3]:
In [4]:
print( 'The current running pipeline is: %s' %NFP)
In [ ]:
#%reset -f -s dhist in out array
In [106]:
scat_geometry = 'saxs' #suport 'saxs', 'gi_saxs', 'ang_saxs' (for anisotropics saxs or flow-xpcs)
#scat_geometry = 'gi_saxs' #suport 'saxs', 'gi_saxs', 'ang_saxs' (for anisotropics saxs or flow-xpcs)
#scat_geometry = 'gi_waxs' #suport 'saxs', 'gi_saxs', 'ang_saxs' (for anisotropics saxs or flow-xpcs)
# gi_waxs define a simple box-shaped ROI
force_compress = False #True #force to compress data
bin_frame = False #generally make bin_frame as False
para_compress = True #parallel compress
run_fit_form = False #run fit form factor
run_waterfall = True #run waterfall analysis
run_t_ROI_Inten = True #run ROI intensity as a function of time
run_one_time = True #run one-time
#run_fit_g2 = True #run fit one-time, the default function is "stretched exponential"
fit_g2_func = 'stretched'
run_two_time = True #False #run two-time
run_four_time = False #True #False #run four-time
run_xsvs= False #False #run visibility analysis
att_pdf_report = True #attach the pdf report to CHX olog
qth_interest = 1 #the intested single qth
use_sqnorm = True #if True, use sq to normalize intensity
use_imgsum_norm=True #if True use imgsum to normalize intensity for one-time calculatoin
pdf_version='_May4_1' #for pdf report name
run_dose = True #False #run dose_depend analysis
if scat_geometry == 'gi_saxs':run_xsvs= False;
if scat_geometry == 'gi_waxs':use_sqnorm = False;
In [6]:
taus=None;g2=None;tausb=None;g2b=None;g12b=None;taus4=None;g4=None;times_xsv=None;contrast_factorL=None; lag_steps = None
In [7]:
#CYCLE= '2017_1' #change clycle here
CYCLE= 'CHX_Results_Pipelines' #change clycle here
#username = getpass.getuser()
#username = 'commissioning'
username = 'Beamline_Paper'
data_dir0 = create_user_folder(CYCLE, username)
print( data_dir0 )
In [8]:
uid = '337e48' # (scan num: 22072) (Measurement: 750Hz, 5k CoralPor )
#uid = '28dd84' # (scan num: 22073) (Measurement: 10Hz, 2k CoralPor )
uid = '7521f3' # (scan num: 22095) (Measurement: 750Hz 5k CoralPor )
#uid = '802671d9' # (scan num: 22097) (Measurement: 20s x2.2k Tr=.000568CoralPor )
uid = '9a2279' # (scan num: 17422) (Measurement: approx. 9kHz 20k (mbs:.1x.4) E9: SiO2 250nm in tween/water 1:2 )
uid = 'a230e1' # (scan num: 17423) (Measurement: 750Hz, 2k E8: SiO2 250nm in tween/water 1:5 )
uid = '701d0d'# (scan num: 17420) (Measurement: approx. 9kHz 10k (mbs:.1x.4) E7: SiO2 250nm in water (diluted from stock) )
uid = 'cb99bd' # (scan num: 19287) (Measurement: E72 fresh prepared in water750Hz 5000fra att=0.1 )
uid = '006b1a' # (scan num: 17547) (Measurement: Silica 250 nm stock solution 10k frames 750Hz )'
########################For Brownian Motion, 4M
uid = 'c8a1fb1f' # (scan num: 17087) (Measurement: 1ms x 2k A5: 15nm citric acid Au in Twee 20 )
#################################################
#uid = '7deec4f4' # (scan num: 19085) (Measurement: D2, AuCit15nm in Wat:Tween=1:1 750Hz 20000fra for dose analysis)
In [10]:
sud = get_sid_filenames(db[uid])
print ('scan_id, full-uid, data path are: %s--%s--%s'%(sud[0], sud[1], sud[2][0] ))
#start_time, stop_time = '2017-2-24 12:23:00', '2017-2-24 13:42:00'
#sids, uids, fuids = find_uids(start_time, stop_time)
In [ ]:
In [11]:
data_dir = os.path.join(data_dir0, '%s/'%uid)
os.makedirs(data_dir, exist_ok=True)
print('Results from this analysis will be stashed in the directory %s' % data_dir)
uidstr = 'uid=%s'%uid
In [12]:
md = get_meta_data( uid )
In [13]:
imgs = load_data( uid, md['detector'], reverse= True )
md.update( imgs.md );Nimg = len(imgs);
#if 'number of images' not in list(md.keys()):
md['number of images'] = Nimg
pixel_mask = 1- np.int_( np.array( imgs.md['pixel_mask'], dtype= bool) )
print( 'The data are: %s' %imgs )
md['acquire period' ] = md['cam_acquire_period']
md['exposure time'] = md['cam_acquire_time']
In [14]:
print_dict( md, ['suid', 'number of images', 'uid', 'scan_id', 'start_time', 'stop_time', 'sample', 'Measurement',
'acquire period', 'exposure time',
'det_distance', 'beam_center_x', 'beam_center_y', ] )
In [15]:
md['beam_center_x']= 1085#1016 #1085
md['beam_center_y']= 1041# 1007 #1041
md['det_distance']= 16.0756*1000 #16.0359 *1000 #16.0756*1000
#md['exposure_time'] = md['count_time']
inc_x0 = None
inc_y0= None
dpix, lambda_, Ldet, exposuretime, timeperframe, center = check_lost_metadata(
md, Nimg, inc_x0 = inc_x0, inc_y0= inc_y0, pixelsize = 7.5*10*(-5) )
setup_pargs=dict(uid=uidstr, dpix= dpix, Ldet=Ldet, lambda_= lambda_, exposuretime=exposuretime,
timeperframe=timeperframe, center=center, path= data_dir)
print_dict( setup_pargs )
In [ ]:
In [16]:
mask_path = '/XF11ID/analysis/2017_1/masks/'
#mask_name = 'Apr10_4M_SAXS16m_mask2.npy'
mask_name = 'Feb23_500K_SAXS6_mask.npy'
mask_name = 'Mar20_4M_SAXS_mask.npy'
mask_name = 'Feb27_4M_SAXS_mask.npy'
mask_name = 'Feb21_4M_SAXS2_mask.npy' #for uid=c8a1fb1f
#mask_name = 'Mar20_4M_SAXS_mask.npy'
In [18]:
mask = load_mask(mask_path, mask_name, plot_ = False, image_name = uidstr + '_mask', reverse= True )
mask *= pixel_mask
show_img(mask,image_name = uidstr + '_mask', save=True, path=data_dir, aspect=1)
mask_load=mask.copy()
imgsa = apply_mask( imgs, mask )
In [19]:
img_choice_N = 3
img_samp_index = random.sample( range(len(imgs)), img_choice_N)
avg_img = get_avg_img( imgsa, img_samp_index, plot_ = False, uid =uidstr)
if avg_img.max() == 0:
print('There are no photons recorded for this uid: %s'%uid)
print('The data analysis should be terminated! Please try another uid.')
In [ ]:
#show_img( imgsa[1000], vmin=.1, vmax= 1e1, logs=True, aspect=1,
# image_name= uidstr + '_img_avg', save=True, path=data_dir, cmap = cmap_albula )
In [20]:
show_img( avg_img, vmin=.1, vmax= 1e1, logs=True, aspect=1,
image_name= uidstr + '_img_avg', save=True, path=data_dir, cmap = cmap_albula )
In [21]:
compress=True
photon_occ = len( np.where(avg_img)[0] ) / ( imgsa[0].size)
#compress = photon_occ < .4 #if the photon ocupation < 0.5, do compress
print ("The non-zeros photon occupation is %s."%( photon_occ))
print("Will " + 'Always ' + ['NOT', 'DO'][compress] + " apply compress process.")
In [22]:
good_start = 5 #5 #make the good_start at least 0
In [23]:
bin_frame = False #True # False # True #generally make bin_frame as False
if bin_frame:
bin_frame_number=4
timeperframe = acquisition_period * bin_frame_number
else:
bin_frame_number =1
In [24]:
import time
t0= time.time()
if bin_frame_number==1:
filename = '/XF11ID/analysis/Compressed_Data' +'/uid_%s.cmp'%md['uid']
else:
filename = '/XF11ID/analysis/Compressed_Data' +'/uid_%s_bined--%s.cmp'%(md['uid'],bin_frame_number)
mask, avg_img, imgsum, bad_frame_list = compress_eigerdata(imgs, mask, md, filename,
force_compress= force_compress, para_compress= para_compress, bad_pixel_threshold = 1e14,
bins=bin_frame_number, num_sub= 100, num_max_para_process= 500, with_pickle=True )
min_inten = 10
good_start = max(good_start, np.where( np.array(imgsum) > min_inten )[0][0] )
print ('The good_start frame number is: %s '%good_start)
FD = Multifile(filename, good_start, len(imgs)//bin_frame_number)
#FD = Multifile(filename, good_start, 100)
uid_ = uidstr + '_fra_%s_%s'%(FD.beg, FD.end)
print( uid_ )
plot1D( y = imgsum[ np.array( [i for i in np.arange(good_start, len(imgsum)) if i not in bad_frame_list])],
title =uidstr + '_imgsum', xlabel='Frame', ylabel='Total_Intensity', legend='imgsum' )
Nimg = Nimg/bin_frame_number
run_time(t0)
In [26]:
show_img( avg_img, vmin=0.0001, vmax= 1e2, logs=True, aspect=1, #save_format='tif',
image_name= uidstr + '_img_avg', save=True, path=data_dir, cmap = cmap_albula )
In [27]:
good_end= None # 2000
if good_end is not None:
FD = Multifile(filename, good_start, min( len(imgs)//bin_frame_number, good_end) )
uid_ = uidstr + '_fra_%s_%s'%(FD.beg, FD.end)
print( uid_ )
In [28]:
re_define_good_start =False
if re_define_good_start:
good_start = 10
good_end = 19700
FD = Multifile(filename, good_start, good_end)
uid_ = uidstr + '_fra_%s_%s'%(FD.beg, FD.end)
print( FD.beg, FD.end)
In [29]:
bad_frame_list = get_bad_frame_list( imgsum, fit=True, plot=True,polyfit_order = 30,
scale=1., good_start = good_start, good_end=good_end, uid= uidstr, path=data_dir)
print( 'The bad frame list length is: %s'%len(bad_frame_list) )
In [30]:
imgsum_y = imgsum[ np.array( [i for i in np.arange( len(imgsum)) if i not in bad_frame_list])]
imgsum_x = np.arange( len( imgsum_y))
save_lists( [imgsum_x, imgsum_y], label=['Frame', 'Total_Intensity'],
filename=uidstr + '_img_sum_t', path= data_dir )
In [31]:
plot1D( y = imgsum_y, title = uidstr + '_img_sum_t', xlabel='Frame',
ylabel='Total_Intensity', legend='imgsum', save=True, path=data_dir)
In [81]:
#fp = 'Au15_roi_16m_4M.pkl'
#fp = 'Au15_roi_16m_4M_dose.pkl'
fp = 'uid=c8a1fb1f_roi_16m.pkl' #16 rings
#fp = 'uid=c8a1fb1f_roi_16m_refined.pkl'
fp = data_dir0 + fp
roi_mask,qval_dict = cpk.load( open(fp, 'rb' ) ) #for load the saved roi data
if scat_geometry =='gi_saxs':
fp = data_dir0 + 'gisaxs_test.pkl'
qr_map, qz_map, ticks, Qrs, Qzs, Qr, Qz, inc_x0 = cpk.load( open(fp, 'rb' ) )
In [82]:
if scat_geometry =='saxs':
## Get circular average| * Do plot and save q~iq
hmask = create_hot_pixel_mask( avg_img, threshold = .1, center=center, center_radius= 400)
qp_saxs, iq_saxs, q_saxs = get_circular_average( avg_img, mask * hmask, pargs=setup_pargs )
plot_circular_average( qp_saxs, iq_saxs, q_saxs, pargs=setup_pargs,
xlim=[q_saxs.min(), q_saxs.max()*0.9], ylim = [iq_saxs.min(), iq_saxs.max()] )
#mask =np.array( mask * hmask, dtype=bool)
In [83]:
if scat_geometry =='saxs':
if run_fit_form:
form_res = fit_form_factor( q_saxs,iq_saxs, guess_values={'radius': 2500, 'sigma':0.05,
'delta_rho':1E-10 }, fit_range=[0.0001, 0.015], fit_variables={'radius': T, 'sigma':T,
'delta_rho':T}, res_pargs=setup_pargs, xlim=[0.0001, 0.015])
qr = np.array( [qval_dict[k][0] for k in sorted( qval_dict.keys())] )
print(len(qr))
show_ROI_on_image( avg_img, roi_mask, center, label_on = False, rwidth = 840, alpha=.9,
save=True, path=data_dir, uid=uidstr, vmin= np.min(avg_img),
vmax= 16, #np.max(avg_img),
aspect=1)
plot_qIq_with_ROI( q_saxs, iq_saxs, qr, logs=True, uid=uidstr, xlim=[0.0001,0.03],
ylim = [iq_saxs.min(), iq_saxs.max()], save=True, path=data_dir)
In [84]:
if scat_geometry =='saxs':
Nimg = FD.end - FD.beg
time_edge = create_time_slice( Nimg, slice_num= 5, slice_width= 1, edges = None )
time_edge = np.array( time_edge ) + good_start
print( time_edge )
qpt, iqst, qt = get_t_iqc( FD, time_edge, mask, pargs=setup_pargs, nx=1500 )
plot_t_iqc( qt, iqst, time_edge, pargs=setup_pargs, xlim=[qt.min(), qt.max()],
ylim = [iqst.min(), iqst.max()], save=True )
In [56]:
if scat_geometry =='gi_saxs':
plot_qzr_map( qr_map, qz_map, inc_x0, ticks = ticks, data= avg_img, uid= uidstr, path = data_dir )
In [57]:
if scat_geometry =='gi_saxs':
roi_masks, qval_dicts = get_gisaxs_roi( Qrs, Qzs, qr_map, qz_map, mask= mask )
show_qzr_roi( avg_img, roi_masks, inc_x0, ticks[:4], alpha=0.5, save=True, path=data_dir, uid=uidstr )
In [58]:
if scat_geometry =='gi_saxs':
Nimg = FD.end - FD.beg
time_edge = create_time_slice( N= Nimg, slice_num= 3, slice_width= 2, edges = None )
time_edge = np.array( time_edge ) + good_start
print( time_edge )
qrt_pds = get_t_qrc( FD, time_edge, Qrs, Qzs, qr_map, qz_map, path=data_dir, uid = uidstr )
plot_qrt_pds( qrt_pds, time_edge, qz_index = 0, uid = uidstr, path = data_dir )
In [59]:
if scat_geometry =='gi_saxs':
if run_waterfall:
xcorners= [ 1100, 1250, 1250, 1100 ]
ycorners= [ 850, 850, 950, 950 ]
waterfall_roi_size = [ xcorners[1] - xcorners[0], ycorners[2] - ycorners[1] ]
waterfall_roi = create_rectangle_mask( avg_img, xcorners, ycorners )
#show_img( waterfall_roi * avg_img, aspect=1,vmin=.001, vmax=1, logs=True, )
wat = cal_waterfallc( FD, waterfall_roi, qindex= 1, bin_waterfall=True,
waterfall_roi_size = waterfall_roi_size,save =True, path=data_dir, uid=uidstr)
In [60]:
if scat_geometry =='gi_saxs':
if run_waterfall:
plot_waterfallc( wat, qindex=1, aspect=None, vmin=1, vmax= np.max( wat), uid=uidstr, save =True,
path=data_dir, beg= FD.beg)
In [61]:
if scat_geometry =='gi_saxs':
show_qzr_roi( avg_img, roi_mask, inc_x0, ticks[:4], alpha=0.5, save=True, path=data_dir, uid=uidstr )
## Get 1D Curve (Q||-intensity¶)
qr_1d_pds = cal_1d_qr( avg_img, Qr, Qz, qr_map, qz_map, inc_x0= None, setup_pargs=setup_pargs )
plot_qr_1d_with_ROI( qr_1d_pds, qr_center=np.unique( np.array(list( qval_dict.values() ) )[:,0] ),
loglog=False, save=True, uid=uidstr, path = data_dir)
In [62]:
if scat_geometry =='gi_waxs':
badpixel = np.where( avg_img[:600,:] >=300 )
roi_mask[badpixel] = 0
show_ROI_on_image( avg_img, roi_mask, label_on = True, alpha=.5,
save=True, path=data_dir, uid=uidstr, vmin=0.1, vmax=5)
In [ ]:
In [85]:
qind, pixelist = roi.extract_label_indices(roi_mask)
noqs = len(np.unique(qind))
In [86]:
nopr = np.bincount(qind, minlength=(noqs+1))[1:]
nopr
Out[86]:
In [ ]:
In [87]:
roi_inten = check_ROI_intensity( avg_img, roi_mask, ring_number= 2, uid =uidstr )
In [92]:
qth_interest = 2 #the second ring.
if scat_geometry =='saxs' or scat_geometry =='gi_waxs':
if run_waterfall:
wat = cal_waterfallc( FD, roi_mask, qindex= qth_interest, save =True, path=data_dir, uid=uidstr)
In [93]:
if scat_geometry =='saxs' or scat_geometry =='gi_waxs':
if run_waterfall:
plot_waterfallc( wat, qth_interest, aspect=None, vmax= 10, uid=uidstr, save =True,
path=data_dir, beg= FD.beg)
In [73]:
ring_avg = None
if run_t_ROI_Inten:
times_roi, mean_int_sets = cal_each_ring_mean_intensityc(FD, roi_mask, timeperframe = None, )
plot_each_ring_mean_intensityc( times_roi, mean_int_sets, uid = uidstr, save=True, path=data_dir )
roi_avg = np.average( mean_int_sets, axis=0)
Note : Enter the number of buffers for Muliti tau one time correlation number of buffers has to be even. More details in https://github.com/scikit-beam/scikit-beam/blob/master/skbeam/core/correlation.py
In [94]:
define_good_series = False
#define_good_series = True
if define_good_series:
good_start = 1500
FD = Multifile(filename, beg = good_start, end = 5000 ) # Nimg)#600)
uid_ = uidstr + '_fra_%s_%s'%(FD.beg, FD.end)
print( uid_ )
In [95]:
if use_sqnorm:norm = get_pixelist_interp_iq( qp_saxs, iq_saxs, roi_mask, center)
else:norm=None
if use_imgsum_norm:imgsum_ = imgsum
else:imgsum_ = None
import time
In [96]:
if run_one_time:
t0 = time.time()
g2, lag_steps = cal_g2p( FD, roi_mask, bad_frame_list,good_start, num_buf = 8, num_lev= None,
imgsum= imgsum_, norm=norm )
run_time(t0)
In [97]:
lag_steps = lag_steps[:g2.shape[0]]
In [98]:
if run_one_time:
taus = lag_steps * timeperframe
g2_pds = save_g2_general( g2, taus=taus,qr=np.array( list( qval_dict.values() ) )[:,0],
uid=uid_+'_g2.csv', path= data_dir, return_res=True )
In [99]:
#g2_pds
In [100]:
if run_one_time:
g2_fit_result, taus_fit, g2_fit = get_g2_fit_general( g2, taus,
function = fit_g2_func, vlim=[0.95, 1.05], fit_range= None,
fit_variables={'baseline':True, 'beta': True, 'alpha':False,'relaxation_rate':True},
guess_values={'baseline':1.03,'beta': 0.15,'alpha':1.0,'relaxation_rate':1,},
guess_limits = dict( baseline =[1, 1.8], alpha=[0, 2],
beta = [0, 1], relaxation_rate= [0.001, 5000]) )
g2_fit_paras = save_g2_fit_para_tocsv(g2_fit_result, filename= uid_ +'_g2_fit_paras.csv', path=data_dir )
In [101]:
if run_one_time:
plot_g2_general( g2_dict={1:g2, 2:g2_fit}, taus_dict={1:taus, 2:taus_fit},vlim=[0.95, 1.05],
qval_dict = qval_dict, fit_res= g2_fit_result, geometry= scat_geometry,filename= uid_+'_g2',
path= data_dir, function= fit_g2_func, ylabel='g2', append_name= '_fit')
In [102]:
if run_one_time:
if True:
fs, fe = 0, 9
fs,fe=0, 12
qval_dict_ = {k:qval_dict[k] for k in list(qval_dict.keys())[fs:fe] }
D0, qrate_fit_res = get_q_rate_fit_general( qval_dict_, g2_fit_paras['relaxation_rate'][fs:fe], geometry= scat_geometry )
plot_q_rate_fit_general( qval_dict_, g2_fit_paras['relaxation_rate'][fs:fe], qrate_fit_res,
geometry= scat_geometry,uid=uid_ , path= data_dir )
else:
D0, qrate_fit_res = get_q_rate_fit_general( qval_dict, g2_fit_paras['relaxation_rate'],
fit_range=[0, 16], geometry= scat_geometry )
plot_q_rate_fit_general( qval_dict, g2_fit_paras['relaxation_rate'], qrate_fit_res,
geometry= scat_geometry,uid=uid_ , path= data_dir, plot_all_range=False)
In [ ]:
#plot1D( x= qr, y=g2_fit_paras['beta'], ls='-', m = 'o', c='b', ylabel=r'$\beta$', xlabel=r'$Q( \AA^{-1} ) $' )
In [103]:
define_good_series = False
#define_good_series = True
if define_good_series:
good_start = 5
FD = Multifile(filename, beg = good_start, end = 1000)
uid_ = uidstr + '_fra_%s_%s'%(FD.beg, FD.end)
print( uid_ )
In [104]:
data_pixel = None
if run_two_time:
data_pixel = Get_Pixel_Arrayc( FD, pixelist, norm= norm ).get_data()
In [105]:
import time
t0=time.time()
g12b=None
if run_two_time:
g12b = auto_two_Arrayc( data_pixel, roi_mask, index = None )
if run_dose:
np.save( data_dir + 'uid=%s_g12b'%uid, g12b)
run_time( t0 )
In [107]:
if run_two_time:
show_C12(g12b, q_ind= 1, N1= FD.beg,logs=False, N2=min( FD.end,5000), vmin= 0.98, vmax=1.25,
timeperframe=timeperframe,save=True, path= data_dir, uid = uid_ )
In [108]:
multi_tau_steps = True
if run_two_time:
if lag_steps is None:
num_bufs=8
noframes = FD.end - FD.beg
num_levels = int(np.log( noframes/(num_bufs-1))/np.log(2) +1) +1
tot_channels, lag_steps, dict_lag = multi_tau_lags(num_levels, num_bufs)
max_taus= lag_steps.max()
#max_taus= lag_steps.max()
max_taus = Nimg
t0=time.time()
#tausb = np.arange( g2b.shape[0])[:max_taus] *timeperframe
if multi_tau_steps:
lag_steps_ = lag_steps[ lag_steps <= g12b.shape[0] ]
g2b = get_one_time_from_two_time(g12b)[lag_steps_]
tausb = lag_steps_ *timeperframe
else:
tausb = (np.arange( g12b.shape[0]) *timeperframe)[:-200]
g2b = (get_one_time_from_two_time(g12b))[:-200]
run_time(t0)
g2b_pds = save_g2_general( g2b, taus=tausb, qr= np.array( list( qval_dict.values() ) )[:,0],
qz=None, uid=uid_ +'_g2b.csv', path= data_dir, return_res=True )
In [109]:
if run_two_time:
g2b_fit_result, tausb_fit, g2b_fit = get_g2_fit_general( g2b, tausb,
function = fit_g2_func, vlim=[0.95, 1.05], fit_range= None,
fit_variables={'baseline':True, 'beta': True, 'alpha':False,'relaxation_rate':True},
guess_values={'baseline':1.03,'beta': 0.15,'alpha':1.0,'relaxation_rate':1,},
guess_limits = dict( baseline =[1, 1.8], alpha=[0, 2],
beta = [0, 1], relaxation_rate= [0.001, 5000]) )
g2b_fit_paras = save_g2_fit_para_tocsv(g2b_fit_result, filename= uid_ +'_g2b_fit_paras.csv', path=data_dir )
In [110]:
#plot1D( x = tausb[1:], y =g2b[1:,0], ylim=[0.95, 1.46], xlim = [0.0001, 10], m='', c='r', ls = '-',
# logx=True, title='one_time_corelation', xlabel = r"$\tau $ $(s)$", )
In [111]:
if run_two_time:
plot_g2_general( g2_dict={1:g2b, 2:g2b_fit}, taus_dict={1:tausb, 2:tausb_fit}, vlim=[0.95, 1.05],
qval_dict=qval_dict, fit_res= g2b_fit_result, geometry=scat_geometry,filename=uid_+'_g2',
path= data_dir, function= fit_g2_func, ylabel='g2', append_name= '_b_fit')
In [112]:
if run_two_time:
if True:
fs, fe = 0,9
fs, fe = 0,12
qval_dict_ = {k:qval_dict[k] for k in list(qval_dict.keys())[fs:fe] }
D0b, qrate_fit_resb = get_q_rate_fit_general( qval_dict_, g2b_fit_paras['relaxation_rate'][fs:fe], geometry= scat_geometry )
plot_q_rate_fit_general( qval_dict_, g2b_fit_paras['relaxation_rate'][fs:fe], qrate_fit_resb,
geometry= scat_geometry,uid=uid_ +'_two_time' , path= data_dir )
else:
D0b, qrate_fit_resb = get_q_rate_fit_general( qval_dict, g2b_fit_paras['relaxation_rate'],
fit_range=[1, 10], geometry= scat_geometry )
plot_q_rate_fit_general( qval_dict, g2b_fit_paras['relaxation_rate'], qrate_fit_resb,
geometry= scat_geometry,uid=uid_ +'_two_time' , path= data_dir, plot_all_range= True )
In [113]:
if run_two_time and run_one_time:
plot_g2_general( g2_dict={1:g2, 2:g2b}, taus_dict={1:taus, 2:tausb},vlim=[0.99, 1.007],
qval_dict=qval_dict, g2_labels=['from_one_time', 'from_two_time'],
geometry=scat_geometry,filename=uid_+'_g2_two_g2', path= data_dir, ylabel='g2', )
In [114]:
if run_dose:
get_two_time_mulit_uids( [uid], roi_mask, norm= norm, bin_frame_number=1,
path= data_dir0, force_generate=False )
In [115]:
try:
print( md['transmission'] )
except:
md['transmission'] =1
In [116]:
if run_dose:
N = len(imgs)
print(N)
exposure_dose = md['transmission'] * exposuretime* np.int_([ N/32, N/16, N/8, N/4 ,N/2, 3*N/4, N*0.99 ])
print( exposure_dose )
In [117]:
if run_dose:
taus_uids, g2_uids = get_series_one_time_mulit_uids( [ uid ], qval_dict, good_start=good_start,
path= data_dir0, exposure_dose = exposure_dose, num_bufs =8, save_g2= False,
dead_time = 0, trans = [ md['transmission'] ] )
In [118]:
if run_dose:
plot_dose_g2( taus_uids, g2_uids, ylim=[.95, 1.3], vshift= 0.00,
qval_dict = qval_dict, fit_res= None, geometry= scat_geometry,
filename= '%s_dose_analysis'%uid_,
path= data_dir, function= None, ylabel='g2_Dose', g2_labels= None, append_name= '' )
In [120]:
if run_dose:
qth_interest = 1
plot_dose_g2( taus_uids, g2_uids, qth_interest= qth_interest, ylim=[0.99, 1.26], vshift= 0.00,
qval_dict = qval_dict, fit_res= None, geometry= scat_geometry,
filename= '%s_dose_analysis'%uidstr,
path= data_dir, function= None, ylabel='g2_Dose', g2_labels= None, append_name= '' )
In [121]:
if run_four_time:
t0=time.time()
g4 = get_four_time_from_two_time(g12b, g2=g2b)[:max_taus]
run_time(t0)
In [122]:
if run_four_time:
taus4 = np.arange( g4.shape[0])*timeperframe
g4_pds = save_g2_general( g4, taus=taus4, qr=np.array( list( qval_dict.values() ) )[:,0],
qz=None, uid=uid_ +'_g4.csv', path= data_dir, return_res=True )
In [123]:
if run_four_time:
plot_g2_general( g2_dict={1:g4}, taus_dict={1:taus4},vlim=[0.95, 1.05], qval_dict=qval_dict, fit_res= None,
geometry=scat_geometry,filename=uid_+'_g4',path= data_dir, ylabel='g4')
In [124]:
run_xsvs = False #True
In [125]:
if run_xsvs:
max_cts = get_max_countc(FD, roi_mask )
max_cts = 15 #for eiger 500 K
qind, pixelist = roi.extract_label_indices( roi_mask )
noqs = len( np.unique(qind) )
nopr = np.bincount(qind, minlength=(noqs+1))[1:]
#time_steps = np.array( utils.geometric_series(2, len(imgs) ) )
time_steps = [0,1] #only run the first two levels
num_times = len(time_steps)
times_xsvs = exposuretime + (2**( np.arange( len(time_steps) ) ) -1 ) * timeperframe
print( 'The max counts are: %s'%max_cts )
In [126]:
if run_xsvs:
if roi_avg is None:
times_roi, mean_int_sets = cal_each_ring_mean_intensityc(FD, roi_mask, timeperframe = None, )
roi_avg = np.average( mean_int_sets, axis=0)
t0=time.time()
spec_bins, spec_his, spec_std = xsvsp( FD, np.int_(roi_mask), norm=None,
max_cts=int(max_cts+2), bad_images=bad_frame_list, only_two_levels=True )
spec_kmean = np.array( [roi_avg * 2**j for j in range( spec_his.shape[0] )] )
run_time(t0)
spec_pds = save_bin_his_std( spec_bins, spec_his, spec_std, filename=uid_+'_spec_res.csv', path=data_dir )
In [127]:
if run_xsvs:
ML_val, KL_val,K_ = get_xsvs_fit( spec_his, spec_kmean, spec_std, max_bins=2, varyK= False ) #True )
#print( 'The observed average photon counts are: %s'%np.round(K_mean,4))
#print( 'The fitted average photon counts are: %s'%np.round(K_,4))
print( 'The difference sum of average photon counts between fit and data are: %s'%np.round(
abs(np.sum( spec_kmean[0,:] - K_ )),4))
print( '#'*30)
qth= 0
print( 'The fitted M for Qth= %s are: %s'%(qth, ML_val[qth]) )
print( K_[qth])
print( '#'*30)
In [ ]:
In [128]:
if run_xsvs:
qr = [qval_dict[k][0] for k in list(qval_dict.keys()) ]
plot_xsvs_fit( spec_his, ML_val, KL_val, K_mean = spec_kmean, spec_std=spec_std,
xlim = [0,10], vlim =[.9, 1.1],
uid=uid_, qth= qth_interest, logy= True, times= times_xsvs, q_ring_center=qr, path=data_dir)
plot_xsvs_fit( spec_his, ML_val, KL_val, K_mean = spec_kmean, spec_std = spec_std,
xlim = [0,15], vlim =[.9, 1.1],
uid=uid_, qth= None, logy= True, times= times_xsvs, q_ring_center=qr, path=data_dir )
In [129]:
if run_xsvs:
contrast_factorL = get_contrast( ML_val)
spec_km_pds = save_KM( spec_kmean, KL_val, ML_val, qs=qr, level_time=times_xsvs, uid=uid_, path = data_dir )
#spec_km_pds
In [130]:
if run_xsvs:
plot_g2_contrast( contrast_factorL, g2b, times_xsvs, tausb, qr,
vlim=[0.8,1.2], qth = qth_interest, uid=uid_,path = data_dir, legend_size=14)
plot_g2_contrast( contrast_factorL, g2b, times_xsvs, tausb, qr,
vlim=[0.8,1.2], qth = None, uid=uid_,path = data_dir, legend_size=4)
In [131]:
#from chxanalys.chx_libs import cmap_vge, cmap_albula, Javascript
In [ ]:
In [132]:
md['mask_file']= mask_path + mask_name
md['mask'] = mask
md['NOTEBOOK_FULL_PATH'] = data_dir + get_current_pipeline_fullpath(NFP).split('/')[-1]
md['good_start'] = good_start
md['bad_frame_list'] = bad_frame_list
md['avg_img'] = avg_img
md['roi_mask'] = roi_mask
md['setup_pargs'] = setup_pargs
if scat_geometry == 'gi_saxs':
md['Qr'] = Qr
md['Qz'] = Qz
md['qval_dict'] = qval_dict
md['beam_center_x'] = inc_x0
md['beam_center_y']= inc_y0
md['beam_refl_center_x'] = refl_x0
md['beam_refl_center_y'] = refl_y0
elif scat_geometry == 'gi_waxs':
md['beam_center_x'] = center[1]
md['beam_center_y']= center[0]
else:
md['qr']= qr
#md['qr_edge'] = qr_edge
md['qval_dict'] = qval_dict
md['beam_center_x'] = center[1]
md['beam_center_y']= center[0]
md['beg'] = FD.beg
md['end'] = FD.end
md['qth_interest'] = qth_interest
md['metadata_file'] = data_dir + 'uid=%s_md.pkl'%uid
psave_obj( md, data_dir + 'uid=%s_md.pkl'%uid ) #save the setup parameters
save_dict_csv( md, data_dir + 'uid=%s_md.csv'%uid, 'w')
Exdt = {}
if scat_geometry == 'gi_saxs':
for k,v in zip( ['md', 'roi_mask','qval_dict','avg_img','mask','pixel_mask', 'imgsum', 'bad_frame_list', 'qr_1d_pds'],
[md, roi_mask, qval_dict, avg_img,mask,pixel_mask, imgsum, bad_frame_list, qr_1d_pds] ):
Exdt[ k ] = v
elif scat_geometry == 'saxs':
for k,v in zip( ['md', 'q_saxs', 'iq_saxs','iqst','qt','roi_mask','qval_dict','avg_img','mask','pixel_mask', 'imgsum', 'bad_frame_list'],
[md, q_saxs, iq_saxs, iqst, qt,roi_mask, qval_dict, avg_img,mask,pixel_mask, imgsum, bad_frame_list] ):
Exdt[ k ] = v
elif scat_geometry == 'gi_waxs':
for k,v in zip( ['md', 'roi_mask','qval_dict','avg_img','mask','pixel_mask', 'imgsum', 'bad_frame_list'],
[md, roi_mask, qval_dict, avg_img,mask,pixel_mask, imgsum, bad_frame_list] ):
Exdt[ k ] = v
if run_waterfall:Exdt['wat'] = wat
if run_t_ROI_Inten:Exdt['times_roi'] = times_roi;Exdt['mean_int_sets']=mean_int_sets
if run_one_time:
for k,v in zip( ['taus','g2','g2_fit_paras'], [taus,g2,g2_fit_paras] ):Exdt[ k ] = v
if run_two_time:
for k,v in zip( ['tausb','g2b','g2b_fit_paras', 'g12b'], [tausb,g2b,g2b_fit_paras,g12b] ):Exdt[ k ] = v
#for k,v in zip( ['tausb','g2b','g2b_fit_paras', ], [tausb,g2b,g2b_fit_paras] ):Exdt[ k ] = v
if run_four_time:
for k,v in zip( ['taus4','g4'], [taus4,g4] ):Exdt[ k ] = v
if run_xsvs:
for k,v in zip( ['spec_kmean','spec_pds','times_xsvs','spec_km_pds','contrast_factorL'],
[ spec_kmean,spec_pds,times_xsvs,spec_km_pds,contrast_factorL] ):Exdt[ k ] = v
In [133]:
export_xpcs_results_to_h5( 'uid=%s_Res.h5'%md['uid'], data_dir, export_dict = Exdt )
#extract_dict = extract_xpcs_results_from_h5( filename = 'uid=%s_Res.h5'%md['uid'], import_dir = data_dir )
In [134]:
#extract_dict = extract_xpcs_results_from_h5( filename = 'uid=%s_Res.h5'%md['uid'], import_dir = data_dir )
In [ ]:
#pdf_version='_@Mar24_2' #for pdf report name
In [136]:
pdf_out_dir = os.path.join('/XF11ID/analysis/', CYCLE, username, 'Results/')
pdf_filename = "XPCS_Analysis_Report_for_uid=%s%s.pdf"%(uid,pdf_version)
if run_xsvs:
pdf_filename = "XPCS_XSVS_Analysis_Report_for_uid=%s%s.pdf"%(uid,pdf_version)
In [137]:
#%run chxanalys_link/chxanalys/Create_Report.py
In [138]:
make_pdf_report( data_dir, uid, pdf_out_dir, pdf_filename, username,
run_fit_form,run_one_time, run_two_time, run_four_time, run_xsvs, run_dose,
report_type= scat_geometry,
md = md )
In [139]:
if att_pdf_report:
os.environ['HTTPS_PROXY'] = 'https://proxy:8888'
os.environ['no_proxy'] = 'cs.nsls2.local,localhost,127.0.0.1'
pname = pdf_out_dir + pdf_filename
atch=[ Attachment(open(pname, 'rb')) ]
try:
update_olog_uid( uid= md['uid'], text='Add XPCS Analysis PDF Report', attachments= atch )
except:
print("I can't attach this PDF: %s due to a duplicated filename. Please give a different PDF file."%pname)
In [140]:
uid
Out[140]:
In [141]:
save_current_pipeline( NFP, data_dir)
In [142]:
get_current_pipeline_fullpath(NFP)
Out[142]:
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