{uKPc @ sd d Z d d l Td d l Z e j d d d l Td d l Z d d l m Z m Z m Z m
Z
m Z m Z m Z d d l
Z
d d l m Z d d l m Z d d l m Z d d l Z d d l m Z d d l Z d d l Z d d l Z d d l Z d d l Z d d l Z d d l Z d d
l m Z m Z e! d d d
d d e" d .
f
i( t *Nt agg( t mktimet strptimet sleept asctimet localtimet struct_timet time( t leastsq( t interpolate( t stats( t erf( t
NullFormattert ScalarFormattert precisioni t linewidthi t Aggt backendc C s t t | t | d S( s#
Median absolute deviation
g)Ǻ?( t mediant abs( t x( ( s\ ../includes/diagnostics/Radiation/1111Spectrometer.ON/ControlSoftware/SpectrometerControl.pyt MAD> s c
C s | d k r- t | | k r- t d n t t | } x< t | D]. } | | d | d c !| | |
| !7+qL W| t | :} t | | d d | | d *t | | d d | | d )| S( s
Simple moving average
i s/ subset_size must be > 1 and less then len(data)i ( t lent
ValueErrort zerost sizet ranget floatt mean( t datat subset_sizet mvavgt i( ( s\ ../includes/diagnostics/Radiation/1111Spectrometer.ON/ControlSoftware/SpectrometerControl.pyt
MovingAverageD s , "c C su t j t t | | } | } d } t | d | d | d | d t | | t t | d } | d } | d } t | d } | d } | d } t | d t d t
| d t | | | d d d t | | | t d | d | | d t
| d | | d | d }
t
|
t |
| | f }
t |
d | }
|
S( s
The most general line shape. xc is position, A amplitude, w width, a skewness, n voitig profile
Line profile is integrated over single pixels
i
i iii i i i ( R
t interp1dt arangeR t linspaceR R t diffR t sqrtt pit expR t reshapet sum( t pR t x_interpt x0t mt xct At wt at nt y( ( s\ ../includes/diagnostics/Radiation/1111Spectrometer.ON/ControlSoftware/SpectrometerControl.pyt UniversalLineShapeV s H
c C s^ t d } | d } | d } t | d | d <| t d | d } | d | d <| d d | | d | t d t | d <| d d | } d | | d t d d | d t d t d t d } d | t d | d | d | d >)7
c s | } | d t | } | | } x> | k rj | t d k rj } d 7 q- W | } | xF d k r | d t d k r d } d 8 q~ W d d k rt | d t d d n | t d t t j d d d f d } | t j d d d f | f } f d }
t |
| d | !d d \ } } }
} } t | d k rt
d- t } n j | } t
|
d |
d } d } d
| d t | d. | t | d f GH| t j j j d | k ra| | | 9} n j | d t | d/ \ } } } | d d k rt | d s t argst full_outputt fvecs. wavelength %4.3f +/- %1.3f; chi^2/doF: %4.2fg?i t rt wheret midt bt postt yerrt fmts r.s b.id s b--t .R5 i t lss --t labelt thresholds wavelength %4.3f +/- %1.3fR s -.t ct gs Center of massR/ t kt tights $\lambda$ [nm]s SNR[-]t loct bests6 wavelength %4.3f +/- %1.3f; chi^2/doF: %4.2f, A: %4.1f( i i ( i i ( i i ( i i ( R R R R/ R5 R ( i i (* R R' R t maxR( R t
inst_widthR R Ro t onest nanR< R+ t scipyR t chi2t isfR t clfR$ R
R# t stept errorbarR% t amint amaxR R t axhlinet axvlinet enumeratet axisR R t legendt titleR R& R t diag( RH t ix0R R t plot_fitt ynR4 R. R3 t p0t funt poptt pcovt infot mesgt successt popt_corrt chisqt doFt line_namet lineR t intervt w_interpt crop_wt
crop_w_100t crop_w_1t colourR! t elementt jR9 ( ( R R RH R s\ ../includes/diagnostics/Radiation/1111Spectrometer.ON/ControlSoftware/SpectrometerControl.pyt peakFitting sx
)
-9(1- )
)
D-1.. * # 3
0
%%c
C s d GHt } t } t | } t | } d } t j j j d | | d d }
| | :} d } xwt r| d 7} | d k r d GHPn t | | d k d d t | } | d | | d | | d | d +t
| |
k r Pn t | }
t | t d |
| t
|
| | ! t d |
| }
| |
} | rt | | d
d t d | d
d d d t d t t | t | t n | j |
| | | \ } } } } } } | j | | | d d | d <| j | | | d d | d <| t j j d | | d 9} | j | | | d | d | d | d | d | | d f t d | | | !| | | !f t t | d d t
| | j d d } t j t | | |
*!!!A!0 (
R R R RI R R R R R R ( ( ( s\ ../includes/diagnostics/Radiation/1111Spectrometer.ON/ControlSoftware/SpectrometerControl.pyR s # ( xt OceanOptics_Specc B sw e Z d Z d Z d Z d Z d Z d Z d Z e d Z
d Z d Z d
Z
d d Z RS(
sD child of class Spectrometer with the Ocean Optics specific functionsc C sL t j | | | t d | _ d | j d ./data/nohup_java.out &(
RR t removeRp t shutilt copyfileR R R= R[ t integTime( RH R+ t java_libraryt run_options( ( s\ ../includes/diagnostics/Radiation/1111Spectrometer.ON/ControlSoftware/SpectrometerControl.pyt start s
/c C sB t | } x/ t | j D] \ } } | | | | 7} q W| S( s,
Apply the wavelength correction polynome
( t copyR t calibrationPolynomeCorrection( RH t old_wavelengtht
new_wavelegthR! R3 ( ( s\ ../includes/diagnostics/Radiation/1111Spectrometer.ON/ControlSoftware/SpectrometerControl.pyt wavelengthCorrection5 s c C s d } t j j | j d s1 t d n t j } | j | j d | j d d } | | j k r t d n | j d d | _ | j d d | _
| j d d | _ | j d d
| _
| j d d } t | | | _ | j d d | _ | j d d
| _ | j d d } | | | _ | j d d } | | | _ y% | j d d } | | | _ Wn t j k
r} d | _ n Xy% | j d d } | | | _ Wn t j k
r} d | _ n X| j d d } | | | _ | j d d | _ | j d d } | | d | _ | j d d } | | d | _ | j d d } | | d | _ | j d d } | | d | _ | j d d } | | | _ t j! | j d d d f | j d d d f d t" d d | _# | j d d! } | | | _$ t j! | j$ d d d f | j$ d d d f d t" d d | _% | j d d" | _& d# G| GHd S($ s3
Load the configuration file of the spectrometer
c S s} | j } t } x[ | D]S } | j d j } | j t x% | D] } | d j t | qN Wq Wt | S( Ns []i( t
splitlinesRC Rb Rc RF R t array( R t fieldR t rowt col( ( s\ ../includes/diagnostics/Radiation/1111Spectrometer.ON/ControlSoftware/SpectrometerControl.pyt parseStringOfFieldF s
s .cfgs) Spectrometer config file does not exists.s Basic parameterss
Serial Numbert WrongSerialNumbert Detectors Optical gratings Wavelength presicion [nm]s Minimum integration time [ms]s Opticaly black pixelss Resolution [px]s min photons/countt Efficienciess Gratting efficiencys Sensor efficiencys Absolute calibrations Overall effectivitys! optical fibers attenuation (dB/m)s fiber lengths Other propertiess Calibration polynome correctioni s Linearity polynome corrections
Hot pixelss wavelength ranges Instrumental broadening functions width(wavelength)Ni R R s skewness(wavelength)s voitig parameters Loaded data of (' RR RS RT R RU RV RW RX RY t detectort
GratingTypRZ R t min_integ_timet int_t black_pixelsR^ R R R R R t
NoOptionErrorRo R R R R5 t linearityPolynomeCorrectiont hotPixelsR R R
R# R t F_inst_widtht
inst_skewnesst F_inst_skewnesst voitig_parameter( RH R> Rd R t tmpstrt err( ( s\ ../includes/diagnostics/Radiation/1111Spectrometer.ON/ControlSoftware/SpectrometerControl.pyR@ B sb
GGc C s; t j } | j d | j d d d | j d d | j | j d d | j | j d d | j | j d d t | j d d | j | j d d | j | j d d
| j
| j d d | j | j d d | j | j d
| j d
d | j
| j d
d | j | j d
d | j | j d
d | j | j d | j d d | j | j d d | j | j d d | j | j d d | j | j d | j d d | j | j d d | j | j d d | j t | j d d } | j | Wd QXd S( s3
Save the configuration file of the spectrometer
s Basic parameterst Types Ocean Optics Spectrometers
Serial NumberR@ s Optical gratingt Dates Wavelength presicion [nm]s Opticaly black pixelss Resolution [px]s Minimum integration time [ms]s min photons/countRA s Gratting efficiencys Sensor efficiencys! Optical fibers attenuation (dB/m)s fiber lengths Other propertiess Calibration polynome corrections linearity polynome corrections
Hot pixelss wavelength ranges Instrumental broadening functions width(wavelength)s skewness(wavelength)s voitig parameters .cfgRf N( RV RW Rh Rg R RB RC R R RF R RD R R R R R R5 RH RI R R RK RM Ri Rj ( RH Rd Rk ( ( s\ ../includes/diagnostics/Radiation/1111Spectrometer.ON/ControlSoftware/SpectrometerControl.pyRl s8
c C s d S( N( ( RH ( ( s\ ../includes/diagnostics/Radiation/1111Spectrometer.ON/ControlSoftware/SpectrometerControl.pyt checkCalibration s c C s d S( N( ( RH t dryRun( ( s\ ../includes/diagnostics/Radiation/1111Spectrometer.ON/ControlSoftware/SpectrometerControl.pyt makeCalibration s c C so t d } | d | d *t | d d | j | d d | d <| j | d | d <| j | d <| S( s
The lines are not fitted by full set of paramathes of the general peak function UniversalShape. Only a few paramethers are used, other are calculated here.
i i i i i ( t emptyR' RJ RL RM ( RH R, t p_full( ( s\ ../includes/diagnostics/Radiation/1111Spectrometer.ON/ControlSoftware/SpectrometerControl.pyt calcParamsForFitting s -
c C s | j | } t | | S( N( RW R6 ( RH R, R RV ( ( s\ ../includes/diagnostics/Radiation/1111Spectrometer.ON/ControlSoftware/SpectrometerControl.pyR s c C sR | j | } t | } t | d d | j | d d | d d ! | _ n | j7 d? } | d k rt
| | d@ d ! | _ n | j7 dA } | d k rt
| | d4 d ! | _ n | j7 dB } | d k rHt | | d d ! | _ n | j7 dC } | d k rt | | d d ! | _ n | j7 dD } | d k r| | d d !}
t8 |
j9 dE j: | _ n | j7 dF } | d k r t | | d
d ! | _) n | j7 dG d k r Pq q W| | j k rO t d | d | j n | j' | j) d: k rt d: | _) n t | j d } t& | d2 | } | j' | dH dH d f | _( xT t* | j D]C } | j+ j, t- | | j( | dH dH | d. f | j | q Wt | j | _3 t | j | _5 n | dI k r
t; | _ | | _ t j j | j dJ s
t d | j dJ d n t& | j dJ | _( t< t6 t= | j( | j> d t6 t? | j( | j> d. d: k r, t dK t= | j( t? | j( | j> d | j> d. f n t j j | j dL sc t d | j dL d n t | j dL d } xV t | D]H \ } } | d. k r t
| | _ n | dM k r t | | _ q q W| j' t j@ | j dL jA | _ dN | _ t j j | j dO s8 t d | j dO d n t& | j dO d2 d, } | dH dH d f | d | j j | _ t j j | j dP r t& | j dP | _ n x t% | j D] } t j j | j dQ tB | d. d s
t d | j dQ tB | d. d d n tC | j dQ tB | d. d } | t4 | 8} | j+ j, t- | | j( | | j | q WtD | | _) n | dR k rt; | _ | | dS | _ t j j | j s
t d | j d n tE jF | j d } tG | jH d, | _ x| jH D]y} | dT k r&| dU k r&| jI | jJ } t
| d | d. | d, | dM | dV | d8 d d d f | _ | j | } x t | D] \ } } | j7 dW d k r| j7 dW } t
| | d4 dX ! | _ n | j7 dY d k rF| j7 dY } t
| | d dZ ! d | _ n | j7 d[ d k r| j7 d[ } | d\ | d] !} qqW| | j k rt d | d | j n | j' | j | } d } t | j } t | j | _( tK } tK } tK } x_t | D]Q\ } } | j7 d^ } | j7 d_ d k rMtL } d } n | j7 d` d k rktK } n | j7 da d k rtL } d } n | j7 db d k rtK } n | j7 dc d k rtL } d } n | j7 dd d k rtK } n | d k r| r%| r%t | | de df ! | | d t6 t? | j( | j> d. d: k r[t dK t= | j( t? | j( | j> d | j> d. f q[n | j | jP k rt d tB | j d tB | jP n | S( s!
Load data from file and create object "shot" containig all necessary informations andou the tokamak shot. It supports many different types of files.
Java_Data_file - file experted from java control program HighSpeedAcquisitionSample.java
Python_Data_file - file exported from this python program
SpectraSuite_xml - file exported from OceanOptics SpectralSuite
SpectraSuite_txt - acsii file exported from OceanOptics SpectralSuite
SpectraSuite_HighSpeed - ascii file exported from OceanOptics SpectralSuite after high speed acquisition
t Java_Data_files .txts
Data file s does not exists.R i s Date and time:i is %Y.%m.%d %H:%M:%Si s Number of spectra:i i s Number pixels in spectra:i i s Integration time [us]:i g @@s Board temperature [C]:i s Spectrometer S/N:s Exact time stamps:s wrong serial number, s != s \s[0-9]+\.[0-9E]+i g .AR R s exposure times from timestampsR5 R s --s exposure time R R s _diff_timestamps.pngt bbox_inchesR s
read out times ; i g ?i s background.txtR i t skip_headers readoutpatterns.txti s RMS^2 of signal:t RMSi i i i
t Python_Data_files
Serial Numbers Date and time (GMT)i s Number of spectrai t
Resolutions Integration time [ms]s Board temperature [C]s Time stamps [ms]s []s Noise RMSs ***************Nt VW_javas wavelength_axis.txts' bad wavelength range %d - %d != %d - %ds settings.txti i s
timing.txts temperature.txtt spectrum_t SpectraSuite_xmls .ProcSpecs OOISignatures.xmls OOIVersion.txti s is is i is s1 s2 s s s
s i it SpectraSuite_txtc S s t | j d d S( Nt ,R ( R Ra ( R ( ( s\ ../includes/diagnostics/Radiation/1111Spectrometer.ON/ControlSoftware/SpectrometerControl.pyR M s t skip_footert
converterss SpectraSuite Data File
s wrong file types corrupted header of files Date:i s %a %b %d %H:%M:%S %Z %Yi$ s$ Number of Sampled Component Spectra:i% s Number of Pixelsis Integration Time (usec):it (t )s Spectrometers:s Spectrometer Serial Number:is Spectra Averageds >>>>>t SpectraSuite_HighSpeeds wrong number of pixels, ( i i (Q t ShotR= RA t DataFileRR RS RT RU Ri R R R R R t n_spectrat n_pixelsR R t temperatureR R t time_stampst ret searcht groupR\ RD R R R& R R0 t ylimRo R t savefigR R$ t
genfromtxtR| R R R RY RF t Spectrumt stdRF R' Ra t isalnumt darkNoiseR t readOutPatternsR R& t float_Rb Rc R R t nanminR t nanmaxR R R RG R t zipfilet ZipFileR t namelistt getinfot date_timeR R t readlinet getctimeR R ( RH RS t typR? t shotR R! R t SNR/ R R R t imaxt integ_time_backgroundt integ_time_readoutpatternst line_headert indt timest myzipR t linesR t channelWavelengthst
sourceSpectrat pixelValuesR t replaceCommaRz t n_avert
first_line( ( s\ ../includes/diagnostics/Radiation/1111Spectrometer.ON/ControlSoftware/SpectrometerControl.pyt loadData s`
" (
)2
#)$
0%
# !
A I?
++0%- B !
!
,# 0" #
! &
!-"IB-( R R R RI R3 R8 R@ Rl RR R RT RW R R< R ( ( ( s\ ../includes/diagnostics/Radiation/1111Spectrometer.ON/ControlSoftware/SpectrometerControl.pyR s 3
O ' Rj c B s e Z d Z d Z d Z e e d Z d e d Z d e e d d Z
d e e d e d Z e d Z d e d e d
Z
d Z d e e e d
Z RS( sR Discharge container class
used for plotting and obtaining discharge data
c C s | | _ | | _ t | _ t | _ t | j | _ t | j | _ d | _
d | _ d | _ t d | _
d | _ d S( Ni
i i R ( R t shot_numRC RY R R R R Rz Ry R t maxSNRRl Ro Rk ( RH R R ( ( s\ ../includes/diagnostics/Radiation/1111Spectrometer.ON/ControlSoftware/SpectrometerControl.pyRI s c C sP t | j d d } x. t | j D] } | j | j | | t | j d d D]' } | j | d j rF| } PqFqFWt
| | j d } d } x8 t | j D]' } | j | j r| d } PqqWt d | } |
| } |
| } t | d
d } t
| d d d d d } x t | D] \ } } | | k rEPn | | d k g } | s}t | d | d g t d d } t d d } t d d } t d } t d | } x| D]} d } t | | k r} d } n t | | k r d } n d
t | GH| | _ d t | d } y t j | } Wn d
t | d
GHqV n Xt d t | d d } | j
| j | j | j
d d d t | }
t | j } x- |
j D]" } | j ri| | j 7} qiqiWd }
x t | j D] \ } } x? t | d D]- \ } } t d | d |
| t |
qWt d | d d t | d | t |
j | t qWqV Wd S( Ni i{ i i R s HR+C1886R t Het Hs shot number s* http://golem.fjfi.cvut.cz/operation/shots/sE /diagnostics/Radiation/1111Spectrometer.ON/data/spectra.txt_Data_.txts does not existR s .txtR2 R^ R R R R/ R5 R i R s ion: i s ; shot #s ; fill gas: ( R R R R/ R5 R ( R R$ R= R R R RA R R Ri Rj RX R| R R R RY R R R RD R R R R R R ( R$ t He_gast H_gasR R R t gasR R R R t integ_spectrumR R R! R R R ( ( s\ ../includes/diagnostics/Radiation/1111Spectrometer.ON/ControlSoftware/SpectrometerControl.pyt Example7M sD
%(c
C s t d } t d | } x | D] } t j j d t | d rN q" n d t | GH| | _ d t | d } y t j | } Wn d t | d GHq" n Xt d t | d d } | j
| j | j q" Wxt
rd
GHt d } | d k rd
} n t | } t d } | d k rGd } n t | } t }
x4 | D], } |
j | j d d d t | qcWt } x] |
D]U } | j t | j x6 | j D]+ }
|
j r| d c |
j 7 RX RY R ( ( ( s\ ../includes/diagnostics/Radiation/1111Spectrometer.ON/ControlSoftware/SpectrometerControl.pyt sj
4
J ^ # 3 $ . ? W l