B
    *XCaFB  ã               @   s$  d dl Z d dlZ d dlZd dlZd dlZd dlmZ d dlZd dlZd dl	Z
d dlZd dlm  mZ d dl	mZ d dlmZmZ d dlmZ d dlmZ d dlmZ d dlmZ d d	lmZ d d
lmZ d dlZd dlZd dlm Z  d dl!m"Z# ddd„Z$ddd„Z%dd„ Z&ddd„Z'dd„ Z(dS )é    N)Úsignal)Úpyplot)ÚconvolveÚBox1DKernel)Úinterpolate)ÚTime)Úcalc_shk)Ú
hk_windows)Úcreate_window)Úmulti_window_calc_shk)Ú	BlackBody)Úunitsé   Fc             C   sD  g }g }g }xlt  | ¡D ]^}t d|¡s*qt j | |¡}	tj|	dd}
t ||
d ¡}t ||
d ¡}t ||
d ¡}qW t 	|¡}t 	|¡}t 	|¡}t 
|¡}|| }|| }|| }|d }|d krÒ|d }|d krâ|d }||k||k@ }|d |d  }|s|d	 }n|}|dkr4tjj ||| ¡}|| || fS )
Nz^lmT)Úunpackr   r   é   é
   éÿÿÿÿg      $@)ÚosÚlistdirÚreÚmatchÚpathÚjoinÚnpZ
genfromtxtÚappendÚarrayÚargsortÚscipyÚndimageÚfiltersÚgaussian_filter)ZfluxdirZminwlZmaxwlÚ
resolutionZresidualZ
wavelengthZres_fluxZ
irradianceÚfÚfpathÚdÚsortZ	angstromsÚselZdwZseries© r'   ú'/home/travis/obs/LCO/nreshk/pipeline.pyÚimport_aligning_spectra8   s>     





r)   c             C   s    |d krt jdt jd}g }| t| |d  tjtjdƒ¡ | t| |d  tjtjdƒ¡ | t| |d  tj	tj
dƒ¡ | t| |d  tjtj
dƒ¡ |S )Né   )Údtyper   Tr   r   é   )r   ÚzerosZfloat32r   r
   ÚhÚcahLamÚlineWidÚcakLamÚlamRÚconWidÚlamB)ÚtarGridÚtargÚoffsetsÚwindowsr'   r'   r(   Úcreate_integration_windowsd   s        r9   c             C   sö  t | ƒ}t |ƒ}g g g}|d  t| tj|tj dƒ¡ |d  t|tj|tj dƒ¡ |d  t| tj|tj dƒ¡ |d  t|tj|tj dƒ¡ |d  t| tj|tj dƒ¡ |d  t|tj|tj dƒ¡ |d  t| tj	|tj dƒ¡ |d  t|tj	|tj dƒ¡ tj
ràt ¡  |d d }	t ||	dk ||	dk ¡ t ¡  t ¡  t ¡  |d d }	t ||	dk ||	dk ¡ t ¡  t ¡  t ¡  |d d }	t ||	dk ||	dk ¡ t ¡  t ¡  g }
x
tdƒD ]þ}|d | }|d | }| |dk }||dk }||dk }||dk }tj
rÄt ¡  |d | }	t | |	dk ||	dk ¡ t ¡  t ¡  t ¡  |d | }	t ||	dk ||	dk ¡ t ¡  t ¡  t||||d|ƒ}|
 |d ¡ |d }qðW |
S )Nr   Tr   Fr   r*   g{®Gázt?)Úlenr   r
   r.   r/   r0   r1   r2   r3   r4   ÚdebugÚpltÚfigureÚplotÚshowÚcloseÚrangeÚcalc_del_lam)ÚlabGridÚlabr5   r6   ÚscaleÚsmoothZllenÚtlenr8   Úcurr7   ÚiZcLabZcTarÚl1Úl2Úl3Úl4ÚoutÚ	labInterpr'   r'   r(   Úfind_window_offsetst   sd            rP   c             C   s®  d}|d |d  }t  dt|ƒ ¡ tjj ||| d ¡}| d | d  }	|}
tj| |
dd}||ƒ}d|d | 	¡ d d …< d|| 	¡ d d d …< t
j||dk< t
j||dk< t
 |¡}t
 |¡}d|t
 |¡< d|t
 |¡< t ||dk | ||dk | d d d… d¡}tt|ƒd d ƒ}td| ƒ}|| t
 ||| || … ¡ }d	}|t
 d| ¡ | }t
 |||| || … d¡}|d  d|d   }t jrät|ƒ t ¡  t tt|ƒƒ|d
¡ t ¡  t ¡  || |d |d   }t  dt|ƒ ¡ t jr¦tjdd\}}|jdd t d¡ t  d¡ t !d¡ t || |d¡ |dkr|tj"t j#dd |dkr–tj"t j$dd t ¡  t ¡  ||fS )Nr   r   zdlam: r   Zextrapolate)Z
fill_valuer   Úfullé   zk-zoffset )é   rR   )ÚfigsizeF)Z	useOffsetz1Unadjusted stellar spectra over reference spectrazWavelength (nm)zScaled irradiancezg-Zblue)ÚxÚcolor)%r.   ZdprintÚstrÚscr   r   r    r   Zinterp1dÚnonzeror   ÚnanZnanmeanÚisnanr   ZfftconvolveÚintr:   ÚargmaxÚarangeÚpolyfitr;   Úprintr<   r=   r>   rA   r?   r@   ZsubplotsZticklabel_formatÚtitleZxlabelZylabelZaxvliner1   r/   )rC   rD   r5   r6   rF   ZtmpDebugZtmpGridScaleZdLamZ	gausdTargZdLabLamZ	gausedLabZ
interpfuncrO   ZrmsxZrmsyZcorrelationZmiddleÚwidthZmvalZfitWidthZxRangeZpolyFuncZxValÚoffsetÚfigÚaxr'   r'   r(   rB   È   s\    


0"





rB   c             C   s¤  d}g }t  | ¡}g }g }x‚|D ]x}|g}	|j}
|
|kr>q"x<|D ]4}|j|jkrD|j|jkrD|j|jk	rnqD|	 |¡ qDW t|	ƒdkr”| |
¡ q"|j}|j}|jd k	r²|j	}n$x|	D ]}| |j¡ q¸W t
dƒ q"g }|j}g }x0|	D ](}| |j¡ | |j¡ | |j¡ qêW t||| ¡ |ƒ}|d }|j}t | ¡ ||j|j||jdd|¡	}| ¡ }|j}t
| ¡ ƒ tjdkr’t |j||d¡ |  |¡ q"W | S )Nr   r   z&sun_daily_data missing header very badTFg333333Ó?)r   ÚasarrayÚmjdÚhourÚdayZnOrdr   r:   ÚheaderÚsiter`   ÚlamGridZ	targOlapfÚwindowr   Úrawr.   ZanalyzedDataÚflatrc   Ú	outputDirÚ	decimalYrÚlabelZpdfModer>   Zpdf_from_intermediate_data)ZinDataZstarNameZlabSpecÚrvÚdoneZallDataZ	datesListZ
sortedListZcurDZsameDZcurMjdÚtrj   rg   rk   r$   ZtargListrl   Z
windowListri   ZshkRetZshkr8   ZcombDatarp   rq   r'   r'   r(   Úsum_daily_data‚  sX    





$rv   )NNr   F)N)r   ))r   Úos.pathr   r   Zscipy.signalr   Zscipy.ndimage.filtersÚnumpyr   Ú
matplotlibZmplrX   Znumpy.polynomial.polynomialZ
polynomialÚpolyr   r<   Zastropy.convolutionr   r   r   Zastropy.timer   r   r	   r
   r   Zplottingr>   Úhelpersr.   Zastropy.modeling.modelsr   Zastropyr   Úur)   r9   rP   rB   rv   r'   r'   r'   r(   Ú<module>   s8   

,
T
 ;