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  Classes needed for the known pulsar search pipeline.

  (C) 2006, 2015 Matthew Pitkin

é    )Úprint_functionÚdivisionz(Matthew Pitkin <matthew.pitkin@ligo.org>z$Date$z
$Revision$N)Úpipeline)ÚRawConfigParser)Údeepcopy)Úoptimize)ÚOrderedDict)Ústring_types)Úpulsarpputilséÿÿÿÿé   z2Error... an error has occurred during DAG creationz@No required data segments were available to perform the analysiséf   c               @   s¦   e Zd Zd,dd„Zdd„ Zdd„ Zdd	„ Zd-dd„Zd.dd„Zd/dd„Z	dd„ Z
dd„ Zdd„ Zdd„ Zd0dd„Zd d!„ Zd"d#„ Zd$d%„ Zd&d'„ Zd(d)„ Zd*d+„ ZdS )1ÚknopeDAGNc       ,         s  dˆ _ dˆ _|ˆ _|dk	r>t|tƒr,|ˆ _ntdƒ tˆ _ dS ˆ jdddddˆ _	d}ˆ j	rÌˆ  dd	¡}|dkrˆtd
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jd tˆ _ dS q,W ˆ j	ršx4ˆ jD ]*}||jkrltdt
jd tˆ _ dS qlW ˆ jddddgdˆ _tˆ jƒdkrÐtdƒ dgˆ _tˆ jƒdkr
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td ƒ ddgˆ _x*ˆ jD ] }	|	d!krtd"ƒ dgˆ _qW ˆ j	rtx4ˆ jD ]*}	|	|jkrFtd#t
jd tˆ _ dS qFW ˆ j	s ˆ jdd$d%d&ˆ _ˆ j dkr¨dS n|jˆ _ˆ j	sâx0ˆ jD ]&}ˆ  ˆ j| ¡ ˆ j dkr¸dS q¸W ˆ  dd'¡ˆ _ˆ j dkr dS t ˆ j¡ˆ _tˆ jtƒrHi }
xˆ jD ]}ˆ jg|
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jd tˆ _ dS q^W xÀtˆ jƒD ]˜}tˆ j| tƒrÂˆ j| gˆ j|< nltˆ j| tƒrtd)d*„ ˆ j| D ƒƒtˆ j| ƒkr.td(t
jd tˆ _ dS ntd(t
jd tˆ _ dS q˜W ntd(t
jd tˆ _ dS ˆ  dd+¡ˆ _ˆ j dkrldS t ˆ j¡ˆ _tˆ jtƒr´i }xˆ jD ]}ˆ jg||< q”W |ˆ _ntˆ jtƒr¢x4ˆ jD ]*}|ˆ jkrÊtd,t
jd tˆ _ dS qÊW xÀtˆ jƒD ]˜}tˆ j| tƒr.ˆ j| gˆ j|< nltˆ j| tƒr‚td-d*„ ˆ j| D ƒƒtˆ j| ƒkrštd,t
jd tˆ _ dS ntd,t
jd tˆ _ dS qW ntd,t
jd tˆ _ dS i ˆ _xZˆ jD ]P}tˆ j| ƒtˆ j| ƒkrtd.t
jd tˆ _ dS tˆ j| ƒˆ j|< qÈW ˆ j	shˆ jdd/d0d1ˆ _ˆ j dkrFdS ˆ jd2krptd3ˆ j ƒ d0ˆ _n|jˆ _ytj d4 }W n   d}Y nX ˆ jdd5d|dˆ _!ˆ j dkr´dS ˆ jd6d7d8d1ˆ _"ˆ j dkrÖdS d9ˆ j"krútd:t
jd tˆ _ dS | #d6d;¡r.| $d6d;¡ˆ _%tˆ j%ƒdkr4dˆ _%ndˆ _%ˆ jddt ¡ d1ˆ _&ˆ  ˆ j&¡ ˆ j dkrfdS ˆ  dd<¡ˆ _'ˆ  ˆ j'¡ ˆ j dkrdS t(t) *¡ j+ƒ}ˆ jdd=d>| d? d1}t|ƒdkrÐd@| d? }tj, -ˆ j'|¡ˆ _.t/j0 1ˆ ˆ j.¡ ˆ jdd=d>| d1}t|ƒdkrd@| }ˆ  2tj, -ˆ j&|¡¡ ˆ jddAdddˆ _3ˆ j dkrVdS ˆ j3r¬ˆ jddBdCd&}ˆ j dkr~dS i ˆ _4xˆ jD ]}|gˆ j4|< qŒW ˆ j4ˆ _4nˆ jˆ _4ˆ  ddD¡ˆ _5tj, 6ˆ j5¡	s tj, 7ˆ j5¡	s tdEˆ j5 t
jd tˆ _ dS ˆ j		r.|j5ˆ j5k	r.tdFt
jd tˆ _ dS g ˆ _8g ˆ _9g ˆ _:tj, 6ˆ j5¡	r¦‡ fdGd*„t ;ˆ j5¡D ƒˆ _<tˆ j<ƒdk	rštdHˆ j5 t
jd tˆ _ dS ˆ j< =¡  n:tj, 7ˆ j5¡	rÂˆ j5gˆ _<ntdIˆ j5 t
jd tˆ _ dS i ˆ _>i ˆ _?ˆ j	s~xJˆ j<D ]>}yt@ A|¡}W n&   tdJ| ƒ dKˆ j?|< 	wþY nX dL|jBk
r`tdM| ƒ dNˆ j?|< 	qþ|dk	
r||dL |k
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r¼tdQ||f ƒ dR| ˆ j?|< 	qþ|dS dkr|dS dTkrtdU|dS |f ƒ dV|dS  ˆ j?|< 	qþ|dW dkrH|dW dXkrHtdY|dW |f ƒ dV|dW  ˆ j?|< 	qþ|ˆ j>|dL < tj, -tj, C|¡dZtj, D|¡ ¡}tj, 7|¡s¶ˆ j9 E|¡ t F|¡jG}ˆ j: E|t(|ƒd[œ¡ n†t(t F|¡jGƒ}t|d\ƒ}y| H¡  I¡ }W n   td]| ƒ d^}Y nX | ¡  ||krˆ j8 E|¡ nˆ j: E||d[œ¡ ˆ j9 E|¡ 	qþW |dk	r~tˆ j>ƒdkr~td_d` -|¡ˆ j5f ƒ tˆ _ dS g ˆ _Jˆ j	sÊˆ  K¡  ˆ j dkr¤dS ˆ jddadddˆ _Lˆ j dkrždS nÔdˆ _Ldˆ _M|dkr
|j8ˆ _8|j9ˆ _9|j>ˆ _>|j?ˆ _?|jNˆ _Nn”i ˆ _NxŒ|D ]„}||j>kr@tdb||f ƒ tˆ _ dS ||j8kr\|j8| ˆ j8|< ||j9krx|j9| ˆ j9|< |j>| ˆ j>|< |jN| ˆ jN|< qW ˆ jLr0x4ˆ j:D ]*}t|dc ddƒ}| O|de ¡ | ¡  q®W xNˆ jJD ]D}tPjQdf|d  dg |dh  didj}| R¡  |jSdkrätdkƒ qäW dS ˆ  T¡  ˆ j dkrHdS ˆ  U¡  x4ˆ j:D ]*}t|dc ddƒ}| O|de ¡ | ¡  qXW xNˆ jJD ]D}tPjQdf|d  dg |dh  didj}| R¡  |jSdkrŽtdkƒ qŽW ttj, -ˆ j&dl¡ddƒ}tVjWˆ j>|ddm | ¡  ttj, -ˆ j&dn¡ddƒ} tVjWˆ j?| ddm |  ¡  ˆ jddodidp}!|!dkrdq|!krhtdr|! ƒ n¤ddlX}"ddlY}#y~y"|# Z¡ }$tj ds }%|%dq |$ }&W n   dt}&Y nX du}'dv|ˆ j[f }(dw})|) \|&|!|'|(¡}*|" ]dx¡}+|+ ^|&|!|*¡ |+ _¡  W n   tdyƒ Y nX dS )zz¾
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isinstanceÚint)Ú.0Úvr   r   ú`/work/yifan.wang/ringdown/master-ringdown-env/lib/python3.7/site-packages/lalapps/knope_utils.pyú
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ephem_pathÚcondorÚaccounting_groupz!ligo.prod.o1.cw.targeted.bayesianzcw.targeted.bayesianzEError... the 'accounting_group' should contain 'cw.targeted.bayesian'Úaccounting_group_userÚlog_dirZdag_namezknope-z.logzknown_pulsar_pipeline-Ú
autonomousZautonomous_initial_startr   Úpulsar_param_dirz=Error... pulsar parameter file/directory '%s' does not exist!zkError... for 'post-processing-only' the pulsar parameter directory must be that same as in the previous runc                sD   g | ]<}d |krt j t j ˆ j|¡¡rd|krt j ˆ j|¡‘qS )z.parz.mod_)ÚosÚpathÚisfileÚjoinr-   )r    Úpf)Úselfr   r"   r#   E  s    z0Error... no pulsar parameter files found in '%s'z?Error... pulsar parameter file or directory '%s' does not existz<Could not read in parameter file '%s'. Skipping this pulsar.z Could not read in parameter fileÚPSRJz<Could not read 'PSRJ' value from '%s'. Skipping this pulsar.zCould not read 'PSRJ' valueÚBINARY)	ZBTZBT1PZBT2PZBTXZELL1ZDDZDDSZMSSZT2zABinary type '%s' in '%s' is not recognised. Skipping this pulsar.z,Binary type '%s' is currenlty not recognisedÚEPHEM)ZDE200ÚDE405ZDE414ZDE421ZDE430ZDE435ZDE436z9Unregconised ephemeris '%s' in '%s'. Skipping this sourcezUnregconised ephemeris '%s'ÚUNITS)ÚTCBÚTDBz:Unregconised time units '%s' in '%s'. Skipping this sourcez.mod_)r   ÚtimeÚrzPWarning... could not read modification time from '%s'. Assuming file is modifiedgÞƒBÊÀó¿zPCould not find any of the listed pulsars '[%s]' in the .par file directory '%s'.z, Úpreprocessing_onlyzSError... specified pulsar '%s' could not be found in previous run pickle file '%s'.r   Úwr;   zcat z >> é   T)ÚshellznWarning... could not append segments to previous segments file. No log of previous segments will be available.zanalysed_pulsars.txt)Úindentzskipped_pulsars.txtÚemail)Ú	allownoneú@zGWarning... email address '%s' is invalid. No notification will be sent.ÚUSERzmatthew.pitkin@ligo.orgzlalapps_knope: successful setupz¢Hi User,

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Regards

lalapps_knope
z#From: {0}
To: {1}
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error_codeÚwarning_codeÚconfigr   r   Ú
pulsarlistÚprintÚKNOPE_ERROR_GENERALÚget_config_optionÚpostonlyÚsysÚstderrÚopenÚpickleÚloadÚcloser.   ÚgetcwdÚrundirr   r   Úlenr   Úmkdirsr   ÚastÚliteral_evalr   r   r$   Ú	ndatasetsÚengineÚenvironr'   r)   Ú
has_optionÚgetr*   r   r+   ÚstrÚuuidÚuuid4Úhexr/   r1   Z
daglogfiler   Ú	CondorDAGÚ__init__Zset_dag_filer,   Úinitial_startr-   Úisdirr0   Úunmodified_pulsarsÚmodified_pulsarsZmodification_filesÚlistdirZparam_filesÚsortÚanalysed_pulsarsZskipped_pulsarsÚpppuÚpsr_parÚ__dict__ÚdirnameÚbasenameÚappendÚstatÚst_mtimeÚreadlineÚstripÚsegment_file_updateÚsetup_preprocessingr=   Ú
remove_jobÚprocessed_filesÚwriteÚspÚPopenÚcommunicateÚ
returncodeÚsetup_parameter_estimationÚsetup_results_pagesÚjsonÚdumpÚsmtplibÚsocketÚgetfqdnÚresults_urlÚformatÚSMTPZsendmailÚquit),r3   ÚcpZconfigfilenamerJ   ZprevdagZpreprocessed_pickleÚfpZallowed_ifosÚifoÚffZstdictZstkeyZetdictZetkeyZdefaultephempathZuniqueidZdaglogZdagnameZinitialstartÚparÚpsrZbintypeZmodtimefileZmodtimeZ
parmodtimeÚfmZ
oldmodtimeZpsrlÚpitemZsfsÚpZfpaZfpsrB   r„   r…   ZHOSTrE   ZFROMÚsubjectZ
messagetxtZemailtemplateÚmessageÚserverr   )r3   r"   re   4   sÄ   
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      
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zknopeDAG.__init__c       -   
   C   sÚ  |   dd¡| _i | _i | _i | _|  | j¡ | jdkr:dS |   dd¡| _| j dddd| _| j dd	d
d| _	t
j | j¡rŠt
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j | j¡rôt
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set_sourceÚset_destinationÚpe_nest2pos_nodesÚ
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set_configÚpe_nest2pos_background_nodesÚcollateNode)-r3   Z
resultexecZcollateexecZcpjobZresultpagejobZ
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 
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zknopeDAG.setup_results_pagesc             C   sv   |   ¡  | jdkrdS | jdkr6|  ¡  | jdkr6dS | jdkrV|  ¡  | jdkrVdS d| _|  ¡  | jdkrrdS dS )zq
    Setup the preprocessing analysis: data finding, segment finding and heterodyne/splinter data processing
    r   Nr%   r&   )Úsetup_datafindrG   r\   Úsetup_heterodyneÚsetup_splinterry   Úconcatenate_files)r3   r   r   r"   rx   …  s    
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 zknopeDAG.setup_preprocessingc       /      C   sþ  | j dddd| _| jdkr dS tj | j¡r>t | jtj¡svtdƒ |  	d¡}|dkrptdt
jd	 t| _dS || _| j dd
dd| _| jdkr–dS i | _i | _t| jƒdkr¸d| _n| j ddddd| _d| _t| jƒdkrô| j ddddd| _| j ddddd| _| jdk r"tdƒ d| _| j dddd| _|  | j¡ | jdkrPdS | j ddddd| _| jdkr°| jdkr”tdt
jd	 t| _dS |  | j¡ | jdkr°dS | j ddddd| _| j ddddd| _| j dd d!d"d| _| j dd#ddd| _| j dd$ddd| _| j dd%dd&d| _| j dd'ddd| _| j dd(d!dd| _| j dd)d!dd| _ | j dd*d!dd| _!| j dd+ddd| _"| j dd,d!dd| _#| j dd-ddd| _$| j dd.dd/d| _%| j dd0ddd| _&| j dd1dd2d| _'| j dd3d!d4d| _(| j dd5ddd| _)| j dd6dd7d| _*| jrBtd8ƒ d| _| j dd9d:d| _+| j+d;krttd<| j+ ƒ d:| _+d| _,t| j-ƒd=krª| jdkrª| j dd>ddd| _,| j dd?ddd| _.| j/d@krÐd| _.| j ddAdBd| _0| j ddCddD| _1| j1dk	r0tj | j1¡s0tdE 2| j1¡t
jd	 t| _dS | j ddFddd| _3| j3r| j ddGddD| _4d| _5| j ddHddD| _6d| _7i | _8yt9 :| j ddIddD¡| _;W n   | j ddIddD| _;Y nX yt9 :| j ddJddD¡| _<W n   | j ddJddD| _<Y nX | j ddKdLd| _=| j ddMddd| _>| j ddNdOd| _?| jdkrBdS tj | j?¡rdt | j?tj¡sžtdPƒ |  	dO¡}|dkr˜tdQt
jd	 t| _dS || _?|   ddR¡| _@| j@dkrÐtdSt
jd	 t| _dS |  | j@¡ | jdkrìdS | jdkrF|   ddT¡| _A| jAdkr*tdUt
jd	 t| _dS |  | jA¡ | jdkrFdS | j ddVddd| _B| j ddWddd| _CtD| j| j| jE| jF| jG| jH| jCdX}tI| j?dY| jE| jF| jG| jHdZ}tJ| jE| jF| jG| jHd[}| jKdkrîtL| jE| jF| jG| jHd[}n| jK}g | _Mx,| jD ]"}| js| jM N|g|d\œ¡ qW | jsL| jM N| jd] O| j¡d\œ¡ i | _Pi | _Qi }| jd }	xtR|	ƒD ]‚}
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qdW t! 9t| j)ƒ¡}0x|+D ]}.|0dM|.  }0q|W t! :dM|0 ¡}0df|0 }1| j(dJkrdM| j)kræ|!dN dkræ|1| j) ;dM¡ | |!dN< dK| j)kr|!dL dkr|1| j) ;dK¡ | |!dL< | j(dOkr¬t| j)ƒdkrT|!dP dkr¬|1d | |!dP< nXdM| j)kr¬dK| j)kr¬|!dQ dkrŒt! <|1¡| |!dQ< |!dR dkr¬t! <|1¡| |!dR< | j=dgkrÚ|dkrÚtdhtjd t| _	|S |dkrx¨|!D ] }%|!|% dkrtdi|% tjd t| _	|S | j=djkr`y|  >|!|% ¡\}2}3W n"   tdk|% tjd t| _	|S nd }3|!|% dl }2| d5|%| j=|3|2f ¡ qêW nú| j?||"dmdMdn\}}}}4| j	dokrÈtdptjd |S d6 |" @¡ ¡}5| dq|5t|ƒf ¡ dr dsdt„ |D ƒ¡}6| du|6 ¡ dr dvdt„ |D ƒ¡}7| du|7 ¡ | dudr dwdt„ |D ƒ¡ ¡ x0|"D ](}8| dudr dxdt„ |"|8 D ƒ¡ ¡ qTW | d¡ | ¡  nìyt|dƒ}W n"   tdy| tjd t| _	|S x®|	D ]¤}|	| d- }|d/krD|	| d0 }t|ƒd2kr"tdz| tjd t| _	|S | d{|||d |d f ¡ qÐt| d6¡ƒ}d7|	| kr~td8  |¡tjd t| _	|S |	| d7 }d9|	| kr¶td:  |¡tjd t| _	|S |	| d9 }t|ƒ|krètd;tjd t| _	|S x4|D ],}t|ƒ|krîtd<tjd t| _	|S qîW d=|	| krJtd>  |¡tjd t| _	|S |	| d= }t|ƒ|kr|td?tjd t| _	|S xV|D ]N}t! "|¡}|j#d |j#d kr‚|j#d |kr‚td@tjd t| _	|S q‚W dA|	| kr tdB  |¡tjd t| _	|S |	| dA }t|ƒ|kr2tdCtjd t| _	|S d0|	tA krª|	| d0 } t| ƒ|krrtdDtjd t| _	|S x:| D ],}t|ƒd2krxtdEtjd t| _	|S qxW nd} | dF  |¡¡ | dG  |¡¡ | dG  t$ %dHdt&|ƒ¡¡¡ | dG  t$ %dHdt&|ƒ¡¡¡ | dI  t$ %dHdt&|ƒ¡¡¡ | dk	rjx6| D ].}| d¡ | dI  t$ %dHdt&|ƒ¡¡¡ q8W | d¡ qÐW | ¡  |S )|aÃ  
    Create the prior file to use for a particular job defined by a set of detectors, or single detector, and
    a set of frequency factors, or a single frequency factor. If creating an prior limit based on a set of given
    amplitude spectral densities (by calculating an estimate of the 95% UL they would produce) then it will
    additionally be scaled by a factor of `scalefactor`.

    Return the full output file and the create prior node
    r4   z%s.priorNz:Error... could not create symbolic link to prior file '%s')r   z%s.corr>   ú	ZDMÚSTARTZFINISHZNTOAZTRESZTZRMJDZTZRFRQZTZRSITEZNITSZELATZELONGz%s_ERRz%s_FITr?   )ZRA_RADZDEC_RADZ_RADr¸   Úgaussian)Ú	priortypeÚrangesú r   Ú
z1 g        ÚEZECCgü©ñÒMbP?ZT0ZOMz0.9999 ÚPBZOMDOTz0 r<   zCError... could not open file '%s' listing previous posterior files.z'Error... could not open prior file '%s'rR  z0Error... no 'priortype' given for parameter '%s'ZgmmrS  z-Error... no 'ranges' given for parameter '%s'r   zMError... 'ranges' for parameter '%s' must be a list or tuple with two entriesZCOSIOTAz%s	%s	%.16le	%.16le
ú:Únmodesz-Error... no 'nmodes' given for parameter '{}'Úmeansz,Error... no 'means' given for parameter '{}'zCError... number of mean values must be equal to the number of modeszHError... number of mean values must be equal to the number of parametersÚcovsz+Error... no 'covs' given for parameter '{}'zRError... number of covariance matrices values must be equal to the number of modesz]Error... number of covariance matrices rows/columns must be equal to the number of parametersÚweightsz.Error... no 'weights' given for parameter '{}'z?Error... number of weights must be equal to the number of modeszCError... number of ranges must be equal to the number of parametersz$Error... ranges must have two valuesz{}	gmm	z{}	z\s+z{}rö   g       @ZC22g      ð?ZC21r÷   ZH0ZI21ZI31g      ð¿zGError... unknown frequency factors or model type in configuration file.z)Error... could not parse prior file '%s'.ZC22ULZH0ULZULZF0rê   z=Error... no corresponding observation times for detector '%s'z1Error... observation time must be a float or int.z&Error... ASD file '%s' does not exist.ú%ú#)Úcommentsz"Error... could not load file '%s'.)r   r   )r   r   g     õ@zDError... frequency range in ASD file does not span pulsar frequency.gš™™™™™%@)rù   Úuniformz5Error... prior type must be 'fermidirac' or 'uniform'z:Error... a required upper limit for '%s' is not available.rù   z9Error... problem deriving the Fermi-Dirac prior for '%s'.gffffffî?Ú
elliptical)ÚtaperÚ
decaywidthr   zBError... could not set GMM prior using previous posterior samples.z
%s	gmm	%d	r  c             S   s,   g | ]$}d d  dd„ | ¡ D ƒ¡ d ‘qS )ú[r  c             S   s   g | ]}t |ƒ‘qS r   )r`   )r    r!   r   r   r"   r#     s    z9knopeDAG.create_prior_file.<locals>.<listcomp>.<listcomp>ú])r1   r  )r    Úvsr   r   r"   r#     s    z.knopeDAG.create_prior_file.<locals>.<listcomp>z[%s]	c             S   s,   g | ]$}d d  dd„ | ¡ D ƒ¡ d ‘qS )rd  r  c             S   s(   g | ] }d d  dd„ |D ƒ¡ d ‘qS )rd  r  c             S   s   g | ]}t |ƒ‘qS r   )r`   )r    Úcar   r   r"   r#     s    zDknopeDAG.create_prior_file.<locals>.<listcomp>.<listcomp>.<listcomp>re  )r1   )r    Úcr   r   r"   r#     s    z9knopeDAG.create_prior_file.<locals>.<listcomp>.<listcomp>re  )r1   r  )r    Úcsr   r   r"   r#     s    c             S   s   g | ]}t |ƒ‘qS r   )r`   )r    r>   r   r   r"   r#     s    c             S   s   g | ]}t |ƒ‘qS r   )r`   )r    Úlimr   r   r"   r#   "  s    z(Error... could not write prior file '%s'z>Error... the ranges in the prior for '%s' are not set properlyz%s	%s	%.16e	%.16e
)Br.   r/   r1   r  ÚsymlinkrK   rO   rP   rL   rG   r  r   r  rQ   r{   rm   Z
float_keysÚreplacerr   rW   rÑ   r  rT   rÊ   Úremover  r  r  r‚   rS   ÚupperÚsplitrˆ   r  ÚarrayÚshapeÚreÚsubr`   r   rÏ   r   Úinfr0   r  r  rÌ   r
  r  r   r   rõ   r   r	  ZloadtxtÚabsZargminÚzerosÚsqrtÚindexÚmaxr  Úfermidirac_rsigmaÚ	gmm_priorÚkeysZ
prioritems)9r3   r   rE  r«   ZfreqfactorsZ
outputpathZscalefactorrâ   Úoutfilerø   ÚcorfilerŒ   ZerritemsZignore_parsZparitemZitemnameræ   ÚeirD  ZeccZposteriorfileZ	prioritemÚptypeZ	rangevalsÚnparsrY  rZ  Úmeanr[  ZcovZnpcovr\  rS  ZrequlsZgmmparsZfppZulsZultÚfreqZasdfilesZobstimesZasdfilestmpZobstimestmpZasdlistZdkZasdZasdvZidxfZmspecZulspecÚbÚarå   ZparssepZmeanstrZcovstrÚgpr   r   r"   r  ƒ  s   



 



DD


"



&




$


"
  
(0""



 
(

"



&




$zknopeDAG.create_prior_fileçš™™™™™Ù?çffffffî?c                s:   d}d| | ‰t  ‡ ‡‡fdd„ˆ¡}|jd }ˆ|fS )aF  
    Calculate the r and sigma parameter of the Fermi-Dirac distribution to be used.

    Based on the definition of the distribution given in https://www.authorea.com/users/50521/articles/65214/_show_article
    the distribution will be defined by a mu parameter at which the distribution has 50% of it's maximum
    probability, and mufrac which is the fraction of mu defining the range from which the distribution falls from
    97.5% of the maximum down to 2.5%. Using an upper limit defining a given cdf of the distribution the parameters
    r and sigma will be returned.
    gR¸…ëQ@g      à?c                sR   ˆ t  dt  ˆ¡ ¡ t  dt  ˆ ¡ ¡ ˆ|   t  dt  ˆ|  ˆ ¡ ¡ S )Ng      ð?)r  ÚlogÚexp)Ús)Úcdfr<   Úulr   r"   Ú<lambda>¨  ó    z,knopeDAG.fermidirac_rsigma.<locals>.<lambda>r   )r   ÚrootÚx)r3   r  ZmufracrŒ  ÚZZsolutionÚsigmar   )rŒ  r<   r  r"   rz  ™  s
    
zknopeDAG.fermidirac_rsigmaé   ç      @c       )   
      sz  yddl m} W n   tdtjd t| _dS d}d}d}	tˆ tƒsftdtjd t| _|||	dfS t	ˆ ƒ}
g }yât|t
jt
jfƒsêtj |¡s¶td| tjd t| _|||	dfS t |¡\}}}xŠˆ D ]}| || ¡  j¡ qÌW nh|jd	 |
kr2xVt|
ƒD ](}| |dd…|f  t	|ƒd	¡¡ qW n td
tjd t| _|||	dfS W n&   tdtjd t| _|||	dfS t
 |¡ ¡ j}xltˆ  ¡ ƒD ]Z\}}d}x0ˆ | D ]"}t
 |¡r¶t
 || ¡}t
 || ¡}|||  }||dd…|f  }t
j t	|dd…|f ƒt!d}|dk	r„||krT|dd…|f d|  | }n:||k r|||dd…|f d|   }ntdtjd q¶t
  t	|dd…|f ƒ¡}|dkrÎt
 "d|d  |d  ¡}n’|dkrêd|||   }nv|dkrt
 "| | ¡}nZ|dkrRt
 #t	|dd…|f ƒ¡}t
 $d|||k  | d  ¡|||k < ntdtjd t
j% &t	|dd…|f ƒ¡|k  '¡ }||dd…f }|dd…|f  d||  7  < |dkrÊt
 |¡}nt
 (||f¡}q¶W |dk	rœt
 (||f¡}qœW t
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 2| |k¡rfd}$x|t.|!| |t
 $t
 3|"¡¡ ‡ fdd„ˆ D ƒ‡ fdd„ˆ D ƒƒD ]:\}%}&}'}(|%|'d|&  k sø|%|(d|&  krÈ|$d	7 }$qÈW |$dkrqf| |!| ¡ | t
 4|t
 4|"|¡¡¡ |	 |#¡ qfW t	|ƒdkrntd tjd t| _|||	|fS )!aÛ  
    Create an ND Gaussian Mixture Model for use as a prior.

    This will use the BayesianGaussianMixture Model from scikit-learn, which fits a Dirichlet Process Gaussian
    Mixture Model to the input data infering the number of components required. The input to this should be
    a previously calculated posterior sample file, or numpy array of samples. If a files is given then the
    parameters given as keys in the `pardict` ordered dictionary will be extracted. For each parameter name
    key in the `pardict` ordered there should be pairs of hard upper an lower limits of the particular parameters.
    If any of these are not +/-infinity then the samples will be duplicated and reflected around that limit. This
    is to avoid edge effects for the inferred Gaussian distributions. `ncomps` sets the hyperparameter used in
    the Dirichlet process related to the number of Gaussian components.

    `taper` sets whether or not to taper-off any reflected samples, and how that tapering happens. Tapering can
    use: a 'gaussian' taper, where the half-width of the Gaussian is set by the range of the samples multiplied
    by `decaywidth`; a 'triangular' taper, which falls from one to zero over the range of the samples; an
    'exponential' taper, where the decay constant is defined by 'decaywidth' multiplied by the range of the
    samples; or, an 'elliptical' taper, where the axis of the ellipse is set by 'decaywidth' multiplied by the
    range of the samples. The default is that no tapering is applied, and it should be noted that tapering can
    still leave artifacts in the final GMM.

    The means, covariance matrices and weights of the Gaussian components will be returned, along with
    the full set of points (including reflected points) used for the estimation.

    An example of using this would be for "H0" versus "COSIOTA", in which case the `pardict` might be:
    >> pardict = OrderedDict()
    >> pardict['H0'] = [0., np.inf]
    >> pardict['COSIOTA'] = [-1., 1.]
    r   )Úmixturez'Error... could not import scikit-learn.)r   )NNNNNz,Error... Input must be an ordered dictionaryz;Error... previous posterior sample file '%s' does not existr?   zHError... input numpy array does not contain correct number of parameterszEError... could not extract posterior samples from file or numpy array)Zdtypeg       @z4Warning... limit is inside the extent of the samplesrQ  g      à¿r   Ú
triangularg      ð?Zexponentialra  zAWarning... unknown tapering has been set, so none will be applied)ZaxisÚfullgš™™™™™©?iô  )Zn_componentsZcovariance_typeÚtolZmax_iterc                s   g | ]}ˆ | d  ‘qS )r   r   )r    r“   )Úpardictr   r"   r#   @  s    z&knopeDAG.gmm_prior.<locals>.<listcomp>c                s   g | ]}ˆ | d  ‘qS )r?   r   )r    r“   )rš  r   r"   r#   @  s    g      @z#Error... no GMM components returned)5Zsklearnr–  rK   rO   rP   rL   rG   r   r   rW   r  ZndarrayZgenericr.   r/   r0   rm   Zpulsar_nest_to_posteriorrr   rn  Zsamplesrq  r  ZreshaperÈ   ZsqueezeÚTrÑ   r|  Úisfinitery  ÚminZonesÚboolrŠ  rv  rw  r  ZrandÚflattenZconcatenateZstdÚidentityZBayesianGaussianMixtureÚfitZpredictÚzipZmeans_Zcovariances_Zweights_ÚanyZdiagÚdot))r3   Zprevpostfilerš  Zncompsrb  rc  r–  rZ  r[  r\  r  Z
allsamplesZpossampsrå   r   ræ   Zallsamplesnpr“   Z
refsamplesrj  ZmaxpZminpZsigmaprã   ZrefidxsZdeltavZprobkeepZthesesamplesZ	parscalesZ	scalesmatZscaledsamplesZdpgmmZparpredr‚  ZcovarÚweightZoutlimsZmusÚsigsZlowlimZhighlimr   )rš  r"   r{  ®  sº    

*






($ 


&L$
zknopeDAG.gmm_priorc       &         sN  | j dddd| _| jdkr dS tj | j¡r>t | jtj¡svtdƒ |  	d¡}|dkrptdt
jd	 t| _dS || _| j dd
dd| _| jdkr–dS | j ddddd| _| j ddddd| _| j ddddd| _|   ddd¡| _| j ddddd| _| j ddddd| _| j ddddd| _| j ddddd| _| jdkrBdS | jr`| jr`tdƒ d| _| j dd d!d"d| _| j dd#dd$d| _| j dd%ddd| _| j dd&ddd| _| jdkrÀdS t| j| j| j| j| j| jd'| jd(}t| j| j| j| j| j| jd)| jd(}i | _i | _ i | _!i }i }x | j"D ]}d||< i ||< q.W xŠ| j"D ]€}|| jkr~td* #|¡t
jd	 t| _dS t$| j| t%ƒr¤| j| g| j|< n*t$| j| t&ƒsPtd+t
jd	 t| _dS qPW x| j'D 
]ü}| j'| }d }	}
|| j(krd}	n|| j)krd}
|  *t+ ,|¡¡\}}}| jdkr>dS i }i | j |< i | j|< 
x€| j"dd… D 
]l}tj -| j.| |¡}|  /|¡ | jdkrœdS tj -|d,¡}|  /|¡ | jdkrÄdS tj -|d'¡}|  /|¡ | jdkrìdS tj -|d)¡}|  /|¡ | jdkrdS tj -|d-¡||< |	r"|| r‚tj -| j.| d.¡| j!|< |  0| j1| | j2| || j!| ¡ | jdkr‚dS yt3 4| j!| || ¡ W n   td/t
jd	 t| _dS || rÎd||< tj -tj 5|| ¡d0¡}tj |¡r„yt 6|¡ W n   td1| ƒ Y nX nb|
r„tj || ¡r†tj -tj 5|| ¡d0¡}tj |¡srt3 4|| |¡ | j7 8|| |f¡ | j9rþtj || ¡rþt:j;d2||  dd3}t<|ƒdkrÞt=| >¡ d4 ƒg| j?|< n td5||  t
jd	 t| _dS | j?| d || kr:t3 4|| | j?| d  || ¡ nJ|| || | j?| d < |  0| j?| | j2| ||| ¡ | jdkr„dS | j@tAkrÖ| j9sÖ| j" 6|¡ t<| j"ƒdkrÌtd6t
jd	 tB| _dS d| _@qhi | j | |< i | j| |< xÞ| jCD ]Ò}|d s:tj -|d7t=|ƒ ¡}tj -|d7t=|ƒ ¡‰ n$tj -|d8| ¡}tj -|d8| ¡‰ |  /|¡ | jdkrxdS |  /ˆ ¡ | jdkr’dS g }| jD| d4krtj -ˆ d9|t=| j?| d ƒt=| j2| d: ƒf ¡}| jrê|d;7 }tEtj -ˆ d<¡|| j| j| jd=}xøtF| jD| ƒD ]ä}| j@tAk	r–| jrntj -|d>|t=| j?| | ƒt=| j2| | ƒf ¡}n4tj -|d?|t=| j?| | ƒt=| j2| | ƒf ¡}tG|ƒ}| jHdk	rÊ| I| jH| | ¡ | J| jK| | ¡ | L| j¡ | M|| ¡ | N| j| | ¡ | O|¡ | j	r&| P¡  | j	r6| Q¡  | R|¡ | Sd¡ | T|¡ | U|¡ | V| j¡ | W| j¡ | X| j¡ | Y|¡ |  Z|¡ | j@tAkrtG|ƒ}| jD| d4k	rÖ|dk	rÌt[|ƒ}| I|¡ | I|¡ tj -ˆ d9|t=| j?| | ƒt=| j2| | ƒf ¡}| 8|¡ | j
r6| J|d; ¡ n
| J|¡ | j
rP| \¡  | M|| ¡ | O|¡ | R|¡ | Sd4¡ | T|¡ | U|¡ | W| j¡ | X| j¡ | V| j¡ | Y|¡ | ]| j¡ | ^|¡ | _|¡ | `|¡ | jr| Q¡  |d:  d;7  < |  Z|¡ | jD| d4kr¼|| jD| d4 krJ| a|¡ |  Z|¡ tj -ˆ d9|t=| j?| d ƒt=| j2| d: ƒf ¡}tb| j| j| j| jd@}tc|ƒ} |  a|¡ |  I|¡ |  Z| ¡ | jD| d4krà|| j | | |< n|| j | | |< | jr|d; }qW |	r2| j@tAkrÎ|g| j| | |< qü|
rü‡ fdAdB„t dˆ ¡D ƒ}!|! e¡  | jrÜxètf|!ƒD ]l\}"}#d;|#krjt:jgdC|# dd3}| h¡ \}$}%|jidkrÈtdD|#|$|%f t
jd	 t| _dS |#d; |!|"< qjW nnxltf|!ƒD ]`\}"}#d;|#kræt:jgdE|# dd3}| h¡ \}$}%|jidkrætdF|#|$|%f t
jd	 t| _dS qæW |!| j| | |< | j@tAkr¶t<|!ƒdkr¬| j" 6|¡ t<| j"ƒdkr¶td6t
jd	 tB| _dS n
d| _@qü| j| | |  8|¡ qüW qhW qÞW t<| j(ƒdkrJxX| j"D ]N}y(tj | j!| ¡r"t 6| j!| ¡ W n   tdG| j!|  ƒ Y nX qøW dS )Hz:
    Setup the coarse and fine heterodyne jobs/nodes.
    r%   Úheterodyne_execZlalapps_heterodyne_pulsar)r   r   NzpWarning... 'heterodyne_exec' in '[heterodyne]' does not exist or is not an executable. Try finding code in path.z=Error... could not find 'lalapps_heterodyne_pulsar' in 'PATH')r   r™   ró   Úfilter_kneerõ   g      Ð?Zcoarse_sample_rater   i @  Zcoarse_resample_rateg      ð?Zchannelsr   Zbinary_outputr   TZgzip_coarse_outputFZcoarse_request_memory)rC   Zcoarse_max_data_lengthi   z`Warning... cannot output coarse heterdyned data as gzip and binary. Defaulting to binary output.Zfine_resample_rateÚstringz1/60Ústddev_threshg      @Zgzip_fine_outputZfine_request_memoryZcoarse)r§   r¤   r¥   r¦   rV   Ú	subprefixrû   Úfinez-Error... could channel not specified for '{}'z6Error... channel must be a string or a list of stringsr°   zsegments.txtzsegments_tmp.txtz:Error... could not copy segment list into pulsar directoryzprevious_segments.txtz?Warning... previous segment list file '%s' could not be removedztail -1 )r@   r?   zAError... could not get end time out of previous segment file '%s'z9Error... no segments were available for any required IFOsz%dfz%.2ffzfine-%s-%d-%d.txtr   z.gzz
concat.sub)Úsubfiler¨   r¤   r¥   r¦   zcoarse-%s-%d-%d.binzcoarse-%s-%d-%d.txt)r¤   r¥   r¦   rV   c                s"   g | ]}d |krt j ˆ |¡‘qS )r¬  )r.   r/   r1   )r    Úhf)Úfreqfacdirfiner   r"   r#   ’	  s    z-knopeDAG.setup_heterodyne.<locals>.<listcomp>zgzip zCError... could not gzip previous fine heterodyned file '%s': %s, %szgunzip zEError... could not gunzip previous fine heterodyned file '%s': %s, %sz7Warning... could not remove temporary segment list '%s')jrM   r§  rG   r.   r/   r0   r»   r¼   rK   r½   rO   rP   rL   Zheterodyne_universeZcoarse_heterodyne_filter_kneeZcoarse_heterodyne_sample_rateZcoarse_heterodyne_resample_rateZcoarse_heterodyne_channelsZcoarse_heterodyne_binary_outputZcoarse_heterodyne_gzip_outputZ coarse_heterodyne_request_memoryZ!coarse_heterodyne_max_data_lengthZfine_heterodyne_resample_rateZfine_heterodyne_stddev_threshÚfine_heterodyne_gzip_outputZfine_heterodyne_request_memoryÚheterodyneJobr)   r*   r+   r   rz   rÜ   Z!modified_pulsars_segment_list_tmpr   rˆ   r   r	   r   rl   ri   rh   r5  rm   rn   r1   r   rX   Úfind_data_segmentsrf   r$   rÇ   Úcopy2rp   rm  rw   rr   r,   r|   Úcheck_outputrW   r   ro  r   rH   ÚKNOPE_WARNING_NO_SEGMENTSÚKNOPE_ERROR_NO_SEGMENTSr   r[   Ú	concatJobr  ÚheterodyneNodeÚdatafind_nodesrÙ   Úset_data_fileÚcache_filesÚset_max_data_lengthÚset_seg_listÚset_channelÚset_output_fileÚset_binoutputÚset_gzip_outputÚset_ifoÚset_het_flagÚ
set_pulsarÚset_param_fileÚset_filter_kneeÚset_sample_rateÚset_resample_rateÚset_freq_factorrÚ   Ú
concatNodeÚset_bininputÚset_stddev_threshÚset_ephem_earth_fileÚset_ephem_sun_fileÚset_ephem_time_filerA  r  r@  rj   rk   rÑ   r}   r~   r   )&r3   ZhetexecZchetjobZfhetjobZgetmodsciencesegsZsegfiletimesr   râ   r   Zmodified_pulsarZunmodified_pulsarrI  rJ  rK  ÚsegfilesrE  ÚdatadirZ	coarsedirZfinedirÚprevsegsr“   Ú
freqfactorZfreqfacdircoarseZfinetmpfilesZ
fineoutputÚ	concatjobÚkZcoarseoutputZ
coarsenodeZfinenodeÚ
concatnoderC  rM  Zhetfilescheckræ   r®  ÚoutÚerrr   )r¯  r"   rï   S  s   
 

   &&

 

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 
" 
 $  

 
 4"64

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


*zknopeDAG.setup_heterodynec           
   C   s~	  | j dddd| _| jdkr dS i | _i | _tj | j¡rJt | jtj	¡s‚t
dƒ |  d¡}|dkr|t
dtjd	 t| _dS || _| j dd
dd| _| jdkr¢dS | j ddddd| _t| j| j| j| j| j| j| jd}t| j| j| j| jd}|   dddd¡| _|   dddddg¡| _|   dddd¡| _|   dddd¡| _|   dddd¡| _|   ddd d!¡| _| jdkrrdS | j| jkr¤t
d" | j| j¡tjd	 t| _dS i | _i | _d| _ d| _!i | _"i | _#d!}d!}t$| j%ƒdkräd}t$| j&ƒdkrød}x~| j'dd… D ]j}tj (| j)| d¡| _*|  +| j*¡ | jdkrBdS xd#D ]ü}tj (| j*|¡}|d$kr|dkrJ|| _ | j%}	i | j|< nqJ|d%krÀ|dkrJ|| _!| j&}	i | j|< nqJtj ,|¡rxft -|¡D ]<}
yt .tj (||
¡¡ W n   t
d&|
|f ƒ Y nX qÚW n|  +|¡ | jdkr6dS x|	D ]}yÜt/ 0|¡}|d' }tj (|tj 1|¡¡}|d$kr„|| j|< |d%kr˜|| j|< t 2||¡ || j#krÄi | j#|< i | j"|< i | j#| |< i | j"| |< tj (| j)| |¡}|  +|¡ | jdkrdS tj (|d(¡}|  +|¡ | jdkr6dS tj (|d¡}|  +|¡ | jdkr^dS xÀ| j3D ]¶}|d) sŒtj (|d*t4|ƒ ¡}ntj (|d+t4|ƒ ¡}tj (|d,||f ¡g| j#| | |< | jrî| j#| | | d  d-7  < |  +|¡ | jdkrdS || j"| | |< qfW W n   t
d.||f ƒ Y nX q>W qJW t$| jƒdkr`d!}t$| jƒdkrtd!}d}|rtj (| j)| d/¡}|  5| j6| | j7| ||¡ | jdkr¾dS | j8t9kr| j' .|¡ t$| j'ƒdkrþt
d0tjd	 t:| _dS d| _8q
d}|rDtj (| j)| d1¡}| j;rtj |¡rt<j=d2| dd3}t$|ƒdkrtt4| >¡ d4 ƒ| j?|< nt
d5| tjd	 t| _dS |  5| j?| | j7| ||¡ | jdkr¼dS | j8t9kr| j' .|¡ t$| j'ƒdkrüt
d6tjd	 t:| _dS d| _8q
tj (| j)| d7¡}tj |¡s4t@ A||¡ | jB C||f¡ x,| j3D ] }|d) sxtj (| j*d*t4|ƒ ¡}ntj (| j*d8| ¡}|  +|¡ | jdkr¦dS ||g}| j | j!g}x°tD||gƒD ]ž\}}|rÊtE|ƒ}| F| jG| d ¡ | H| jI| ¡ | J|¡ | K|| ¡ | L|| ¡ | M|¡ | N|¡ | O| j¡ | P| j¡ | Q| j¡ | R| jd ¡ | S| jd4 ¡ | T| j¡ | U| jV¡ | jr¬| W¡  |dkrÆ|| j| |< n|| j| |< |  X|¡ xˆ|	D ]€}t/ 0|¡}|d' }tY|ƒ}tj (|d,||f ¡}| j	r(|d-7 }| Z|¡ | [| j#| | | d ¡ | F|¡ |  X|¡ qäW qÊW qNW q
W dS )9z6
    Setup the Spectral Interpolation jobs/nodes.
    r&   Úsplinter_execZlalapps_SplInter)r   r   NzlWarning... 'splinter_exec' in '[splinter]' does not exist or is not an executable. Try finding code in path.z4Error... could not find 'lalapps_SplInter' in 'PATH')r   r™   ró   Úsplinter_request_memoryr   T)rC   )r§   r¤   r¥   r¦   rV   rû   )r¤   r¥   r¦   rV   Ú	bandwidthrõ   g333333Ó?Z
freq_ranger   g      >@g     @Ÿ@rª  g      @Zmin_seg_lengthi  Zmax_seg_lengthi`T  Zgzip_outputr   Fz\Error... minimum segment length ({}) for SplInter is larger than maximum segment length ({}))ÚmodifiedÚ
unmodifiedrÜ  rÝ  zRWarning... problem removing par file '%s' from '%s'. This file may be overwritten.r4   r°   g      ð?z%dfz%.3ffzSplInter_%s_%sz.gzzXWarning... could not create link to par file '%s' in '%s'. This file may be overwritten.zsegments_modified.txtz?Error... no segments could were available for any required IFOszsegments_unmodified.txtztail -1 )r@   r?   zAError... could not get end time out of previous segment file '%s'z9Error... no segments were available for any required IFOszprevious_segments.txtz%.2ff)\rM   rÙ  rG   r9  r:  r.   r/   r0   r»   r¼   rK   r½   rO   rP   rL   Zsplinter_universerÚ  ÚsplinterJobr)   r*   r+   r   r  Zsplinter_bandwidthZsplinter_freq_rangeZsplinter_stddev_threshZsplinter_min_seg_lengthZsplinter_max_seg_lengthÚsplinter_gzip_outputrˆ   rÝ   r;  Zsplinter_modified_pulsar_dirZsplinter_unmodified_pulsar_dirÚsplinter_data_locationrz   rW   ri   rh   r   r1   r   Zsplinter_dirrX   rg   rj   rm  rm   rn   rq   rk  r   r   r²  rf   r$   rH   rµ  r¶  r,   r|   r´  ro  r   rÇ   r³  rw   rr   rÑ   ÚsplinterNoderÙ   r¹  Úset_sft_lalcacher»  Úset_output_dirÚset_param_dirr½  rÉ  rÂ  Úset_bandwidthÚset_min_seg_lengthÚset_max_seg_lengthÚset_start_freqÚset_end_freqrÌ  Úset_ephem_dirr'   rÁ  rÚ   r<  rÖ   r×   ) r3   ZsplexecZspljobrB  ZmodparsZ	unmodparsr   Z	modsuffixÚpardirZparlistrü   r   r   râ   ZparlinkrE  rÑ  ZsplintercpydirrÓ  rí   Z
modsegfileZunmodsegfiler“   rÒ  ZsplinterdirZsplsegfilesZ
splpardirsÚidxZsplboolZsplnoderL  Zsplinterfiler   r   r"   rð   Å	  sŒ   
 

 $    




 

 

 



 
 
 
&
 "    

 



 




zknopeDAG.setup_splinterc             C   sü   |d }|dkrd}|d }|dkr(d}t j | jd| ¡}t j | jd| ¡}|dkrjt j | jd	¡}nt j | jd
¡}t j |¡s¢td| tjd t| _	dS t j |¡sÊtd| tjd t| _	dS t j |¡sòtd| tjd t| _	dS |||fS )zQ
    Get the ephemeris file information based on the content of the psr file
    r6   Nr7   r8   r9   zearth00-40-%s.dat.gzzsun00-40-%s.dat.gzr:   ztdb_2000-2040.dat.gzzte405_2000-2040.dat.gzz1Error... Earth ephemeris file '%s' does not exist)r   z/Error... Sun ephemeris file '%s' does not existz0Error... time ephemeris file '%s' does not exist)
r.   r/   r1   r'   r0   rK   rO   rP   rL   rG   )r3   r   ZephemZunitsrI  rJ  rK  r   r   r"   r5  ×
  s0    zknopeDAG.get_ephemerisc             C   sT  t | j| j| j| jd}|| _i | _x(| jD ]}| j| }x
|D ] }|| }xð|D ]æ}|| }d}d}	d}
d}d}| jdkr’t	|ƒdkr8|| jkr¬i | j|< || j| krÈi | j| |< t
j |d ¡ d¡d }t
j |d ¡ d¡d	 }| d
d¡}| dd¡}t
j t
j |d ¡d|||f ¡}| jrH|d }|}y| j| | | }W n   d}Y nX t
j t
j |d ¡d¡}	n¦| jdkr8t
 | j| | | ¡}
t	|
ƒdkrètd| j| | |  ƒ t| _dS || jkrt| j| d ƒ}nºt	|
ƒdkrŒyt
j |
¡ d¡d }W n4   td|
| j| f ƒ t| j| d ƒ}Y nX t
j | j| | | |
d ¡|g}nt| j| d ƒ}y| j| | }W n   d}Y nX t| j| d ƒ}t
j | j| | | dt
j |d ¡ d¡||f ¡}| jr|d }t
j | j| | | d¡}	|	dk	rº|dk	rºt|	|| j| j| jd}t |ƒ}| !|¡ |dk	rŠ| "|¡ |  #|¡ || j| | |< |g| j| | |< t	|ƒdksÒ| jdkr\|dkr\t$|ƒ}|
dkr| %t
j | j| | | |
d ¡¡ | !|¡ |	dk	r:|dk	r:| "|¡ |  #|¡ q\W qFW q.W dS )zü
    Create jobs to concatenate fine heterodyned/Splinter data files in cases where multiple files exist (e.g. in automated search).
    Go though the processed file list and find ones that have more than one file, also also remove previous files.
    )r¤   r¥   r¦   rV   Nr%   r?   r   ú-r   r   é   z.txtr¸   z.gzzfine-%s-%s-%s.txtz
concat.subr&   z?Error... more than one previous Splinter file in directory '%s'zoWarning... could not get previous start time from Splinter file name '%s'. Using start time from this run: '%d'z%s-%s-%s.txt)r­  r¨   r¤   r¥   r¦   )&r  r)   r*   r+   r   ry   rÛ   rz   r\   rW   r.   r/   rq   ro  rl  r1   rp   r°  rÜ   rj   rà  rK   rL   rG   r9  r`   r   r;  r$   rv   rß  r·  rÊ  rA  rÙ   rÚ   r@  rr   )r3   rC  r’   ZpifosZpifoZffsrŽ   Z	finefilesrÖ  ZsublocZprevfileZnewfinefileZcatfilesZ
firststartZlastendÚparentZ	startnameZendnamerÔ  rM  r   r   r"   rñ      s–    


$
&
8



 
&

zknopeDAG.concatenate_filesFc          
   C   sv  d}|dks|dks|dkr‚y| j  ||¡}W nN   |sxt|tƒsbtd||f tjd t| _ntd|||f ƒ |}Y nX nð|dkrðy| j  	||¡}W nN   |sæt|t
ƒsÐtd||f tjd t| _ntd	|||f ƒ |}Y nX n‚|d
krdy| j  ||¡}W nR   |sZt|tƒsDtd||f tjd t| _ntd|||f ƒ |}Y nX n|dkrØy| j  ||¡}W nR   |sÎt|tƒs¸td||f tjd t| _ntd|||f ƒ |}Y nX nš|dkrjy*t | j  ||¡¡}t|tƒs
|g}W nX   |s`t|tƒsDtd||f tjd t| _ntd||d |¡f ƒ |}Y nX n|dkrZyŒt | j  ||¡¡}t|tƒs¾t|tƒr¾td||t|ƒf ƒ |}n@t|tƒsþt|tƒsþ|sútd||f tjd t| _nd}W nV   |sRt|tƒs8td||f tjd t| _ntd||t|ƒf ƒ |}Y nX ntd| tjd t| _|S )zº
    Get a value of type cftype ('string', 'int', 'float', 'boolean', 'list', 'dict' or 'dir') from the configuration parser object.

    Return value on success and None on failure
    Nr©  r   z9Error... could not parse '%s' option from '[%s]' section.)r   zMWarning... could not parse '%s' option from '[%s]' section. Defaulting to %s.rõ   z?Error... could not parse '%s' float option from '[%s]' section.zSWarning... could not parse '%s' float option from '[%s]' section. Defaulting to %f.r   zAError... could not parse '%s' boolean option from '[%s]' section.zUWarning... could not parse '%s' boolean option from '[%s]' section. Defaulting to %r.r   z=Error... could not parse '%s' int option from '[%s]' section.zQWarning... could not parse '%s' int option from '[%s]' section. Defaulting to %d.r   z>Error... could not parse '%s' list option from '[%s]' section.zTWarning... could not parse '%s' list option from '[%s]' section. Defaulting to [%s].z, r   zXWarning... could not parse '%s' dictionary option from '[%s]' section. Defaulting to %s.zDError... could not parse '%s' dictionary option from '[%s]' section.zHError... unknown trying to get unknown type '%s' from configuration file)rI   r_   r   r`   rK   rO   rP   rL   rG   Úgetfloatrõ   Ú
getbooleanrž  Úgetintr   rY   rZ   r   r1   r   )r3   ÚsectionÚoptionr   r   rC   Úvaluer   r   r"   rM   x  s”    






zknopeDAG.get_config_optionc             C   s   |dkrdS dS dS )zC
    Check Condor universe is 'local', 'vanilla' or 'standard'
    )rš   ró   ÚstandardTFNr   )r3   r™   r   r   r"   Úcheck_universeÖ  s    zknopeDAG.check_universec             C   s  i | _ d| _| j dd¡r.| jddddd}|dk	rt xþ| jD ]ô}||kr–td| ƒ |  d¡}|dkr„td	tj	d
 t
| _dS | j dd|¡ qBt|| tƒs²|| g||< g | j |< xx|| D ]l}tj |¡s"td| ƒ |  d¡}|dkrtd	tj	d
 t
| _dS | j dd|¡ qÆ| j |  |¡ qÆW qBW t| j ƒt| jƒk r,t t| j ¡ ƒd | j| j¡| _n¸|  dd¡}tj |¡rÂt |tj¡rÂt t| j ¡ ƒd | j| j¡| _njtd| ƒ |  d¡}|dkrútd	tj	d
 t
| _dS | j dd|¡ t t| j ¡ ƒd | j| j¡| _n^|  d¡}|dkrZtd	tj	d
 t
| _dS | j dd|¡ t t| j ¡ ƒd | j| j¡| _| jdk	rü| j d| j¡ | jdk	rÄ| j d| j¡ | j tj | j d¡¡ t| j ƒt| jƒk r|  !¡  nd| _"dS )z.
    Create and setup the data find jobs.
    Nr(   Údatafindr   T)r   rC   zVWarning... no frame/SFT cache file given for %s, try using system gw_data_find insteadZgw_data_findz5Error... could not find 'gw_data_find' in your 'PATH')r   zZWarning... frame/SFT cache file '%s' does not exist, try using system gw_data_find insteadr   zpWarning... data find executable '%s' does not exist, or is not executable, try using system gw_data_find insteadr)   r*   zdatafind.sub)#r»  Údatafind_jobrI   r^   rM   r   rK   r½   rO   rP   rL   rG   rÂ   r   r   r.   r/   r0   rr   rW   r   ZLSCDataFindJobr   rÌ   r+   r»   r¼   Úadd_condor_cmdr)   r*   Úset_sub_filer1   r   Úset_datafind_nodesr¹  )r3   rø  r   ZdatafindexecÚ	cachefiler   r   r"   rî   à  sn    




$$

$

"
zknopeDAG.setup_datafindc       
      C   s  i | _ | j dd¡rLt | j dd¡¡}t|tƒsdtdt	j
d t| _dS ntdt	j
d t| _dS x˜| jD ]Œ}g }||krœtd| t	j
d t| _dS t|| tƒrÒxŠt| j| ƒD ]}| || ¡ qºW ndt|| tƒr|| }t|ƒ| j| kr6tdt	j
d t| _dS ntd	 |¡t	j
d t| _dS || jkrDqng | j |< g | j|< | jd
krœttj | j| d¡tj | j| d¡| j| j| jd}xÜt| j| ƒD ]Ê}t  | j!¡}| "|d ¡ | #|| ¡ | $| j%| | ¡ | &| j'| | ¡ | j| dkr&tj | j| d¡}ntj | j| d |¡¡}| j|  |¡ | (|¡ | j |  |¡ |  )|¡ q¬W | jd
krn| j| dkrnt*|ƒ}| +| j| ¡ x| j | D ]}	| ,|	¡ q¶W |  )|¡ |g| j |< tj | j| d¡g| j|< qnW dS )z6
    Add data find nodes to a dictionary of nodes
    rø  ÚtypezOError... the data find 'types' must be a dictionary of values for each detector)r   Nz0Error... no frame 'type' specified for data findz!Error... no data find type for %szPError... the number of frame types must be the same as the number of start timeszJError... frame types for '{}' must be a single string or a list of stringsr&   z
concat.subz	cache.lcf)r­  r¨   r¤   r¥   r¦   r   r?   zcache_{}.lcf)-r¹  rI   r^   rY   rZ   r_   r   r   rK   rO   rP   rL   rG   r   r	   r  r[   rr   r   rW   rˆ   r»  r\   r·  r.   r/   r1   r   r)   r*   r+   r   ZLSCDataFindNoderù  Zset_observatoryÚset_typeZ	set_startrf   Zset_endr$   Z
set_outputrÚ   rÊ  rA  rÙ   )
r3   Zfrtypesr   Z
frtypelistræ   rÔ  Zdfnoderý  rÖ  Údfnr   r   r"   rü  8  sp    


8


zknopeDAG.set_datafind_nodesc          	   C   s‚  | j ddddd}|dk	r–||kr8td| ƒ t| _dS || }tj |¡sbtd| ƒ t| _dS yt ||¡ W n   td	| ƒ t| _Y nX dS yd
dl	m
} W n" tk
rÈ   tdƒ t| _dS X | j dddd}| j dddd}	| j ddddd}
||	kr"td| tjd t| _dS t|tƒrHt|tƒrH|g}|g}nšt|tƒrÐt|tƒrÐt|ƒt|ƒkrŠtdtjd t| _dS x:t||ƒD ],\}}||kr–tdtjd t| _dS q–W |}|}ntdƒ t| _dS d
}yt|dƒ}W n$ tk
r   tdƒ t| _dS X xXt||ƒD ]H\}}t|	| tƒržt|	| | tƒshtdƒ t| _dS t|	| ƒt|ƒkrtdƒ t| _dS |	| | }n*t|	| tƒsÀtdƒ t| _dS |	| }dd„ | d¡D ƒ}d}xVtt|ƒƒD ]D}|j|| |||d}|j}|
dk	r||
krt|
| tƒr’t|
| | tƒs\td ƒ t| _dS t|
| ƒt|ƒkr„td!ƒ t| _dS |
| | }n*t|
| tƒs´td ƒ t| _dS |
| }t|ƒd
krd"d„ | d¡D ƒ}x8tt|ƒƒD ](}|j|| |||d}||j @ }qìW |dkr,| ¡ }n||@ }qðW x,|D ]$}tt|d
 ƒt|d# ƒ|d q@W |d#7 }q(W | ¡  dS )$a  
    Find data segments and output them to an acsii text segment file containing the start and end times of
    each segment. Pairs of start and end times in the `starttime` and `endtime` lists will be iterated over
    and all segments within those pair will be concatenated into the final file.

    Args:
        starttime (list): a list of GPS start times
        endtime (list): a list of GPS end times
        ifo (str): a detector name, e.g., 'H1'
        outfile (str): the file to output the segment list file to
    ZsegmentfindZsegfindr   T)r   rC   Nz'Error... No segment file given for '%s'z*Error... segment file '%s' does not exist.z9Error... could not copy segment file to location of '%s'.r   )ÚDataQualityFlagz3Error... gwpy is required for finding segment listsr–   zhttps://segments.ligo.org)r   Úsegmenttype)r   ÚexcludetypezError... No segment type for %s)r   zNError... list of start and end times for the segments are not the same lengthsz*Error... start time comes before end time!zBError... start and end times must be integers or lists of integersr>   z)Error... could not open segment list filez'Error... segment types must be a stringzMError... number of segment types is not the same as the number of start timesc             S   s   g | ]}|  ¡ ‘qS r   )rv   )r    Ústsr   r   r"   r#   þ  s    z/knopeDAG.find_data_segments.<locals>.<listcomp>r  )Úurlz'Error... exclude types must be a stringzMError... number of exclude types is not the same as the number of start timesc             S   s   g | ]}|  ¡ ‘qS r   )rv   )r    r  r   r   r"   r#     s    r?   )rM   rK   rL   rG   r.   r/   r0   rÇ   rË   Zgwpy.segmentsr  ÚImportErrorrO   rP   r   r   r   rW   r¢  rQ   ÚIOErrorr	   ro  r  Zquery_dqsegdbÚactiverÈ   rT   )r3   r   r$   r   r}  rÐ  Zsegfiler  r–   ZsegmenttypesZexcludesegsr  ZetsÚstÚetZsidxZsegfpr  ZsegtypesZsegqueryræ   Úqueryr  Z
segextypesrD  ZexqueryZthissegr   r   r"   r²    sÒ    







$zknopeDAG.find_data_segmentsc             C   sj   t j |¡rt  |t j¡r|S xFt jd  t j¡D ]0}t j ||¡}t j |¡r2t  |t j¡r2|S q2W dS )zf
    Search through the PATH environment for the first instance of the executable file "filename"
    ÚPATHN)	r.   r/   r0   r»   r¼   r]   ro  Úpathsepr1   )r3   ÚfilenameÚdZ	filecheckr   r   r"   r½   4  s    zknopeDAG.find_exec_filec             C   sV   t  |t j¡rt j |¡rdS yt  |¡ W n$   td| tjd t	| _
Y nX dS )z
    Helper function. Make the given directory, creating intermediate
    dirs if necessary, and don't complain about it already existing.
    Nz#Error... cannot make directory '%s')r   )r.   r»   ÚW_OKr/   rg   ÚmakedirsrK   rO   rP   rL   rG   )r3   r/   r   r   r"   rX   E  s     zknopeDAG.mkdirs)N)rN  )r‡  rˆ  )r”  Nr•  )NNF)Ú__name__Ú
__module__Ú__qualname__re   r   rx   r€   r  rz  r{  rï   rð   r5  rñ   rM   r÷  rî   rü  r²  r½   rX   r   r   r   r"   r   3   sH   
   e  q   i
    

 &  t  )x
^
XU (r   c               @   s   e Zd ZdZddd„ZdS )r±  z=
  A lalapps_heterodyne_pulsar job to heterodyne the data.
  ró   Nr¸   c	       	      C   sú   || _ || _tj | | j| j ¡ tj | d ¡ |d krB|  d|¡ |d krV|  d|¡ |  dd¡ |d k	r€t|tƒr€|  d|¡ |d kr²|  	t
j |d¡¡ |  t
j |d¡¡ n|  	d¡ |  d¡ |d krè|  t
j ||d ¡¡ n|  |d ¡ d S )	Nr)   r*   ÚgetenvÚTrueÚrequest_memoryzheterodyne-$(cluster).outzheterodyne-$(cluster).errzheterodyne.sub)Z_heterodyneJob__executableZ_heterodyneJob__universer   ÚCondorDAGJobre   ÚAnalysisJobrú  r   r   Úset_stdout_filer.   r/   r1   Úset_stderr_filerû  )	r3   Úexecur§   r¤   r¥   r¦   rV   r«  rû   r   r   r"   re   \  s(      


zheterodyneJob.__init__)ró   NNNNr¸   N)r  r  r  Ú__doc__re   r   r   r   r"   r±  X  s   r±  c               @   s  e Zd ZdZdd„ Zdd„ Zdd„ Zdd	„ Zd
d„ Zdd„ Z	dd„ Z
dd„ Zdd„ Zdd„ Zdd„ Zdd„ Zdd„ Zdd„ Zdd„ Zd d!„ Zd"d#„ Zd$d%„ Zd&d'„ Zd(d)„ Zd*d+„ Zd,d-„ Zd.d/„ Zd0d1„ Zd2d3„ Zd4d5„ Zd6d7„ Zd8d9„ Zd:d;„ Z d<d=„ Z!d>d?„ Z"d@S )Ar¸  zU
  A heterodyneNode runs an instance of lalapps_heterodyne_pulsar in a condor DAG.
  c             C   sŠ   t j | |¡ t j | ¡ d| _d| _d| _d| _d| _d| _	d| _
d| _d| _d| _
d| _d| _d| _d| _d| _d| _d| _d| _dS )zT
    job = A CondorDAGJob that can run an instance of lalapps_heterodyne_pulsar
    NF)r   ÚCondorDAGNodere   ÚAnalysisNodeÚ_heterodyneNode__ifoÚ_heterodyneNode__param_fileÚ_heterodyneNode__freq_factorÚ_heterodyneNode__filter_kneeÚ_heterodyneNode__sample_rateÚ_heterodyneNode__resample_rateÚ_heterodyneNode__data_fileÚ_heterodyneNode__channelÚ_heterodyneNode__seg_listÚ_heterodyneNode__output_fileÚ_heterodyneNode__het_flagÚ_heterodyneNode__pulsarZ_heterodyneNode__high_passZ_heterodyneNode__scale_facÚ_heterodyneNode__manual_epochÚ_heterodyneNode__gzipÚ _heterodyneNode__max_data_length)r3   Újobr   r   r"   re   }  s(    zheterodyneNode.__init__c             C   s   |   d|¡ || _d S )Nz	data-file)Úadd_var_optr&  )r3   Z	data_filer   r   r"   rº  ˜  s    zheterodyneNode.set_data_filec             C   s   |   d|¡ || _d S )Nzdata-chunk-length)r0  r.  )r3   Zmaxdatalengthr   r   r"   r¼    s    z"heterodyneNode.set_max_data_lengthc             C   s   |   d|¡ || _d S )Nzoutput-file)r0  r)  )r3   Zoutput_filer   r   r"   r¿  ¢  s    zheterodyneNode.set_output_filec             C   s   |   d|¡ || _d S )Nzseg-file)r0  r(  )r3   Zseg_listr   r   r"   r½  §  s    zheterodyneNode.set_seg_listc             C   s   |   d|¡ || _d S )Nr   )r0  r   )r3   r   r   r   r"   rÂ  ¬  s    zheterodyneNode.set_ifoc             C   s   |   d|¡ || _d S )Nz
param-file)r0  r!  )r3   Z
param_filer   r   r"   rÅ  ±  s    zheterodyneNode.set_param_filec             C   s   |   d|¡ || _d S )Nzfreq-factor)r0  r"  )r3   Zfreq_factorr   r   r"   rÉ  ¶  s    zheterodyneNode.set_freq_factorc             C   s   |   d|¡ d S )Nzparam-file-update)r0  )r3   Zparam_file_updater   r   r"   Úset_param_file_update»  s    z$heterodyneNode.set_param_file_updatec             C   s   |   d|¡ || _d S )Nzmanual-epoch)r0  r,  )r3   Zmanual_epochr   r   r"   Úset_manual_epoch¿  s    zheterodyneNode.set_manual_epochc             C   s   |   d|¡ d S )Nzephem-earth-file)r0  )r3   Zephem_earth_filer   r   r"   rÍ  Ä  s    z#heterodyneNode.set_ephem_earth_filec             C   s   |   d|¡ d S )Nzephem-sun-file)r0  )r3   Zephem_sun_filer   r   r"   rÎ  È  s    z!heterodyneNode.set_ephem_sun_filec             C   s   |   d|¡ d S )Nzephem-time-file)r0  )r3   Zephem_time_filer   r   r"   rÏ  Ì  s    z"heterodyneNode.set_ephem_time_filec             C   s   |   d|¡ || _d S )NÚpulsar)r0  r+  )r3   r3  r   r   r"   rÄ  Ð  s    zheterodyneNode.set_pulsarc             C   s   |   d|¡ || _d S )Nzheterodyne-flag)r0  r*  )r3   Zhet_flagr   r   r"   rÃ  Õ  s    zheterodyneNode.set_het_flagc             C   s   |   d|¡ || _d S )Nzfilter-knee)r0  r#  )r3   r¨  r   r   r"   rÆ  Ú  s    zheterodyneNode.set_filter_kneec             C   s   |   d|¡ || _d S )NÚchannel)r0  r'  )r3   r4  r   r   r"   r¾  ß  s    zheterodyneNode.set_channelc             C   s   |   d|¡ || _d S )Nzsample-rate)r0  r$  )r3   Zsample_rater   r   r"   rÇ  ä  s    zheterodyneNode.set_sample_ratec             C   s   |   d|¡ || _d S )Nzresample-rate)r0  r%  )r3   Zresample_rater   r   r"   rÈ  é  s    z heterodyneNode.set_resample_ratec             C   s   |   d|¡ d S )Nzstddev-thresh)r0  )r3   rª  r   r   r"   rÌ  î  s    z heterodyneNode.set_stddev_threshc             C   s   |   dd¡ d S )NZ	calibrater¸   )r0  )r3   r   r   r"   Úset_calibrateò  s    zheterodyneNode.set_calibratec             C   s   |   dd¡ d S )NÚverboser¸   )r0  )r3   r   r   r"   Úset_verboseö  s    zheterodyneNode.set_verbosec             C   s   |   dd¡ d S )Nzbinary-inputr¸   )r0  )r3   r   r   r"   rË  ú  s    zheterodyneNode.set_bininputc             C   s   |   dd¡ d S )Nzbinary-outputr¸   )r0  )r3   r   r   r"   rÀ  þ  s    zheterodyneNode.set_binoutputc             C   s   |   dd¡ d| _d S )Nzgzip-outputr¸   T)r0  r-  )r3   r   r   r"   rÁ    s    zheterodyneNode.set_gzip_outputc             C   s   |   d|¡ d S )Nzresponse-file)r0  )r3   Zresponse_functionr   r   r"   Úset_response_function  s    z$heterodyneNode.set_response_functionc             C   s   |   d|¡ d S )Nzcoefficient-file)r0  )r3   Zcoefficient_filer   r   r"   Úset_coefficient_file  s    z#heterodyneNode.set_coefficient_filec             C   s   |   d|¡ d S )Nzsensing-function)r0  )r3   Zsensing_functionr   r   r"   Úset_sensing_function  s    z#heterodyneNode.set_sensing_functionc             C   s   |   d|¡ d S )Nzopen-loop-gain)r0  )r3   Zopen_loop_gainr   r   r"   Úset_open_loop_gain  s    z!heterodyneNode.set_open_loop_gainc             C   s   |   d|¡ d S )Nzscale-factor)r0  )r3   Z	scale_facr   r   r"   Úset_scale_fac  s    zheterodyneNode.set_scale_facc             C   s   |   d|¡ d S )Nzhigh-pass-freq)r0  )r3   Z	high_passr   r   r"   Úset_high_pass  s    zheterodyneNode.set_high_passN)#r  r  r  r  re   rº  r¼  r¿  r½  rÂ  rÅ  rÉ  r1  r2  rÍ  rÎ  rÏ  rÄ  rÃ  rÆ  r¾  rÇ  rÈ  rÌ  r5  r7  rË  rÀ  rÁ  r8  r9  r:  r;  r<  r=  r   r   r   r"   r¸  y  s@   r¸  c               @   s   e Zd ZdZddd„ZdS )rÞ  z1
  A lalapps_SplInter job to process SFT data.
  ró   Nc             C   sò   || _ || _tj | | j| j ¡ tj | d ¡ |d krB|  d|¡ |d krV|  d|¡ |  dd¡ |d k	r€t|tƒr€|  d|¡ |d kr²|  	t
j |d¡¡ |  t
j |d¡¡ n|  	d¡ |  d¡ |d krä|  t
j |d¡¡ n
|  d¡ d S )	Nr)   r*   r  r  r  zsplinter-$(cluster).outzsplinter-$(cluster).errzsplinter.sub)Z_splinterJob__executableZ_splinterJob__universer   r  re   r  rú  r   r   r  r.   r/   r1   r  rû  )r3   r  r§   r¤   r¥   r¦   rV   rû   r   r   r"   re   $  s(      


zsplinterJob.__init__)ró   NNNNN)r  r  r  r  re   r   r   r   r"   rÞ     s   rÞ  c               @   s°   e Zd ZdZdd„ Zdd„ Zdd„ Zdd	„ Zd
d„ Zdd„ Z	dd„ Z
dd„ Zdd„ Zdd„ Zdd„ Zdd„ Zdd„ Zdd„ Zdd„ Zd d!„ Zd"d#„ Zd$d%„ Zd&d'„ Zd(d)„ Zd*S )+rá  zJ
  A splinterNode runs an instance of lalapps_Splinter in a condor DAG.
  c             C   s–   t j | |¡ t j | ¡ d| _d| _d| _d| _d| _d| _	d| _
d| _d| _d| _d| _d| _d| _d| _d| _d| _d| _d| _d| _d| _dS )zK
    job = A CondorDAGJob that can run an instance of lalapps_SplInter
    NF)r   r  re   r  Ú_splinterNode__ifoÚ_splinterNode__param_fileÚ_splinterNode__param_dirÚ_splinterNode__start_freqZ_splinterNode__end_freqÚ_splinterNode__freq_factorZ_splinterNode__data_fileÚ_splinterNode__seg_listÚ_splinterNode__sft_cacheÚ_splinterNode__sft_locÚ_splinterNode__sft_lalcacheÚ_splinterNode__output_dirÚ_splinterNode__stddev_threshÚ_splinterNode__bandwidthÚ_splinterNode__min_seg_lengthÚ_splinterNode__max_seg_lengthÚ_splinterNode__starttimeÚ_splinterNode__endtimeÚ_splinterNode__ephem_dirÚ_splinterNode__gzip)r3   r/  r   r   r"   re   E  s,    zsplinterNode.__init__c             C   s   |   d|¡ || _d S )Nz
start-freq)r0  rA  )r3   rü   r   r   r"   rè  b  s    zsplinterNode.set_start_freqc             C   s   |   d|¡ d S )Nzend-freq)r0  )r3   rü   r   r   r"   ré  g  s    zsplinterNode.set_end_freqc             C   s   |   d|¡ || _d S )Nz	sft-cache)r0  rD  )r3   rü   r   r   r"   Úset_sft_cachek  s    zsplinterNode.set_sft_cachec             C   s   |   d|¡ || _d S )Nzsft-lalcache)r0  rF  )r3   rü   r   r   r"   râ  p  s    zsplinterNode.set_sft_lalcachec             C   s   |   d|¡ || _d S )Nzsft-loc)r0  rE  )r3   rü   r   r   r"   Úset_sft_locu  s    zsplinterNode.set_sft_locc             C   s   |   d|¡ || _d S )Nz
output-dir)r0  rG  )r3   rü   r   r   r"   rã  z  s    zsplinterNode.set_output_dirc             C   s   |   d|¡ || _d S )Nzseg-file)r0  rC  )r3   rü   r   r   r"   r½    s    zsplinterNode.set_seg_listc             C   s   |   d|¡ || _d S )Nr   )r0  r>  )r3   r   r   r   r"   rÂ  „  s    zsplinterNode.set_ifoc             C   s   |   d|¡ || _d S )Nz
param-file)r0  r?  )r3   rü   r   r   r"   rÅ  ‰  s    zsplinterNode.set_param_filec             C   s   |   d|¡ || _d S )Nz	param-dir)r0  r@  )r3   rü   r   r   r"   rä  Ž  s    zsplinterNode.set_param_dirc             C   s   |   d|¡ || _d S )Nzfreq-factor)r0  rB  )r3   rü   r   r   r"   rÉ  “  s    zsplinterNode.set_freq_factorc             C   s   |   d|¡ || _d S )NrÛ  )r0  rI  )r3   rü   r   r   r"   rå  ˜  s    zsplinterNode.set_bandwidthc             C   s   |   d|¡ || _d S )Nzmin-seg-length)r0  rJ  )r3   rü   r   r   r"   ræ    s    zsplinterNode.set_min_seg_lengthc             C   s   |   d|¡ || _d S )Nzmax-seg-length)r0  rK  )r3   rü   r   r   r"   rç  ¢  s    zsplinterNode.set_max_seg_lengthc             C   s   |   d|¡ || _d S )Nz	ephem-dir)r0  rN  )r3   rü   r   r   r"   rê  §  s    zsplinterNode.set_ephem_dirc             C   s   |   d|¡ || _d S )NZstddevthresh)r0  rH  )r3   rü   r   r   r"   rÌ  ¬  s    zsplinterNode.set_stddev_threshc             C   s   |   dd¡ d| _d S )NÚgzipr¸   T)r0  rO  )r3   r   r   r"   rÁ  ±  s    zsplinterNode.set_gzip_outputc             C   s   |   d|¡ || _d S )Nr   )r0  rL  )r3   rü   r   r   r"   Úset_starttime¶  s    zsplinterNode.set_starttimec             C   s   |   d|¡ || _d S )Nr$   )r0  rM  )r3   rü   r   r   r"   Úset_endtime»  s    zsplinterNode.set_endtimeN)r  r  r  r  re   rè  ré  rP  râ  rQ  rã  r½  rÂ  rÅ  rä  rÉ  rå  ræ  rç  rê  rÌ  rÁ  rS  rT  r   r   r   r"   rá  A  s*   rá  c               @   s   e Zd ZdZddd„ZdS )r·  zb
  A concatenation job (using "cat" and output to stdout - a new job is needed for each pulsar)
  Nc             C   sä   d| _ d| _tj | | j| j ¡ tj | d ¡ |d krB|  d|¡ |d krV|  d|¡ |d krxtdtj	d t 
d¡ n
|  |¡ |d kr¤tdtj	d t 
d¡ n
|  |¡ |d krÌ|  tj |d	¡¡ n
|  d	¡ |  d
¡ d S )Nz/bin/catrš   r)   r*   z7Error... Condor sub file required for concatenation job)r   r?   z3Error... output file required for concatenation jobzconcat-$(cluster).errz$(macrocatfiles))Z_concatJob__executableZ_concatJob__universer   r  re   r  rú  rK   rO   rP   Úexitrû  r  r  r.   r/   r1   Úadd_arg)r3   r­  r¨   r¤   r¥   r¦   r   r   r"   re   È  s(      


zconcatJob.__init__)NNNNN)r  r  r  r  re   r   r   r   r"   r·  Ä  s   r·  c               @   s    e Zd ZdZdd„ Zdd„ ZdS )rÊ  z
  A node for a concatJob
  c             C   s$   t j | |¡ t j | ¡ d| _dS )zU
    job = A CondorDAGJob that can run an instance of parameter estimation code.
    N)r   r  re   r  Ú_concatNode__files)r3   r/  r   r   r"   re   ë  s    zconcatNode.__init__c             C   s   |   dd |¡¡ || _d S )NZmacrocatfilesrT  )Ú	add_macror1   rW  )r3   r®   r   r   r"   rA  ô  s    zconcatNode.set_filesN)r  r  r  r  re   rA  r   r   r   r"   rÊ  æ  s   	rÊ  c               @   s   e Zd ZdZddd„ZdS )r  z/
  A remove job (using "rm" to remove files)
  Nc             C   sÒ   d| _ d| _tj | | j| j ¡ tj | d ¡ |d krB|  d|¡ |d krV|  d|¡ |d krˆ|  tj	 
|d¡¡ |  tj	 
|d¡¡ n|  d¡ |  d¡ |  d¡ |d krÄ|  tj	 
|d¡¡ n
|  d¡ d S )	Nz/bin/rmrš   r)   r*   zrm-$(cluster).outzrm-$(cluster).errz-f $(macrormfiles)zrm.sub)Z_removeJob__executableZ_removeJob__universer   r  re   r  rú  r  r.   r/   r1   r  rV  rû  )r3   r¤   r¥   r¦   rV   r   r   r"   re     s"      


zremoveJob.__init__)NNNN)r  r  r  r  re   r   r   r   r"   r  ý  s   r  c               @   s    e Zd ZdZdd„ Zdd„ ZdS )r@  z1
  An instance of a removeJob in a condor DAG.
  c             C   s.   t j | |¡ t j | ¡ d| _|  d¡ dS )z>
    job = A CondorDAGJob that can run an instance of rm.
    Nr?   )r   r  re   r  Ú_removeNode__filesÚ	set_retry)r3   r/  r   r   r"   re     s    zremoveNode.__init__c             C   s   |   dd |¡¡ || _d S )NZmacrormfilesrT  )rX  r1   rY  )r3   r®   r   r   r"   rA  )  s    zremoveNode.set_filesN)r  r  r  r  re   rA  r   r   r   r"   r@    s   
r@  c               @   s   e Zd ZdZddd„ZdS )r  z+
  A move job (using "mv" to move files)
  Nc             C   sÒ   d| _ d| _tj | | j| j ¡ tj | d ¡ |d krB|  d|¡ |d krV|  d|¡ |d krˆ|  tj	 
|d¡¡ |  tj	 
|d¡¡ n|  d¡ |  d¡ |  d¡ |d krÄ|  tj	 
|d¡¡ n
|  d¡ d S )	Nz/bin/mvrš   r)   r*   zmv-$(cluster).outzmv-$(cluster).errz"$(macrosource) $(macrodestination)zmv.sub)Z_moveJob__executableZ_moveJob__universer   r  re   r  rú  r  r.   r/   r1   r  rV  rû  )r3   r¤   r¥   r¦   rV   r   r   r"   re   6  s"      


zmoveJob.__init__)NNNN)r  r  r  r  re   r   r   r   r"   r  2  s   r  c               @   s(   e Zd ZdZdd„ Zdd„ Zdd„ ZdS )	r<  z/
  An instance of a moveJob in a condor DAG.
  c             C   s4   t j | |¡ t j | ¡ d| _d| _|  d¡ dS )z>
    job = A CondorDAGJob that can run an instance of mv.
    Nr?   )r   r  re   r  Z_moveNode__sourcefileÚ_moveNode__destinationfilerZ  )r3   r/  r   r   r"   re   T  s
    zmoveNode.__init__c             C   s   |   d|¡ || _d S )NÚmacrosource)rX  Z_moveNode__sourcefiles)r3   Úsfiler   r   r"   rÖ   _  s    zmoveNode.set_sourcec             C   s   |   d|¡ || _d S )NÚmacrodestination)rX  r[  )r3   Údfiler   r   r"   r×   d  s    zmoveNode.set_destinationN)r  r  r  r  re   rÖ   r×   r   r   r   r"   r<  P  s   r<  c               @   s   e Zd ZdZddd„ZdS )r¾   z+
  A copy job (using "cp" to copy files)
  Nc             C   sÒ   d| _ d| _tj | | j| j ¡ tj | d ¡ |d krB|  d|¡ |d krV|  d|¡ |d krˆ|  tj	 
|d¡¡ |  tj	 
|d¡¡ n|  d¡ |  d¡ |  d¡ |d krÄ|  tj	 
|d¡¡ n
|  d¡ d S )	Nz/bin/cprš   r)   r*   zcp-$(cluster).outzcp-$(cluster).errz"$(macrosource) $(macrodestination)zcp.sub)Z_copyJob__executableZ_copyJob__universer   r  re   r  rú  r  r.   r/   r1   r  rV  rû  )r3   r¤   r¥   r¦   rV   r   r   r"   re   q  s"      


zcopyJob.__init__)NNNN)r  r  r  r  re   r   r   r   r"   r¾   m  s   r¾   c               @   s(   e Zd ZdZdd„ Zdd„ Zdd„ ZdS )	rÕ   z/
  An instance of a copyJob in a condor DAG.
  c             C   s4   t j | |¡ t j | ¡ d| _d| _|  d¡ dS )z>
    job = A CondorDAGJob that can run an instance of mv.
    Nr?   )r   r  re   r  Z_copyNode__sourcefileÚ_copyNode__destinationfilerZ  )r3   r/  r   r   r"   re     s
    zcopyNode.__init__c             C   s   |   d|¡ || _d S )Nr\  )rX  Z_copyNode__sourcefiles)r3   r]  r   r   r"   rÖ   š  s    zcopyNode.set_sourcec             C   s   |   d|¡ || _d S )Nr^  )rX  r`  )r3   r_  r   r   r"   r×   Ÿ  s    zcopyNode.set_destinationN)r  r  r  r  re   rÖ   r×   r   r   r   r"   rÕ   ‹  s   rÕ   c               @   s   e Zd ZdZddd„ZdS )r  z 
  A parameter estimation job
  ró   Nc             C   sü   || _ || _tj | | j| j ¡ tj | d ¡ |d krB|  d|¡ |d krV|  d|¡ |  dd¡ |d k	r€t|tƒr€|  d|¡ |d kr²|  	t
j |d¡¡ |  t
j |d¡¡ n|  	d¡ |  d¡ |d krä|  t
j |d¡¡ n
|  d¡ |  d	¡ d S )
Nr)   r*   r  r  r  zppe$(logname)-$(cluster).outzppe$(logname)-$(cluster).errzppe.subz$(macroargs))Z_ppeJob__executableZ_ppeJob__universer   r  re   r  rú  r   r   r  r.   r/   r1   r  rû  rV  )r3   r  r§   r¤   r¥   r¦   rV   rû   r   r   r"   re   ¬  s*      



zppeJob.__init__)ró   NNNNN)r  r  r  r  re   r   r   r   r"   r  ¨  s   r  c               @   sÊ  e Zd ZdZdrdd„Zdd„ Zdd„ Zd	d
„ Zdd„ Zdd„ Z	dd„ Z
dd„ Zdd„ Zdd„ Zdd„ Zdd„ Zdd„ Zdd„ Zdd „ Zd!d"„ Zd#d$„ Zd%d&„ Zd'd(„ Zd)d*„ Zd+d,„ Zd-d.„ Zd/d0„ Zd1d2„ Zd3d4„ Zd5d6„ Zd7d8„ Zd9d:„ Zd;d<„ Z d=d>„ Z!d?d@„ Z"dAdB„ Z#dCdD„ Z$dEdF„ Z%dGdH„ Z&dIdJ„ Z'dKdL„ Z(dMdN„ Z)dOdP„ Z*dQdR„ Z+dSdT„ Z,dUdV„ Z-dWdX„ Z.dYdZ„ Z/d[d\„ Z0d]d^„ Z1d_d`„ Z2dadb„ Z3dcdd„ Z4dedf„ Z5dgdh„ Z6didj„ Z7dkdl„ Z8dmdn„ Z9dodp„ Z:dqS )sr  zN
  A pes runs an instance of the parameter estimation code in a condor DAG.
  r¸   c             C   s”  t j | |¡ t j | ¡ d| _d| _d| _d| _d| _d| _	d| _
d| _d| _d| _d| _d| _d| _d| _d| _d| _d| _d| _d| _d| _d| _d| _d| _d| _d| _d| _d| _d| _d| _ d| _!d| _"d| _#d| _$d| _%d| _&d| _'d| _(d| _)d| _*d| _+d| _,d| _-d| _.d| _/d| _0d| _1d| _2d| _3d| _4d| _5d| _6d| _7d| _8|  9dd¡ t:|ƒdkr„|  9dd| ¡ n|  9dd¡ dS )zU
    job = A CondorDAGJob that can run an instance of parameter estimation code.
    NFÚ	macroargsr¸   r   Úlognamerí  );r   r  re   r  Ú_ppeNode__detectorsÚ_ppeNode__par_fileÚ_ppeNode__cor_fileÚ_ppeNode__input_filesÚ_ppeNode__outfileÚ_ppeNode__chunk_minÚ_ppeNode__chunk_maxÚ_ppeNode__psi_binsÚ_ppeNode__time_binsÚ_ppeNode__prior_fileÚ_ppeNode__ephem_earthÚ_ppeNode__ephem_sunÚ_ppeNode__ephem_timeÚ_ppeNode__harmonicsÚ_ppeNode__biaxialÚ_ppeNode__gaussian_likeÚ_ppeNode__randomiseÚ_ppeNode__starttimeÚ_ppeNode__endtimeÚ_ppeNode__truncate_timeÚ_ppeNode__truncate_samplesÚ_ppeNode__truncate_fractionÚ_ppeNode__veto_thresholdÚ_ppeNode__NliveÚ_ppeNode__NmcmcÚ_ppeNode__NmcmcinitialÚ_ppeNode__NrunsÚ_ppeNode__toleranceÚ_ppeNode__randomseedÚ_ppeNode__use_roqÚ_ppeNode__roq_ntrainingÚ_ppeNode__roq_toleranceÚ_ppeNode__roq_uniformÚ_ppeNode__roq_output_weightsÚ_ppeNode__roq_input_weightsÚ_ppeNode__temperatureZ_ppeNode__ensmeble_walkÚ_ppeNode__ensemble_stretchÚ_ppeNode__diffevÚ_ppeNode__inject_fileÚ_ppeNode__inject_outputÚ_ppeNode__fake_dataÚ_ppeNode__fake_psdÚ_ppeNode__fake_startsÚ_ppeNode__fake_lengthsÚ_ppeNode__fake_dtÚ_ppeNode__scale_snrÚ_ppeNode__sample_filesÚ_ppeNode__sample_nlivesÚ_ppeNode__prior_cellÚ_ppeNode__oldChunksÚ_ppeNode__sourceModelÚ_ppeNode__verboserX  rW   )r3   r/  r   r   r   r"   re   Ï  sv    zppeNode.__init__c             C   sT   |   d|¡ || _d|  ¡ kr,|  ¡ d }nd}|d | dd¡ }|  d|¡ d S )Nr«   rb  r¸   rí  r  )r0  rc  Úget_optsrl  rX  )r3   r«   Úcurmacrovalr   r   r"   r    s    zppeNode.set_detectorsc             C   s   |   dd¡ d| _d S )Nr6  r¸   T)r0  r–  )r3   r   r   r"   r7  +  s    zppeNode.set_verbosec             C   s   |   d|¡ || _d S )Nzpar-file)r0  rd  )r3   r±   r   r   r"   r  0  s    zppeNode.set_par_filec             C   s@   d|   ¡ kr|   ¡ d }nd}|d | }|  d|¡ || _d S )Nra  r¸   z --cor-file )r—  rX  re  )r3   r~  r˜  r   r   r"   r  5  s    zppeNode.set_cor_filec             C   s   |   d|¡ || _d S )Nzinput-files)r0  rf  )r3   rH  r   r   r"   r1  B  s    zppeNode.set_input_filesc             C   s   |   d|¡ || _d S )Nr}  )r0  rg  )r3   Zofr   r   r"   r(  G  s    zppeNode.set_outfilec             C   s   |   d|¡ || _d S )Nz	chunk-min)r0  rh  )r3   Zcminr   r   r"   Úset_chunk_minL  s    zppeNode.set_chunk_minc             C   s   |   d|¡ || _d S )Nz	chunk-max)r0  ri  )r3   Zcmaxr   r   r"   Úset_chunk_maxQ  s    zppeNode.set_chunk_maxc             C   s   |   d|¡ || _d S )Nz
start-time)r0  rt  )r3   r   r   r   r"   r#  V  s    zppeNode.set_start_timec             C   s   |   d|¡ || _|| _d S )Nzend-time)r0  ru  rv  )r3   r$   r   r   r"   r$  [  s    zppeNode.set_end_timec             C   s&   | j d kr"|  d|¡ || _|| _ d S )Nztruncate-time)ru  r0  rv  )r3   Útruncr   r   r"   r%  a  s    
zppeNode.set_truncate_timec             C   s   |   d|¡ || _d S )Nztruncate-samples)r0  rw  )r3   r›  r   r   r"   r&  h  s    zppeNode.set_truncate_samplesc             C   s   |   d|¡ || _d S )Nztruncate-fraction)r0  rx  )r3   r›  r   r   r"   r'  m  s    zppeNode.set_truncate_fractionc             C   s   |   d|¡ || _d S )Nzveto-threshold)r0  ry  )r3   Zvetor   r   r"   Úset_veto_thresholdr  s    zppeNode.set_veto_thresholdc             C   s   |   d|¡ || _d S )Nzpsi-bins)r0  rj  )r3   Zpbr   r   r"   Úset_psi_binsw  s    zppeNode.set_psi_binsc             C   s   |   d|¡ || _d S )Nz	time-bins)r0  rk  )r3   Útbr   r   r"   Úset_time_bins|  s    zppeNode.set_time_binsc             C   s   |   d|¡ || _d S )Nz
prior-file)r0  rl  )r3   r2   r   r   r"   r    s    zppeNode.set_prior_filec             C   s   |   d|¡ || _d S )Nzephem-earth)r0  rm  )r3   Úeer   r   r"   r6  †  s    zppeNode.set_ephem_earthc             C   s   |   d|¡ || _d S )Nz	ephem-sun)r0  rn  )r3   Úesr   r   r"   r7  ‹  s    zppeNode.set_ephem_sunc             C   s   |   d|¡ || _d S )Nzephem-timecorr)r0  ro  )r3   r
  r   r   r"   r8    s    zppeNode.set_ephem_timec             C   s   |   d|¡ || _d S )Nr³   )r0  rp  )r3   Úhr   r   r"   r  •  s    zppeNode.set_harmonicsc             C   s   |   d|¡ || _d S )NÚNlive)r0  rz  )r3   Únlr   r   r"   r  š  s    zppeNode.set_Nlivec             C   s   |   d|¡ || _d S )NZNmcmc)r0  r{  )r3   Únmr   r   r"   r   Ÿ  s    zppeNode.set_Nmcmcc             C   s   |   d|¡ || _d S )NZNmcmcinitial)r0  r|  )r3   r¥  r   r   r"   r!  ¤  s    zppeNode.set_Nmcmcinitialc             C   s   |   d|¡ || _d S )NZNruns)r0  r}  )r3   Únrr   r   r"   Ú	set_Nruns©  s    zppeNode.set_Nrunsc             C   s   |   d|¡ || _d S )Nrô   )r0  r~  )r3   r™  r   r   r"   r"  ®  s    zppeNode.set_tolerancec             C   s   |   d|¡ || _d S )NZ
randomseed)r0  r  )r3   Úrsr   r   r"   r  ³  s    zppeNode.set_randomseedc             C   s   |   d|¡ || _d S )NZensembleStretch)r0  r‡  )r3   rü   r   r   r"   Úset_ensemble_stretch¸  s    zppeNode.set_ensemble_stretchc             C   s   |   d|¡ || _d S )NZensembleWalk)r0  Z_ppeNode__ensemble_walk)r3   rü   r   r   r"   Úset_ensemble_walk½  s    zppeNode.set_ensemble_walkc             C   s   |   d|¡ || _d S )NZtemperature)r0  r†  )r3   Útempr   r   r"   Úset_temperatureÂ  s    zppeNode.set_temperaturec             C   s   |   d|¡ || _d S )NZdiffev)r0  rˆ  )r3   Úder   r   r"   Ú
set_diffevÇ  s    zppeNode.set_diffevc             C   s   |   d|¡ || _d S )Nzinject-file)r0  r‰  )r3   Zifilr   r   r"   Úset_inject_fileÌ  s    zppeNode.set_inject_filec             C   s   |   d|¡ || _d S )Nzinject-output)r0  rŠ  )r3   Zioutr   r   r"   Úset_inject_outputÑ  s    zppeNode.set_inject_outputc             C   s   |   d|¡ || _d S )Nz	fake-data)r0  r‹  )r3   Úfdr   r   r"   Úset_fake_dataÖ  s    zppeNode.set_fake_datac             C   s   |   d|¡ || _d S )Nzfake-psd)r0  rŒ  )r3   rŒ   r   r   r"   Úset_fake_psdÛ  s    zppeNode.set_fake_psdc             C   s   |   d|¡ || _d S )Nzfake-starts)r0  r  )r3   Úfsr   r   r"   Úset_fake_startsà  s    zppeNode.set_fake_startsc             C   s   |   d|¡ || _d S )Nzfake-lengths)r0  rŽ  )r3   Úflr   r   r"   Úset_fake_lengthså  s    zppeNode.set_fake_lengthsc             C   s   |   d|¡ || _d S )Nzfake-dt)r0  r  )r3   Zfdtr   r   r"   Úset_fake_dtê  s    zppeNode.set_fake_dtc             C   s   |   d|¡ || _d S )Nz	scale-snr)r0  r  )r3   Zssnrr   r   r"   Úset_scale_snrï  s    zppeNode.set_scale_snrc             C   s   |   d|¡ || _d S )Nzsample-files)r0  r‘  )r3   Zssfr   r   r"   Úset_sample_filesô  s    zppeNode.set_sample_filesc             C   s   |   d|¡ || _d S )Nzsample-nlives)r0  r’  )r3   Zsnlr   r   r"   Úset_sample_nlivesù  s    zppeNode.set_sample_nlivesc             C   s   |   d|¡ || _d S )Nz
prior-cell)r0  r“  )r3   Zpcr   r   r"   Úset_prior_cellþ  s    zppeNode.set_prior_cellc             C   s   |   dd¡ d| _d S )NZ	oldChunksr¸   T)r0  r”  )r3   r   r   r"   Úset_OldChunks  s    zppeNode.set_OldChunksc             C   s<   d|   ¡ kr|   ¡ d }nd}|d }|  d|¡ d| _d S )Nra  r¸   z --source-modelT)r—  rX  r•  )r3   r˜  r   r   r"   r3    s    zppeNode.set_source_modelc             C   s<   d|   ¡ kr|   ¡ d }nd}|d }|  d|¡ d| _d S )Nra  r¸   z
 --biaxialT)r—  rX  rq  )r3   r˜  r   r   r"   r4    s    zppeNode.set_biaxialc             C   s   |   dd¡ d| _d S )Nzgaussian-liker¸   T)r0  rr  )r3   r   r   r"   r2     s    zppeNode.set_gaussian_likec             C   s@   d|   ¡ kr|   ¡ d }nd}|d | }|  d|¡ || _d S )Nra  r¸   z --randomise )r—  rX  rs  )r3   rü   r˜  r   r   r"   r0  %  s    zppeNode.set_randomisec             C   s<   d|   ¡ kr|   ¡ d }nd}|d }|  d|¡ d| _d S )Nra  r¸   z --roqT)r—  rX  r€  )r3   r˜  r   r   r"   r)  1  s    zppeNode.set_roqc             C   s@   d|   ¡ kr|   ¡ d }nd}|d | }|  d|¡ || _d S )Nra  r¸   z --ntraining )r—  rX  r  )r3   rü   r˜  r   r   r"   r+  =  s    zppeNode.set_roq_ntrainingc             C   s@   d|   ¡ kr|   ¡ d }nd}|d | }|  d|¡ || _d S )Nra  r¸   z --roq-tolerance )r—  rX  r‚  )r3   rü   r˜  r   r   r"   r,  H  s    zppeNode.set_roq_tolerancec             C   s<   d|   ¡ kr|   ¡ d }nd}|d }|  d|¡ d| _d S )Nra  r¸   z --roq-uniformT)r—  rX  rƒ  )r3   r˜  r   r   r"   r.  S  s    zppeNode.set_roq_uniformc             C   s@   d|   ¡ kr|   ¡ d }nd}|d | }|  d|¡ || _d S )Nra  r¸   z --input-weights )r—  rX  r…  )r3   rü   r˜  r   r   r"   r/  ^  s    zppeNode.set_roq_inputweightsc             C   s@   d|   ¡ kr|   ¡ d }nd}|d | }|  d|¡ || _d S )Nra  r¸   z --output-weights )r—  rX  r„  )r3   rü   r˜  r   r   r"   r-  i  s    zppeNode.set_roq_outputweightsc             C   sD   d|   ¡ kr|   ¡ d }nd}|d | }|  d|¡ t|ƒ| _d S )Nra  r¸   z --chunk-max )r—  rX  r   ri  )r3   rü   r˜  r   r   r"   r*  t  s    zppeNode.set_roq_chunkmaxN)r¸   );r  r  r  r  re   r  r7  r  r  r1  r(  r™  rš  r#  r$  r%  r&  r'  rœ  r  rŸ  r  r6  r7  r8  r  r  r   r!  r§  r"  r  r©  rª  r¬  r®  r¯  r°  r²  r³  rµ  r·  r¸  r¹  rº  r»  r¼  r½  r3  r4  r2  r0  r)  r+  r,  r.  r/  r-  r*  r   r   r   r"   r  Ë  sp   
Or  c               @   s   e Zd Zddd„ZdS )r¿   rš   Nc             C   sÞ   || _ || _tj | | j| j ¡ tj | d ¡ |d krB|  d|¡ |d krV|  d|¡ |  dd¡ |d kr”|  tj	 
|d¡¡ |  tj	 
|d¡¡ n|  d¡ |  d¡ |d krÆ|  tj	 
|d¡¡ n
|  d¡ |  d¡ d S )	Nr)   r*   r  r  zresultpage-$(cluster).outzresultpage-$(cluster).errzresultpage.subz$(macroconfigfile))Z_resultpageJob__executableZ_resultpageJob__universer   r  re   r  rú  r  r.   r/   r1   r  rû  rV  )r3   r  r§   r¤   r¥   r¦   rV   r   r   r"   re   „  s$      


zresultpageJob.__init__)rš   NNNN)r  r  r  re   r   r   r   r"   r¿   ƒ  s   r¿   c               @   s    e Zd ZdZdd„ Zdd„ ZdS )rÞ   zR
  A resultpageNode runs an instance of the result page script in a condor DAG.
  c             C   s$   t j | |¡ t j | ¡ d| _dS )zT
    job = A CondorDAGJob that can run an instance of lalapps_knope_result_page
    N)r   r  re   r  Ú_resultpageNode__configfile)r3   r/  r   r   r"   re   £  s    zresultpageNode.__init__c             C   s   |   d|¡ || _d S )NÚmacroconfigfile)rX  r¾  )r3   Ú
configfiler   r   r"   rß   ¬  s    zresultpageNode.set_configN)r  r  r  r  re   rß   r   r   r   r"   rÞ   Ÿ  s   	rÞ   c               @   s   e Zd Zddd„ZdS )rÀ   rš   Nc             C   sÞ   || _ || _tj | | j| j ¡ tj | d ¡ |d krB|  d|¡ |d krV|  d|¡ |  dd¡ |d kr”|  tj	 
|d¡¡ |  tj	 
|d¡¡ n|  d¡ |  d¡ |d krÆ|  tj	 
|d¡¡ n
|  d¡ |  d¡ d S )	Nr)   r*   r  r  zcollate-$(cluster).outzcollate-$(cluster).errzcollate.subz$(macroconfigfile))Z_collateJob__executableZ_collateJob__universer   r  re   r  rú  r  r.   r/   r1   r  rû  rV  )r3   r  r§   r¤   r¥   r¦   rV   r   r   r"   re   µ  s$      


zcollateJob.__init__)rš   NNNN)r  r  r  re   r   r   r   r"   rÀ   ´  s   rÀ   c               @   s    e Zd ZdZdd„ Zdd„ ZdS )rá   zY
  A collateNode runs an instance of the result page collation script in a condor DAG.
  c             C   s$   t j | |¡ t j | ¡ d| _dS )zX
    job = A CondorDAGJob that can run an instance of lalapps_knope_collate_results
    N)r   r  re   r  Ú_collateNode__configfile)r3   r/  r   r   r"   re   Ô  s    zcollateNode.__init__c             C   s   |   d|¡ || _d S )Nr¿  )rX  rÁ  )r3   rÀ  r   r   r"   rß   Ý  s    zcollateNode.set_configN)r  r  r  r  re   rß   r   r   r   r"   rá   Ð  s   	rá   c               @   s   e Zd ZdZddd„ZdS )r  zD
  A merge nested sampling files job to use lalinference_nest2pos
  rš   Nc             C   sè   || _ || _tj | | j| j ¡ tj | d ¡ |d krB|  d|¡ |d krV|  d|¡ |  dd¡ |d kr”|  tj	 
|d¡¡ |  tj	 
|d¡¡ n|  d¡ |  d¡ |  d¡ |  d¡ |d krÚ|  tj	 
|d	¡¡ n
|  d	¡ d S )
Nr)   r*   r  r  zn2p-$(cluster).outzn2p-$(cluster).errz--non-strict-versionsz$(macroinputfiles)zn2p.sub)Z_nest2posJob__executableZ_nest2posJob__universer   r  re   r  rú  r  r.   r/   r1   r  rV  rû  )r3   r  r§   r¤   r¥   r¦   rV   r   r   r"   re   æ  s&      



znest2posJob.__init__)rš   NNNN)r  r  r  r  re   r   r   r   r"   r  â  s   r  c               @   s@   e Zd ZdZdd„ Zdd„ Zdd„ Zdd	„ Zd
d„ Zdd„ Z	dS )r>  z~
  A nest2posNode runs a instance of the lalinference_nest2pos to combine individual nested
  sample files in a condor DAG.
  c             C   sL   t j | |¡ t j | ¡ |  d¡ d| _d| _d| _d| _d| _	d| _
dS )zV
    job = A CondorDAGJob that can run an of the nested sample combination script
    r?   NF)r   r  re   r  rZ  Ú_nest2posNode__nest_filesÚ_nest2posNode__nest_liveÚ_nest2posNode__outfileÚ_nest2posNode__headerÚ_nest2posNode__nposÚ_nest2posNode__gzip)r3   r/  r   r   r"   re     s    
znest2posNode.__init__c             C   sh   || _ tj |d ¡d  ¡ }|dkrR|dkrR|d  d¡d }|| _|  d|¡ |  dd	 	|¡¡ d S )
Nr   r   z.hdfz.h5z.gzz_params.txtÚheadersZmacroinputfilesrT  )
rÂ  r.   r/   r=  ÚlowerÚrstriprÅ  r0  rX  r1   )r3   rF  ZfeÚheaderr   r   r"   r?    s    znest2posNode.set_nest_filesc             C   s   |   d|¡ || _d S )Nr£  )r0  rÃ  )r3   Znestliver   r   r"   Úset_nest_live#  s    znest2posNode.set_nest_livec             C   s   |   d|¡ || _d S )NÚpos)r0  rÄ  )r3   r}  r   r   r"   r(  (  s    znest2posNode.set_outfilec             C   s   |   d|¡ || _d S )NÚnpos)r0  rÆ  )r3   rÎ  r   r   r"   Ú
set_numpos-  s    znest2posNode.set_numposc             C   s   |   dd¡ d| _d S )NrR  r¸   T)r0  rÇ  )r3   r   r   r"   Úset_gzip2  s    znest2posNode.set_gzipN)
r  r  r  r  re   r?  rÌ  r(  rÏ  rÐ  r   r   r   r"   r>    s   r>  c               @   s   e Zd ZdZdd„ ZdS )ÚcreateresultspageJobz7
  A job to create an individual pulsar results page
  c             C   s¸   || _ d| _tj | | j| j ¡ tj | d ¡ |  dd¡ |  d|¡ |  d|¡ |  |d ¡ |  |d ¡ |  	d¡ |  
d	¡ |  
d
¡ |  
d¡ |  
d¡ |  
d¡ |  
d¡ d S )Nró   r  r  r)   r*   z#/create_results_page-$(cluster).outz#/create_results_page-$(cluster).errzcreate_results_page.subz	$(macrom)z
$(macrobk)z	$(macroi)z	$(macrof)z	$(macrow)z	$(macros))Z!_createresultspageJob__executableZ_createresultspageJob__universer   r  re   r  rú  r  r  rû  rV  )r3   r  Úlogpathr¤   r¥   r   r   r"   re   <  s     





zcreateresultspageJob.__init__N)r  r  r  r  re   r   r   r   r"   rÑ  8  s   rÑ  c               @   s€   e Zd ZdZdd„ Zdd„ Zdd„ Zdd	„ Zd
d„ Zdd„ Z	dd„ Z
dd„ Zdd„ Zdd„ Zdd„ Zdd„ Zdd„ Zdd„ ZdS )ÚcreateresultspageNodez@
    A createresultspage node to run as part of a condor DAG.
  c             C   s`   t j | |¡ t j | ¡ d| _d| _g | _d| _g | _d| _	g | _
d| _g | _d| _d| _dS )zK
    job = A CondorDAGJob that can run the segment list finding script
    NF)r   r  re   r  Ú_createresultspageNode__outpathÚ_createresultspageNode__domcmcÚ _createresultspageNode__mcmcdirsÚ _createresultspageNode__donestedÚ#_createresultspageNode__nestedfilesÚ_createresultspageNode__parfileÚ_createresultspageNode__BkfilesZ!_createresultspageNode__priorfileÚ_createresultspageNode__ifosÚ _createresultspageNode__histbinsÚ_createresultspageNode__epsout)r3   r/  r   r   r"   re   V  s    zcreateresultspageNode.__init__c             C   s   | j d|dd || _d S )NÚoT)Úshort)r0  rÔ  )r3   Úvalr   r   r"   Úset_outpathj  s    z!createresultspageNode.set_outpathc             C   s   | j dddd d| _d S )NÚMr¸   T)rß  )r0  rÕ  )r3   r   r   r"   Ú
set_domcmcn  s    z createresultspageNode.set_domcmcc             C   s@   d}x|D ]}d||f }q
W |   d|¡ |   dd¡ || _d S )Nr¸   z%s-m %s ÚmacromÚmacrof)rX  rÖ  )r3   rà  Úmacrovalrü   r   r   r"   Úset_mcmcdirr  s    
z!createresultspageNode.set_mcmcdirc             C   s   |   dd¡ d| _d S )NÚnestedr¸   T)r0  r×  )r3   r   r   r"   Úset_donested{  s    z"createresultspageNode.set_donestedc             C   s@   d}x|D ]}d||f }q
W |   d|¡ |   dd¡ || _d S )Nr¸   z%s-f %s rå  rä  )rX  rØ  )r3   rà  ræ  rü   r   r   r"   Úset_nestedfiles  s    
z%createresultspageNode.set_nestedfilesc             C   s   | j d|dd || _d S )Nr“   T)rß  )r0  rÙ  )r3   rà  r   r   r"   Úset_parfileˆ  s    z!createresultspageNode.set_parfilec             C   s4   d}x|D ]}d||f }q
W |   d|¡ || _d S )Nr¸   z%s-b %s Zmacrobk)rX  rÚ  )r3   rà  ræ  rü   r   r   r"   Úset_bkfilesŒ  s
    
z!createresultspageNode.set_bkfilesc             C   s   | j d|dd d | _d S )Nr<   T)rß  )r0  Z _createresultspageNode__priordir)r3   rà  r   r   r"   Úset_priordir”  s    z"createresultspageNode.set_priordirc             C   s4   d}x|D ]}d||f }q
W |   d|¡ || _d S )Nr¸   z%s-i %s Zmacroi)rX  rÛ  )r3   rà  ræ  rü   r   r   r"   Úset_ifos˜  s
    
zcreateresultspageNode.set_ifosc             C   s   | j d|dd || _d S )NÚnT)rß  )r0  rÜ  )r3   rà  r   r   r"   Úset_histbins   s    z"createresultspageNode.set_histbinsc             C   s   | j dddd d| _d S )NÚer¸   T)rß  )r0  rÝ  )r3   r   r   r"   Ú
set_epsout¤  s    z createresultspageNode.set_epsoutc             C   s"   |r|   dd¡ n|   dd¡ d S )NÚmacrosz--sw-injr¸   )rX  )r3   Zisswinjr   r   r"   Ú	set_swinj¨  s    zcreateresultspageNode.set_swinjc             C   s"   |r|   dd¡ n|   dd¡ d S )NZmacrowz--hw-injr¸   )rX  )r3   Zishwinjr   r   r"   Ú	set_hwinj®  s    zcreateresultspageNode.set_hwinjN)r  r  r  r  re   rá  rã  rç  ré  rê  rë  rì  rí  rî  rð  rò  rô  rõ  r   r   r   r"   rÓ  R  s   		rÓ  c               @   s   e Zd ZdZdd„ ZdS )ÚcollateresultsJobz>
  A job to collate all the individual pulsar results pages
  c             C   s†   || _ d| _tj | | j| j ¡ tj | d ¡ |  dd¡ |  d|¡ |  d|¡ |  |d ¡ |  |d ¡ |  	d¡ |  
d	¡ d S )
Nró   r  r  r)   r*   z/collate_results-$(cluster).outz/collate_results-$(cluster).errzcollate_results.subz$(macroifo))Z_collateresultsJob__executableZ_collateresultsJob__universer   r  re   r  rú  r  r  rû  rV  )r3   r  rÒ  r¤   r¥   r   r   r"   re   ¹  s    
zcollateresultsJob.__init__N)r  r  r  r  re   r   r   r   r"   rö  µ  s   rö  c               @   sx   e Zd ZdZdd„ Zdd„ Zdd„ Zdd	„ Zd
d„ Zdd„ Z	dd„ Z
dd„ Zdd„ Zdd„ Zdd„ Zdd„ Zdd„ ZdS )ÚcollateresultsNodez=
    A collateresults node to run as part of a condor DAG.
  c             C   sf   t j | |¡ t j | ¡ d| _d| _d| _d| _d| _g | _	g | _
g | _d| _d| _d| _d| _dS )zK
    job = A CondorDAGJob that can run the segment list finding script
    NF)r   r  re   r  Ú_collateresultsNode__outpathÚ_collateresultsNode__inpathÚ_collateresultsNode__parfileÚ!_collateresultsNode__compilelatexÚ_collateresultsNode__sorttypeÚ_collateresultsNode__ifosÚ_collateresultsNode__outputlimsÚ_collateresultsNode__outputvalsÚ_collateresultsNode__outputhistÚ!_collateresultsNode__outputulplotÚ_collateresultsNode__withpriorÚ_collateresultsNode__epsout)r3   r/  r   r   r"   re   Ð  s    zcollateresultsNode.__init__c             C   s   | j d|dd || _d S )NrÞ  T)rß  )r0  rø  )r3   rà  r   r   r"   rá  å  s    zcollateresultsNode.set_outpathc             C   s   | j d|dd || _d S )NÚzT)rß  )r0  rù  )r3   rà  r   r   r"   Ú
set_inpathé  s    zcollateresultsNode.set_inpathc             C   s   | j d|dd || _d S )Nr“   T)rß  )r0  rú  )r3   rà  r   r   r"   rë  í  s    zcollateresultsNode.set_parfilec             C   s   | j dddd d| _d S )NÚlr¸   T)rß  )r0  rû  )r3   r   r   r"   Úset_compilelatexñ  s    z#collateresultsNode.set_compilelatexc             C   s   | j d|dd || _d S )Nr‹  T)rß  )r0  rü  )r3   rà  r   r   r"   Úset_sorttypeõ  s    zcollateresultsNode.set_sorttypec             C   s4   d}x|D ]}d||f }q
W |   d|¡ || _d S )Nr¸   z%s-i %s Zmacroifo)rX  rý  )r3   rà  ræ  rü   r   r   r"   rî  ù  s
    
zcollateresultsNode.set_ifosc             C   s4   d}x|D ]}d||f }q
W |   d|¡ || _d S )Nr¸   z%s-u %s Zmacrou)rX  rþ  )r3   rà  ræ  rü   r   r   r"   Úset_outputlims  s
    
z!collateresultsNode.set_outputlimsc             C   s4   d}x|D ]}d||f }q
W |   d|¡ || _d S )Nr¸   z%s-n %s Zmacron)rX  rÿ  )r3   rà  ræ  rü   r   r   r"   Úset_outputvals	  s
    
z!collateresultsNode.set_outputvalsc             C   s   | j dddd d| _d S )NrÕ  r¸   T)rß  )r0  r   )r3   r   r   r"   Úset_outputhist  s    z!collateresultsNode.set_outputhistc             C   s   | j dddd d| _d S )NÚtr¸   T)rß  )r0  r  )r3   r   r   r"   Úset_outputulplot  s    z#collateresultsNode.set_outputulplotc             C   s   | j dddd d| _d S )Nr>   r¸   T)rß  )r0  r  )r3   r   r   r"   Úset_withprior  s    z collateresultsNode.set_withpriorc             C   s   | j dddd d| _d S )Nrñ  r¸   T)rß  )r0  r  )r3   r   r   r"   rò    s    zcollateresultsNode.set_epsoutN)r  r  r  r  re   rá  r  rë  r  r  rî  r	  r
  r  r  r  rò  r   r   r   r"   r÷  Ì  s   r÷  )Kr  Ú
__future__r   r   Ú
__author__Ú__date__Ú__version__r.   rr  Zgluer   rO   rY   r‚   Ú
subprocessr|   rÇ   ra   Zsix.moves.configparserr   Zsix.moves.urllib.parseÚmovesÚurllibÚparserÅ   rÈ   r   Únumpyr  rR   Zscipyr   Úcollectionsr   Úsixr	   Zlalappsr
   rm   rL   r¶  ZKNOPE_ERROR_GENERAL_MSGZKNOPE_ERROR_NO_SEGMENTS_MSGZKNOPE_ERRORrµ  rd   r   r  r  r±  r  r  r¸  rÞ  rá  r·  rÊ  r  r@  r  r<  r¾   rÕ   r  r  r¿   rÞ   rÀ   rá   r  r>  rÑ  rÓ  rö  r÷  r   r   r   r"   Ú<module>   sª                             ?! (! "#   ; 6c