B }^ÆJã@sÜdZddlmZddlmZddlZddlZddlmZm Z m Z ddl m Z ddl mZmZmZmZmZmZmZddlZddlmZdd lmZmZdd lmZddlZddlZddlZddl Z ddl!Z!Gd d „d eƒZ"dS) uð Created on 12 Apr 2016 @author: Éric Piel Gives ability to acquire a set of streams multiple times over time. This is free and unencumbered software released into the public domain. Anyone is free to copy, modify, publish, use, compile, sell, or distribute this software, either in source code form or as a compiled binary, for any purpose, commercial or non-commercial, and by any means. In jurisdictions that recognize copyright laws, the author or authors of this software dedicate any and all copyright interest in the software to the public domain. We make this dedication for the benefit of the public at large and to the detriment of our heirs and successors. We intend this dedication to be an overt act of relinquishment in perpetuity of all present and future rights to this software under copyright law. The software is provided "as is", without warranty of any kind, express or implied, including but not limited to the warranties of merchantability, fitness for a particular purpose and non-infringement. In no event shall the authors be liable for any claim, damages or other liability, whether in an action of contract, tort or otherwise, arising from, out of or in connection with the software or the use or other dealings in the software. é)Údivision)Ú OrderedDictN)ÚmodelÚdataioÚacq)Ústream)ÚMonochromatorSettingsStreamÚARStreamÚSpectrumStreamÚ UNDEFINED_ROIÚ StaticStreamÚ LiveStreamÚStream)Úget_acqui_conf)ÚPluginÚAcquisitionDialog)ÚsplitextcsüeZdZdZdZdZdZeddddœfd d ej j ifd d d ej j dœfdej j ddœfdiffƒZ ‡fdd„Zdd„Zd8dd„Zdd„Zdd„Zdd„Zd d!„Zd"d#„Zd9d%d&„Zd'd(„Zd)d*„Zd+d,„Zd-d.„Zd/d0„Zd:d2d3„Zd4d5„Zd6d7„Z‡ZS);ÚTimelapsePluginZ Timelapsez2.0u Éric Pielz Public domainÚperiodzTime between each acquisitionÚlog)ÚtooltipZscaleÚnumberOfAcquisitionsÚ control_typeÚ semOnlyOnLastzSEM only on the lastz1Acquire SEM images only once, after the timelapse)ÚlabelrrÚfilenamez=TIFF files (*.tiff, *tif)|*.tiff;*.tif|HDF5 Files (*.h5)|*.h5)rZwildcardÚexpectedDurationcsÎtt|ƒ ||¡|sdStjddd|jd|_t dd¡|_t  d¡|_ t  d¡|_ tj d dd d |_|j |j¡|j |j¡|jd kr tjj|jd d<d|_| d|j¡t ¡|_g|_d|_dS)Né )gü©ñÒMbP?i'Ús)ÚunitÚsetteréd)éi †Fza.h5éT)rÚreadonly)ZsecomZdelphirrzAcquisition/Timelapse... Ctrl+T)ÚsuperrÚ__init__rZFloatContinuousÚ _setPeriodrZ IntContinuousrZ BooleanVArZStringVArZVigilantAttributerÚ subscribeÚ_update_exp_durÚroleÚodemisÚguiZ CONTROL_CHECKÚvaconfÚ_dlgZaddMenuÚstartÚqueueÚQueueÚ _to_storeÚ _sthreadsÚ _exporter)ÚselfZ microscopeÚmain_app)Ú __class__©úY/tmp/pip-install-m1v76eul/Odemis/Odemis-3.0.0.data/data/share/odemis/plugins/timelapse.pyr&Ts$      zTimelapsePlugin.__init__cCs&tƒ}tj |jdt d¡|jf¡S)Nz%s%sz %Y%m%d-%H%M%S)rÚosÚpathÚjoinZ last_pathÚtimeÚstrftimeZlast_extension)r5Úconfr8r8r9Ú_get_new_filenamepsz!TimelapsePlugin._get_new_filenameNc CsŽ|jj}|jj}| ¡\}}t |¡}t d|t|ƒ¡t d||ƒ}||||d}|rt|t ||¡|7}|j j t   |¡dddS)zN Called when VA that affects the expected duration is changed z*Estimating %g s acquisition for %d streamsrr#T)Z force_writeN)rÚvaluerÚ_get_acq_streamsrÚ estimateTimeÚloggingÚdebugÚlenÚmaxrZ _set_valueÚmathÚceil) r5Ú_ÚnbÚpÚssÚlast_ssÚsacqtÚintpÚdurr8r8r9r)ws  zTimelapsePlugin._update_exp_durcCsRd}x4| ¡dD]$}| ¡}td|tjƒ}||7}qWtt||ƒ|jjdƒS)Nrgü©ñÒMbP?r#)rBÚestimateAcquisitionTimerGrÚSETUP_OVERHEADÚminrÚrange)r5rZtot_timerZacqtr8r8r9r'Šs  zTimelapsePlugin._setPeriodcCsbt|jjƒ}t|dƒrÁsz3TimelapsePlugin._get_acq_streams..cSsg|]}t|tjƒr|‘qSr8)r\rÚEMStream)r`rr8r8r9ú Ìsz4TimelapsePlugin._get_acq_streams..cSsg|]}t|tjƒs|‘qSr8)r\rrd)r`rr8r8r9reÍs)r.ÚviewZ getStreamsÚ hidden_viewrDrErFr6Ú main_dataÚtabrAÚtab_data_modelrYr_r\rZMultipleDetectorStreamÚanyrXÚappendr)r5r]Zacq_strMZacsrNr8)rbr9rBªs,     z TimelapsePlugin._get_acq_streamscCsÚ|jjjj}|jdkrFt |jjddtjtj B¡}|  ¡|  ¡dSyD|j j jjtkrˆt |jjddtjtj B¡}|  ¡|  ¡dSWntk ržYnX|j ¡| ¡|j_t|ddƒ}||_| ||j¡| |j ¡}xD|D]<}t|tttfƒrt d|¡|j |ddqè|  |¡qèW| !d ¡|j!d |j"d d |j#j|j#_|j$j%j&j'|j(d d|j)j%j&j'|j(d d|  ¡}|dkršt d¡n"|dkr°t d¡n t *d|¡|j$j%j& +|j(¡|  ¡dS)N)Z secom_liveZ sparc_acquiz?Timelapse acquisition must be done from the acquisition stream.z"Timelapse acquisition not possiblez+You need to select a region of acquisition.zTimelapse acquisitionzœThe same streams will be acquired multiple times, defined by the 'number of acquisitions'. The time separating each acquisition is defined by the 'period'. z>Not showing stream %s, for which the live image is not spatial)ÚindexZCancelZAcquireZblue)Z face_colourT)ÚinitrzAcquisition cancelledr#zAcquisition completedzGot unknown return code %s),r6rhrirAÚnameÚwxZ MessageDialogZ main_frameÚOKZ ICON_STOPZ ShowModalZDestroyrjZ semStreamZroir ÚAttributeErrorÚstreambar_controllerÚ pauseStreamsr@rrr.Z addSettingsr-r^r\r r rrDÚinfoZ addStreamZ addButtonÚacquirerrfZ stream_treeZflatr(r)rgÚwarningZ unsubscribe)r5riZboxÚdlgrMrZansr8r8r9r/ÑsV                zTimelapsePlugin.startc CsŒzxyTxN|j ¡\}}|dkr*|j ¡dSt d||¡|j ||¡|j ¡qWWntk rtt d¡YnXWdt  d|¡XdS)NzSaving data %s in thread %dzFailure in the saving threadzSaving thread %d done) r2ÚgetÚ task_donerDrur4ÚexportÚ ExceptionÚ exceptionrE)r5ÚiÚfnÚdasr8r8r9Ú_saving_threads zTimelapsePlugin._saving_threadécCsT|jrt d¡| ¡x6t|ƒD]*}tj|j|fd}| ¡|j  |¡q"WdS)z1 n (int >= 1): number of threads z:The previous saving threads were not stopped, stopping now)ÚtargetÚargsN) r3rDrwÚ_stop_saving_threadsrUÚ threadingÚThreadrr/rl)r5Únr~Útr8r8r9Ú_start_saving_threads's z%TimelapsePlugin._start_saving_threadscCsHx|jD]}|j d¡qW|j ¡x|jD] }| ¡q.Wg|_dS)zi Blocks until all the data has been stored Can be called multiple times in a row )NNN)r3r2Úputr<)r5rJr‰r8r8r9r…4s     z$TimelapsePlugin._stop_saving_threadscCs|j ||f¡dS)zO Queue the requested DataArrays to be stored in the given file N)r2r‹)r5rr€r8r8r9Ú _save_dataCszTimelapsePlugin._save_datac CsÜ|jj}|jjj}| ¡}| ¡| d¡| ¡\}}t   |¡}|j j}|j j} zht |ƒdkrªt|dtƒrª| dkrª|dkrª||tjkrªt d¡| ||d|¡n| |||¡Wd| ¡Xt d¡| ¡dS)Nr‚r#rr"éz9Fast timelapse detected, will acquire as fast as possiblezClosing dialog)r6rhrirArsrtZ pauseSettingsrŠrBrrCrrrFr\r rrSrDruÚ_fast_acquire_oneÚ_acquire_multir…rEÚClose) r5rxrhZstr_ctrlZ stream_pausedrMrNrOrLrKr8r8r9rvIs&       zTimelapsePlugin.acquirec CsT|jj}|jj}t |¡|_t|ƒ\}}|d|}t ¡|_ t   ¡} |j | _ || _|rr|d8}t |g|¡} nd} | || ||| ¡z<|  ¡| | ¡d|j_|j  ¡|  ¡rÂ| ¡dSWdd|j_t d|¡| |¡X|r>t d¡|g|} | jt ¡t | ¡d t | ¡ ¡\} } | ||f| ¡|  ¡|  !d¡dS) a Acquires one stream, *as fast as possible* (ie, the period is not used). Only works with LiveStreams (and not with MDStreams) st (LiveStream) last_ss (list of Streams): all the streams to be acquire on the last time z-%.5dr#rTNFzRestoring stream %sz0Acquiring last acquisition, with all the streams)Úend)"rrArrÚfind_fittest_converterr4rr†ÚEventÚ_acq_completedrÚProgressiveFutureÚ_cancel_fast_acquireÚtask_cancellerÚ_streamrrCÚ_hijack_live_streamÚset_running_or_notify_cancelÚ showProgressÚ is_activeÚwaitÚ cancelledÚresumeSettingsrDrEÚ_restore_live_streamÚ set_progressr=rvÚresultrŒr…Ú set_result)r5rxÚstrNrKrÚbsÚextÚfn_patÚfÚ extra_durrMr€Úer8r8r9rŽjsB           z!TimelapsePlugin._fast_acquire_onecCsd|jj_|j ¡dS)NFT)r˜rœrAr”Úset)r5r¨r8r8r9r–¢s  z$TimelapsePlugin._cancel_fast_acquirercsPˆjˆ_dd„ˆ_dˆ_ˆ ¡tj‰‡‡‡‡‡‡‡fdd„}ˆjˆ_|ˆ_dS)NcSsdS)Nr8r8r8r8r9Ú©óz5TimelapsePlugin._hijack_live_stream..rcs¦ˆj}ˆjd7_t d|¡ˆjˆkrHt d¡dˆj_ˆj ¡nˆjˆkr`t d¡dSˆ ˆ|fˆjdg¡ˆ|}ˆ|ˆ}ˆj t   ¡|ddS)Nr#zReceived data %dzStopping the streamFzSkipping extra datar)r‘) Ú_data_receivedrDrErœrAr”r«rŒÚrawr¡r=)r~ÚleftrQ)Údur_oner©r¨r§rKr5r¤r8r9Ústore_raw_data¯s       z;TimelapsePlugin._hijack_live_stream..store_raw_data)Ú_shouldUpdateHistogramÚ_old_shouldUpdateHistogramr®rRrrSÚ_shouldUpdateImageÚ_old_shouldUpdateImage)r5r¤r¨rKr§r©r²r8)r±r©r¨r§rKr5r¤r9r™§s z#TimelapsePlugin._hijack_live_streamcCs|j|_|`|j|_|`dS)N)r¶rµr´r³)r5r¤r8r8r9r Æsz$TimelapsePlugin._restore_live_streamcCs†|jj}|jj}|jj}t |¡|_t|ƒ\}}|d|} t  |¡} t d|| ƒ} || krjt   d| |¡t  ¡} dd„| _|  ¡| | ¡xàt|ƒD]Ô} || }| || |d}|dkrÞ|rÞ||7}|t  |¡| 7}t ¡}| j||dt |¡ ¡\}}|  ¡r| ¡dS| | | f|¡|dkr˜||t ¡}|dkr^t |¡q˜t  d| ¡q˜W| ¡|  d¡dS) Nz-%.5drzLAcquisition will take %g s, but period between acquisition must be only %g scSsdS)NTr8)Úlr8r8r9r¬àr­z0TimelapsePlugin._acquire_multi..r#)r‘z0Immediately starting next acquisition, %g s late)rrArrrr’r4rrrCrGrDrwrr•r—ršr›rUr=r¡rvr¢ržrŸrŒÚsleeprur…r£)r5rxrMrNrLrKrr¥r¦r§rOrPr¨r~r°rQZstarttr€rªZsleeptr8r8r9rÌsH          zTimelapsePlugin._acquire_multi)N)r‚)r) Ú__name__Ú __module__Ú __qualname__roÚ __version__Ú __author__Ú __license__rr+r,Z CONTROL_INTZ CONTROL_NONEZCONTROL_SAVE_FILEr-r&r@r)r'r^rBr/rrŠr…rŒrvrŽr–r™r rÚ __classcell__r8r8)r7r9r5sF     'G !8 r)#Ú__doc__Ú __future__rÚ collectionsrrDrHr+rrrZ odemis.acqrZodemis.acq.streamrr r r r r rZ odemis.guiZodemis.gui.confrZodemis.gui.pluginrrZodemis.util.dataiorr:r0r†r=rprr8r8r8r9Ús"   $