2?j}<dZddlmZddlZddlZddlmZmZmZmZm Z m Z m Z m Z m Z mZddlZddlZddlmZmZmZddlmZmZejeZGdd ZGd d ZGd d eZdejde ee e e!ffdZ"dS)aRead SPE files. This plugin supports reading files saved in the Princeton Instruments SPE file format. Parameters ---------- check_filesize : bool The number of frames in the file is stored in the file header. However, this number may be wrong for certain software. If this is `True` (default), derive the number of frames also from the file size and raise a warning if the two values do not match. char_encoding : str Deprecated. Exists for backwards compatibility; use ``char_encoding`` of ``metadata`` instead. sdt_meta : bool Deprecated. Exists for backwards compatibility; use ``sdt_control`` of ``metadata`` instead. Methods ------- .. note:: Check the respective function for a list of supported kwargs and detailed documentation. .. autosummary:: :toctree: SpePlugin.read SpePlugin.iter SpePlugin.properties SpePlugin.metadata )datetimeN) AnyCallableDictIteratorListMappingOptionalSequenceTupleUnion)RequestIOModeInitializationError)PluginV3ImagePropertiesc&eZdZdZdddddddZid d d d ejgd dfdddddddddddddddddd d!d"d#d$d%d&d'd(d)d*d+d,id-d.d/d0d1d2d3d4d5d6d7d8d9d:d;d<d=d>d?d@dAdBdCdDdEdFdGdHdIdJdKdLdMdNdOdPdQdRdSdTdUddVdWdXdYddZ Zd[Zejej ejej ejej ejej ejej d\Zgd]Zgd^Zd_gZd`S)aSpecaWSPE file specification data Tuples of (offset, datatype, count), where offset is the offset in the SPE file and datatype is the datatype as used in `numpy.fromfile`() `data_start` is the offset of actual image data. `dtypes` translates SPE datatypes (0...4) to numpy ones, e. g. dtypes[0] is dtype(" J?B@ jABF :GBBH zIBJ zKBL zMBN jOBP ZQBR jSBT ZUBV lWBX LYBZ k[B\ K]B^ K_B` +aBb +cBd  eBf $gBh [iBBj$! "!"#(%$#'CBBBHHJ 28BJ   28BH   28BH   28BI   28BI   F   K"A@@M IIIrrc eZdZdZiddddddddd dd d d d dd ddddddddddddddddddZdd d!d"d#ZGd$d%Zid&ed ed'd(ed)ed ed(d*ed+ed ed,de d-eded.d/e d0d1ed edd2e d3ed ed4d5ed6ed d2d7d8ed d9d:d;ed edd?d@ed edAd<e dBdCed eddfdDdEed ed5dAe d0dFeded,d edGededdHe dIdJeded dedKededHd<e d0ededdeededDescribe how to extract a metadata entry from a comment stringnslicecvtNscalec>||_||_||_||_dSN)rrrr)selfrrrrs r__init__z#SDTControlSpec.CommentDesc.__init__s$DFDJDHDJJJr)rrrrint__annotations__rrstrrr floatr rrrr CommentDescrsLL 7 > seSj !!!!<T5[!!!!1 ),%)    3%*%  E?      rrsdt_major_versionrRDsdt_minor_versionFsdt_controller_namer exposure_timerPIgư> color_coder/detection_channelsr1background_subtractionc|dkS)NBrxs rzSDTControlSpec.s 18r em_active c|dkS)NErrs rrzSDTControlSpec.s a3hrem_gainmodulation_active!c|dkS)NArrs rrzSDTControlSpec. s a3hr pixel_sizeg? sequence_typecj|Sr)sequence_types)r __class__s rrzSDTControlSpec. s9+CA+Frgridn_macro delay_macrogMbP?n_mini delay_mini%OrB7)n_micro delay_micro n_subpics delay_shutterdelay_prebleach bleach_time recovery_timebleach_piezo_active"#c|dkS)Nzrrs rrzSDTControlSpec.s 1PS8r))rfr)rfrwrdreturnc|ddddkrdS t|dddt|dddfS#t$rYdSwxYw)a-Get the version of SDT-control metadata encoded in the comments Parameters ---------- comments List of SPE file comments, typically ``metadata["comments"]``. Returns ------- Major and minor version. ``-1, -1`` if detection failed. r5rLCOMVER)rNP)r ValueError)rds rget_comment_versionz"SDTControlSpec.get_comment_version!s} A;r"u  ) )6 x{2b5)**C BrE0B,C,CC C   66 s9A A A versionc i}t|ddzD]} j|d|f}n#t$rY%wxYw|D]}\}} |||j|j}|j ||jz}|||<H#t$r)}tj d|d|d||<Yd}~vd}~wwxYw| jvrTd td j} tj d|dd |dd d | d |d|d z} | |d<|S)aCExtract SDT-control metadata from comments Parameters ---------- comments List of SPE file comments, typically ``metadata["comments"]``. version Major and minor version of SDT-control metadata format Returns ------- Dict of metadata rwrNz-Failed to decode SDT-control metadata field `z`: z, c*|dd|ddS)Nr.rw02rrs rrz/SDTControlSpec.parse_comments..]s111!111rz)Unsupported SDT-control metadata version rrz. Only versions z@ are supported. Some or all SDT-control metadata may be missing.rcomment)rangecomment_fieldsKeyErroritemsrrrr Exceptionwarningswarnjoinmapstrip) rdrsdt_mdminorcmtnamespecve supported_verrrs rparse_commentszSDTControlSpec.parse_comments5s"71:>** ( (E  .wqz5/@A    !iikk ( ( d ($&!1$*!=>>Az-TZ#$F4LL (((MTTTQRTT$(F4LLLLLL ( ( )2 2 2 II1193KLLM MCGAJCCQRZCC!.CCC    1+ +#MMOOy s(5 AAAB!! C+CCr9timeNc  j|dd}tt|dd|t|ddt|ddt|ddt|ddS#t$r)}td|dYd }~d Sd }~wwxYw) aiTurn date and time saved by SDT-control into proper datetime object Parameters ---------- date SPE file date, typically ``metadata["date"]``. time SPE file date, typically ``metadata["time_local"]``. Returns ------- File's datetime if parsing was succsessful, else None. rrfrrr5r+z1Failed to decode date from SDT-control metadata: rN)monthsrrrloggerinfo)r9rmonthrrs r get_datetimezSDTControlSpec.get_datetimehs R$T!A#Y/ED1ID1ID1ID1ID1I   R R R KKPAPPP Q Q Q Q Q Q Q Q Q RsBB CCClatin1meta char_encodingc|d}td|DrtddS|d|}|d|||d|d}|r/||d<|d|d|d} |||d <|dn$#t$rtj d YnwxYw|d |d dS) arExtract SDT-control metadata from SPE metadata SDT-control stores some metadata in comments and other fields. Extract them and remove unused entries. Parameters ---------- meta SPE file metadata. Modified in place. char_encoding Character encoding used to decode strings in the metadata. rdc3"K|] }|dkV dS)rNr.0cs r z2SDTControlSpec.extract_metadata..s&%%q1u%%%%%%rzSDT-control comments not found.Nr9rSrrmmodulation_scriptzHFailed to decode SDT-control laser modulation script. Bad char_encoding?rVr8) ranyrdebugrpopupdaterdecodeUnicodeDecodeErrorrr )rrcomversdt_metadtsp4rs rextract_metadatazSDTControlSpec.extract_metadatas..tJ/?@@ %%f%%% % %  LL: ; ; ; F++D,,>??  {{1eeBmmS99  Q4F4F!G!G  ++ar2sCC  [[55B<|jd t0j|j}|t jz }||jd |jdz|jjzz}||jkrGtjd|j jd|jd|dt=||j|_|jt jdS#t>$rt dwxYw)aInstantiate a new SPE file plugin object Parameters ---------- request : Request A request object representing the resource to be operated on. check_filesize : bool If True, compute the number of frames from the filesize, compare it to the frame count in the file header, and raise a warning if the counts don't match. (Certain software may create files with char_encoding : str Deprecated. Exists for backwards compatibility; use ``char_encoding`` of ``metadata`` instead. sdt_meta : bool Deprecated. Exists for backwards compatibility; use ``sdt_control`` of ``metadata`` instead. zcannot write SPE filesNz{Passing `char_encoding` to the constructor is deprecated. Use `char_encoding` parameter of the `metadata()` method instead.ztPassing `sdt_meta` to the constructor is deprecated. Use `sdt_control` parameter of the `metadata()` method instead.rr rrrrrxrrrwzThe file header of z claims there are z frames, but there are actually z frames.z)SPE plugin cannot read the provided file.) superrr6io_moderwriterrr DeprecationWarning_char_encoding _sdt_metar7get_file_file _parse_headerrr_file_header_verr_dtype_shape_lenseekosSEEK_ENDtellritemsizefilenameminr) rr7r8rr.rdata_endliners rrzSpePlugin.__init__sO4 !!! < 6< / /%&>?? ?  $ M#     ,   M#     "\**,,  S%%dj(;;D$():$;D !+d:&67DK<f6DK[)DI 5 )*a//#$78HHJOOAr{333#z00H$/1Q$+a.84;;OOO49$$MUdl.CUU9UUFJUUU!$D$) 4 4DI JOODO , , , , , S S S%&QRR R Ss 1E1H$$H>.indexrQcf|tur@tj}|jd|jdz|jz}|jg|jR}n|dkrt d|d||jkrt d|d|jdtj||jdz|jdz|jjzz}|jd|jdz}|j}|j |tj |j|j|}| |S)a<Read a frame or all frames from the file Parameters ---------- index : int Select the index-th frame from the file. If index is `...`, select all frames and stack them along a new axis. Returns ------- A Numpy array of pixel values. rrwzIndex `z` is smaller than 0.z5` exceeds the number of frames stored in this file (`z`).rcount) EllipsisrrrErF IndexErrorrDrKrArGrfromfilereshape)rrQ read_offsetrT out_shapedatas rreadzSpePlugin.reads9 H  /KKNT[^3di?E1T[11II QYYBuBBBCC C di  d%ddVZV_ddd  $+a.(4;q>9DK.0s1==q  ""======r)rrF)rs`riterzSpePlugin.iter(s)>===E$),<,<====rrexclude_applied sdt_controlc|jdkr2|j|j}|j|j}|||S|S)uaSPE specific metadata. Parameters ---------- index : int Ignored as SPE files only store global metadata. exclude_applied : bool Ignored. Exists for API compatibility. char_encoding : str The encoding to use when parsing strings. sdt_control : bool If `True`, decode special metadata written by the SDT-control software if present. Returns ------- metadata : dict Key-value pairs of metadata. Notes ----- SPE v3 stores metadata as XML, whereas SPE v2 uses a binary format. .. rubric:: Supported SPE v2 Metadata fields ROIs : list of dict Regions of interest used for recording images. Each dict has the "top_left" key containing x and y coordinates of the top left corner, the "bottom_right" key with x and y coordinates of the bottom right corner, and the "bin" key with number of binned pixels in x and y directions. comments : list of str The SPE format allows for 5 comment strings of 80 characters each. controller_version : int Hardware version logic_output : int Definition of output BNC amp_hi_cap_low_noise : int Amp switching mode mode : int Timing mode exp_sec : float Alternative exposure in seconds date : str Date string detector_temp : float Detector temperature detector_type : int CCD / diode array type st_diode : int Trigger diode delay_time : float Used with async mode shutter_control : int Normal, disabled open, or disabled closed absorb_live : bool on / off absorb_mode : int Reference strip or file can_do_virtual_chip : bool True or False whether chip can do virtual chip threshold_min_live : bool on / off threshold_min_val : float Threshold minimum value threshold_max_live : bool on / off threshold_max_val : float Threshold maximum value time_local : str Experiment local time time_utc : str Experiment UTC time adc_offset : int ADC offset adc_rate : int ADC rate adc_type : int ADC type adc_resolution : int ADC resolution adc_bit_adjust : int ADC bit adjust gain : int gain sw_version : str Version of software which created this file spare_4 : bytes Reserved space readout_time : float Experiment readout time type : str Controller type clockspeed_us : float Vertical clock speed in microseconds readout_mode : ["full frame", "frame transfer", "kinetics", ""] Readout mode. Empty string means that this was not set by the Software. window_size : int Window size for Kinetics mode file_header_ver : float File header version chip_size : [int, int] x and y dimensions of the camera chip virt_chip_size : [int, int] Virtual chip x and y dimensions pre_pixels : [int, int] Pre pixels in x and y dimensions post_pixels : [int, int], Post pixels in x and y dimensions geometric : list of {"rotate", "reverse", "flip"} Geometric operations sdt_major_version : int (only for files created by SDT-control) Major version of SDT-control software sdt_minor_version : int (only for files created by SDT-control) Minor version of SDT-control software sdt_controller_name : str (only for files created by SDT-control) Controller name exposure_time : float (only for files created by SDT-control) Exposure time in seconds color_code : str (only for files created by SDT-control) Color channels used detection_channels : int (only for files created by SDT-control) Number of channels background_subtraction : bool (only for files created by SDT-control) Whether background subtraction war turned on em_active : bool (only for files created by SDT-control) Whether EM was turned on em_gain : int (only for files created by SDT-control) EM gain modulation_active : bool (only for files created by SDT-control) Whether laser modulation (“attenuate”) was turned on pixel_size : float (only for files created by SDT-control) Camera pixel size sequence_type : str (only for files created by SDT-control) Type of sequnce (standard, TOCCSL, arbitrary, …) grid : float (only for files created by SDT-control) Sequence time unit (“grid size”) in seconds n_macro : int (only for files created by SDT-control) Number of macro loops delay_macro : float (only for files created by SDT-control) Time between macro loops in seconds n_mini : int (only for files created by SDT-control) Number of mini loops delay_mini : float (only for files created by SDT-control) Time between mini loops in seconds n_micro : int (only for files created by SDT-control) Number of micro loops delay_micro : float (only for files created by SDT-control) Time between micro loops in seconds n_subpics : int (only for files created by SDT-control) Number of sub-pictures delay_shutter : float (only for files created by SDT-control) Camera shutter delay in seconds delay_prebleach : float (only for files created by SDT-control) Pre-bleach delay in seconds bleach_time : float (only for files created by SDT-control) Bleaching time in seconds recovery_time : float (only for files created by SDT-control) Recovery time in seconds comment : str (only for files created by SDT-control) User-entered comment. This replaces the "comments" field. datetime : datetime.datetime (only for files created by SDT-control) Combines the "date" and "time_local" keys. The latter two plus "time_utc" are removed. modulation_script : str (only for files created by SDT-control) Laser modulation script. Replaces the "spare_4" key. bleach_piezo_active : bool (only for files created by SDT-control) Whether piezo for bleaching was enabled rx)rCr>r?_metadata_pre_v3_metadata_post_v3)rrQrarrbs rrzSpePlugin.metadata2s[X  1 $ $". $ 3 ~)"n (( DD D%%'''rc |tj| dd}|dkrdn|}t dd| d< fddD d< fdd D d < fd d D d < fddD d<d dD d<g} dd}|dzr|d|dzr|d|dzr|d| d< d}d|cxkrt tjkrnntj|dz  d<nd d< d}d|cxkrt tjkrnntj|dz  d<nd d<dD]}t | |<|rt | S)aZExtract metadata from SPE v2 files Parameters ---------- char_encoding String character encoding sdt_control If `True`, try to decode special metadata written by the SDT-control software. Returns ------- dict mapping metadata names to values. r!Nrwr"c<g|]}|dSrr)r#kms r z.SpePlugin._metadata_pre_v3..s%IIIQ!%%4..IIIr)r*r, chip_sizec<g|]}|dSrrhris rrlz.SpePlugin._metadata_pre_v3..s%RRR!quuQ~~RRRr)r.r0virt_chip_sizec<g|]}|dSrrhris rrlz.SpePlugin._metadata_pre_v3.. s%PPPa155D>>PPPr)rnrp pre_pixelsc<g|]}|dSrrhris rrlz.SpePlugin._metadata_pre_v3..!s%SSSqAEE!TNNSSSr)rorq post_pixelsc,g|]}t|Sr)rr"s rrlz.SpePlugin._metadata_pre_v3..$s777AQ777rrdrgrrotaterreverser5fliprsru)rErIrKrO) rBrrr)roi_array_to_dictappendlenrrboolrr1) rrrbnrgftrrjrks @rrdzSpePlugin._metadata_pre_v3st"   t}m < < UU8T " "q&&QQb%ain55& JIII2HIII+RRRR7QRRR PPPP3OPPP,SSSS4RSSS-87:777*   EE+q ! ! q5  HHX    q5 HHY    q5  HHV   + fI  * * * *S)** * * * * *(Q/AfIIAfI n   , , , ,S+,, , , , , , $ 21q5 9An   $An    A !::AaDD  >  + +A} = = =rc|tjd}|j|d|j}d|iS)zExtract XML metadata from SPE v3 files Returns ------- dict with key `"__xml"`, whose value is the XML metadata rr__xml)rBrrrArGr\)rrxmls rrezSpePlugin._metadata_post_v3LsP!!$*h77 01222joo~rc|tur+t|jg|jR|j|jdSt|j|jdS)aStandardized ndimage metadata. Parameters ---------- index : int If the index is an integer, select the index-th frame and return its properties. If index is an Ellipsis (...), return the properties of all frames in the file stacked along a new batch dimension. Returns ------- properties : ImageProperties A dataclass filled with standardized image metadata. T)shapern_imagesis_batchF)rrr)rUrrFrErD)rrQs r propertieszSpePlugin.propertiesYs`" H  "y/4;//k   T[ eTTTTrrcPi}tjfd}|D]\}}|j|dt |dkrdn|d}tj|j|d|}|jjdkrC|tj vr5 ||}n(#t$rtj d|d YnwxYw |}n$#t$rtj|}YnwxYw|||<|S) aGet information from SPE file header Parameters ---------- spec Maps header entry name to its location, data type description and optionally number of entries. See :py:attr:`Spec.basic` and :py:attr:`Spec.metadata`. char_encoding String character encoding Returns ------- Dict mapping header entry name to its value c.|Sr)r+)rrs rrz)SpePlugin._parse_header..s(?(?rrrxrwrrSSzFailed to decode "z3" metadata string. Check `char_encoding` parameter.)r vectorizerrArGrzrWrkindrrrrr itemrsqueeze) rrrretr+rspcntrs ` rrBzSpePlugin._parse_headerssa&????@@   HD" JOOBqE " " "2ww{{!!1C DJbe3???Aw|s""t4>'A'Aq AA MCTCCC  "FFHH " " "JqMM "CII s$2 B>>"C#"C#'C<<DD)TNN).TrT).)rrrrr{r rrrrndarrayr\rr`rrrrdrerrr r rBr3r4s@rr6r6s& $'+#' NSNSNSNS } NS 4. NS  NSNSNSNSNSNS`$'#'#'#'S#'2:#'#'#'#'J>hrz*>>>> $% R(R(R(R( R(  R( c3h R(R(R(R(hDcDDcSVhDDDDL 4S>    UUUoUUUU4,CJ',8;, c3h,,,,,,,,rr6arcg}|gd}|D]x\}}}}}}t|t|gt|t|gt|t|gd}||y|S)a\Convert the `ROIs` structured arrays to :py:class:`dict` Parameters ---------- a Structured array containing ROI data Returns ------- One dict per ROI. Keys are "top_left", "bottom_right", and "bin", values are tuples whose first element is the x axis value and the second element is the y axis value. )r#r&r$r'r%r()top_left bottom_rightbin)rry) r dict_listsxsyexeygxgyroi_dicts rrxrxsI B B BCA"###BBBR#b''* WWc"gg.GGSWW%   """" r)#rrloggingrHtypingrrrrrr r r r r rnumpyr core.requestrrrcore.v3_plugin_apirr getLoggerrrrrr6rrrrxrrrrs!!F                         ??????????::::::::  8 $ $~~~~~~~~Bn!n!n!n!n!n!n!n!bmmmmmmmm`T#tCy.-A(Br