o 9ήc`@sdZddlmZddlZddlZddlmZmZmZmZm Z m Z m Z ddl Z ddlmZeeZGdddZGd d d ZGd d d eZd dZdS)u Read SPE files. Backend: internal This plugin supports reading files saved in the Princeton Instruments SPE file format. Parameters for reading ---------------------- char_encoding : str Character encoding used to decode strings in the metadata. Defaults to "latin1". 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. sdt_meta : bool If set to `True` (default), check for special metadata written by the `SDT-control` software. Does not have an effect for files written by other software. Metadata for reading -------------------- 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. )datetimeN)AnyCallableDictMappingOptionalSequenceUnion)Formatc@sxeZdZdZdddddddZid d d d egd 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[Zeej eej eej eej eej 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("ed d?d@d8dAed edBd=e dCdDed eddfdEd8dFed ed5dBe d0dGeded,d edHededdIe dJdKeded dedLededId=e d0ededdeeded=dMe d0ededdeeded/dNe d0ededMdOe d0ededOdPe d0ededPd.e d0dQZ e dRe e dSeedTffdUdVZe dWe dXe dSeedTfffdYdZ Ze d`d\ed]e ffd^d_ ZZS)aSDTControlSpeca&Extract metadata written by the SDT-control software Some of it is encoded in the comment strings (see :py:meth:`parse_comments`). Also, date and time are encoded in a peculiar way (see :py:meth:`get_datetime`). Use :py:meth:`extract_metadata` to update the metadata dict. uJänrnJanFebr uMärroMarAprr,Mair]MayJunr"JulAugr.Sep Oktr OctNov Dez DecstandardTOCCSLru arbitrary)SEQUSETOKINESEARc @szeZdZUdZeed< eed< eege fed< e de fed< edfdededeege fde e fddZ dS) zSDTControlSpec.CommentDescz>Describe how to extract a metadata entry from a comment stringnslicecvtNscalecCs||_||_||_||_dSN)rrrr)selfrrrrrrr__init__s z#SDTControlSpec.CommentDesc.__init__)rvrwrxryint__annotations__rrstrrr floatrrrrrr CommentDesczs*  rsdt_major_versionrIDsdt_minor_versionFsdt_controller_namer exposure_timerGIgư> color_coder&detection_channelsr(background_subtractioncC|dkS)NBrxrrrzSDTControlSpec. em_active cCr)NErrrrrrrem_gainmodulation_active!cCr)NArrrrrrr pixel_sizeg? sequence_typecs j|Sr)sequence_typesr __class__rrrs gridn_macro delay_macrogMbP?n_mini delay_mini%Or97)n_micro delay_micro n_subpics delay_shutterdelay_prebleach bleach_time recovery_timer[returnNc Csi}|ddddkrtddSi}tjD]=\}}z|||j|j}|jdur4||j9}Wnt yR}ztd|d|WYd}~nd}~ww|||<q|d|d }| |d <|S) a6Extract SDT-control metadata from comments Parameters ---------- comments List of SPE file comments, typically ``metadata["comments"]``. Returns ------- If SDT-control comments were detected, return a dict of metadata, else `None`. r,rN COMVER0500zSDT-control comments not found.z-Failed to decode SDT-control metadata field "z": rr comment) loggerdebugrr[itemsrrrr Exceptionstrip)r[sdt_mdnamespecverrrrparse_commentss*     zSDTControlSpec.parse_commentsr0timec sz1j|dd}tt|dd|t|ddt|ddt|ddt|ddWStyM}ztd|dWYd }~d Sd }~ww) 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. r r]rrr,r"z1Failed to decode date from SDT-control metadata: .N)monthsrrrrinfo)r0rmonthrrrr get_datetimes zSDTControlSpec.get_datetimelatin1meta char_encodingcs|d}|s dS|d|||d|d}|r/||d<|d|d|d}z|||d<|dWntyOtdYnw|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. r[Nr0rJrrdmodulation_scriptzHFailed to decode SDT-control laser modulation script. Bad char_encoding?rMr/)rpopupdaterdecodeUnicodeDecodeErrorrwarning)rrsdt_metadtsp4rrrextract_metadatas*      zSDTControlSpec.extract_metadata)r)rvrwrxryrrrrrrrr[ staticmethodrr rrrrrr __classcell__rrrrrTs          !$"rc@s2eZdZdZddZddZGdddejZdS) SpeFormatzSee :mod:`imageio.plugins.spe`cCs |j|jvSr) extension extensionsrrequestrrr _can_reads zSpeFormat._can_readcCsdS)NFrrrrr _can_writeszSpeFormat._can_writec@sNeZdZdddZddZddZd d Zd d Zd dZddZ ddZ dS)zSpeFormat.ReaderrTcCs|j|_||_|tj}|d|_tj|d|_ |d|df|_ |d|_ ||_ |rn|ddkr9|dnt j|j}|tj}||j d|j d |j j}||j krntd |jj|j |t||j |_ d|_dS) NrrrrrrorrrnzSThe file header of %s claims there are %s frames, but there are actually %s frames.)rget_file_file_char_encoding _parse_headerr rz_file_header_verr_dtype_shape_len _sdt_metaospathgetsizeget_local_filenamer~itemsizerrfilenamemin_meta)rrcheck_filesizerrdata_endlinerrr_open"s0          zSpeFormat.Reader._opencCs0|jdur|jdkr||jS||jS)Nro)rr_init_meta_data_pre_v3_init_meta_data_post_v3)rindexrrr_get_meta_dataEs  zSpeFormat.Reader._get_meta_datacCsdSrrrrrr_closeMszSpeFormat.Reader._closecCs|tj|_|jdd}|dkrdn|}t|jdd||jd<|jdd|jddg|jd<|jdd|jddg|jd <|jd d|jd dg|jd <|jd d|jddg|jd<dd|jdD|jd<g}|jdd}|d@r|d|d@r|d|d@r|d||jd<|jd}d|krttjkrnn tj|d|jd<nd|jd<|jd}d|krttj krnn tj |d|jd<nd|jd<dD] }t |j||j|<q|j |jd<|j r t |j|jdSdS)Nrrnrr!r# chip_sizer%r'virt_chip_sizererg pre_pixelsrfrh post_pixelscSsg|]}t|qSr)r).0crrr ksz;SpeFormat.Reader._init_meta_data_pre_v3..r[r^rrotater reverser,fliprjrl)r<r@rBrF frame_shape)r r r}rrroi_array_to_dictappendlenrrboolrrrrr )rnrgftmkrrrrQsP                  z'SpeFormat.Reader._init_meta_data_pre_v3c si}tfdd}|D]_\}}j|dt|dkr#dn|d}tjj|d|d}|jjdkrU|t j vrUz||}Wnt yTt d |Ynwz|}Wntyit|}Ynw|||<q|S) Ncs |jSr)rr rr#rrrs z0SpeFormat.Reader._parse_header..rrornr r|countSzGFailed to decode "{}" metadata string. Check `char_encoding` parameter.)r{ vectorizerr seekr3fromfiler|kindr rrrrformatitem ValueErrorsqueeze)rrretrrspcntrrr#rr s,     zSpeFormat.Reader._parse_headercCs4|tj}|j|d|j}d|i|_dS)Nr__xml)r r rzr r?readr)rrxmlrrrr s  z(SpeFormat.Reader._init_meta_data_post_v3cCs|jjddvr dS|jS)NrnvV)rr-rr#rrr _get_lengthszSpeFormat.Reader._get_lengthcCs |dkr td|||jkrtd||jf|jjddvrO|dkr(td|jtjtj |j|j |j d|j d|jd}| |jf|j }n/|jtj||j d|j d|j j tj |j|j |j d|j dd}| |j }|||fS)NrzImage index %i < 0zImage index %i > %irnrLz"Index has to be 0 in v and V modesr;) IndexErrorrrr-r r?r r~r{r@rrreshaperr")rr!datarrr _get_datas0   zSpeFormat.Reader._get_dataN)rTT) rvrwrxrr"r$rr r rMrQrrrrReader!s #C rRN)rvrwrxryrr r rRrrrrrs rc Csdg}|gd}|D]%\}}}}}}t|t|gt|t|gt|t|gd}||q |S)aConvert the `ROIs` structured arrays to :py:class:`dict` Parameters ---------- a : numpy.ndarray: Structured array containing ROI data Returns ------- list of dict One dict per ROI. Keys are "top_left", "bottom_right", and "bin", values are tuples whose first element is the x axis value and the second element is the y axis value. )rrrrrr)top_left bottom_rightbin)rr2) a dict_listsxsyexeygxgyroi_dictrrrr1s  r1)ryrloggingrtypingrrrrrrr numpyr{corer getLoggerrvrr rrr1rrrrs  C$  E B