U ?h}@sdZddlmZddlZddlZddlmZmZmZmZm Z m Z m Z m Z m Z mZddlZddlZddlmZmZmZddlmZmZeeZGdd d ZGd d d ZGd d d eZeje ee e e!fdddZ"dS)a Read 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)PluginV3ImagePropertiesc0@seZdZdZdddddddZd d ed d d dddgdfddddddddddddddd d!d"d#d$d%d&d'd(d)d*d+d,d-d.d/d0d1d2d3d4d5d6d7d8dd9d:d;dZeej eej eej eej eej d?Zd@dAdBdCdDdEdFdGdHdIdJdKg ZdLdMdNgZdOgZdPS)QSpecaWSPE 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("d? Ze dDee dAfdBdC ZZS)ESDTControlSpeca&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. r`r rar*rCr&r+ r% )uJänJanFebuMärMarAprZMaiMayJunJulAugSepZOktOctNovZDezDecstandardZTOCCSLrb arbitrary)ZSEQUZSETOZKINEZSEARc@sleZdZUdZeed<eed<eege fed<e de fed<edfeeeege fe e ddd Z dS) zSDTControlSpec.CommentDescz>Describe how to extract a metadata entry from a comment stringnslicecvtNscalerrrrcCs||_||_||_||_dSNr)selfrrrrrprprq__init__sz#SDTControlSpec.CommentDesc.__init__)rcrdrerfint__annotations__rrstrrr floatr rrprprprq CommentDescs  rr8DFrr7Igư>r(r)cCs|dkS)NBrpxrprprqzSDTControlSpec. cCs|dkS)NErprrprprqr r!cCs|dkS)NArprrprprqr rg?cs j|Sr)sequence_typesr __class__rprqrrgMbP?%Or07)Zsdt_major_versionZsdt_minor_versionZsdt_controller_nameZ exposure_timeZ color_codeZdetection_channelsZbackground_subtractionZ em_activeZem_gainZmodulation_activeZ pixel_sizeZ sequence_typegridZn_macroZ delay_macroZn_miniZ delay_miniZn_microZ delay_microZ n_subpicsZ delay_shutterZdelay_prebleachZ bleach_timeZ recovery_timeZbleach_piezo_active"#cCs|dkS)Nzrprrprprqrr))rCr)rCr`)rWreturncCs^|ddddkrdSz*t|dddt|dddfWStk rXYdSXdS) 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. r*rLZCOMVER)rNPN)r ValueError)rWrprprqget_comment_version"s *z"SDTControlSpec.get_comment_version)rWversionrc s>i}t|ddD]}zj|d|f}Wntk rFYqYnX|D]\}}z6|||j|j}|jdk r||j9}|||<WqPtk r}z"t d|d|d||<W5d}~XYqPXqPq|jkrd t ddj} t d |dd |dd d | d |d|d} | |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 r`rNz-Failed to decode SDT-control metadata field `z`: z, cSs|dd|ddS)Nr.r`02rprrprprqr^rz/SDTControlSpec.parse_comments..z)Unsupported SDT-control metadata version rrz. Only versions z@ are supported. Some or all SDT-control metadata may be missing.r comment)rangecomment_fieldsKeyErroritemsrrrr Exceptionwarningswarnjoinmapstrip) rWrZsdt_mdminorZcmtnamespecveZ supported_verrrrprqparse_comments6s6       zSDTControlSpec.parse_commentsN)rPtimerc szbj|dd}tt|dd|t|ddt|ddt|ddt|ddWStk r}ztd|dW5d }~XYnXd S) 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 rCrtrr*r&z1Failed to decode date from SDT-control metadata: rN)monthsrrrloggerinfo)rPrmonthrrrprq get_datetimeiszSDTControlSpec.get_datetimelatin1)meta char_encodingcs|d}tdd|Dr.tddS|d|}|d|||d|d}|r||d<|d|d|d }z|||d <|d Wnt k rt d YnX|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. rWcss|]}|dkVqdS)rNrp.0crprprq sz2SDTControlSpec.extract_metadata..zSDT-control comments not found.NrPrUrrYZmodulation_scriptzHFailed to decode SDT-control laser modulation script. Bad char_encoding?rVrO) ranyrdebugrpopupdaterdecodeUnicodeDecodeErrorrr)rrZcomversdt_metadtZsp4rrprqextract_metadatas,       zSDTControlSpec.extract_metadata)r)rcrdrerfrrrrrrrr staticmethodr r rrrrr rrrr __classcell__rprprrqrrs  "  2 rrcseZdZdeeeeeeddfdd Zddee j dd d Z e e j d d d Z deeeeeeefdddZeeeeefdddZeeefd ddZdeedddZeeefeeeefdddZZS) SpePluginTN)requestcheck_filesizerrrc szt||jjtjkr"td|dk r6tdt ||_ |dk rPtdt ||_ |j |_z|tjd}|d|_tj|d|_|d|d f|_|d |_|rF|dd kr|d }n|jd tj|j}|tj}||jd |jd|jj}||jkrFtd|j jd|jd|dt||j|_|jtjWntk rttdYnXdS)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.rrrrrrrarrr`zThe file header of z claims there are z frames, but there are actually z frames.z)SPE plugin cannot read the provided file.) superrrNZio_moderwriterrrDeprecationWarning_char_encoding _sdt_metarZget_file_file _parse_headerrrg_file_header_verrl_dtype_shape_lenseekosSEEK_ENDtellrkitemsizefilenameminr)rrrrrrZdata_endlinerrprqrsJ          zSpePlugin.__init__.index)rrcCs|tkr8tj}|jd|jd|j}|jf|j}n~|dkrRtd|dnd||jkrvtd|d|jdn@tj||jd|jd|jj}|jd|jd}|j}|j |t j |j|j|d}| |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. rr`zIndex `z` is smaller than 0.z5` exceeds the number of frames stored in this file (`z`).ricount) Ellipsisrrkrr IndexErrorrrrrrhfromfileZreshape)rr read_offsetrZ out_shapedatarprprqreads&  zSpePlugin.read)rcsfddtjDS)zrIterate over the frames in the file Yields ------ A Numpy array of pixel values. c3s|]}j|dVqdS)rN)r)rirrprqr1sz!SpePlugin.iter..)rrrrprrqiter)szSpePlugin.iterr)rexclude_appliedr sdt_controlrcCs>|jdkr6|jdk r|j}|jdk r*|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 raN)rrr_metadata_pre_v3_metadata_post_v3)rrrrrrprprqrj3sM    zSpePlugin.metadata)rrrc s|tj|dd}|dkr&dn|}tdd|d<fdddDd<fd dd Dd <fd dd Dd<fdddDd<dddDd<g}dd}|d@r|d|d@r|d|d@r|d|d<d}d|kr$ttjkrsz.SpePlugin._metadata_pre_v3..)rJrKZ chip_sizecsg|]}|dqSrrrr rprqr  s)rLrMZvirt_chip_sizecsg|]}|dqSrrrr rprqr !s)rZr\Z pre_pixelscsg|]}|dqSrrrr rprqr "s)r[r]Z post_pixelscSsg|] }t|qSrp)rrrprprqr %srWrXrrotater reverser*flipr^r_)rQrRrSrT) rrrjrroi_array_to_dictappendlenrmrnboolrrr) rrrnrgftrrrpr rqrs>     "" zSpePlugin._metadata_pre_v3cCs0|tjd}|j|d|j}d|iS)zExtract XML metadata from SPE v3 files Returns ------- dict with key `"__xml"`, whose value is the XML metadata rrZ__xml)rrrgrrr)rrxmlrprprqrMs zSpePlugin._metadata_post_v3cCs8|tkr&t|jf|j|j|jddSt|j|jddS)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)shaperiZn_imagesis_batchF)rrir)rrrrr)rrrprprq propertiesZs zSpePlugin.properties)rrrc si}tfdd}|D]\}}|j|dt|dkrFdn|d}tj|j|d|d}|jjdkr|t j krz ||}Wn&t k rt d |d YnXz |}Wntk rt|}YnX|||<q|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 cs |Sr)rrrrprqrrz)SpePlugin._parse_header..rrar`r rSzFailed to decode "z3" metadata string. Check `char_encoding` parameter.)rhZ vectorizerrrrrrikindrrorrritemrZsqueeze) rrrretrrspZcntrrprrqrts&    zSpePlugin._parse_header)TNN).TrT).)rcrdrerrr rrrrhndarrayrrrrrrjrrrrrr rrrprprrqrs>P%  UF   r)arc Cslg}|ddddddg}|D]J\}}}}}}t|t|gt|t|gt|t|gd}||q|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. rr"r r#r!r$)top_left bottom_rightbin)rr) r#Z dict_listsxZsyexZeyZgxgyZroi_dictrprprqrs r)#rfrloggingrtypingrrrrrrr r r r rnumpyrhZ core.requestrrrZcore.v3_plugin_apirr getLoggerrcrrrrrr"rrrrprprprqs$# 0  rs