U Z$d`@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)Formatc0@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("Describe how to extract a metadata entry from a comment stringnslicecvtNscaler~rrrcCs||_||_||_||_dSNr)selfr~rrrririrj__init__sz#SDTControlSpec.CommentDesc.__init__)r\r]r^r_int__annotations__rrstrrr floatrrriririrj CommentDesczs  rr1DFrr0Igư>r!r"cCs|dkS)NBrixririrjzSDTControlSpec. cCs|dkS)NErirririrjrr!cCs|dkS)NArirririrjrrg?cs j|Sr)sequence_typesr __class__rirjrrgMbP?%Or)7)Zsdt_major_versionZsdt_minor_versionZsdt_controller_nameZ exposure_timeZ color_codeZdetection_channelsZbackground_subtractionZ em_activeZem_gainZmodulation_activeZ pixel_sizeZ sequence_typeZgridZn_macroZ delay_macroZn_miniZ delay_miniZn_microZ delay_microZ n_subpicsZ delay_shutterZdelay_prebleachZ bleach_timeZ recovery_timeN)rPreturnc Csi}|ddddkr&tddSi}tjD]x\}}z.|||j|j}|jdk rh||j9}Wn8t k r}ztd|d|W5d}~XYnX|||<q4|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#rNZ COMVER0500zSDT-control comments not found.z-Failed to decode SDT-control metadata field "z": rr comment) loggerdebugrkrPitemsrr~rr Exceptionstrip)rPZsdt_mdnamespecverririrjparse_commentss$    zSDTControlSpec.parse_comments)rItimerc 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 r<rmrr#rz1Failed to decode date from SDT-control metadata: .N)monthsrrrrinfo)rIrmonthrrrirj get_datetimeszSDTControlSpec.get_datetimelatin1)meta char_encodingcs|d}|sdS|d|||d|d}|r^||d<|d|d|d}z|||d<|dWntk rtdYnX|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. rPNrIrNrrRZmodulation_scriptzHFailed to decode SDT-control laser modulation script. Bad char_encoding?rOrH)rpopupdaterdecodeUnicodeDecodeErrorrwarning)rrsdt_metadtZsp4rrirjextract_metadatas(      zSDTControlSpec.extract_metadata)r)r\r]r^r_rrrrrrrrP staticmethodrr rrrrrr __classcell__ririrrjrkTsx  ! rkc@s2eZdZdZddZddZGdddejZdS) SpeFormatzSee :mod:`imageio.plugins.spe`cCs |j|jkSr) extension extensionsrrequestririrj _can_readszSpeFormat._can_readcCsdS)NFrirririrj _can_writeszSpeFormat._can_writec@sNeZdZdddZddZddZd d Zd d Zd dZddZ ddZ dS)zSpeFormat.ReaderrTcCs|j|_||_|tj}|d|_tj|d|_ |d|df|_ |d|_ ||_ |r|ddkrr|dnt j|j}|tj}||j d|j d |j j}||j krtd |jj|j |t||j |_ d|_dS) NrrrrrrZrrrYzSThe file header of %s claims there are %s frames, but there are actually %s frames.)rZget_file_file_char_encoding _parse_headerr r`_file_header_verre_dtype_shape_len _sdt_metaospathgetsizeZget_local_filenamerditemsizerrfilenamemin_meta)rrZcheck_filesizerrZdata_endlineririrj_open"s0        zSpeFormat.Reader._opencCs,|jdkr&|jdkr|n||jS)NrZ)rr_init_meta_data_pre_v3_init_meta_data_post_v3)rindexririrj_get_meta_dataEs    zSpeFormat.Reader._get_meta_datacCsdSrrirririrj_closeMszSpeFormat.Reader._closecCs"|tj|_|jdd}|dkr(dn|}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$|d|d@r8|d||jd<|jd}d|krjttjkrnntj|d|jd<n d|jd<|jd}d|krttj krnntj |d|jd<n d|jd<dD]}t |j||j|<q|j |jd<|j rt |j|jdS)NrArYrBrCrDZ chip_sizerErFZvirt_chip_sizerSrUZ pre_pixelsrTrVZ post_pixelscSsg|] }t|qSri)r).0cririrj ksz;SpeFormat.Reader._init_meta_data_pre_v3..rPrQrrotater reverser#ZfliprWrX)rJrKrLrMZ frame_shape)rr rcrrroi_array_to_dictappendlenrfrgboolrrrkrr)rnrgftmkririrjrQsN                "  "  z'SpeFormat.Reader._init_meta_data_pre_v3c si}tfdd}|D]\}}j|dt|dkrFdn|d}tjj|d|d}|jjdkr|t j krz ||}Wn$t k rt d |YnXz |}Wntk rt|}YnX|||<q|S) Ncs |jSr)rrrrrirjrrz0SpeFormat.Reader._parse_header..rrZrYr rbcountSzGFailed to decode "{}" metadata string. Check `char_encoding` parameter.)raZ vectorizerrseekrfromfilerbkindr rhrrrformatitem ValueErrorZsqueeze)rrretrrspZcntrrirrjrs*    zSpeFormat.Reader._parse_headercCs4|tj}|j|d|j}d|i|_dS)NrZ__xml)rr r`rrreadr)rrxmlririrjrs  z(SpeFormat.Reader._init_meta_data_post_v3cCs|jjddkrdS|jSdS)NrYvV)rrGrrririrj _get_lengthszSpeFormat.Reader._get_lengthcCs |dkrtd|||jkr0td||jf|jjddkr|dkrPtd|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 > %irYrz"Index has to be 0 in v and V modesr) IndexErrorrrrGrrr rdrarrrZreshaperr)rrdataririrj _get_datas4   zSpeFormat.Reader._get_dataN)rTT) r\r]r^rrrrrrrrriririrjReader!s #CrN)r\r]r^r_rrr rriririrjrsrc Cslg}|ddddddg}|D]J\}}}}}}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)Ztop_leftZ bottom_rightbin)rr) aZ dict_listZsxZsyexZeyZgxgyZroi_dictririrjrs r)r_rloggingrtypingrrrrrrr Znumpyracorer getLoggerr\rr rkrrriririrjsC $  EB