U f{j @sdZddlmZmZddlmZmZddlmZm Z ddl Z ddl mZdd lmZmZmZmZmZmZmZdd lmZmZdd lmZdd lmZdd lmZddlm Z ddl!m"Z"ddlm#Z#m$Z$ddl%m&Z&m'Z'ddl(m)Z)dZ*dZ+dZ,ddZ-Gddde.Z/eGdddeZ0ddZ1dd Z2Gd!d"d"eZ3d#d$Z4ed3d%d&Z5ed4d'd(Z6d5d)d*Z7ed6d/d0Z8ed7d1d2Z9dS)8zhConversion tool from SQD to FIF. RawKIT class is adapted from Denis Engemann et al.'s mne_bti2fiff.py. ) defaultdict OrderedDict)sincos)SEEK_CURpathN pick_types)verboseloggerwarnfill_doc _check_option _stamp_to_dt _check_fname) apply_trans als_ras_trans)BaseRaw) _mult_cal_one) BaseEpochs)FIFF) _empty_info)KITLEGACY_AMP_PARAMS)read_mrk _set_dig_kit) read_eventsz.sz&_call_digitization..rZaxiseeg_digdigZ dev_head_tZ hpi_resultsz=mrk, elp and hsp need to be provided as a group (all or none))getr$listnpZmeanZ_unlockr ValueErrorinfor r!r"kit_infor#r#r(_call_digitization%s       r4c@seZdZdZddZdS)UnsupportedKITFormatz4Our reader is not guaranteed to work with old files.cOs||_tj|f||dS)N) sqd_versionr0__init__)selfr6argskwargsr#r#r(r7AszUnsupportedKITFormat.__init__N)__name__ __module__ __qualname____doc__r7r#r#r#r(r5>sr5c sDeZdZdZedfdd Zdd d Zed dZddZ Z S)RawKITa Raw object from KIT SQD file. Parameters ---------- input_fname : str Path to the sqd file. mrk : None | str | array_like, shape (5, 3) | list of str or array_like Marker points representing the location of the marker coils with respect to the MEG Sensors, or path to a marker file. If list, all of the markers will be averaged together. elp : None | str | array_like, shape (8, 3) Digitizer points representing the location of the fiducials and the marker coils with respect to the digitized head shape, or path to a file containing these points. hsp : None | str | array, shape (n_points, 3) Digitizer head shape points, or path to head shape file. If more than 10,000 points are in the head shape, they are automatically decimated. stim : list of int | '<' | '>' | None Channel-value correspondence when converting KIT trigger channels to a Neuromag-style stim channel. For '<', the largest values are assigned to the first channel (default). For '>', the largest values are assigned to the last channel. Can also be specified as a list of trigger channel indexes. If None, no synthesized channel is generated. slope : '+' | '-' How to interpret values on KIT trigger channels when synthesizing a Neuromag-style stim channel. With '+', a positive slope (low-to-high) is interpreted as an event. With '-', a negative slope (high-to-low) is interpreted as an event. stimthresh : float The threshold level for accepting voltage changes in KIT trigger channels as a trigger event. If None, stim must also be set to None. %(preload)s stim_code : 'binary' | 'channel' How to decode trigger values from stim channels. 'binary' read stim channel events as binary code, 'channel' encodes channel number. allow_unknown_format : bool Force reading old data that is not officially supported. Alternatively, read and re-save the data with the KIT MEG Laboratory application. %(standardize_names)s %(verbose)s Notes ----- ``elp`` and ``hsp`` are usually the exported text files (*.txt) from the Polhemus FastScan system. hsp refers to the headshape surface points. elp refers to the points in head-space that corresponds to the HPI points. Currently, '*.elp' and '*.hsp' files are NOT supported. See Also -------- mne.io.Raw : Documentation of attribute and methods. N>-rFbinaryc std|t|}d|_tdt|| | \} }||d<||d<|dtjkr^tdtd|d d g}|g|_ | | || t t |j | |||g|j | d t|j||||d |_td dS)Nz$Extracting SQD Parameters from %s...FzCreating Raw.info structure...slope stimthreshacq_typez5SQD file contains epochs, not raw data. Wrong reader.zCreating Info structure... n_samplesr) last_samps filenamesZ raw_extrasr r1Ready.)r r2opabspathpreload get_kit_infor CONTINUOUS TypeError _raw_extras_set_stimchannelssuperr?r7r4)r8 input_fnamer r!r"stimrCrDrL stim_codeallow_unknown_formatstandardize_namesr r2r3rG __class__r#r(r7}sB    zRawKIT.__init__j@c Cst|}t|j}t|jd}t|jdddgd}tjd|ftjd}t|||D]>}||}||||fd}||dd|||j df<qT|S)a Read events from data. Parameter --------- buffer_size : int The size of chunk to by which the data are scanned. Returns ------- events : array, [samples] The event vector (1 x samples). rFT)megref_megrTexcludedtyperN) intZ first_sampZ last_sampr r2r/emptyZint64rangeshape) r8 buffer_sizestartstoppickstim_chZb_startZb_stopxr#r#r( read_stim_chs    zRawKIT.read_stim_chcCs&|jrtdtd|ddg|dk rt|trrt|}|dkrR|ddd}q|dkr`|}qtd t|n' Can be submitted as list of trigger channels. If a list is not specified, the default triggers extracted from misc channels will be used with specified directionality. '<' means that largest values assigned to the first channel in sequence. '>' means the largest trigger assigned to the last channel in sequence. stim_code : 'binary' | 'channel' How to decode trigger values from stim channels. 'binary' read stim channel events as binary code, 'channel' encodes channel number. z,Can't change stim channel after loading datarUrBchannelN' or '<', not %rrnchanz.Got stim=%s, but sqd file only has %i channelsrchs?zSTI 014 ) callognoscannorbunitunit_mulch_name coil_typelockind coord_framerT)rLNotImplementedErrorrr$r%_default_stim_chsr0r/Zasarrayr`maxrPappenddictr CALIB_FACTORrZFIFF_UNIT_NONEZFIFF_UNITM_NONEZFIFFV_COIL_NONEfullnanZ FIFFV_STIM_CHZFIFFV_COORD_UNKNOWN_update_redundant)r8r2rTrUZpicksrnr#r#r(rQsJ     zRawKIT._set_stimchannelsc Csv|j|}|d} ||| } |d} |dj} | dksr r7rjrrQr __classcell__r#r#rXr(r?Fs5  9r?cCst|dddgdddS)z+Return default stim channels for SQD files.FT)r[r\miscr]Nr )r2r#r#r(r}s  r}cCs|dkr||k}n|dkr$||k}ntd|dkrHdtt|}n|dkr`tdt|||ddtjf}tj|jd d dd S) z=Create synthetic stim channel from multiple trigger channels.+rAzslope needs to be '+' or '-'rBrrkz/stim_code must be 'binary' or 'channel', got %sNrr*)Zndmin)r0r/rlenreprnewaxisarraysum)Z trigger_chsrC thresholdrUZtrigger_valuesZ trig_chs_binZtrig_chsr#r#r(rs  rcs.eZdZdZed fdd ZddZZS) EpochsKITa@Epochs Array object from KIT SQD file. Parameters ---------- input_fname : str Path to the sqd file. events : str | array, shape (n_events, 3) Path to events file. If array, it is the events typically returned by the read_events function. If some events don't match the events of interest as specified by event_id,they will be marked as 'IGNORED' in the drop log. event_id : int | list of int | dict | None The id of the event to consider. If dict, the keys can later be used to access associated events. Example: dict(auditory=1, visual=3). If int, a dict will be created with the id as string. If a list, all events with the IDs specified in the list are used. If None, all events will be used with and a dict is created with string integer names corresponding to the event id integers. tmin : float Start time before event. baseline : None or tuple of length 2 (default (None, 0)) The time interval to apply baseline correction. If None do not apply it. If baseline is (a, b) the interval is between "a (s)" and "b (s)". If a is None the beginning of the data is used and if b is None then b is set to the end of the interval. If baseline is equal to (None, None) all the time interval is used. The baseline (a, b) includes both endpoints, i.e. all timepoints t such that a <= t <= b. reject : dict | None Rejection parameters based on peak-to-peak amplitude. Valid keys are 'grad' | 'mag' | 'eeg' | 'eog' | 'ecg'. If reject is None then no rejection is done. Example:: reject = dict(grad=4000e-13, # T / m (gradiometers) mag=4e-12, # T (magnetometers) eeg=40e-6, # V (EEG channels) eog=250e-6 # V (EOG channels) ) flat : dict | None Rejection parameters based on flatness of signal. Valid keys are 'grad' | 'mag' | 'eeg' | 'eog' | 'ecg', and values are floats that set the minimum acceptable peak-to-peak amplitude. If flat is None then no rejection is done. reject_tmin : scalar | None Start of the time window used to reject epochs (with the default None, the window will start with tmin). reject_tmax : scalar | None End of the time window used to reject epochs (with the default None, the window will end with tmax). mrk : None | str | array_like, shape = (5, 3) | list of str or array_like Marker points representing the location of the marker coils with respect to the MEG Sensors, or path to a marker file. If list, all of the markers will be averaged together. elp : None | str | array_like, shape = (8, 3) Digitizer points representing the location of the fiducials and the marker coils with respect to the digitized head shape, or path to a file containing these points. hsp : None | str | array, shape = (n_points, 3) Digitizer head shape points, or path to head shape file. If more than 10`000 points are in the head shape, they are automatically decimated. allow_unknown_format : bool Force reading old data that is not officially supported. Alternatively, read and re-save the data with the KIT MEG Laboratory application. %(standardize_names)s %(verbose)s Notes ----- ``elp`` and ``hsp`` are usually the exported text files (*.txt) from the Polhemus FastScan system. hsp refers to the headshape surface points. elp refers to the points in head-space that corresponds to the HPI points. Currently, '*.elp' and '*.hsp' files are NOT supported. See Also -------- mne.Epochs : Documentation of attribute and methods. NrFcst|trt|}t|ddd}td|t|| |\|_}|j|d|g|_g|_ t ||jddkrxt d|jdd t j krt j|jdd <ntd |dkrd d t|dddfD}|D],\}}||dddfkrt d||fq|}|j|jdd|jd|jddfkssz&EpochsKIT.__init__..rz-No matching events found for %s (event id %i)rn frame_lengthrsfreq)rejectflat reject_tmin reject_tmaxfilenamer r1rI)r$r%rrr r2rMupdaterPrrr0rEPOCHSINTrOr/uniqueitems_read_kit_datarcrrRrr7r4)r8rSeventsevent_idZtminZbaselinerrrrr r!r"rVrWr r3keyvalrZtmaxrXr#r(r7|sn      zEpochsKIT.__init__c Cs|jd}|d}|d}|d}|d}|d}|d}t|ddd 6}||d tjd ||} tj||| d } W5QRX| ||fj} | |d } | |||f} | d} | S)zRead epochs data. Returns ------- data : array, [channels x samples] the data matrix (channels x samples). times : array, [samples] returns the time values corresponding to the samples. rrrrFrSr_rnrrrrrr)rrr) rPrrrrr/rrTZ transpose) r8r2Z epoch_lengthrrFrSr_rnrrrr#r#r(rs   zEpochsKIT._read_kit_data) NrNNNNNNNNFNN)r;r<r=r>r r7rrr#r#rXr(r*s Q/rc CsHtt|tddt|tddt|tddt|tdddS)Nrr)rsize max_countr)rr/rUINT32INT32)rr#r#r( _read_dirs rcCstt}|t|t|dddD],}td|d||t|q(t||tj dkspt |S)Nrrrz KIT dir entry z @ ) r.rrrbr debugtellrrZ DIR_INDEX_DIRr)rr riir#r#r( _read_dirssrccCs t}||d<d}t|ddd :}t||d<}||tjdt|td\}} |dksr|dkr| d krd || f} |rd }t d | nt | d | ft|tdd} t |dd} t |dd} t t|tdd|d<}t |dd}t|td\}}|tj d tt|tdd}|tj d tt|tdd}|tj d tt|tdd}|tj d tt|tdd}|tj dt|dks|dkr| d krtt|tdd}nt|tdd}t|td \}}}| dd} | dd} | dd} | dd} d|dd| d}tdtd|td| td| td | td!|td"|td#|td$|td%|td&|td'|d(td)|td*|| d+| d,|d-| }|d.dks*ttd/|d.|d0<|tjkrttj}|t||d}t d1| | | ||f|}|tj}|d|d2}} g|d3<}!t}"t|D]r}#||| |#t|td\}$| d4kr|#d5kr|$tjkrtj}$|$tj krz|$tj!kr2t"d6|$|!#|$tj|td7d8d9|$tj$kr2|d:tt ||$|!d;d<<n|$tj%kr t|td\}%|d=tt ||$}&|!#|$|%|&d>|$tj&tj'fkr2|$tj&krd?nd.}'||'t|"#t|tddn(|$tjkr&|!#d@|$in t(dA|$qt)|"}"||tj*dtj|t|dd8}(|df|(_+|(j,\})}*|)dk-st||tj.dt|tdd}+|dBkr&|+dC@dD?},|+dE@dF?}-|+dG@dH?}.tj/|,tj/|-tj/|.}/|+dI@d.?}0|+dJ@d:?}1|+d @d?}2nP|+dK@dL?}3|+dM@d?}4tj/|3tj/|4}/|+dM@d=?}0|+dI@d.?}1|+dN@dO?}2tj|\}5}6}7tj0|5|0|dP<tj1|6|1|dQ<tj2|7|2|dR<||tj3dt|td\|dS<\}8t|td\|dT<|8tj4kr.|tj tt|td\|dU<n|8tj5ksF|8tj6krt|td\|dV<t|td\|dW<t|td\|dX<t|td\|dY<|8tj5kr|dV|dU<n|dV|dY|dU<nt(dZ|8f|tj7}9|tj8}:t};t}<|9d[dk rX|:d[dk rX||9dt|9d[D]T}=t |d.d}&|&9}&t|td }>|&rr|&|;ksht|>|;|&<n |<#|>q*g}?d\D]4}@|@|;krt:|;|@-r|?#|;;|@qt)|?}?t)||?d ||:dt?|?j+dd d f}Ad gd7}Bt|:d[D]}=t|tdd}C|d:tj@d:tj@tt|tdd}D|C s q:|Dt>|Ak sttt>|AD]L}Et|td=\}F}G}H}ItA|I|B|E<|d tj@tt|td |A|E< q|dt q:t-|B sHtBd_tC|Bdt>|Bd`|?d gd |B}?|A|B}A|jD|<|?|AdaW5QRX| r| tEk rt(db| ftE| \}}t)dcdd|!D}J|d(|}K|K|/|*}LtF|J|L|K}Mdedd|!D}N|"d(|dO}"|K|"|"dk<|"|M|N<|MdfdftjGf|dg<tHt|dT}O|OjDtI|df|dQ|dP| |dhtBdig|Odj<}PtJdkdl}QtK|dm<tL|!dD]J\}R}S|Sd@tj k r|SMd%d, check your data for correctness, including channel scales and filter settings!rchannels4zNKIT channel type %i can not be read. 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Parameters ---------- input_fname : str Path to the sqd file. mrk : None | str | array_like, shape (5, 3) | list of str or array_like Marker points representing the location of the marker coils with respect to the MEG Sensors, or path to a marker file. If list, all of the markers will be averaged together. elp : None | str | array_like, shape (8, 3) Digitizer points representing the location of the fiducials and the marker coils with respect to the digitized head shape, or path to a file containing these points. hsp : None | str | array, shape (n_points, 3) Digitizer head shape points, or path to head shape file. If more than 10,000 points are in the head shape, they are automatically decimated. stim : list of int | '<' | '>' Channel-value correspondence when converting KIT trigger channels to a Neuromag-style stim channel. For '<', the largest values are assigned to the first channel (default). For '>', the largest values are assigned to the last channel. Can also be specified as a list of trigger channel indexes. slope : '+' | '-' How to interpret values on KIT trigger channels when synthesizing a Neuromag-style stim channel. With '+', a positive slope (low-to-high) is interpreted as an event. With '-', a negative slope (high-to-low) is interpreted as an event. stimthresh : float The threshold level for accepting voltage changes in KIT trigger channels as a trigger event. %(preload)s stim_code : 'binary' | 'channel' How to decode trigger values from stim channels. 'binary' read stim channel events as binary code, 'channel' encodes channel number. allow_unknown_format : bool Force reading old data that is not officially supported. Alternatively, read and re-save the data with the KIT MEG Laboratory application. %(standardize_names)s %(verbose)s Returns ------- raw : instance of RawKIT A Raw object containing KIT data. See Also -------- mne.io.Raw : Documentation of attribute and methods. Notes ----- If mrk, hsp or elp are array_like inputs, then the numbers in xyz coordinates should be in units of meters. rSr r!r"rTrCrDrLrUrVrWr )r?rr#r#r( read_raw_kitXs< rc Cst|||||||||d } | S)aReader function for Ricoh/KIT epochs files. Parameters ---------- input_fname : str Path to the sqd file. %(events_epochs)s %(event_id)s mrk : None | str | array_like, shape (5, 3) | list of str or array_like Marker points representing the location of the marker coils with respect to the MEG Sensors, or path to a marker file. If list, all of the markers will be averaged together. elp : None | str | array_like, shape (8, 3) Digitizer points representing the location of the fiducials and the marker coils with respect to the digitized head shape, or path to a file containing these points. hsp : None | str | array, shape (n_points, 3) Digitizer head shape points, or path to head shape file. If more than 10,000 points are in the head shape, they are automatically decimated. allow_unknown_format : bool Force reading old data that is not officially supported. Alternatively, read and re-save the data with the KIT MEG Laboratory application. %(standardize_names)s %(verbose)s Returns ------- epochs : instance of Epochs The epochs. Notes ----- .. versionadded:: 0.9.0 ) rSrrr r!r"rVrWr )r) rSrrr r!r"rVrWr epochsr#r#r(read_epochs_kits&r)N)NN)NN) NNNr@rArFrBFFN)NNNNFFN):r> collectionsrrmathrrosrrrJnumpyr/rgr utilsr r rrrrrZ transformsrrbaserrrr constantsrZ meas_inforrrZcoregrreventrrrrr4r0r5r?r}rrrrrMrrrr#r#r#r(sl  $      K!  x  B