U f{j @sddlZddlZddlZddlmZmZmZddl m Z m Z ddl m Z mZmZmZmZmZmZddlmZddlmZmZmZmZdd lmZggd d fd d ZGdddeZddZ ddZ!ddZ"ddZ#edej$ddddddfddddZ%eddej$ddddddf ddddZ&edej$dddddd d ddf ddddZ'eddej$dddddd d ddf dddd Z(ed2ddd"d#Z)ed3ddd$d%Z*d4d&d'Z+d5d(d)Z,ed6ddd*d+Z-d,d-Z.d.d/Z/d7d0d1Z0dS)8N) _cwt_arraymorlet _get_nfft) pick_channels _picks_to_idx)loggerverbosewarncopy_function_doc_to_method_doc ProgressBar _check_fname_import_h5io_funcsplot_csd)_compute_mt_params _mt_spectra _csd_from_mt_psd_from_mt_adaptive) parallel_funcFTc s|r tj|||d}g}jjD]6}t|}||ddfdd|f}|t|q*fdd|D} t |j_| _S)amPick channels from cross-spectral density matrix. Parameters ---------- csd : instance of CrossSpectralDensity The CSD object to select the channels from. include : list of str List of channels to include (if empty, include all available). exclude : list of str Channels to exclude (if empty, do not exclude any). ordered : bool If True (default False), ensure that the order of the channels in the modified instance matches the order of ``include``. .. versionadded:: 0.20.0 copy : bool If True (the default), return a copy of the CSD matrix with the modified channels. If False, channels are modified in-place. .. versionadded:: 0.20.0 Returns ------- res : instance of CrossSpectralDensity Cross-spectral density restricted to selected channels. )includeexcludeorderedNcsg|]}j|qS)ch_names.0icsdrU/var/www/html/bwave/python/venv/lib/python3.8/site-packages/mne/time_frequency/csd.py <sz%pick_channels_csd..) copyrr_dataT_vector_to_sym_matappend_sym_mat_to_vectornparray) r rrrr#seldatavecmatrrrr!pick_channels_csds  r/c@seZdZdZd*ddZeddZeddZd d Zd d Z d+d dZ d,ddZ ddZ d-ddZ d.ddZeed/ddZddZdd Zd!d"Zeddd#d$d%Zd&d'Zd0d(d)ZdS)1CrossSpectralDensityaZCross-spectral density. Given a list of time series, the CSD matrix denotes for each pair of time series, the cross-spectral density. This matrix is symmetric and internally stored as a vector. This object can store multiple CSD matrices: one for each frequency. Use ``.get_data(freq)`` to obtain an CSD matrix as an ndarray. Parameters ---------- data : ndarray, shape ((n_channels**2 + n_channels) // 2, n_frequencies) For each frequency, the cross-spectral density matrix in vector format. ch_names : list of str List of string names for each channel. frequencies : float | list of float | list of list of float Frequency or frequencies for which the CSD matrix was calculated. When averaging across frequencies (see the :func:`CrossSpectralDensity.mean` function), this will be a list of lists that contains for each frequency bin, the frequencies that were averaged. Frequencies should always be sorted. n_fft : int The number of FFT points or samples that have been used in the computation of this CSD. tmin : float | None Start of the time window for which CSD was calculated in seconds. Can be ``None`` (the default) to indicate no timing information is available. tmax : float | None End of the time window for which CSD was calculated in seconds. Can be ``None`` (the default) to indicate no timing information is available. projs : list of Projection | None List of projectors to apply to timeseries data when using this CSD object to compute a DICS beamformer. Defaults to ``None``, which means no projectors will be applied. See Also -------- csd_fourier csd_multitaper csd_morlet csd_array_fourier csd_array_multitaper csd_array_morlet NcCst|}|jdkr(|ddtjf}n|jdkr:td||_t|tt|kr\tdt||_ ||_ ||_ t |t jr|g}t||jdkrtdt||jdf||_||_|dkrg|_n t||_dS)Nrrz)`data` should be either a 1D or 2D array.zNNumber of ch_names does not match the number of time series in the CSD matrix.z]Number of frequencies does not match the number of CSD matrices in the data array (%d != %d).)r)asarrayndimnewaxis ValueErrorr$len_n_dims_from_triulistrtmintmax isinstancenumbersNumbershape frequenciesn_fftprojscpdeepcopy)selfr,rr>r?r8r9r@rrr!__init__rs,     zCrossSpectralDensity.__init__cCs t|jS)z1Number of time series defined in this CSD object.)r5rrCrrr! n_channelsszCrossSpectralDensity.n_channelscCst|jdtj S)z>Whether the CSD matrix represents a sum (or average) of freqs.r)r:r>r;r<rErrr!_is_sumszCrossSpectralDensity._is_sumcCs t|jS)zReturn number of frequencies. Returns ------- n_freqs : int The number of frequencies. )r5r>rErrr!__len__szCrossSpectralDensity.__len__c Csg}|jD]^}t|tjr*|t|q t|dkrJ|t|dq |dt |t |q d |d}|j dk r|j dk rd|j |j }nd}d|j||S) Nrrz{}-{}z, z Hz.z {} to {} sunknownz?)r>r:r;r<r'strr5formatr)minmaxjoinr8r9rF)rCZ freq_strsfZfreq_strZtime_strrrr!__repr__s"    zCrossSpectralDensity.__repr__c sjrtd|dkr8|dkr8jdg}jdg}n\t|tjrJ|g}t|tjr\|g}|dkrxjdgt|}|dkrjdgt|}tddt||Drt dfdd |D}fd d |D}t|t|krt d t|}t j j j d|fj jd }g}tt||D]L\}\} } j dd| | fjd d|dd|f<|j| | q(t|jjj|jjd} | S)aCalculate the sum CSD in the given frequency range(s). If the exact given frequencies are not available, the nearest frequencies will be chosen. Parameters ---------- fmin : float | list of float | None Lower bound of the frequency range in Hertz. Defaults to the lowest frequency available. When a list of frequencies is given, these are used as the lower bounds (inclusive) of frequency bins and the sum is taken for each bin. fmax : float | list of float | None Upper bound of the frequency range in Hertz. Defaults to the highest frequency available. When a list of frequencies is given, these are used as the upper bounds (inclusive) of frequency bins and the sum is taken for each bin. Returns ------- csd : instance of CrossSpectralDensity The CSD matrix, summed across the given frequency range(s). zDThis CSD matrix already represents a mean or sum across frequencies.Nrcss|]\}}||kVqdSNr)rZfmin_Zfmax_rrr! sz+CrossSpectralDensity.sum..zASome lower bounds are higher than the corresponding upper bounds.csg|]}|qSr_get_frequency_indexrrOrErr!r"sz,CrossSpectralDensity.sum..csg|]}|dqS)rrTrVrErr!r"sz5The length of fmin does not match the length of fmax.dtyperZaxisr,rr8r9r>r?r@)rG RuntimeErrorr>r:r;r<r5anyzipr4r)zerosr$r=rX enumeratesumr'r0rr8r9r?r@) rCfminfmaxZ fmin_indsZ fmax_indsZn_binsZnew_dataZnew_frequenciesrZmin_indZmax_indZcsd_outrrEr!r`sF   *zCrossSpectralDensity.sumcCsB|||}t|jD]&\}}|jdd|ft|<q|S)aCalculate the mean CSD in the given frequency range(s). Parameters ---------- fmin : float | list of float | None Lower bound of the frequency range in Hertz. Defaults to the lowest frequency available. When a list of frequencies is given, these are used as the lower bounds (inclusive) of frequency bins and the mean is taken for each bin. fmax : float | list of float | None Upper bound of the frequency range in Hertz. Defaults to the highest frequency available. When a list of frequencies is given, these are used as the upper bounds (inclusive) of frequency bins and the mean is taken for each bin. Returns ------- csd : instance of CrossSpectralDensity The CSD matrix, averaged across the given frequency range(s). N)r`r_r>r$r5)rCrarbr rrOrrr!means  zCrossSpectralDensity.meancCsN|jrtdtt|j|}t|}||}|dkrJtd||S)aFind the index of the given frequency in ``self.frequencies``. If the exact given frequency is not available, the nearest frequencies will be chosen, up to a difference of 1 Hertz. Parameters ---------- freq : float The frequency to find the index for Returns ------- index : int The index of the frequency nearest to the requested frequency. zYThis CSD object represents a mean across frequencies. Cannot select a specific frequency.rzFrequency %f is not available.)rGr4r)absr1r>argmin IndexError)rCfreqZdistanceindexZmin_distrrr!rUs  z)CrossSpectralDensity._get_frequency_indexcCsD|dkr|dkrtdn"|dk r<|dk r2td||}||S)aGet a CrossSpectralDensity object with only the given frequency. Parameters ---------- freq : float | None Return the CSD matrix for a specific frequency. Only available when no averaging across frequencies has been done. index : int | None Return the CSD matrix for the frequency or frequency-bin with the given index. Returns ------- csd : instance of CrossSpectralDensity A CSD object containing a single CSD matrix that corresponds to the requested frequency or frequency-bin. See Also -------- get_data NzKUse either the "freq" or "index" parameter to select the desired frequency.*Cannot specify both a frequency and index.)r4rU)rCrgrhrrr!pick_frequency7s  z#CrossSpectralDensity.pick_frequencyFcCs|dkr.|dkr.|jjddkr(tdd}n"|dk rP|dk rFtd||}t|jdd|f}|rddlm}|||jg|j|j dS|SdS) aLGet the CSD matrix for a given frequency as NumPy array. If there is only one matrix defined in the CSD object, calling this method without any parameters will return it. If multiple matrices are defined, use either the ``frequency`` or ``index`` parameter to select one. Parameters ---------- frequency : float | None Return the CSD matrix for a specific frequency. Only available when no averaging across frequencies has been done. index : int | None Return the CSD matrix for the frequency or frequency-bin with the given index. as_cov : bool Whether to return the data as a numpy array (`False`, the default), or pack it in a :class:`mne.Covariance` object (`True`). .. versionadded:: 0.20 Returns ------- csd : ndarray, shape (n_channels, n_channels) | instance of Covariance The CSD matrix corresponding to the requested frequency. See Also -------- pick_frequency Nrz^Specify either the frequency or index of the frequency bin for which to obtain the CSD matrix.rrir) Covariance)Zbadsr@Znfree) r$r=r4rUr&Zcovrkrr@r?)rCZ frequencyrhZas_covr,rkrrr!get_dataYs  zCrossSpectralDensity.get_datar Tviridisc Cst|||||||dS)N)infomodecolorbarcmapn_colsshowr)rCrnrorprqrrrsrrr!plots  zCrossSpectralDensity.plotcsdddlm|d|_|d|_|d|_|d|_|d|_|d|_fd d |d D|_dS) Nr Projectionr,r8r9rr>r?csg|]}f|qSrr)rprojrurr!r"sz5CrossSpectralDensity.__setstate__..r@) rwrvr$r8r9rr>r?r@)rCstaterrur! __setstate__s       z!CrossSpectralDensity.__setstate__c Cs$t|j|j|j|j|j|j|jdS)N)r,r8r9rr>r?r@)dictr$r8r9rr>r?r@rErrr! __getstate__sz!CrossSpectralDensity.__getstate__c Cs>t|jdd|f|j|j|jt|j||j |j dS)a Subselect frequencies. Parameters ---------- sel : ndarray Array of frequency indices to subselect. Returns ------- csd : instance of CrossSpectralDensity A new CSD instance with the subset of frequencies. NrZ) r0r$rr8r9r)Z atleast_1dr>tolistr?r@)rCr+rrr! __getitem__s z CrossSpectralDensity.__getitem__) overwriter cCs@t\}}|ds|d7}t||d}|||ddddS)aSave the CSD to an HDF5 file. Parameters ---------- fname : str The name of the file to save the CSD to. The extension '.h5' will be appended if the given filename doesn't have it already. %(overwrite)s .. versionadded:: 1.0 %(verbose)s .. versionadded:: 1.0 See Also -------- read_csd : For reading CSD objects from a file. .h5)r~Tconpy)r~titleN)rendswithrr{)rCfnamer~r _Z write_hdf5rrr!saves    zCrossSpectralDensity.savecCs t|S)zReturn copy of the CrossSpectralDensity object. Returns ------- copy : instance of CrossSpectralDensity A copy of the object. )rArBrErrr!r#szCrossSpectralDensity.copycCst||g|ddS)a?Pick channels from this cross-spectral density matrix. Parameters ---------- ch_names : list of str List of channels to keep. All other channels are dropped. ordered : bool If True (default False), ensure that the order of the channels matches the order of ``ch_names``. Returns ------- csd : instance of CrossSpectralDensity. The modified cross-spectral density object. Notes ----- Operates in-place. .. versionadded:: 0.20.0 F)rrrr#)r/)rCrrrrr!rsz"CrossSpectralDensity.pick_channels)NNN)NN)NN)NN)NNF)Nr TrmNT)F)__name__ __module__ __qualname____doc__rDpropertyrFrGrHrPr`rcrUrjrlr rrtryr{r}r rr#rrrrr!r0Cs8.     E  " 3    r0cCsttt|ddS)aCompute matrix dims from number of elements in the upper triangle. Parameters ---------- n : int Number of elements in the upper triangle of the symmetric matrix. Returns ------- dim : int The dimensions of the symmetric matrix. rr)intr)ceilsqrt)nrrr!r6s r6cCstt|}tj||f|jdd|jd}||t|<|t|d}t |jtj rx|t |d<n|t |d<|S)aConvert vector to a symmetric matrix. The upper triangle of the matrix (including the diagonal) will be filled with the values of the vector. Parameters ---------- vec : list or 1d-array The vector to convert to a symmetric matrix. Returns ------- mat : 2d-array The symmetric matrix. See Also -------- _sym_mat_to_vector rNrWr) r6r5r)r^r=rXZ triu_indicesZrollaxisconjZ issubdtypeintegerZ diag_indices)r-dimr.rrr!r& s "r&cCs|t|S)aConvert a symmetric matrix to a vector. The upper triangle of the matrix (including the diagonal) will be used as the values of the vector. Parameters ---------- mat : 2d-array The symmetric matrix to convert to a vector Returns ------- vec : 1d-array A vector consisting of the values of the upper triangle of the matrix. See Also -------- _vector_to_sym_mat )r)Ztriu_indices_from)r.rrr!r(3sr(cCs2t\}}|ds|d7}||dd}tf|S)aRead a CrossSpectralDensity object from an HDF5 file. Parameters ---------- fname : str The name of the file to read the CSD from. The extension '.h5' will be appended if the given filename doesn't have it already. Returns ------- csd : instance of CrossSpectralDensity The CSD that was stored in the file. See Also -------- CrossSpectralDensity.save : For saving CSD objects. rr)r)rrr0)rZ read_hdf5rZcsd_dictrrr!read_csdJs    rr c  CsBt|||||\}}t||jd|j|||||j|||| d S)aEstimate cross-spectral density from an array using short-time fourier. Parameters ---------- epochs : instance of Epochs The epochs to compute the CSD for. fmin : float Minimum frequency of interest, in Hertz. fmax : float | np.inf Maximum frequency of interest, in Hertz. tmin : float | None Minimum time instant to consider, in seconds. If ``None`` start at first sample. tmax : float | None Maximum time instant to consider, in seconds. If ``None`` end at last sample. %(picks_good_data_noref)s n_fft : int | None Length of the FFT. If ``None``, the exact number of samples between ``tmin`` and ``tmax`` will be used. projs : list of Projection | None List of projectors to store in the CSD object. Defaults to ``None``, which means the projectors defined in the Epochs object will by copied. %(n_jobs)s %(verbose)s Returns ------- csd : instance of CrossSpectralDensity The computed cross-spectral density. See Also -------- csd_array_fourier csd_array_morlet csd_array_multitaper csd_morlet csd_multitaper sfreq) rt0rarbr8r9rr?r@n_jobsr ) _prepare_csdcsd_array_fourierrlrnr8r) epochsrarbr8r9picksr?r@rr rrr! csd_fourierds*rc  Csddlm} t|||||||\}} }}}}|dkr8dnt| |d}|dkrTdnt| |d}|dddd||f}| ||} t| }|dkr|n|}| |d|}||k||k@}||}t|dkrtdt|| |t||||g||| | | d S)a-Estimate cross-spectral density from an array using short-time fourier. Parameters ---------- X : array-like, shape (n_epochs, n_channels, n_times) The time series data consisting of n_epochs separate observations of signals with n_channels time-series of length n_times. sfreq : float Sampling frequency of observations. t0 : float Time of the first sample relative to the onset of the epoch, in seconds. Defaults to 0. fmin : float Minimum frequency of interest, in Hertz. fmax : float | np.inf Maximum frequency of interest, in Hertz. tmin : float | None Minimum time instant to consider, in seconds. If ``None`` start at first sample. tmax : float | None Maximum time instant to consider, in seconds. If ``None`` end at last sample. ch_names : list of str | None A name for each time series. If ``None`` (the default), the series will be named 'SERIES###'. n_fft : int | None Length of the FFT. If ``None``, the exact number of samples between ``tmin`` and ``tmax`` will be used. projs : list of Projection | None List of projectors to store in the CSD object. Defaults to ``None``, which means no projectors are stored. %(n_jobs)s %(verbose)s Returns ------- csd : instance of CrossSpectralDensity The computed cross-spectral density. See Also -------- csd_array_morlet csd_array_multitaper csd_fourier csd_morlet csd_multitaper rrfftfreqN绽|=?No discrete fourier transform results within the given frequency window. Please widen either the frequency window or the time windowparamsr?rr@rr ) scipy.fftr_prepare_csd_arrayr) searchsortedr5r4_execute_csd_function _csd_fourier)Xrrrarbr8r9rr?r@rr rtimeststarttstopn_timesorig_frequencies freq_maskr>rrr!rs:3     rc  CsHt||||| \}} t||jd|j|||||j|||| | | | dS)aEstimate cross-spectral density from epochs using a multitaper method. Parameters ---------- epochs : instance of Epochs The epochs to compute the CSD for. fmin : float | None Minimum frequency of interest, in Hertz. fmax : float | np.inf Maximum frequency of interest, in Hertz. tmin : float Minimum time instant to consider, in seconds. If ``None`` start at first sample. tmax : float | None Maximum time instant to consider, in seconds. If ``None`` end at last sample. %(picks_good_data_noref)s n_fft : int | None Length of the FFT. If ``None``, the exact number of samples between ``tmin`` and ``tmax`` will be used. bandwidth : float | None The bandwidth of the multitaper windowing function in Hz. adaptive : bool Use adaptive weights to combine the tapered spectra into PSD. low_bias : bool Only use tapers with more than 90%% spectral concentration within bandwidth. projs : list of Projection | None List of projectors to store in the CSD object. Defaults to ``None``, which means the projectors defined in the Epochs object will by copied. %(n_jobs)s %(verbose)s Returns ------- csd : instance of CrossSpectralDensity The computed cross-spectral density. See Also -------- csd_array_fourier csd_array_morlet csd_array_multitaper csd_fourier csd_morlet r)rrrarbr8r9rr? bandwidthadaptivelow_biasr@rr )rcsd_array_multitaperrlrnr8r) rrarbr8r9rr?rrrr@rr rrr!csd_multitapers 2rc Csddlm}t|||||||\}}}}}}|dkr8dnt||d}|dkrTdnt||d}|dddd||f}|||}t|}|dkr|n|}t||| | | \}}}||d|}||k||k@}||}t|dkrtdt|||t ||||||| g||| | |d S)aUEstimate cross-spectral density from an array using a multitaper method. Parameters ---------- X : array-like, shape (n_epochs, n_channels, n_times) The time series data consisting of n_epochs separate observations of signals with n_channels time-series of length n_times. sfreq : float Sampling frequency of observations. t0 : float Time of the first sample relative to the onset of the epoch, in seconds. Defaults to 0. fmin : float Minimum frequency of interest, in Hertz. fmax : float | np.inf Maximum frequency of interest, in Hertz. tmin : float | None Minimum time instant to consider, in seconds. If ``None`` start at first sample. tmax : float | None Maximum time instant to consider, in seconds. If ``None`` end at last sample. ch_names : list of str | None A name for each time series. If ``None`` (the default), the series will be named 'SERIES###'. n_fft : int | None Length of the FFT. If ``None``, the exact number of samples between ``tmin`` and ``tmax`` will be used. bandwidth : float | None The bandwidth of the multitaper windowing function in Hz. adaptive : bool Use adaptive weights to combine the tapered spectra into PSD. low_bias : bool Only use tapers with more than 90%% spectral concentration within bandwidth. projs : list of Projection | None List of projectors to store in the CSD object. Defaults to ``None``, which means no projectors are stored. %(n_jobs)s %(verbose)s Returns ------- csd : instance of CrossSpectralDensity The computed cross-spectral density. See Also -------- csd_array_fourier csd_array_morlet csd_fourier csd_morlet csd_multitaper rrNrrrr) rrrr)rr5rr4r_csd_multitaper)rrrrarbr8r9rr?rrrr@rr rrrrr window_funeigvalsZ mt_adaptiverrr>rrr!r!sF;    rc  CsDt|||||\}}t||jd||j|||j||||| | d S)aEstimate cross-spectral density from epochs using Morlet wavelets. Parameters ---------- epochs : instance of Epochs The epochs to compute the CSD for. frequencies : list of float The frequencies of interest, in Hertz. tmin : float | None Minimum time instant to consider, in seconds. If ``None`` start at first sample. tmax : float | None Maximum time instant to consider, in seconds. If ``None`` end at last sample. %(picks_good_data_noref)s n_cycles : float | list of float | None Number of cycles to use when constructing Morlet wavelets. Fixed number or one per frequency. Defaults to 7. use_fft : bool Whether to use FFT-based convolution to compute the wavelet transform. Defaults to True. decim : int | slice To reduce memory usage, decimation factor during time-frequency decomposition. Defaults to 1 (no decimation). If `int`, uses tfr[..., ::decim]. If `slice`, uses tfr[..., decim]. projs : list of Projection | None List of projectors to store in the CSD object. Defaults to ``None``, which means the projectors defined in the Epochs object will be copied. %(n_jobs)s %(verbose)s Returns ------- csd : instance of CrossSpectralDensity The computed cross-spectral density. See Also -------- csd_array_fourier csd_array_morlet csd_array_multitaper csd_fourier csd_multitaper r) rr>rr8r9rn_cyclesuse_fftdecimr@rr )rcsd_array_morletrlrnr8r) rr>r8r9rrrrr@rr rrr! csd_morlet}s3rc  Cs6t|||||\}} }}}}t| }t|||}t|t|d}d}}|dk rpt| |}td||}|dk rt| |}t|||}|dddd||f}| ||} |dkrdnt| |d}|dkrdnt| |d}t||}| |} t |||}t || |t |||||| gd|| | | d S)aEstimate cross-spectral density from an array using Morlet wavelets. Parameters ---------- X : array-like, shape (n_epochs, n_channels, n_times) The time series data consisting of n_epochs separate observations of signals with n_channels time-series of length n_times. sfreq : float Sampling frequency of observations. frequencies : list of float The frequencies of interest, in Hertz. t0 : float Time of the first sample relative to the onset of the epoch, in seconds. Defaults to 0. tmin : float | None Minimum time instant to consider, in seconds. If ``None`` start at first sample. tmax : float | None Maximum time instant to consider, in seconds. If ``None`` end at last sample. ch_names : list of str | None A name for each time series. If ``None`` (the default), the series will be named 'SERIES###'. n_cycles : float | list of float | None Number of cycles to use when constructing Morlet wavelets. Fixed number or one per frequency. Defaults to 7. use_fft : bool Whether to use FFT-based convolution to compute the wavelet transform. Defaults to True. decim : int | slice To reduce memory usage, decimation factor during time-frequency decomposition. Defaults to 1 (no decimation). If `int`, uses tfr[..., ::decim]. If `slice`, uses tfr[..., decim]. projs : list of Projection | None List of projectors to store in the CSD object. Defaults to ``None``, which means the projectors defined in the Epochs object will be copied. %(n_jobs)s %(verbose)s Returns ------- csd : instance of CrossSpectralDensity The computed cross-spectral density. See Also -------- csd_array_fourier csd_array_multitaper csd_fourier csd_morlet csd_multitaper rNrrrr) rr5rr)rerrMrLslicerr _csd_morlet)rrr>rr8r9rrrrr@rr rrrwaveletsZ wave_lengthrrZ csd_tstartZ csd_tstopZ csd_tslicenfftrrr!rs:;       rcCs|jd|jd}|dk r6||jd|kr6td|dk rX||jd|krXtd|dk rx|dk rx||krxtd|jdkr|jdd krtd t|j|d d d }||}|dkr|jd}||fS)zDo some checking and preprocessing of common csd_* parameters. See the csd_* functions for documentation of the parameters. rrN7tmin should be larger than the smallest data time pointrQ7tmax should be smaller than the largest data time pointtmax must be larger than tminZhighpassg?zhEpochs are not baseline corrected or enough highpass filtered. Cross-spectral density may be inaccurate.r,F)Z with_ref_megr@)rr4Zbaselinernr rr#pick)rr8r9rr@tsteprrr!rs rc Cstj|td}|jdkr td|jd}d|}t|||} |dkrT| }|dkrd| }||krttd|| d|krtd || d |krtd |dk r|dk r||krtd || ||||fS) zDo some checking and preprocessing of common csd_r=array_* parameters. See the csd_array_* functions for documentation of the parameters. rWz*X must be n_epochs x n_channels x n_times.rrNrrrrQrzfmax must be larger than fmin) r)r1floatr2r4r=ZarangerMrL) rrrr8r9rarbrrrrrr!r1s&  rc  s |j\} } } tdt|} tj| | dd| ftjd}t||| d\}}tt | t |}t t |ddD]F}||||d|}|fdd |D}|tj |d d 7}qx|| }td |d krddt | D}t|||d |d|||dS)aEstimate cross-spectral density with a given function. This function will apply the given CSD function in parallel across epochs. Parameters ---------- X : array-like, shape (n_epochs, n_channels, n_times) The time series data consisting of n_epochs separate observations of signals with n_channels time-series of length n_times. times : float Timestamps for each sample. frequencies : list of float The frequencies of interest for which the CSD is going to be computed. csd_function : function Function that performs the actual CSD computation params : list List of parameters to pass the CSD function. n_fft : int Number of FFT points. This is stored in the CSD object. ch_names : list of str | None A name for each time series. If ``None`` (the default), the series will be named 'SERIES###'. projs : list of Projection | None List of projectors to store in the CSD object. Defaults to ``None``, which means the projectors defined in the Epochs object will be copied. %(n_jobs)s %(verbose)s Returns ------- csd : instance of CrossSpectralDensity The computed cross-spectral density. z/Computing cross-spectral density from epochs...rrrWrzCSD epoch blocks)Zmesgc3s|]}|fVqdSrRr)rZ this_epochZmy_csdrrr!rSsz(_execute_csd_function..rrYz[done]NcSsg|]}d|dqS)z SERIES%03drrrrrr!r"sz)_execute_csd_function..rQ)rr8r9r>r?r@)r=r rnr5r)r^Z complex128rrrrr ranger`r0)rrr>Z csd_functionrr?rr@rr Zn_epochsrFrZn_freqsZ csds_meanparallelZn_blocksrZ epoch_blockcsdsrrr!rSs8%     rc st|t|||\}}tdgddtjtjtjf}|dddd|f}|ddtjddddf}t|d|jdddg}tj|ddddgd}tj|ddddgd} t|||| tfdd t jd Dj |d 9|S) aCompute cross spectral density (CSD) using short-time fourier transform. Computes the CSD for a single epoch of data. Parameters ---------- X : ndarray, shape (n_channels, n_times) The time series data consisting of n_channels time-series of length n_times. sfreq : float The sampling frequency of the data in Hertz. n_times : int Number of time samples freq_mask : ndarray Which frequencies to use. n_fft : int Length of the FFT. rNrrrrZaxescs&g|]}tdddd|fqSrRr(rrrr!r"sz _csd_fourier..rQgUUUUUU@) rr)Zhanningr*r3tiler= transposerrr%) rrrrr?x_mtrweightsy_mt weights_yrrr!rs" rc s<t||||\}} |rdt|||dd\} } | ddtjddddf} t| d|jdddg} n t|tjtjddtjf} |dddd|f}|ddtjddddf}t|d|jdddg}tj|ddddgd} tj| ddddgd} t|| | | t fd d t jd Dj |S) a+Compute cross spectral density (CSD) using multitaper module. Computes the CSD for a single epoch of data. Parameters ---------- X : ndarray, shape (n_channels, n_times) The time series data consisting of n_channels time-series of length n_times. sfreq : float The sampling frequency of the data in Hertz. n_times : int Number of time samples window_fun : ndarray Window function(s) of length n_times. This corresponds to first output of `dpss_windows`. eigvals : ndarray | float Eigenvalues associated with window functions. freq_mask : ndarray Which frequencies to use. n_fft : int Length of the FFT. adaptive : bool Use adaptive weights to combine the tapered spectra into PSD. T)Zreturn_weightsNrrrrrcs&g|]}tdddd|fqSrRrrrrr!r"sz#_csd_multitaper..rQ) rrr)r3rr=rrrr*rr%) rrrrrrr?rrrrrrrrr!rs&   rc st|||d||d|dk r|jdkr*dn|j|}|jdkrBdn|j|}|jdkrZdn|j|} t||| }dddd|ft|jd} tfddt | D} | |} | S)aCompute cross spectral density (CSD) using the given Morlet wavelets. Computes the CSD for a single epoch of data. Parameters ---------- data : ndarray, shape (n_channels, n_times) The time series data consisting of n_channels time-series of length n_times. sfreq : float The sampling frequency of the data in Hertz. wavelets : list of ndarray The Morlet wavelets for which to compute the CSD's. These have been created by the `mne.time_frequency.tfr.morlet` function. nfft : int The number of FFT points. tslice : slice | None The desired time samples to compute the CSD over. If None, defaults to including all time samples. use_fft : bool Whether to use FFT-based convolution to compute the wavelet transform. Defaults to True. decim : int | slice To reduce memory usage, decimation factor during time-frequency decomposition. Defaults to 1 (no decimation). Only used in 'cwt_morlet' mode. If `int`, uses tfr[..., ::decim]. If `slice`, uses tfr[..., decim]. Returns ------- csd : ndarray, shape ((n_channels**2 + n_channels) / 2 , n_wavelets) For each wavelet, the upper triangle of the cross spectral density matrix. See Also -------- _vector_to_sym_mat : For converting the CSD to a full matrix. Zsame)rorrNrcs,g|]$}tj|g|dddqS)NrrY)r)rcrZpsdsZ psds_conjrr!r"@sz_csd_morlet..) rstartstopsteprr)rr=Zvstackr) r,rrrZtslicerrrrrrFrrrr!rs +    r)NNNrTrNN) rNNNrTrNN)NNNN)NN)NNN)NTr)1r#rAr;numpyr)ZtfrrrrZio.pickrrutilsr r r r r rrZviz.miscrZtime_frequency.multitaperrrrrrrr/objectr0r6r&r(rinfrrrrrrrrrrrrrrrr!s$  ,=& 0 P : [:\  "F1<