def calc_freq2ix(freq, start_ix = 20): _, ix, err = misc.closest(ix2freq[start_ix:], freq, log = True) if err>1: raise 'Large error encountered. (%f)' % err return ix
def calc_fft_following(psth_smoo, rr, npips, remfirst = True): if remfirst: pip_start = 1. else: pip_start = 0. trial_start = np.int32(1000 * pip_start/rr) trial_end = np.int32(1000 * npips/rr) psth_smoo = psth_smoo[trial_start:trial_end] P = np.abs(np.fft.fftshift(np.fft.fft(psth_smoo))) P_freq = np.fft.fftshift(np.fft.fftfreq(psth_smoo.size, d = 0.001)) [_, ix] = misc.closest(P_freq, rr) power = P[ix[0]] / psth_smoo.sum() return power
cf_ix = np.int32(np.round(RF.find_cf(cfs, np.int32(penno)))) cf = ix2freq[20:][cf_ix] # perform analysis if len(rr_path) > 0: rr_file = h5py.File(rr_path, 'r') rr_rast = rr_file['rast'].value rr_stimparams = rr_file['stimID'].value rr_file.close() # rr_rast = rr_rast[1:, :] # rr_stimparams = rr_stimparams[:-1, :] ufreqs = np.unique(rr_stimparams[:, 0]) urrs = np.unique(rr_stimparams[:, 1]) freq_played, freq_ix_played, _ = misc.closest(ufreqs, cf, log = True) rr_bins = np.arange(0, 6, 0.05) rr_psth_stim, usp = Spikes.calc_psth_by_stim(rr_rast, rr_stimparams, bins = rr_bins) cf_psth = rr_psth_stim[freq_ix_played, :, :] noise_psth = rr_psth_stim[0, :, :] fig = plt.figure() nrrs = cf_psth.shape[0] ax = [] for i in range(nrrs): ax.append(fig.add_subplot(nrrs, 1, i+1)) ax[-1].plot(rr_bins[:-1], cf_psth[i, :]) RR.plot_tone_pips(urrs[i], 6, 0.05, 0.025, ax = ax[-1], color = 'r') if i>0: ax[-1].set_xticklabels('')
frr = h5py.File(rrpath, 'r') rast = frr['rast'].value stimparams = frr['stimID'].value frr.close() # if not np.isnan(spktimes[0]): cf = cfs[cfs[:, 0]==unitnum, 1][0] cf_hz = ix2freq[20:][int(cf)] freqs = stimparams[:, 0] rrs = stimparams[:, 1] ufreqs = np.unique(freqs) urrs = np.unique(rrs) nrrs = urrs.size # now we determine which of the frequencies we played is closest to this neuron's CF thisfreq, thisfreq_ix, thisfreq_err = misc.closest(ufreqs, cf_hz, log = True) if np.abs(thisfreq_err) > 0.2: print 'No close frequency found!' thisfreq = ufreqs[thisfreq_ix] # isolate the parts of the raster for this frequency and build a psth for each RR ix = RF.get_trials(stimparams, np.array([thisfreq, np.nan])) thisrast = rast[ix, :1050] thisstims = stimparams[ix, :] psths, ustims = Spikes.calc_psth_by_stim(thisrast, thisstims) rrtf = RR.calc_rrtf_all(thisrast, thisstims, thisfreq, urrs) db.resize(db.size+1) db[-1] = np.array((gen, exp, sess, unitnum, cf_hz, rrtf, urrs), dtype = dtype)
def rr_make_contactsheets(): ''' loop through all the sessions and plot the rrtfs ''' fig = plt.figure(figsize = (30, 18)); txt_suptitle = fig.suptitle('') ax_cfrrtf = fig.add_axes((0.76, 0.76, 0.24, 0.23)); ax_cfvs = ax_cfrrtf.twinx(); ax_cfcircpsthall = fig.add_axes((0.62, (11/14.)-0.02, 0.1, (1/7.)+0.04), polar = True) ax_cfcircpsthall.set_xticklabels(''); ax_cfcircpsthall.set_yticklabels(''); ax_rf = fig.add_axes((0.67, 0.51, 0.33, 0.23)); ax_rfrast = fig.add_axes((0.67, 0.25, 0.33, 0.24)); ax_rfrast.set_xticklabels(''); ax_rfpsth = fig.add_axes((0.67, 0.01, 0.33, 0.24)); ax_cfrr = [fig.add_axes((0.03, 1-((i+1)/7.), 0.35, 1/7.)) for i in np.arange(nrrs)] ax_cfalignedpsth = [fig.add_axes((0.38, 1-((i+1)/7.), 0.17, 1/7.)) for i in np.arange(nrrs)] ax_cfcircpsth = [fig.add_axes((0.53, 1-((i+1)/7.), 0.1, 1/7.), polar = True) for i in np.arange(nrrs)] # ax_noiserr = [fig.add_subplot(nrrs, 3, i) for i in np.arange(1, 3*nrrs, 3)] for sessionpath in sessionpaths: session = os.path.split(sessionpath)[1] unitinfos = fileconversion.get_session_unitinfo(sessionpath, onlycomplete = ('RF', 'RR', 'VOC')) for unitkey in unitinfos.keys(): txt_suptitle.set_text('%s %s' % (session, unitkey)) unitinfo = unitinfos[unitkey] rf_ix = unitinfo['stimtype'].index('RF') f_rf = h5py.File(unitinfo['fpath'][rf_ix], 'r') rf_rast = f_rf['rast'].value rf_stimparams = f_rf['stimID'].value cf_ix = f_rf['cf'].value f_rf.close() cf = ix2freq[20:][int(cf_ix)] ''' calculate and plot RF, psth, and sorted raster''' rf = RF.calc_rf(rf_rast, rf_stimparams) rf_psth = Spikes.calc_psth(rf_rast) RF.plot_rf(rf, cf = cf_ix, axes_on = False, ax = ax_rf) # plot RF ax_rf.axvline(cf_ix, color = 'r', lw = 1.5) Spikes.plot_sorted_raster(rf_rast, rf_stimparams, ax = ax_rfrast) # plot raster ax_rfpsth.plot(t_rf, Spikes.exp_smoo(rf_psth, tau = 0.005)) # plot PSTH ''' calcualte and plot RRTFs for CF and noise stimuli ''' rr_ix = unitinfo['stimtype'].index('RR') f_rr = h5py.File(unitinfo['fpath'][rr_ix], 'r') rr_rast = f_rr['rast'].value rr_stimparams = f_rr['stimID'].value f_rr.close() # find the played CF rr_ufreqs = np.unique(rr_stimparams[:, 0]) urrs = np.unique(rr_stimparams[:, 1]) npips = (urrs*4).astype(int) rr_freq, rr_ufreq_ix, _ = misc.closest(rr_ufreqs, cf, log = True) ax_rf.axvline(RF.calc_freq2ix(rr_freq), color = 'g', lw = 1.5) # calculate the PSTHs for each repetition rate tmp = Spikes.calc_psth_by_stim(rr_rast, rr_stimparams) rr_cfpth = tmp[0][rr_ufreq_ix, :, :] # rrtf_noisepsth = tmp[0][0, :, :] # plot the aligned psths RR.aligned_psth_separate_all(rr_rast, rr_stimparams, rr_freq, npips, axs = ax_cfalignedpsth) [a.set_yticklabels('') for a in ax_cfalignedpsth] [a.set_xticklabels('') for a in ax_cfalignedpsth[:-1]] # plot circular psths r, V, theta = RR.circ_psth_all(rr_rast, rr_stimparams, rr_freq, npips, axs = ax_cfcircpsth) [a.set_yticklabels('') for a in ax_cfcircpsth] [a.set_xticklabels('') for a in ax_cfcircpsth] # plot all circular summed vector strengths ax_cfcircpsthall.plot(theta, V, '.-') [ax_cfcircpsthall.plot([0, th], [0, v], color = 'b', alpha = 1-(i/10.)) for i, (th, v) in enumerate(zip(theta, V))] # plot RRTF rrtf = RR.calc_rrtf_all(rr_rast, rr_stimparams, rr_freq, urrs, npips) ax_cfrrtf.plot(rrtf, '.-', ms = 10) ax_cfvs.plot(V*np.cos(theta), 'g.-', ms = 10) for tick in ax_cfvs.yaxis.get_major_ticks(): tick.set_pad(-5) tick.label2.set_horizontalalignment('right') # plot repetition rate PSTHs for i in xrange(nrrs): # RR.plot_rrtf(t_rrtf, rrtf_noisepsth[i, :], urrs[i], int(4*urrs[i]), onset = 0.05, duration = 0.025, ax = ax_noiserr[i]) RR.plot_rrtf(t_rrtf, rr_cfpth[i, :], urrs[i], int(4*urrs[i]), onset = 0.05, duration = 0.025, ax = ax_cfrr[i]) # ax_noiserr[0].set_title('Noise RRTFs') ax_cfrr[0].set_title('CF RRTFs (%.0f kHz)' % (cf/1000)) # [a.set_xlim(0, 4.5) for a in ax_noiserr] [a.set_xlim(0, 4.5) for a in ax_cfrr] misc.sameyaxis(ax_cfrr+ax_cfalignedpsth) figsavepath = os.path.join(studydir, 'Sheets', 'RRTFs', '%s_%s_RRTF.png' % (session, unitkey)) print figsavepath fig.savefig(figsavepath) [a.cla() for a in fig.get_axes()] # clear all axes
def analyze(): gens = [] exps = [] sesss = [] unitnums = [] cfs = [] noise_rrtfs = [] cf_rrtfs = [] for session in sessions: _, gen, exp, _ = session.split("_") unitinfos = fileconversion.get_session_unitinfo(session, onlycomplete=("RF", "RR", "VOC")) for unitkey in unitinfos.iterkeys(): unitinfo = unitinfos[unitkey] print unitinfo["session"], unitinfo["unitnum"] rr_ix = unitinfo["stimtype"].index("RR") f = h5py.File(unitinfo["fpath"][rr_ix], "r") rast = f["rast"].value stimparams = f["stimID"].value cf_ix = f["cf"].value f.close() ufreqs = np.unique(stimparams[:, 0]) nfreqs = ufreqs.size urrs = np.unique(stimparams[:, 1]) cf = RF.ix2freq[20:][np.round(cf_ix).astype(int)] _, ix, err = misc.closest(ufreqs, cf, log=True) if np.abs(err) > 0.5: print "Repetition rate stimuli not present for this unit (nearest tone %2.2f octaves away)" % err continue ufreq_played = ufreqs[ix] npips = urrs * 4 noise_rrtf = RR.calc_rrtf_all(rast, stimparams, 0.0, urrs, npips=npips) cf_rrtf = RR.calc_rrtf_all(rast, stimparams, ufreq_played, urrs, npips=npips) gens.append(gen) exps.append(exp) sesss.append(session) unitnums.append(unitinfo["unitnum"]) cfs.append(cf_ix) noise_rrtfs.append(noise_rrtf) cf_rrtfs.append(cf_rrtf) df = pd.DataFrame( dict(gen=gens, exp=exps, sess=sesss, unit=unitnums, cf=cfs, noise_rrtf=noise_rrtfs, cf_rrtf=cf_rrtfs) ) d = pd.HDFStore(os.path.join(studydir, "Analysis", "rrtf_data.h5")) d["df"] = df d.close() return df
def add_field(): savepath = '/Users/robert/Documents/Work/Bao/Fmr1_RR/Analysis/RRTFs.h5' fsave = h5py.File(savepath, 'a') sessnames = fsave.keys() for sessname in sessnames: fsess = fsave[sessname] rrblocks = fsess.keys() for rrblock in rrblocks: rrpath = os.path.join(basedir, 'Sessions', 'full_window', 'good', sessname, 'fileconversion', rrblock + '.h5') p = re.compile('RR') rfpath_ = p.sub('RF', rrblock) rfpath = os.path.join(basedir, 'Sessions', 'full_window', 'good', sessname, 'fileconversion', rfpath_+'.h5') p = re.compile('(\d+)') unitnum = np.int32(p.findall(rrblock)[0]) funit = fsess[rrblock] # d = funit.require_dataset('unit', (), 'i4') # d.write_direct(np.array([unitnum])) if verbose: print rrblock print rfpath # LOAD RF FILECONVERSION FILE frf = h5py.File(rfpath, 'r') cf_ix = np.int32(frf['cf'].value) frf.close() cf = ix2freq[20:][cf_ix] # LOAD RR FILECONVERSION FILE frr = h5py.File(rrpath, 'r') rast = frr['rast'].value stimparams = frr['stimID'].value frr.close() # CALCULATE FREQ PLAYED TO THIS UNIT'S CF freqs = np.unique(stimparams[:, 0]) rrs = np.unique(stimparams[:, 1]) freq, _, freq_err = misc.closest(freqs, cf, log = True) freq = np.round(freq, 0) assert freq_err<0.3 # COMPUTE NEW FIELD on, off = Spikes.calc_on_off(funit['ev_psth'].value) # vs, vs_p = RR.calc_vs_all(rast, stimparams, [0.], rrs) # rrtf = RR.calc_rrtf_all(rast, stimparams, freq, rrs) # ADD NEW FIELD d = funit.require_dataset('on_halfmax', (1,), float) d.write_direct(np.array([on])) d = funit.require_dataset('off_halfmax', (1,), float) d.write_direct(np.array([off])) # open the RR file, get rast and stimparams, then close it # frf = h5py.File(rfpath, 'r') # RF.add_rf_analysis(frf, funit) # frf.close() fsave.close()