def make_descr_fits(cellNum,
data_path=basePath + data_suff,
fit_rvc=1,
fit_sf=1,
rvcMod=1,
sfMod=0,
loss_type=2,
vecF1=1,
onsetCurr=None,
rvcName=rvcName,
sfName=sfName,
toSave=1,
fracSig=1,
nBoots=0,
n_repeats=25,
jointSf=0,
resp_thresh=(-1e5, 0),
veThresh=-1e5,
sfModRef=1,
phAdvCorr=True):
''' Separate fits for DC, F1
-- for DC: [maskOnly, mask+base]
-- for F1: [maskOnly, mask+base {@mask TF}]
For asMulti fits (i.e. when done in parallel) we do the following to reduce multiple loading of files/race conditions
--- we'll pass in the previous fits as fit_rvc and/or fit_sf
--- we'll pass in [cellNum, cellName] as cellNum
'''
rvcFits_curr_toSave = None
sfFits_curr_toSave = None
# default to None, in case we don't actually do those fits
expName = 'sfBB_core'
if not isinstance(cellNum, int):
cellNum, unitNm = cellNum
print('cell %d {%s}' % (cellNum, unitNm))
else:
dlName = hf.get_datalist('V1_BB/')
dataList = hf.np_smart_load(data_path + dlName)
unitNm = dataList['unitName'][cellNum - 1]
print('loading cell')
cell = hf.np_smart_load('%s%s_sfBB.npy' % (data_path, unitNm))
expInfo = cell[expName]
byTrial = expInfo['trial']
if fit_rvc == 1 or fit_rvc is not None: # load existing rvcFits, if there
rvcNameFinal = hf.rvc_fit_name(rvcName, rvcMod, None, vecF1)
if fit_rvc == 1:
if os.path.isfile(data_path + rvcNameFinal):
rvcFits = hf.np_smart_load(data_path + rvcNameFinal)
else:
rvcFits = dict()
else: # otherwise, we have passed it in as fit_sf to avoid race condition during multiprocessing (i.e. multiple threads trying to load the same file)
rvcFits = fit_rvc
try:
rvcFits_curr_toSave = rvcFits[cellNum - 1]
except:
rvcFits_curr_toSave = dict()
if fit_sf == 1 or fit_sf is not None:
modStr = hf.descrMod_name(sfMod)
sfNameFinal = hf.descrFit_name(loss_type,
descrBase=sfName,
modelName=modStr,
joint=jointSf)
# descrLoss order is lsq/sqrt/poiss/sach
if fit_sf == 1:
if os.path.isfile(data_path + sfNameFinal):
sfFits = hf.np_smart_load(data_path + sfNameFinal)
else:
sfFits = dict()
else: # otherwise, we have passed it in as fit_sf to avoid race condition during multiprocessing (i.e. multiple threads trying to load the same file)
sfFits = fit_sf
try:
sfFits_curr_toSave = sfFits[cellNum - 1]
print('---prev sf!')
except:
sfFits_curr_toSave = dict()
print('---NO PREV sf!')
# Set up whether we will bootstrap straight away
resample = False if nBoots <= 0 else True
if cross_val is not None:
# we also set to True if cross_val is not None
resample = True
nBoots = 1 if nBoots <= 0 else nBoots
if nBoots > 1:
ftol = 5e-9
#ftol = 1e-6;
else:
ftol = 2.220446049250313e-09
# the default value, per scipy guide (scipy.optimize, for L-BFGS-B)
#########
### Get the responses - base only, mask+base [base F1], mask only (mask F1)
### _____ MAKE THIS A FUNCTION???
#########
# 1. Get the mask only response (f1 at mask TF)
_, _, gt_respMatrixDC_onlyMask, gt_respMatrixF1_onlyMask = hf_sf.get_mask_resp(
expInfo,
withBase=0,
maskF1=1,
vecCorrectedF1=vecF1,
onsetTransient=onsetCurr,
returnByTr=1,
phAdvCorr=phAdvCorr)
# i.e. get the maskONLY response
# 2f1. get the mask+base response (but f1 at mask TF)
_, _, _, gt_respMatrixF1_maskTf = hf_sf.get_mask_resp(
expInfo,
withBase=1,
maskF1=1,
vecCorrectedF1=vecF1,
onsetTransient=onsetCurr,
returnByTr=1,
phAdvCorr=phAdvCorr)
# i.e. get the maskONLY response
# 2dc. get the mask+base response (f1 at base TF)
_, _, gt_respMatrixDC, _ = hf_sf.get_mask_resp(expInfo,
withBase=1,
maskF1=0,
vecCorrectedF1=vecF1,
onsetTransient=onsetCurr,
returnByTr=1,
phAdvCorr=phAdvCorr)
# i.e. get the base response for F1
if cross_val == 2.0:
nBoots = np.multiply(*gt_respMatrixDC_onlyMask.shape[0:2], )
print('# boots is %03d' % nBoots)
resample = False
# then we DO NOT want to resample
for boot_i in range(nBoots):
######
# 3a. Ensure we have the right responses (incl. resampling, taking mean)
######
# --- Note that all hf_sf.resample_all_cond(resample, arr, axis=X) calls are X=2, because all arrays are [nSf x nCon x respPerTrial x ...]
# - o. DC responses are easy - simply resample, then take the mean/s.e.m. across all trials of a given condition
respMatrixDC_onlyMask_resample = hf_sf.resample_all_cond(
resample, np.copy(gt_respMatrixDC_onlyMask), axis=2)
respMatrixDC_onlyMask = np.stack(
(np.nanmean(respMatrixDC_onlyMask_resample, axis=-1),
sem(respMatrixDC_onlyMask_resample, axis=-1, nan_policy='omit')),
axis=-1)
respMatrixDC_resample = hf_sf.resample_all_cond(
resample, np.copy(gt_respMatrixDC), axis=2)
respMatrixDC = np.stack(
(np.nanmean(respMatrixDC_resample, axis=-1),
sem(respMatrixDC_resample, axis=-1, nan_policy='omit')),
axis=-1)
# - F1 responses are different - vector math (i.e. hf.polar_vec_mean call)
# --- first, resample the data, then do the vector math
# - i. F1, only mask
respMatrixF1_onlyMask_resample = hf_sf.resample_all_cond(
resample, np.copy(gt_respMatrixF1_onlyMask), axis=2)
# --- however, polar_vec_mean must be computed by condition, to handle NaN (which might be unequal across conditions):
respMatrixF1_onlyMask = np.empty(
respMatrixF1_onlyMask_resample.shape[0:2] +
respMatrixF1_onlyMask_resample.shape[3:])
respMatrixF1_onlyMask_phi = np.copy(respMatrixF1_onlyMask)
for conds in itertools.product(
*[range(x)
for x in respMatrixF1_onlyMask_resample.shape[0:2]]):
r_mean, phi_mean, r_sem, phi_sem = hf.polar_vec_mean(
[
hf.nan_rm(respMatrixF1_onlyMask_resample[conds +
(slice(None), 0)])
], [
hf.nan_rm(respMatrixF1_onlyMask_resample[conds +
(slice(None), 1)])
],
sem=1) # return s.e.m. rather than std (default)
# - and we only care about the R value (after vec. avg.)
respMatrixF1_onlyMask[conds] = [r_mean[0], r_sem[0]]
# r...[0] to unpack (it's nested inside array, since f is vectorized
respMatrixF1_onlyMask_phi[conds] = [phi_mean[0], phi_sem[0]]
if phAdvCorr and vecF1:
maskCon, maskSf = expInfo['maskCon'], expInfo['maskSF']
opt_params, phAdv_model = hf_sf.phase_advance_fit_core(
respMatrixF1_onlyMask, respMatrixF1_onlyMask_phi, maskCon,
maskSf)
for msI, mS in enumerate(maskSf):
curr_params = opt_params[msI]
# the phAdv model applies per-SF
for mcI, mC in enumerate(maskCon):
curr_r, curr_phi = respMatrixF1_onlyMask[
mcI, msI, 0], respMatrixF1_onlyMask_phi[mcI, msI, 0]
refPhi = phAdv_model(*curr_params, curr_r)
new_r = np.multiply(
curr_r,
np.cos(np.deg2rad(refPhi) - np.deg2rad(curr_phi)))
respMatrixF1_onlyMask[mcI, msI, 0] = new_r
# - ii. F1, both (@ maskTF)
respMatrixF1_maskTf_resample = hf_sf.resample_all_cond(
resample, np.copy(gt_respMatrixF1_maskTf), axis=2)
# --- however, polar_vec_mean must be computed by condition, to handle NaN (which might be unequal across conditions):
respMatrixF1_maskTf = np.empty(
respMatrixF1_maskTf_resample.shape[0:2] +
respMatrixF1_maskTf_resample.shape[3:])
respMatrixF1_maskTf_phi = np.copy(respMatrixF1_maskTf)
for conds in itertools.product(
*[range(x) for x in respMatrixF1_maskTf_resample.shape[0:2]]):
r_mean, phi_mean, r_sem, phi_var = hf.polar_vec_mean(
[
hf.nan_rm(respMatrixF1_maskTf_resample[conds +
(slice(None), 0)])
], [
hf.nan_rm(respMatrixF1_maskTf_resample[conds +
(slice(None), 1)])
],
sem=1) # return s.e.m. rather than std (default)
# - and we only care about the R value (after vec. avg.)
respMatrixF1_maskTf[conds] = [r_mean[0], r_sem[0]]
# r...[0] is to unpack (it's nested inside array, since func is vectorized
respMatrixF1_maskTf_phi[conds] = [phi_mean[0], phi_sem[0]]
if phAdvCorr and vecF1:
maskCon, maskSf = expInfo['maskCon'], expInfo['maskSF']
opt_params, phAdv_model = hf_sf.phase_advance_fit_core(
respMatrixF1_maskTf, respMatrixF1_maskTf_phi, maskCon, maskSf)
for msI, mS in enumerate(maskSf):
curr_params = opt_params[msI]
# the phAdv model applies per-SF
for mcI, mC in enumerate(maskCon):
curr_r, curr_phi = respMatrixF1_maskTf[
mcI, msI, 0], respMatrixF1_maskTf_phi[mcI, msI, 0]
refPhi = phAdv_model(*curr_params, curr_r)
new_r = np.multiply(
curr_r,
np.cos(np.deg2rad(refPhi) - np.deg2rad(curr_phi)))
respMatrixF1_maskTf[mcI, msI, 0] = new_r
if cross_val == 2.0:
n_sfs, n_cons = gt_respMatrixF1_maskTf.shape[
0], gt_respMatrixF1_maskTf.shape[1]
con_ind, sf_ind = np.floor(np.divide(boot_i,
n_sfs)).astype('int'), np.mod(
boot_i,
n_sfs).astype('int')
print('holding out con/sf indices %02d/%02d' % (con_ind, sf_ind))
for measure in [0, 1]:
if measure == 0:
baseline = np.nanmean(
hf.resample_array(resample, expInfo['blank']['resps']))
if cross_val == 2.0:
# --- so, "nan" out that condition in all of the responses
mask_only_ref = np.copy(respMatrixDC_onlyMask)
mask_base_ref = np.copy(respMatrixDC)
# the above establish the reference values; below, we nan out the current condition
mask_only = np.copy(respMatrixDC_onlyMask)
mask_base = np.copy(respMatrixDC)
mask_only[sf_ind, con_ind] = np.nan
mask_base[sf_ind, con_ind] = np.nan
else:
mask_only = respMatrixDC_onlyMask
mask_base = respMatrixDC
mask_only_all = None
# as of 22.06.15
fix_baseline = False
elif measure == 1:
baseline = 0
if cross_val == 2.0:
# --- so, "nan" out that condition in all of the responses
mask_only_ref = np.copy(respMatrixF1_onlyMask)
mask_base_ref = np.copy(respMatrixF1_maskTf)
# the above establish the reference values; below, we nan out the current condition
mask_only = np.copy(respMatrixF1_onlyMask)
mask_base = np.copy(respMatrixF1_maskTf)
mask_only[sf_ind, con_ind] = np.nan
mask_base[sf_ind, con_ind] = np.nan
else:
mask_only = respMatrixF1_onlyMask
mask_base = respMatrixF1_maskTf
mask_only_all = None
# as of 22.06.15; ignore the above line
fix_baseline = True
resp_str = hf_sf.get_resp_str(respMeasure=measure)
if cross_val is not None: # set up what is the test data!
nan_val = -1e3
# make sure we nan out any existing NaN values in the reference data
mask_only_ref[np.isnan(mask_only_ref)] = nan_val
# make sure we nan out any NaN values in the training data
mask_only_tr = np.copy(mask_only)
mask_only_tr[np.isnan(mask_only_tr)] = nan_val
heldout = np.abs(
mask_only_tr - mask_only_ref
) > 1e-6 # if the idff. is g.t. this, it means they are different values
test_mask_only = np.nan * np.zeros_like(mask_only_tr)
test_mask_base = np.nan * np.zeros_like(mask_only_tr)
test_mask_only[heldout] = mask_only_ref[heldout]
test_mask_base[heldout] = mask_base_ref[heldout]
heldouts = [test_mask_only]
# update to include ...base IF below lines (which*) include both
else:
heldouts = [None]
whichAll = [mask_only_all]
whichResp = [mask_only] #, mask_base];
whichKey = ['mask'] #, 'both'];
if fit_rvc == 1 or fit_rvc is not None:
''' Fit RVCs responses (see helper_fcns.rvc_fit for details) for:
--- F0: mask alone (7 sfs)
mask + base together (7 sfs)
--- F1: mask alone (7 sfs; at maskTf)
mask+ + base together (7 sfs; again, at maskTf)
NOTE: Assumes only sfBB_core
'''
if resp_str not in rvcFits_curr_toSave:
rvcFits_curr_toSave[resp_str] = dict()
cons = expInfo['maskCon']
# first, mask only; then mask+base
for wR, wK, wA in zip(whichResp, whichKey, whichAll):
# create room for an empty dict, if not already present
if wK not in rvcFits_curr_toSave[resp_str]:
rvcFits_curr_toSave[resp_str][wK] = dict()
adjMeans = np.transpose(wR[:, :, 0])
# just the means
# --- in new version of code [to allow boot], we can get masked array; do the following to save memory
adjMeans = adjMeans.data if isinstance(
adjMeans, np.ma.MaskedArray) else adjMeans
consRepeat = [cons] * len(adjMeans)
# get a previous fit, if present
try:
rvcFit_curr = rvcFits_curr_toSave[resp_str][
wK] if not resample else None
except:
rvcFit_curr = None
# do the fitting!
_, all_opts, all_conGains, all_loss = hf.rvc_fit(
adjMeans,
consRepeat,
var=None,
mod=rvcMod,
fix_baseline=fix_baseline,
prevFits=rvcFit_curr,
n_repeats=n_repeats)
# compute variance explained!
varExpl = [
hf.var_explained(
hf.nan_rm(dat),
hf.nan_rm(hf.get_rvcResp(prms, cons, rvcMod)),
None) for dat, prms in zip(adjMeans, all_opts)
]
# now, package things
if resample:
if boot_i == 0: # i.e. first time around
# - then we create empty lists to which we append the result of each success iteration
# --- note that we do not include adjMeans here (don't want nBoots iterations of response means saved!)
rvcFits_curr_toSave[resp_str][wK][
'boot_loss'] = []
rvcFits_curr_toSave[resp_str][wK][
'boot_params'] = []
rvcFits_curr_toSave[resp_str][wK][
'boot_conGain'] = []
rvcFits_curr_toSave[resp_str][wK][
'boot_varExpl'] = []
# then -- append!
rvcFits_curr_toSave[resp_str][wK]['boot_loss'].append(
all_loss)
rvcFits_curr_toSave[resp_str][wK][
'boot_params'].append(all_opts)
rvcFits_curr_toSave[resp_str][wK][
'boot_conGain'].append(all_conGains)
rvcFits_curr_toSave[resp_str][wK][
'boot_varExpl'].append(varExpl)
else: # we will never be here more than once, since if not resample, then nBoots = 1
rvcFits_curr_toSave[resp_str][wK]['loss'] = all_loss
rvcFits_curr_toSave[resp_str][wK]['params'] = all_opts
rvcFits_curr_toSave[resp_str][wK][
'conGain'] = all_conGains
rvcFits_curr_toSave[resp_str][wK][
'adjMeans'] = adjMeans
rvcFits_curr_toSave[resp_str][wK]['varExpl'] = varExpl
########
# END of rvc fit (for this measure, boot iteration)
########
if fit_sf == 1 or fit_sf is not None:
''' Fit SF tuning responses (see helper_fcns.dog_fit for details) for:
--- F0: mask alone (7 cons)
mask + base together (7 cons)
--- F1: mask alone (7 cons; at maskTf)
mask+ + base together (7 cons; again, at maskTf)
NOTE: Assumes only sfBB_core
'''
if resp_str not in sfFits_curr_toSave:
sfFits_curr_toSave[resp_str] = dict()
cons, sfs = expInfo['maskCon'], expInfo['maskSF']
stimVals = [[0], cons, sfs]
valConByDisp = [np.arange(0, len(cons))]
# all cons are valid in sfBB experiment
for wR, wK, wA, heldout in zip(whichResp, whichKey, whichAll,
heldouts):
if wK not in sfFits_curr_toSave[resp_str]:
sfFits_curr_toSave[resp_str][wK] = dict()
# get a previous fit, if present
try:
sfFit_curr = sfFits_curr_toSave[resp_str][
wK] if not resample else None
except:
sfFit_curr = None
# try to load isolated fits...
if jointSf > 0:
try: # load non_joint fits as a reference (see hf.dog_fit or S. Sokol thesis for details)
modStr = hf.descrMod_name(sfMod)
ref_fits = hf.np_smart_load(
data_path + hf.descrFit_name(loss_type,
descrBase=sfName,
modelName=modStr,
joint=0))
isolFits = ref_fits[cellNum -
1][resp_str][wK]['params']
if sfMod == sfModRef:
ref_varExpl = ref_fits[
cellNum - 1][resp_str][wK]['varExpl']
else:
# otherwise, load the DoG
vExp_ref_fits = hf.np_smart_load(
data_path + hf.descrFit_name(
loss_type,
descrBase=sfName,
modelName=hf.descrMod_name(sfModRef),
joint=0))
ref_varExpl = vExp_ref_fits[
cellNum - 1][resp_str][wK]['varExpl']
except:
isolFits = None
ref_varExpl = None
else:
isolFits = None
ref_varExpl = None
allCurr = np.expand_dims(
np.transpose(
wA, [1, 0, 2]), axis=0) if wA is not None else None
# -- by default, loss_type=2 (meaning sqrt loss); why expand dims and transpose? dog fits assumes the data is in [disp,sf,con] and we just have [con,sf]
nll, prms, vExp, pSf, cFreq, totNLL, totPrm, success = hf.dog_fit(
[
np.expand_dims(np.transpose(wR[:, :, 0]),
axis=0), allCurr,
np.expand_dims(np.transpose(wR[:, :, 1]), axis=0),
baseline
],
sfMod,
loss_type=2,
disp=0,
expInd=None,
stimVals=stimVals,
validByStimVal=None,
valConByDisp=valConByDisp,
prevFits=sfFit_curr,
noDisp=1,
fracSig=fracSig,
n_repeats=n_repeats,
isolFits=isolFits,
ref_varExpl=ref_varExpl,
veThresh=veThresh,
joint=jointSf,
ftol=ftol,
resp_thresh=resp_thresh
) # noDisp=1 means that we don't index dispersion when accessins prevFits
if resample or cross_val is not None:
if boot_i == 0: # i.e. first time around
if cross_val is not None:
# first, pre-define empty lists for all of the needed results, if they are not yet defined
sfFits_curr_toSave[resp_str][wK][
'boot_NLL_cv_test'] = np.empty(
(nBoots, ) + nll.shape,
dtype=np.float32)
sfFits_curr_toSave[resp_str][wK][
'boot_vExp_cv_test'] = np.empty(
(nBoots, ) + vExp.shape,
dtype=np.float32)
sfFits_curr_toSave[resp_str][wK][
'boot_NLL_cv_train'] = np.empty(
(nBoots, ) + nll.shape,
dtype=np.float32)
sfFits_curr_toSave[resp_str][wK][
'boot_vExp_cv_train'] = np.empty(
(nBoots, ) + vExp.shape,
dtype=np.float32)
# --- these are all implicitly based on training data
sfFits_curr_toSave[resp_str][wK][
'boot_cv_params'] = np.empty(
(nBoots, ) + prms.shape,
dtype=np.float32)
sfFits_curr_toSave[resp_str][wK][
'boot_cv_prefSf'] = np.empty(
(nBoots, ) + pSf.shape,
dtype=np.float32)
sfFits_curr_toSave[resp_str][wK][
'boot_cv_charFreq'] = np.empty(
(nBoots, ) + cFreq.shape,
dtype=np.float32)
else: # otherwise, the things we put only if we didn't have cross-validation
# - pre-allocate empty array of length nBoots (save time over appending each time around)
sfFits_curr_toSave[resp_str][wK][
'boot_loss'] = np.empty(
(nBoots, ) + nll.shape,
dtype=np.float32)
sfFits_curr_toSave[resp_str][wK][
'boot_params'] = np.empty(
(nBoots, ) + prms.shape,
dtype=np.float32)
sfFits_curr_toSave[resp_str][wK][
'boot_varExpl'] = np.empty(
(nBoots, ) + vExp.shape,
dtype=np.float32)
sfFits_curr_toSave[resp_str][wK][
'boot_prefSf'] = np.empty(
(nBoots, ) + pSf.shape,
dtype=np.float32)
sfFits_curr_toSave[resp_str][wK][
'boot_charFreq'] = np.empty(
(nBoots, ) + cFreq.shape,
dtype=np.float32)
# and the below apply whether or not we did cross-validation!
if jointSf > 0:
sfFits_curr_toSave[resp_str][wK][
'boot_totalNLL'] = np.empty(
(nBoots, ) + totNLL.shape,
dtype=np.float32)
sfFits_curr_toSave[resp_str][wK][
'boot_paramList'] = np.empty(
(nBoots, ) + totPrm.shape,
dtype=np.float32)
sfFits_curr_toSave[resp_str][wK][
'boot_success'] = np.empty((nBoots, ),
dtype=np.bool_)
else: # only if joint=0 will success be an array (and not just one value)
sfFits_curr_toSave[resp_str][wK][
'boot_success'] = np.empty(
(nBoots, ) + success.shape,
dtype=np.bool_)
# then -- put in place (we reach here for all boot_i)
if cross_val is not None:
### then, we need to compute test loss/vExp!
test_nlls = np.nan * np.zeros_like(nll)
test_vExps = np.nan * np.zeros_like(vExp)
# set up ref_params, ref_rc_val; will only be used IF applicable
ref_params = None
ref_rc_val = None
if sfMod == 3:
try:
all_xc = prms[:, 1]
# xc
ref_params = [np.nanmin(all_xc), 1]
except:
pass
else:
try:
ref_params = prms[-1]
# high contrast condition
ref_rc_val = totPrm[
2] if jointSf > 0 else None
# even then, only used for jointSf==5
except:
pass
for ii, prms_curr in enumerate(prms):
# we'll iterate over the parameters, which are fit for each contrast (the final dimension of test_mn)
if np.any(np.isnan(prms_curr)):
continue
non_nans = np.where(~np.isnan(heldout[:, ii,
0]))[0]
# check -- from the heldout data at contrast ii, which sfs are not NaN
curr_sfs = stimVals[2][non_nans]
# get those sf values
resps_curr = heldout[non_nans, ii, 0]
# and get those responses, to pass into DoG_loss
test_nlls[ii] = hf.DoG_loss(
prms_curr,
resps_curr,
curr_sfs,
resps_std=None,
loss_type=loss_type,
DoGmodel=sfMod,
dir=dir,
joint=0,
baseline=baseline,
ref_params=ref_params,
ref_rc_val=ref_rc_val
) # why not enforce max? b/c fewer resps means more varied range of max, don't want to wrongfully penalize
test_vExps[ii] = hf.var_explained(
resps_curr,
prms_curr,
curr_sfs,
sfMod,
baseline=baseline,
ref_params=ref_params,
ref_rc_val=ref_rc_val)
### done with computing test loss, so save everything
sfFits_curr_toSave[resp_str][wK][
'boot_NLL_cv_test'][boot_i] = test_nlls
sfFits_curr_toSave[resp_str][wK][
'boot_vExp_cv_test'][boot_i] = test_vExps
sfFits_curr_toSave[resp_str][wK][
'boot_NLL_cv_train'][boot_i] = nll
sfFits_curr_toSave[resp_str][wK][
'boot_vExp_cv_train'][boot_i] = vExp
# --- these are all implicitly based on training data
sfFits_curr_toSave[resp_str][wK]['boot_cv_params'][
boot_i] = prms
sfFits_curr_toSave[resp_str][wK]['boot_cv_prefSf'][
boot_i] = pSf
sfFits_curr_toSave[resp_str][wK][
'boot_cv_charFreq'][boot_i] = cFreq
else:
sfFits_curr_toSave[resp_str][wK]['boot_loss'][
boot_i] = nll
sfFits_curr_toSave[resp_str][wK]['boot_params'][
boot_i] = prms
sfFits_curr_toSave[resp_str][wK]['boot_charFreq'][
boot_i] = cFreq
sfFits_curr_toSave[resp_str][wK]['boot_varExpl'][
boot_i] = vExp
sfFits_curr_toSave[resp_str][wK]['boot_prefSf'][
boot_i] = pSf
# these apply regardless of c-v or not
sfFits_curr_toSave[resp_str][wK]['boot_success'][
boot_i] = success
if jointSf > 0:
try:
sfFits_curr_toSave[resp_str][wK][
'boot_totalNLL'][boot_i] = totNLL
sfFits_curr_toSave[resp_str][wK][
'boot_paramList'][boot_i] = totPrm
except:
pass
else: # otherwise, we'll only be here once
sfFits_curr_toSave[resp_str][wK]['NLL'] = nll.astype(
np.float32)
sfFits_curr_toSave[resp_str][wK][
'params'] = prms.astype(np.float32)
sfFits_curr_toSave[resp_str][wK][
'varExpl'] = vExp.astype(np.float32)
sfFits_curr_toSave[resp_str][wK][
'prefSf'] = pSf.astype(np.float32)
sfFits_curr_toSave[resp_str][wK][
'charFreq'] = cFreq.astype(np.float32)
sfFits_curr_toSave[resp_str][wK][
'success'] = success #.astype(np.bool_);
if jointSf > 0:
try:
sfFits_curr_toSave[resp_str][wK][
'totalNLL'] = totNLL.astype(np.float32)
except:
sfFits_curr_toSave[resp_str][wK][
'totalNLL'] = totNLL
# if it's None, or [], or...
try:
sfFits_curr_toSave[resp_str][wK][
'paramList'] = totPrm.astype(np.float32)
except:
sfFits_curr_toSave[resp_str][wK][
'paramList'] = totPrm
# if it's None, or [], or...
########
# END of sf fit (for this measure, boot iteration)
########
########
# END of measure (i.e. handled both measures, go back for more boot_iter, if specified)
########
########
# END of all boot iters (i.e. handled both measures, go back for more boot_iter, if specified)
########
###########
# NOW, save (if saving); otherwise, we return the values
###########
# if we are saving, save; otherwise, return the curr_rvc, curr_sf fits
if toSave:
if fit_rvc:
# load fits again in case some other run has saved/made changes
if os.path.isfile(data_path + rvcNameFinal):
print('reloading rvcFits...')
rvcFits = hf.np_smart_load(data_path + rvcNameFinal)
if cellNum - 1 not in rvcFits:
rvcFits[cellNum - 1] = dict()
# now save
rvcFits[cellNum - 1] = rvcFits_curr_toSave
np.save(data_path + rvcNameFinal, rvcFits)
print('Saving %s, %s @ %s' % (resp_str, wK, rvcNameFinal))
if fit_sf:
pass_check = False
while not pass_check: # keep saving/reloading until the fit has properly saved everything...
# load fits again in case some other run has saved/made changes
if os.path.isfile(data_path + sfNameFinal):
print('reloading sfFits...')
sfFits = hf.np_smart_load(data_path + sfNameFinal)
if cellNum - 1 not in sfFits:
sfFits[cellNum - 1] = dict()
sfFits[cellNum - 1] = sfFits_curr_toSave
# now save
np.save(data_path + sfNameFinal, sfFits)
print('Saving %s, %s @ %s' % (resp_str, wK, sfNameFinal))
# now check...
check = hf.np_smart_load(data_path + sfNameFinal)
if resample: # check that the boot stuff is there
if 'boot_params' in check[cellNum -
1]['dc']['mask'].keys():
pass_check = True
else:
if 'NLL' in check[cellNum - 1]['dc']['mask'].keys(
): # just check that any relevant key is there
pass_check = True
# --- and if neither pass_check was triggered, then we go back and reload, etc
### End of saving (both RVC and SF)
else:
return rvcFits_curr_toSave, sfFits_curr_toSave
### RVCFITS
#rvcBase = 'rvcFits_200507'; # direc flag & '.npy' are added
#rvcBase = 'rvcFits_191023'; # direc flag & '.npy' are adde
#rvcBase = 'rvcFits_200714'; # direc flag & '.npy' are adde
#rvcBase = 'rvcFits_200507';
rvcBase = 'rvcFits_210517'
# -- rvcAdj = -1 means, yes, load the rvcAdj fits, but with vecF1 correction rather than ph fit; so, we'll
rvcAdjSigned = rvcAdj
rvcAdj = np.abs(rvcAdj)
##################
### Spatial frequency
##################
modStr = hf.descrMod_name(descrMod)
fLname = hf.descrFit_name(descrLoss, descrBase=descrBase, modelName=modStr)
descrFits = hf.np_smart_load(data_loc + fLname)
pause_tm = 2.5 * np.random.rand()
time.sleep(pause_tm)
# set the save directory to save_loc, then create the save directory if needed
subDir = fLname.replace('Fits', '').replace('.npy', '')
save_loc = str(save_loc + subDir + '/')
if not os.path.exists(save_loc):
os.makedirs(save_loc)
dataList = hf.np_smart_load(data_loc + expName)
cellName = dataList['unitName'][cellNum - 1]
try:
cellType = dataList['unitType'][cellNum - 1]
print('rvc? %d -- sf? %d -- sfMod,joint %d,%d' %
(fit_rvc, fit_sf, sf_mod, jointSf))
fracSig = 1
# why fracSig =1? For V1 fits, we want to contrasin the upper-half sigma of the two-half gaussian as a fraction of the lower half
if asMulti:
from functools import partial
import multiprocessing as mp
nCpu = mp.cpu_count()
# to avoid race conditions, load the previous fits beforehand; and the datalist
rvcNameFinal = hf.rvc_fit_name(rvcName, rvc_mod, None, vecF1=1)
# DEFAULT is vecF1 adjustment
modStr = hf.descrMod_name(sf_mod)
sfNameFinal = hf.descrFit_name(loss_type,
descrBase=sfName,
modelName=modStr,
joint=jointSf)
# descrLoss order is lsq/sqrt/poiss/sach
pass_rvc = hf.np_smart_load(
'%s%s%s' %
(basePath, data_suff, rvcNameFinal)) if fit_rvc else None
pass_sf = hf.np_smart_load(
'%s%s%s' % (basePath, data_suff, sfNameFinal)) if fit_sf else None
dataList = hf.np_smart_load(
'%s%s%s' % (basePath, data_suff, hf.get_datalist('V1_BB/')))
if nBoots > 1:
n_repeats = 3 if jointSf > 0 else 5
# fewer if repeat
### DESCRLIST
hpc_str = 'HPC' if isHPC else ''
descrBase = 'descrFits%s_220720vEs' % hpc_str
#descrBase = 'descrFits%s_220410' % hpc_str;
### RVCFITS
rvcBase = 'rvcFits%s_220718' % hpc_str
#rvcBase = 'rvcFits%s_220609' % hpc_str;
##################
### Spatial frequency
##################
modStr = hf.descrMod_name(descrMod)
fLname = hf.descrFit_name(descrLoss,
descrBase=descrBase,
modelName=modStr,
joint=joint,
phAdj=1 if phAdjSigned == 1 else None)
descrFits = hf.np_smart_load(data_loc + fLname)
pause_tm = 2.0 * np.random.rand()
time.sleep(pause_tm)
# set the save directory to save_loc, then create the save directory if needed
subDir = fLname.replace('Fits', '').replace('.npy', '')
save_loc = str(save_loc + subDir + '/')
if not os.path.exists(save_loc):
os.makedirs(save_loc)
dataList = hf.np_smart_load(data_loc + expName)
cellName = dataList['unitName'][cellNum - 1]
if rpt_fit:
is_rpt = '_rpt'
else:
is_rpt = ''
conDig = 3
# round contrast to the 3rd digit
dataList = np.load(str(dataPath + expName), encoding='latin1').item()
cellStruct = np.load(str(dataPath + dataList['unitName'][which_cell - 1] +
'_sfm.npy'),
encoding='latin1').item()
# #### Load descriptive model fits, comp. model fits
descrFitName = hf.descrFit_name(descr_fit_type)
modParams = np.load(str(dataPath + fitListName), encoding='latin1').item()
modParamsCurr = modParams[which_cell - 1]['params']
# ### Organize data
# #### determine contrasts, center spatial frequency, dispersions
data = cellStruct['sfm']['exp']['trial']
ignore, modRespAll = mod_resp.SFMGiveBof(modParamsCurr,
cellStruct,
normType=norm_type,
lossType=lossType,
expInd=expInd)
print('norm type %02d' % (norm_type))
lossSuf = '_poiss.npy'
elif lossType == 3:
lossSuf = '_modPoiss.npy'
elif lossType == 4:
lossSuf = '_chiSq.npy'
fitName = str(fitBase + fitSuf + lossSuf)
# set the save directory to save_loc, then create the save directory if needed
subDir = fitName.replace('fitList', 'fits').replace('.npy', '')
save_loc = str(save_loc + subDir + '/')
if not os.path.exists(save_loc):
os.makedirs(save_loc)
# load descrFits
descrExpName = descrFit_name(descrLossType)
descrModName = descrFit_name(descrLossType, fitName)
nFam = 5
nCon = 2
plotSteps = 100
# how many steps for plotting descriptive functions?
sfPlot = np.logspace(-1, 1, plotSteps)
# for bandwidth/prefSf descriptive stuff
muLoc = 2
# mu is in location '2' of parameter arrays
height = 1 / 2.
# measure BW at half-height
sf_range = [0.01, 10]
# allowed values of 'mu' for fits - see descr_fit.py for details
vecF1 = -1
else:
rvcMod = 1
# i.e. Naka-rushton (1)
dMod_num = 3
# d-dog-s
rvcDir = None
# None if we're doing vec-corrected
if expDir == 'altExp/':
vecF1 = 0
else:
vecF1 = 1
dFits_mod = hf.descrMod_name(dMod_num)
descrFits_name = hf.descrFit_name(lossType=dLoss_num,
descrBase=dFits_base,
modelName=dFits_mod,
phAdj=1 if vecF1 == -1 else None)
## now, let it run
dataPath = basePath + expDir + 'structures/'
save_loc = basePath + expDir + 'figures/'
save_locSuper = save_loc + 'superposition_220713/'
if use_mod_resp == 1:
save_locSuper = save_locSuper + '%s/' % fitBase
dataList = hf.np_smart_load(dataPath + dataListNm)
print('Trying to load descrFits at: %s' % (dataPath + descrFits_name))
descrFits = hf.np_smart_load(dataPath + descrFits_name)
if use_mod_resp == 1 or use_mod_resp == 2:
fitList = hf.np_smart_load(dataPath + fitList_nm)
else:
def plot_save_superposition(which_cell, expDir, use_mod_resp=0, fitType=2, excType=1, useHPCfit=1, conType=None, lgnFrontEnd=None, force_full=1, f1_expCutoff=2, to_save=1):
if use_mod_resp == 2:
rvcAdj = -1; # this means vec corrected F1, not phase adjustment F1...
_applyLGNtoNorm = 0; # don't apply the LGN front-end to the gain control weights
recenter_norm = 1;
newMethod = 1; # yes, use the "new" method for mrpt (not that new anymore, as of 21.03)
lossType = 1; # sqrt
_sigmoidSigma = 5;
basePath = os.getcwd() + '/'
if 'pl1465' in basePath or useHPCfit:
loc_str = 'HPC';
else:
loc_str = '';
rvcName = 'rvcFits%s_220531' % loc_str if expDir=='LGN/' else 'rvcFits%s_220609' % loc_str
rvcFits = None; # pre-define this as None; will be overwritten if available/needed
if expDir == 'altExp/': # we don't adjust responses there...
rvcName = None;
dFits_base = 'descrFits%s_220609' % loc_str if expDir=='LGN/' else 'descrFits%s_220631' % loc_str
if use_mod_resp == 1:
rvcName = None; # Use NONE if getting model responses, only
if excType == 1:
fitBase = 'fitList_200417';
elif excType == 2:
fitBase = 'fitList_200507';
lossType = 1; # sqrt
fitList_nm = hf.fitList_name(fitBase, fitType, lossType=lossType);
elif use_mod_resp == 2:
rvcName = None; # Use NONE if getting model responses, only
if excType == 1:
fitBase = 'fitList%s_210308_dG' % loc_str
if recenter_norm:
#fitBase = 'fitList%s_pyt_210312_dG' % loc_str
fitBase = 'fitList%s_pyt_210331_dG' % loc_str
elif excType == 2:
fitBase = 'fitList%s_pyt_210310' % loc_str
if recenter_norm:
#fitBase = 'fitList%s_pyt_210312' % loc_str
fitBase = 'fitList%s_pyt_210331' % loc_str
fitList_nm = hf.fitList_name(fitBase, fitType, lossType=lossType, lgnType=lgnFrontEnd, lgnConType=conType, vecCorrected=-rvcAdj);
# ^^^ EDIT rvc/descrFits/fitList names here;
############
# Before any plotting, fix plotting paramaters
############
plt.style.use('https://raw.githubusercontent.com/paul-levy/SF_diversity/master/paul_plt_style.mplstyle');
from matplotlib import rcParams
rcParams['font.size'] = 20;
rcParams['pdf.fonttype'] = 42 # should be 42, but there are kerning issues
rcParams['ps.fonttype'] = 42 # should be 42, but there are kerning issues
rcParams['lines.linewidth'] = 2.5;
rcParams['axes.linewidth'] = 1.5;
rcParams['lines.markersize'] = 8; # this is in style sheet, just being explicit
rcParams['lines.markeredgewidth'] = 0; # no edge, since weird tings happen then
rcParams['xtick.major.size'] = 15
rcParams['xtick.minor.size'] = 5; # no minor ticks
rcParams['ytick.major.size'] = 15
rcParams['ytick.minor.size'] = 0; # no minor ticks
rcParams['xtick.major.width'] = 2
rcParams['xtick.minor.width'] = 2;
rcParams['ytick.major.width'] = 2
rcParams['ytick.minor.width'] = 0
rcParams['font.style'] = 'oblique';
rcParams['font.size'] = 20;
############
# load everything
############
dataListNm = hf.get_datalist(expDir, force_full=force_full);
descrFits_f0 = None;
dLoss_num = 2; # see hf.descrFit_name/descrMod_name/etc for details
if expDir == 'LGN/':
rvcMod = 0;
dMod_num = 1;
rvcDir = 1;
vecF1 = -1;
else:
rvcMod = 1; # i.e. Naka-rushton (1)
dMod_num = 3; # d-dog-s
rvcDir = None; # None if we're doing vec-corrected
if expDir == 'altExp/':
vecF1 = 0;
else:
vecF1 = 1;
dFits_mod = hf.descrMod_name(dMod_num)
descrFits_name = hf.descrFit_name(lossType=dLoss_num, descrBase=dFits_base, modelName=dFits_mod, phAdj=1 if vecF1==-1 else None);
## now, let it run
dataPath = basePath + expDir + 'structures/'
save_loc = basePath + expDir + 'figures/'
save_locSuper = save_loc + 'superposition_220713/'
if use_mod_resp == 1:
save_locSuper = save_locSuper + '%s/' % fitBase
dataList = hf.np_smart_load(dataPath + dataListNm);
print('Trying to load descrFits at: %s' % (dataPath + descrFits_name));
descrFits = hf.np_smart_load(dataPath + descrFits_name);
if use_mod_resp == 1 or use_mod_resp == 2:
fitList = hf.np_smart_load(dataPath + fitList_nm);
else:
fitList = None;
if not os.path.exists(save_locSuper):
os.makedirs(save_locSuper)
cells = np.arange(1, 1+len(dataList['unitName']))
zr_rm = lambda x: x[x>0];
# more flexible - only get values where x AND z are greater than some value "gt" (e.g. 0, 1, 0.4, ...)
zr_rm_pair = lambda x, z, gt: [x[np.logical_and(x>gt, z>gt)], z[np.logical_and(x>gt, z>gt)]];
# zr_rm_pair = lambda x, z: [x[np.logical_and(x>0, z>0)], z[np.logical_and(x>0, z>0)]] if np.logical_and(x!=[], z!=[])==True else [], [];
# here, we'll save measures we are going use for analysis purpose - e.g. supperssion index, c50
curr_suppr = dict();
############
### Establish the plot, load cell-specific measures
############
nRows, nCols = 6, 2;
cellName = dataList['unitName'][which_cell-1];
expInd = hf.get_exp_ind(dataPath, cellName)[0]
S = hf.np_smart_load(dataPath + cellName + '_sfm.npy')
expData = S['sfm']['exp']['trial'];
# 0th, let's load the basic tuning characterizations AND the descriptive fit
try:
dfit_curr = descrFits[which_cell-1]['params'][0,-1,:]; # single grating, highest contrast
except:
dfit_curr = None;
# - then the basics
try:
basic_names, basic_order = dataList['basicProgName'][which_cell-1], dataList['basicProgOrder']
basics = hf.get_basic_tunings(basic_names, basic_order);
except:
try:
# we've already put the basics in the data structure... (i.e. post-sorting 2021 data)
basic_names = ['','','','',''];
basic_order = ['rf', 'sf', 'tf', 'rvc', 'ori']; # order doesn't matter if they are already loaded
basics = hf.get_basic_tunings(basic_names, basic_order, preProc=S, reducedSave=True)
except:
basics = None;
### TEMPORARY: save the "basics" in curr_suppr; should live on its own, though; TODO
curr_suppr['basics'] = basics;
try:
oriBW, oriCV = basics['ori']['bw'], basics['ori']['cv'];
except:
oriBW, oriCV = np.nan, np.nan;
try:
tfBW = basics['tf']['tfBW_oct'];
except:
tfBW = np.nan;
try:
suprMod = basics['rfsize']['suprInd_model'];
except:
suprMod = np.nan;
try:
suprDat = basics['rfsize']['suprInd_data'];
except:
suprDat = np.nan;
try:
cellType = dataList['unitType'][which_cell-1];
except:
# TODO: note, this is dangerous; thus far, only V1 cells don't have 'unitType' field in dataList, so we can safely do this
cellType = 'V1';
############
### compute f1f0 ratio, and load the corresponding F0 or F1 responses
############
f1f0_rat = hf.compute_f1f0(expData, which_cell, expInd, dataPath, descrFitName_f0=descrFits_f0)[0];
curr_suppr['f1f0'] = f1f0_rat;
respMeasure = 1 if f1f0_rat > 1 else 0;
if vecF1 == 1:
# get the correct, adjusted F1 response
if expInd > f1_expCutoff and respMeasure == 1:
respOverwrite = hf.adjust_f1_byTrial(expData, expInd);
else:
respOverwrite = None;
if (respMeasure == 1 or expDir == 'LGN/') and expDir != 'altExp/' : # i.e. if we're looking at a simple cell, then let's get F1
if vecF1 == 1:
spikes_byComp = respOverwrite
# then, sum up the valid components per stimulus component
allCons = np.vstack(expData['con']).transpose();
blanks = np.where(allCons==0);
spikes_byComp[blanks] = 0; # just set it to 0 if that component was blank during the trial
else:
if rvcName is not None:
try:
rvcFits = hf.get_rvc_fits(dataPath, expInd, which_cell, rvcName=rvcName, rvcMod=rvcMod, direc=rvcDir, vecF1=vecF1);
except:
rvcFits = None;
else:
rvcFits = None
spikes_byComp = hf.get_spikes(expData, get_f0=0, rvcFits=rvcFits, expInd=expInd);
spikes = np.array([np.sum(x) for x in spikes_byComp]);
rates = True if vecF1 == 0 else False; # when we get the spikes from rvcFits, they've already been converted into rates (in hf.get_all_fft)
baseline = None; # f1 has no "DC", yadig?
else: # otherwise, if it's complex, just get F0
respMeasure = 0;
spikes = hf.get_spikes(expData, get_f0=1, rvcFits=None, expInd=expInd);
rates = False; # get_spikes without rvcFits is directly from spikeCount, which is counts, not rates!
baseline = hf.blankResp(expData, expInd)[0]; # we'll plot the spontaneous rate
# why mult by stimDur? well, spikes are not rates but baseline is, so we convert baseline to count (i.e. not rate, too)
spikes = spikes - baseline*hf.get_exp_params(expInd).stimDur;
#print('###\nGetting spikes (data): rates? %d\n###' % rates);
_, _, _, respAll = hf.organize_resp(spikes, expData, expInd, respsAsRate=rates); # only using respAll to get variance measures
resps_data, stimVals, val_con_by_disp, _, _ = hf.tabulate_responses(expData, expInd, overwriteSpikes=spikes, respsAsRates=rates, modsAsRate=rates);
if fitList is None:
resps = resps_data; # otherwise, we'll still keep resps_data for reference
elif fitList is not None: # OVERWRITE the data with the model spikes!
if use_mod_resp == 1:
curr_fit = fitList[which_cell-1]['params'];
modResp = mod_resp.SFMGiveBof(curr_fit, S, normType=fitType, lossType=lossType, expInd=expInd, cellNum=which_cell, excType=excType)[1];
if f1f0_rat < 1: # then subtract baseline..
modResp = modResp - baseline*hf.get_exp_params(expInd).stimDur;
# now organize the responses
resps, stimVals, val_con_by_disp, _, _ = hf.tabulate_responses(expData, expInd, overwriteSpikes=modResp, respsAsRates=False, modsAsRate=False);
elif use_mod_resp == 2: # then pytorch model!
resp_str = hf_sf.get_resp_str(respMeasure)
curr_fit = fitList[which_cell-1][resp_str]['params'];
model = mrpt.sfNormMod(curr_fit, expInd=expInd, excType=excType, normType=fitType, lossType=lossType, lgnFrontEnd=lgnFrontEnd, newMethod=newMethod, lgnConType=conType, applyLGNtoNorm=_applyLGNtoNorm)
### get the vec-corrected responses, if applicable
if expInd > f1_expCutoff and respMeasure == 1:
respOverwrite = hf.adjust_f1_byTrial(expData, expInd);
else:
respOverwrite = None;
dw = mrpt.dataWrapper(expData, respMeasure=respMeasure, expInd=expInd, respOverwrite=respOverwrite); # respOverwrite defined above (None if DC or if expInd=-1)
modResp = model.forward(dw.trInf, respMeasure=respMeasure, sigmoidSigma=_sigmoidSigma, recenter_norm=recenter_norm).detach().numpy();
if respMeasure == 1: # make sure the blank components have a zero response (we'll do the same with the measured responses)
blanks = np.where(dw.trInf['con']==0);
modResp[blanks] = 0;
# next, sum up across components
modResp = np.sum(modResp, axis=1);
# finally, make sure this fills out a vector of all responses (just have nan for non-modelled trials)
nTrialsFull = len(expData['num']);
modResp_full = np.nan * np.zeros((nTrialsFull, ));
modResp_full[dw.trInf['num']] = modResp;
if respMeasure == 0: # if DC, then subtract baseline..., as determined from data (why not model? we aren't yet calc. response to no stim, though it can be done)
modResp_full = modResp_full - baseline*hf.get_exp_params(expInd).stimDur;
# TODO: This is a work around for which measures are in rates vs. counts (DC vs F1, model vs data...)
stimDur = hf.get_exp_params(expInd).stimDur;
asRates = False;
#divFactor = stimDur if asRates == 0 else 1;
#modResp_full = np.divide(modResp_full, divFactor);
# now organize the responses
resps, stimVals, val_con_by_disp, _, _ = hf.tabulate_responses(expData, expInd, overwriteSpikes=modResp_full, respsAsRates=asRates, modsAsRate=asRates);
predResps = resps[2];
respMean = resps[0]; # equivalent to resps[0];
respStd = np.nanstd(respAll, -1); # take std of all responses for a given condition
# compute SEM, too
findNaN = np.isnan(respAll);
nonNaN = np.sum(findNaN == False, axis=-1);
respSem = np.nanstd(respAll, -1) / np.sqrt(nonNaN);
############
### first, fit a smooth function to the overall pred V measured responses
### --- from this, we can measure how each example superposition deviates from a central tendency
### --- i.e. the residual relative to the "standard" input:output relationship
############
all_resps = respMean[1:, :, :].flatten() # all disp>0
all_preds = predResps[1:, :, :].flatten() # all disp>0
# a model which allows negative fits
# myFit = lambda x, t0, t1, t2: t0 + t1*x + t2*x*x;
# non_nan = np.where(~np.isnan(all_preds)); # cannot fit negative values with naka-rushton...
# fitz, _ = opt.curve_fit(myFit, all_preds[non_nan], all_resps[non_nan], p0=[-5, 10, 5], maxfev=5000)
# naka rushton
myFit = lambda x, g, expon, c50: hf.naka_rushton(x, [0, g, expon, c50])
non_neg = np.where(all_preds>0) # cannot fit negative values with naka-rushton...
try:
if use_mod_resp == 1: # the reference will ALWAYS be the data -- redo the above analysis for data
predResps_data = resps_data[2];
respMean_data = resps_data[0];
all_resps_data = respMean_data[1:, :, :].flatten() # all disp>0
all_preds_data = predResps_data[1:, :, :].flatten() # all disp>0
non_neg_data = np.where(all_preds_data>0) # cannot fit negative values with naka-rushton...
fitz, _ = opt.curve_fit(myFit, all_preds_data[non_neg_data], all_resps_data[non_neg_data], p0=[100, 2, 25], maxfev=5000)
else:
fitz, _ = opt.curve_fit(myFit, all_preds[non_neg], all_resps[non_neg], p0=[100, 2, 25], maxfev=5000)
rel_c50 = np.divide(fitz[-1], np.max(all_preds[non_neg]));
except:
fitz = None;
rel_c50 = -99;
############
### organize stimulus information
############
all_disps = stimVals[0];
all_cons = stimVals[1];
all_sfs = stimVals[2];
nCons = len(all_cons);
nSfs = len(all_sfs);
nDisps = len(all_disps);
maxResp = np.maximum(np.nanmax(respMean), np.nanmax(predResps));
# by disp
clrs_d = cm.viridis(np.linspace(0,0.75,nDisps-1));
lbls_d = ['disp: %s' % str(x) for x in range(nDisps)];
# by sf
val_sfs = hf.get_valid_sfs(S, disp=1, con=val_con_by_disp[1][0], expInd=expInd) # pick
clrs_sf = cm.viridis(np.linspace(0,.75,len(val_sfs)));
lbls_sf = ['sf: %.2f' % all_sfs[x] for x in val_sfs];
# by con
val_con = all_cons;
clrs_con = cm.viridis(np.linspace(0,.75,len(val_con)));
lbls_con = ['con: %.2f' % x for x in val_con];
############
### create the figure
############
fSuper, ax = plt.subplots(nRows, nCols, figsize=(10*nCols, 8*nRows))
sns.despine(fig=fSuper, offset=10)
allMix = [];
allSum = [];
### plot reference tuning [row 1 (i.e. 2nd row)]
## on the right, SF tuning (high contrast)
sfRef = hf.nan_rm(respMean[0, :, -1]); # high contrast tuning
ax[1, 1].plot(all_sfs, sfRef, 'k-', marker='o', label='ref. tuning (d0, high con)', clip_on=False)
ax[1, 1].set_xscale('log')
ax[1, 1].set_xlim((0.1, 10));
ax[1, 1].set_xlabel('sf (c/deg)')
ax[1, 1].set_ylabel('response (spikes/s)')
ax[1, 1].set_ylim((-5, 1.1*np.nanmax(sfRef)));
ax[1, 1].legend(fontsize='x-small');
#####
## then on the left, RVC (peak SF)
#####
sfPeak = np.argmax(sfRef); # stupid/simple, but just get the rvc for the max response
v_cons_single = val_con_by_disp[0]
rvcRef = hf.nan_rm(respMean[0, sfPeak, v_cons_single]);
# now, if possible, let's also plot the RVC fit
if rvcFits is not None:
rvcFits = hf.get_rvc_fits(dataPath, expInd, which_cell, rvcName=rvcName, rvcMod=rvcMod);
rel_rvc = rvcFits[0]['params'][sfPeak]; # we get 0 dispersion, peak SF
plt_cons = np.geomspace(all_cons[0], all_cons[-1], 50);
c50, pk = hf.get_c50(rvcMod, rel_rvc), rvcFits[0]['conGain'][sfPeak];
c50_emp, c50_eval = hf.c50_empirical(rvcMod, rel_rvc); # determine c50 by optimization, numerical approx.
if rvcMod == 0:
rvc_mod = hf.get_rvc_model();
rvcmodResp = rvc_mod(*rel_rvc, plt_cons);
else: # i.e. mod=1 or mod=2
rvcmodResp = hf.naka_rushton(plt_cons, rel_rvc);
if baseline is not None:
rvcmodResp = rvcmodResp - baseline;
ax[1, 0].plot(plt_cons, rvcmodResp, 'k--', label='rvc fit (c50=%.2f, gain=%0f)' %(c50, pk))
# and save it
curr_suppr['c50'] = c50; curr_suppr['conGain'] = pk;
curr_suppr['c50_emp'] = c50_emp; curr_suppr['c50_emp_eval'] = c50_eval
else:
curr_suppr['c50'] = np.nan; curr_suppr['conGain'] = np.nan;
curr_suppr['c50_emp'] = np.nan; curr_suppr['c50_emp_eval'] = np.nan;
ax[1, 0].plot(all_cons[v_cons_single], rvcRef, 'k-', marker='o', label='ref. tuning (d0, peak SF)', clip_on=False)
# ax[1, 0].set_xscale('log')
ax[1, 0].set_xlabel('contrast (%)');
ax[1, 0].set_ylabel('response (spikes/s)')
ax[1, 0].set_ylim((-5, 1.1*np.nanmax(rvcRef)));
ax[1, 0].legend(fontsize='x-small');
# plot the fitted model on each axis
pred_plt = np.linspace(0, np.nanmax(all_preds), 100);
if fitz is not None:
ax[0, 0].plot(pred_plt, myFit(pred_plt, *fitz), 'r--', label='fit')
ax[0, 1].plot(pred_plt, myFit(pred_plt, *fitz), 'r--', label='fit')
for d in range(nDisps):
if d == 0: # we don't care about single gratings!
dispRats = [];
continue;
v_cons = np.array(val_con_by_disp[d]);
n_v_cons = len(v_cons);
# plot split out by each contrast [0,1]
for c in reversed(range(n_v_cons)):
v_sfs = hf.get_valid_sfs(S, d, v_cons[c], expInd)
for s in v_sfs:
mixResp = respMean[d, s, v_cons[c]];
allMix.append(mixResp);
sumResp = predResps[d, s, v_cons[c]];
allSum.append(sumResp);
# print('condition: d(%d), c(%d), sf(%d):: pred(%.2f)|real(%.2f)' % (d, v_cons[c], s, sumResp, mixResp))
# PLOT in by-disp panel
if c == 0 and s == v_sfs[0]:
ax[0, 0].plot(sumResp, mixResp, 'o', color=clrs_d[d-1], label=lbls_d[d], clip_on=False)
else:
ax[0, 0].plot(sumResp, mixResp, 'o', color=clrs_d[d-1], clip_on=False)
# PLOT in by-sf panel
sfInd = np.where(np.array(v_sfs) == s)[0][0]; # will only be one entry, so just "unpack"
try:
if d == 1 and c == 0:
ax[0, 1].plot(sumResp, mixResp, 'o', color=clrs_sf[sfInd], label=lbls_sf[sfInd], clip_on=False);
else:
ax[0, 1].plot(sumResp, mixResp, 'o', color=clrs_sf[sfInd], clip_on=False);
except:
pass;
#pdb.set_trace();
# plot baseline, if f0...
# if baseline is not None:
# [ax[0, i].axhline(baseline, linestyle='--', color='k', label='spon. rate') for i in range(2)];
# plot averaged across all cons/sfs (i.e. average for the whole dispersion) [1,0]
mixDisp = respMean[d, :, :].flatten();
sumDisp = predResps[d, :, :].flatten();
mixDisp, sumDisp = zr_rm_pair(mixDisp, sumDisp, 0.5);
curr_rats = np.divide(mixDisp, sumDisp)
curr_mn = geomean(curr_rats); curr_std = np.std(np.log10(curr_rats));
# curr_rat = geomean(np.divide(mixDisp, sumDisp));
ax[2, 0].bar(d, curr_mn, yerr=curr_std, color=clrs_d[d-1]);
ax[2, 0].set_yscale('log')
ax[2, 0].set_ylim(0.1, 10);
# ax[2, 0].yaxis.set_ticks(minorticks)
dispRats.append(curr_mn);
# ax[2, 0].bar(d, np.mean(np.divide(mixDisp, sumDisp)), color=clrs_d[d-1]);
# also, let's plot the (signed) error relative to the fit
if fitz is not None:
errs = mixDisp - myFit(sumDisp, *fitz);
ax[3, 0].bar(d, np.mean(errs), yerr=np.std(errs), color=clrs_d[d-1])
# -- and normalized by the prediction output response
errs_norm = np.divide(mixDisp - myFit(sumDisp, *fitz), myFit(sumDisp, *fitz));
ax[4, 0].bar(d, np.mean(errs_norm), yerr=np.std(errs_norm), color=clrs_d[d-1])
# and set some labels/lines, as needed
if d == 1:
ax[2, 0].set_xlabel('dispersion');
ax[2, 0].set_ylabel('suppression ratio (linear)')
ax[2, 0].axhline(1, ls='--', color='k')
ax[3, 0].set_xlabel('dispersion');
ax[3, 0].set_ylabel('mean (signed) error')
ax[3, 0].axhline(0, ls='--', color='k')
ax[4, 0].set_xlabel('dispersion');
ax[4, 0].set_ylabel('mean (signed) error -- as frac. of fit prediction')
ax[4, 0].axhline(0, ls='--', color='k')
curr_suppr['supr_disp'] = dispRats;
### plot averaged across all cons/disps
sfInds = []; sfRats = []; sfRatStd = [];
sfErrs = []; sfErrsStd = []; sfErrsInd = []; sfErrsIndStd = []; sfErrsRat = []; sfErrsRatStd = [];
curr_errNormFactor = [];
for s in range(len(val_sfs)):
try: # not all sfs will have legitmate values;
# only get mixtures (i.e. ignore single gratings)
mixSf = respMean[1:, val_sfs[s], :].flatten();
sumSf = predResps[1:, val_sfs[s], :].flatten();
mixSf, sumSf = zr_rm_pair(mixSf, sumSf, 0.5);
rats_curr = np.divide(mixSf, sumSf);
sfInds.append(s); sfRats.append(geomean(rats_curr)); sfRatStd.append(np.std(np.log10(rats_curr)));
if fitz is not None:
#curr_NR = myFit(sumSf, *fitz); # unvarnished
curr_NR = np.maximum(myFit(sumSf, *fitz), 0.5); # thresholded at 0.5...
curr_err = mixSf - curr_NR;
sfErrs.append(np.mean(curr_err));
sfErrsStd.append(np.std(curr_err))
curr_errNorm = np.divide(mixSf - curr_NR, mixSf + curr_NR);
sfErrsInd.append(np.mean(curr_errNorm));
sfErrsIndStd.append(np.std(curr_errNorm))
curr_errRat = np.divide(mixSf, curr_NR);
sfErrsRat.append(np.mean(curr_errRat));
sfErrsRatStd.append(np.std(curr_errRat));
curr_normFactors = np.array(curr_NR)
curr_errNormFactor.append(geomean(curr_normFactors[curr_normFactors>0]));
else:
sfErrs.append([]);
sfErrsStd.append([]);
sfErrsInd.append([]);
sfErrsIndStd.append([]);
sfErrsRat.append([]);
sfErrsRatStd.append([]);
curr_errNormFactor.append([]);
except:
pass
# get the offset/scale of the ratio so that we can plot a rescaled/flipped version of
# the high con/single grat tuning for reference...does the suppression match the response?
offset, scale = np.nanmax(sfRats), np.nanmax(sfRats) - np.nanmin(sfRats);
sfRef = hf.nan_rm(respMean[0, val_sfs, -1]); # high contrast tuning
sfRefShift = offset - scale * (sfRef/np.nanmax(sfRef))
ax[2,1].scatter(all_sfs[val_sfs][sfInds], sfRats, color=clrs_sf[sfInds], clip_on=False)
ax[2,1].errorbar(all_sfs[val_sfs][sfInds], sfRats, sfRatStd, color='k', linestyle='-', clip_on=False, label='suppression tuning')
# ax[2,1].plot(all_sfs[val_sfs][sfInds], sfRats, 'k-', clip_on=False, label='suppression tuning')
ax[2,1].plot(all_sfs[val_sfs], sfRefShift, 'k--', label='ref. tuning', clip_on=False)
ax[2,1].axhline(1, ls='--', color='k')
ax[2,1].set_xlabel('sf (cpd)')
ax[2,1].set_xscale('log')
ax[2,1].set_xlim((0.1, 10));
#ax[2,1].set_xlim((np.min(all_sfs), np.max(all_sfs)));
ax[2,1].set_ylabel('suppression ratio');
ax[2,1].set_yscale('log')
#ax[2,1].yaxis.set_ticks(minorticks)
ax[2,1].set_ylim(0.1, 10);
ax[2,1].legend(fontsize='x-small');
curr_suppr['supr_sf'] = sfRats;
### residuals from fit of suppression
if fitz is not None:
# mean signed error: and labels/plots for the error as f'n of SF
ax[3,1].axhline(0, ls='--', color='k')
ax[3,1].set_xlabel('sf (cpd)')
ax[3,1].set_xscale('log')
ax[3,1].set_xlim((0.1, 10));
#ax[3,1].set_xlim((np.min(all_sfs), np.max(all_sfs)));
ax[3,1].set_ylabel('mean (signed) error');
ax[3,1].errorbar(all_sfs[val_sfs][sfInds], sfErrs, sfErrsStd, color='k', marker='o', linestyle='-', clip_on=False)
# -- and normalized by the prediction output response + output respeonse
val_errs = np.logical_and(~np.isnan(sfErrsRat), np.logical_and(np.array(sfErrsIndStd)>0, np.array(sfErrsIndStd) < 2));
norm_subset = np.array(sfErrsInd)[val_errs];
normStd_subset = np.array(sfErrsIndStd)[val_errs];
ax[4,1].axhline(0, ls='--', color='k')
ax[4,1].set_xlabel('sf (cpd)')
ax[4,1].set_xscale('log')
ax[4,1].set_xlim((0.1, 10));
#ax[4,1].set_xlim((np.min(all_sfs), np.max(all_sfs)));
ax[4,1].set_ylim((-1, 1));
ax[4,1].set_ylabel('error index');
ax[4,1].errorbar(all_sfs[val_sfs][sfInds][val_errs], norm_subset, normStd_subset, color='k', marker='o', linestyle='-', clip_on=False)
# -- AND simply the ratio between the mixture response and the mean expected mix response (i.e. Naka-Rushton)
# --- equivalent to the suppression ratio, but relative to the NR fit rather than perfect linear summation
val_errs = np.logical_and(~np.isnan(sfErrsRat), np.logical_and(np.array(sfErrsRatStd)>0, np.array(sfErrsRatStd) < 2));
rat_subset = np.array(sfErrsRat)[val_errs];
ratStd_subset = np.array(sfErrsRatStd)[val_errs];
#ratStd_subset = (1/np.log(2))*np.divide(np.array(sfErrsRatStd)[val_errs], rat_subset);
ax[5,1].scatter(all_sfs[val_sfs][sfInds][val_errs], rat_subset, color=clrs_sf[sfInds][val_errs], clip_on=False)
ax[5,1].errorbar(all_sfs[val_sfs][sfInds][val_errs], rat_subset, ratStd_subset, color='k', linestyle='-', clip_on=False, label='suppression tuning')
ax[5,1].axhline(1, ls='--', color='k')
ax[5,1].set_xlabel('sf (cpd)')
ax[5,1].set_xscale('log')
ax[5,1].set_xlim((0.1, 10));
ax[5,1].set_ylabel('suppression ratio (wrt NR)');
ax[5,1].set_yscale('log', basey=2)
# ax[2,1].yaxis.set_ticks(minorticks)
ax[5,1].set_ylim(np.power(2.0, -2), np.power(2.0, 2));
ax[5,1].legend(fontsize='x-small');
# - compute the variance - and put that value on the plot
errsRatVar = np.var(np.log2(sfErrsRat)[val_errs]);
curr_suppr['sfRat_VAR'] = errsRatVar;
ax[5,1].text(0.1, 2, 'var=%.2f' % errsRatVar);
# compute the unsigned "area under curve" for the sfErrsInd, and normalize by the octave span of SF values considered
val_errs = np.logical_and(~np.isnan(sfErrsRat), np.logical_and(np.array(sfErrsIndStd)>0, np.array(sfErrsIndStd) < 2));
val_x = all_sfs[val_sfs][sfInds][val_errs];
ind_var = np.var(np.array(sfErrsInd)[val_errs]);
curr_suppr['sfErrsInd_VAR'] = ind_var;
# - and put that value on the plot
ax[4,1].text(0.1, -0.25, 'var=%.3f' % ind_var);
else:
curr_suppr['sfErrsInd_VAR'] = np.nan
curr_suppr['sfRat_VAR'] = np.nan
#########
### NOW, let's evaluate the derivative of the SF tuning curve and get the correlation with the errors
#########
mod_sfs = np.geomspace(all_sfs[0], all_sfs[-1], 1000);
mod_resp = hf.get_descrResp(dfit_curr, mod_sfs, DoGmodel=dMod_num);
deriv = np.divide(np.diff(mod_resp), np.diff(np.log10(mod_sfs)))
deriv_norm = np.divide(deriv, np.maximum(np.nanmax(deriv), np.abs(np.nanmin(deriv)))); # make the maximum response 1 (or -1)
# - then, what indices to evaluate for comparing with sfErr?
errSfs = all_sfs[val_sfs][sfInds];
mod_inds = [np.argmin(np.square(mod_sfs-x)) for x in errSfs];
deriv_norm_eval = deriv_norm[mod_inds];
# -- plot on [1, 1] (i.e. where the data is)
ax[1,1].plot(mod_sfs, mod_resp, 'k--', label='fit (g)')
ax[1,1].legend();
# Duplicate "twin" the axis to create a second y-axis
ax2 = ax[1,1].twinx();
ax2.set_xscale('log'); # have to re-inforce log-scale?
ax2.set_ylim([-1, 1]); # since the g' is normalized
# make a plot with different y-axis using second axis object
ax2.plot(mod_sfs[1:], deriv_norm, '--', color="red", label='g\'');
ax2.set_ylabel("deriv. (normalized)",color="red")
ax2.legend();
sns.despine(ax=ax2, offset=10, right=False);
# -- and let's plot rescaled and shifted version in [2,1]
offset, scale = np.nanmax(sfRats), np.nanmax(sfRats) - np.nanmin(sfRats);
derivShift = offset - scale * (deriv_norm/np.nanmax(deriv_norm));
ax[2,1].plot(mod_sfs[1:], derivShift, 'r--', label='deriv(ref. tuning)', clip_on=False)
ax[2,1].legend(fontsize='x-small');
# - then, normalize the sfErrs/sfErrsInd and compute the correlation coefficient
if fitz is not None:
norm_sfErr = np.divide(sfErrs, np.nanmax(np.abs(sfErrs)));
norm_sfErrInd = np.divide(sfErrsInd, np.nanmax(np.abs(sfErrsInd))); # remember, sfErrsInd is normalized per condition; this is overall
non_nan = np.logical_and(~np.isnan(norm_sfErr), ~np.isnan(deriv_norm_eval))
corr_nsf, corr_nsfN = np.corrcoef(deriv_norm_eval[non_nan], norm_sfErr[non_nan])[0,1], np.corrcoef(deriv_norm_eval[non_nan], norm_sfErrInd[non_nan])[0,1]
curr_suppr['corr_derivWithErr'] = corr_nsf;
curr_suppr['corr_derivWithErrsInd'] = corr_nsfN;
ax[3,1].text(0.1, 0.25*np.nanmax(sfErrs), 'corr w/g\' = %.2f' % corr_nsf)
ax[4,1].text(0.1, 0.25, 'corr w/g\' = %.2f' % corr_nsfN)
else:
curr_suppr['corr_derivWithErr'] = np.nan;
curr_suppr['corr_derivWithErrsInd'] = np.nan;
# make a polynomial fit
try:
hmm = np.polyfit(allSum, allMix, deg=1) # returns [a, b] in ax + b
except:
hmm = [np.nan];
curr_suppr['supr_index'] = hmm[0];
for j in range(1):
for jj in range(nCols):
ax[j, jj].axis('square')
ax[j, jj].set_xlabel('prediction: sum(components) (imp/s)');
ax[j, jj].set_ylabel('mixture response (imp/s)');
ax[j, jj].plot([0, 1*maxResp], [0, 1*maxResp], 'k--')
ax[j, jj].set_xlim((-5, maxResp));
ax[j, jj].set_ylim((-5, 1.1*maxResp));
ax[j, jj].set_title('Suppression index: %.2f|%.2f' % (hmm[0], rel_c50))
ax[j, jj].legend(fontsize='x-small');
fSuper.suptitle('Superposition: %s #%d [%s; f1f0 %.2f; szSupr[dt/md] %.2f/%.2f; oriBW|CV %.2f|%.2f; tfBW %.2f]' % (cellType, which_cell, cellName, f1f0_rat, suprDat, suprMod, oriBW, oriCV, tfBW))
if fitList is None:
save_name = 'cell_%03d.pdf' % which_cell
else:
save_name = 'cell_%03d_mod%s.pdf' % (which_cell, hf.fitType_suffix(fitType))
pdfSv = pltSave.PdfPages(str(save_locSuper + save_name));
pdfSv.savefig(fSuper)
pdfSv.close();
#########
### Finally, add this "superposition" to the newest
#########
if to_save:
if fitList is None:
from datetime import datetime
suffix = datetime.today().strftime('%y%m%d')
super_name = 'superposition_analysis_%s.npy' % suffix;
else:
super_name = 'superposition_analysis_mod%s.npy' % hf.fitType_suffix(fitType);
pause_tm = 5*np.random.rand();
print('sleeping for %d secs (#%d)' % (pause_tm, which_cell));
time.sleep(pause_tm);
if os.path.exists(dataPath + super_name):
suppr_all = hf.np_smart_load(dataPath + super_name);
else:
suppr_all = dict();
suppr_all[which_cell-1] = curr_suppr;
np.save(dataPath + super_name, suppr_all);
return curr_suppr;