def __init__(self, path, animal=None):
self.level = 2 # level in the hierarchy
self.treebuf = StringIO.StringIO() # string buffer to print tree hierarchy to
self.path = path
self.animal = animal
if animal != None:
# update parent animal's track dict, in case self wasn't loaded by its parent
animal.tr[self.id] = self
self.r = dictattr() # store recordings in a dictionary with attrib access
def __init__(self, path, animal=None):
self.level = 2 # level in the hierarchy
self.treebuf = StringIO() # string buffer to print tree hierarchy to
self.path = path
self.animal = animal
if animal != None:
# update parent animal's track dict, in case self wasn't loaded by its parent
animal.tr[self.id] = self
self.r = dictattr(
) # store recordings in a dictionary with attrib access
def build(self):
"""Build the sweep table.
A Variable's dim value relative to the dim values of all the other
Variables determines its order in the nested for loops that generate
the combinations of values for each sweep: the Variable with the lowest
dim value becomes the outermost for loop and changes least often;
the Variable with the highest dim value becomes the innermost for loop
and changes on every sweep. dim must be an integer. Variables with the
same dim value are part of the same Dimension, are shuffled/randomized
together, and must therefore be of the same length and have the same
shuffle and random flags"""
e = self.experiment # synonym
# Build the dimensions
self.builddimensions()
# Build the dimension index table
self.builddimitable()
# Now use dimitable to build the sweep table
self.data = dictattr(
) # holds the actual sweep table, a dict with attribute access
for dim in self.dimensions:
for var in dim.variables:
# get the entire column of indices into the values of this dimension:
dimi = self.dimitable[:, dim.dim]
# convert to array to enable multiple value selection:
vals = np.asarray(var.vals)[dimi]
self.data[var.name] = vals # store it as an array
# Check to make sure that all the variables in self.data have the same number of vals
try:
nvals = len(list(self.data.values())[0])
except IndexError: # there aren't any variables at all
nvals = 0
for varname in self.data:
if len(self.data[varname]) != nvals:
raise ValueError(
'%s length in sweep table does not match expected length %d'
% (varname, nvals))
# For convenience the main stimulus loop, add non-varying dynamic params to self.data:
nvals = max(nvals,
1) # make sure the sweep table has at least one entry
for paramname, paramval in e.dynamic.items():
if paramname not in self.data:
# paramval was already checked to be a scalar in Experiment.check():
self.data[paramname] = np.tile(paramval, nvals)
def build(self):
"""Build the sweep table.
A Variable's dim value relative to the dim values of all the other
Variables determines its order in the nested for loops that generate
the combinations of values for each sweep: the Variable with the lowest
dim value becomes the outermost for loop and changes least often;
the Variable with the highest dim value becomes the innermost for loop
and changes on every sweep. dim must be an integer. Variables with the
same dim value are part of the same Dimension, are shuffled/randomized
together, and must therefore be of the same length and have the same
shuffle and random flags"""
e = self.experiment # synonym
# Build the dimensions
self.builddimensions()
# Build the dimension index table
self.builddimitable()
# Now use dimitable to build the sweep table
self.data = dictattr() # holds the actual sweep table, a dict with attribute access
for dim in self.dimensions:
for var in dim.variables:
dimi = self.dimitable[:, dim.dim] # get the entire column of indices into the values of this dimension
vals = np.asarray(var.vals)[
dimi
] # convert to array so you can select multiple values with a sequence of indices
self.data[var.name] = vals # store it as an array
# Check to make sure that all the variables in self.data have the same number of vals
try:
nvals = len(self.data.values()[0])
except IndexError: # there aren't any variables at all
nvals = 0
for varname in self.data:
assert len(self.data[varname]) == nvals, "%s length in sweep table does not match expected length %d" % (
varname,
nvals,
)
# For convenience in the main stimulus loop, add the non-varying dynamic params to self.data
nvals = max(nvals, 1) # make sure the sweep table has at least one entry
for paramname, paramval in e.dynamic.iteritems():
if paramname not in self.data:
self.data[paramname] = np.tile(
paramval, nvals
) # paramval was already checked to be a scalar in Experiment.check()
get_ipython().user_ns['VARNAME']
"""
# __future__ imports don't seem to work when executing this file in IPython, see main.py:
# from __future__ import division
# from __future__ import print_function
import os
from core import mergeuniquedictvals, dictattr
DATAROOTPATH = os.path.expanduser("~/data")
LABPATHNAME = "slab"
# LABPATHNAME = 'blab'
DATAPATH = os.path.join(DATAROOTPATH, LABPATHNAME)
MOVIEPATH = os.path.join(DATAPATH, "mov")
MOVIES = dictattr()
# for each recording, load all Sorts, or just the most recent one?
LOADALLSORTS = False
"""Mean spike rate that delineates normal vs "quiet" neurons. 0.1 Hz seems reasonable if you
plot mean spike rate distributions for all the neurons in a given track. But, if you want a
reasonable looking DJS histogram without a lot of missing netstates, you need to exclude
more low firing rate cells, 0.5 works better"""
MINRATE = 0.05 # Hz
"""Calculate a TrackNeuron's meanrate according to its trange (period between its first and
last spike), or according to its track's entire duration. Need to reload the track or call
Track.calc_meanrates() after changing this on the fly"""
TRACKNEURONPERIOD = "track" # 'trange' or 'track'
# ditto for recordings:
RECNEURONPERIOD = "recording" # 'trange' or 'recording'
def __init__(self, path):
self.level = 1 # level in the hierarchy
self.treebuf = StringIO.StringIO() # string buffer to print tree hierarchy to
self.path = path
self.tr = dictattr() # store tracks in a dictionary with attrib access
def load_din(self):
self.din = np.fromfile(self.path,
dtype=np.int64).reshape(-1,
2) # reshape to 2 cols
# look for a .textheader:
try:
txthdrpath = rstrip(self.path, '.din') + '.textheader'
f = open(txthdrpath, 'rU') # use universal newline support
self.textheader = f.read() # read it all in
f.close()
except IOError:
print("WARNING: couldn't load text header associated with '%s'" %
self.name)
self.textheader = '' # set to empty
if self.textheader != '':
# comment out all lines starting with "from dimstim"
self.textheader = self.textheader.replace('from dimstim',
'#from dimstim')
# execute any remaining 'import' lines first, so that any modules imported
# aren't artefactually detected as having been added to the namespace:
for line in self.textheader.splitlines():
if line.startswith('import'):
exec(line)
thns = {} # textheader namespace
# compiling to code and then executing it is supposed to be faster than directly
# executing a string, according to
# http://lucumr.pocoo.org/2011/2/1/exec-in-python/, but doesn't seem to make
# a difference here:
code = compile(self.textheader, "<string>", "exec")
# don't exec in current namespace, load name:val pairs into thns instead:
exec(code, None, thns)
try:
# dimstim up to ptc15 didn't have a version, neither did NVS display
self.__version__ = thns['__version__'] # a string
except KeyError:
self.__version__ = '0.0'
if float(self.__version__
) >= 0.16: # after major refactoring of dimstim
for name, val in thns.items():
# bind each variable in the textheader as an attrib of self
self.__setattr__(name, val)
# this doesn't work for textheaders generated by dimstim 0.16, since
# xorigDeg and yorigDeg were accidentally omitted from all the experiment
# scripts and hence the textheaders too:
'''
self.e.xorig = deg2pix(self.e.static.xorigDeg, self.I) + self.I.SCREENWIDTH / 2
self.e.yorig = deg2pix(self.e.static.yorigDeg, self.I) + self.I.SCREENHEIGHT / 2
'''
self.REFRESHTIME = intround(1 / float(self.I.REFRESHRATE) *
1000000) # us
# prevent replication of movie frame data in memory
if type(self.e) == Movie:
fname = os.path.split(
self.e.static.fname)[-1] # pathless fname
uns = get_ipython().user_ns
if fname not in uns['MOVIES']:
# add movie experiment, indexed according to movie data file name,
# to prevent from ever loading its frames more than once
uns['MOVIES'][fname] = self.e
else:
self.oldparams = dictattr()
for name, val in thns.items():
# bind each variable in the textheader to oldparams
self.oldparams[name] = val
self.loadptc15exp()
else:
# use the time difference between the first two din instead
self.REFRESHTIME = self.din[1, 0] - self.din[0, 0]
# add an extra refresh time after last din, that's when screen actually turns off
self.trange = (self.din[0, 0], self.din[-1, 0] + self.REFRESHTIME)
def loadptc15exp(self):
## TODO: - fake a .e dimstim.Experiment object, to replace what used to be the
## .stims object for movie experiments
''' - self.movie = self.experiment.stims[0]
- need to convert sweeptimeMsec to sweepSec
- assert len(self.experiment.stims) == 1
- self.movie = self.experiment.stims[0]
- self.movie.load() # ensure the movie's data is loaded
if self.movie.oname == 'mseq32':
frameis = frameis[frameis != 65535] # remove all occurences of 65535
elif self.movie.oname == 'mseq16':
frameis = frameis[frameis != 16383] # remove all occurences of 16383
'''
# Add .static and .dynamic params to fake dimstim experiment
self.e = dictattr()
self.I = dictattr() # fake InternalParams object
self.e.static = dictattr() # fake StaticParams object
self.e.dynamic = dictattr() # fake DynamicParams object
# maps ptc15 param names to dimstim 0.16 param types and names, wherever possible
## TODO: fill in params for experiment types other than Movie??
_15to16 = {
'EYE': ('I', 'EYE'),
'PIXPERCM': ('I', 'PIXPERCM'),
'REFRESHRATE': ('I', 'REFRESHRATE'),
'SCREENDISTANCECM': ('I', 'SCREENDISTANCECM'),
'SCREENHEIGHT': ('I', 'SCREENHEIGHT'),
'SCREENHEIGHTCM': ('I', 'SCREENHEIGHTCM'),
'SCREENWIDTH': ('I', 'SCREENWIDTH'),
'SCREENWIDTHCM': ('I', 'SCREENWIDTHCM'),
'fname': ('static', 'fname'),
'preexpSec': ('static', 'preexpSec'),
'postexpSec': ('static', 'postexpSec'),
'orioff': ('static', 'orioff'),
'regionwidthDeg': ('static', 'widthDeg'),
'regionheightDeg': ('static', 'heightDeg'),
'mask': ('static', 'mask'),
'diameterDeg': ('static', 'diameterDeg'),
'GAMMA': ('static', 'gamma'),
'framei': ('dynamic', 'framei'),
'ori': ('dynamic', 'ori'),
'polarity': ('dynamic', 'invert'),
'bgbrightness': ('dynamic', 'bgbrightness'),
'sweeptimeMsec': ('dynamic', 'sweepSec'),
'postsweepMsec': ('dynamic', 'postsweepSec'),
}
# collect any ptc15 movie attribs and add them to self.oldparams
try:
# can't really handle more than 1 movie, since dimstim 0.16 doesn't
assert len(np.unique(self.oldparams.playlist)) == 1
# bind it, movie was the only possible stim object anyway in ptc15
self.movie = self.oldparams.playlist[0]
# returns dict of name:val pair attribs excluding __ and methods:
movieparams = self.oldparams[self.movie.oname].__dict__
self.oldparams.update(movieparams)
except AttributeError:
# no playlist, no movies, and therefore no movie attribs to deal with
pass
# convert ptc15 params to dimstim 0.16
for oldname, val in self.oldparams.items():
if 'msec' in oldname.lower():
val = val / 1000. # convert to sec
elif oldname == 'polarity':
val = bool(val) # convert from 0/1 to boolean
if oldname == 'origDeg': # split old origDeg into new separate xposDeg and yposDeg
self.e.dynamic.xposDeg = val[0]
self.e.dynamic.yposDeg = val[1]
else:
try:
paramtype, newname = _15to16[oldname]
if paramtype == 'I':
# bind InternalParams directly to self, not to self.e:
self.I[newname] = val
self.e[paramtype][newname] = val
except KeyError: # oldname doesn't have a newname equivalent
pass
try:
m = self.movie
except AttributeError:
m = None
if m:
# make fake dimstim experiment a ptc15 Movie object, bind all of the attribs of
# the existing fake dimstim experiment
old_e = self.e
self.e = m
for name, val in old_e.__dict__.items():
# bind each variable in the textheader as an attrib of self
self.e.__setattr__(name, val)
# deal with movie filename:
# didn't have a chance to pass this exp as the parent in the movie init,
# so just set the attribute manually:
m.e = self
# if fname refers to a movie whose local name is different, rename it to match
# the local movie name
old2new = {'mseq16.m': 'MSEQ16', 'mseq32.m': 'MSEQ32'}
try:
m.fname = old2new[m.fname]
except KeyError:
pass # old name not in old2new, leave it be
self.e.static.fname = m.fname # update fake dimstim experiment's fname too
# extensionless fname, fname should've been defined in the textheader
m.name = os.path.splitext(m.fname)[0]
uns = get_ipython().user_ns
if m.name not in uns['MOVIES']:
# and it very well may not be, cuz the textheader inits movies with no args,
# leaving fname==None at first, which prevents it from being added to
# MOVIES
uns['MOVIES'][m.name] = m # add m to MOVIES dictattr
# Search self.e.moviepath string (from textheader) for 'Movies' word. Everything
# after that is the relative path to your base movies folder. Eg, if
# self.e.moviepath = 'C:\\Desktop\\Movies\\reliability\\e\\single\\', then set
# self.e.relpath = '\\reliability\\e\\single\\'
spath = self.oldparams.moviepath.split(
'\\') # ptc15 has purely MS path separators
matchi = spath.index('Movies')
relpath = joinpath(spath[matchi + 1::])
MOVIEPATH = get_ipython().user_ns['MOVIEPATH']
path = os.path.join(MOVIEPATH, relpath)
m.fname = os.path.join(path, m.fname)
self.e.static.fname = m.fname # update
try:
self.REFRESHTIME = intround(1 / float(self.oldparams.REFRESHRATE) *
1000000) # us
except AttributeError:
pass
def load(self):
f = open(self.path, 'rb')
self.din = np.fromfile(f, dtype=np.int64).reshape(-1, 2) # reshape to nrows x 2 cols
f.close()
try:
txthdrpath = rstrip(self.path, '.din') + '.textheader'
f = open(txthdrpath, 'rU') # use universal newline support
self.textheader = f.read() # read it all in
f.close()
except IOError:
warn("couldn't load text header associated with '%s'" % self.name)
self.textheader = '' # set to empty
treestr = self.level*TAB + self.name + '/'
# print string to tree hierarchy and screen
self.writetree(treestr + '\n')
print(treestr)
if self.textheader != '':
# comment out all lines starting with "from dimstim"
self.textheader = self.textheader.replace('from dimstim', '#from dimstim')
names1 = locals().copy() # namespace before execing the textheader
exec(self.textheader)
names2 = locals().copy() # namespace after
# names that were added to the namespace, excluding the 'names1' name itself:
newnames = [ n2 for n2 in names2 if n2 not in names1 and n2 != 'names1' ]
try:
# dimstim up to Cat 15 didn't have a version, neither did NVS display
self.__version__ = eval('__version__')
except NameError:
self.__version__ = 0.0
if self.__version__ >= 0.16: # after major refactoring of dimstim
for newname in newnames:
# bind each variable in the textheader as an attrib of self
self.__setattr__(newname, eval(newname))
self.sweeptable = SweepTable(experiment=self.e) # build the sweep table
self.st = self.sweeptable.data # synonym, used a lot by experiment subclasses
# this doesn't work for textheaders generated by dimstim 0.16, since
# xorigDeg and yorigDeg were accidentally omitted from all the experiment
# scripts and hence the textheaders too:
'''
self.e.xorig = deg2pix(self.e.static.xorigDeg, self.I) + self.I.SCREENWIDTH / 2
self.e.yorig = deg2pix(self.e.static.yorigDeg, self.I) + self.I.SCREENHEIGHT / 2
'''
self.REFRESHTIME = intround(1 / float(self.I.REFRESHRATE) * 1000000) # us
# prevent replication of movie frame data in memory
if type(self.e) == Movie:
fname = os.path.split(self.e.static.fname)[-1] # pathless fname
if fname not in _MOVIES:
# add movie experiment, indexed according to movie data file name,
# to prevent from ever loading its frames more than once
_MOVIES[fname] = e
else:
self.oldparams = dictattr()
for newname in newnames:
# bind each variable in the textheader to oldparams
self.oldparams[newname] = eval(newname)
self.loadCat15exp()
else:
# use the time difference between the first two din instead
self.REFRESHTIME = self.din[1, 0] - self.din[0, 0]
# add an extra refresh time after last din, that's when screen actually turns off
self.trange = (self.din[0, 0], self.din[-1, 0] + self.REFRESHTIME)
def loadCat15exp(self):
## TODO: - fake a .e dimstim.Experiment object, to replace what used to be the
## .stims object for movie experiments
''' - self.movie = self.experiment.stims[0]
- need to convert sweeptimeMsec to sweepSec
- assert len(self.experiment.stims) == 1
- self.movie = self.experiment.stims[0]
- self.movie.load() # ensure the movie's data is loaded
if self.movie.oname == 'mseq32':
frameis = frameis[frameis != 65535] # remove all occurences of 65535
elif self.movie.oname == 'mseq16':
frameis = frameis[frameis != 16383] # remove all occurences of 16383
'''
# Add .static and .dynamic params to fake dimstim experiment
self.e = dictattr()
self.I = dictattr() # fake InternalParams object
self.e.static = dictattr() # fake StaticParams object
self.e.dynamic = dictattr() # fake DynamicParams object
# maps Cat 15 param names to dimstim 0.16 param types and names, wherever possible
## TODO: fill in params for experiment types other than Movie??
_15to16 = {'EYE': ('I', 'EYE'),
'PIXPERCM': ('I', 'PIXPERCM'),
'REFRESHRATE': ('I', 'REFRESHRATE'),
'SCREENDISTANCECM': ('I', 'SCREENDISTANCECM'),
'SCREENHEIGHT': ('I', 'SCREENHEIGHT'),
'SCREENHEIGHTCM': ('I', 'SCREENHEIGHTCM'),
'SCREENWIDTH': ('I', 'SCREENWIDTH'),
'SCREENWIDTHCM': ('I', 'SCREENWIDTHCM'),
'fname': ('static', 'fname'),
'preexpSec': ('static', 'preexpSec'),
'postexpSec': ('static', 'postexpSec'),
'orioff': ('static', 'orioff'),
'regionwidthDeg': ('static', 'widthDeg'),
'regionheightDeg': ('static', 'heightDeg'),
'mask': ('static', 'mask'),
'diameterDeg': ('static', 'diameterDeg'),
'GAMMA': ('static', 'gamma'),
'framei': ('dynamic', 'framei'),
'ori': ('dynamic', 'ori'),
'polarity': ('dynamic', 'invert'),
'bgbrightness': ('dynamic', 'bgbrightness'),
'sweeptimeMsec': ('dynamic', 'sweepSec'),
'postsweepMsec': ('dynamic', 'postsweepSec'),
}
# collect any Cat 15 movie attribs and add them to self.oldparams
try:
# can't really handle more than 1 movie, since dimstim 0.16 doesn't
assert len(np.unique(self.oldparams.playlist)) == 1
# bind it, movie was the only possible stim object anyway in Cat 15
self.movie = self.oldparams.playlist[0]
# returns dict of name:val pair attribs excluding __ and methods:
movieparams = self.oldparams[self.movie.oname].__dict__
self.oldparams.update(movieparams)
except AttributeError:
# no playlist, no movies, and therefore no movie attribs to deal with
pass
# convert Cat 15 params to dimstim 0.16
for oldname, val in self.oldparams.items():
if 'msec' in oldname.lower():
val = val / 1000. # convert to sec
elif oldname == 'polarity':
val = bool(val) # convert from 0/1 to boolean
if oldname == 'origDeg': # split old origDeg into new separate xposDeg and yposDeg
self.e.dynamic.xposDeg = val[0]
self.e.dynamic.yposDeg = val[1]
else:
try:
paramtype, newname = _15to16[oldname]
if paramtype == 'I':
# bind InternalParams directly to self, not to self.e:
self.I[newname] = val
self.e[paramtype][newname] = val
except KeyError: # oldname doesn't have a newname equivalent
pass
try:
m = self.movie
except AttributeError:
m = None
if m:
# make fake dimstim experiment a Cat15Movie object, bind all of the attribs of
# the existing fake dimstim experiment
old_e = self.e
self.e = m
for name, val in old_e.__dict__.items():
# bind each variable in the textheader as an attrib of self
self.e.__setattr__(name, val)
# deal with movie filename:
# didn't have a chance to pass this exp as the parent in the movie init,
# so just set the attribute manually:
m.e = self
# if fname refers to a movie whose local name is different, rename it to match
# the local movie name
_old2new = {'mseq16.m': MSEQ16, 'mseq32.m': MSEQ32}
try:
m.fname = _old2new[m.fname]
except KeyError:
pass # old name not in _old2new, leave it be
self.e.static.fname = m.fname # update fake dimstim experiment's fname too
# extensionless fname, fname should've been defined in the textheader
m.name = os.path.splitext(m.fname)[0]
if m.name not in _MOVIES:
# and it very well may not be, cuz the textheader inits movies with no args,
# leaving fname==None at first, which prevents it from being added to
# _MOVIES
_MOVIES[m.name] = m # add m to _MOVIES dictattr
# Search self.e.moviepath string (from textheader) for 'Movies' word. Everything
# after that is the relative path to your base movies folder. Eg, if
# self.e.moviepath = 'C:\\Desktop\\Movies\\reliability\\e\\single\\', then set
# self.e.relpath = '\\reliability\\e\\single\\'
spath = self.oldparams.moviepath.split('\\') # Cat15 has purely windows seperators
matchi = spath.index('Movies')
relpath = joinpath(spath[matchi+1 ::])
MOVIEPATH = get_ipython().user_ns['MOVIEPATH']
path = os.path.join(MOVIEPATH, relpath)
m.fname = os.path.join(path, m.fname)
self.e.static.fname = m.fname # update
# Generate the sweeptable:
# dict of lists, ie sweeptable={'ori':[0,45,90], 'sfreq':[1,1,1]}, so you index
# into it with self.sweeptable['var'][sweepi]
#self.sweeptable = {[]}
#vars = self.sweeptable.keys()
# need to check if varlist exists, if so use it (we're dealing with Cat 15),
# if not, use revamped dimstim.SweepTable class
varvals = {} # init a dictionary that will contain variable values
for var in m.varlist:
# generate dict with var:val entries, to pass to buildSweepTable
varvals[var] = eval('m.' + var)
# pass varlist by reference, dim indices end up being modified:
m.sweepTable = self.buildCat15SweepTable(m.varlist, varvals, m.nruns,
m.shuffleRuns, m.blankSweep,
m.shuffleBlankSweeps,
makeSweepTableText=0)[0]
else: # this is a simple stim (not object oriented movie)
varvals = {} # init a dictionary that will contain variable values
for var in self.oldparams.varlist:
# generate dict with var:val entries, to pass to buildSweepTable
varvals[var] = eval('self.oldparams.' + var)
# pass varlist by reference, dim indices end up being modified:
self.sweepTable = self.buildCat15SweepTable(self.oldparams.varlist, varvals,
self.oldparams.nruns,
self.oldparams.shuffleRuns,
self.oldparams.blankSweep,
self.oldparams.shuffleBlankSweeps,
makeSweepTableText=0)[0]
try:
self.REFRESHTIME = intround(1 / float(self.oldparams.REFRESHRATE) * 1000000) # us
except AttributeError:
pass
def __init__(self, path):
self.level = 1 # level in the hierarchy
self.treebuf = StringIO() # string buffer to print tree hierarchy to
self.path = path
self.tr = dictattr() # store tracks in a dictionary with attrib access
def load(self):
f = open(self.path, 'rb')
self.din = np.fromfile(f, dtype=np.int64).reshape(-1, 2) # reshape to 2 cols
f.close()
try:
txthdrpath = rstrip(self.path, '.din') + '.textheader'
f = open(txthdrpath, 'rU') # use universal newline support
self.textheader = f.read() # read it all in
f.close()
except IOError:
print("WARNING: couldn't load text header associated with '%s'" % self.name)
self.textheader = '' # set to empty
treestr = self.level*TAB + self.name + '/'
# print string to tree hierarchy and screen
self.writetree(treestr + '\n')
print(treestr)
if self.textheader != '':
# comment out all lines starting with "from dimstim"
self.textheader = self.textheader.replace('from dimstim', '#from dimstim')
# execute any remaining 'import' lines first, so that any modules imported
# aren't artefactually detected as having been added to the namespace:
for line in self.textheader.splitlines():
if line.startswith('import'):
exec(line)
thns = {} # textheader namespace
# compiling to code and then executing that is supposed to be faster than directly
# executing a string, according to
# http://lucumr.pocoo.org/2011/2/1/exec-in-python/, but doesn't seem to make
# a difference here:
code = compile(self.textheader, "<string>", "exec")
# don't exec in current namespace, load name:val pairs into thns instead:
exec(code, None, thns)
try:
# dimstim up to ptc15 didn't have a version, neither did NVS display
self.__version__ = thns['__version__']
except KeyError:
self.__version__ = 0.0
if self.__version__ >= 0.16: # after major refactoring of dimstim
for name, val in thns.items():
# bind each variable in the textheader as an attrib of self
self.__setattr__(name, val)
# this doesn't work for textheaders generated by dimstim 0.16, since
# xorigDeg and yorigDeg were accidentally omitted from all the experiment
# scripts and hence the textheaders too:
'''
self.e.xorig = deg2pix(self.e.static.xorigDeg, self.I) + self.I.SCREENWIDTH / 2
self.e.yorig = deg2pix(self.e.static.yorigDeg, self.I) + self.I.SCREENHEIGHT / 2
'''
self.REFRESHTIME = intround(1 / float(self.I.REFRESHRATE) * 1000000) # us
# prevent replication of movie frame data in memory
if type(self.e) == Movie:
fname = os.path.split(self.e.static.fname)[-1] # pathless fname
uns = get_ipython().user_ns
if fname not in uns['MOVIES']:
# add movie experiment, indexed according to movie data file name,
# to prevent from ever loading its frames more than once
uns['MOVIES'][fname] = self.e
else:
self.oldparams = dictattr()
for name, val in thns.items():
# bind each variable in the textheader to oldparams
self.oldparams[name] = val
self.loadptc15exp()
else:
# use the time difference between the first two din instead
self.REFRESHTIME = self.din[1, 0] - self.din[0, 0]
# add an extra refresh time after last din, that's when screen actually turns off
self.trange = (self.din[0, 0], self.din[-1, 0] + self.REFRESHTIME)
# these are static, no need for properties:
self.dt = self.trange[1] - self.trange[0] # duration (us)
self.dtsec = self.dt / 1e6
self.dtmin = self.dtsec / 60
self.dthour = self.dtmin / 60
"""Global variables that can be modified by the user at the IPython command line.
Access programatically using:
get_ipython().user_ns['VARNAME']
"""
import os
from core import mergeuniquedictvals, dictattr
import colour as clr
DATAPATH = os.path.expanduser('~/data')
#BLABPATH = os.path.join(DATAPATH, 'blab') # Busse Lab
BLABPATH = os.path.join(DATAPATH, 'blab', 'natstate') # Busse Lab
SLABPATH = os.path.join(DATAPATH, 'slab') # Swindale Lab
MOVIEPATH = os.path.join(SLABPATH, 'mov')
MOVIES = dictattr()
# for each recording, load all Sorts, or just the most recent one?
LOADALLSORTS = False
"""Mean spike rate that delineates normal vs "quiet" neurons. 0.1 Hz seems reasonable if you
plot mean spike rate distributions for all the neurons in a given track. But, if you want a
reasonable looking DJS histogram without a lot of missing netstates, you need to exclude
more low firing rate cells, 0.5 works better"""
MINRATE = 0.05 # Hz
"""Calculate a TrackNeuron's meanrate according to its trange (period between its first and
last spike), or according to its track's entire duration. Need to reload the track or call
Track.calc_meanrates() after changing this on the fly"""
TRACKNEURONPERIOD = 'track' # 'trange' or 'track'
# ditto for recordings:
RECNEURONPERIOD = 'recording' # 'trange' or 'recording'
"""NeuronCode (Ising matrix) and network state parameters"""
CODEKIND = 'binary'
