def loadinputdata(self, datafile, savefile=None):
rdd = load(self.sc, datafile, preprocessmethod="dff-percentile")
self.rdd = rdd
self.datafile = datafile
if savefile is not None:
self.savefile = savefile
self.modelfile = os.path.join(os.path.split(self.datafile)[0], 'stim')
def test_ica(self):
ica_data = os.path.join(DATA_DIR, "ica.txt")
ica_results = os.path.join(DATA_DIR, "results/ica")
data = load(self.sc, ica_data, "raw")
w, sigs = ica(data, 4, 4, svdmethod="direct", seed=1)
w_true = loadmat(os.path.join(ica_results, "w.mat"))["w"]
sigs_true = loadmat(os.path.join(ica_results, "sigs.mat"))["sigs"]
tol = 10e-02
assert allclose(w, w_true, atol=tol)
assert allclose(transpose(sigs.map(lambda (_, v): v).collect()), sigs_true, atol=tol)
def test_ica(self):
ica_data = os.path.join(DATA_DIR, "ica.txt")
ica_results = os.path.join(DATA_DIR, "results/ica")
data = load(self.sc, ica_data, "raw")
w, sigs = ica(data, 4, 4, svdmethod="direct", seed=1)
w_true = loadmat(os.path.join(ica_results, "w.mat"))["w"]
sigs_true = loadmat(os.path.join(ica_results, "sigs.mat"))["sigs"]
tol = 10e-02
assert (allclose(w, w_true, atol=tol))
assert (allclose(transpose(sigs.map(lambda (_, v): v).collect()),
sigs_true,
atol=tol))
method = SigProcessingMethod.load("stats", statistic=statistic)
vals = method.calc(data)
return vals
if __name__ == "__main__":
parser = argparse.ArgumentParser(description="compute summary statistics on time series data")
parser.add_argument("master", type=str)
parser.add_argument("datafile", type=str)
parser.add_argument("outputdir", type=str)
parser.add_argument("mode", choices=("mean", "median", "std", "norm"), help="which summary statistic")
parser.add_argument("--preprocess", choices=("raw", "dff", "dff-highpass", "sub"), default="raw", required=False)
args = parser.parse_args()
egg = glob.glob(os.path.join(os.environ["THUNDER_EGG"], "*.egg"))
sc = SparkContext(args.master, "ref", pyFiles=egg)
data = load(sc, args.datafile, args.preprocess).cache()
vals = stats(data, args.mode)
outputdir = (args.outputdir + "-stats",)
outputdir = args.outputdir + "-stats"
if not os.path.exists(outputdir):
os.makedirs(outputdir)
save(vals, outputdir, "stats_" + args.mode, "matlab")
return corr
if __name__ == "__main__":
parser = argparse.ArgumentParser(
description="correlate time series with neighbors")
parser.add_argument("master", type=str)
parser.add_argument("datafile", type=str)
parser.add_argument("outputdir", type=str)
parser.add_argument("sz", type=int)
parser.add_argument("--preprocess",
choices=("raw", "dff", "dff-highpass", "sub"),
default="raw",
required=False)
args = parser.parse_args()
sc = SparkContext(args.master, "localcorr")
if args.master != "local":
egg = glob.glob(os.path.join(os.environ['THUNDER_EGG'], "*.egg"))
sc.addPyFile(egg[0])
data = load(sc, args.datafile, args.preprocess).cache()
corrs = localcorr(data, args.sz)
outputdir = args.outputdir + "-localcorr"
save(corrs, outputdir, "corr", "matlab")
parser.add_argument("--tuningmode", choices=("circular", "gaussian"), default="gaussian", required=False, help="form of tuning curve")
parser.add_argument("--basename", type=str, default="-", required=False)
parser.add_argument("--stim", type=str, default="-", required=False)
args = parser.parse_args()
sc = SparkContext(args.master, "myscript")
if args.master != "local":
egg = glob.glob(os.path.join(os.environ['THUNDER_EGG'], "*.egg"))
sc.addPyFile(egg[0])
# load data file
datafile = os.path.join(args.datafolder, args.imagename)
outputdir = os.path.join(args.datafolder,"spark")
data = load(sc, datafile, args.preprocess, 4)
# drop key
data = data.map(lambda (k, v): (k[0:3], v))
data.cache()
# compute mean map
vals = stats(data,"mean")
save(vals,outputdir,"mean_vals","matlab")
# compute local cor
if args.neighbourhood != 0:
cor = localcorr(data,args.neighbourhood)
save(cor,outputdir,"local_corr","matlab")
# if stim argument is not default
