def plot_interlevels(file, persFile, output, interval, r, mask=False):
"""
plots interlevels sets for specified numpy file
from the height values in associated persFile (USE .BETTI FILE)
output is directory for output files (indv. names come from file + height)
interval provides info on what frames to save
(i.e. interval==2 means every other frame )
r perburation to height function (use half of desired window)
Use half interval to capture every height value (if all height values present)
if mask==True all sublevel values are set to 1
"""
if not output.endswith("/"):
output += "/"
with open(persFile, "r") as f:
s = f.read()
f.close()
data = numpy.load(file)
heightList = [x[1:-1] for x in re.findall("\[[^\]]*\]", s)]
# d = numpy.where(data>int(heightList[100]))
# data[d] = 0
# rp . save_npy_as_png(data,output+file.split('/')[-1].rstrip('.npy'))
for ind, h in enumerate(heightList):
if ind % interval == 0:
temp = data.copy()
lower = int(h) - r
upper = int(h) + r
temp[(temp > upper) | (temp < lower)] = 0
if mask:
temp[numpy.where(temp != 0)] = 1
outName = file.split("/")[-1].rstrip(".npy") + "_" + h + "-" + str(lower) + "-" + str(upper)
rp.save_npy_as_png(temp, output + outName + ".png")
def plot_sublevels_comp(file, slice, output, interval, persFile="NULL", mask=False):
"""
plots sublevel sets for specified numpy file
from the height values in associated persFile
output is directory for output files (indv. names come from file + height)
interval provides info on what frames to save
(i.e. interval==2 means every other frame )
if mask==True all sublevel values are set to 1
"""
if not output.endswith("/"):
output += "/"
data = numpy.load(file)[slice]
if persFile != "NULL":
with open(persFile, "r") as f:
s = f.read()
f.close()
heightList = [x[1:-1] for x in re.findall("\[[^\]]*\]", s)]
else:
tempMin = data[numpy.where(data > data.min())].min()
avg = (data.max() - tempMin) / 50
heightList = numpy.arange(tempMin, data.max(), avg)
# d = numpy.where(data>int(heightList[100]))
# data[d] = 0
# rp . save_npy_as_png(data,output+file.split('/')[-1].rstrip('.npy'))
for ind, h in enumerate(heightList):
if ind % interval == 0:
temp = data.copy()
temp[numpy.where(temp > int(h))] = 0
if mask:
temp[numpy.where(temp != 0)] = 1
outName = file.split("/")[-1].rstrip(".npy") + "_" + str(slice) + "_" + str(h)
rp.save_npy_as_png(temp, output + outName + ".png")
