def get_from_filelist(self, xml_file_list):
from kt_simul import simul_spindle as sim
from kt_simul import attachment_state as atst
self.defects = {}
self.mero_types = {}
self.xml_file_list = xml_file_list
for i, in range(len(xml_file_list))[::num_ech]:
for j in num_ech:
mp = sim.get_fromfile( i * num_ech + j)
if i * j == 0:
self.defects, were_defects = atst.defect_histories(mp.KD)
balance, self.mero_types = atst.balance_histories(mp.KD)
else:
defects, were_defects = atst.defect_histories(mp.KD)
balance, mero_types = atst.balance_histories(mp.KD)
for defect in defects.keys():
self.defects[defect] = hstack((self.defects[defect],
defects[defect]))
for mero_type in mero_types.keys():
self.mero_types[mero_type] = hstack((self.mero_types[mero_type],
mero_types[mero_type]))
del defects, were_defects, balance
del mp
if mod(i,20) == 0:
print '%i / %i'%(i, len(xml_file_list))
def compute_defects(xml_file_list, base_name):
from kt_simul import simul_spindle as sim
from kt_simul import attachment_state as atst
all_defects = {}
all_merotelic_types = {}
all_pcs1s = []#load(base_name+'_pcs1s.npy')
all_auroras = []#load(base_name+'_auroras.npy')
#base_shape = (pcs1s.size, auroras.size)
for i, fname in enumerate(xml_file_list):
mp = sim.get_fromfile(os.path.join(base_name,fname))
if i == 0:
all_defects, all_were_defects = atst.defect_histories(mp.KD)
all_balance, all_merotelic_types = atst.balance_histories(mp.KD)
else:
defects, were_defects = atst.defect_histories(mp.KD)
balance, merotelic_types = atst.balance_histories(mp.KD)
trans_mat = atst.transition_matrix(mp.KD)
for defect in defects.keys():
all_defects[defect] = hstack((all_defects[defect],
defects[defect]))
for mero_type in merotelic_types.keys():
all_merotelic_types[mero_type] = hstack((all_merotelic_types[mero_type],
merotelic_types[mero_type]))
del defects, were_defects, balance, trans_mat
all_pcs1s.append(mp.KD.params['orientation'])
all_auroras.append(mp.KD.params['aurora'])
if mod(i,20) == 0:
print '%i / %i'%(i, len(xml_file_list))
del mp
return all_pcs1s, all_auroras, all_defects, all_merotelic_types