def test_info(self):
'''
Test the info module.
'''
for patch in self._name_list:
test_patch = Patch(os.path.join(self._dir, patch))
test_patch.scan()
for index, cluster in enumerate(test_patch):
# Testing basic information loading
test_start = abs(cluster.start - self._patch_list[patch][index]['start'])
if test_start > 0.0001:
print('Module Info "start" test failed')
print('Expected: {}, Obtained: {}'.format(self._patch_list[patch][index]['start'],
cluster.start))
test_open_period = sum((cluster.open_period - self._patch_list[patch][index]['open_period'])**2)
if test_open_period > 0.0001:
print('Module Info "open_period" test failed')
print('Total difference: {}'.format(test_open_period))
test_shut_period = sum((cluster.shut_period - self._patch_list[patch][index]['shut_period'])**2)
if test_shut_period > 0.0001:
print('Module Info "shut_period" test failed')
print('Total difference: {}'.format(test_shut_period))
test_open_amp = sum((cluster.open_amp - self._patch_list[patch][index]['open_amp'])**2)
if test_open_amp > 0.0001:
print('Module Info "open_amp" test failed')
print('Total difference: {}'.format(test_open_amp))
test_shut_amp = sum((cluster.shut_amp - self._patch_list[patch][index]['shut_amp'])**2)
if test_shut_amp > 0.0001:
print('Module Info "shut_amp" test failed')
print('Total difference: {}'.format(test_shut_amp))
def scan_folder(self, clear = True):
'''
Scan and collect all the clusters in the folder.
'''
if clear:
self._cluster_list = []
for folder in self._folder_list:
patch_list = [csv for csv in os.listdir(folder) if csv[-4:] == '.csv']
for patch in patch_list:
current_path = os.path.join(folder, patch)
current_patch = Patch(current_path)
current_patch.scan()
for cluster in current_patch:
self._cluster_list.append(cluster)
return self._cluster_list
def test_PlotComputation_using_PlotMPL(self):
'''
Testing the PlotComputation using the PlotMPL module which uses Matplotlib as backend.
'''
for patch in self._name_list:
test_patch = Patch(os.path.join(self._dir, patch))
test_patch.scan()
for index, cluster in enumerate(test_patch):
cluster.compute_mode()
cluster.compute_mode_detail()
test_plot = PlotSingle(self._dir)
test_plot.load_cluster(cluster)
test_plot.plot_original()
test_plot.plot_popen_on_original()
test_plot.plot_open_close()
test_plot.plot_cost_difference()
def scan_orded_folder(self, func = _add_cluster, clear = True, export = False):
'''
Scan the folder and apply the func to every clusters in the folder.
If func is not provided, a whole list of the clusters in the folder
will be generated.
'''
if clear:
self._cluster_list = []
for folder in self._folder_list:
current_path = folder
current_folder_list = list_folder(current_path)
for receptor in current_folder_list:
current_path_R = os.path.join(current_path, receptor)
current_folder_list_R = list_folder(current_path_R)
for mutation in current_folder_list_R:
current_path_M = os.path.join(current_path_R, mutation)
current_folder_list_M = list_folder(current_path_M)
for composition in current_folder_list_M:
current_path_C = os.path.join(current_path_M, composition)
current_folder_list_C = list_folder(current_path_C)
for agonist in current_folder_list_C:
current_path_A = os.path.join(current_path_C, agonist)
current_folder_list_A = list_folder(current_path_A)
for concentration in current_folder_list_A:
path = os.path.join(current_path_A, concentration)
patch_list = [csv for csv in os.listdir(path)
if csv[-4:] == '.csv']
for patch in patch_list:
filepath = os.path.join(path, patch)
current_patch = Patch(filepath)
current_patch.scan()
for cluster in current_patch:
func(self, cluster,
receptor = receptor,
mutation = mutation,
composition = composition,
agonist = agonist,
concentration = concentration)
if export:
return self._cluster_list
def test_batch_analysis(self):
'''
test the batch analysis.
'''
cluster_list = []
for patch in self._name_list:
test_patch = Patch(os.path.join(self._dir, patch))
test_patch.scan()
for cluster in test_patch:
cluster.compute_mode()
cluster.compute_mode_detail()
cluster_list.append(cluster)
# Test BatchAnalysis class
batch_analysis = BatchAnalysis(list(cluster_list))
test_dict = batch_analysis.compute_cluster_summary()
for patchname in self._name_list:
for cluster_no in range(1, self.cluster_num+1):
test_dict = batch_analysis.compute_cluster_summary(
patchname = patchname, cluster_no = cluster_no)
temp_amp = np.mean(self._patch_list[patchname][cluster_no-1]['open_amp']
-
self._patch_list[patchname][cluster_no-1]['shut_amp'])
if abs(test_dict['mean_amp'] - temp_amp) > 0.0001:
print('Amplitude error')
temp_duration = (sum(self._patch_list[patchname][cluster_no-1]['open_period'])
+
sum(self._patch_list[patchname][cluster_no-1]['shut_period']))
if abs(test_dict['duration'] - temp_duration) > 0.0001:
print('Duration error')
temp_popen = sum(self._patch_list[patchname][cluster_no-1]['open_period']) / temp_duration
if abs(test_dict['popen'] - temp_popen) > 0.0001:
print('Popen error')
# Test StretchSummary class
batch_analysis.compute_stretch_summary()
def test_scn_write():
intervals = np.hstack((np.arange(1,501),np.arange(1,501)))
amplitudes = np.ones(1000)*-1
amplitudes[::2] = 0
amplitudes = amplitudes.astype('int')
flags = np.zeros(1000)
flags = flags.astype('int')
dcio.scn_write(intervals, amplitudes, flags, filename='./test.SCN')
new_patch = Patch('./test.SCN')
new_patch.read_scn(tres=0, tcrit=500)
new_patch.write_scn()
new_patch = Patch('./modified_test.SCN')
new_patch.read_scn(tres=0, tcrit=np.inf)
period = new_patch[1].period
print(sum(intervals[3:-1]-period))
def test_batch_query(self):
'''
test the batch_query module.
'''
cluster_list = []
for patch in self._name_list:
test_patch = Patch(os.path.join(self._dir, patch))
test_patch.scan()
for cluster in test_patch:
cluster_list.append(cluster)
# Test search orded folder scan
choice_dict = OrderedDict([('receptor', ['NMDA', 'AMPA']),
('mutation', ['S219P', 'S200T']),
('composition', ['a1','ab']),
('agonist', ['glycine', 'taurine']),
('concentration', ['100', '0.1'])])
organisation = {keys:{key: [] for key in choice_dict[keys]} for keys in choice_dict}
for index in range(len(self._name_list)):
temp_filepath = self._dir
for key in choice_dict:
choice = random.choice(choice_dict[key])
temp_filepath = os.path.join(temp_filepath, choice)
organisation[key][choice].extend([index]*self.cluster_num)
try:
os.makedirs(temp_filepath)
except FileExistsError:
pass
shutil.copy2(os.path.join(self._dir, self._name_list[index]),
os.path.join(temp_filepath, self._name_list[index]))
test_batch = Batch(folder_list = self._dir)
if len(test_batch.scan_folder()) != len(cluster_list):
print('scan_folder error')
test_cluster_list = test_batch.scan_orded_folder(clear = True,export = True)
copy_organisation = copy.deepcopy(organisation)
for cluster in test_cluster_list:
index = self._name_list.index(cluster.patchname)
for key in organisation:
if not index in organisation[key][getattr(cluster, key)]:
print('scan_orded_folder error')
else:
copy_organisation[key][getattr(cluster, key)].remove(index)
for i in copy_organisation:
for j in copy_organisation[i]:
if copy_organisation[i][j]:
print('scan_orded_folder error')
# Test query
copy_organisation = copy.deepcopy(organisation)
for i in organisation:
for j in organisation[i]:
if organisation[i][j]:
query_list = test_batch.query(**{i: j})
for cluster in query_list:
index = self._name_list.index(cluster.patchname)
try:
copy_organisation[i][j].remove(index)
except ValueError:
print('query error')
for i in copy_organisation:
for j in copy_organisation[i]:
if copy_organisation[i][j]:
print('query error')
cluster_list = []
data = np.loadtxt('./ekdist_paramteters.csv',
delimiter=',', dtype={
'names': ('filename', 'concentration', 'res', 'tcrit'),
'formats': ('S8', 'S3', 'f4', 'f4')})
concentrations = [1,3,10,100]
for concentration in concentrations:
for patch in data:
if float(patch['concentration']) == concentration:
filename = "./ekdist_traces/{}.scn".format(patch['filename'].decode('utf8'))
#
# filename = "./raw trace/{}/{}.scn".format(patch['concentration'].decode('utf8'),
# patch['filename'].decode('utf8'))
patch = Patch(filename)
patch.read_scn(tres=patch['res']*1e-6, tcrit=patch['tcrit']*1e-6)
cluster_list.extend(patch.get_cluster_list())
batch_analysis = BatchAnalysis(cluster_list)
summary = batch_analysis.compute_cluster_summary()
summary['start'] /= 1000
summary['end'] /= 1000
np.savetxt('temp.csv', summary, delimiter=',', fmt = '%s,%.18e,%.18e,%.18e,%.18e,%.18e,%.18e,%.18e,%.18e,%.18e,%.18e,%.18e')
col_name = str(summary.dtype.names)
col_name = col_name[1:-1] + '\n'
f = open('temp.csv','r')
string = f.read()
'15072411',
'15080408'
]
tres = [
20,
30,
20
]
tcrit = [
100,
70,
100
]
popen =[]
for index, name in enumerate(name_list):
patch = Patch('/Users/zhiyiwu/Documents/pharmfit/raw trace/3/{}.SCN'.format(name))
patch.read_scn(tres=tres[index], tcrit=tcrit[index])
maxopen = 1
maxshut = float('inf')
def rule(cluster, maxopen, maxshut):
if (cluster.mean_open > maxopen) or (cluster.mean_shut > maxshut):
return False
else:
return True
for i in range(3):
patch = Patch('/Users/zhiyiwu/Documents/pharmfit/raw trace/3/{}.SCN'.format(name_list[i]))
patch.read_scn(tres=tres[i], tcrit=tcrit[i])
patch.filter_cluster(rule, maxopen, maxshut)
# -*- coding: utf-8 -*-
"""
Created on Fri May 20 11:26:23 2016
@author: zhiyiwu
"""
from info import Cluster,Patch
from dcpyps import dataset
from PlotAnalysis import PlotSingle
from batch_analysis import BatchAnalysis
import matplotlib.pyplot as plt
patch_F = Patch('/Users/zhiyiwu/Documents/pharmfit/raw trace/1/15071710.SCN')
patch_F.read_scn(tres=30, tcrit=100)
plt.plot(patch_F.mean_open, patch_F.mean_shut,'o', alpha=0.5, label = 'F')
patch_G = Patch('/Users/zhiyiwu/Documents/pharmfit/raw trace/1/15080500.SCN')
patch_G.read_scn(tres=20, tcrit=300)
plt.plot(patch_G.mean_open, patch_G.mean_shut,'o', alpha=0.5, label = 'G')
patch_H = Patch('/Users/zhiyiwu/Documents/pharmfit/raw trace/1/15080705.SCN')
patch_H.read_scn(tres=20, tcrit=300)
plt.plot(patch_H.mean_open, patch_H.mean_shut,'o', alpha=0.5, label = 'H')
plt.legend()
from info import Cluster,Patch
from dcpyps import dataset
from PlotAnalysis import PlotSingle
from batch_analysis import BatchAnalysis
import matplotlib.pyplot as plt
import numpy as np
maxopen = 1
maxshut = float('inf')
def rule(cluster, maxopen, maxshut):
if (cluster.mean_open > maxopen) or (cluster.mean_shut > maxshut):
return False
else:
return True
patch_G = Patch('/Users/zhiyiwu/Documents/pharmfit/raw trace/1/15080500.SCN')
patch_G.read_scn(tres=20, tcrit=300)
patch_H = Patch('/Users/zhiyiwu/Documents/pharmfit/raw trace/1/15080705.SCN')
patch_H.read_scn(tres=20, tcrit=300)
patch_G.filter_cluster(rule, maxopen, maxshut)
patch_G.write_scn()
patch_H.filter_cluster(rule, maxopen, maxshut)
patch_H.write_scn()
def change(name, tres, tcrit, minPopen = 0, maxPopen = 1.1):
new_patch = Patch('./set/{}.SCN'.format(name))
new_patch.read_scn(tres=tres, tcrit=tcrit)
new_patch.filter_cluster(rule, minPopen, maxPopen)
new_patch.write_scn()
# -*- coding: utf-8 -*-
"""
Created on Tue Jun 7 09:32:25 2016
@author: zhiyiwu
"""
import numpy as np
import matplotlib.pyplot as plt
from info import Patch
from binary_search import BFS
patch = Patch('/Users/zhiyiwu/Documents/pharmfit/12061415.csv')
patch.scan()
cluster = patch[1]
opening = cluster.open_period
log_opening = np.log10(opening)
plt.hist(log_opening)
sep_open = sorted(BFS(log_opening[:, np.newaxis]))
print(sep_open)
shutting = cluster.shut_period
plt.hist(np.log10(shutting))
log_shutting = np.log10(shutting)
plt.hist(log_shutting)
sep_shut = sorted(BFS(log_shutting[:, np.newaxis]))
print(sep_shut)
period = cluster.period