def __init__(self, log_dir, process_names=[]):
os.chdir(log_dir)
if process_names is None:
process_names = []
self.process_names = process_names
for device_dir in self.list_device_dirs():
logger.info('create report for %s' % device_dir)
core_num = 1
try:
with open(os.path.join(device_dir, 'corenum.txt'), 'r') as f:
core_num = int(f.read())
except:
pass
file_names = self.filter_file_names(device_dir)
logger.debug('%s' % file_names)
if file_names:
book_name = '%s-%s.xlsx' % (device_dir, datetime.now().strftime('%Y.%m.%d-%H.%M.%S'))
excel = Excel(book_name)
for file_name in file_names:
name = file_name.split('.')[0]
info = INFO_CONFIG.get(name)(device_dir, file_name, process_names, core_num)
for sheet in info.get_sheet_list():
logger.info('add sheet %s' % sheet[0])
excel.add_sheet(*sheet)
logger.info('wait to save %s' % book_name)
excel.save()
def onButton_data(self, event):
"""
This method is fired when its corresponding button is pressed
"""
openDirDialog = wx.DirDialog(self.panel1, 'Choose input directory', '.', wx.DD_DEFAULT_STYLE | wx.DD_DIR_MUST_EXIST)
#
if openDirDialog.ShowModal() != wx.ID_CANCEL:
# ----------------------------------------
# Get all data files
# ----------------------------------------
patients = {}
for filename in glob.glob(openDirDialog.GetPath() + os.sep + '*.txt'):
file_content = AminoacidAnalyzes_file(filename)
if file_content.patient not in patients:
patients[file_content.patient] = Patient()
patients[file_content.patient].add_data(file_content)
#
# ----------------------------------------
# Create result folder
# ----------------------------------------
folder = ''.join((openDirDialog.GetPath(), os.sep, '..', os.sep, 'result', os.sep))
if not os.path.isdir(folder):
os.makedirs(folder)
# ----------------------------------------
# Go through each patient data and create an excel file for each
# ----------------------------------------
uptakes = {}
for patient in patients:
print patient
patients[patient].calculate_average()
# ----------------------------------------
# Create Excel file
# ----------------------------------------
excelfile = Excel()
# ----------------------------------------
# Raw data
# ----------------------------------------
excelfile.add_sheet('raw data', patients[patient].raw_data()[1])
# ----------------------------------------
# Concentration
# ----------------------------------------
excelfile.add_sheet('concentration', patients[patient].raw_data()[0])
# ----------------------------------------
# Mean + Std
# ----------------------------------------
excelfile.add_sheet('mean', patients[patient].mean_std())
# ----------------------------------------
# Normalized to aminoacid
# ----------------------------------------
for i in xrange(len(patients[patient].aa)):
#
new = np.array(patients[patient].normalized(-1, i))
if i == 0:
a = new
else:
a = np.concatenate((a, new), axis = 1)
#
excelfile.add_sheet('normalized', a)
# ----------------------------------------
# Uptake
# ----------------------------------------
excelfile.add_sheet('uptake', patients[patient].normalized(0, -1))
# ----------------------------------------
# Uptake normalized
# ----------------------------------------
for i in xrange(len(patients[patient].aa)):
new = np.array(patients[patient].normalized(0, i))
if i == 0:
a = new
else:
a = np.concatenate((a, new), axis = 1)
#
excelfile.add_sheet('uptake normalized', a)
# ----------------------------------------
# Save Excel datafile
# ----------------------------------------
excelfile.save_excel_file(folder + patient + '.xls')
# ----------------------------------------
# Uptake is Arg
# ----------------------------------------
uptakes[patient] = patients[patient].uptake(7)
# ----------------------------------------
# Create a file with all results
# ----------------------------------------
excelfile = Excel()
groups = list(set([key.split('-')[0] for key in uptakes.keys()]))
groups.sort()
patient_data = [['patient'] + patients[uptakes.keys()[0]].samples]
for group in groups:
keys = []
group_data = []
for key in uptakes.keys():
if group in key:
keys.append(key)
group_data.append(uptakes[key])
group_data = np.array(group_data)
mean = group_data.mean(axis = 0)
std = group_data.std(axis = 0)
for key in keys:
patient_data.append([key] + uptakes[key])
patient_data.append(['' for _ in xrange(len(mean)+1)])
patient_data.append(['Mean'] + list(mean))
patient_data.append(['Std'] + list(std))
patient_data.append(['' for _ in xrange(len(mean)+1)])
patient_data.append(['' for _ in xrange(len(mean)+1)])
patient_data = np.array(patient_data)
excelfile.add_sheet('patient_data', patient_data.T)
excelfile.save_excel_file(folder + 'patients.xls')
# ----------------------------------------
# Finish
# ----------------------------------------
self.button_data.Label = 'Saved!'
#
openDirDialog.Destroy()
#
return None
