def __import_dptfile(conn, filepath, mid):
"""
Inheritently Private Function, determines peaks of .sp File and imports to database
:param conn: Database connection
:param filepath: Path to import file
:param mid: Molecule ID
:return:
"""
from analysis import peak_finder
# Get data from file
frequencies = []
intensities = []
with open(filepath) as f:
for line in f:
point = line.split(",")
frequencies.append(float(point[0])) # get frequency
intensities.append(float(point[1])) # get actual intensity (logx ^ x)
print "[Data Points collected: " + str(len(frequencies)) + "]"
# Determine Peaks
frequencies, intensities = peak_finder.peak_finder(frequencies, intensities, 0.2)
print "[Peaks found: " + str(len(frequencies)) + "]"
# Store peaks into file
for i in range(0, len(frequencies)):
conn.execute('INSERT INTO peaks(mid, frequency, intensity) VALUES (?,?,?)',(mid, frequencies[i], intensities[i])) # insert into peak table
# Commit Changes
conn.commit()
print "[ Added entry peaks ] "
def __import_dptfile(conn, filepath, mid):
"""
Inheritently Private Function, determines peaks of .sp File and imports to database
:param conn: Database connection
:param filepath: Path to import file
:param mid: Molecule ID
:return:
"""
from analysis import peak_finder
# Get data from file as numpy arrays
data = np.loadtxt(filepath)
frequencies = data[:, 0]
intensities = data[:, 1]
print("[Data Points collected: " + str(len(frequencies)) + "]")
# Determine Peaks
frequencies, intensities = peak_finder.peak_finder(frequencies,
intensities)
print "[Peaks found: " + str(len(frequencies)) + "]"
# Store peaks into file
for i in range(0, len(frequencies)):
conn.execute(
'INSERT INTO peaks(mid, frequency, intensity) VALUES (?,?,?)',
(mid, frequencies[i], intensities[i])) # insert into peak table
# Commit Changes
conn.commit()
print "[ Added entry peaks ] "
def __import_ftbfile(conn, filepath, mid, peaks=False):
"""
Inheritently Private Function, determines peaks of .sp File and imports to database
:param conn: Database connection
:param filepath: Path to import file
:param mid: Molecule ID
:return:
"""
from analysis import peak_finder
import re
delimiters = ["ftmfreq:", "shots:", "dipole:", " ", "#intensity "]
regex = '|'.join((map(re.escape, delimiters)))
# Get data from file
frequencies = []
intensities = []
line_num = 0
with open(filepath) as f:
for line in f:
line += 1
if line is not None or line is not "" or line[0] is '#':
point = re.split(regex, line.strip())
try:
frequencies.append(float(point[1])) # get frequency
intensities.append(float(
point[7])) # get actual intensity (logx ^ x)
except IndexError:
print "IndexError in line: " + str(line_num)
except ValueError:
print "ValueError in line: " + str(line_num)
print "PEAKS!!" + str(len(frequencies))
if peaks is False:
# Determine Peaks
frequencies, intensities = peak_finder.peak_finder(
frequencies, intensities, 0.2)
# Store peaks into file
for i in range(0, len(frequencies)):
conn.execute(
'INSERT INTO peaks(mid, frequency, intensity) VALUES (?,?,?)',
(mid, frequencies[i], intensities[i])) # insert into peak table
# Commit Changes
conn.commit()
print "[ Added entry peaks ] "
def __import_ftbfile(conn, filepath, mid, peaks=False):
"""
Inheritently Private Function, determines peaks of .sp File and imports to database
:param conn: Database connection
:param filepath: Path to import file
:param mid: Molecule ID
:return:
"""
from analysis import peak_finder
import re
delimiters = ["ftmfreq:", "shots:", "dipole:", " ", "#intensity "]
regex = '|'.join((map(re.escape, delimiters)))
# Get data from file
frequencies = []
intensities = []
line_num = 0
with open(filepath) as f:
for line in f:
line += 1
if line is not None or line is not "" or line[0] is '#':
point = re.split(regex, line.strip())
try:
frequencies.append(float(point[1])) # get frequency
intensities.append(float(point[7])) # get actual intensity (logx ^ x)
except IndexError:
print "IndexError in line: " + str(line_num)
except ValueError:
print "ValueError in line: " + str(line_num)
print "PEAKS!!" + str(len(frequencies))
if peaks is False:
# Determine Peaks
frequencies, intensities = peak_finder.peak_finder(frequencies, intensities, 0.2)
# Store peaks into file
for i in range(0, len(frequencies)):
conn.execute('INSERT INTO peaks(mid, frequency, intensity) VALUES (?,?,?)',
(mid, frequencies[i], intensities[i])) # insert into peak table
# Commit Changes
conn.commit()
print "[ Added entry peaks ] "
def __import_txtfile(conn, filepath, mid, peaks=False):
"""
Inheritently Private Function, determines peaks of .sp File and imports to database
:param conn: Database connection
:param filepath: Path to import file
:param mid: Molecule ID
:return:
"""
from analysis import peak_finder
import re
delimiters = [" ", "\t", ",", ", "]
with open(filepath) as f:
data_string = f.read()
for delimiter in delimiters:
# Replace all types of delimiters into comma
# separated
data_string = data_string.replace(delimiter, ",")
with open(filepath + ".csv", "w+") as f:
f.write(data_string)
# Load in data as numpy array and skip the first line
data = np.loadtxt(filepath + ".csv",
dtype=float,
skiprows=1,
delimiter=",")
frequencies = data[:, 0]
intensities = data[:, 1]
if peaks is False:
# Determine Peaks
frequencies, intensities = peak_finder.peak_finder(
frequencies, intensities)
# Store peaks into file
for frequency, intensity in zip(frequencies, intensities):
conn.execute(
'INSERT INTO peaks(mid, frequency, intensity) VALUES (?,?,?)',
(mid, frequency, intensity)) # insert into peak table
# Commit Changes
conn.commit()
print "[ Added entry peaks ] "