def write(self, file_root):
"""
@summary: Writes the entire raw data to two files, one
'file_root'.I.csv (intensities) and 'file_root'.mz.csv
(m/z values).
This method writes two CSV files, containing intensities
and corresponding m/z values. In general these are not
two-dimensional matrices, because different scans may
have different number of m/z values recorded.
@param file_root: The root for the output file names
@type file_root: StringType
@author: Vladimir Likic
"""
if not is_str(file_root):
error("'file_root' must be a string")
file_name1 = file_root + ".I.csv"
file_name2 = file_root + ".mz.csv"
print " -> Writing intensities to '%s'" % ( file_name1 )
print " -> Writing m/z values to '%s'" % ( file_name2 )
fp1 = open_for_writing(file_name1)
fp2 = open_for_writing(file_name2)
for ii in range(len(self.__scan_list)):
scan = self.__scan_list[ii]
intensity_list = scan.get_intensity_list()
mass_list = scan.get_mass_list()
for ii in range(len(intensity_list)):
v = intensity_list[ii]
if ii == 0:
fp1.write("%.4f" % (v))
else:
fp1.write(",%.4f" % (v))
fp1.write("\n")
for ii in range(len(mass_list)):
v = mass_list[ii]
if ii == 0:
fp2.write("%.4f" % (v))
else:
fp2.write(",%.4f" % (v))
fp2.write("\n")
close_for_writing(fp1)
close_for_writing(fp2)
def write(self, file_root):
"""
@summary: Writes the entire raw data to two files, one
'file_root'.I.csv (intensities) and 'file_root'.mz.csv
(m/z values).
This method writes two CSV files, containing intensities
and corresponding m/z values. In general these are not
two-dimensional matrices, because different scans may
have different number of m/z values recorded.
@param file_root: The root for the output file names
@type file_root: StringType
@author: Vladimir Likic
"""
if not is_str(file_root):
error("'file_root' must be a string")
file_name1 = file_root + ".I.csv"
file_name2 = file_root + ".mz.csv"
print " -> Writing intensities to '%s'" % ( file_name1 )
print " -> Writing m/z values to '%s'" % ( file_name2 )
fp1 = open_for_writing(file_name1)
fp2 = open_for_writing(file_name2)
for ii in range(len(self.__scan_list)):
scan = self.__scan_list[ii]
intensity_list = scan.get_intensity_list()
mass_list = scan.get_mass_list()
for ii in range(len(intensity_list)):
v = intensity_list[ii]
if ii == 0:
fp1.write("%.4f" % (v))
else:
fp1.write(",%.4f" % (v))
fp1.write("\n")
for ii in range(len(mass_list)):
v = mass_list[ii]
if ii == 0:
fp2.write("%.4f" % (v))
else:
fp2.write(",%.4f" % (v))
fp2.write("\n")
close_for_writing(fp1)
close_for_writing(fp2)
def write_intensities_stream(self, file_name):
"""
@summary: Writes all intensities to a file
@param file_name: Output file name
@type file_name: StringType
This function loop over all scans, and for each scan
writes intensities to the file, one intenisity per
line. Intensities from different scans are joined
without any delimiters.
@author: Vladimir Likic
"""
if not is_str(file_name):
error("'file_name' must be a string")
N = len(self.__scan_list)
print" -> Writing scans to a file"
fp = open_for_writing(file_name)
for ii in range(len(self.__scan_list)):
scan = self.__scan_list[ii]
intensities = scan.get_intensity_list()
for I in intensities:
fp.write("%8.4f\n" % ( I ) )
close_for_writing(fp)
def write(self, file_name, minutes=False):
"""
@summary: Writes the ion chromatogram to the specified file
@param file_name: Output file name
@type file_name: StringType
@param minutes: A boolean value indicating whether to write
time in minutes
@type minutes: BooleanType
@return: none
@rtype: NoneType
@author: Lewis Lee
@author: Vladimir Likic
"""
if not is_str(file_name):
error("'file_name' must be a string")
fp = open_for_writing(file_name)
time_list = copy.deepcopy(self.__time_list)
if minutes:
for ii in range(len(time_list)):
time_list[ii] = time_list[ii]/60.0
for ii in range(len(time_list)):
fp.write("%8.4f %#.6e\n" % (time_list[ii], self.__ia[ii]))
close_for_writing(fp)
def write_intensities_stream(self, file_name):
"""
@summary: Writes all intensities to a file
@param file_name: Output file name
@type file_name: StringType
This function loop over all scans, and for each scan
writes intensities to the file, one intenisity per
line. Intensities from different scans are joined
without any delimiters.
@author: Vladimir Likic
"""
if not is_str(file_name):
error("'file_name' must be a string")
N = len(self.__scan_list)
print" -> Writing scans to a file"
fp = open_for_writing(file_name)
for ii in range(len(self.__scan_list)):
scan = self.__scan_list[ii]
intensities = scan.get_intensity_list()
for I in intensities:
fp.write("%8.4f\n" % ( I ) )
close_for_writing(fp)
def write(self, file_name, minutes=False):
"""
@summary: Writes the ion chromatogram to the specified file
@param file_name: Output file name
@type file_name: StringType
@param minutes: A boolean value indicating whether to write
time in minutes
@type minutes: BooleanType
@return: none
@rtype: NoneType
@author: Lewis Lee
@author: Vladimir Likic
"""
if not is_str(file_name):
error("'file_name' must be a string")
fp = open_for_writing(file_name)
time_list = copy.deepcopy(self.__time_list)
if minutes:
for ii in range(len(time_list)):
time_list[ii] = time_list[ii]/60.0
for ii in range(len(time_list)):
fp.write("%8.4f %#.6e\n" % (time_list[ii], self.__ia[ii]))
close_for_writing(fp)
def export_leco_csv(self, file_name):
"""
@summary: Exports data in LECO CSV format
@param file_name: File name
@type file_name: StringType
@return: none
@rtype: NoneType
@author: Andrew Isaac
@author: Vladimir Likic
"""
if not is_str(file_name):
error("'file_name' is not a string")
mass_list = self.__mass_list
time_list = self.__time_list
vals = self.__intensity_matrix
fp = open_for_writing(file_name)
# Format is text header with:
# "Scan","Time",...
# and the rest is "TIC" or m/z as text, i.e. "50","51"...
# The following lines are:
# scan_number,time,value,value,...
# scan_number is an int, rest seem to be fixed format floats.
# The format is 0.000000e+000
# write header
fp.write("\"Scan\",\"Time\"")
for ii in mass_list:
if is_number(ii):
fp.write(",\"%d\"" % int(ii))
else:
error("mass list datum not a number")
fp.write("\r\n") # windows CR/LF
# write lines
for ii in range(len(time_list)):
fp.write("%s,%#.6e" % (ii, time_list[ii]))
for jj in range(len(vals[ii])):
if is_number(vals[ii][jj]):
fp.write(",%#.6e" % (vals[ii][jj]))
else:
error("datum not a number")
fp.write("\r\n")
close_for_writing(fp)
def export_leco_csv(self, file_name):
"""
@summary: Exports data in LECO CSV format
@param file_name: File name
@type file_name: StringType
@return: none
@rtype: NoneType
@author: Andrew Isaac
@author: Vladimir Likic
"""
if not is_str(file_name):
error("'file_name' is not a string")
mass_list = self.__mass_list
time_list = self.__time_list
vals = self.__intensity_matrix
fp = open_for_writing(file_name)
# Format is text header with:
# "Scan","Time",...
# and the rest is "TIC" or m/z as text, i.e. "50","51"...
# The following lines are:
# scan_number,time,value,value,...
# scan_number is an int, rest seem to be fixed format floats.
# The format is 0.000000e+000
# write header
fp.write("\"Scan\",\"Time\"")
for ii in mass_list:
if is_number(ii):
fp.write(",\"%d\"" % int(ii))
else:
error("mass list datum not a number")
fp.write("\r\n") # windows CR/LF
# write lines
for ii in range(len(time_list)):
fp.write("%s,%#.6e" % (ii, time_list[ii]))
for jj in range(len(vals[ii])):
if is_number(vals[ii][jj]):
fp.write(",%#.6e" % (vals[ii][jj]))
else:
error("datum not a number")
fp.write("\r\n")
close_for_writing(fp)
