def export_ascii(self, root_name, format='dat'):
"""
@summary: Exports the intensity matrix, retention time vector, and
m/z vector to the ascii format
By default, export_ascii("NAME") will create NAME.im.dat, NAME.rt.dat,
and NAME.mz.dat where these are the intensity matrix, retention
time vector, and m/z vector in tab delimited format. If format='csv',
the files will be in the CSV format, named NAME.im.csv, NAME.rt.csv,
and NAME.mz.csv.
@param root_name: Root name for the output files
@type root_name: StringType
@return: none
@rtype: NoneType
@author: Milica Ng
@author: Andrew Isaac
@author: Vladimir Likic
"""
if not is_str(root_name):
error("'root_name' is not a string")
if format == 'dat':
separator = " "
extension = ".dat"
elif format == 'csv':
separator = ","
extension = ".csv"
else:
error("unkown format '%s'. Only 'dat' or 'csv' supported" % format)
# export 2D matrix of intensities
vals = self.__intensity_matrix
save_data(root_name+'.im'+extension, vals, sep=separator)
# export 1D vector of m/z's, corresponding to rows of
# the intensity matrix
mass_list = self.__mass_list
save_data(root_name+'.mz'+extension, mass_list, sep=separator)
# export 1D vector of retention times, corresponding to
# columns of the intensity matrix
time_list = self.__time_list
save_data(root_name+'.rt'+extension, time_list, sep=separator)
def export_ascii(self, root_name, format='dat'):
"""
@summary: Exports the intensity matrix, retention time vector, and
m/z vector to the ascii format
By default, export_ascii("NAME") will create NAME.im.dat, NAME.rt.dat,
and NAME.mz.dat where these are the intensity matrix, retention
time vector, and m/z vector in tab delimited format. If format='csv',
the files will be in the CSV format, named NAME.im.csv, NAME.rt.csv,
and NAME.mz.csv.
@param root_name: Root name for the output files
@type root_name: StringType
@return: none
@rtype: NoneType
@author: Milica Ng
@author: Andrew Isaac
@author: Vladimir Likic
"""
if not is_str(root_name):
error("'root_name' is not a string")
if format == 'dat':
separator = " "
extension = ".dat"
elif format == 'csv':
separator = ","
extension = ".csv"
else:
error("unkown format '%s'. Only 'dat' or 'csv' supported" % format)
# export 2D matrix of intensities
vals = self.__intensity_matrix
save_data(root_name+'.im'+extension, vals, sep=separator)
# export 1D vector of m/z's, corresponding to rows of
# the intensity matrix
mass_list = self.__mass_list
save_data(root_name+'.mz'+extension, mass_list, sep=separator)
# export 1D vector of retention times, corresponding to
# columns of the intensity matrix
time_list = self.__time_list
save_data(root_name+'.rt'+extension, time_list, sep=separator)
def export_ascii(
self,
root_name: PathLike,
fmt: AsciiFiletypes = AsciiFiletypes.ASCII_DAT,
):
"""
Exports the intensity matrix, retention time vector, and m/z vector to the ascii format.
By default, export_ascii("NAME") will create NAME.im.dat, NAME.rt.dat,
and NAME.mz.dat where these are the intensity matrix, retention time
vector, and m/z vector in tab delimited format.
If ``format`` == ``<AsciiFiletypes.ASCII_CSV>``, the files will be in the CSV format, named
NAME.im.csv, NAME.rt.csv, and NAME.mz.csv.
:param root_name: Root name for the output files
:param fmt: Format of the output file, either ``<AsciiFiletypes.ASCII_DAT>`` or ``<AsciiFiletypes.ASCII_CSV>``
:authors: Milica Ng, Andrew Isaac, Vladimir Likic, Dominic Davis-Foster (pathlib support)
"""
if not is_path(root_name):
raise TypeError("'root_name' must be a string or a pathlib.Path object")
root_name = prepare_filepath(root_name, mkdirs=True)
fmt = AsciiFiletypes(fmt)
if fmt is AsciiFiletypes.ASCII_DAT:
separator = ' '
extension = "dat"
elif fmt is AsciiFiletypes.ASCII_CSV:
separator = ','
extension = "csv"
# export 2D matrix of intensities
vals = self._intensity_array
save_data(f"{root_name}.im.{extension}", vals, sep=separator)
# export 1D vector of m/z's, corresponding to rows of
# the intensity matrix
mass_list = self._mass_list
save_data(f"{root_name}.mz.{extension}", mass_list, sep=separator)
# export 1D vector of retention times, corresponding to
# columns of the intensity matrix
time_list = self._time_list
save_data(f"{root_name}.rt.{extension}", time_list, sep=separator)
# IntensityMatrix
# must build intensity matrix before accessing any intensity matrix methods.
# default, float masses with interval (bin interval) of one from min mass
print "default intensity matrix, bin interval = 1, boundary +/- 0.5"
im = build_intensity_matrix(data)
#
# Saving data
#
# save the intensity matrix values to a file
mat = im.get_matrix_list()
print "saving intensity matrix intensity values..."
save_data("output/im.dat", mat)
# Export the entire IntensityMatrix as CSV. This will create
# data.im.csv, data.mz.csv, and data.rt.csv where
# these are the intensity matrix, retention time
# vector, and m/z vector in the CSV format
print "exporting intensity matrix data..."
im.export_ascii("output/data")
# Export the entire IntensityMatrix as LECO CSV. This is
# useful for import into AnalyzerPro
print "exporting intensity matrix data to LECO CSV format..."
im.export_leco_csv("output/data_leco.csv")
#
# Import saved data
# IntensityMatrix
# must build intensity matrix before accessing any intensity matrix methods.
# default, float masses with interval (bin interval) of one from min mass
print "default intensity matrix, bin interval = 1, boundary +/- 0.5"
im = build_intensity_matrix(data)
#
# Saving data
#
# save the intensity matrix values to a file
mat = im.get_matrix_list()
print "saving intensity matrix intensity values..."
save_data("output/im.dat", mat)
# Export the entire IntensityMatrix as CSV. This will create
# data.im.csv, data.mz.csv, and data.rt.csv where
# these are the intensity matrix, retention time
# vector, and m/z vector in the CSV format
print "exporting intensity matrix data..."
im.export_ascii("output/data")
# Export the entire IntensityMatrix as LECO CSV. This is
# useful for import into AnalyzerPro
print "exporting intensity matrix data to LECO CSV format..."
im.export_leco_csv("output/data_leco.csv")
#
# Import saved data