def loadPeakMap(path=None):
""" loads mzXML, mzML and mzData files
If *path* is missing, a dialog for file selection is opened
instead.
"""
# local import in order to keep namespaces clean
import ms
import os.path
import sys
from pyopenms import MSExperiment, FileHandler
from libms.DataStructures import PeakMap
if isinstance(path, unicode):
path = path.encode(sys.getfilesystemencoding())
elif path is None:
path = ms.askForSingleFile(extensions="mzML mzXML mzData".split())
if path is None:
return None
# open-ms returns empty peakmap if file not exists, so we
# check ourselves:
if not os.path.exists(path):
raise Exception("file %s does not exist" % path)
if not os.path.isfile(path):
raise Exception("path %s is not a file" % path)
experiment = MSExperiment()
fh = FileHandler()
if sys.platform == "win32":
path = path.replace("/","\\") # needed for network shares
fh.loadExperiment(path, experiment)
return PeakMap.fromMSExperiment(experiment)
def loadPeakMap(path=None):
""" loads mzXML, mzML and mzData files
If *path* is missing, a dialog for file selection is opened
instead.
"""
# local import in order to keep namespaces clean
import os.path
import sys
from pyopenms import MSExperiment, FileHandler
from ..core.data_types import PeakMap
path = _prepare_path(path, extensions=["mzML", "mzXML", "mzData"])
if path is None:
return None
# open-ms returns empty peakmap if file not exists, so we
# check ourselves:
if not os.path.exists(path):
raise Exception("file %s does not exist" % path)
if not os.path.isfile(path):
raise Exception("path %s is not a file" % path)
experiment = MSExperiment()
fh = FileHandler()
if sys.platform == "win32":
path = path.replace("/", "\\") # needed for network shares
fh.loadExperiment(path, experiment)
return PeakMap.fromMSExperiment(experiment)
def read_ms1_experiment(filepath):
source_experiment = MSExperiment()
file_handler = FileHandler()
# bytes is required by `loadExperiment()` called below
typed_fp = filepath if isinstance(filepath, bytes) else filepath.encode()
file_handler.loadExperiment(typed_fp, source_experiment)
ms1_experiment = MSExperiment()
for spectrum in source_experiment:
if spectrum.getMSLevel() == 1:
ms1_experiment.addSpectrum(spectrum)
return ms1_experiment
def read_ms1_experiment(filepath):
# pylint: disable=import-outside-toplevel,no-name-in-module,import-error
from pyopenms import FileHandler, MSExperiment
source_experiment = MSExperiment()
file_handler = FileHandler()
# bytes is required by `loadExperiment()` called below
typed_fp = filepath if isinstance(filepath,
bytes) else filepath.encode()
file_handler.loadExperiment(typed_fp, source_experiment)
ms1_experiment = MSExperiment()
for spectrum in source_experiment:
if spectrum.getMSLevel() == 1:
ms1_experiment.addSpectrum(spectrum)
return ms1_experiment