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 loadCSV(path=None, sep=";", keepNone = False, **specialFormats):
# local import in order to keep namespaces clean
import ms
import csv, os.path, sys, re
from libms.DataStructures.Table import (Table, common_type_for,\
bestConvert, guessFormatFor)
if isinstance(path, unicode):
path = path.encode(sys.getfilesystemencoding())
elif path is None:
path = ms.askForSingleFile(extensions=["csv"])
if path is None:
return None
with open(path,"r") as fp:
# remove clutter at right margin
reader = csv.reader(fp, delimiter=sep)
# reduce multiple spaces to single underscore
colNames = [ re.sub(" +", "_", n.strip()) for n in reader.next()]
if keepNone:
conv = bestConvert
else:
conv = lambda v: None if v=="None" else bestConvert(v)
rows = [ [conv(c.strip()) for c in row] for row in reader]
columns = [[row[i] for row in rows] for i in range(len(colNames))]
types = [common_type_for(col) for col in columns]
#defaultFormats = {float: "%.2f", str: "%s", int: "%d"}
formats = dict([(name, guessFormatFor(name,type_)) for (name, type_)\
in zip(colNames, types)])
formats.update(specialFormats)
formats = [formats[n] for n in colNames]
title = os.path.basename(path)
meta = dict(loaded_from=os.path.abspath(path))
return Table._create(colNames, types, formats, rows, title, meta)
def loadTable(path=None):
""" load pickled table
If *path* is missing, a dialog for file selection is opened
instead.
"""
# local import in order to keep namespaces clean
import ms
import sys
from libms.DataStructures.Table import Table, compressPeakMaps
if isinstance(path, unicode):
path = path.encode(sys.getfilesystemencoding())
elif path is None:
path = ms.askForSingleFile(extensions=["table"])
if path is None:
return None
result = Table.load(path)
compressPeakMaps(result)
return result
