def save(self, filename):
"""
Save time vector states and inputs to file filename
"""
from itertools import chain as ch
f = open(filename, 'w')
f.write('Time, ' + ', '.join(ch(self.sol['states'].keys())) + ', ' +
', '.join(ch(self.sol['inputs'].keys())) + '\n')
np.savetxt(f, np.vstack((self.sol['t'],
self.sol['states'].values(),
self.sol['inputs'].values())).T,
delimiter=', ')
f.close()
def save(self, filename):
"""
Save time vector states and inputs to file filename
"""
from itertools import chain as ch
f = open(filename, 'w')
f.write('Time, ' + ', '.join(ch(self.sol['states'].keys())) + ', ' +
', '.join(ch(self.sol['inputs'].keys())) + '\n')
np.savetxt(f,
np.vstack((self.sol['t'], self.sol['states'].values(),
self.sol['inputs'].values())).T,
delimiter=', ')
f.close()
def __init__(self, filename):
self.filename = filename
self.mzid = open(filename, "r")
self.tree = xml.parse(self.mzid)
self.root = self.tree.getroot()
assert "mzIdentML" in self.root.tag, "%s does not appear to be a valid mzIdentML file."
if self.root.get("version") != "1.1.0":
print((
"Multiplierz mzIdentML reader was written against the specification "
"for mzIdentML version 1.1.0; this file is version %s, so there may "
"be discrepancies in the results." % self.root.get("version")))
self.getSourceMode()
self.pfx = self.root.tag[:-9] # Take out "mzIdentML", when present.
# (There's probably a more proper way to do this!)
# The below be done as-needed
# or at least in a single iterator (but it seems fast enough.)
self.parentMap = dict(
sum([[(c.get("id"), p.get("id"))
for c in p if c.get("id") and p.get("id")]
for p in ch(
self.tree.getiterator(self.pfx + "ProteinAmbiguityGroup"),
self.tree.getiterator(self.pfx +
"SpectrumIdentificationResult"))],
[]))
proteinElements = self.root.getiterator(self.pfx +
"ProteinDetectionHypothesis")
self.proteinLookup = {prot.get("id"): prot for prot in proteinElements}
spectrumElements = self.root.getiterator(
self.pfx + "SpectrumIdentificationResult")
self.spectrumLookup = {
spec.get("id"): spec
for spec in spectrumElements
}
pepIdElements = self.root.getiterator(self.pfx +
"SpectrumIdentificationItem")
self.pepIdLookup = {pepid.get("id"): pepid for pepid in pepIdElements}
evidenceElements = self.root.getiterator(self.pfx + "PeptideEvidence")
self.evidenceLookup = {evi.get("id"): evi for evi in evidenceElements}
dbElements = self.root.getiterator(self.pfx + "DBSequence")
self.dbLookup = {db.get("id"): db for db in dbElements}
peptideElements = self.root.getiterator(self.pfx + "Peptide")
self.peptideLookup = {pep.get("id"): pep for pep in peptideElements}
fileElements = self.root.getiterator(self.pfx + "SpectraData")
self.fileLookup = {data.get("id"): data for data in fileElements}
self.dataFileScans = {}
self.filePointers = {}
def __init__(self, filename):
self.filename = filename
self.mzid = open(filename, "r")
self.tree = xml.parse(self.mzid)
self.root = self.tree.getroot()
assert "mzIdentML" in self.root.tag, "%s does not appear to be a valid mzIdentML file."
if self.root.get("version") != "1.1.0":
print ("Multiplierz mzIdentML reader was written against the specification "
"for mzIdentML version 1.1.0; this file is version %s, so there may "
"be discrepancies in the results." % self.root.get("version"))
self.pfx = self.root.tag[:-9] # Take out "mzIdentML"
#print "Indexing file..." # Really this could all be done on an as-needed basis.
self.parentMap = dict(sum([[(c.get("id"),p.get("id")) for c in p if c.get("id") and p.get("id")]
for p in ch(self.tree.getiterator(self.pfx + "ProteinAmbiguityGroup"),
self.tree.getiterator(self.pfx + "SpectrumIdentificationResult"))], []))
proteinElements = self.root.getiterator(self.pfx + "ProteinDetectionHypothesis")
#self.proteinLookup = {prot.get("id"):prot for prot in proteinElements}
self.proteinLookup = dict([(prot.get("id"), prot) for prot in proteinElements])
spectrumElements = self.root.getiterator(self.pfx + "SpectrumIdentificationResult")
#self.spectrumLookup = {spec.get("id"):spec for spec in spectrumElements}
self.spectrumLookup = dict([(spec.get("id"), spec) for spec in spectrumElements])
pepIdElements = self.root.getiterator(self.pfx + "SpectrumIdentificationItem")
#self.pepIdLookup = {pepid.get("id"):pepid for pepid in pepIdElements}
self.pepIdLookup = dict([(pepid.get("id"), pepid) for pepid in pepIdElements])
evidenceElements = self.root.getiterator(self.pfx + "PeptideEvidence")
#self.evidenceLookup = {evi.get("id"):evi for evi in evidenceElements}
self.evidenceLookup = dict([(evi.get("id"), evi) for evi in evidenceElements])
dbElements = self.root.getiterator(self.pfx + "DBSequence")
#self.dbLookup = {db.get("id"):db for db in dbElements}
self.dbLookup = dict([(db.get("id"), db) for db in dbElements])
peptideElements = self.root.getiterator(self.pfx + "Peptide")
#self.peptideLookup = {pep.get("id"):pep for pep in peptideElements}
self.peptideLookup = dict([(pep.get("id"), pep) for pep in peptideElements])
fileElements = self.root.getiterator(self.pfx + "SpectraData")
#self.fileLookup = {data.get("id"):data for data in fileElements}
self.fileLookup = dict([(data.get("id"), data) for data in fileElements])
#print "Indexing complete."
self.dataFileScans = {}
self.filePointers = {}
def handle_photo(photo_path, method, frame_count=None, full_path=False):
paths = ['{}/{}'.format(photo_path, file_path) for file_path in os.listdir(photo_path)]
files = ['{}/{}'.format(p, f) for p in ifil(os.path.isdir, paths) for f in os.listdir(p)]
files = list(ch(files, list(ifil(os.path.isfile, paths))))
finalimage = None
result_name = '{count}'.format(count=frame_count) if frame_count else ''
for i, file_path in enumerate(files):
what = imghdr.what(file_path)
if what in [None, 'gif']:
files.pop(i)
continue
currentimage = Image.open(file_path)
if what in ['png']:
try:
bg = Image.new("RGB", currentimage.size, (255, 255, 255))
bg.paste(currentimage, mask=currentimage)
currentimage = bg
except ValueError:
pass
if finalimage is None:
finalimage = currentimage
continue
if frame_count and i != 1 and i % frame_count:
continue
if method == 'both':
lighter = handle_photo(photo_path, 'lighter', frame_count, full_path=True)
darker = handle_photo(photo_path, 'darker', frame_count, full_path=True)
l_img = Image.open(lighter)
d_img = Image.open(darker)
res = ImageChops.blend(l_img, d_img, 0.5)
path, name = save_result(res, photo_path, result_name, method)
return name
if method == 'diff':
if i < 1:
continue
prev = Image.open(files[i - 1])
diff = ImageChops.difference(currentimage, prev)
finalimage = ImageChops.add(finalimage, diff)
if method == 'lighter':
finalimage = ImageChops.lighter(finalimage, currentimage)
if method == 'darker':
finalimage = ImageChops.darker(finalimage, currentimage)
path, name = save_result(finalimage, photo_path, result_name, method)
return path if full_path else name