def test_Parsing(self):
bibtex = """
@article{delaRosaTrevin2013,
title = "Xmipp 3.0: An improved software suite for image processing in electron microscopy ",
journal = "Journal of Structural Biology ",
volume = "184",
number = "2",
pages = "321 - 328",
year = "2013",
issn = "1047-8477",
doi = "http://dx.doi.org/10.1016/j.jsb.2013.09.015",
url = "http://www.sciencedirect.com/science/article/pii/S1047847713002566",
author = "J.M. de la Rosa-Trevín and J. Otón and R. Marabini and A. Zaldívar and J. Vargas and J.M. Carazo and C.O.S. Sorzano",
keywords = "Electron microscopy, Single particles analysis, Image processing, Software package "
}
@incollection{Sorzano2013,
title = "Semiautomatic, High-Throughput, High-Resolution Protocol for Three-Dimensional Reconstruction of Single Particles in Electron Microscopy",
booktitle = "Nanoimaging",
year = "2013",
isbn = "978-1-62703-136-3",
volume = "950",
series = "Methods in Molecular Biology",
editor = "Sousa, Alioscka A. and Kruhlak, Michael J.",
doi = "10.1007/978-1-62703-137-0_11",
url = "http://dx.doi.org/10.1007/978-1-62703-137-0_11",
publisher = "Humana Press",
keywords = "Single particle analysis; Electron microscopy; Image processing; 3D reconstruction; Workflows",
author = "Sorzano, CarlosOscar and Rosa Trevín, J.M. and Otón, J. and Vega, J.J. and Cuenca, J. and Zaldívar-Peraza, A. and Gómez-Blanco, J. and Vargas, J. and Quintana, A. and Marabini, Roberto and Carazo, JoséMaría",
pages = "171-193",
}
"""
prettyDict(utils.parseBibTex(bibtex))
def main():
# Get arguments.
args = get_parser().parse_args()
setObj = EMSet(filename=args.setFile)
firstItem = setObj.getFirstItem()
root = pwutils.findRootFrom(args.setFile, firstItem.getFileName())
print("ROOT: ", root)
if args.output_text:
with open(args.output, 'w') as f:
for movie in setObj:
f.write('%s\n' % movie.getFileName())
elif args.print:
for item in setObj:
print(item.getFileName())
elif args.copy:
for item in setObj:
fn = os.path.join(root, item.getFileName())
print('Copying %s to %s' % (fn, args.output))
pwutils.copyFile(fn, args.output)
elif args.check_dims:
from pwem.emlib.image import ImageHandler
ih = ImageHandler()
counter = {}
for item in setObj:
fn = os.path.join(root, item.getFileName())
dims = ih.getDimensions(fn)
counter[dims] = 1 if dims not in counter else counter[dims] + 1
print('%s: %s' % (os.path.basename(fn), dims))
pwutils.prettyDict(counter)
def exportParticlesStep(self, particlesId):
""" Create the input file in STAR format as expected by Relion.
If the input particles comes from Relion, just link the file.
"""
imgSet = self.inputParticles.get()
self._stackType = self.stackType.get()
self._ih = em.ImageHandler()
self._stackDict = {}
particlesPath = self._getPath('Particles')
pwutils.cleanPath(particlesPath)
pwutils.makePath(particlesPath)
alignType = imgSet.getAlignment() if self.useAlignment else em.ALIGN_NONE
# Create links to binary files and write the relion .star file
writeSetOfParticles(imgSet, self._getPath("particles.star"),
outputDir=self._getExtraPath(),
alignType=alignType,
postprocessImageRow=self._postprocessImageRow,
fillMagnification=True)
pwutils.prettyDict(self._stackDict)
def test_Parsing(self):
bibtex = """
@article{delaRosaTrevin2013,
title = "Xmipp 3.0: An improved software suite for image processing in electron microscopy ",
journal = "Journal of Structural Biology ",
volume = "184",
number = "2",
pages = "321 - 328",
year = "2013",
issn = "1047-8477",
doi = "http://dx.doi.org/10.1016/j.jsb.2013.09.015",
url = "http://www.sciencedirect.com/science/article/pii/S1047847713002566",
author = "J.M. de la Rosa-Trevín and J. Otón and R. Marabini and A. Zaldívar and J. Vargas and J.M. Carazo and C.O.S. Sorzano",
keywords = "Electron microscopy, Single particles analysis, Image processing, Software package "
}
@incollection{Sorzano2013,
title = "Semiautomatic, High-Throughput, High-Resolution Protocol for Three-Dimensional Reconstruction of Single Particles in Electron Microscopy",
booktitle = "Nanoimaging",
year = "2013",
isbn = "978-1-62703-136-3",
volume = "950",
series = "Methods in Molecular Biology",
editor = "Sousa, Alioscka A. and Kruhlak, Michael J.",
doi = "10.1007/978-1-62703-137-0_11",
url = "http://dx.doi.org/10.1007/978-1-62703-137-0_11",
publisher = "Humana Press",
keywords = "Single particle analysis; Electron microscopy; Image processing; 3D reconstruction; Workflows",
author = "Sorzano, CarlosOscar and Rosa Trevín, J.M. and Otón, J. and Vega, J.J. and Cuenca, J. and Zaldívar-Peraza, A. and Gómez-Blanco, J. and Vargas, J. and Quintana, A. and Marabini, Roberto and Carazo, JoséMaría",
pages = "171-193",
}
"""
f = StringIO()
f.write(bibtex)
f.seek(0, 0)
parser = BibTexParser(f)
from pyworkflow.utils import prettyDict
prettyDict(parser.get_entry_dict())
def exportParticlesStep(self, particlesId):
""" Create the input file in STAR format as expected by Relion.
If the input particles comes from Relion, just link the file.
"""
imgSet = self.inputParticles.get()
self._stackType = self.stackType.get()
self._ih = em.ImageHandler()
self._stackDict = {}
particlesPath = self._getPath('Particles')
pwutils.cleanPath(particlesPath)
pwutils.makePath(particlesPath)
alignType = imgSet.getAlignment(
) if self.useAlignment else em.ALIGN_NONE
# Create links to binary files and write the relion .star file
writeSetOfParticles(imgSet,
self._getPath("particles.star"),
outputDir=self._getExtraPath(),
alignType=alignType,
postprocessImageRow=self._postprocessImageRow,
fillMagnification=True)
pwutils.prettyDict(self._stackDict)
def checkPlugins():
""" Discover all plugins and print some info.
"""
plugins = Domain.getPlugins()
env = createEnvironment()
print("Plugins:")
for k, plugin in plugins.iteritems():
print("-", plugin.__name__)
plugin.Plugin.defineBinaries(env)
print("\nDefined binaries: ")
print(env.printHelp())
if args.verbosity > 0:
print("Objects")
pwutils.prettyDict(Domain.getObjects())
print("Protocols")
pwutils.prettyDict(Domain.getProtocols())
print("Viewers")
pwutils.prettyDict(Domain.getViewers())
dataFn = getDataFile(SESSIONS_FILE)
sMan = SessionManager(dataFn)
sessionsSet = sMan.getSessions()
counters = sessionsSet.counters.get()
print("Counters: ")
def cmpKey(key1, key2):
if key1 == key2:
return 0
l1, l2 = len(key1), len(key2)
if l1 == l2:
return -1 if key1 < key2 else 1
return -1 if l1 < l2 else 1
if '--as-params' in sys.argv:
params = []
keys = sorted(counters.keys())
for k in keys:
v = counters[k]
params.append({"label": k, "value": v})
form = {"params": params}
print(json.dumps(form, indent=4))
else:
pwutils.prettyDict(counters)
'cem': 0,
'fac': 0,
'sll': 0,
'dbb': 0,
'mmk': 0
}
}
wrongGroups = []
for r in reservations:
d = stats[r.resource.get()]
group = r.user.getGroup()
if r.isNationalFacility():
d['cem'] += r.getTotalDays()
else:
if group not in d:
wrongGroups.append((group, r.username.get()))
else:
d[group] += r.getTotalDays()
printReservations(reservations)
print("Reservations: %d" % len(reservations))
pwutils.prettyDict(stats)
if wrongGroups:
print("ERROR: Wrong groups: ")
for group, username in wrongGroups:
print(" group: '%s', user: %s" % (group, username))
if len(sys.argv) > 2:
outputStar = sys.argv[2]
else:
outputStar = pwutils.removeExt(inputStar) + '_existing.star'
outputMd = md.MetaData()
fnDict = {}
index = None
IMG = 'rlnImageName'
MIC = 'rlnMicrographName'
for row in md.iterRows(inputStar):
label = IMG if row.hasLabel(IMG) else MIC
fn = row.getValue(label)
if '@' in fn:
index, fn = fn.split('@')
if fn not in fnDict:
fnDict[fn] = os.path.exists(fn)
# Copy the item to the output md if the filename exists
if fnDict[fn]:
row.addToMd(outputMd)
print "Writing output to: %s" % outputStar
outputMd.write(outputStar)
pwutils.prettyDict(fnDict)
return ''
n = len(sys.argv)
if n > 4:
usage("Incorrect number of input parameters")
if n == 1: # List all plugins
plugins = Domain.getPlugins()
print("Plugins:")
for k, v in iteritems(plugins):
print("-", k)
print("Objects")
pwutils.prettyDict(Domain.getObjects())
print("Protocols")
pwutils.prettyDict(Domain.getProtocols())
print("Viewers")
pwutils.prettyDict(Domain.getViewers())
elif n == 2:
if sys.argv[1] in ['-h', '--help', 'help']:
usage()
pluginName = sys.argv[1]
plugin = Domain.getPlugin(pluginName)
print("Plugin: %s" % pluginName)
for subName in [