def getDefaultBoxSize(self):
""" This function is used by the wizard to estimate the box size. """
boxSize = None
ci = self.getImportClass()
if hasattr(ci, 'getBoxSize'):
boxSize = ci.getBoxSize([f for f, _ in self.iterFiles()][0])
if boxSize is not None and self.scale != 1.:
boxSize = int(boxSize * self.scale.get())
return boxSize
boxSize = 100
importFrom = self.getImportFrom()
scale = self.scale.get()
if importFrom == ProtImportCoordinates.IMPORT_FROM_XMIPP:
configfile = join(self.filesPath.get(), 'config.xmd')
existsConfig = exists(configfile)
if existsConfig:
md = xmipp.MetaData('properties@' + configfile)
configobj = md.firstObject()
boxSize = md.getValue(xmipp.MDL_PICKING_PARTICLE_SIZE, configobj)
if importFrom == ProtImportCoordinates.IMPORT_FROM_EMAN:
# Read the boxSize from the e2boxercache/base.json
jsonFnbase = join(self.filesPath.get(), 'e2boxercache', 'base.json')
from pyworkflow.em.packages.eman2 import loadJson
jsonBoxDict = loadJson(jsonFnbase)
boxSize = int(jsonBoxDict["box_size"])
boxSize = (int)(boxSize * scale)
return boxSize
def getDefaultBoxSize(self):
""" This function is used by the wizard to estimate the box size. """
boxSize = None
ci = self.getImportClass()
if hasattr(ci, 'getBoxSize'):
boxSize = ci.getBoxSize([f for f, _ in self.iterFiles()][0])
if boxSize is not None and self.scale != 1.:
boxSize = int(boxSize * self.scale.get())
return boxSize
boxSize = 100
importFrom = self.getImportFrom()
scale = self.scale.get()
if importFrom == ProtImportCoordinates.IMPORT_FROM_XMIPP:
configfile = join(self.filesPath.get(), 'config.xmd')
existsConfig = exists(configfile)
if existsConfig:
md = xmipp.MetaData('properties@' + configfile)
configobj = md.firstObject()
boxSize = md.getValue(xmipp.MDL_PICKING_PARTICLE_SIZE,
configobj)
if importFrom == ProtImportCoordinates.IMPORT_FROM_EMAN:
# Read the boxSize from the e2boxercache/base.json
jsonFnbase = join(self.filesPath.get(), 'e2boxercache',
'base.json')
from pyworkflow.em.packages.eman2 import loadJson
jsonBoxDict = loadJson(jsonFnbase)
boxSize = int(jsonBoxDict["box_size"])
boxSize = (int)(boxSize * scale)
return boxSize
def importCoordinates(self, fileName, addCoordinate):
if exists(fileName):
ext = getExt(fileName)
if ext == ".json":
print "importando un json"
jsonPosDict = loadJson(fileName)
if jsonPosDict.has_key("boxes"):
boxes = jsonPosDict["boxes"]
for box in boxes:
x, y = box[:2]
coord = Coordinate()
coord.setPosition(x, y)
addCoordinate(coord)
elif ext == ".box":
md = MetaData()
md.readPlain(fileName, 'xcoor ycoor xSize ySize')
for objId in md:
x = md.getValue(MDL_XCOOR, objId)
y = md.getValue(MDL_YCOOR, objId)
coord = Coordinate()
coord.setPosition(x, y)
addCoordinate(coord)
else:
print "importando un queseyo"
def readCoordinates(mic, fileName, coordsSet):
if exists(fileName):
jsonPosDict = loadJson(fileName)
if jsonPosDict.has_key("boxes"):
boxes = jsonPosDict["boxes"]
for box in boxes:
x, y = box[:2]
coord = Coordinate()
coord.setPosition(x, y)
coord.setMicrograph(mic)
coordsSet.append(coord)
def readSetOfCoordinates(workDir, micSet, coordSet):
""" Read from Eman .json files.
It is expected a file named: base.json under the workDir.
Params:
workDir: where the Eman boxer output files are located.
micSet: the SetOfMicrographs to associate the .json, which
name should be the same of the micrographs.
coordSet: the SetOfCoordinates that will be populated.
"""
# Read the boxSize from the e2boxercache/base.json
jsonFnbase = join(workDir, 'e2boxercache', 'base.json')
jsonBoxDict = loadJson(jsonFnbase)
size = int(jsonBoxDict["box_size"])
jsonFninfo = join(workDir, 'info/')
for mic in micSet:
micPosFn = ''.join(glob.glob(jsonFninfo + '*' + removeBaseExt(mic.getFileName()) + '_info.json'))
readCoordinates(mic, micPosFn, coordSet)
coordSet.setBoxSize(size)
def getDefaultBoxSize(self):
import xmipp
boxSize = 100
importFrom = self.getImportFrom()
scale = self.scale.get()
if importFrom == ProtImportCoordinates.IMPORT_FROM_XMIPP:
configfile = join(self.filesPath.get(), 'config.xmd')
existsConfig = exists(configfile)
if existsConfig:
md = xmipp.MetaData('properties@' + configfile)
configobj = md.firstObject()
boxSize = md.getValue(xmipp.MDL_PICKING_PARTICLE_SIZE, configobj)
if importFrom == ProtImportCoordinates.IMPORT_FROM_EMAN:
# Read the boxSize from the e2boxercache/base.json
jsonFnbase = join(self.filesPath.get(), 'e2boxercache', 'base.json')
from pyworkflow.em.packages.eman2 import loadJson
jsonBoxDict = loadJson(jsonFnbase)
boxSize = int(jsonBoxDict["box_size"])
boxSize = (int)(boxSize * scale)
return boxSize