def importCoordinates(self, fileName, addCoordinate):
if exists(fileName):
ext = getExt(fileName)
if ext == ".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 particleSize")
size = md.getValue(MDL_PICKING_PARTICLE_SIZE, md.firstObject())
if size is None:
print ">>> WARNING: Error parsing coordinate file: %s" % fileName
print " Skipping this file."
else:
half = size / 2
for objId in md:
x = md.getValue(MDL_XCOOR, objId)
y = md.getValue(MDL_YCOOR, objId)
coord = Coordinate()
coord.setPosition(x+half, y+half)
addCoordinate(coord)
else:
raise Exception('Unknown extension "%s" to import Eman coordinates' % ext)
def getBoxSize(self, coordFile):
""" Try to infer the box size from the given coordinate file.
In the case of .box files, the size is the 3rd column
In the case of .json files, we will look for file
e2boxercache/base.json
"""
if coordFile.endswith('.box'):
md = MetaData()
md.readPlain(coordFile, "xcoor ycoor particleSize")
return md.getValue(MDL_PICKING_PARTICLE_SIZE, md.firstObject())
elif coordFile.endswith('.json'):
infoDir = pwutils.dirname(coordFile)
# Still go one level up of info dir
jsonBase = pwutils.join(pwutils.dirname(infoDir), 'e2boxercache',
'base.json')
jsonBase2 = pwutils.join(infoDir, 'project.json')
if pwutils.exists(jsonBase):
jsonDict = loadJson(jsonBase)
if jsonDict.has_key('box_size'):
return int(jsonDict["box_size"])
elif pwutils.exists(jsonBase2):
jsonDict = loadJson(jsonBase2)
if jsonDict.has_key('global.boxsize'):
return int(jsonDict["global.boxsize"])
return None
def getBoxSize(self, coordFile):
""" Try to infer the box size from the given coordinate file.
In the case of .box files, the size is the 3rd column
In the case of .json files, we will look for file e2boxercache/base.json
"""
if coordFile.endswith('.box'):
md = MetaData()
md.readPlain(coordFile, "xcoor ycoor particleSize")
return md.getValue(MDL_PICKING_PARTICLE_SIZE, md.firstObject())
elif coordFile.endswith('.json'):
infoDir = dirname(coordFile)
# Still go one level up of info dir
jsonBase = join(dirname(infoDir), 'e2boxercache', 'base.json')
if exists(jsonBase):
jsonDict = loadJson(jsonBase)
if jsonDict.has_key('box_size'):
return int(jsonDict["box_size"])
return None
