def runObjectCommand(self, cmd, inputStrId, objStrId):
try:
objId = int(objStrId)
project = self.project
if os.path.isfile(inputStrId) and os.path.exists(inputStrId):
from pwem.utils import loadSetFromDb
inputObj = loadSetFromDb(inputStrId)
else:
inputId = int(inputStrId)
inputObj = project.mapper.selectById(inputId)
func = self._OBJECT_COMMANDS.get(cmd, None)
if func is None:
print("Error, command '%s' not found. " % cmd)
else:
def myfunc():
func(inputObj, objId)
inputObj.close()
self.enqueue(myfunc)
except Exception as ex:
print("There was an error executing object command !!!:")
print(ex)
def createSetObject(self):
_dbName, self._dbPrefix = self.sqliteFile.get().split(',')
self._dbName = self._getPath('subset.sqlite')
os.rename(_dbName, self._dbName)
if self._dbPrefix.endswith('_'):
self._dbPrefix = self._dbPrefix[:-1]
from pwem.utils import loadSetFromDb
# Ignoring self._dbPrefix here, since we want to load
# the top-level set in the sqlite file
setObj = loadSetFromDb(self._dbName)
return setObj
def createSetObject(self):
""" Moves the sqlite with the enable/disable status to its own
path to keep it and names it subset.sqlite"""
_dbName, self._dbPrefix = self.sqliteFile.get().split(',')
self._dbName = self._getPath('subset.sqlite')
os.rename(_dbName, self._dbName)
if self._dbPrefix.endswith('_'):
self._dbPrefix = self._dbPrefix[:-1]
from pwem.utils import loadSetFromDb
# Ignoring self._dbPrefix here, since we want to load
# the top-level set in the sqlite file
setObj = loadSetFromDb(self._dbName)
return setObj
def main():
parser = argparse.ArgumentParser(prog=CONVERT_ENTRY_POINT,
usage="pwem command to convert metadata "
"coordinates from several em formats "
"(eman, relion, gautomatch "
"and bsoft) to xmipp metadata")
parser.add_argument('--coordinates',
help='Convert coordinates',
action="store_true")
parser.add_argument('--fromType', help='Convert from input type')
parser.add_argument('--toType', help='Convert to output type')
parser.add_argument('--input', help='Input file or folder', required=True)
parser.add_argument('--output', help='Output file or folder')
parser.add_argument('--extra', help='To add extra parameters')
args = parser.parse_args()
fromType = args.fromType
toType = args.toType
input = args.input
output = args.output
if args.coordinates:
micSet = loadSetFromDb(input)
outputDir = output
coordsfn = os.path.join(outputDir, 'coordinates.sqlite')
cleanPath(coordsfn)
coordSet = SetOfCoordinates(filename=coordsfn)
coordSet.setMicrographs(micSet)
if fromType == 'eman2':
if toType == 'xmipp':
readSetOfCoordinates = pwutils.Config.getDomain(
).importFromPlugin('eman2.convert',
'readSetOfCoordinates',
doRaise=True)
elif fromType == 'dogpicker':
if toType == 'xmipp':
readSetOfCoordinates = pwutils.Config.getDomain(
).importFromPlugin('appion.convert',
'readSetOfCoordinates',
doRaise=True)
elif fromType == 'relion':
if toType == 'xmipp':
def readSetOfCoordinates(outputDir, micSet, coordSet):
readSetOfCoordinates = pwutils.Config.getDomain(
).importFromPlugin('relion.convert',
'readSetOfCoordinates',
doRaise=True)
inputCoords = args.extra
starFiles = [
os.path.join(inputCoords,
"mic_%06d_autopick.star" % mic.getObjId())
for mic in micSet
]
readSetOfCoordinates(coordSet, starFiles)
elif fromType == 'gautomatch':
if toType == 'xmipp':
readSetOfCoordinates = pwutils.Config.getDomain(
).importFromPlugin('gautomatch.convert',
'readSetOfCoordinates',
doRaise=True)
else:
raise Exception('Unknown coordinates type: %s' % fromType)
readSetOfCoordinates(outputDir, micSet, coordSet)
writeSetOfCoordinatesWithState = pwutils.Config.getDomain(
).importFromPlugin('xmipp3.convert',
'writeSetOfCoordinatesWithState',
doRaise=True)
writeSetOfCoordinatesWithState(outputDir, coordSet, state='Automatic')