def switchDataset(dataset):
"""Load the appropriate dbconfig project based on the dataset name"""
# Switch on the dataset
if dataset == 'hayworth5nm':
import dbconfighayworth5nm
return dbconfighayworth5nm.dbConfigHayworth5nm()
elif dataset == 'bock11':
import dbconfigbock11
return dbconfigbock11.dbConfigBock11()
elif dataset == 'kasthuri11':
import dbconfigkasthuri11
return dbconfigkasthuri11.dbConfigKasthuri11()
elif dataset == 'will':
import dbconfigwill
return dbconfigwill.dbConfigWill()
elif dataset == 'drosophila':
import dbconfigdrosophila
return dbconfigdrosophila.dbConfigDrosophila()
elif dataset == 'kat11iso':
import dbconfigkat11iso
return dbconfigkat11iso.dbConfigKasthuri11Isotropic()
elif dataset == 'weiler':
import dbconfigweiler
return dbconfigweiler.dbConfigWeiler()
elif dataset == 'autism':
import dbconfigautism
return dbconfigautism.dbConfigAutism()
else:
# RBTODO make this a dbconfig exception
raise DBConfigError("Could not find dataset = %s" % dataset)
def main():
parser = argparse.ArgumentParser(description='Cutout a portion of the database.')
parser.add_argument('xlow', action="store", type=int )
parser.add_argument('xhigh', action="store", type=int)
parser.add_argument('ylow', action="store", type=int)
parser.add_argument('yhigh', action="store", type=int)
parser.add_argument('zlow', action="store", type=int)
parser.add_argument('zhigh', action="store", type=int)
result = parser.parse_args()
dbcfg = dbconfighayworth5nm.dbConfigHayworth5nm()
annoDB = anndb.AnnotateDB ( dbcfg )
voxlist= []
for k in range (result.zlow,result.zhigh):
for j in range (result.ylow,result.yhigh):
for i in range (result.xlow,result.xhigh):
voxlist.append ( [ i,j,k] )
print voxlist
# Build a grayscale file and display
entityid = annoDB.addEntity ( voxlist )
print "Added entity with identifier = ", entityid
def main():
# Specify the database to ingest
#dbcfg = dbconfigbock11.dbConfigBock11()
dbcfg = dbconfighayworth5nm.dbConfigHayworth5nm()
cdb = cubedb.CubeDB ( dbcfg )
# for all specified resolutions
for resolution in dbcfg.resolutions:
print "Building DB for resolution ", resolution, " imagesize ", dbcfg.imagesz[resolution]
cdb.generateDB ( resolution )
return
def main():
parser = argparse.ArgumentParser(description='Cutout a portion of the database.')
parser.add_argument('xlow', action="store", type=int )
parser.add_argument('xhigh', action="store", type=int)
parser.add_argument('ylow', action="store", type=int)
parser.add_argument('yhigh', action="store", type=int)
parser.add_argument('zslice', action="store", type=int, default=0)
result = parser.parse_args()
dbcfg = dbconfighayworth5nm.dbConfigHayworth5nm()
annoDB = anndb.AnnotateDB ( dbcfg )
corner = [ result.xlow, result.ylow, result.zslice ]
dim = [ result.xhigh - result.xlow, result.yhigh - result.ylow, 1 ]
# Build a grayscale file and display
xyplane = annoDB.cutout ( corner, dim, dbcfg.annotateres )
print xyplane.data
def hayworth5nm ( webargs ): """Use the hayworth5nm data set""" dbcfg = dbconfighayworth5nm.dbConfigHayworth5nm() return selectService ( webargs, dbcfg )