def read_all_mysql(self):
print "reading observations from %s database" % (self.params.backend)
if self.params.backend == 'MySQL':
from xfel.cxi.merging_database import manager
elif self.params.backend == 'SQLite':
from xfel.cxi.merging_database_sqlite3 import manager
else:
from xfel.cxi.merging_database_fs import manager
CART = manager(self.params)
self.millers_mysql = CART.read_indices()
self.millers = self.millers_mysql
self.observations_mysql = CART.read_observations()
parser = column_parser()
parser.set_int("hkl_id", self.observations_mysql["hkl_id"])
parser.set_double("i", self.observations_mysql["i"])
parser.set_double("sigi", self.observations_mysql["sigi"])
parser.set_int("frame_id", self.observations_mysql["frame_id"])
parser.set_int("H", self.observations_mysql["original_h"])
parser.set_int("K", self.observations_mysql["original_k"])
parser.set_int("L", self.observations_mysql["original_l"])
self._observations_mysql = parser
self.observations = dict(
hkl_id=parser.get_int("hkl_id"),
i=parser.get_double("i"),
sigi=parser.get_double("sigi"),
frame_id=parser.get_int("frame_id"),
H=parser.get_int("H"),
K=parser.get_int("K"),
L=parser.get_int("L"),
)
self.frames_mysql = CART.read_frames()
parser = column_parser()
parser.set_int("frame_id", self.frames_mysql["frame_id"])
parser.set_double("wavelength", self.frames_mysql["wavelength"])
parser.set_double("cc", self.frames_mysql["cc"])
try:
parser.set_double("slope", self.frames_mysql["slope"])
parser.set_double("offset", self.frames_mysql["offset"])
if self.params.scaling.report_ML:
parser.set_double("domain_size_ang",
self.frames_mysql["domain_size_ang"])
parser.set_double("half_mosaicity_deg",
self.frames_mysql["half_mosaicity_deg"])
except KeyError:
pass
self._frames_mysql = parser
CART.join()
def read_all_mysql(self):
print "reading observations from %s database"%(self.params.backend)
if self.params.backend == 'MySQL':
from xfel.cxi.merging_database import manager
elif self.params.backend == 'SQLite':
from xfel.cxi.merging_database_sqlite3 import manager
else:
from xfel.cxi.merging_database_fs import manager
CART = manager(self.params)
self.millers_mysql = CART.read_indices()
self.millers = self.millers_mysql
self.observations_mysql = CART.read_observations()
parser = column_parser()
parser.set_int("hkl_id",self.observations_mysql["hkl_id"])
parser.set_double("i",self.observations_mysql["i"])
parser.set_double("sigi",self.observations_mysql["sigi"])
parser.set_int("frame_id",self.observations_mysql["frame_id"])
parser.set_int("H",self.observations_mysql["original_h"])
parser.set_int("K",self.observations_mysql["original_k"])
parser.set_int("L",self.observations_mysql["original_l"])
self._observations_mysql = parser
self.observations = dict(hkl_id=parser.get_int("hkl_id"),
i=parser.get_double("i"),
sigi=parser.get_double("sigi"),
frame_id=parser.get_int("frame_id"),
H=parser.get_int("H"),
K=parser.get_int("K"),
L=parser.get_int("L"),
)
self.frames_mysql = CART.read_frames()
parser = column_parser()
parser.set_int("frame_id",self.frames_mysql["frame_id"])
parser.set_double("wavelength",self.frames_mysql["wavelength"])
parser.set_double("cc",self.frames_mysql["cc"])
try:
parser.set_double("slope",self.frames_mysql["slope"])
parser.set_double("offset",self.frames_mysql["offset"])
if self.params.scaling.report_ML:
parser.set_double("domain_size_ang",self.frames_mysql["domain_size_ang"])
parser.set_double("half_mosaicity_deg",self.frames_mysql["half_mosaicity_deg"])
except KeyError: pass
self._frames_mysql = parser
CART.join()
def read_all(self):
# XXX Should not be used any more--migrate C++ into
# cxi/merging_database_fs.py?
print "reading observations from flat-file database"
self.frames = dict( frame_id=flex.int(),
wavelength=flex.double(),
cc=flex.double(),
slope=flex.double(),
offset=flex.double(),
odd_numbered=flex.bool(),
orientation=[],
unit_cell=[])
self.millers = dict(merged_asu_hkl=flex.miller_index())
G = open(self.params.output.prefix+"_miller.db","r")
for line in G.xreadlines():
tokens = line.strip().split()
self.millers["merged_asu_hkl"].append((int(tokens[1]),int(tokens[2]),int(tokens[3])))
# --- start C++ read
parser = column_parser()
parser.set_int("hkl_id",0)
parser.set_double("i",1)
parser.set_double("sigi",2)
parser.set_int("frame_id",5)
parser.set_int("H",7)
parser.set_int("K",8)
parser.set_int("L",9)
G = open(self.params.output.prefix+"_observation.db","r")
for line in G.xreadlines():
parser.parse_from_line(line)
self.observations = dict(hkl_id=parser.get_int("hkl_id"),
i=parser.get_double("i"),
sigi=parser.get_double("sigi"),
frame_id=parser.get_int("frame_id"),
H=parser.get_int("H"),
K=parser.get_int("K"),
L=parser.get_int("L"),
)
self._observations = parser
G.close()
# --- done with C++ read
G = open(self.params.output.prefix+"_frame.db","r")
for line in G.xreadlines():
tokens = line.strip().split()
self.frames["frame_id"].append(int(tokens[0]))
self.frames["wavelength"].append(float(tokens[1]))
self.frames["cc"].append(float(tokens[5]))
self.frames["slope"].append(float(tokens[6]))
self.frames["offset"].append(float(tokens[7]))
self.frames["odd_numbered"].append( is_odd_numbered(tokens[17]) )
# components of orientation direct matrix
odm = (float(tokens[8]), float(tokens[9]), float(tokens[10]),
float(tokens[11]), float(tokens[12]), float(tokens[13]),
float(tokens[14]), float(tokens[15]), float(tokens[16]),)
CO = crystal_orientation(odm, False)
self.frames["orientation"].append(CO)
self.frames["unit_cell"].append(CO.unit_cell())
G.close()
parser = column_parser()
parser.set_int("frame_id",0)
parser.set_double("wavelength",1)
parser.set_double("cc",5)
parser.set_double("slope",6)
parser.set_double("offset",7)
G = open(self.params.output.prefix+"_frame.db","r")
for line in G.xreadlines():
parser.parse_from_line(line)
self._frames = parser
