def read_frames(self):
from xfel.cxi.util import is_odd_numbered
cursor = self._db.cursor()
cursor.execute("""SELECT
frame_id_1_base,wavelength,c_c,slope,offset,res_ori_1,res_ori_2,res_ori_3,
res_ori_4,res_ori_5,res_ori_6,res_ori_7,res_ori_8,res_ori_9,
unique_file_name
FROM _frame""")
ALL = cursor.fetchall()
from cctbx.crystal_orientation import crystal_orientation
orientations = [
crystal_orientation(
(a[5], a[6], a[7], a[8], a[9], a[10], a[11], a[12], a[13]),
False) for a in ALL
]
return dict(frame_id=flex.int([a[0] - 1 for a in ALL]),
wavelength=flex.double([a[1] for a in ALL]),
cc=flex.double([a[2] for a in ALL]),
slope=flex.double([a[3] for a in ALL]),
offset=flex.double([a[4] for a in ALL]),
odd_numbered=flex.bool(
[is_odd_numbered(a[14]) for a in ALL]),
orientation=orientations,
unit_cell=[CO.unit_cell() for CO in orientations],
unique_file_name=[a[14] for a in ALL])
def read_frames_updated_detail(self):
from cctbx.crystal_orientation import crystal_orientation
from xfel.cxi.util import is_odd_numbered
frames = {'frame_id': flex.int(),
'wavelength': flex.double(),
'cc': flex.double(),
'G': flex.double(),
'BFACTOR': flex.double(),
'RS': flex.double(),
'odd_numbered': flex.bool(),
'thetax': flex.double(),
'thetay': flex.double(),
'orientation': [],
'unit_cell': [],
'unique_file_name': []}
stream = open(self.params.output.prefix + '_frame.db', 'r')
for row in stream:
items = row.split()
CO = crystal_orientation([float(t) for t in items[8:17]], True)
unique_file_name = eval(items[19])
frames['frame_id'].append(int(items[0]))
frames['wavelength'].append(float(items[1]))
frames['cc'].append(float(items[20]))
frames['G'].append(float(items[5]))
frames['BFACTOR'].append(float(items[6]))
frames['RS'].append(float(items[7]))
frames['thetax'].append(float(items[17]))
frames['thetay'].append(float(items[18]))
frames['odd_numbered'].append(is_odd_numbered(unique_file_name))
frames['orientation'].append(CO)
frames['unit_cell'].append(CO.unit_cell())
frames['unique_file_name'].append(unique_file_name)
stream.close()
return frames
def read_frames_legacy_detail(self):
from cctbx.crystal_orientation import crystal_orientation
from xfel.cxi.util import is_odd_numbered
# XXX issues with spaces in the file name, and leading and
# trailing single quotes (stripped below).
frames = {
'frame_id': flex.int(),
'wavelength': flex.double(),
'cc': flex.double(),
'slope': flex.double(),
'offset': flex.double(),
'odd_numbered': flex.bool(),
'domain_size_ang': flex.double(),
'half_mosaicity_deg': flex.double(),
'orientation': [],
'unit_cell': [],
'unique_file_name': []
}
stream = open(self.params.output.prefix + '_frame.db', 'r')
for row in stream:
items = row.split()
CO = crystal_orientation([float(t) for t in items[8:17]], False)
unique_file_name = eval(items[24])
frames['frame_id'].append(int(items[0]))
frames['wavelength'].append(float(items[1]))
frames['cc'].append(float(items[5]))
frames['slope'].append(float(items[6]))
frames['offset'].append(float(items[7]))
frames['domain_size_ang'].append(float(items[23]))
frames['half_mosaicity_deg'].append(float(items[20]))
frames['odd_numbered'].append(
is_odd_numbered(unique_file_name,
use_hash=self.params.hash_filenames))
frames['orientation'].append(CO)
frames['unit_cell'].append(CO.unit_cell())
frames['unique_file_name'].append(unique_file_name)
stream.close()
return frames
def read_frames(self):
from xfel.cxi.util import is_odd_numbered
db = self.connection()
cursor = db.cursor()
cursor.execute("""SELECT
frame_id_1_base,wavelength,c_c,slope,offset,res_ori_1,res_ori_2,res_ori_3,
res_ori_4,res_ori_5,res_ori_6,res_ori_7,res_ori_8,res_ori_9,
unique_file_name
FROM `%s_frame`"""%self.params.mysql.runtag)
ALL = cursor.fetchall()
from cctbx.crystal_orientation import crystal_orientation
orientations = [crystal_orientation(
(a[5],a[6],a[7],a[8],a[9],a[10],a[11],a[12],a[13]),False) for a in ALL]
return dict( frame_id = flex.int( [a[0]-1 for a in ALL] ),
wavelength = flex.double( [a[1] for a in ALL] ),
cc = flex.double( [a[2] for a in ALL] ),
slope = flex.double( [a[3] for a in ALL] ),
offset = flex.double( [a[4] for a in ALL] ),
odd_numbered = flex.bool( [is_odd_numbered(a[14]) for a in ALL] ),
orientation = orientations,
unit_cell = [CO.unit_cell() for CO in orientations],
unique_file_name = [a[14] for a in ALL] )
def read_frames_updated_detail(self):
from cctbx.crystal_orientation import crystal_orientation
from xfel.cxi.util import is_odd_numbered
frames = {
'frame_id': flex.int(),
'wavelength': flex.double(),
'cc': flex.double(),
'G': flex.double(),
'BFACTOR': flex.double(),
'RS': flex.double(),
'odd_numbered': flex.bool(),
'thetax': flex.double(),
'thetay': flex.double(),
'orientation': [],
'unit_cell': [],
'unique_file_name': []
}
stream = open(self.params.output.prefix + '_frame.db', 'r')
for row in stream:
items = row.split()
CO = crystal_orientation([float(t) for t in items[8:17]], True)
unique_file_name = eval(items[19])
frames['frame_id'].append(int(items[0]))
frames['wavelength'].append(float(items[1]))
frames['cc'].append(float(items[20]))
frames['G'].append(float(items[5]))
frames['BFACTOR'].append(float(items[6]))
frames['RS'].append(float(items[7]))
frames['thetax'].append(float(items[17]))
frames['thetay'].append(float(items[18]))
frames['odd_numbered'].append(
is_odd_numbered(unique_file_name,
use_hash=self.params.hash_filenames))
frames['orientation'].append(CO)
frames['unit_cell'].append(CO.unit_cell())
frames['unique_file_name'].append(unique_file_name)
stream.close()
return frames
def read_frames_legacy_detail(self):
from cctbx.crystal_orientation import crystal_orientation
from xfel.cxi.util import is_odd_numbered
# XXX issues with spaces in the file name, and leading and
# trailing single quotes (stripped below).
frames = {'frame_id': flex.int(),
'wavelength': flex.double(),
'cc': flex.double(),
'slope': flex.double(),
'offset': flex.double(),
'odd_numbered': flex.bool(),
'domain_size_ang': flex.double(),
'half_mosaicity_deg': flex.double(),
'orientation': [],
'unit_cell': [],
'unique_file_name': []}
stream = open(self.params.output.prefix + '_frame.db', 'r')
for row in stream:
items = row.split()
CO = crystal_orientation([float(t) for t in items[8:17]], False)
unique_file_name = eval(items[24])
frames['frame_id'].append(int(items[0]))
frames['wavelength'].append(float(items[1]))
frames['cc'].append(float(items[5]))
frames['slope'].append(float(items[6]))
frames['offset'].append(float(items[7]))
frames['domain_size_ang'].append(float(items[23]))
frames['half_mosaicity_deg'].append(float(items[20]))
frames['odd_numbered'].append(is_odd_numbered(unique_file_name))
frames['orientation'].append(CO)
frames['unit_cell'].append(CO.unit_cell())
frames['unique_file_name'].append(unique_file_name)
stream.close()
return frames
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
