def __establish_tmp_file_name(self):
'''
Called internally to establish temporary file name member variables
'''
self.__gen_tmp_file_name()
while (db_check_dict(self.__tmp_db_name)):
self.__gen_tmp_file_name()
def check(options, verbose):
error = False
if (options.sep < 1):
if verbose > 0:
print(
"Error: the --sep argument must be greater than zero, currently it is %d"
% (options.sep))
error = True
if (options.nofilecheck == False):
if os.path.exists(options.outfile):
if (not options.force):
if verbose > 0:
print("File %s exists, will not write over, exiting" %
options.outfile)
error = True
if not os.path.exists(options.simmxfile) and not db_check_dict(
options.simmxfile):
if verbose > 0:
print(
"Error: the similarity matrix file (%s) was not found, cannot run e2classify.py"
% (options.simmxfile))
error = True
else:
num_sim = EMUtil.get_image_count(options.simmxfile)
if (num_sim < 5):
if verbose > 0:
print(
"Error, the similarity matrix did not contain 5 images - be sure to use the --saveali argument when running e2simmx.py"
)
error = True
return error
def get_gui_arg_img_sets(filenames):
'''
returns the img_sets list required to intialized the GUI correctly
'''
img_sets = []
if db_check_dict("bdb:e2ctf.parms"):
db_parms = db_open_dict("bdb:e2ctf.parms", ro=True)
else:
return img_sets
for file in filenames:
name = get_file_tag(file)
if not db_parms.has_key(name):
print "error, you must first run auto fit before running the gui - there are no parameters for", name
return []
img_set = db_parms[name]
ctf = EMAN2Ctf()
ctf.from_string(
img_set[0]) # convert to ctf object seeing as it's a string
img_set[0] = ctf
actual = [file]
actual.extend(img_set)
img_sets.append(actual)
return img_sets
def __establish_tmp_file_name(self): ''' Called internally to establish temporary file name member variables ''' self.__gen_tmp_file_name() while (db_check_dict(self.__tmp_db_name)): self.__gen_tmp_file_name()
def check(options,verbose): error = False if (options.sep < 1): if verbose>0: print "Error: the --sep argument must be greater than zero, currently it is %d" %(options.sep) error = True if ( options.nofilecheck == False ): if os.path.exists(options.outfile): if (not options.force): if verbose>0: print "File %s exists, will not write over, exiting" %options.outfile error = True if not os.path.exists(options.simmxfile) and not db_check_dict(options.simmxfile): if verbose>0: print "Error: the similarity matrix file (%s) was not found, cannot run e2classify.py" %(options.simmxfile) error = True else: num_sim = EMUtil.get_image_count(options.simmxfile) if (num_sim<5): if verbose>0: print "Error, the similarity matrix did not contain 5 images - be sure to use the --saveali argument when running e2simmx.py" error = True return error
def remove_tmp_file(self): ''' removes the temporary file ''' if (db_check_dict(self.__tmp_db_name)): db_remove_dict(self.__tmp_db_name) else: pass
def remove_tmp_file(self):
'''
removes the temporary file
'''
if (db_check_dict(self.__tmp_db_name)):
db_remove_dict(self.__tmp_db_name)
else:
pass
def _checkfiles(self, filename): files = filename.split() for f in files: if not os.access(f, os.F_OK) and not db_check_dict(f): self._onBadFile(f) # Display the rubbish file to the user self.filenamebox.setText(filename) return False return True
def __init__(self,file_name):
'''
@param file_name the name of the file that which is being overwritten
@exception RuntimeError raised of the file_name is not a valid bdb style database handle
'''
if not db_check_dict(file_name): raise RuntimeError("%s is not a valid database name" %file_name)
self.__orig_db_name = file_name
EMTmpFileHandleBase.__init__(self)
self.__tmp_db_name = ""
self.__establish_tmp_file_name()
def __init__(self,file_name):
'''
@param file_name the name of the file that which is being overwritten
@exception RuntimeError raised of the file_name is not a valid bdb style database handle
'''
if not db_check_dict(file_name): raise RuntimeError("%s is not a valid database name" %file_name)
self.__orig_db_name = file_name
EMTmpFileHandleBase.__init__(self)
self.__tmp_db_name = ""
self.__establish_tmp_file_name()
def _checkfiles(self, filename):
# Posional arguments must be space delimted for multiple files, whereas options must be comma delimted
if self.getPositional():
files = filename.split()
else:
files = filename.split(",")
# If we have too many files, the user will have to wait a LOOONG time for the image check, so we just skip it
if len(files) > 20:
try:
tst = EMData(files[0], 0)
nx, ny, nz = tst["nx"], tst["ny"], tst["nz"]
except:
nx, ny, nz = 0, 0, 0
if nx > 0:
self.infolabel.setText("Files: %d %dx%dx%d" %
(len(files), nx, ny, nz))
else:
self.infolabel.setText("Files: %d" % (len(files)))
return True
# Check each file
numimages = 0
nx, ny, nz = 0, 0, 0
for f in files:
if not os.access(f, os.F_OK) and not db_check_dict(f):
self._onBadFile(f)
# Display the rubbish file to the user
self.filenamebox.setText(filename)
return False
try:
numimages += EMUtil.get_image_count(f)
tst = EMData(files[0], 0)
nx, ny, nz = tst["nx"], tst["ny"], tst["nz"]
except:
nx, ny, nz = 0, 0, 0
if nx > 0:
self.infolabel.setText("Files: %d Images: %d %dx%dx%d" %
(len(files), numimages, nx, ny, nz))
else:
self.infolabel.setText("Files: %d Images: %d" %
(len(files), numimages))
return True
def _checkfiles(self, filename):
# Posional arguments must be space delimted for multiple files, whereas options must be comma delimted
if self.getPositional():
files = filename.split()
else:
files = filename.split(",")
# If we have too many files, the user will have to wait a LOOONG time for the image check, so we just skip it
if len(files)>20 :
try:
tst=EMData(files[0],0)
nx,ny,nz=tst["nx"],tst["ny"],tst["nz"]
except: nx,ny,nz=0,0,0
if nx>0: self.infolabel.setText("Files: %d %dx%dx%d"%(len(files),nx,ny,nz))
else : self.infolabel.setText("Files: %d"%(len(files)))
return True
# Check each file
numimages = 0
nx,ny,nz=0,0,0
for f in files:
if not os.access(f, os.F_OK) and not db_check_dict(f):
self._onBadFile(f)
# Display the rubbish file to the user
self.filenamebox.setText(filename)
return False
try:
numimages += EMUtil.get_image_count(f)
tst=EMData(files[0],0)
nx,ny,nz=tst["nx"],tst["ny"],tst["nz"]
except:
nx,ny,nz=0,0,0
if nx>0: self.infolabel.setText("Files: %d Images: %d %dx%dx%d"%(len(files),numimages,nx,ny,nz))
else : self.infolabel.setText("Files: %d Images: %d"%(len(files),numimages))
return True
def get_gui_arg_img_sets(filenames):
'''
returns the img_sets list required to intialized the GUI correctly
'''
img_sets = []
if db_check_dict("bdb:e2ctf.parms"):
db_parms=db_open_dict("bdb:e2ctf.parms",ro=True)
else: return img_sets
for file in filenames:
name = get_file_tag(file)
if not db_parms.has_key(name):
print "error, you must first run auto fit before running the gui - there are no parameters for",name
return []
img_set = db_parms[name]
ctf=EMAN2Ctf()
ctf.from_string(img_set[0]) # convert to ctf object seeing as it's a string
img_set[0] = ctf
actual = [file]
actual.extend(img_set)
img_sets.append(actual)
return img_sets
def isac_substack(args):
from utilities import get_im, write_text_file
from EMAN2db import db_open_dict, db_check_dict
from e2bdb import makerelpath
# To make the execution exit upon fatal error by ERROR in global_def.py
global_def.BATCH = True
# Check error conditions
subcommand_name = "isac_substack"
if not db_check_dict(args.input_bdb_stack_path, readonly=True):
ERROR(
"Input BDB image stack file does not exist. Please check the file path and restart the program.",
subcommand_name) # action=1 - fatal error, exit
if not os.path.exists(args.input_isac_class_avgs_path):
ERROR(
"Input ISAC class average stack file does not exist. Please check the file path and restart the program.",
subcommand_name) # action=1 - fatal error, exit
if os.path.exists(args.output_directory):
ERROR(
"Output directory exists. Please change the name and restart the program.",
subcommand_name) # action=1 - fatal error, exit
if args.substack_basename.strip() == "":
ERROR("Substack basename cannot be empty string or only white spaces.",
subcommand_name) # action=1 - fatal error, exit
assert (db_check_dict(args.input_bdb_stack_path, readonly=True))
assert (os.path.exists(args.input_isac_class_avgs_path))
assert (not os.path.exists(args.output_directory))
assert (args.substack_basename.strip() != "")
# Create output directory
os.mkdir(args.output_directory)
# Retrieve original particle IDs of member particles listed in ISAC class average stack
n_img_processed = EMUtil.get_image_count(args.input_isac_class_avgs_path)
isac_substack_particle_id_list = []
for i_img in xrange(n_img_processed):
isac_substack_particle_id_list += get_im(
args.input_isac_class_avgs_path, i_img).get_attr("members")
isac_substack_particle_id_list.sort()
# Save the substack particle id list
isac_substack_particle_id_list_file_path = os.path.join(
args.output_directory,
"{0}_particle_id_list.txt".format(args.substack_basename))
write_text_file(isac_substack_particle_id_list,
isac_substack_particle_id_list_file_path)
# Open the output BDB dictionary
assert (args.output_directory != "")
output_virtual_bdb_stack_real_path = "bdb:{0}#{1}".format(
args.output_directory, args.substack_basename)
output_virtual_bdb_stack = db_open_dict(output_virtual_bdb_stack_real_path)
# Convert an absolute path to the actual output data to a relative path by eliminating any symbolic links
output_virtual_bdb_stack_real_path = os.path.realpath(
output_virtual_bdb_stack.path) + "/"
# Open the input BDB dictionary
input_bdb_stack = db_open_dict(args.input_bdb_stack_path,
ro=True) # Read only
# Copy the header from input to output BDB dictionary
n_img_detected = len(isac_substack_particle_id_list)
print(" ")
print_progress("Detected %d ISAC validated particles in %s" %
(n_img_detected, args.input_isac_class_avgs_path))
# Loop through all ISAC validated particles
print(" ")
n_img_processed = 0
n_img_of_10_percent = n_img_detected // 10
for i_img_detected, isac_substack_particle_id in enumerate(
isac_substack_particle_id_list):
# Print progress
if i_img_detected % n_img_of_10_percent == 0:
try:
print_progress(
"Progress %5.2f%%: Processing entry %6d (Particle ID %6d)."
% (float(i_img_detected) / n_img_detected * 100.0,
i_img_detected, isac_substack_particle_id))
sys.stdout.flush()
except:
pass
# Read a particle image header from input bdb stack
try:
img_header = input_bdb_stack.get(
isac_substack_particle_id,
nodata=1).get_attr_dict() # Need only header information
except:
# ERROR("Failed to read image header of particle #%d from %s. Skipping this image..."%(isac_substack_particle_id, args.input_bdb_stack_path), subcommand_name, action = 0) # action = 0 - non-fatal, print a warning;
# continue
ERROR(
"Failed to read image header of particle #%d from %s. Please make sure input_bdb_stack_path (%s) and input_isac_class_avgs_path (%s) are correct pair and run the command again..."
% (isac_substack_particle_id, args.input_bdb_stack_path,
args.input_bdb_stack_path, args.input_isac_class_avgs_path),
subcommand_name) # action=1 - fatal error, exit
# Convert an absolute path to the actual input data to a relative path by eliminating any symbolic links
try:
input_bdb_stack_real_path = os.path.realpath(
input_bdb_stack.get_data_path(isac_substack_particle_id))
# Conver the path to OS specific format
if os.name == "nt":
output_virtual_bdb_stack_real_path = output_virtual_bdb_stack_real_path.replace(
"\\", "/")
input_bdb_stack_real_path = input_bdb_stack_real_path.replace(
"\\", "/")
# Takes a pair of paths /a/b/c/d and /a/b/e/f/g and returns a relative path to b from a, ../../e/f/g
common_relative_path = makerelpath(
output_virtual_bdb_stack_real_path, input_bdb_stack_real_path)
except:
ERROR(
"Failure to find common relative data path for particle image #%d. Skipping this image..."
% (isac_substack_particle_id),
subcommand_name,
action=0) # action = 0 - non-fatal, print a warning;
continue
# Update the image header for output
img_header["data_path"] = common_relative_path
img_header["data_n"] = isac_substack_particle_id
img_header["data_source"] = args.input_bdb_stack_path
# Register the image header to output virtual bdb stack
output_virtual_bdb_stack[n_img_processed] = img_header
# Increment process image counts
n_img_processed += 1
# Close input and output bdb stacks
output_virtual_bdb_stack.close()
input_bdb_stack.close()
# Print summary of processing
print(" ")
print_progress("Summary of processing...")
print_progress("Detected : %6d" % (n_img_detected))
print_progress("Processed : %6d" % (n_img_processed))
print(" ")
def updateTable(self):
""" Update FSC table"""
dirs = []
for pattern in self.patterns:
dirs.extend(glob.glob("%s*"%pattern))
self.tablewidget.setRowCount(len(dirs))
for i, directory in enumerate(sorted(dirs)):
# load each directory
qwi_dirname = QtGui.QTableWidgetItem(str(directory))
self.tablewidget.setItem(i, 0, qwi_dirname)
#load info from DB
db_name = "bdb:"+str(directory)+"#convergence.results"
if not db_check_dict(db_name):
continue
db = db_open_dict(db_name,ro=True)
keys = db.keys()
# count iterations, refinement
rcount = 0
ccount = 0
for key in keys:
if "init_00_fsc" == key:
rcount+=1
#do I need to increment ccount too?
continue
if ("%02d_%02d_fsc"%(rcount,rcount+1)) == key:
rcount+=1
continue
if ("conv_even_odd_%02d"%(ccount+1)) == key :
ccount+=1
# no need for further processing
if rcount == 0 and ccount == 0:
continue
# load refinement results
if rcount > 0:
qwi_iterations = QtGui.QTableWidgetItem(str(rcount))
qwi_iterations.setTextAlignment(QtCore.Qt.AlignCenter)
self.tablewidget.setItem(i, 1, qwi_iterations)
# get res estimates, I jacked this from David
reo = EMAN2fsc.get_e2refine_even_odd_results_list(keys)
eo = EMAN2fsc.get_e2eotest_results_list(keys)
if len(reo) > 0:
# get the latest one, this will be the last as guaranteed by sorted results
last_res = reo[-1]
[xaxis,yaxis] = db[last_res]
resolution = self.find_first_point_5_crossing(xaxis,yaxis,.143) # with this test, the .143 threshold is reasonable
qwi_res = QtGui.QTableWidgetItem(str(resolution))
qwi_res.setTextAlignment(QtCore.Qt.AlignCenter)
self.tablewidget.setItem(i, 2, qwi_res)
if len(eo) > 0:
last_res = eo[-1]
[xaxis,yaxis] = db[last_res]
resolution = self.find_first_point_5_crossing(xaxis,yaxis)
qwi_eotest = QtGui.QTableWidgetItem(str(resolution))
qwi_eotest.setTextAlignment(QtCore.Qt.AlignCenter)
self.tablewidget.setItem(i, 3, qwi_eotest)