def extractData():
parser = OptionParser()
parser.add_option("--inputDir", dest="inputDir", help="Input directory", metavar="DIRECTORY")
parser.add_option("--mrc_number", dest="mrc_number", help="Number of mrc files to be trained.", metavar="VALUE", default=-1)
parser.add_option("--coordinate_symbol", dest="coordinate_symbol", help="The symbol of the coordinate file, like '_manualPick'", metavar="STRING")
parser.add_option("--particle_size", dest="particle_size", help="the size of the particle.", metavar="VALUE", default=-1)
parser.add_option("--save_dir", dest="save_dir", help="save the training samples to this directory", metavar="DIRECTORY", default="../trained_model")
parser.add_option("--save_file", dest="save_file", help="save the training samples to file", metavar="FILE")
(opt, args) = parser.parse_args()
inputDir = opt.inputDir
particle_size = int(opt.particle_size)
coordinate_symbol = opt.coordinate_symbol
mrc_number = int(opt.mrc_number)
output_dir = opt.save_dir
output_filename = opt.save_file
if not os.path.isdir(output_dir):
os.mkdir(output_dir)
if particle_size == -1:
print("particle size should be a positive value!")
return
output_filename = os.path.join(output_dir, output_filename)
DataLoader.extractData(inputDir, particle_size, coordinate_symbol, mrc_number, output_filename)
def extractData():
parser = OptionParser()
parser.add_option("--inputDir",
dest="inputDir",
help="Input directory",
metavar="DIRECTORY")
parser.add_option("--mrc_number",
dest="mrc_number",
help="Number of mrc files to be trained.",
metavar="VALUE",
default=-1)
parser.add_option(
"--coordinate_symbol",
dest="coordinate_symbol",
help="The symbol of the coordinate file, like '_manualPick'",
metavar="STRING")
parser.add_option("--particle_size",
dest="particle_size",
help="the size of the particle.",
metavar="VALUE",
default=-1)
parser.add_option("--save_dir",
dest="save_dir",
help="save the training samples to this directory",
metavar="DIRECTORY",
default="../trained_model")
parser.add_option("--save_file",
dest="save_file",
help="save the training samples to file",
metavar="FILE")
(opt, args) = parser.parse_args()
inputDir = opt.inputDir
particle_size = int(opt.particle_size)
coordinate_symbol = opt.coordinate_symbol
mrc_number = int(opt.mrc_number)
output_dir = opt.save_dir
output_filename = opt.save_file
if not os.path.isdir(output_dir):
os.mkdir(output_dir)
if particle_size == -1:
print("particle size should be a positive value!")
return
output_filename = os.path.join(output_dir, output_filename)
DataLoader.extractData(inputDir, particle_size, coordinate_symbol,
mrc_number, output_filename)
def extractData():
parser = OptionParser()
parser.add_option("--inputDir",
dest="inputDir",
help="Input directory",
metavar="DIRECTORY")
parser.add_option("--mrc_number",
dest="mrc_number",
help="Number of mrc files to be trained.",
metavar="VALUE",
default=-1)
parser.add_option(
"--coordinate_symbol",
dest="coordinate_symbol",
help="The symbol of the coordinate file, like '_manualPick'",
metavar="STRING")
parser.add_option("--particle_size",
dest="particle_size",
help="the size of the particle.",
metavar="VALUE",
default=-1)
parser.add_option("--save_dir",
dest="save_dir",
help="save the training samples to this directory",
metavar="DIRECTORY",
default="../trained_model")
parser.add_option("--save_file",
dest="save_file",
help="save the training samples to file",
metavar="FILE")
parser.add_option("--produce_negative",
dest="produce_negative",
help="whether to produce negative samples",
metavar="BOOL",
default=True)
parser.add_option("--class_number",
dest="class_number",
help="ClassNumber",
metavar="STRING",
default='0')
(opt, args) = parser.parse_args()
inputDir = opt.inputDir
particle_size = int(opt.particle_size)
coordinate_symbol = opt.coordinate_symbol
mrc_number = int(opt.mrc_number)
output_dir = opt.save_dir
#output_filename = opt.save_file
produce_negative = opt.produce_negative
class_number = int(opt.class_number)
print "produce_negative =", produce_negative
if not os.path.isdir(output_dir):
os.mkdir(output_dir)
print 'mkdir!'
if particle_size == -1:
print("particle size should be a positive value!")
return
#output_filename = os.path.join(output_dir, output_filename)
print 'begin extracting!'
if class_number == 0:
output_filename = os.path.join(output_dir, opt.save_file)
print("saved_file >>> ", output_filename)
sys.stdout.flush()
DataLoader.extractData(inputDir,
particle_size,
coordinate_symbol,
mrc_number,
output_filename,
produce_negative=produce_negative)
else:
#for i in range(1, class_number+1):
# output_filename = "class%d.pickle" % i
# output_filename = os.path.join(output_dir, output_filename)
# print (coordinate_symbol+str(i), " >>> ", output_filename)
# sys.stdout.flush()
# DataLoader.extractData(inputDir, particle_size, coordinate_symbol+str(i), mrc_number, output_filename, produce_negative=produce_negative)
DataLoader.extractData(inputDir,
particle_size,
coordinate_symbol,
mrc_number,
output_dir,
class_number,
produce_negative=produce_negative)
