def __init__( self, eprimerOptions ):
self.programName = "EPrimer3"
self.options = eprimerOptions
primer3corePath = utils.search_file( "primer3_core" )
if primer3corePath is None:
raise utils.ProgramNotFoundException( "primer3_core", "Please ensure that the primer3 package is installed on your system. It can be obtained from http://primer3.sourceforge.net/" )
eprimerPath = utils.search_file( "eprimer3" )
if eprimerPath is None:
raise utils.ProgramNotFoundException( 'eprimer3', "Please ensure that the EMBOSS package is installed and configured on your system." )
self.primer3core = primer3corePath
self.eprimer3 = eprimerPath
def deployRepoAttempt(self, attempt, deployPath):
utils.vagrant_pip_clear()
setup_files = utils.search_file(deployPath, 'setup.py')
LOG.info('setup.py: ' + str(setup_files))
if len(setup_files):
return ATTEMPT_STATUS_NOT_AN_APPLICATION
setting_files = utils.search_file(deployPath, 'settings.py')
LOG.info('settings.py: ' + str(setting_files))
if not len(setting_files):
return ATTEMPT_STATUS_MISSING_REQUIRED_FILES
manage_files = utils.search_file(deployPath, 'manage.py')
LOG.info('manage.py: ' + str(manage_files))
if not len(manage_files):
return ATTEMPT_STATUS_MISSING_REQUIRED_FILES
self.requirement_files = utils.search_file(deployPath, 'requirements.txt')
LOG.info('REQUIREMENTS: ' + str(self.requirement_files))
manage_paths = [os.path.dirname(manage_file) for manage_file in manage_files]
LOG.info("MANAGE_PATHS: " + str(manage_paths))
setting_paths = [os.path.dirname(os.path.dirname(setting_file)) for setting_file in setting_files]
LOG.info("setting_paths: " + str(setting_paths))
base_dirs = set.intersection(set(manage_paths), set(setting_paths))
if not base_dirs:
LOG.error('can not find base directory')
return ATTEMPT_STATUS_MISSING_REQUIRED_FILES
base_dir = next(iter(base_dirs))
LOG.info('BASE_DIR: ' + base_dir)
manage_file = next(name for name in manage_files if name.startswith(base_dir))
setting_file = next(name for name in setting_files if name.startswith(base_dir))
# Database
attempt.database = self.getDatabase(setting_file)
LOG.info('DATABASE: ' + attempt.database.name)
# Base Dir
attempt.base_dir = base_dir.split('/', 1)[1]
LOG.info('BASE_DIR: ' + attempt.base_dir)
# Settings Dir
attempt.setting_dir = os.path.basename(os.path.dirname(setting_file))
LOG.info('SETTING_DIR: ' + attempt.setting_dir)
# Try to deploy!
return self.tryDeploy(attempt, manage_file, setting_file)
def compile():
if settings["download_missing_files"]:
version = repository.Version.get_version_file()
repo.compare_tree(version.branch) if version.commit_hash is None else repo.compare_tree(version.commit_hash)
locales.adv_print("BUILDING")
if not os.path.exists("gradlew.bat"):
with open("gradlew.bat", "w") as f:
f.write(requests.get("https://raw.githubusercontent.com/michel-kraemer/gradle-download-task/master/gradlew.bat").text)
process = subprocess.Popen(["gradlew.bat", "RatPoison"])
process.communicate()
return_code = process.returncode
utils.kill_jdk()
if return_code == 0:
delete_libs_folder()
bat_file = utils.get_bat_name()
for path in utils.search_file("java.exe"):
if utils.verify_path(path):
java_exe = str(path)
with open(bat_file, "r") as rFile:
prev_lines = rFile.readlines()
prev_lines[4] = prev_lines[4].replace("java", f"\"{java_exe}\"", 1)
with open(bat_file, "w") as wFile:
wFile.writelines(prev_lines)
break
if locales.adv_input("RANDOMIZE_FILE_NAMES_INPUT") in locales.yes:
randomize_file_names()
replace_bat_path()
else:
if locales.adv_input("RETRY_BUILD_INPUT"):
settings["skip_jdk_checks"] = False
settings["force_install_jdk"] = True
jdk_tools.download_jdk()
compile()
def __init__( self ):
self.programName = "PrimerSearch"
primerSearchPath = utils.search_file( "primersearch" )
if primerSearchPath is None:
raise utils.ProgramNotFoundException( "primersearch", "Please ensure that the EMBOSS package is installed on your system." )
self.primerSearch = primerSearchPath
def deploy_repo_attempt(self, deploy_path):
LOG.info(utils.configure_env(self.base_path))
manage_files = utils.search_file(deploy_path, 'manage.py')
if not manage_files:
return ATTEMPT_STATUS_MISSING_REQUIRED_FILES
manage_paths = [os.path.dirname(manage_file) for manage_file in manage_files]
base_dir = next(name for name in manage_paths if 'lib/python2.7/site-packages/' not in name)
manage_path = next(name for name in manage_paths if name.startswith(base_dir))
LOG.info('manage.py path: {}'.format(manage_path))
with open(os.path.join(manage_path, 'manage.py'), 'r') as manage_file:
s = re.search('os.environ.setdefault\("DJANGO_SETTINGS_MODULE", "(.*)"\)', manage_file.read())
if s:
setting_path = s.group(1)
else:
return ATTEMPT_STATUS_MISSING_REQUIRED_FILES
setting_path = setting_path.replace('.', '/')
if os.path.isdir(os.path.join(manage_path, setting_path)):
setting_path = os.path.join(manage_path, setting_path)
for setting_file in sorted(os.listdir(setting_path)):
if os.path.isfile(os.path.join(setting_path, setting_file)):
setting_path = os.path.join(setting_path, setting_file)
break
self.setting_path = setting_path
elif os.path.isfile(os.path.join(manage_path, setting_path + '.py')):
setting_path = os.path.join(manage_path, setting_path + '.py')
self.setting_path = setting_path
else:
for candidate_setting_files in utils.search_file_regex(deploy_path, '^settings.*\.py$'):
setting_path = os.path.join(manage_path, setting_path + '.py')
utils.copy_file(candidate_setting_files, setting_path)
self.setting_path = setting_path
break
if self.setting_path == None:
return ATTEMPT_STATUS_MISSING_REQUIRED_FILES
LOG.info('setting.py path: {}'.format(setting_path))
requirement_files = utils.search_file(deploy_path, 'requirements.txt')
if requirement_files:
LOG.info('requirements.txt path: {}'.format(requirement_files))
return self.try_deploy(manage_path, requirement_files)
def deploy_repo_attempt(self, deploy_path):
LOG.info(utils.configure_env(self.base_path))
manage_files = utils.search_file(deploy_path, 'manage.py')
if not manage_files:
return ATTEMPT_STATUS_MISSING_REQUIRED_FILES
manage_paths = [os.path.dirname(manage_file) for manage_file in manage_files]
base_dir = next(name for name in manage_paths if 'lib/python2.7/site-packages/' not in name)
manage_path = next(name for name in manage_paths if name.startswith(base_dir))
LOG.info('manage.py path: {}'.format(manage_path))
with open(os.path.join(manage_path, 'manage.py'), 'r') as manage_file:
s = re.search('os.environ.setdefault\("DJANGO_SETTINGS_MODULE", "(.*)"\)', manage_file.read())
if s:
setting_path = s.group(1)
else:
return ATTEMPT_STATUS_MISSING_REQUIRED_FILES
setting_path = setting_path.replace('.', '/')
if os.path.isdir(os.path.join(manage_path, setting_path)):
setting_path = os.path.join(manage_path, setting_path)
for setting_file in sorted(os.listdir(setting_path)):
if os.path.isfile(os.path.join(setting_path, setting_file)):
setting_path = os.path.join(setting_path, setting_file)
break
self.setting_path = setting_path
elif os.path.isfile(os.path.join(manage_path, setting_path + '.py')):
setting_path = os.path.join(manage_path, setting_path + '.py')
self.setting_path = setting_path
else:
for candidate_setting_files in utils.search_file_regex(deploy_path, '^settings.*\.py$'):
setting_path = os.path.join(manage_path, setting_path + '.py')
utils.copy_file(candidate_setting_files, setting_path)
self.setting_path = setting_path
break
if self.setting_path == None:
return ATTEMPT_STATUS_MISSING_REQUIRED_FILES
LOG.info('setting.py path: {}'.format(setting_path))
requirement_files = utils.search_file(deploy_path, 'requirements.txt')
if requirement_files:
LOG.info('requirements.txt path: {}'.format(requirement_files))
return self.try_deploy(manage_path, requirement_files)
def __init__( self ):
#if we can't find the nucemer binary, throw
nucmerPath = utils.search_file( 'nucmer' )
ProgramBase.__init__( self )
if nucmerPath is None:
raise utils.ProgramNotFoundException( 'nucmer', "Please ensure that the MUMmer package is installed and configured on your system." )
self.nucmer = nucmerPath
self.programName = "nucmer"
self.outputExtension = ".coords"
def deploy_repo_attempt(self, deploy_path):
rake_files = utils.search_file(deploy_path, 'Rakefile')
if not rake_files:
LOG.error('No rakefile found!')
return ATTEMPT_STATUS_MISSING_REQUIRED_FILES
rakefile_paths = [
os.path.dirname(rake_file) for rake_file in rake_files
]
gem_files = utils.search_file(deploy_path, 'Gemfile')
if not gem_files:
LOG.error('No gemfile found!')
return ATTEMPT_STATUS_MISSING_REQUIRED_FILES
gemfile_paths = [os.path.dirname(gem_file) for gem_file in gem_files]
base_dirs = sorted(
set.intersection(set(rakefile_paths), set(gemfile_paths)))
if not base_dirs:
LOG.error('Can not find base directory!')
return ATTEMPT_STATUS_MISSING_REQUIRED_FILES
base_dir = next(iter(base_dirs))
config_files = utils.search_file_regex(
os.path.join(base_dir, 'config'), '.*yml.*')
for config_file in config_files:
if '.example' in config_file:
new_config_file = config_file.replace('.example', '')
utils.copy_file(config_file, new_config_file)
elif '/example' in config_file:
new_config_file = config_file.replace('/example', '')
utils.copy_file(config_file, new_config_file)
elif '-sample' in config_file:
new_config_file = config_file.replace('-sample', '')
utils.copy_file(config_file, new_config_file)
elif '.tmpl' in config_file:
new_config_file = config_file.replace('.tmpl', '')
utils.copy_file(config_file, new_config_file)
self.setting_path = base_dir
return self.try_deploy(base_dir)
def get_urls(self):
setting_files = utils.search_file(BaseDeployer.TMP_DEPLOY_PATH, 'settings.py')[0]
dirname = os.path.dirname(setting_files)
sys.path.append(dirname)
proj_name = os.path.basename(setting_files)
command = "python " + utils.to_vm_path('get_urls.py') + ' ' + utils.to_vm_path(dirname) + ' ' + proj_name
out = utils.vagrant_run_command(command).strip()
if not out:
urls = []
else:
urls = out.splitlines()
return urls
def deploy_repo_attempt(self, deploy_path):
install_phps = utils.search_file(deploy_path, 'install.php')
if len(install_phps) == 0:
return ATTEMPT_STATUS_MISSING_REQUIRED_FILES
base_dir = sorted([os.path.dirname(install_php) for install_php in install_phps])[0]
self.setting_path = base_dir
return self.try_deploy(base_dir)
## DEF
## CLASS
def deploy_repo_attempt(self, deploy_path):
rake_files = utils.search_file(deploy_path, 'Rakefile')
if not rake_files:
LOG.error('No rakefile found!')
return ATTEMPT_STATUS_MISSING_REQUIRED_FILES
rakefile_paths = [os.path.dirname(rake_file) for rake_file in rake_files]
gem_files = utils.search_file(deploy_path, 'Gemfile')
if not gem_files:
LOG.error('No gemfile found!')
return ATTEMPT_STATUS_MISSING_REQUIRED_FILES
gemfile_paths = [os.path.dirname(gem_file) for gem_file in gem_files]
base_dirs = sorted(set.intersection(set(rakefile_paths), set(gemfile_paths)))
if not base_dirs:
LOG.error('Can not find base directory!')
return ATTEMPT_STATUS_MISSING_REQUIRED_FILES
base_dir = next(iter(base_dirs))
config_files = utils.search_file_regex(os.path.join(base_dir, 'config'), '.*yml.*')
for config_file in config_files:
if '.example' in config_file:
new_config_file = config_file.replace('.example', '')
utils.copy_file(config_file, new_config_file)
elif '/example' in config_file:
new_config_file = config_file.replace('/example', '')
utils.copy_file(config_file, new_config_file)
elif '-sample' in config_file:
new_config_file = config_file.replace('-sample', '')
utils.copy_file(config_file, new_config_file)
elif '.tmpl' in config_file:
new_config_file = config_file.replace('.tmpl', '')
utils.copy_file(config_file, new_config_file)
self.setting_path = base_dir
return self.try_deploy(base_dir)
def deploy_repo_attempt(self, deploy_path):
install_phps = utils.search_file(deploy_path, 'install.php')
if len(install_phps) == 0:
return ATTEMPT_STATUS_MISSING_REQUIRED_FILES
base_dir = sorted(
[os.path.dirname(install_php) for install_php in install_phps])[0]
self.setting_path = base_dir
return self.try_deploy(base_dir)
## DEF
## CLASS
def deploy_repo_attempt(self, deploy_path):
if self.database.name != 'MySQL':
return ATTEMPT_STATUS_DATABASE_ERROR
grailsw_files = utils.search_file(deploy_path, 'grailsw')
if not grailsw_files:
LOG.error('No grailsw found!')
return ATTEMPT_STATUS_MISSING_REQUIRED_FILES
base_dir = sorted([
os.path.dirname(grailsw_file) for grailsw_file in grailsw_files
])[0]
self.setting_path = base_dir
return self.try_deploy(base_dir)
## DEF
## CLASS
def compile():
if settings["download_missing_files"]:
version = repository.Version.get_version_file()
repo.compare_tree(version.branch) if version.commit_hash is None else repo.compare_tree(version.commit_hash)
locales.adv_print("BUILDING")
subprocess.check_call(["gradlew.bat", "RatPoison"])
delete_libs_folder()
utils.kill_jdk()
bat_file = utils.get_bat_name()
for path in utils.search_file("java.exe"):
if utils.verify_path(str(path)):
java_exe = str(path)
with open(bat_file, "r") as rFile:
prev_lines = rFile.readlines()
prev_lines[4] = prev_lines[4].replace("java", f"\"{java_exe}\"", 1)
with open(bat_file, "w") as wFile:
wFile.writelines(prev_lines)
break
if locales.adv_input("RANDOMIZE_FILE_NAMES_INPUT") in locales.yes:
randomize_file_names()
replace_bat_path()
def deploy_repo_attempt(self, deploy_path):
package_jsons = utils.search_file(deploy_path, 'package.json')
if not package_jsons:
LOG.error('No package.json found!')
return ATTEMPT_STATUS_MISSING_REQUIRED_FILES
base_dir = sorted([os.path.dirname(package_json) for package_json in package_jsons])[0]
for main_filename in ['server.js', 'app.js', 'main.js']:
if utils.search_file_norecur(base_dir, main_filename):
self.main_filename = main_filename
break
if self.main_filename == None:
LOG.error('No main file found!')
return ATTEMPT_STATUS_MISSING_REQUIRED_FILES
self.setting_path = base_dir
return self.try_deploy(base_dir)
## DEF
## CLASS
from utils import search_file
import cv2
import numpy as np
from utils import COLOR_DICT
from utils import dense_crf
from utils import intersectionAndUnion
from PIL import Image
os.environ["CUDA_VISIBLE_DEVICES"] = "3"
# 是否使用cuda
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
num_classes = 2
num_channels = 3
batch_size = 4
size = (256, 256)
root = "data/membrane/test"
img_file = search_file(root, [".png"])
# print(img_file)
if __name__ == "__main__":
model = U_Net(num_channels, num_classes).to(device)
model.load_state_dict(torch.load('UNet_weights_bilinear_weight.pth'))
model.eval()
with torch.no_grad():
for i in range(1):
print(img_file[i])
input = cv2.imread(img_file[i], cv2.IMREAD_COLOR)
input = cv2.resize(input, size)
original_img = input
print(
os.path.join(
"data/membrane/result1",
os.path.splitext(os.path.basename(img_file[i]))[0] +
def deploy_repo_attempt(self, deploy_path):
LOG.info(utils.configure_env(self.base_path))
self.clear_database()
if self.repo.setup_scripts != None:
project_path = utils.search_dir(deploy_path, self.repo.repo_name())
LOG.info("Project Path: {}".format(project_path))
LOG.info("Setup Scripts: {} && {} && {} && {}".format(
utils.to_env(self.base_path),
"unset DJANGO_SETTINGS_MODULE",
"cd {}".format(project_path),
self.repo.setup_scripts))
code, stdout, stderr = utils.run_command("{} && {} && {} && {}".format(
utils.to_env(self.base_path),
"unset DJANGO_SETTINGS_MODULE",
"cd {}".format(project_path),
self.repo.setup_scripts))
LOG.info("Setup Return Code: {}".format(code))
LOG.debug("Setup Return STDOUT:{}".format(stdout))
LOG.debug("Setup Return STDERR:{}".format(stderr))
if 'myproject' in self.repo.setup_scripts:
deploy_path = os.path.join(deploy_path, 'myproject')
manage_files = utils.search_file(deploy_path, 'manage.py')
if not manage_files:
LOG.error("Can not find manage.py!")
return ATTEMPT_STATUS_MISSING_REQUIRED_FILES
manage_paths = [os.path.dirname(manage_file) for manage_file in manage_files]
base_dir = next(name for name in manage_paths if 'lib/python2.7/site-packages/' not in name)
manage_path = next(name for name in manage_paths if name.startswith(base_dir))
LOG.info('manage.py path: {}'.format(manage_path))
with open(os.path.join(manage_path, 'manage.py'), 'r') as manage_file:
s = re.search('os.environ.setdefault\("DJANGO_SETTINGS_MODULE", "(.*)"\)', manage_file.read())
if s:
setting_path = s.group(1)
else:
setting_paths = utils.search_file(deploy_path, 'settings.py')
if len(setting_paths) > 0:
setting_path = setting_paths[0][:-3]
else:
LOG.error("Can not find settings.py")
return ATTEMPT_STATUS_MISSING_REQUIRED_FILES
setting_path = setting_path.replace('.', '/')
if os.path.isdir(os.path.join(manage_path, setting_path)):
setting_path = os.path.join(manage_path, setting_path)
for setting_file in sorted(os.listdir(setting_path)):
if os.path.isfile(os.path.join(setting_path, setting_file)):
setting_path = os.path.join(setting_path, setting_file)
break
self.setting_path = setting_path
elif os.path.isfile(os.path.join(manage_path, setting_path + '.py')):
setting_path = os.path.join(manage_path, setting_path + '.py')
self.setting_path = setting_path
else:
for candidate_setting_files in utils.search_file_regex(deploy_path, '^settings.*\.py$'):
setting_path = os.path.join(manage_path, setting_path + '.py')
utils.copy_file(candidate_setting_files, setting_path)
self.setting_path = setting_path
break
if self.setting_path == None:
LOG.error("Can not find settings.py!")
return ATTEMPT_STATUS_MISSING_REQUIRED_FILES
LOG.info('setting.py path: {}'.format(setting_path))
requirement_files = utils.search_file(deploy_path, 'requirements.txt')
if requirement_files:
LOG.info('requirements.txt path: {}'.format(requirement_files))
return self.try_deploy(manage_path, requirement_files)
from network import U_Net
from utils import search_file
import cv2
import numpy as np
from utils import COLOR_DICT
from utils import dense_crf
from PIL import Image
os.environ["CUDA_VISIBLE_DEVICES"] = "1"
# 是否使用cuda
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
num_classes = 3
num_channels = 3
batch_size = 4
size = (512, 384)
root = "membrane/test"
img_file = search_file(root, [".jpg"])
print(len(img_file))
# print(img_file)
if __name__ == "__main__":
model = U_Net(num_channels, num_classes).to(device)
model.load_state_dict(torch.load('UNet_weights_bilinear_weight.pth'))
model.eval()
with torch.no_grad():
for i in range(len(img_file)):
print(img_file[i])
save_path = os.path.join(
"membrane1/result",
os.path.basename(img_file[i])[0:-4] + ".png")
print(save_path)
input = cv2.imread(img_file[i], cv2.IMREAD_COLOR)
input = cv2.resize(input, size)
