def main():
print("SCT info:")
print("- version: {}".format(sct.__version__))
print("- path: {0}".format(sct.__sct_dir__))
# initialization
install_software = 0
e = 0
complete_test = param.complete_test
os_running = 'not identified'
# Check input parameters
parser = get_parser()
arguments = parser.parse_args()
if arguments.complete:
complete_test = 1
# use variable "verbose" when calling sct.run for more clarity
verbose = complete_test
# complete test
if complete_test:
print(sct.run('date', verbose))
print(sct.run('whoami', verbose))
print(sct.run('pwd', verbose))
bash_profile = os.path.expanduser("~/.bash_profile")
if os.path.isfile(bash_profile):
with io.open(bash_profile, "r") as f:
print(f.read())
bashrc = os.path.expanduser("~/.bashrc")
if os.path.isfile(bashrc):
with io.open(bashrc, "r") as f:
print(f.read())
# check OS
platform_running = sys.platform
if platform_running.find('darwin') != -1:
os_running = 'osx'
elif platform_running.find('linux') != -1:
os_running = 'linux'
print('OS: ' + os_running + ' (' + platform.platform() + ')')
# Check number of CPU cores
from multiprocessing import cpu_count
output = int(os.getenv('ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS', 0))
print('CPU cores: Available: {}, Used by SCT: {}'.format(
cpu_count(), output))
# check RAM
sct.checkRAM(os_running, 0)
# check if Python path is within SCT path
print_line('Check Python executable')
path_python = sys.executable
if sct.__sct_dir__ in path_python:
print_ok()
print(' Using bundled python {} at {}'.format(sys.version,
path_python))
else:
print_warning()
print(' Using system python which is unsupported: {}'.format(
path_python))
# check if data folder is empty
print_line('Check if data are installed')
if os.path.isdir(sct.__data_dir__):
print_ok()
else:
print_fail()
for dep_pkg, dep_ver_spec in get_dependencies():
if dep_ver_spec is None:
print_line('Check if %s is installed' % (dep_pkg))
else:
print_line('Check if %s (%s) is installed' %
(dep_pkg, dep_ver_spec))
try:
module_name, suppress_stderr = resolve_module(dep_pkg)
module = module_import(module_name, suppress_stderr)
version = get_version(module)
if dep_ver_spec is None and version is not None:
ver_pip_setup = dict(
get_dependencies(
os.path.join(sct.__sct_dir__,
"requirements.txt"))).get(dep_pkg, None)
if ver_pip_setup is None:
print_ok(more=(" (%s)" % version))
elif ver_pip_setup is not None and version.startswith(
ver_pip_setup):
print_ok(more=(" (%s)" % version))
else:
print_warning(more=(" (%s != %s reference version))" %
(version, ver_pip_setup)))
elif dep_ver_spec == version:
print_ok()
else:
print_warning(more=(" (%s != %s mandated version))" %
(version, dep_ver_spec)))
except ImportError as err:
print_fail()
print(err)
install_software = 1
print_line('Check if spinalcordtoolbox is installed')
try:
importlib.import_module('spinalcordtoolbox')
print_ok()
except ImportError:
print_fail()
install_software = 1
# Check ANTs integrity
print_line('Check ANTs compatibility with OS ')
cmd = 'isct_test_ants'
status, output = sct.run(cmd, verbose=0, raise_exception=False)
if status == 0:
print_ok()
else:
print_fail()
print(output)
e = 1
if complete_test:
print('>> ' + cmd)
print((status, output), '\n')
# check PropSeg compatibility with OS
print_line('Check PropSeg compatibility with OS ')
status, output = sct.run('isct_propseg',
verbose=0,
raise_exception=False,
is_sct_binary=True)
if status in (0, 1):
print_ok()
else:
print_fail()
print(output)
e = 1
if complete_test:
print((status, output), '\n')
print_line('Check if DISPLAY variable is set')
try:
os.environ['DISPLAY']
print_ok()
# Further check with PyQt specifically
print_line('Check if figure can be opened with PyQt')
from PyQt5.QtWidgets import QApplication, QLabel
try:
app = QApplication([])
label = QLabel('Hello World!')
label.show()
label.close()
print_ok()
except Exception as err:
print_fail()
print(err)
except KeyError:
print_fail()
print('')
sys.exit(e + install_software)
def main():
# initialization
fsl_is_working = 1
# ants_is_installed = 1
# isct_c3d_is_installed = 1
install_software = 0
e = 0
restart_terminal = 0
create_log_file = param.create_log_file
file_log = 'sct_check_dependencies.log'
complete_test = param.complete_test
os_running = 'not identified'
print
# Check input parameters
try:
opts, args = getopt.getopt(sys.argv[1:], 'hlc')
except getopt.GetoptError:
usage()
for opt, arg in opts:
if opt == '-h':
usage()
elif opt in ('-c'):
complete_test = 1
elif opt in ('-l'):
create_log_file = 1
# use variable "verbose" when calling sct.run for more clarity
verbose = complete_test
# redirect to log file
if create_log_file:
orig_stdout = sys.stdout
handle_log = file(file_log, 'w')
sys.stdout = handle_log
# complete test
if complete_test:
print sct.run('date', verbose)
print sct.run('whoami', verbose)
print sct.run('pwd', verbose)
if os.path.isfile('~/.bash_profile'):
(status, output) = sct.run('more ~/.bash_profile', verbose)
print output
if os.path.isfile('~/.bashrc'):
(status, output) = sct.run('more ~/.bashrc', verbose)
print output
# check if user is root (should not be!)
if os.geteuid() == 0:
print 'Looks like you are root. Please run this script without sudo. Exit program\n'
sys.exit(2)
# check OS
print 'Check which OS is running... '
platform_running = sys.platform
if (platform_running.find('darwin') != -1):
os_running = 'osx'
elif (platform_running.find('linux') != -1):
os_running = 'linux'
print ' '+os_running+' ('+platform.platform()+')'
# check RAM
print 'Check RAM... '
sct.checkRAM(os_running)
# check installation packages
print 'Check which Python is running ... '
print ' '+sys.executable
# get path of the toolbox
status, output = sct.run('echo $SCT_DIR', verbose)
path_sct = output
if complete_test:
print (status, output), '\n'
# fetch version of the toolbox
print 'Fetch version of the Spinal Cord Toolbox... '
with open (path_sct+"/version.txt", "r") as myfile:
version_sct = myfile.read().replace('\n', '')
print " version: "+version_sct
# check pillow
print_line("Check if pillow is installed ")
try:
import PIL
print_ok()
except ImportError:
print_fail()
print ' pillow is not installed! Please install it via miniconda (https://sourceforge.net/p/spinalcordtoolbox/wiki/install_python/)'
install_software = 1
# check numpy
print_line('Check if numpy is installed ')
try:
import numpy
print_ok()
except ImportError:
print_fail()
print ' numpy is not installed! Please install it via miniconda (https://sourceforge.net/p/spinalcordtoolbox/wiki/install_python/)'
install_software = 1
# check scipy
print_line('Check if scipy is installed ')
try:
import scipy
print_ok()
except ImportError:
print_fail()
print ' scipy is not installed! Please install it via miniconda (https://sourceforge.net/p/spinalcordtoolbox/wiki/install_python/)'
install_software = 1
# check sympy
print_line('Check if sympy is installed ')
try:
import sympy
print_ok()
except ImportError:
print_fail()
print ' sympy is not installed! Please install it via miniconda (https://sourceforge.net/p/spinalcordtoolbox/wiki/install_python/)'
install_software = 1
# check matplotlib
print_line('Check if matplotlib is installed ')
try:
import matplotlib
print_ok()
except ImportError:
print_fail()
print ' matplotlib is not installed! Please install it via miniconda (https://sourceforge.net/p/spinalcordtoolbox/wiki/install_python/)'
install_software = 1
# check nibabel
print_line('Check if nibabel is installed ')
try:
import nibabel
print_ok()
except ImportError:
print_fail()
print ' nibabel is not installed! See instructions (https://sourceforge.net/p/spinalcordtoolbox/wiki/install_python/)'
install_software = 1
# check dipy
print_line('Check if dipy is installed ')
try:
import dipy
print_ok()
except ImportError:
print_fail()
print ' dipy is not installed! You can install it using: http://nipy.org/dipy/installation.html'
install_software = 1
# check if FSL is declared
print_line('Check if FSL is declared ')
cmd = 'which fsl'
status, output = commands.getstatusoutput(cmd)
if output:
print_ok()
path_fsl = output[:-7]
print ' '+path_fsl
else:
print_fail()
print ' FSL is either not installed or not declared.'
print ' - To install it: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation.'
print ' - To declare it: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/ShellSetup'
e = 1
# check if git is installed
print_line('Check if git is installed ')
cmd = 'which git'
status, output = commands.getstatusoutput(cmd)
if output:
print_ok()
else:
print_fail()
print ' git is not installed.'
print ' - To install it: http://git-scm.com/book/en/v1/Getting-Started-Installing-Git'
e = 1
if complete_test:
print '>> '+cmd
print (status, output), '\n'
# # check if FSL is installed
# if not fsl_is_working:
# print_line('Check if FSL is installed ')
# # check first under /usr for faster search
# (status, output) = commands.getstatusoutput('find /usr -name "flirt" -type f -print -quit 2>/dev/null')
# if output:
# print_ok()
# path_fsl = output[:-10]
# print ' '+path_fsl
# else:
# # some users might have installed it under /home, so check it...
# (status, output) = commands.getstatusoutput('find /home -name "flirt" -type f -print -quit 2>/dev/null')
# if output:
# print_ok()
# path_fsl = output[:-10]
# print ' '+path_fsl
# else:
# print_fail()
# print ' FSL is either not installed.'
# print ' - To install it: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation.'
# fsl_is_installed = 0
# install_software = 1
# # check ANTs
# print_line('Check which ANTs is running ')
# # (status, output) = commands.getstatusoutput('command -v isct_antsRegistration >/dev/null 2>&1 || { echo >&2 "nope";}')
# cmd = 'which isct_antsRegistration'
# status, output = commands.getstatusoutput(cmd)
# if output:
# print_ok()
# path_ants = output[:-20]
# print ' '+path_ants
# else:
# print_warning()
# print ' ANTs is not declared.'
# e = 1
# if complete_test:
# print '>> '+cmd
# print (status, output), '\n'
# check if ANTs is compatible with OS
print_line('Check ANTs compatibility with OS ')
cmd = 'isct_antsRegistration'
status, output = commands.getstatusoutput(cmd)
if status in [0, 256]:
print_ok()
else:
print_fail()
e = 1
if complete_test:
print '>> '+cmd
print (status, output), '\n'
# # check isct_c3d
# print_line('Check which isct_c3d is running ')
# # (status, output) = commands.getstatusoutput('command -v isct_c3d >/dev/null 2>&1 || { echo >&2 "nope";}')
# status, output = commands.getstatusoutput('which isct_c3d')
# if output:
# print_ok()
# path_isct_c3d = output[:-7]
# print ' '+path_isct_c3d
# else:
# print_warning()
# print ' isct_c3d is not installed or not declared.'
# install_software = 1
# if complete_test:
# print (status, output), '\n'
# check isct_c3d compatibility with OS
print_line('Check c3d compatibility with OS ')
(status, output) = commands.getstatusoutput('isct_c3d -h')
if status in [0, 256]:
print_ok()
else:
print_fail()
install_software = 1
if complete_test:
print (status, output), '\n'
# check PropSeg compatibility with OS
print_line('Check PropSeg compatibility with OS ')
(status, output) = commands.getstatusoutput('sct_propseg')
if status in [0, 256]:
print_ok()
else:
print_fail()
e = 1
if complete_test:
print (status, output), '\n'
# Check ANTs integrity
print_line('Check integrity of ANTs output ')
cmd_ants_test = 'isct_test_ants'
# if not complete_test:
# cmd_ants_test += ' -v 0'
(status, output) = commands.getstatusoutput(cmd_ants_test)
if status in [0]:
print_ok()
else:
print_fail()
print output
e = 1
if complete_test:
print (status, output), '\n'
print
# close log file
if create_log_file:
sys.stdout = orig_stdout
handle_log.close()
print "File generated: "+file_log+'\n'
sys.exit(e + install_software)
def main():
print("SCT info:")
print("- version: {}".format(sct.__version__))
print("- path: {0}".format(sct.__sct_dir__))
# initialization
fsl_is_working = 1
# ants_is_installed = 1
install_software = 0
e = 0
restart_terminal = 0
create_log_file = param.create_log_file
file_log = 'sct_check_dependencies.log'
complete_test = param.complete_test
os_running = 'not identified'
dipy_version = '0.10.0dev'
# Check input parameters
parser = get_parser()
arguments = parser.parse_args()
if arguments.complete:
complete_test = 1
# use variable "verbose" when calling sct.run for more clarity
verbose = complete_test
# complete test
if complete_test:
print(sct.run('date', verbose))
print(sct.run('whoami', verbose))
print(sct.run('pwd', verbose))
bash_profile = os.path.expanduser("~/.bash_profile")
if os.path.isfile(bash_profile):
with io.open(bash_profile, "r") as f:
print(f.read())
bashrc = os.path.expanduser("~/.bashrc")
if os.path.isfile(bashrc):
with io.open(bashrc, "r") as f:
print(f.read())
# check OS
platform_running = sys.platform
if platform_running.find('darwin') != -1:
os_running = 'osx'
elif platform_running.find('linux') != -1:
os_running = 'linux'
print('OS: ' + os_running + ' (' + platform.platform() + ')')
# Check number of CPU cores
from multiprocessing import cpu_count
output = int(os.getenv('ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS', 0))
print('CPU cores: Available: {}, Used by SCT: {}'.format(cpu_count(), output))
# check RAM
sct.checkRAM(os_running, 0)
# check if Python path is within SCT path
print_line('Check Python executable')
path_python = sys.executable
if sct.__sct_dir__ in path_python:
print_ok()
print(' Using bundled python {} at {}'.format(sys.version, path_python))
else:
print_warning()
print(' Using system python which is unsupported: {}'.format(path_python))
# check if data folder is empty
print_line('Check if data are installed')
if os.path.isdir(sct.__data_dir__):
print_ok()
else:
print_fail()
for dep_pkg, dep_ver_spec in get_dependencies():
if dep_ver_spec is None:
print_line('Check if %s is installed' % (dep_pkg))
else:
print_line('Check if %s (%s) is installed' % (dep_pkg, dep_ver_spec))
try:
module_name, suppress_stderr = resolve_module(dep_pkg)
module = module_import(module_name, suppress_stderr)
version = getattr(module, "__version__", getattr(module, "__VERSION__", None))
if dep_ver_spec is None and version is not None:
ver_pip_setup = dict(get_dependencies(os.path.join(sct.__sct_dir__, "requirements.txt"))).get(dep_pkg, None)
if ver_pip_setup is None:
print_ok(more=(" (%s)" % version))
elif ver_pip_setup is not None and version.startswith(ver_pip_setup):
print_ok(more=(" (%s)" % version))
else:
print_warning(more=(" (%s != %s reference version))" % (version, ver_pip_setup)))
elif dep_ver_spec == version:
print_ok()
else:
print_warning(more=(" (%s != %s mandated version))" % (version, dep_ver_spec)))
except ImportError:
print_fail()
install_software = 1
print_line('Check if spinalcordtoolbox is installed')
try:
importlib.import_module('spinalcordtoolbox')
print_ok()
except ImportError:
print_fail()
install_software = 1
# CHECK EXTERNAL MODULES:
# Check if dipy is installed
# print_line('Check if dipy ('+dipy_version+') is installed')
# try:
# module = importlib.import_module('dipy')
# if module.__version__ == dipy_version:
# print_ok()
# else:
# print_warning()
# print(' Detected version: '+version+'. Required version: '+dipy_version)
# except ImportError:
# print_fail()
# install_software = 1
# Check ANTs integrity
print_line('Check ANTs compatibility with OS ')
cmd = 'isct_test_ants'
status, output = sct.run(cmd, verbose=0, raise_exception=False)
if status == 0:
print_ok()
else:
print_fail()
print(output)
e = 1
if complete_test:
print('>> ' + cmd)
print((status, output), '\n')
# check if ANTs is compatible with OS
# print_line('Check ANTs compatibility with OS ')
# cmd = 'isct_antsRegistration'
# status, output = sct.run(cmd)
# if status in [0, 256]:
# print_ok()
# else:
# print_fail()
# e = 1
# if complete_test:
# print('>> '+cmd)
# print((status, output), '\n')
# check PropSeg compatibility with OS
print_line('Check PropSeg compatibility with OS ')
status, output = sct.run('isct_propseg', verbose=0, raise_exception=False, is_sct_binary=True)
if status in (0, 1):
print_ok()
else:
print_fail()
print(output)
e = 1
if complete_test:
print((status, output), '\n')
# check if figure can be opened (in case running SCT via ssh connection)
print_line('Check if figure can be opened')
import warnings
with warnings.catch_warnings():
warnings.simplefilter("ignore")
import matplotlib.pyplot as plt
try:
plt.figure()
plt.close()
print_ok()
except Exception:
print_fail()
print('')
sys.exit(e + install_software)
def main():
# initialization
fsl_is_working = 1
# ants_is_installed = 1
# isct_c3d_is_installed = 1
install_software = 0
e = 0
restart_terminal = 0
create_log_file = param.create_log_file
file_log = 'sct_check_dependencies.log'
complete_test = param.complete_test
os_running = 'not identified'
print
# Check input parameters
try:
opts, args = getopt.getopt(sys.argv[1:], 'hlc')
except getopt.GetoptError:
usage()
for opt, arg in opts:
if opt == '-h':
usage()
elif opt in ('-c'):
complete_test = 1
elif opt in ('-l'):
create_log_file = 1
# use variable "verbose" when calling sct.run for more clarity
verbose = complete_test
# redirect to log file
if create_log_file:
orig_stdout = sys.stdout
handle_log = file(file_log, 'w')
sys.stdout = handle_log
# complete test
if complete_test:
print sct.run('date', verbose)
print sct.run('whoami', verbose)
print sct.run('pwd', verbose)
if os.path.isfile('~/.bash_profile'):
(status, output) = sct.run('more ~/.bash_profile', verbose)
print output
if os.path.isfile('~/.bashrc'):
(status, output) = sct.run('more ~/.bashrc', verbose)
print output
# check if user is root (should not be!)
if os.geteuid() == 0:
print 'Looks like you are root. Please run this script without sudo. Exit program\n'
sys.exit(2)
# check OS
print 'Check which OS is running... '
platform_running = sys.platform
if (platform_running.find('darwin') != -1):
os_running = 'osx'
elif (platform_running.find('linux') != -1):
os_running = 'linux'
print ' ' + os_running + ' (' + platform.platform() + ')'
# check RAM
print 'Check RAM... '
sct.checkRAM(os_running)
# check installation packages
print 'Check which Python is running ... '
print ' ' + sys.executable
# get path of the toolbox
status, output = sct.run('echo $SCT_DIR', verbose)
path_sct = output
if complete_test:
print(status, output), '\n'
# fetch version of the toolbox
print 'Fetch version of the Spinal Cord Toolbox... '
with open(path_sct + "/version.txt", "r") as myfile:
version_sct = myfile.read().replace('\n', '')
print " version: " + version_sct
# loop across python packages -- CONDA
version_requirements = get_version_requirements()
for i in version_requirements:
if i == 'pillow':
module = 'PIL'
else:
module = i
print_line('Check if ' + i + ' (' + version_requirements.get(i) +
') is installed')
try:
module = importlib.import_module(module)
# get version
if i == 'pillow':
version = module.PILLOW_VERSION
else:
version = module.__version__
# check if version matches requirements
if check_package_version(version, version_requirements, i):
print_ok()
else:
print_warning()
print ' Detected version: ' + version + '. Required version: ' + version_requirements[
i]
except ImportError:
print_fail()
install_software = 1
# loop across python packages -- PIP
version_requirements_pip = get_version_requirements_pip()
for i in version_requirements_pip:
if i == 'scikit-image':
module = 'skimage'
else:
module = i
print_line('Check if ' + i + ' (' + version_requirements_pip.get(i) +
') is installed')
try:
module = importlib.import_module(module)
# get version
version = module.__version__
# check if version matches requirements
if check_package_version(version, version_requirements_pip, i):
print_ok()
else:
print_warning()
print ' Detected version: ' + version + '. Required version: ' + version_requirements_pip[
i]
except ImportError:
print_fail()
install_software = 1
# check if git is installed
print_line('Check if git is installed ')
cmd = 'which git'
status, output = commands.getstatusoutput(cmd)
if output:
print_ok()
else:
print_fail()
print ' git is not installed.'
print ' - To install it: http://git-scm.com/book/en/v1/Getting-Started-Installing-Git'
e = 1
if complete_test:
print '>> ' + cmd
print(status, output), '\n'
# check if ANTs is compatible with OS
print_line('Check ANTs compatibility with OS ')
cmd = 'isct_antsRegistration'
status, output = commands.getstatusoutput(cmd)
if status in [0, 256]:
print_ok()
else:
print_fail()
e = 1
if complete_test:
print '>> ' + cmd
print(status, output), '\n'
# check isct_c3d compatibility with OS
print_line('Check c3d compatibility with OS ')
(status, output) = commands.getstatusoutput('isct_c3d -h')
if status in [0, 256]:
print_ok()
else:
print_fail()
install_software = 1
if complete_test:
print(status, output), '\n'
# check PropSeg compatibility with OS
print_line('Check PropSeg compatibility with OS ')
(status, output) = commands.getstatusoutput('sct_propseg')
if status in [0, 256]:
print_ok()
else:
print_fail()
e = 1
if complete_test:
print(status, output), '\n'
# Check ANTs integrity
print_line('Check integrity of ANTs output ')
cmd_ants_test = 'isct_test_ants'
# if not complete_test:
# cmd_ants_test += ' -v 0'
(status, output) = commands.getstatusoutput(cmd_ants_test)
if status in [0]:
print_ok()
else:
print_fail()
print output
e = 1
if complete_test:
print(status, output), '\n'
print
# close log file
if create_log_file:
sys.stdout = orig_stdout
handle_log.close()
print "File generated: " + file_log + '\n'
sys.exit(e + install_software)
sct.log.info('Hostname: {}'.format(platform.node()))
# Check number of CPU cores
sct.log.info('CPU Thread on local machine: {} '.format(cpu_count()))
sct.log.info(' Requested threads: {} '.format(jobs))
if __MPI__:
sct.log.info(
"Running in MPI mode with mpi4py.futures's MPIPoolExecutor")
else:
sct.log.info(
"Running with python concurrent.futures's ProcessPoolExecutor")
# check RAM
sct.checkRAM(os_running, 0)
# display command
sct.log.info('\nCommand(s):')
for args in list_args:
sct.log.info(' ' + function_to_test + ' ' + args)
sct.log.info('Dataset: ' + path_data)
sct.log.info('Test integrity: ' + str(test_integrity))
# test function
try:
# retrieve subjects list
list_subj = get_list_subj(path_data,
data_specifications=data_specifications,
fname_database=fname_database)
# during testing, redirect to standard output to avoid stacking error messages in the general log
def main():
path_sct = os.environ.get("SCT_DIR",
os.path.dirname(os.path.dirname(__file__)))
print("SCT info:")
print("- version: {}".format(sct.__version__))
print("- path: {0}".format(path_sct))
# initialization
fsl_is_working = 1
# ants_is_installed = 1
install_software = 0
e = 0
restart_terminal = 0
create_log_file = param.create_log_file
file_log = 'sct_check_dependencies.log'
complete_test = param.complete_test
os_running = 'not identified'
dipy_version = '0.10.0dev'
# Check input parameters
parser = get_parser()
arguments = parser.parse_args()
if arguments.complete:
complete_test = 1
if arguments.generate_log:
create_log_file = 1
# use variable "verbose" when calling sct.run for more clarity
verbose = complete_test
# redirect to log file
if create_log_file:
handle_log = sct.ForkStdoutToFile(file_log)
# complete test
if complete_test:
print(sct.run('date', verbose))
print(sct.run('whoami', verbose))
print(sct.run('pwd', verbose))
bash_profile = os.path.expanduser("~/.bash_profile")
if os.path.isfile(bash_profile):
with io.open(bash_profile, "r") as f:
print(f.read())
bashrc = os.path.expanduser("~/.bashrc")
if os.path.isfile(bashrc):
with io.open(bashrc, "r") as f:
print(f.read())
# check OS
platform_running = sys.platform
if (platform_running.find('darwin') != -1):
os_running = 'osx'
elif (platform_running.find('linux') != -1):
os_running = 'linux'
print('OS: ' + os_running + ' (' + platform.platform() + ')')
# Check number of CPU cores
from multiprocessing import cpu_count
output = int(os.getenv('ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS', 0))
print('CPU cores: Available: {}, Used by SCT: {}'.format(
cpu_count(), output))
# check RAM
sct.checkRAM(os_running, 0)
# check if Python path is within SCT path
print_line('Check Python executable')
path_python = sys.executable
if path_sct in path_python:
print_ok()
print(' Using bundled python {} at {}'.format(sys.version,
path_python))
else:
print_warning()
print(' Using system python which is unsupported: {}'.format(
path_python))
# check if data folder is empty
print_line('Check if data are installed')
if os.listdir(os.path.join(path_sct, "data")):
print_ok()
else:
print_fail()
# loop across python packages -- CONDA
version_requirements = get_version_requirements()
for i in version_requirements:
module_name, suppress_stderr = resolve_module(i)
if module_name is None:
continue
print_line('Check if %s (%s) is installed' %
(i, version_requirements.get(i)))
try:
module = module_import(module_name, suppress_stderr)
# get version
try:
version = module.__version__
except:
try:
version = module.__VERSION__
except:
# skip if module doesn't have __version__ nor __VERSION__ (e.g., xlutils)
version = version_requirements[i]
# check if version matches requirements
if check_package_version(version, version_requirements, i):
print_ok()
else:
print_warning()
print(' Detected version: ' + version +
'. Required version: ' + version_requirements[i])
except ImportError:
print_fail()
install_software = 1
# loop across python packages -- PIP
version_requirements_pip = get_version_requirements_pip()
for i in version_requirements_pip:
module_name, suppress_stderr = resolve_module(i)
print_line('Check if ' + i + ' (' + version_requirements_pip.get(i) +
') is installed')
try:
module = module_import(module_name, suppress_stderr)
if module_name in ("raven", ):
version = module.VERSION
else:
try:
version = module.__version__
except AttributeError:
# Futures package as no embedded version info
version = version_requirements_pip[i]
# check if version matches requirements
if check_package_version(version, version_requirements_pip, i):
print_ok()
else:
print_warning()
print(' Detected version: ' + version +
'. Required version: ' + version_requirements_pip[i])
except ImportError:
print_fail()
install_software = 1
# CHECK DEPENDENT MODULES (installed by nibabel/dipy):
sys.stdout.write('Check if numpy is installed')
sys.stdout.flush()
try:
np = importlib.import_module('numpy')
sys.stdout.write(' ({})'.format(np.__version__).ljust(25, '.'))
print_ok()
except ImportError:
sys.stdout.write(' (........................')
print_fail()
install_software = 1
sys.stdout.write('Check if scipy is installed')
sys.stdout.flush()
try:
sp = importlib.import_module('scipy')
sys.stdout.write(' ({})'.format(sp.__version__).ljust(25, '.'))
print_ok()
except ImportError:
print_fail()
install_software = 1
print_line('Check if spinalcordtoolbox is installed')
try:
importlib.import_module('spinalcordtoolbox')
print_ok()
except ImportError:
print_fail()
install_software = 1
# CHECK EXTERNAL MODULES:
# Check if dipy is installed
# print_line('Check if dipy ('+dipy_version+') is installed')
# try:
# module = importlib.import_module('dipy')
# if module.__version__ == dipy_version:
# print_ok()
# else:
# print_warning()
# print(' Detected version: '+version+'. Required version: '+dipy_version)
# except ImportError:
# print_fail()
# install_software = 1
# Check ANTs integrity
print_line('Check ANTs compatibility with OS ')
cmd = 'isct_test_ants'
status, output = sct.run(cmd, verbose=0, raise_exception=False)
if status == 0:
print_ok()
else:
print_fail()
print(output)
e = 1
if complete_test:
print('>> ' + cmd)
print((status, output), '\n')
# check if ANTs is compatible with OS
# print_line('Check ANTs compatibility with OS ')
# cmd = 'isct_antsRegistration'
# status, output = sct.run(cmd)
# if status in [0, 256]:
# print_ok()
# else:
# print_fail()
# e = 1
# if complete_test:
# print('>> '+cmd)
# print((status, output), '\n')
# check PropSeg compatibility with OS
print_line('Check PropSeg compatibility with OS ')
status, output = sct.run('isct_propseg', verbose=0, raise_exception=False)
if status in (0, 1):
print_ok()
else:
print_fail()
print(output)
e = 1
if complete_test:
print((status, output), '\n')
# check if figure can be opened (in case running SCT via ssh connection)
print_line('Check if figure can be opened')
import warnings
with warnings.catch_warnings():
warnings.simplefilter("ignore")
import matplotlib.pyplot as plt
try:
plt.figure()
plt.close()
print_ok()
except Exception:
if "MPLBACKEND" not in os.environ:
print("\nSecond attempt to plot ...")
print("\nOverwriting environment variable $MPLBACKEND=agg")
try:
os.environ["MPLBACKEND"] = "agg"
plt.figure()
plt.close()
print_ok()
except Exception:
print_fail()
print(sys.exc_info())
else:
print(
"Please try manually setting environment variable $MPLBACKEND=agg"
)
print_fail()
print('')
sys.exit(e + install_software)
if (platform_running.find('darwin') != -1):
os_running = 'osx'
elif (platform_running.find('linux') != -1):
os_running = 'linux'
print 'OS: '+os_running+' ('+platform.platform()+')'
# check hostname
print 'Hostname:', platform.node()
# Check number of CPU cores
from multiprocessing import cpu_count
# status, output = sct.run('echo $ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS', 0)
print 'CPU cores: ' + str(cpu_count()) # + ', Used by SCT: '+output
# check RAM
sct.checkRAM(os_running, 0)
# test function
try:
results = test_function(function_to_test, dataset, parameters, nb_cpu, json_requirements, verbose)
pd.set_option('display.max_rows', 500)
pd.set_option('display.max_columns', 500)
pd.set_option('display.width', 1000)
results_subset = results.drop('script', 1).drop('dataset', 1).drop('parameters', 1).drop('output', 1)
results_display = results_subset
# save panda structure
if create_log:
results_subset.to_pickle(file_log+'.pickle')
# mean
def main():
# initialization
fsl_is_working = 1
# ants_is_installed = 1
install_software = 0
e = 0
restart_terminal = 0
create_log_file = param.create_log_file
file_log = 'sct_check_dependencies.log'
complete_test = param.complete_test
os_running = 'not identified'
print
# Check input parameters
parser = get_parser()
arguments = parser.parse(sys.argv[1:])
if '-c' in arguments:
complete_test = 1
if '-log' in arguments:
create_log_file = 1
# use variable "verbose" when calling sct.run for more clarity
verbose = complete_test
# redirect to log file
if create_log_file:
orig_stdout = sys.stdout
handle_log = file(file_log, 'w')
sys.stdout = handle_log
# complete test
if complete_test:
print sct.run('date', verbose)
print sct.run('whoami', verbose)
print sct.run('pwd', verbose)
if os.path.isfile('~/.bash_profile'):
(status, output) = sct.run('more ~/.bash_profile', verbose)
print output
if os.path.isfile('~/.bashrc'):
(status, output) = sct.run('more ~/.bashrc', verbose)
print output
# check if user is root (should not be!)
if os.geteuid() == 0:
print 'Looks like you are root. Please run this script without sudo. Exit program\n'
sys.exit(2)
# check OS
print 'Check which OS is running... '
platform_running = sys.platform
if (platform_running.find('darwin') != -1):
os_running = 'osx'
elif (platform_running.find('linux') != -1):
os_running = 'linux'
print '.. '+os_running+' ('+platform.platform()+')'
# Check number of CPU cores
print 'Check number of CPU cores...'
from multiprocessing import cpu_count
print '.. Available: ' + str(cpu_count())
status, output = sct.run('echo $ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS', 0)
print '.. Used by SCT: ' + output
# check RAM
print 'Check RAM... '
sct.checkRAM(os_running)
# check installation packages
print 'Check which Python is running...'
print '.. '+sys.executable
# get path of the toolbox
print 'Check SCT path...'
status, output = sct.run('echo $SCT_DIR', verbose)
path_sct = output
print '.. '+path_sct
# fetch version of the toolbox
print 'Check SCT version... '
with open (path_sct+"/version.txt", "r") as myfile:
version_sct = myfile.read().replace('\n', '')
print ".. "+version_sct
# loop across python packages -- CONDA
version_requirements = get_version_requirements()
for i in version_requirements:
if i == 'scikit-image':
module = 'skimage'
else:
module = i
print_line('Check if '+i+' ('+version_requirements.get(i)+') is installed')
try:
module = importlib.import_module(module)
# get version
version = module.__version__
# check if version matches requirements
if check_package_version(version, version_requirements, i):
print_ok()
else:
print_warning()
print ' Detected version: '+version+'. Required version: '+version_requirements[i]
except ImportError:
print_fail()
install_software = 1
# loop across python packages -- PIP
version_requirements_pip = get_version_requirements_pip()
for i in version_requirements_pip:
module = i
print_line('Check if '+i+' ('+version_requirements_pip.get(i)+') is installed')
try:
module = importlib.import_module(module)
# get version
version = module.__version__
# check if version matches requirements
if check_package_version(version, version_requirements_pip, i):
print_ok()
else:
print_warning()
print ' Detected version: '+version+'. Required version: '+version_requirements_pip[i]
except ImportError:
print_fail()
install_software = 1
# CHECK EXTERNAL MODULES:
# Check if ornlm is installed
print_line('Check if ornlm is installed')
# sys.path.append(path_sct + '/external/denoise/ornlm') # append to PYTHONPATH
try:
importlib.import_module('ornlm')
print_ok()
except ImportError:
print_fail()
install_software = 1
# Check if dipy is installed
print_line('Check if dipy is installed')
try:
importlib.import_module('dipy')
print_ok()
except ImportError:
print_fail()
install_software = 1
# check if ANTs is compatible with OS
print_line('Check ANTs compatibility with OS ')
cmd = 'isct_antsRegistration'
status, output = commands.getstatusoutput(cmd)
if status in [0, 256]:
print_ok()
else:
print_fail()
e = 1
if complete_test:
print '>> '+cmd
print (status, output), '\n'
# check PropSeg compatibility with OS
print_line('Check PropSeg compatibility with OS ')
(status, output) = commands.getstatusoutput('sct_propseg')
if status in [0, 256]:
print_ok()
else:
print_fail()
e = 1
if complete_test:
print (status, output), '\n'
# close log file
if create_log_file:
sys.stdout = orig_stdout
handle_log.close()
print "File generated: "+file_log+'\n'
print ''
sys.exit(e + install_software)
def main():
print("SCT info:")
print("- version: {}".format(sct.__version__))
print("- path: {0}".format(sct.__sct_dir__))
# initialization
fsl_is_working = 1
# ants_is_installed = 1
install_software = 0
e = 0
restart_terminal = 0
create_log_file = param.create_log_file
file_log = 'sct_check_dependencies.log'
complete_test = param.complete_test
os_running = 'not identified'
dipy_version = '0.10.0dev'
# Check input parameters
parser = get_parser()
arguments = parser.parse_args()
if arguments.complete:
complete_test = 1
# use variable "verbose" when calling sct.run for more clarity
verbose = complete_test
# complete test
if complete_test:
print(sct.run('date', verbose))
print(sct.run('whoami', verbose))
print(sct.run('pwd', verbose))
bash_profile = os.path.expanduser("~/.bash_profile")
if os.path.isfile(bash_profile):
with io.open(bash_profile, "r") as f:
print(f.read())
bashrc = os.path.expanduser("~/.bashrc")
if os.path.isfile(bashrc):
with io.open(bashrc, "r") as f:
print(f.read())
# check OS
platform_running = sys.platform
if (platform_running.find('darwin') != -1):
os_running = 'osx'
elif (platform_running.find('linux') != -1):
os_running = 'linux'
print('OS: ' + os_running + ' (' + platform.platform() + ')')
# Check number of CPU cores
from multiprocessing import cpu_count
output = int(os.getenv('ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS', 0))
print('CPU cores: Available: {}, Used by SCT: {}'.format(cpu_count(), output))
# check RAM
sct.checkRAM(os_running, 0)
# check if Python path is within SCT path
print_line('Check Python executable')
path_python = sys.executable
if sct.__sct_dir__ in path_python:
print_ok()
print(' Using bundled python {} at {}'.format(sys.version, path_python))
else:
print_warning()
print(' Using system python which is unsupported: {}'.format(path_python))
# check if data folder is empty
print_line('Check if data are installed')
if os.path.isdir(sct.__data_dir__):
print_ok()
else:
print_fail()
for dep_pkg, dep_ver_spec in get_dependencies():
if dep_ver_spec is None:
print_line('Check if %s is installed' % (dep_pkg))
else:
print_line('Check if %s (%s) is installed' % (dep_pkg, dep_ver_spec))
try:
module_name, suppress_stderr = resolve_module(dep_pkg)
module = module_import(module_name, suppress_stderr)
version = getattr(module, "__version__", getattr(module, "__VERSION__", None))
if dep_ver_spec is None and version is not None:
ver_pip_setup = dict(get_dependencies(os.path.join(sct.__sct_dir__, "requirements.txt"))).get(dep_pkg, None)
if ver_pip_setup is None:
print_ok(more=(" (%s)" % version))
elif ver_pip_setup is not None and version.startswith(ver_pip_setup):
print_ok(more=(" (%s)" % version))
else:
print_warning(more=(" (%s != %s reference version))" % (version, ver_pip_setup)))
elif dep_ver_spec == version:
print_ok()
else:
print_warning(more=(" (%s != %s mandated version))" % (version, dep_ver_spec)))
except ImportError:
print_fail()
install_software = 1
print_line('Check if spinalcordtoolbox is installed')
try:
importlib.import_module('spinalcordtoolbox')
print_ok()
except ImportError:
print_fail()
install_software = 1
# CHECK EXTERNAL MODULES:
# Check if dipy is installed
# print_line('Check if dipy ('+dipy_version+') is installed')
# try:
# module = importlib.import_module('dipy')
# if module.__version__ == dipy_version:
# print_ok()
# else:
# print_warning()
# print(' Detected version: '+version+'. Required version: '+dipy_version)
# except ImportError:
# print_fail()
# install_software = 1
# Check ANTs integrity
print_line('Check ANTs compatibility with OS ')
cmd = 'isct_test_ants'
status, output = sct.run(cmd, verbose=0, raise_exception=False)
if status == 0:
print_ok()
else:
print_fail()
print(output)
e = 1
if complete_test:
print('>> ' + cmd)
print((status, output), '\n')
# check if ANTs is compatible with OS
# print_line('Check ANTs compatibility with OS ')
# cmd = 'isct_antsRegistration'
# status, output = sct.run(cmd)
# if status in [0, 256]:
# print_ok()
# else:
# print_fail()
# e = 1
# if complete_test:
# print('>> '+cmd)
# print((status, output), '\n')
# check PropSeg compatibility with OS
print_line('Check PropSeg compatibility with OS ')
status, output = sct.run('isct_propseg', verbose=0, raise_exception=False, is_sct_binary=True)
if status in (0, 1):
print_ok()
else:
print_fail()
print(output)
e = 1
if complete_test:
print((status, output), '\n')
# check if figure can be opened (in case running SCT via ssh connection)
print_line('Check if figure can be opened')
import warnings
with warnings.catch_warnings():
warnings.simplefilter("ignore")
import matplotlib.pyplot as plt
try:
plt.figure()
plt.close()
print_ok()
except Exception:
print_fail()
print('')
sys.exit(e + install_software)
def main():
# initialization
fsl_is_working = 1
# ants_is_installed = 1
install_software = 0
e = 0
restart_terminal = 0
create_log_file = param.create_log_file
file_log = 'sct_check_dependencies.log'
complete_test = param.complete_test
os_running = 'not identified'
dipy_version = '0.10.0dev'
print
# Check input parameters
parser = get_parser()
arguments = parser.parse(sys.argv[1:])
if '-c' in arguments:
complete_test = 1
if '-log' in arguments:
create_log_file = 1
# use variable "verbose" when calling sct.run for more clarity
verbose = complete_test
# redirect to log file
if create_log_file:
orig_stdout = sys.stdout
handle_log = file(file_log, 'w')
sys.stdout = handle_log
# complete test
if complete_test:
print sct.run('date', verbose)
print sct.run('whoami', verbose)
print sct.run('pwd', verbose)
if os.path.isfile('~/.bash_profile'):
(status, output) = sct.run('more ~/.bash_profile', verbose)
print output
if os.path.isfile('~/.bashrc'):
(status, output) = sct.run('more ~/.bashrc', verbose)
print output
# check OS
platform_running = sys.platform
if (platform_running.find('darwin') != -1):
os_running = 'osx'
elif (platform_running.find('linux') != -1):
os_running = 'linux'
print 'OS: '+os_running+' ('+platform.platform()+')'
# Check number of CPU cores
from multiprocessing import cpu_count
status, output = sct.run('echo $ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS', 0)
print 'CPU cores: Available: ' + str(cpu_count()) + ', Used by SCT: '+output
# check RAM
sct.checkRAM(os_running, 0)
# get path of the toolbox
path_sct = os.path.dirname(os.path.dirname(__file__))
if path_sct is None:
raise EnvironmentError("SCT_DIR, which is the path SCT install needs to be set")
print ('SCT path: {0}'.format(path_sct))
# fetch true commit number and branch (do not use commit.txt which is wrong)
path_curr = os.path.abspath(os.curdir)
os.chdir(path_sct)
# first, make sure there is a .git folder
if os.path.isdir('.git'):
print 'Installation type: git'
sct_commit = commands.getoutput('git rev-parse HEAD')
sct_branch = commands.getoutput('git branch | grep \*').strip('* ')
if not (sct_commit.isalnum()):
sct_commit = 'unknown'
sct_branch = 'unknown'
print ' commit: '+sct_commit
print ' branch: '+sct_branch
else:
print 'Installation type: package'
# fetch version
with open(path_sct + '/version.txt', 'r') as myfile:
version_sct = myfile.read().replace('\n', '')
print ' version: '+version_sct
os.chdir(path_curr)
# # fetch version of the toolbox
# with open (path_sct+"/version.txt", "r") as myfile:
# version_sct = myfile.read().replace('\n', '')
# with open (path_sct+"/commit.txt", "r") as myfile:
# commit_sct = myfile.read().replace('\n', '')
# print "SCT version: "+version_sct+'-'+commit_sct
# check if Python path is within SCT path
print_line('Check Python path')
path_python = sys.executable
if path_sct in path_python:
print_ok()
else:
print_fail()
print ' Python path: '+path_python
# check if data folder is empty
print_line('Check if data are installed')
if os.listdir(path_sct+"/data"):
print_ok()
else:
print_fail()
# loop across python packages -- CONDA
version_requirements = get_version_requirements()
for i in version_requirements:
# need to adapt import name and module name in specific cases
if i == 'scikit-image':
module = 'skimage'
elif i == 'scikit-learn':
module = 'sklearn'
elif i == 'pyqt':
module = 'PyQt4'
else:
module = i
print_line('Check if '+i+' ('+version_requirements.get(i)+') is installed')
try:
module = importlib.import_module(module)
# get version
try:
version = module.__version__
except:
try:
version = module.__VERSION__
except:
# skip if module doesn't have __version__ nor __VERSION__ (e.g., xlutils)
version = version_requirements[i]
# check if version matches requirements
if check_package_version(version, version_requirements, i):
print_ok()
else:
print_warning()
print ' Detected version: '+version+'. Required version: '+version_requirements[i]
except ImportError:
print_fail()
install_software = 1
# loop across python packages -- PIP
version_requirements_pip = get_version_requirements_pip()
for i in version_requirements_pip:
module = i
print_line('Check if '+i+' ('+version_requirements_pip.get(i)+') is installed')
try:
module = importlib.import_module(module)
# get version
version = module.__version__
# check if version matches requirements
if check_package_version(version, version_requirements_pip, i):
print_ok()
else:
print_warning()
print ' Detected version: '+version+'. Required version: '+version_requirements_pip[i]
except ImportError:
print_fail()
install_software = 1
# CHECK DEPENDENT MODULES (installed by nibabel/dipy):
print_line('Check if numpy is installed')
try:
importlib.import_module('numpy')
print_ok()
except ImportError:
print_fail()
install_software = 1
print_line('Check if scipy is installed')
try:
importlib.import_module('scipy')
print_ok()
except ImportError:
print_fail()
install_software = 1
# CHECK EXTERNAL MODULES:
# Check if dipy is installed
# print_line('Check if dipy ('+dipy_version+') is installed')
# try:
# module = importlib.import_module('dipy')
# if module.__version__ == dipy_version:
# print_ok()
# else:
# print_warning()
# print ' Detected version: '+version+'. Required version: '+dipy_version
# except ImportError:
# print_fail()
# install_software = 1
# Check ANTs integrity
print_line('Check ANTs compatibility with OS ')
cmd = 'isct_test_ants'
# here, cannot use commands.getstatusoutput because status is wrong (because of launcher)
# status = os.system(cmd+" &> /dev/null")
# status, output = sct.run(cmd, 0)
# import subprocess
# process = subprocess.Popen(cmd, shell=True, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
# status = subprocess.call(cmd, shell=True)
# status = process.returncode
(status, output) = commands.getstatusoutput(cmd)
# from subprocess import call
# status, output = call(cmd)
# print status
# print output
# if status in [0, 256]:
if status == 0:
print_ok()
else:
print_fail()
print output
e = 1
if complete_test:
print '>> '+cmd
print (status, output), '\n'
# check if ANTs is compatible with OS
# print_line('Check ANTs compatibility with OS ')
# cmd = 'isct_antsRegistration'
# status, output = commands.getstatusoutput(cmd)
# if status in [0, 256]:
# print_ok()
# else:
# print_fail()
# e = 1
# if complete_test:
# print '>> '+cmd
# print (status, output), '\n'
# check PropSeg compatibility with OS
print_line('Check PropSeg compatibility with OS ')
(status, output) = commands.getstatusoutput('isct_propseg')
if status in [0, 256]:
print_ok()
else:
print_fail()
print output
e = 1
if complete_test:
print (status, output), '\n'
# check if figure can be opened (in case running SCT via ssh connection)
print_line('Check if figure can be opened')
try:
import warnings
with warnings.catch_warnings():
warnings.simplefilter("ignore")
import matplotlib.pyplot as plt
plt.figure()
plt.close()
print_ok()
except:
print_fail()
print sys.exc_info()
# close log file
if create_log_file:
sys.stdout = orig_stdout
handle_log.close()
print "File generated: "+file_log+'\n'
print ''
sys.exit(e + install_software)
def main():
# initialization
fsl_is_working = 1
# ants_is_installed = 1
install_software = 0
e = 0
restart_terminal = 0
create_log_file = param.create_log_file
file_log = 'sct_check_dependencies.log'
complete_test = param.complete_test
os_running = 'not identified'
dipy_version = '0.10.0dev'
print
# Check input parameters
parser = get_parser()
arguments = parser.parse(sys.argv[1:])
if '-c' in arguments:
complete_test = 1
if '-log' in arguments:
create_log_file = 1
# use variable "verbose" when calling sct.run for more clarity
verbose = complete_test
# redirect to log file
if create_log_file:
orig_stdout = sys.stdout
handle_log = file(file_log, 'w')
sys.stdout = handle_log
# complete test
if complete_test:
print sct.run('date', verbose)
print sct.run('whoami', verbose)
print sct.run('pwd', verbose)
if os.path.isfile('~/.bash_profile'):
(status, output) = sct.run('more ~/.bash_profile', verbose)
print output
if os.path.isfile('~/.bashrc'):
(status, output) = sct.run('more ~/.bashrc', verbose)
print output
# check OS
platform_running = sys.platform
if (platform_running.find('darwin') != -1):
os_running = 'osx'
elif (platform_running.find('linux') != -1):
os_running = 'linux'
print 'OS: ' + os_running + ' (' + platform.platform() + ')'
# Check number of CPU cores
from multiprocessing import cpu_count
status, output = sct.run('echo $ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS', 0)
print 'CPU cores: Available: ' + str(
cpu_count()) + ', Used by SCT: ' + output
# check RAM
sct.checkRAM(os_running, 0)
# get path of the toolbox
path_sct = os.path.dirname(os.path.dirname(__file__))
if path_sct is None:
raise EnvironmentError(
"SCT_DIR, which is the path SCT install needs to be set")
print('SCT path: {0}'.format(path_sct))
# fetch true commit number and branch (do not use commit.txt which is wrong)
path_curr = os.path.abspath(os.curdir)
os.chdir(path_sct)
# first, make sure there is a .git folder
if os.path.isdir('.git'):
print 'Installation type: git'
sct_commit = commands.getoutput('git rev-parse HEAD')
sct_branch = commands.getoutput('git branch | grep \*').strip('* ')
if not (sct_commit.isalnum()):
sct_commit = 'unknown'
sct_branch = 'unknown'
print ' commit: ' + sct_commit
print ' branch: ' + sct_branch
else:
print 'Installation type: package'
# fetch version
with open(path_sct + '/version.txt', 'r') as myfile:
version_sct = myfile.read().replace('\n', '')
print ' version: ' + version_sct
os.chdir(path_curr)
# # fetch version of the toolbox
# with open (path_sct+"/version.txt", "r") as myfile:
# version_sct = myfile.read().replace('\n', '')
# with open (path_sct+"/commit.txt", "r") as myfile:
# commit_sct = myfile.read().replace('\n', '')
# print "SCT version: "+version_sct+'-'+commit_sct
# check if Python path is within SCT path
print_line('Check Python path')
path_python = sys.executable
if path_sct in path_python:
print_ok()
else:
print_fail()
print ' Python path: ' + path_python
# check if data folder is empty
print_line('Check if data are installed')
if os.listdir(path_sct + "/data"):
print_ok()
else:
print_fail()
# loop across python packages -- CONDA
version_requirements = get_version_requirements()
for i in version_requirements:
# need to adapt import name and module name in specific cases
if i == 'scikit-image':
module = 'skimage'
elif i == 'scikit-learn':
module = 'sklearn'
elif i == 'pyqt':
module = 'PyQt4'
else:
module = i
print_line('Check if ' + i + ' (' + version_requirements.get(i) +
') is installed')
try:
module = importlib.import_module(module)
# get version
try:
version = module.__version__
except:
try:
version = module.__VERSION__
except:
# skip if module doesn't have __version__ nor __VERSION__ (e.g., xlutils)
version = version_requirements[i]
# check if version matches requirements
if check_package_version(version, version_requirements, i):
print_ok()
else:
print_warning()
print ' Detected version: ' + version + '. Required version: ' + version_requirements[
i]
except ImportError:
print_fail()
install_software = 1
# loop across python packages -- PIP
version_requirements_pip = get_version_requirements_pip()
for i in version_requirements_pip:
module = i
print_line('Check if ' + i + ' (' + version_requirements_pip.get(i) +
') is installed')
try:
module = importlib.import_module(module)
# get version
version = module.__version__
# check if version matches requirements
if check_package_version(version, version_requirements_pip, i):
print_ok()
else:
print_warning()
print ' Detected version: ' + version + '. Required version: ' + version_requirements_pip[
i]
except ImportError:
print_fail()
install_software = 1
# CHECK DEPENDENT MODULES (installed by nibabel/dipy):
print_line('Check if numpy is installed')
try:
importlib.import_module('numpy')
print_ok()
except ImportError:
print_fail()
install_software = 1
print_line('Check if scipy is installed')
try:
importlib.import_module('scipy')
print_ok()
except ImportError:
print_fail()
install_software = 1
print_line('Check if spinalcordtoolbox is installed')
try:
importlib.import_module('spinalcordtoolbox')
print_ok()
except ImportError:
print_fail()
install_software = 1
# CHECK EXTERNAL MODULES:
# Check if dipy is installed
# print_line('Check if dipy ('+dipy_version+') is installed')
# try:
# module = importlib.import_module('dipy')
# if module.__version__ == dipy_version:
# print_ok()
# else:
# print_warning()
# print ' Detected version: '+version+'. Required version: '+dipy_version
# except ImportError:
# print_fail()
# install_software = 1
# Check ANTs integrity
print_line('Check ANTs compatibility with OS ')
cmd = 'isct_test_ants'
# here, cannot use commands.getstatusoutput because status is wrong (because of launcher)
# status = os.system(cmd+" &> /dev/null")
# status, output = sct.run(cmd, 0)
# import subprocess
# process = subprocess.Popen(cmd, shell=True, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
# status = subprocess.call(cmd, shell=True)
# status = process.returncode
(status, output) = commands.getstatusoutput(cmd)
# from subprocess import call
# status, output = call(cmd)
# print status
# print output
# if status in [0, 256]:
if status == 0:
print_ok()
else:
print_fail()
print output
e = 1
if complete_test:
print '>> ' + cmd
print(status, output), '\n'
# check if ANTs is compatible with OS
# print_line('Check ANTs compatibility with OS ')
# cmd = 'isct_antsRegistration'
# status, output = commands.getstatusoutput(cmd)
# if status in [0, 256]:
# print_ok()
# else:
# print_fail()
# e = 1
# if complete_test:
# print '>> '+cmd
# print (status, output), '\n'
# check PropSeg compatibility with OS
print_line('Check PropSeg compatibility with OS ')
(status, output) = commands.getstatusoutput('isct_propseg')
if status in [0, 256]:
print_ok()
else:
print_fail()
print output
e = 1
if complete_test:
print(status, output), '\n'
# check if figure can be opened (in case running SCT via ssh connection)
print_line('Check if figure can be opened')
try:
import warnings
with warnings.catch_warnings():
warnings.simplefilter("ignore")
import matplotlib.pyplot as plt
plt.figure()
plt.close()
print_ok()
except:
print_fail()
print sys.exc_info()
# close log file
if create_log_file:
sys.stdout = orig_stdout
handle_log.close()
print "File generated: " + file_log + '\n'
print ''
sys.exit(e + install_software)
def main():
# initialization
fsl_is_working = 1
# ants_is_installed = 1
# isct_c3d_is_installed = 1
install_software = 0
e = 0
restart_terminal = 0
create_log_file = param.create_log_file
file_log = 'sct_check_dependencies.log'
complete_test = param.complete_test
os_running = 'not identified'
print
# Check input parameters
try:
opts, args = getopt.getopt(sys.argv[1:], 'hlc')
except getopt.GetoptError:
usage()
for opt, arg in opts:
if opt == '-h':
usage()
elif opt in ('-c'):
complete_test = 1
elif opt in ('-l'):
create_log_file = 1
# use variable "verbose" when calling sct.run for more clarity
verbose = complete_test
# redirect to log file
if create_log_file:
orig_stdout = sys.stdout
handle_log = file(file_log, 'w')
sys.stdout = handle_log
# complete test
if complete_test:
print sct.run('date', verbose)
print sct.run('whoami', verbose)
print sct.run('pwd', verbose)
if os.path.isfile('~/.bash_profile'):
(status, output) = sct.run('more ~/.bash_profile', verbose)
print output
if os.path.isfile('~/.bashrc'):
(status, output) = sct.run('more ~/.bashrc', verbose)
print output
# check if user is root (should not be!)
if os.geteuid() == 0:
print 'Looks like you are root. Please run this script without sudo. Exit program\n'
sys.exit(2)
# check OS
print 'Check which OS is running... '
platform_running = sys.platform
if (platform_running.find('darwin') != -1):
os_running = 'osx'
elif (platform_running.find('linux') != -1):
os_running = 'linux'
print ' '+os_running+' ('+platform.platform()+')'
# check RAM
print 'Check RAM... '
sct.checkRAM(os_running)
# check installation packages
print 'Check which Python is running ... '
print ' '+sys.executable
# get path of the toolbox
status, output = sct.run('echo $SCT_DIR', verbose)
path_sct = output
if complete_test:
print (status, output), '\n'
# fetch version of the toolbox
print 'Fetch version of the Spinal Cord Toolbox... '
with open (path_sct+"/version.txt", "r") as myfile:
version_sct = myfile.read().replace('\n', '')
print " version: "+version_sct
# loop across python packages -- CONDA
version_requirements = get_version_requirements()
for i in version_requirements:
if i == 'pillow':
module = 'PIL'
else:
module = i
print_line('Check if '+i+' ('+version_requirements.get(i)+') is installed')
try:
module = importlib.import_module(module)
# get version
if i == 'pillow':
version = module.PILLOW_VERSION
else:
version = module.__version__
# check if version matches requirements
if check_package_version(version, version_requirements, i):
print_ok()
else:
print_warning()
print ' Detected version: '+version+'. Required version: '+version_requirements[i]
except ImportError:
print_fail()
install_software = 1
# loop across python packages -- PIP
version_requirements_pip = get_version_requirements_pip()
for i in version_requirements_pip:
if i == 'scikit-image':
module = 'skimage'
else:
module = i
print_line('Check if '+i+' ('+version_requirements_pip.get(i)+') is installed')
try:
module = importlib.import_module(module)
# get version
version = module.__version__
# check if version matches requirements
if check_package_version(version, version_requirements_pip, i):
print_ok()
else:
print_warning()
print ' Detected version: '+version+'. Required version: '+version_requirements_pip[i]
except ImportError:
print_fail()
install_software = 1
# check if git is installed
print_line('Check if git is installed ')
cmd = 'which git'
status, output = commands.getstatusoutput(cmd)
if output:
print_ok()
else:
print_fail()
print ' git is not installed.'
print ' - To install it: http://git-scm.com/book/en/v1/Getting-Started-Installing-Git'
e = 1
if complete_test:
print '>> '+cmd
print (status, output), '\n'
# check if ANTs is compatible with OS
print_line('Check ANTs compatibility with OS ')
cmd = 'isct_antsRegistration'
status, output = commands.getstatusoutput(cmd)
if status in [0, 256]:
print_ok()
else:
print_fail()
e = 1
if complete_test:
print '>> '+cmd
print (status, output), '\n'
# check isct_c3d compatibility with OS
print_line('Check c3d compatibility with OS ')
(status, output) = commands.getstatusoutput('isct_c3d -h')
if status in [0, 256]:
print_ok()
else:
print_fail()
install_software = 1
if complete_test:
print (status, output), '\n'
# check PropSeg compatibility with OS
print_line('Check PropSeg compatibility with OS ')
(status, output) = commands.getstatusoutput('sct_propseg')
if status in [0, 256]:
print_ok()
else:
print_fail()
e = 1
if complete_test:
print (status, output), '\n'
# Check ANTs integrity
print_line('Check integrity of ANTs output ')
cmd_ants_test = 'isct_test_ants'
# if not complete_test:
# cmd_ants_test += ' -v 0'
(status, output) = commands.getstatusoutput(cmd_ants_test)
if status in [0]:
print_ok()
else:
print_fail()
print output
e = 1
if complete_test:
print (status, output), '\n'
print
# close log file
if create_log_file:
sys.stdout = orig_stdout
handle_log.close()
print "File generated: "+file_log+'\n'
sys.exit(e + install_software)