def validate(self):
errors = []
if self.MaskMode=="Binary mask" and not os.path.exists(self.MaskFile):
errors.append(self.MaskFile+" does not exist")
if which("nma_diag_arpack")=="":
errors.append("Cannot find nma_diag_arpack in the PATH")
if which("nma_diagrtb")=="":
errors.append("Cannot find nma_diagrtb in the PATH")
return errors
def validate(self):
errors = []
md = MetaData()
md.read(self.ImgMd, 1) # Read only the first object in md
if md.containsLabel(MDL_IMAGE):
if not getattr(self, 'Is2D', False):
self._validateInputSize('Ref3D', 'Reference volume', True, md, errors)
self._validateInputSize('ReferenceMask', 'Reference mask', False, md, errors)
self._validateInputSize('SolventMask','Solvent mask', False, md, errors)
else:
errors.append("Input metadata <%s> doesn't contains image label" % self.ImgMd)
if self.DoCTFCorrection and not self._containsCTF(md):
errors.append("CTF correction selected and input metadata <%s> doesn't contains CTF information" % self.ImgMd)
# Check relion is installed
if len(which('relion_refine')) == 0:
errors.append('<relion_refine> was not found.')
if len(which('relion_movie_handler')) == 0:
errors.append('''program "relion_movie_handler" is missing.
Are you sure you have relion version 1.2?.''')
if self.DoContinue:
errors += self.__validateContinue()
if self.PrevRun:
errors += self._validateContinue()
else:
errors += self._validate()
if not findAcquisitionInfo(self.ImgMd):
errors.append("""Acquisition file for metadata %s is not available.
Either import images before using them
or create a file named acquisition_info.xmd
(see example below) and place it in the same directory than
the %s file
EXAMPLE:
# XMIPP_STAR_1 *
# change XXXXX by the sampling rate
data_noname
_sampling_rate XXXXX
""" %(self.ImgMd,self.ImgMd))
return errors
def detectMatlab():
from protlib_utils import which
matlab_home = None
matlab = which('matlab')
if matlab:
from os.path import dirname
from protlib_filesystem import findRealFile
matlab_home = dirname(dirname(findRealFile(matlab)))
return matlab_home
def detectJava():
from protlib_utils import which
java_home = None
javac = which('javac')
if javac:
from os.path import dirname
from protlib_filesystem import findRealFile
java_home = dirname(dirname(findRealFile(javac)))
return java_home
