def checkConflicts(self):
if self.params['align'] and not self.params['defergpu']:
exename = 'dosefgpu_driftcorr'
gpuexe = subprocess.Popen("which "+exename, shell=True, stdout=subprocess.PIPE).stdout.read().strip()
if not os.path.isfile(gpuexe):
apDisplay.printError('Correction program "%s" not available' % exename)
# We don't have gpu locking
if self.params['parallel']:
apDisplay.printWarning('Make sure that you use different gpuid for each parallel process')
# Local directory creating and permission checking
if self.params['tempdir']:
try:
fileutil.mkdirs(self.params['tempdir'])
os.access(self.params['tempdir'],os.W_OK|os.X_OK)
except:
raise
apDisplay.printError('Local temp directory not writable')
else:
# makes no sense to save gain corrected ddstack in tempdir if no alignment
# will be done on the same machine
if self.params['tempdir']:
apDisplay.printWarning('tempdir is not neccessary without aligning on the same host. Reset to None')
self.params['tempdir'] = None
# Stack cleaning should not be done in some cases
if not self.params['keepstack']:
if self.params['defergpu']:
apDisplay.printWarning('The gain/dark-corrected stack must be saved if alignment is deferred')
self.params['keepstack'] = True
else:
apDisplay.printError('Why making only gain/dark-corrected ddstacks but not keeping them')
def saveImageFromImageData(self,datainst): old_image_path = datainst['session']['image path'] bits = old_image_path.split(datainst['session']['name']) tail = bits[-1] # assumes that the path separator is '/' while tail[0] == '/': tail = tail[1:] new_image_path = os.path.join(self.output_base_path,datainst['session']['name'],tail) fileutil.mkdirs(new_image_path) filename = datainst['filename']+'.mrc' source = os.path.join(old_image_path,filename) destination = os.path.join(new_image_path,filename) print 'copy to ', destination shutil.copy(source,destination)
def saveImageFromImageData(self, datainst):
old_image_path = datainst['session']['image path']
bits = old_image_path.split(datainst['session']['name'])
tail = bits[-1]
# assumes that the path separator is '/'
while tail[0] == '/':
tail = tail[1:]
new_image_path = os.path.join(self.output_base_path,
datainst['session']['name'], tail)
fileutil.mkdirs(new_image_path)
filename = datainst['filename'] + '.mrc'
source = os.path.join(old_image_path, filename)
destination = os.path.join(new_image_path, filename)
print 'copy to ', destination
shutil.copy(source, destination)
def makeFrameDir(self,newdir): fileutil.mkdirs(newdir)