def convertMask(img, outputPath, newPix=None, newDim=None, threshold=True):
""" Convert mask to mrc format read by Relion.
Params:
img: input image to be converted.
outputPath: it can be either a directory or a file path.
If it is a directory, the output name will be inferred from input
and put into that directory. If it is not a directory,
it is assumed is the output filename.
newPix: output pixel size (equals input if None)
newDim: output box size
Return:
new file name of the mask.
"""
index, filename = img.getLocation()
imgFn = locationToRelion(index, filename)
inPix = img.getSamplingRate()
if os.path.isdir(outputPath):
outFn = os.path.join(outputPath, pwutils.replaceBaseExt(imgFn, 'mrc'))
else:
outFn = outputPath
params = '--i %s --o %s --angpix %0.5f' % (imgFn, outFn, inPix)
if newPix is not None:
params += ' --rescale_angpix %0.5f' % newPix
if newDim is not None:
params += ' --new_box %d' % newDim
if threshold:
params += ' --threshold_above 1 --threshold_below 0'
pwutils.runJob(None,
'relion_image_handler',
params,
env=Plugin.getEnviron())
return outFn
def runRelionProgram(cmd):
print(">>>", cmd)
cmd = cmd.split()
p = subprocess.Popen(cmd, env=Plugin.getEnviron())
return p.wait()