def boxMaskStack(bmstackf, partdatas, box, xmask, ymask, falloff, imask=None, norotate=False):
from appionlib.apSpider import operations
from appionlib import apEMAN
import os
# create blank image for mask using SPIDER
maskfile = "boxmask.spi"
operations.createBoxMask(maskfile,box,xmask,ymask,falloff,imask)
# convert mask to MRC
apEMAN.executeEmanCmd("proc2d boxmask.spi boxmask.mrc",verbose=False,showcmd=False)
os.remove("boxmask.spi")
maskarray = mrc.read("boxmask.mrc")
# box particles
maskedparts = []
for i in range(len(partdatas)):
if norotate is True:
rotatemask = maskarray
else:
angle = (-partdatas[i]['angle'])-90
rotatemask = ndimage.rotate(maskarray, angle=angle, reshape=False, order=1)
maskedparts.append(rotatemask)
# write to stack
apImagicFile.writeImagic(maskedparts, bmstackf)
os.remove("boxmask.mrc")
return bmstackf
def boxMask(self,infile,outfile,spirots=None):
from appionlib.apSpider import operations
# boxmask the particles
apDisplay.printMsg("masking the particles with a rectangular box")
nump = apStack.getNumberStackParticlesFromId(self.params['stackid'])
box = self.stackdata['boxsize']
apix = self.stackdata['pixelsize']*1e10
if self.params['mask'] is None:
mask = box/2-2
else:
mask = int(self.params['mask']/apix)
imask = int(self.params['imask']/apix)
length = int(self.params['length']/apix)
falloff = self.params['falloff']/apix
mask -= falloff/2
length = (length/2)-(falloff/2)
# create blank image for mask
maskfile = "boxmask.spi"
operations.createBoxMask(maskfile,box,mask,length,falloff,imask)
mySpi = spyder.SpiderSession(dataext=".spi", logo=False, log=False)
mySpi.toSpiderQuiet("CP",
spyder.fileFilter(maskfile),"_4")
mySpi.toSpider("do x10=1,%i"%nump)
if self.params['vertical'] is not True:
mySpi.toSpider("UD IC x10,x30",
spyder.fileFilter(spirots),
"x30 = -1*x30",
"RT B",
"_4",
"_9",
"(x30)",
"(0)",
"MU",
spyder.fileFilter(infile)+"@{******x10}",
"_9")
else:
mySpi.toSpider("MU",
spyder.fileFilter(infile)+"@{******x10}",
"_4")
mySpi.toSpider(spyder.fileFilter(outfile)+"@{******x10}",
"*",
"enddo")
if self.params['vertical'] is not True:
mySpi.toSpider("UD ICE",spyder.fileFilter(spirots))
mySpi.close()
def boxMask(self, infile, outfile, spirots=None):
from appionlib.apSpider import operations
# boxmask the particles
apDisplay.printMsg("masking the particles with a rectangular box")
nump = apStack.getNumberStackParticlesFromId(self.params['stackid'])
box = self.stackdata['boxsize']
apix = self.stackdata['pixelsize'] * 1e10
if self.params['mask'] is None:
mask = box / 2 - 2
else:
mask = int(self.params['mask'] / apix)
imask = int(self.params['imask'] / apix)
length = int(self.params['length'] / apix)
falloff = self.params['falloff'] / apix
mask -= falloff / 2
length = (length / 2) - (falloff / 2)
# create blank image for mask
maskfile = "boxmask.spi"
operations.createBoxMask(maskfile, box, mask, length, falloff, imask)
mySpi = spyder.SpiderSession(dataext=".spi", logo=False, log=False)
mySpi.toSpiderQuiet("CP", spyder.fileFilter(maskfile), "_4")
mySpi.toSpider("do x10=1,%i" % nump)
if self.params['vertical'] is not True:
mySpi.toSpider("UD IC x10,x30", spyder.fileFilter(spirots),
"x30 = -1*x30", "RT B", "_4", "_9", "(x30)", "(0)",
"MU",
spyder.fileFilter(infile) + "@{******x10}", "_9")
else:
mySpi.toSpider("MU",
spyder.fileFilter(infile) + "@{******x10}", "_4")
mySpi.toSpider(
spyder.fileFilter(outfile) + "@{******x10}", "*", "enddo")
if self.params['vertical'] is not True:
mySpi.toSpider("UD ICE", spyder.fileFilter(spirots))
mySpi.close()
