def shiftStep(self):
"""call xmipp program to shift the particles"""
centermd = self._getExtraPath("center_particles.xmd")
args = '-i "%s" -o "%s" ' % (self._getExtraPath("input_particles.xmd"), centermd)
if self.option:
self.x = self.xin.get()
self.y = self.yin.get()
self.z = self.zin.get()
else:
fnvol = self.inputMask.get().getFileName()
if fnvol.endswith('.mrc'):
fnvol += ':mrc'
vol = Volume()
vol.setFileName(fnvol)
vol = ih().read(vol.getFileName())
masscenter = vol.centerOfMass()
self.x = masscenter[0]
self.y = masscenter[1]
self.z = masscenter[2]
args += '--shift_to %f %f %f ' % (self.x, self.y, self.z)
program = "xmipp_transform_geometry"
if not self.interp.get():
interp = 'linear'
else:
interp = 'spline'
args += ' --apply_transform --dont_wrap --interp %s' % interp
if self.inv.get():
args += ' --inverse'
self.runJob(program, args)
if not self.boxSizeBool.get():
box = self.boxSize.get()
self.runJob('xmipp_transform_window', '-i "%s" -o "%s" --size %d %d %d --save_metadata_stack' %
(centermd, self._getExtraPath("crop_particles.stk"), box, box, 1))
def createOutputStep(self):
vol1 = self.vol1.get()
volume = Volume()
volume.setSamplingRate(vol1.getSamplingRate())
if vol1.getFileName().endswith('mrc'):
origin = Transform()
ccp4header = headers.Ccp4Header(vol1.getFileName(), readHeader=True)
shifts = ccp4header.getOrigin()
origin.setShiftsTuple(shifts)
volume.setOrigin(origin)
volume.setFileName(self._getExtraPath("output_volume.mrc"))
filename = volume.getFileName()
if filename.endswith('.mrc') or filename.endswith('.map'):
volume.setFileName(filename + ':mrc')
self._defineOutputs(outputVolume=volume)