def _showVolumesChimera(self):
tmpFileNameCMD = self.protocol._getTmpPath("chimera.cmd")
f = open(tmpFileNameCMD, "w")
dim = self.protocol.inputVolumes.get().getDim()[0]
sampling = self.protocol.inputVolumes.get().getSamplingRate()
tmpFileName = os.path.abspath(self.protocol._getTmpPath("axis.bild"))
Chimera.createCoordinateAxisFile(dim,
bildFileName=tmpFileName,
sampling=sampling)
f.write("open %s\n" % tmpFileName)
f.write("cofr 0,0,0\n") # set center of coordinates
_inputVol = self.protocol.inputVolumes.get()
_outputVol = self.protocol.outputVolume
inputVolFileName = os.path.abspath(ImageHandler.removeFileType(
_inputVol.getFileName()))
# input vol origin coordinates
x_input, y_input, z_input = _inputVol.getShiftsFromOrigin()
f.write("open %s\n" % inputVolFileName)
f.write("volume #1 style mesh level 0.001 voxelSize %f origin "
"%0.2f,%0.2f,%0.2f\n"
% (_inputVol.getSamplingRate(), x_input, y_input, z_input))
outputVolFileName = os.path.abspath(ImageHandler.removeFileType(
_outputVol.getFileName()))
# output vol origin coordinates
x_output, y_output, z_output = _outputVol.getShiftsFromOrigin()
f.write("open %s\n" % outputVolFileName)
f.write("volume #2 style surface level 0.001 voxelSize %f origin "
"%0.2f,%0.2f,%0.2f\n"
% (_outputVol.getSamplingRate(), x_output, y_output, z_output))
cMap = ['red', 'yellow', 'green', 'cyan', 'blue']
d = {}
d['outerRadius'] = self.protocol.outerRadius.get() * sampling
d['innerRadius'] = self.protocol.innerRadius.get() * sampling
d['symmetry'] = Chimera.getSymmetry(self.protocol.symmetryGroup.get())
if self.protocol.symmetryGroup >= SYM_I222:
f.write("shape icosahedron mesh true radius %(outerRadius)d "
"orientation %(symmetry)s\n" % d)
step = (d['outerRadius'] - d['innerRadius']) / float(len(cMap) - 1)
f.write("scolor #2 geom radial center 0,0,0 cmap ")
counter = 0
s = ""
for color in cMap:
s += "%d,%s:" % (d['innerRadius'] + counter * step, color)
counter += 1
f.write(s[:-1] + '\n')
f.close()
return [ChimeraView(tmpFileNameCMD)]
def visualize(self, obj, **kwargs):
cls = type(obj)
if issubclass(cls, AtomStruct):
# if attribute _chimeraScript exists then protocol
# has create a script file USE IT
if hasattr(obj, '_chimeraScript'):
fn = obj._chimeraScript.get()
ChimeraView(fn).show()
return
# if not create a script file with: coordinates axis, PDB and
# volume (if available)
else:
fn = obj.getFileName()
# check if tmp dir exists, if not use /tmp
# tmp does not exists if you try to visualize something (eye)
# before irunning the protocol
tmpPath = self.protocol._getTmpPath()
if not os.path.exists(tmpPath):
tmpPath = "/tmp"
fnCmd = os.path.join(tmpPath, "chimera.cmd")
f = open(fnCmd, 'w')
f.write("cofr 0,0,0\n") # set center of coordinates
if obj.hasVolume():
volID = 0
volumeObject = obj.getVolume()
dim = volumeObject.getDim()[0]
sampling = volumeObject.getSamplingRate()
f.write("open %s\n" % os.path.abspath(
ImageHandler.removeFileType(
volumeObject.getFileName())))
f.write("volume #%d style surface voxelSize %f\n" %
(volID, sampling))
x, y, z = volumeObject.getShiftsFromOrigin()
f.write("volume #%d origin %0.2f,%0.2f,%0.2f\n" %
(volID, x, y, z))
else:
dim = 150 # eventually we will create a PDB library that
# computes PDB dim
sampling = 1.
# Construct the coordinate file
bildFileName = os.path.abspath(
os.path.join(tmpPath, "axis.bild"))
Chimera.createCoordinateAxisFile(dim,
bildFileName=bildFileName,
sampling=sampling)
f.write("open %s\n" % bildFileName)
f.write("open %s\n" % os.path.abspath(fn))
f.close()
ChimeraView(fnCmd).show()
# FIXME: there is an asymmetry between ProtocolViewer and Viewer
# for the first, the visualize method return a list of View's
# (that are shown)
# for the second, the visualize directly shows the objects.
# the first approach is better
else:
raise Exception('ChimeraViewer.visualize: '
'can not visualize class: %s' % obj.getClassName())
def _showVolumesChimera(self):
""" Create a chimera script to visualize selected volumes. """
tmpFileNameCMD = self.protocol._getTmpPath("chimera.cmd")
f = open(tmpFileNameCMD, "w")
sampling, _setOfVolumes = self._createSetOfVolumes()
count = 0 # first model in chimera is a volume
if len(_setOfVolumes) == 1:
count = 1 # first model in chimera is the bild file
# if we have a single volume then create axis
# as bild file. Chimera must read the bild file first
# otherwise system of coordinates will not
# be in the center of the window
dim = self.protocol.outputVolume.getDim()[0]
tmpFileNameBILD = os.path.abspath(self.protocol._getTmpPath(
"axis.bild"))
Chimera.createCoordinateAxisFile(dim,
bildFileName=tmpFileNameBILD,
sampling=sampling)
f.write("open %s\n" % tmpFileNameBILD)
f.write("cofr 0,0,0\n") # set center of coordinates
count = 1 # skip first model because is not a 3D map
for vol in _setOfVolumes:
localVol = os.path.abspath(ImageHandler.removeFileType(
vol.getFileName()))
if localVol.endswith("stk"):
errorWindow(None, "Extension .stk is not supported")
f.write("open %s\n" % localVol)
f.write("volume#%d style surface voxelSize %f\n" %
(count, sampling))
count += 1
if len(_setOfVolumes) > 1:
f.write('tile\n')
else:
x, y, z = vol.getShiftsFromOrigin()
f.write("volume#1 origin %0.2f,%0.2f,%0.2f\n" % (x, y, z))
f.close()
return [ChimeraView(tmpFileNameCMD)]
