def _visualize(self, obj, **args):
import os
fnCmd = self.protocol._getPath('result_strain_chimera.cmd')
if os.path.exists(fnCmd):
self._views.append(ChimeraView(fnCmd))
fnCmd = self.protocol._getPath('result_localrot_chimera.cmd')
if os.path.exists(fnCmd):
self._views.append(ChimeraView(fnCmd))
fnCmd = self.protocol._getPath('result_morph_chimera.cmd')
if os.path.exists(fnCmd):
self._views.append(ChimeraView(fnCmd))
return self._views
def _doShowStrain(self, param=None):
scriptFile = self.protocol._getPath('strain_chimera.cxc')
fhCmd = open(scriptFile, 'w')
fnbase = removeExt(self.protocol._getFileName('fnInputVol'))
ext = getExt(self.protocol._getFileName('fnInputVol'))
fninput = abspath(fnbase + ext[0:4])
smprt = self.protocol.outputVolume.getSamplingRate()
fnbase2 = removeExt(self.protocol._getFileName('fnOutVol'))
fnStrain = abspath(fnbase2)
fhCmd.write(self.OPEN_FILE % fninput)
fhCmd.write(self.OPEN_FILE % (fnStrain + "_strain.mrc"))
counter = 1
fhCmd.write(self.VOXEL_SIZE % (counter, str(smprt)))
counter += 1
fhCmd.write(self.VOXEL_SIZE % (counter, str(smprt)))
fhCmd.write(self.VOL_HIDE % counter)
fhCmd.write('color sample #%d map #%d palette rainbow\n' %
(counter - 1, counter))
fhCmd.write(self.VIEW)
fhCmd.close()
view = ChimeraView(scriptFile)
return [view]
def _showVolumesChimera(self):
tmpFileNameCMD = self.protocol._getExtraPath("chimera.cxc")
f = open(tmpFileNameCMD, "w")
dim = self.protocol.inputVolumes.get().getDim()[0]
sampling = self.protocol.inputVolumes.get().getSamplingRate()
tmpFileName = os.path.abspath(self.protocol._getExtraPath("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 #2 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 #3 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 = {}
innerRadius = self.protocol.innerRadius.get()
d['outerRadius'] = self.protocol.outerRadius.get() * sampling
if innerRadius < 0:
innerRadius = 0
d['innerRadius'] = innerRadius * sampling
d['innerRadius'] = self.protocol.innerRadius.get() * sampling
d['symmetry'] = Chimera.getSymmetry(XMIPP_TO_SCIPION[self.protocol.symmetryGroup.get()])
if self.protocol.symmetryGroup >= XMIPP_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("color radial #3 center 0,0,0 palette -")
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 _doShowDeformedOrigRef(self, param=None):
scriptFile = self.protocol._getPath('morph_deformed_ref_chimera.cxc')
fhCmd = open(scriptFile, 'w')
fnbase = removeExt(self.protocol._getFileName('fnOutVol'))
ext = getExt(self.protocol._getFileName('fnOutVol'))
fninput = abspath(fnbase + ext[0:4])
smprt = self.protocol.outputVolume.getSamplingRate()
fnbase2 = removeExt(self.protocol._getFileName('fnRefVol'))
ext2 = getExt(self.protocol._getFileName('fnRefVol'))
fnref = abspath(fnbase2 + ext2[0:4])
fhCmd.write(self.OPEN_FILE % fninput)
fhCmd.write(self.OPEN_FILE % fnref)
counter = 1
fhCmd.write(self.VOXEL_SIZE % (counter, str(smprt)))
fhCmd.write(self.VOL_HIDE % counter)
counter += 1
fhCmd.write(self.VOXEL_SIZE % (counter, str(smprt)))
# fhCmd.write("focus\n")
fhCmd.write(self.VOL_HIDE % counter)
fhCmd.write("volume morph #%d,%d frames 500\n" %
(counter - 1, counter))
fhCmd.write(self.VIEW)
fhCmd.close()
view = ChimeraView(scriptFile)
return [view]
def _visualize_norm_pdb(self, obj, **args):
self._create_legend(1.5);
fnCmd = self.protocol._getExtraPath("chimera_output.py")
f = open(fnCmd, 'a')
f.write("run(session, 'open %s')\n" % self.protocol._getFileName(PDB_NORM_FILE))
if self.displayNormPDB == self.RESIDUE:
f.write("run(session, 'cartoon')\n")
f.write("run(session, 'hide target ab')\n")
f.write("run(session, 'color byattribute occupancy palette"
" -1.5,red:-1.0,orange:-0.5,gold:0,yellow:0.5,lime:1.0,cyan:1.5,#1e90ff"
" ave residue')\n")
else:
f.write("run(session, 'cartoon hide')\n")
f.write("run(session, 'show target ab')\n")
f.write("run(session, 'style stick')\n")
f.write("run(session, 'color byattribute occupancy palette"
" -1.5,red:-1.0,orange:-0.5,gold:0,yellow:0.5,lime:1.0,cyan:1.5,#1e90ff')\n")
f.close()
view = ChimeraView(fnCmd)
return [view]
def _showChimera(self, param=None):
if (exists(self.protocol._getExtraPath("MG_Chimera_resolution.mrc"))):
fnResVol = self.protocol._getExtraPath("MG_Chimera_resolution.mrc")
else:
fnResVol = self.protocol._getExtraPath(OUTPUT_RESOLUTION_FILE_CHIMERA)
if self.sharpenedMap.get():
fnOrigMap = self.sharpenedMap.get().getFileName()
sampRate = self.sharpenedMap.get().getSamplingRate()
else:
if self.protocol.useHalfVolumes.get():
if self.protocol.hasHalfVolumesFile.get():
vol = self.protocol.associatedHalves.get().getHalfMaps()
fnOrigMap, _unused = vol.split(',')
sampRate = self.protocol.associatedHalves.get().getSamplingRate()
else:
vol = self.protocol.halfMap1.get()
fnOrigMap = vol.getFileName()
sampRate = vol.getSamplingRate()
else:
vol = self.protocol.fullMap.get()
fnOrigMap = vol.getFileName()
sampRate = vol.getSamplingRate()
cmdFile = self.protocol._getExtraPath('chimera_resolution_map.py')
self.createChimeraScript(cmdFile, fnResVol, fnOrigMap, sampRate,
numColors=self.intervals.get(),
lowResLimit=self.highest.get(),
highResLimit=self.lowest.get())
view = ChimeraView(cmdFile)
return [view]
def _viewStrain(self, e=None):
import os
protToShow = self.protToShow.get()
protId = protToShow.getObjId()
views = []
fnCmd = self.protocol._getPath('%d_result_strain_chimera.cmd' % protId)
if os.path.exists(fnCmd):
views.append(ChimeraView(fnCmd))
fnCmd = self.protocol._getPath('%d_result_localrot_chimera.cmd' %
protId)
if os.path.exists(fnCmd):
views.append(ChimeraView(fnCmd))
fnCmd = protToShow._getPath('result_morph_chimera.cmd')
if os.path.exists(fnCmd):
views.append(ChimeraView(fnCmd))
return views
def _showVolumesChimera(self):
""" Create a chimera script to visualize selected volumes. """
tmpFileNameCMD = self.protocol._getExtraPath("chimera.cxc")
f = open(tmpFileNameCMD, "w")
sampling, _setOfVolumes = self._createSetOfVolumes()
count = 1 # chimeraX stars counting in 1 (chimera in 0)
if len(_setOfVolumes) == 1:
# 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._getExtraPath("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 = 2 # skip first model because is not a 3D map
for vol in _setOfVolumes:
localVol = os.path.abspath(
image.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 level 0.001 voxelSize %f\n" %
(count, sampling))
count += 1
if len(_setOfVolumes) > 1:
f.write('tile\n')
else:
x, y, z = vol.getShiftsFromOrigin()
f.write("volume #2 origin %0.2f,%0.2f,%0.2f\n" % (x, y, z))
if vol.getHalfMaps():
for halfMap in vol.getHalfMaps().split(','):
if not os.path.abspath(halfMap).endswith(".mrc"):
f.write(
"open %s\n" %
(os.path.abspath(halfMap).split(".")[0] + ".mrc"))
else:
f.write("open %s\n" % os.path.abspath(halfMap))
f.write(
"volume #%d style surface level 0.001 voxelSize %f\n" %
(count, sampling))
f.write("volume #%d origin %0.2f,%0.2f,%0.2f\n" %
(count, x, y, z))
f.write("tile\n")
count += 1
f.write("view\n")
f.close()
return [ChimeraView(tmpFileNameCMD)]
def _showVolumesChimera(self):
""" Create a chimera script to visualize selected volumes. """
volume = self._getVolumeName()
cmdFile = self.protocol._getExtraPath('chimera_volumes.cxc')
with open(cmdFile, 'w+') as f:
localVol = os.path.relpath(volume, self.protocol._getExtraPath())
if os.path.exists(volume):
f.write("open %s\n" % localVol)
view = ChimeraView(cmdFile)
return [view]
def _showChimera(self, param=None):
fnResVol = self.protocol._getFileName(FN_RESOLMAP)
fnOrigMap = self.protocol.inputVolume.get().getFileName()
cmdFile = self.protocol._getExtraPath('chimera_resolution_map.py')
sampRate = self.protocol.resolution_Volume.getSamplingRate()
self.createChimeraScript(cmdFile, fnResVol, fnOrigMap, sampRate,
numColors=self.intervals.get(),
lowResLimit=self.highest.get(),
highResLimit=self.lowest.get())
view = ChimeraView(cmdFile)
return [view]
def _showVolumesChimera(self):
""" Create a chimera script to visualize selected volumes. """
volumes = self._getVolumeNames()
cmdFile = self.protocol._getExtraPath('chimera_volumes.cmd')
with open(cmdFile, 'w+') as f:
for vol in volumes:
# We assume that the chimera script will be generated
# at the same folder as 3DFSC volumes
if os.path.exists(vol):
localVol = os.path.relpath(vol,
self.protocol._getExtraPath())
f.write("open %s\n" % localVol)
f.write('tile\n')
view = ChimeraView(cmdFile)
return [view]
def _showVolumesChimera(self):
""" Create a chimera script to visualize selected volumes. """
volumes = self.getVolumeNames()
cmdFile = self._getFinalPath('chimera_volumes.cxc')
with open(cmdFile, 'w+') as f:
for vol in volumes:
# We assume that the chimera script will be generated
# at the same folder than spider volumes
localVol = os.path.basename(vol)
if os.path.exists(vol):
f.write("open %s format spider\n" % localVol)
f.write('tile\n')
view = ChimeraView(cmdFile)
return [view]
def _showVolumesChimera(self):
""" Create a chimera script to visualize selected volumes. """
volumes = self._getVolumeNames()
cmdFile = self.protocol._getExtraPath('chimera_volumes.cxc')
with open(cmdFile, 'w+') as f:
for vol in volumes:
# remove ":mrc" extension needed by xmipp
vol = vol.replace(":mrc", "")
# We assume that the chimera script will be generated
# at the same folder as relion volumes
localVol = os.path.basename(vol)
if os.path.exists(vol):
f.write("open %s\n" % localVol)
f.write('tile\n')
view = ChimeraView(cmdFile)
return [view]
def _showChimera(self, param=None):
fnResVol = self.protocol._getFileName(OUTPUT_RESOLUTION_FILE_CHIMERA)
fnOrigMap = self.protocol._getFileName(RESIZE_VOL)
sampRate = 1.0 # Res volume and original volume are at different scales
cmdFile = self.protocol._getExtraPath('chimera_resolution_map.py')
self.createChimeraScript(cmdFile,
fnResVol,
fnOrigMap,
sampRate,
numColors=self.intervals.get(),
lowResLimit=self.highest.get(),
highResLimit=self.lowest.get())
view = ChimeraView(cmdFile)
return [view]
def _doShowPDB(self, obj, **kwargs):
scriptFile = self.protocol._getPath('pdb_deform_chimera.cxc')
fhCmd = open(scriptFile, 'w')
inputFile = os.path.abspath(self.protocol.inputPDB.get().getFileName())
outputFile = os.path.abspath(self.protocol.outputPDB.getFileName())
fhCmd.write(self.OPEN_FILE % inputFile)
fhCmd.write(self.OPEN_FILE % outputFile)
# fhCmd.write("start Model Panel\n")
fhCmd.write("show cartoons\n")
fhCmd.write("cartoon style width 1.5 thick 1.5\n")
fhCmd.write("style stick\n")
fhCmd.write("color bymodel\n")
fhCmd.close()
view = ChimeraView(scriptFile)
return [view]
def _showTomogramsChimera(self):
""" Create a chimera script to visualize selected tomograms. """
tmpFileNameCMD = self._getExtraFolder("chimera.cxc")
f = open(tmpFileNameCMD, "w")
sampling, _setOfObjects = self._getSetAndSampling()
count = 1 # first model in chimera is a tomogram
if len(_setOfObjects) == 1:
count = 2 # first model in chimera is the bild file
# if we have a single tomogram 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 = _setOfObjects.getDim()[0]
tmpFileNameBILD = os.path.abspath(
self._getExtraFolder("axis.bild"))
viewers.viewer_chimera.Chimera.createCoordinateAxisFile(
dim, bildFileName=tmpFileNameBILD, sampling=sampling)
f.write("open %s\n" % tmpFileNameBILD)
f.write("cofr 0,0,0\n") # set center of coordinates
oldFileName = ""
for tomo in _setOfObjects:
fileName = tomo.getFileName()
if fileName == oldFileName:
continue
else:
oldFileName = fileName
localTomo = os.path.abspath(
ImageHandler.removeFileType(tomo.getFileName()))
if localTomo.endswith("stk"):
self.showError("Extension .stk is not supported")
f.write("open %s\n" % localTomo)
f.write("volume #%d style surface voxelSize %f\n" %
(count, sampling))
f.write("volume #%d level 1\n" % count)
count += 1
if len(_setOfObjects) > 1:
f.write('tile\n')
else:
x, y, z = tomo.getShiftsFromOrigin()
f.write("volume #2 origin %0.2f,%0.2f,%0.2f\n" % (x, y, z))
f.close()
view = ChimeraView(tmpFileNameCMD)
return [view]
def _doShowMorph(self, obj, **kwargs):
scriptFile = self.protocol._getPath('pdb_deform_chimera.cxc')
fhCmd = open(scriptFile, 'w')
inputFile = os.path.abspath(self.protocol.inputPDB.get().getFileName())
outputFile = os.path.abspath(self.protocol.outputPDB.getFileName())
fhCmd.write(self.OPEN_FILE % inputFile)
fhCmd.write(self.OPEN_FILE % outputFile)
fhCmd.write("hide models\n")
fhCmd.write("morph #1,2 frames 50 play false\n")
fhCmd.write("coordset #3 1,\n")
fhCmd.write("wait 50\n")
fhCmd.write("coordset #3 50,1\n")
fhCmd.close()
view = ChimeraView(scriptFile)
return [view]
def _showVolumesChimera(self):
""" Create a chimera script to visualize selected volumes. """
prot = self.protocol
volumes = self._getVolumeNames()
extra = prot._getExtraPath()
cmdFile = prot._getExtraPath('chimera_volumes.cxc')
with open(cmdFile, 'w+') as f:
for vol in volumes:
localVol = os.path.relpath(vol, extra)
if os.path.exists(vol):
f.write("open %s\n" % localVol)
f.write('tile\n')
view = ChimeraView(cmdFile)
return [view]
def _showVolumesChimera(self, volumes):
""" Create a chimera script to visualize selected volumes. """
if len(volumes) > 1:
cmdFile = self.protocol._getExtraPath('chimera_volumes.cxc')
f = open(cmdFile, 'w+')
f.write('windowsize 800 600\n')
for volFn in volumes:
vol = os.path.relpath(volFn, self.protocol._getExtraPath())
f.write("open %s\n" % vol)
f.write('tile\n')
f.close()
view = ChimeraView(cmdFile)
else:
#view = CommandView('xmipp_chimera_client --input "%s" --mode projector 256 &' % volumes[0])
view = ChimeraClientView(volumes[0], showProjection=True)
return [view]
def _showVolumesChimera(self):
""" Create a chimera script to visualize selected volumes. """
volumes = self._getVolumeNames()
if len(volumes) > 1:
cmdFile = self.protocol._getExtraPath('chimera_volumes.cmd')
f = open(cmdFile, 'w+')
for volFn in volumes:
# We assume that the chimera script will be generated
# in the same folder as xmipp volumes
localVol = os.path.basename(volFn)
if exists(volFn):
f.write("open %s\n" % localVol)
f.write('tile\n')
f.close()
view = ChimeraView(cmdFile)
else:
view = ChimeraClientView(volumes[0])
return [view]
def _visualize_norm_vol(self, obj, **args):
self._create_legend(1.5);
fnCmd = self.protocol._getExtraPath("chimera_output.py")
f = open(fnCmd, 'a')
f.write("run(session, 'open %s')\n" % self.protocol._getFileName(OUTPUT_PDBMRC_FILE))
f.write("run(session, 'open %s')\n" % self.protocol._getFileName(RESTA_FILE_NORM))
f.write("run(session, 'volume #2 voxelSize %s step 1')\n" %
self.protocol.inputVolume.get().getSamplingRate() )
f.write("run(session, 'volume #3 voxelSize %s')\n" %
self.protocol.inputVolume.get().getSamplingRate() )
f.write("run(session, 'vol #3 hide')\n")
f.write("run(session, 'color sample #2 map #3 palette"
" -1.5,red:-1.0,orange:-0.5,gold:0,yellow:0.5,lime:1.0,cyan:1.5,#1e90ff')\n")
f.close()
view = ChimeraView(fnCmd)
return [view]
def _showChimera(self, param=None):
self.createChimeraScriptDoA(OUTPUT_DOA_FILE_CHIMERA, CHIMERA_CMD_DOA,
CHIMERA_ELLIP)
cmdFile = self.protocol._getPath('chimera_DoA.cmd')
view = ChimeraView(cmdFile)
return [view]
def _visualize(self, obj, **args):
# Input map(s) are a parameter from the protocol
dim = 150.
sampling = 1.
_inputVol = None
_inputHalf1 = None
_inputHalf2 = None
listVol = []
directory = self.protocol._getExtraPath()
if self.protocol.useHalfMapsInsteadVol.get():
if self.protocol.halfMapsAttached.get():
if self.protocol.inputVolume.get() is not None:
_inputVol = self.protocol.inputVolume.get()
dim = _inputVol.getDim()[0]
sampling = _inputVol.getSamplingRate()
listVol.append(_inputVol)
else:
if self.protocol.inputHalf1.get() is not None:
_inputHalf1 = self.protocol.inputHalf1.get()
_inputHalf2 = self.protocol.inputHalf2.get()
dim = _inputHalf1.getDim()[0]
sampling = _inputHalf1.getSamplingRate()
listVol.append(_inputHalf1)
listVol.append(_inputHalf2)
else:
if self.protocol.inputVolume.get() is not None:
_inputVol = self.protocol.inputVolume.get()
dim = _inputVol.getDim()[0]
sampling = _inputVol.getSamplingRate()
listVol.append(_inputVol)
bildFileName = self.protocol._getExtraPath("axis_output.bild")
Chimera.createCoordinateAxisFile(dim,
bildFileName=bildFileName,
sampling=sampling)
fnCxc = self.protocol._getExtraPath("chimera_output.cxc")
f = open(fnCxc, 'w')
# change to workingDir
# If we do not use cd and the project name has an space
# the protocol fails even if we pass absolute paths
f.write('cd %s\n' % os.getcwd())
f.write("open %s\n" % bildFileName)
f.write("cofr 0,0,0\n") # set center of coordinates
counter = 1
for vol in listVol:
counter += 1
self._visInputVolume(f, vol, counter)
for filename in sorted(os.listdir(directory)):
if filename.endswith(".mrc"):
counter += 1
volFileName = os.path.join(directory, filename)
vol = Volume()
vol.setFileName(volFileName)
if self.protocol.useHalfMapsInsteadVol.get():
if self.protocol.halfMapsAttached.get():
inVol = self.protocol.inputVolume.get()
else:
inVol = self.protocol.inputHalf1.get()
else:
inVol = self.protocol.inputVolume.get()
vol.setSamplingRate(inVol.getSamplingRate())
vol.setOrigin(inVol.getOrigin(True))
self._visInputVolume(f, vol, counter)
f.write("volume #%d level %0.3f\n" % (counter, 0.001))
f.close()
return [ChimeraView(fnCxc)]
