def _getImgPath(self, mdFn, imgFn):
""" Get ups and ups until finding the relative location to images. """
path = os.path.dirname(mdFn)
index, fn = emlib.FileName(imgFn).decompose()
while path and path != '/':
newFn = os.path.join(path, fn)
if os.path.exists(newFn):
if index:
newFn = '%d@%s' % (index, newFn)
return newFn
path = os.path.dirname(path)
return None
def openPath(self, path):
"""Try to open the selected path"""
path = expandPattern(path)
# If the path is a dir, open it with scipion browser dir <path>
if os.path.isdir(path):
dpath = (path if os.path.isabs(path) else os.path.join(
os.getcwd(), path))
subprocess.Popen([pw.PYTHON, pw.getViewerScript(), dpath])
return
# If it is a file, interpret it correctly and open it with DataView
dirname = os.path.dirname(path)
fname = os.path.basename(path)
if '@' in fname:
path = os.path.join(dirname, fname.split('@', 1)[-1])
else:
path = os.path.join(dirname, fname)
if os.path.exists(path):
from pwem import emlib
fn = emlib.FileName(path)
if fn is not None and (fn.isImage() or fn.isMetaData()):
# fn is None if xmippLib is the xmippLib ghost library
from pwem.viewers import DataView
DataView(path).show()
else:
_open_cmd(path)
else:
# This is probably one special reference, like sci-open:... that
# can be interpreted with our handlers.
tag = path.split(':', 1)[0] if ':' in path else None
if tag in self.handlers:
self.handlers[tag](path.split(':', 1)[-1])
else:
print("Can't find %s" % path)
def runCreateOutputStep(self):
''' Create standard output results_images, result_classes'''
#creating results files
imgSet = self.inputParticles.get()
lastIter = self.numberOfIterations.get()
Ts = imgSet.getSamplingRate()
if self.numberOfReferences != 1:
inDocfile = self._getFileName('docfileInputAnglesIters', iter=lastIter)
ClassFnTemplate = '%(rootDir)s/reconstruction_Ref3D_%(ref)03d.vol'
allExpImagesinDocfile = emlib.FileName()
all_exp_images = "all_exp_images"
allExpImagesinDocfile.compose(all_exp_images, inDocfile)
dataClasses = self._getFileName('sqliteClasses')
createClassesFromImages(imgSet, str(allExpImagesinDocfile),
dataClasses, SetOfClasses3D, emlib.MDL_REF3D,
ClassFnTemplate, lastIter)
classes = self._createSetOfClasses3D(imgSet)
clsSet = SetOfClasses3D(dataClasses)
classes.appendFromClasses(clsSet)
volumes = self._createSetOfVolumes()
volumes.setSamplingRate(Ts)
for refN in self.allRefs():
volFn = self._getFileName('reconstructedFileNamesIters',
iter=lastIter,
ref=refN)
volFn = convertToMrc(self, volFn, Ts, True)
vol = Volume()
vol.setFileName(volFn)
volumes.append(vol)
self._defineOutputs(outputVolumes=volumes)
self._defineOutputs(outputClasses=classes)
self._defineSourceRelation(self.inputParticles, volumes)
self._defineSourceRelation(self.inputParticles, classes)
self._defineSourceRelation(self.input3DReferences, volumes)
self._defineSourceRelation(self.input3DReferences, classes)
else:
volFn = self._getFileName('reconstructedFileNamesIters',
iter=lastIter,
ref=1)
halfMap1 = self._getFileName('reconstructedFileNamesItersSplit1',
iter=lastIter,
ref=1)
halfMap2 = self._getFileName('reconstructedFileNamesItersSplit2',
iter=lastIter,
ref=1)
volFn = convertToMrc(self, volFn, Ts, True)
halfMap1 = convertToMrc(self, halfMap1, Ts, True)
halfMap2 = convertToMrc(self, halfMap2, Ts, True)
vol = Volume()
vol.setFileName(volFn)
vol.setSamplingRate(Ts)
vol.setHalfMaps([halfMap1, halfMap2])
self._defineOutputs(outputVolume=vol)
self._defineSourceRelation(self.inputParticles, vol)
self._defineSourceRelation(self.input3DReferences, vol)
#create set of images
imgSetOut = self._createSetOfParticles("_iter_%03d" % lastIter)
self._fillParticlesFromIter(imgSetOut, lastIter)
self._defineOutputs(outputParticles=imgSetOut)
self._defineSourceRelation(self.inputParticles, imgSetOut)
self._defineSourceRelation(self.input3DReferences, imgSetOut)