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.getScipionScript(), 'view', 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):
import xmippLib
fn = xmippLib.FileName(path)
if fn.isImage() or fn.isMetaData():
from pyworkflow.em.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 _checkOutputs(self, outputs, random=False, errorthreshold=0.001):
""" Check that all output files are produced
and are equivalent to the ones in goldStandard folder.
"""
import xmippLib
for out in outputs:
outFile = os.path.join(self._testDir, self.outputDir, out)
fileGoldStd = os.path.join(self.goldDir, out)
# Check the expect output file was produced
msg = "Missing expected output file:\n output: %s" % outFile
self.assertTrue(os.path.exists(outFile), red(msg))
if random:
print(yellow("WARNING: %s was created using a random seed, check skipped..." % outFile))
else:
fnGoldStd = xmippLib.FileName(fileGoldStd)
if fnGoldStd.isImage():
im1 = xmippLib.Image(fileGoldStd)
im2 = xmippLib.Image(outFile)
msg = "Images are not equal (+-%f):\n output: %s\n gold: %s" % \
(errorthreshold, outFile, fileGoldStd)
self.assertTrue(im1.equal(im2, errorthreshold), red(msg))
elif fnGoldStd.isMetaData():
msg = "MetaDatas are not equal:\n output: %s\n gold: %s" % (outFile, fileGoldStd)
self.assertTrue(xmippLib.compareTwoMetadataFiles(outFile, fileGoldStd), red(msg))
else:
msg = "Files are not equal:\n output: %s\n gold: %s" % (outFile, fileGoldStd)
self.assertTrue(xmippLib.compareTwoFiles(outFile, fileGoldStd, 0), red(msg))
def createMetaDataFromPattern(pattern, isStack=False, label="image"):
''' Create a metadata from files matching pattern'''
import glob
files = glob.glob(pattern)
files.sort()
label = xmippLib.str2Label(label) #Check for label value
mD = xmippLib.MetaData()
inFile = xmippLib.FileName()
nSize = 1
for file in files:
fileAux = file
if isStack:
if file.endswith(".mrc"):
fileAux = file + ":mrcs"
x, x, x, nSize = xmippLib.getImageSize(fileAux)
if nSize != 1:
counter = 1
for jj in range(nSize):
inFile.compose(counter, fileAux)
objId = mD.addObject()
mD.setValue(label, inFile, objId)
mD.setValue(xmippLib.MDL_ENABLED, 1, objId)
counter += 1
else:
objId = mD.addObject()
mD.setValue(label, fileAux, objId)
mD.setValue(xmippLib.MDL_ENABLED, 1, objId)
return mD
def _getImgPath(self, mdFn, imgFn):
""" Get ups and ups until finding the relative location to images. """
path = dirname(mdFn)
index, fn = xmippLib.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 = dirname(path)
return None
def xmippExists(path):
return xmippLib.FileName(path).exists()
def isImageFile(cls, imgFn):
""" Check if imgFn has an image extension. The function
is implemented in the Xmipp binding.
"""
return xmippLib.FileName(imgFn).isImage()
def runCreateOutputStep(self):
''' Create standard output results_images, result_classes'''
#creating results files
imgSet = self.inputParticles.get()
lastIter = self.numberOfIterations.get()
if self.numberOfReferences != 1:
inDocfile = self._getFileName('docfileInputAnglesIters', iter=lastIter)
ClassFnTemplate = '%(rootDir)s/reconstruction_Ref3D_%(ref)03d.vol'
allExpImagesinDocfile = xmippLib.FileName()
all_exp_images = "all_exp_images"
allExpImagesinDocfile.compose(all_exp_images, inDocfile)
dataClasses = self._getFileName('sqliteClasses')
createClassesFromImages(imgSet, str(allExpImagesinDocfile),
dataClasses, SetOfClasses3D,
xmippLib.MDL_REF3D, ClassFnTemplate, lastIter)
classes = self._createSetOfClasses3D(imgSet)
clsSet = SetOfClasses3D(dataClasses)
classes.appendFromClasses(clsSet)
volumes = self._createSetOfVolumes()
volumes.setSamplingRate(imgSet.getSamplingRate())
for refN in self.allRefs():
volFn = self._getFileName('reconstructedFileNamesIters',
iter=lastIter,
ref=refN)
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)
vol = Volume()
vol.setFileName(volFn)
vol.setSamplingRate(imgSet.getSamplingRate())
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)