def importCoordinates(self, fileName, addCoordinate):
if exists(fileName):
ext = getExt(fileName)
if ext == ".json":
jsonPosDict = loadJson(fileName)
if jsonPosDict.has_key("boxes"):
boxes = jsonPosDict["boxes"]
for box in boxes:
x, y = box[:2]
coord = Coordinate()
coord.setPosition(x, y)
addCoordinate(coord)
elif ext == ".box":
md = MetaData()
md.readPlain(fileName, "xcoor ycoor particleSize")
size = md.getValue(MDL_PICKING_PARTICLE_SIZE, md.firstObject())
if size is None:
print ">>> WARNING: Error parsing coordinate file: %s" % fileName
print " Skipping this file."
else:
half = size / 2
for objId in md:
x = md.getValue(MDL_XCOOR, objId)
y = md.getValue(MDL_YCOOR, objId)
coord = Coordinate()
coord.setPosition(x+half, y+half)
addCoordinate(coord)
else:
raise Exception('Unknown extension "%s" to import Eman coordinates' % ext)
def importCoordinates(self, fileName, addCoordinate):
if exists(fileName):
ext = getExt(fileName)
if ext == ".json":
print "importando un json"
jsonPosDict = loadJson(fileName)
if jsonPosDict.has_key("boxes"):
boxes = jsonPosDict["boxes"]
for box in boxes:
x, y = box[:2]
coord = Coordinate()
coord.setPosition(x, y)
addCoordinate(coord)
elif ext == ".box":
md = MetaData()
md.readPlain(fileName, 'xcoor ycoor xSize ySize')
for objId in md:
x = md.getValue(MDL_XCOOR, objId)
y = md.getValue(MDL_YCOOR, objId)
coord = Coordinate()
coord.setPosition(x, y)
addCoordinate(coord)
else:
print "importando un queseyo"
def convertBinaryFiles(imgSet, outputDir, extension='mrcs'):
""" Convert binary images files to a format read by Relion.
Params:
imgSet: input image set to be converted.
outputDir: where to put the converted file(s)
Return:
A dictionary with old-file as key and new-file as value
If empty, not conversion was done.
"""
filesDict = {}
ih = em.ImageHandler()
# This approach can be extended when
# converting from a binary file format that
# is not read from Relion
def createBinaryLink(fn):
""" Just create a link named .mrcs to Relion understand
that it is a binary stack file and not a volume.
"""
newFn = join(outputDir, replaceBaseExt(fn, extension))
createLink(fn, newFn)
return newFn
def convertStack(fn):
""" Convert from a format that is not read by Relion
to an spider stack.
"""
newFn = join(outputDir, replaceBaseExt(fn, 'stk'))
ih.convertStack(fn, newFn)
return newFn
ext = getExt(imgSet.getFirstItem().getFileName())[1:] # remove dot in extension
print "extension = ", extension
print "ext = ", ext
if ext == extension:
mapFunc = createBinaryLink
elif ext == 'mrc' and extension == 'mrcs':
mapFunc = createBinaryLink
elif ext.endswith('.hdf'): # assume eman .hdf format
mapFunc = convertStack
else:
mapFunc = None
if mapFunc is not None:
for fn in imgSet.getFiles():
filesDict[fn] = mapFunc(fn) # convert and map new filename
return filesDict
def _warnings(self):
warnings = []
firstMic = self.inputMicrographs.get().getFirstItem()
fnLower = firstMic.getFileName().lower()
ext = getExt(fnLower)
if ext in ['.tif', '.dm3'] and not self.invertY.get():
warnings.append(
'We have seen a flip in Y when using %s files in EMAN2' % ext)
warnings.append(
'The generated coordinates may or may not be valid in Scipion.'
)
warnings.append(
'TIP: Activate "Invert Y coordinates" if you find it wrong.')
return warnings
def _insertAllSteps(self):
self._params = {}
# diameter must be passed in Armstrongs and therefore should be converted
self._params['diam'] = self.diameter.get() * self.getInputMicrographs().getSamplingRate()
# self._params['num-slices'] = self.numberSizes.get()
# self._params['size-range'] = self.sizeRange.get()
self._params['apix'] = self.inputMicrographs.get().getSamplingRate()
self._params['thresh'] = self.threshold.get()
# self._params['max-thresh'] = self.maxThreshold.get()
# self._params['max-area'] = self.maxArea.get()
# self._params['max-peaks'] = self.maxPeaks.get()
args = ""
for par, val in self._params.iteritems():
args += " --%s=%s" % (par, str(val))
if self.invert:
args += " --invert"
args += " " + self.extraParams.get('')
deps = [] # Store all steps ids, final step createOutput depends on all of them
ih = ImageHandler()
for mic in self.inputMicrographs.get():
# Create micrograph folder
micName = mic.getFileName()
micDir = self._getTmpPath(removeBaseExt(micName))
makePath(micDir)
# If needed convert micrograph to mrc format, otherwise link it
if getExt(micName) != ".mrc":
fnMicBase = replaceBaseExt(micName, 'mrc')
inputMic = join(micDir, fnMicBase)
ih.convert(mic.getLocation(), inputMic)
else:
inputMic = join(micDir, basename(micName))
createLink(micName, inputMic)
# Insert step to execute program
stepId = self._insertFunctionStep('executeDogpickerStep', inputMic, args)
deps.append(stepId)
self._insertFinalSteps(deps)
def _insertAllSteps(self):
self._params = {}
# diameter must be passed in Angstrongs and therefore should be converted
self._params['diam'] = self.diameter.get() * self.getInputMicrographs().getSamplingRate()
# self._params['num-slices'] = self.numberSizes.get()
# self._params['size-range'] = self.sizeRange.get()
self._params['apix'] = self.inputMicrographs.get().getSamplingRate()
self._params['thresh'] = self.threshold.get()
# self._params['max-thresh'] = self.maxThreshold.get()
# self._params['max-area'] = self.maxArea.get()
# self._params['max-peaks'] = self.maxPeaks.get()
args = ""
for par, val in self._params.iteritems():
args += " --%s=%s" % (par, str(val))
if self.invert:
args += " --invert"
args += " " + self.extraParams.get('')
deps = [] # Store all steps ids, final step createOutput depends on all of them
ih = ImageHandler()
for mic in self.inputMicrographs.get():
# Create micrograph folder
micName = mic.getFileName()
micDir = self._getTmpPath(removeBaseExt(micName))
makePath(micDir)
# If needed convert micrograph to mrc format, otherwise link it
if getExt(micName) != ".mrc":
fnMicBase = replaceBaseExt(micName, 'mrc')
inputMic = join(micDir, fnMicBase)
ih.convert(mic.getLocation(), inputMic)
else:
inputMic = join(micDir, basename(micName))
createLink(micName, inputMic)
# Insert step to execute program
stepId = self._insertFunctionStep('executeDogpickerStep', inputMic, args)
deps.append(stepId)
self._insertFinalSteps(deps)
def convertBinaryFiles(imgSet, outputDir, extension='mrcs'):
""" Convert binary images files to a format read by Relion.
Params:
imgSet: input image set to be converted.
outputDir: where to put the converted file(s)
Return:
A dictionary with old-file as key and new-file as value
If empty, not conversion was done.
"""
filesDict = {}
ih = em.ImageHandler()
def getUniqueFileName(fn, extension):
""" Get an unique file for either link or convert files.
It is possible that the base name overlap if they come
from different runs. (like partices.mrcs after relion preprocess)
"""
newFn = join(outputDir, replaceBaseExt(fn, extension))
newRoot = removeExt(newFn)
values = filesDict.values()
counter = 1
while newFn in values:
counter += 1
newFn = '%s_%05d.%s' % (newRoot, counter, extension)
return newFn
def createBinaryLink(fn):
""" Just create a link named .mrcs to Relion understand
that it is a binary stack file and not a volume.
"""
newFn = getUniqueFileName(fn, extension)
createLink(fn, newFn)
return newFn
def convertStack(fn):
""" Convert from a format that is not read by Relion
to an spider stack.
"""
newFn = getUniqueFileName(fn, 'stk')
ih.convertStack(fn, newFn)
return newFn
ext = getExt(imgSet.getFirstItem().getFileName())[1:] # remove dot in extension
if ext == extension:
mapFunc = createBinaryLink
print "convertBinaryFiles: creating soft links."
elif ext == 'mrc' and extension == 'mrcs':
mapFunc = createBinaryLink
print "convertBinaryFiles: creating soft links (mrcs -> mrc)."
elif ext.endswith('hdf'): # assume eman .hdf format
mapFunc = convertStack
print "convertBinaryFiles: converting stacks. (%s -> %s)" % (extension, ext)
else:
mapFunc = None
if mapFunc is not None:
for fn in imgSet.getFiles():
newFn = mapFunc(fn) # convert or link
filesDict[fn] = newFn # map new filename
print " %s -> %s" % (newFn, fn)
return filesDict
def convertBinaryFiles(imgSet, outputDir, extension='mrcs'):
""" Convert binary images files to a format read by Relion.
Params:
imgSet: input image set to be converted.
outputDir: where to put the converted file(s)
Return:
A dictionary with old-file as key and new-file as value
If empty, not conversion was done.
"""
filesDict = {}
ih = em.ImageHandler()
def getUniqueFileName(fn, extension):
""" Get an unique file for either link or convert files.
It is possible that the base name overlap if they come
from different runs. (like partices.mrcs after relion preprocess)
"""
newFn = join(outputDir, replaceBaseExt(fn, extension))
newRoot = removeExt(newFn)
values = filesDict.values()
counter = 1
while newFn in values:
counter += 1
newFn = '%s_%05d.%s' % (newRoot, counter, extension)
return newFn
def createBinaryLink(fn):
""" Just create a link named .mrcs to Relion understand
that it is a binary stack file and not a volume.
"""
newFn = getUniqueFileName(fn, extension)
createLink(fn, newFn)
return newFn
def convertStack(fn):
""" Convert from a format that is not read by Relion
to an spider stack.
"""
newFn = getUniqueFileName(fn, 'stk')
ih.convertStack(fn, newFn)
return newFn
ext = getExt(
imgSet.getFirstItem().getFileName())[1:] # remove dot in extension
if ext == extension:
mapFunc = createBinaryLink
print "convertBinaryFiles: creating soft links."
elif ext == 'mrc' and extension == 'mrcs':
mapFunc = createBinaryLink
print "convertBinaryFiles: creating soft links (mrcs -> mrc)."
elif ext.endswith('hdf'): # assume eman .hdf format
mapFunc = convertStack
print "convertBinaryFiles: converting stacks. (%s -> %s)" % (extension,
ext)
else:
mapFunc = None
if mapFunc is not None:
for fn in imgSet.getFiles():
newFn = mapFunc(fn) # convert or link
filesDict[fn] = newFn # map new filename
print " %s -> %s" % (newFn, fn)
return filesDict
