def _fillMicName(self, img, filename):
from pyworkflow.em import Micrograph
if isinstance(img, Micrograph):
filePaths = self.getMatchFiles()
commPath = pwutils.commonPath(filePaths)
micName = filename.replace(commPath + "/", "").replace("/", "_")
img.setMicName(micName)
def _fillMicName(self, img, filename, pattern):
from pwem.objects import Micrograph
if isinstance(img, Micrograph):
filePaths = self.getMatchFiles(pattern=pattern)
commPath = pwutils.commonPath(filePaths)
micName = filename.replace(commPath + "/", "").replace("/", "_")
img.setMicName(micName)
def _getUniqueFileName(self, filename, filePaths=None):
if filePaths is None:
filePaths = [re.split(r'[$*#?]', self.getPattern())[0]]
commPath = pwutils.commonPath(filePaths)
return filename.replace(commPath + "/", "").replace("/", "_")
def _getUniqueFileName(self, filename, filePaths=None):
if filePaths is None:
filePaths = [re.split(r'[$*#?]', self.getPattern())[0]]
commPath = pwutils.commonPath(filePaths)
return filename.replace(commPath + "/", "").replace("/", "_")
def convertBinaryFiles(imgSet,
outputDir,
extension='mrcs',
forceConvert=False):
""" Convert binary images files to a format read by Relion.
Or create links if there is no need to convert the binary files.
Params:
imgSet: input image set to be converted.
outputDir: where to put the converted file(s)
extension: extension accepted by the program
forceConvert: if True, the files will be converted and no root will be used
Return:
A dictionary with old-file as key and new-file as value
If empty, not conversion was done.
"""
filesDict = {}
ih = ImageHandler()
outputRoot = outputDir if forceConvert else os.path.join(
outputDir, 'input')
# Get the extension without the dot
stackFiles = imgSet.getFiles()
ext = pwutils.getExt(next(iter(stackFiles)))[1:]
rootDir = pwutils.commonPath(list(stackFiles))
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 particles.mrcs after relion preprocess)
"""
newFn = os.path.join(outputRoot, pwutils.replaceBaseExt(fn, extension))
newRoot = pwutils.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)
if not os.path.exists(newFn):
pwutils.createLink(fn, newFn)
print(" %s -> %s" % (newFn, fn))
return newFn
def convertStack(fn):
""" Convert from a format that is not read by Relion
to an spider stack.
"""
newFn = getUniqueFileName(fn, 'mrcs')
ih.convertStack(fn, newFn)
print(" %s -> %s" % (newFn, fn))
return newFn
def replaceRoot(fn):
""" Link create to the root folder, so just replace that
in the name, no need to do anything else.
"""
return fn.replace(rootDir, outputRoot)
if forceConvert:
print("convertBinaryFiles: forceConvert = True")
mapFunc = convertStack
elif ext == extension:
print("convertBinaryFiles: creating soft links.")
print(" Root: %s -> %s" % (outputRoot, rootDir))
mapFunc = replaceRoot
# FIXME: There is a bug in pwutils.createLink when input is a single folder
# pwutils.createLink(rootDir, outputRoot)
# relativeOutput = os.path.join(os.path.relpath(rootDir, outputRoot), rootDir)
# If the rootDir is a prefix in the outputRoot (usually Runs)
# we need to prepend that basename to make the link works
if rootDir in outputRoot:
relativeOutput = os.path.join(os.path.relpath(rootDir, outputRoot),
os.path.basename(rootDir))
else:
relativeOutput = os.path.relpath(rootDir,
os.path.dirname(outputRoot))
if not os.path.exists(outputRoot):
os.symlink(relativeOutput, outputRoot)
elif ext == 'mrc' and extension == 'mrcs':
print("convertBinaryFiles: creating soft links (mrcs -> mrc).")
mapFunc = createBinaryLink
elif ext.endswith('hdf'): # assume eman .hdf format
print("convertBinaryFiles: converting stacks. (%s -> %s)" %
(extension, ext))
mapFunc = convertStack
else:
mapFunc = None
if mapFunc is not None:
pwutils.makePath(outputRoot)
for fn in stackFiles:
newFn = mapFunc(fn) # convert or link
filesDict[fn] = newFn # map new filename
return filesDict