def _validate(self):
errors = []
if (not self.patternUntilted.get() or not self.patternTilted.get()):
errors.append(Message.ERROR_PATTERN_EMPTY)
else:
filePathsUntilted = glob(expandPattern(self.patternUntilted.get()))
filePathsTilted = glob(expandPattern(self.patternTilted.get()))
if (len(filePathsUntilted) == 0 or len(filePathsTilted) == 0):
errors.append(Message.ERROR_PATTERN_FILES)
return errors
def _validate(self):
errors = []
if (not self.patternUntilted.get() or not self.patternTilted.get()):
errors.append(Message.ERROR_PATTERN_EMPTY)
else:
filePathsUntilted = glob(expandPattern(self.patternUntilted.get()))
filePathsTilted = glob(expandPattern(self.patternTilted.get()))
if (len(filePathsUntilted) == 0 or len(filePathsTilted) == 0):
errors.append(Message.ERROR_PATTERN_FILES)
return errors
def getPattern(self):
""" Expand the pattern using environ vars or username
and also replacing special character # by digit matching.
"""
self._idRegex = None
filesPath = self.filesPath.get('').strip()
filesPattern = self.filesPattern.get('').strip()
if filesPattern:
fullPattern = join(filesPath, filesPattern)
else:
fullPattern = filesPath
pattern = expandPattern(fullPattern.replace("$", ""))
match = re.match('[^#]*(#+)[^#]*', pattern)
if match is not None:
g = match.group(1)
n = len(g)
# prepare regex pattern - place ids, handle *, handle ?
idregex = pattern.replace(g, '(%s)' % ('[0-9]' * n))
idregex = idregex.replace('*', '.*')
idregex = idregex.replace('?', '.')
self._idRegex = re.compile(idregex)
pattern = pattern.replace(g, '[0-9]' * n)
return pattern
def getPattern(self):
""" Expand the pattern using environ vars or username
and also replacing special character # by digit matching.
"""
self._idRegex = None
filesPath = self.filesPath.get('').strip()
filesPattern = self.filesPattern.get('').strip()
if filesPattern:
fullPattern = join(filesPath, filesPattern)
else:
fullPattern = filesPath
pattern = expandPattern(fullPattern.replace("$", ""))
match = re.match('[^#]*(#+)[^#]*', pattern)
if match is not None:
g = match.group(1)
n = len(g)
# prepare regex pattern - place ids, handle *, handle ?
idregex = pattern.replace(g, '(%s)' % ('[0-9]'*n))
idregex = idregex.replace('*','.*')
idregex = idregex.replace('?', '.')
self._idRegex = re.compile(idregex)
pattern = pattern.replace(g, '[0-9]'*n)
return pattern
def importMicrographs(self, pattern, suffix, voltage, sphericalAberration,
amplitudeContrast):
""" Copy images matching the filename pattern
Register other parameters.
"""
filePaths = glob(expandPattern(pattern))
#imgSet = SetOfMicrographs(filename=self.micsPairsSqlite, prefix=suffix)
imgSet = self._createSetOfMicrographs(suffix=suffix)
acquisition = imgSet.getAcquisition()
# Setting Acquisition properties
acquisition.setVoltage(voltage)
acquisition.setSphericalAberration(sphericalAberration)
acquisition.setAmplitudeContrast(amplitudeContrast)
# Call a function that should be implemented by each subclass
self._setOtherPars(imgSet)
outFiles = [imgSet.getFileName()]
imgh = ImageHandler()
img = imgSet.ITEM_TYPE()
n = 1
size = len(filePaths)
filePaths.sort()
for i, fn in enumerate(filePaths):
# ext = os.path.splitext(basename(f))[1]
dst = self._getExtraPath(basename(fn))
if self.copyToProj:
copyFile(fn, dst)
else:
createLink(fn, dst)
if n > 1:
for index in range(1, n + 1):
img.cleanObjId()
img.setFileName(dst)
img.setIndex(index)
imgSet.append(img)
else:
img.cleanObjId()
img.setFileName(dst)
# Fill the micName if img is a Micrograph.
self._fillMicName(img, fn, pattern)
imgSet.append(img)
outFiles.append(dst)
sys.stdout.write("\rImported %d/%d" % (i + 1, size))
sys.stdout.flush()
print "\n"
imgSet.write()
return imgSet
def importMicrographs(self, pattern, suffix, voltage, sphericalAberration, amplitudeContrast):
""" Copy images matching the filename pattern
Register other parameters.
"""
filePaths = glob(expandPattern(pattern))
#imgSet = SetOfMicrographs(filename=self.micsPairsSqlite, prefix=suffix)
imgSet = self._createSetOfMicrographs(suffix=suffix)
acquisition = imgSet.getAcquisition()
# Setting Acquisition properties
acquisition.setVoltage(voltage)
acquisition.setSphericalAberration(sphericalAberration)
acquisition.setAmplitudeContrast(amplitudeContrast)
# Call a function that should be implemented by each subclass
self._setOtherPars(imgSet)
outFiles = [imgSet.getFileName()]
imgh = ImageHandler()
img = imgSet.ITEM_TYPE()
n = 1
size = len(filePaths)
filePaths.sort()
for i, fn in enumerate(filePaths):
# ext = os.path.splitext(basename(f))[1]
dst = self._getExtraPath(basename(fn))
if self.copyToProj:
copyFile(fn, dst)
else:
createLink(fn, dst)
if n > 1:
for index in range(1, n+1):
img.cleanObjId()
img.setFileName(dst)
img.setIndex(index)
imgSet.append(img)
else:
img.cleanObjId()
img.setFileName(dst)
# Fill the micName if img is a Micrograph.
self._fillMicName(img, fn, pattern)
imgSet.append(img)
outFiles.append(dst)
sys.stdout.write("\rImported %d/%d" % (i+1, size))
sys.stdout.flush()
print "\n"
imgSet.write()
return imgSet
def getPattern(self):
""" Expand the pattern using environ vars or username
and also replacing special character # by digit matching.
"""
self._idRegex = None
filesPath = self.filesPath.get('').strip()
filesPattern = self.filesPattern.get('').strip()
if filesPattern:
fullPattern = join(filesPath, filesPattern)
else:
fullPattern = filesPath
pattern = expandPattern(fullPattern)
match = re.match('[^#]*(#+)[^#]*', pattern)
if match is not None:
g = match.group(1)
n = len(g)
self._idRegex = re.compile(pattern.replace(g, '(%s)' % ('\d' * n)))
pattern = pattern.replace(g, '[0-9]' * n)
return pattern
def getPattern(self):
""" Expand the pattern using environ vars or username
and also replacing special character # by digit matching.
"""
self._idRegex = None
filesPath = self.filesPath.get('').strip()
filesPattern = self.filesPattern.get('').strip()
if filesPattern:
fullPattern = join(filesPath, filesPattern)
else:
fullPattern = filesPath
pattern = expandPattern(fullPattern)
match = re.match('[^#]*(#+)[^#]*', pattern)
if match is not None:
g = match.group(1)
n = len(g)
self._idRegex = re.compile(pattern.replace(g, '(%s)' % ('\d'*n)))
pattern = pattern.replace(g, '[0-9]'*n)
return pattern
def _iterFiles(self, pattern):
filePaths = glob(expandPattern(pattern))
for fn in filePaths:
yield fn