def _insertAllSteps(self):
importFrom = self.importFrom.get()
ci = self.getImportClass()
if ci is None:
ProtImportImages._insertAllSteps(self)
else:
self._insertFunctionStep('importParticlesStep', importFrom,
self.importFilePath)
def _insertAllSteps(self):
importFrom = self.importFrom.get()
ci = self.getImportClass()
if ci is None:
ProtImportImages._insertAllSteps(self)
else:
self._insertFunctionStep('importParticlesStep', importFrom,
self.importFilePath)
def _getImportChoices(self):
""" Return a list of possible choices
from which the import can be done.
(usually packages formas such as: xmipp3, eman2, relion...etc.
"""
choices = ProtImportImages._getImportChoices(self)
return choices + ['emx', 'xmipp3', 'scipion']
def _getImportChoices(self):
""" Return a list of possible choices
from which the import can be done.
(usually packages formas such as: xmipp3, eman2, relion...etc.
"""
choices = ProtImportImages._getImportChoices(self)
return choices
def _defineAcquisitionParams(self, form):
group = ProtImportImages._defineAcquisitionParams(self, form)
group.addParam(
'samplingRateMode',
params.EnumParam,
choices=[Message.LABEL_SAMP_MODE_1, Message.LABEL_SAMP_MODE_2],
default=SAMPLING_FROM_IMAGE,
label=Message.LABEL_SAMP_MODE,
help=Message.TEXT_SAMP_MODE)
group.addParam('samplingRate',
params.FloatParam,
default=1.0,
condition='samplingRateMode==%d' % SAMPLING_FROM_IMAGE,
label=Message.LABEL_SAMP_RATE,
help=Message.TEXT_SAMP_RATE)
group.addParam('scannedPixelSize',
params.FloatParam,
default=7.0,
condition='samplingRateMode==%d' %
SAMPLING_FROM_SCANNER,
label=Message.LABEL_SCANNED,
help='')
return group
def _getImportChoices(self):
""" Return a list of possible choices
from which the import can be done.
(usually packages formas such as: xmipp3, eman2, relion...etc.
"""
choices = ProtImportImages._getImportChoices(self)
return choices + ['emx', 'xmipp3', 'relion', 'scipion', 'frealign']#the order of this list is related to the constants defined
def _defineAcquisitionParams(self, form):
form.addParam('samplingRate',
params.FloatParam,
default=1.,
label=Message.LABEL_SAMP_RATE)
group = ProtImportImages._defineAcquisitionParams(self, form)
group.expertLevel.set(LEVEL_ADVANCED)
def _defineAcquisitionParams(self, form):
form.addParam('samplingRate', params.FloatParam, default=1.,
label=Message.LABEL_SAMP_RATE)
group = ProtImportImages._defineAcquisitionParams(self, form)
group.expertLevel.set(LEVEL_ADVANCED)
# Change some params properties
patternParam = form.getParam('filesPattern')
patternParam.condition.set('0')
def _getImportChoices(self):
""" Return a list of possible choices
from which the import can be done.
(usually packages formas such as: xmipp3, eman2, relion...etc.
"""
choices = ProtImportImages._getImportChoices(self)
# Do not change the order of this list since
# it is related to the constants defined
return choices + self.importFormats
def _getImportChoices(self):
""" Return a list of possible choices
from which the import can be done.
(usually packages formas such as: xmipp3, eman2, relion...etc.
"""
choices = ProtImportImages._getImportChoices(self)
return choices + [
'emx', 'xmipp3', 'relion', 'scipion', 'frealign'
] #the order of this list is related to the constants defined
def _getImportChoices(self):
""" Return a list of possible choices
from which the import can be done.
(usually packages formas such as: xmipp3, eman2, relion...etc.
"""
choices = ProtImportImages._getImportChoices(self)
# Do not change the order of this list since
# it is related to the constants defined
return choices + self.importFormats
def _validate(self):
ci = self.getImportClass()
if ci is None:
return ProtImportImages._validate(self)
else:
errors = self._validateFileExtension()
if errors:
return errors
else:
return ci.validateParticles()
def _validate(self):
ci = self.getImportClass()
if ci is None:
return ProtImportImages._validate(self)
else:
errors = self._validateFileExtension()
if errors:
return errors
else:
return ci.validateParticles()
def _defineAcquisitionParams(self, form):
group = ProtImportImages._defineAcquisitionParams(self, form)
group.addParam('samplingRateMode', EnumParam,
choices=[Message.LABEL_SAMP_MODE_1, Message.LABEL_SAMP_MODE_2],
default=SAMPLING_FROM_IMAGE,
label=Message.LABEL_SAMP_MODE,
help=Message.TEXT_SAMP_MODE)
group.addParam('samplingRate', FloatParam, default=1.0,
condition='samplingRateMode==%d' % SAMPLING_FROM_IMAGE,
label=Message.LABEL_SAMP_RATE,
help=Message.TEXT_SAMP_RATE)
group.addParam('scannedPixelSize', FloatParam, default=7.0,
condition='samplingRateMode==%d' % SAMPLING_FROM_SCANNER,
label=Message.LABEL_SCANNED,
help='')
return group
def loadAcquisitionInfo(self):
""" Return a proper acquistionInfo (dict)
or an error message (str).
"""
if self.importFrom != self.IMPORT_FROM_FILES:
return ProtImportImages.loadAcquisitionInfo(self)
result = "Could not find acquistion information"
for fileName, fileId in self.iterFiles():
baseName = pwutils.removeExt(fileName)
xml1 = baseName.replace('_frames', '.xml')
if os.path.exists(xml1):
result = self._parseXML(xml1)
else:
xml2 = baseName + '.xml'
result = self._parseXML(xml2)
return result
def loadAcquisitionInfo(self):
""" Return a proper acquistionInfo (dict)
or an error message (str).
"""
if self.importFrom != self.IMPORT_FROM_FILES:
return ProtImportImages.loadAcquisitionInfo(self)
result = "Could not find acquistion information"
for fileName, fileId in self.iterFiles():
baseName = pwutils.removeExt(fileName)
xml1 = baseName.replace('_frames', '.xml')
if os.path.exists(xml1):
result = self._parseXML(xml1)
else:
xml2 = baseName + '.xml'
result = self._parseXML(xml2)
return result
def _validate(self):
errors = ProtImportImages._validate(self)
errors += self._validateBlacklist()
return errors
def _summary(self):
if self.importFrom == self.IMPORT_FROM_FILES:
return ProtImportImages._summary(self)
else:
return [self.summaryVar.get('')]
def _defineParams(self, form):
ProtImportImages._defineParams(self, form)
def _defineAcquisitionParams(self, form):
group = ProtImportImages._defineAcquisitionParams(self, form)
group.addParam('samplingRate',
params.FloatParam,
label=Message.LABEL_SAMP_RATE)
def _defineAcquisitionParams(self, form):
form.addParam('samplingRate', params.FloatParam, default=1.,
label=Message.LABEL_SAMP_RATE)
group = ProtImportImages._defineAcquisitionParams(self, form)
group.expertLevel.set(LEVEL_ADVANCED)
def _summary(self):
if self.importFrom == self.IMPORT_FROM_FILES:
return ProtImportImages._summary(self)
else:
return [self.summaryVar.get('')]
def __init__(self, **args):
ProtImportImages.__init__(self, **args)
def _defineAcquisitionParams(self, form):
group = ProtImportImages._defineAcquisitionParams(self, form)
group.addParam('samplingRate', params.FloatParam,
label=Message.LABEL_SAMP_RATE)
def _validate(self):
ci = self.getImportClass()
if ci is None:
return ProtImportImages._validate(self)
else:
return ci.validateParticles()
def _validate(self):
ci = self.getImportClass()
if ci is None:
return ProtImportImages._validate(self)
else:
return ci.validateParticles()
def __init__(self, **args):
ProtImportImages.__init__(self, **args)
def _defineParams(self, form):
ProtImportImages._defineParams(self, form)