def __init__(self, **kwargs):
ProtFilterParticles.__init__(self, **kwargs)
SpiderProtocol.__init__(self, **kwargs)
self._op = "FQ"
self._params = {'ext': 'stk',
'particles': 'particles_filtered',
'particlesSel': 'particles_filtered_sel'}
def __init__(self, **kwargs):
ProtCreateMask2D.__init__(self, **kwargs)
SpiderProtocol.__init__(self, **kwargs)
self._params = {'ext': 'stk',
'inputImage': 'input_image',
'outputMask': 'output_mask'
}
def __init__(self, **kwargs):
ProtCreateMask2D.__init__(self, **kwargs)
SpiderProtocol.__init__(self, **kwargs)
self._params = {'ext': 'stk',
'inputImage': 'input_image',
'outputMask': 'output_mask'
}
def __init__(self, **kwargs):
ProtFilterParticles.__init__(self, **kwargs)
SpiderProtocol.__init__(self, **kwargs)
self._op = "FQ"
self._params = {
'ext': 'stk',
'particles': 'particles_filtered',
'particlesSel': 'particles_filtered_sel'
}
def __init__(self, **kwargs):
ProtCreateMask2D.__init__(self, **kwargs)
SpiderProtocol.__init__(self, **kwargs)
# To avoid showing MPI box due to duplicated init
self.allowMpi = False
self._params = {'ext': 'stk',
'inputImage': 'input_image',
'outputMask': 'output_mask'
}
def __init__(self, **kwargs):
ProtCreateMask2D.__init__(self, **kwargs)
SpiderProtocol.__init__(self, **kwargs)
# To avoid showing MPI box due to duplicated init
self.allowMpi = False
self._params = {
'ext': 'stk',
'inputImage': 'input_image',
'outputMask': 'output_mask'
}
def __init__(self, script, alignDir, **args):
ProtAlign2D.__init__(self, **args)
SpiderProtocol.__init__(self, **args)
self._script = script
self._alignDir = alignDir
self._params = {'ext': 'stk',
'particles': 'input_particles',
'particlesSel': 'input_particles_sel',
'average': join(self._alignDir, 'rfreeavg001'), # If change the name, change it in template batch
'particlesAligned': join(self._alignDir, 'stkaligned')
}
def __init__(self, **kwargs):
ProtFilterParticles.__init__(self, **kwargs)
SpiderProtocol.__init__(self, **kwargs)
# To avoid showing MPI box due to duplicated init
self.allowMpi = False
self._op = "FQ"
self._params = {
'ext': 'stk',
'particles': 'particles_filtered',
'particlesSel': 'particles_filtered_sel'
}
def __init__(self, script, classDir, **kwargs):
ProtClassify2D.__init__(self, **kwargs)
SpiderProtocol.__init__(self, **kwargs)
self._script = script
self._classDir = classDir
self._params = {'ext': 'stk',
'[class_dir]': self._classDir,
'particles': 'input_particles',
'particlesSel': 'input_particles_sel',
'dendroPs': 'dendrogram',
'dendroDoc': '%s/docdendro' % self._classDir,
'averages': 'averages',
}
def __init__(self, script, classDir, **kwargs):
ProtClassify2D.__init__(self, **kwargs)
SpiderProtocol.__init__(self, **kwargs)
self._script = script
self._classDir = classDir
self._params = {'ext': 'stk',
'[class_dir]': self._classDir,
'particles': 'input_particles',
'particlesSel': 'input_particles_sel',
'dendroPs': 'dendrogram',
'dendroDoc': '%s/docdendro' % self._classDir,
'averages': 'averages'
}
def __init__(self, script, alignDir, **args):
ProtAlign2D.__init__(self, **args)
SpiderProtocol.__init__(self, **args)
# To avoid showing MPI box due to duplicated init
self.allowMpi = False
self._script = script
self._alignDir = alignDir
self._params = {'ext': 'stk',
'particles': 'input_particles',
'particlesSel': 'input_particles_sel',
'average': join(self._alignDir, 'rfreeavg001'), # If change the name, change it in template batch
'particlesAligned': join(self._alignDir, 'stkaligned')
}
def __init__(self, script, alignDir, **args):
ProtAlign2D.__init__(self, **args)
SpiderProtocol.__init__(self, **args)
self._script = script
self._alignDir = alignDir
self._params = {
'ext': 'stk',
'particles': 'input_particles',
'particlesSel': 'input_particles_sel',
'average':
join(self._alignDir, 'rfreeavg001'
), # If change the name, change it in template batch
'particlesAligned': join(self._alignDir, 'stkaligned')
}
def __init__(self, script, classDir, **kwargs):
ProtClassify2D.__init__(self, **kwargs)
SpiderProtocol.__init__(self, **kwargs)
# To avoid showing MPI box due to duplicated init
self.allowMpi = False
self._script = script
self._classDir = classDir
self._params = {'ext': 'stk',
'[class_dir]': self._classDir,
'particles': 'input_particles',
'particlesSel': 'input_particles_sel',
'dendroPs': 'dendrogram',
'dendroDoc': '%s/docdendro' % self._classDir,
'averages': 'averages'
}
def __init__(self, script, alignDir, **args):
ProtAlign2D.__init__(self, **args)
SpiderProtocol.__init__(self, **args)
# To avoid showing MPI box due to duplicated init
self.allowMpi = False
self._script = script
self._alignDir = alignDir
self._params = {
'ext': 'stk',
'particles': 'input_particles',
'particlesSel': 'input_particles_sel',
'average':
join(self._alignDir, 'rfreeavg001'
), # If change the name, change it in template batch
'particlesAligned': join(self._alignDir, 'stkaligned')
}
def __init__(self, **kwargs):
SpiderProtocol.__init__(self, **kwargs)
self._caDir = 'CA'
self._caPrefix = 'cas'
caFilePrefix = join(self._caDir, self._caPrefix + '_')
self._params = {'ext': 'stk',
'particles': 'input_particles',
'particlesSel': 'input_particles_sel',
'outputParticles': 'output_particles',
'mask': 'mask',
# TO DO: read tags in case filenames change in SPIDER procedure
'imcFile': caFilePrefix + 'IMC',
'seqFile': caFilePrefix + 'SEQ',
'eigFile': caFilePrefix + 'EIG',
'eigenimages': join(self._caDir, 'stkeigenimg'),
'reconstituted': join(self._caDir, 'stkreconstituted')
}
def __init__(self, **kwargs):
ProtCreateMask2D.__init__(self, **kwargs)
SpiderProtocol.__init__(self, **kwargs)
self._params = {"ext": "stk", "inputImage": "input_image", "outputMask": "output_mask"}