def __init__(self, initializer={}):
self.__types = OrderedDict(self.typemap())
for t in self.__types.values():
if t not in validators and not hasattr(t, 'validator'):
raise RuntimeError('no validator for type %s' % (t, ))
## initialize all items defined by typemap
complete_init = OrderedDict(initializer)
for key, value in self.__types.items():
if key not in initializer:
complete_init[key] = None
super(TypedDict, self).__init__(complete_init)
blobsm = commonsteps.ImageMarker('blobsm')
blobsm.setDependency('image', input)
blobsm.setDependency('points', blobs)
latfilt = commonsteps.LatticeFilter('lattice')
latfilt.setDependency('input', blobs)
latm = commonsteps.ImageMarker('latm')
latm.setDependency('image', input)
latm.setDependency('points', latfilt)
# first a list of steps
templatefinder = [
input,
template,
tempcor,
threshold,
blobs,
blobsm,
latfilt,
latm,
]
# then an ordered dict
templatefinder = OrderedDict([(step.name, step) for step in templatefinder])
if __name__ == '__main__':
test = workflow.WorkflowCLI(templatefinder)
test.loop()
return results
##############################################################
### Create instances of those classes and build my workflow.
### Also using the class InputImage from commonsteps.py
##############################################################
## The complete workflow will contain 4 steps. I create the instances and
## give them each a unique name.
input = commonsteps.ImageInput('input')
rotate = RotN90('rotate')
maximum = MaximumPixel('maximum')
shift = Shifter('shift')
## connect them together properly:
rotate.setDependency('image', input)
maximum.setDependency('image', rotate)
shift.setDependency('points', maximum)
## Group them together into a container. Use our OrderedDict class:
myworkflow = OrderedDict()
myworkflow['input'] = input
myworkflow['rotate'] = rotate
myworkflow['maximum'] = maximum
myworkflow['shift'] = shift
## Now we have a complete workflow. We can plug it into Leginon (not yet)
## Or we can test it using our command line interface...
test = workflow.WorkflowCLI(myworkflow)
test.loop()
def types(self):
return OrderedDict(self.__types)
