def visualize(self, obj, **args):
"""Open the Protocol GUI Form given a Protocol instance"""
from gui.form import FormWindow
self.setProtocol(obj)
self.windows = args.get('windows', None)
self.formWindow = FormWindow("Protocol Viewer: " + self.getClassName(),
self, self._viewAll, self.windows,
visualizeDict=self.__getVisualizeWrapperDict(),
visualizeMode=True)
self.formWindow.visualizeMode = True
self.showInfo = self.formWindow.showInfo
self.showError = self.formWindow.showError
self._tkRoot = self.formWindow.root
self.formWindow.show(center=True)
def visualize(self, obj, **args):
"""Open the Protocol GUI Form given a Protocol instance"""
from gui.form import FormWindow
self.setProtocol(obj)
self.windows = args.get('windows', None)
self.formWindow = FormWindow("Protocol Viewer: " + self.getClassName(),
self, self._viewAll, self.windows,
visualizeDict=self.__getVisualizeWrapperDict(),
visualizeMode=True)
self.formWindow.visualizeMode = True
self.showInfo = self.formWindow.showInfo
self.showError = self.formWindow.showError
self._tkRoot = self.formWindow.root
self.formWindow.show(center=True)
class ProtocolViewer(Protocol, Viewer):
""" Special kind of viewer that have a Form to organize better
complex visualization associated with protocol results.
If should provide a mapping between form params and the corresponding
functions that will return the corresponding Views.
"""
def __init__(self, **kwargs):
# Here we are going to intercept the original _defineParams function
# and replace by an empty one, this is to postpone the definition of
# params until the protocol is set and then self.protocol can be used
# for a more dynamic definition
object.__setattr__(self, '_defineParamsBackup', self._defineParams)
object.__setattr__(self, '_defineParams', self._defineParamsEmpty)
Protocol.__init__(self, **kwargs)
Viewer.__init__(self, **kwargs)
self.allowHeader.set(False)
# This flag will be used to display a plot or return the plotter
self.showPlot = True
self._tkRoot = None
self.formWindow = None
self.setWorkingDir(self.getProject().getTmpPath())
def getWindow(self):
return self.formWindow
def getTkRoot(self):
return self._tkRoot
def _defineParamsEmpty(self, form):
""" Just do nothing and postpone the real definition. """
pass
def setProtocol(self, protocol):
""" Set the protocol instance to the viewer and
call the definition of the parameters.
"""
self.protocol = protocol
self._defineParamsBackup(self._definition)
self._createVarsFromDefinition()
def visualize(self, obj, **args):
"""Open the Protocol GUI Form given a Protocol instance"""
from gui.form import FormWindow
self.setProtocol(obj)
self.windows = args.get('windows', None)
self.formWindow = FormWindow(
"Protocol Viewer: " + self.getClassName(),
self,
self._viewAll,
self.windows,
visualizeDict=self.__getVisualizeWrapperDict(),
visualizeMode=True)
self.formWindow.visualizeMode = True
self.showInfo = self.formWindow.showInfo
self.showError = self.formWindow.showError
self._tkRoot = self.formWindow.root
self.formWindow.show(center=True)
def _visualizeParam(self, paramName=None):
""" Call handler to get viewers and visualize each one. """
errors = self.validate()
if errors:
errorMsg = '\n'.join(errors)
self.showError(errorMsg, "Validation errors")
else:
views = self._getVisualizeDict()[paramName](paramName)
if views:
for v in views:
v.show()
def __getVisualizeWrapperDict(self):
""" Replace the True attributes handler by the generic one. """
d = {}
for k in self._getVisualizeDict():
d[k] = self._visualizeParam
return d
def _getVisualizeDict(self):
""" Create the visualization dict for view individual params. """
return {}
def _viewAll(self, *args):
""" Visualize all data give the parameters. """
for k, v in self._getVisualizeDict().iteritems():
print "k: %s, v: %s" % (k, v)
if self.getAttributeValue(k, False):
print " calling v..."
v(k)
def _citations(self):
return self.protocol._citations()
#TODO: This method should not be necessary, instead NumericListParam should
# return a list and not a String
def _getListFromRangeString(self, rangeStr):
''' Create a list of integer from a string with range definitions
Examples:
"1,5-8,10" -> [1,5,6,7,8,10]
"2,6,9-11" -> [2,6,9,10,11]
"2 5, 6-8" -> [2,5,6,7,8]
'''
elements = rangeStr.split(',')
values = []
for e in elements:
if '-' in e:
limits = e.split('-')
values += range(int(limits[0]), int(limits[1]) + 1)
else:
# If values are separated by comma also splitted
values += map(int, e.split())
return values
def createVolumesSqlite(self,
files,
path,
samplingRate,
updateItemCallback=None):
from em import SetOfVolumes, Volume
cleanPath(path)
volSet = SetOfVolumes(filename=path)
volSet.setSamplingRate(samplingRate)
for volFn in files:
vol = Volume()
vol.setFileName(volFn)
if updateItemCallback:
updateItemCallback(vol)
volSet.append(vol)
volSet.write()
volSet.close()
return volSet
def createAngDistributionSqlite(self, sqliteFn, numberOfParticles,
itemDataIterator):
import pyworkflow.em.metadata as md
if not os.path.exists(sqliteFn):
# List of list of 3 elements containing angleTilt, anglePsi, weight
projectionList = []
def getCloseProjection(angleRot, angleTilt):
""" Get an existing projection close to angleRot, angleTilt.
Return None if not found close enough.
"""
for projection in projectionList:
if (abs(projection[0] - angleRot) <= 0.5
and abs(projection[1] - angleTilt) <= 0.5):
return projection
return None
weight = 1. / numberOfParticles
for angleRot, angleTilt in itemDataIterator:
projection = getCloseProjection(angleRot, angleTilt)
if projection is None:
projectionList.append([angleRot, angleTilt, weight])
else:
projection[2] = projection[2] + weight
mdProj = md.MetaData()
for projection in projectionList:
mdRow = md.Row()
mdRow.setValue(md.MDL_ANGLE_ROT, projection[0])
mdRow.setValue(md.MDL_ANGLE_TILT, projection[1])
mdRow.setValue(md.MDL_WEIGHT, projection[2])
mdRow.writeToMd(mdProj, mdProj.addObject())
mdProj.write(sqliteFn)
class ProtocolViewer(Protocol, Viewer):
""" Special kind of viewer that have a Form to organize better
complex visualization associated with protocol results.
If should provide a mapping between form params and the corresponding
functions that will return the corresponding Views.
"""
def __init__(self, **kwargs):
# Here we are going to intercept the original _defineParams function
# and replace by an empty one, this is to postpone the definition of
# params until the protocol is set and then self.protocol can be used
# for a more dynamic definition
object.__setattr__(self, '_defineParamsBackup', self._defineParams)
object.__setattr__(self, '_defineParams', self._defineParamsEmpty)
Protocol.__init__(self, **kwargs)
Viewer.__init__(self, **kwargs)
self.allowHeader.set(False)
# This flag will be used to display a plot or return the plotter
self.showPlot = True
self._tkRoot = None
self.formWindow = None
self.setWorkingDir(self.getProject().getTmpPath())
def getWindow(self):
return self.formWindow
def getTkRoot(self):
return self._tkRoot
def _defineParamsEmpty(self, form):
""" Just do nothing and postpone the real definition. """
pass
def setProtocol(self, protocol):
""" Set the protocol instance to the viewer and
call the definition of the parameters.
"""
self.protocol = protocol
self._defineParamsBackup(self._definition)
self._createVarsFromDefinition()
def visualize(self, obj, **args):
"""Open the Protocol GUI Form given a Protocol instance"""
from gui.form import FormWindow
self.setProtocol(obj)
self.windows = args.get('windows', None)
self.formWindow = FormWindow("Protocol Viewer: " + self.getClassName(),
self, self._viewAll, self.windows,
visualizeDict=self.__getVisualizeWrapperDict(),
visualizeMode=True)
self.formWindow.visualizeMode = True
self.showInfo = self.formWindow.showInfo
self.showError = self.formWindow.showError
self._tkRoot = self.formWindow.root
self.formWindow.show(center=True)
def _visualizeParam(self, paramName=None):
""" Call handler to get viewers and visualize each one. """
errors = self.validate()
if errors:
errorMsg = '\n'.join(errors)
self.showError(errorMsg, "Validation errors")
else:
views = self._getVisualizeDict()[paramName](paramName)
if views:
for v in views:
v.show()
def __getVisualizeWrapperDict(self):
""" Replace the True attributes handler by the generic one. """
d = {}
for k in self._getVisualizeDict():
d[k] = self._visualizeParam
return d
def _getVisualizeDict(self):
""" Create the visualization dict for view individual params. """
return {}
def _viewAll(self, *args):
""" Visualize all data give the parameters. """
for k, v in self._getVisualizeDict().iteritems():
print "k: %s, v: %s" % (k, v)
if self.getAttributeValue(k, False):
print " calling v..."
v(k)
def _citations(self):
return self.protocol._citations()
#TODO: This method should not be necessary, instead NumericListParam should
# return a list and not a String
def _getListFromRangeString(self, rangeStr):
''' Create a list of integer from a string with range definitions
Examples:
"1,5-8,10" -> [1,5,6,7,8,10]
"2,6,9-11" -> [2,6,9,10,11]
"2 5, 6-8" -> [2,5,6,7,8]
'''
elements = rangeStr.split(',')
values = []
for e in elements:
if '-' in e:
limits = e.split('-')
values += range(int(limits[0]), int(limits[1])+1)
else:
# If values are separated by comma also splitted
values += map(int, e.split())
return values
def createVolumesSqlite(self, files, path, samplingRate,
updateItemCallback=None):
from em import SetOfVolumes, Volume
cleanPath(path)
volSet = SetOfVolumes(filename=path)
volSet.setSamplingRate(samplingRate)
for volFn in files:
vol = Volume()
vol.setFileName(volFn)
if updateItemCallback:
updateItemCallback(vol)
volSet.append(vol)
volSet.write()
volSet.close()
return volSet
def createAngDistributionSqlite(self, sqliteFn, numberOfParticles,
itemDataIterator):
import pyworkflow.em.metadata as md
if not os.path.exists(sqliteFn):
# List of list of 3 elements containing angleTilt, anglePsi, weight
projectionList = []
def getCloseProjection(angleRot, angleTilt):
""" Get an existing projection close to angleRot, angleTilt.
Return None if not found close enough.
"""
for projection in projectionList:
if (abs(projection[0] - angleRot) <= 0.5 and
abs(projection[1] - angleTilt) <= 0.5):
return projection
return None
weight = 1./numberOfParticles
for angleRot, angleTilt in itemDataIterator:
projection = getCloseProjection(angleRot, angleTilt)
if projection is None:
projectionList.append([angleRot, angleTilt, weight])
else:
projection[2] = projection[2] + weight
mdProj = md.MetaData()
for projection in projectionList:
mdRow = md.Row()
mdRow.setValue(md.MDL_ANGLE_ROT, projection[0])
mdRow.setValue(md.MDL_ANGLE_TILT, projection[1])
mdRow.setValue(md.MDL_WEIGHT, projection[2])
mdRow.writeToMd(mdProj, mdProj.addObject())
mdProj.write(sqliteFn)
