def initModules(self):
self.module = PropertyMgr(self)
oldModuleName = self._currentModuleName
for m in BaseModuleMgr.__subclasses__():
print "DataMgr initializing module:", m.name
self._currentModuleName = m.name
self.module[m.name] = m(self)
self._currentModuleName = oldModuleName
def initModules(self):
self.module = PropertyMgr(self)
mods = BaseModuleDataItemMgr.__subclasses__()
for m in mods:
self.module[m.name] = m(self)
self.module[m.name].overlayMgr = self.overlayMgr
def initModules(self):
self.module = PropertyMgr(self)
oldModuleName = self._currentModuleName
for m in BaseModuleMgr.__subclasses__():
print "DataMgr initializing module:", m.name
self._currentModuleName = m.name
self.module[m.name] = m(self)
self._currentModuleName = oldModuleName
def initModules(self):
self.module = PropertyMgr(self)
mods = BaseModuleDataItemMgr.__subclasses__()
for m in mods:
self.module[m.name] = m(self)
self.module[m.name].overlayMgr = self.overlayMgr
class DataMgr():
"""
Manages Project structure and associated files, e.g. images volumedata
"""
# does not unload _data, maybe implement some sort of reference
# counting if memory scarceness manifests itself
def __init__(self, featureCacheFile=None):
self._dataItems = []
self.featureLock = threading.Semaphore(1) #prevent chaining of _activeImageNumber during thread stuff
self._dataItemsLoaded = []
self.channels = -1
self._activeImage = None
self._activeImageNumber = 0
self._currentModuleName = None
self.initModules()
def initModules(self):
self.module = PropertyMgr(self)
oldModuleName = self._currentModuleName
for m in BaseModuleMgr.__subclasses__():
print "DataMgr initializing module:", m.name
self._currentModuleName = m.name
self.module[m.name] = m(self)
self._currentModuleName = oldModuleName
def onNewImage(self, dataItemImage):
if len(self._dataItems) == 1:
self._activeImage = self._dataItems[0]
dataItemImage.overlayMgr.dataMgr = self
oldModuleName = self._currentModuleName
for v in dataItemImage.module.values():
v.globalMgr = self.module[v.name]
for v in self.module.values():
self._currentModuleName = v.__class__.name
v.onNewImage(dataItemImage)
self._currentModuleName = oldModuleName
def onRemoveImage(self, dataItemIndex):
self._dataItems[dataItemIndex].overlayMgr.dataMgr = self
oldModuleName = self._currentModuleName
for v in self.module.values():
self._currentModuleName = v.__class__.name
v.onDeleteImage(self._dataItems[dataItemIndex])
self._currentModuleName = oldModuleName
def append(self, dataItem, alreadyLoaded=False):
dataItem.dataMgr = self
if alreadyLoaded == False:
try:
dataItem.loadFromFile()
except Exception, e:
print e
traceback.print_exc(file=sys.stdout)
QtGui.QErrorMessage.qtHandler().showMessage("Not enough Memory to load this file !")
raise e
alreadyLoaded = True
if self.channels == -1 or dataItem.shape[-1] == self.channels:
self.channels = dataItem.shape[-1]
self.selectedChannels = range(self.channels)
self._dataItems.append(dataItem)
self._dataItemsLoaded.append(alreadyLoaded)
self.onNewImage(dataItem)
else:
raise TypeError('DataMgr.append: DataItem has wrong number of channels, a project can contain only images that have the same number of channels !')
class DataItemImage(DataItemBase):
def __init__(self, fileName):
DataItemBase.__init__(self, fileName)
self._dataVol = None
self._featureM = None
self._readBegin = (0,0,0)
self._readEnd = (0,0,0)
self._writeBegin = (0,0,0)
self._writeEnd = (0,0,0)
self.overlayMgr = overlayMgr.OverlayMgr(self)
self.dataMgr = None
self.initModules()
def initModules(self):
self.module = PropertyMgr(self)
mods = BaseModuleDataItemMgr.__subclasses__()
for m in mods:
self.module[m.name] = m(self)
self.module[m.name].overlayMgr = self.overlayMgr
def setDataVol(self, dataVol):
self._dataVol = dataVol
self._writeBegin = (0,0,0)
self._writeEnd = (dataVol.shape[1], dataVol.shape[2], dataVol.shape[3])
def setReadBounds(self, begin, end):
self._readBegin = begin
self._readEnd = end
def setWriteBounds(self, begin, end, shape):
self._writeBegin = begin
self._writeEnd = end
self._writeShape = shape
def __getitem__(self, args):
return self._dataVol._data[args]
def __setitem__(self, args, data):
self._dataVol._data[args] = data
def __getattr__(self, name):
if name == "dtype":
return self._dataVol._data.dtype
elif name == "shape":
return self._dataVol._data.shape
else:
raise AttributeError, name
def unLoadData(self):
# TODO: delete permanently here for better garbage collection
self._dataVol = None
self._data = None
def loadFromFile(self):
f = h5py.File(self.fileName, 'r')
g = f["volume"]
self.deserialize(g)
def serialize(self, h5G, destbegin = (0,0,0), destend = (0,0,0), srcbegin = (0,0,0), srcend = (0,0,0), destshape = (0,0,0) ):
if destend != (0,0,0):
self._dataVol.serialize(h5G, destbegin, destend, srcbegin, srcend, destshape)
elif self._writeEnd != (0,0,0):
destbegin = self._writeBegin
destend = self._writeEnd
srcbegin = self._readBegin
srcend = self._readEnd
destshape = self._writeShape
self._dataVol.serialize(h5G, "data", destbegin, destend, srcbegin, srcend, destshape)
else:
self._dataVol.serialize(h5G)
for k in self.module.keys():
if hasattr(self.module[k], "serialize"):
print "serializing ", k
try:
self.module[k].serialize(h5G, destbegin, destend, srcbegin, srcend, destshape)
except Exception as e:
print e
print traceback.print_exc()
print "couldn't serialize something"
def updateOverlays(self):
ov = overlayMgr.OverlayItem(self._dataVol._data, color = QtGui.QColor(255, 255, 255), alpha = 1.0, colorTable = None, autoAdd = True, autoVisible = True, autoAlphaChannel = False, min = 0, max = 255)
self.overlayMgr["Raw Data"] = ov
def deserialize(self, h5G, offsets = (0,0,0), shape = (0,0,0)):
self._dataVol = DataAccessor.deserialize(h5G, "data", offsets, shape)
#load obsolete file format parts (pre version 0.5)
#and store them in the properties
#the responsible modules will take care of them
for k in self.module.keys():
if hasattr(self.module[k], "deserialize"):
print "Deserializing", k
self.module[k].deserialize(h5G, offsets, shape)
self.updateOverlays()
class DataMgr():
"""
Manages Project structure and associated files, e.g. images volumedata
"""
# does not unload _data, maybe implement some sort of reference
# counting if memory scarceness manifests itself
def __init__(self, featureCacheFile=None):
self._dataItems = []
self.featureLock = threading.Semaphore(
1) #prevent chaining of _activeImageNumber during thread stuff
self._dataItemsLoaded = []
self.channels = -1
self._activeImage = None
self._activeImageNumber = 0
self._currentModuleName = None
self.initModules()
def initModules(self):
self.module = PropertyMgr(self)
oldModuleName = self._currentModuleName
for m in BaseModuleMgr.__subclasses__():
print "DataMgr initializing module:", m.name
self._currentModuleName = m.name
self.module[m.name] = m(self)
self._currentModuleName = oldModuleName
def onNewImage(self, dataItemImage):
if len(self._dataItems) == 1:
self._activeImage = self._dataItems[0]
dataItemImage.overlayMgr.dataMgr = self
oldModuleName = self._currentModuleName
for v in dataItemImage.module.values():
v.globalMgr = self.module[v.name]
for v in self.module.values():
self._currentModuleName = v.__class__.name
v.onNewImage(dataItemImage)
self._currentModuleName = oldModuleName
def onRemoveImage(self, dataItemIndex):
self._dataItems[dataItemIndex].overlayMgr.dataMgr = self
oldModuleName = self._currentModuleName
for v in self.module.values():
self._currentModuleName = v.__class__.name
v.onDeleteImage(self._dataItems[dataItemIndex])
self._currentModuleName = oldModuleName
def append(self, dataItem, alreadyLoaded=False):
dataItem.dataMgr = self
if alreadyLoaded == False:
try:
dataItem.loadFromFile()
except Exception, e:
print e
traceback.print_exc(file=sys.stdout)
QtGui.QErrorMessage.qtHandler().showMessage(
"Not enough Memory to load this file !")
raise e
alreadyLoaded = True
if self.channels == -1 or dataItem.shape[-1] == self.channels:
self.channels = dataItem.shape[-1]
self.selectedChannels = range(self.channels)
self._dataItems.append(dataItem)
self._dataItemsLoaded.append(alreadyLoaded)
self.onNewImage(dataItem)
else:
raise TypeError(
'DataMgr.append: DataItem has wrong number of channels, a project can contain only images that have the same number of channels !'
)
class DataItemImage(DataItemBase):
def __init__(self, fileName):
DataItemBase.__init__(self, fileName)
self._dataVol = None
self._featureM = None
self._readBegin = (0, 0, 0)
self._readEnd = (0, 0, 0)
self._writeBegin = (0, 0, 0)
self._writeEnd = (0, 0, 0)
self.overlayMgr = overlayMgr.OverlayMgr(self)
self.dataMgr = None
self.initModules()
def initModules(self):
self.module = PropertyMgr(self)
mods = BaseModuleDataItemMgr.__subclasses__()
for m in mods:
self.module[m.name] = m(self)
self.module[m.name].overlayMgr = self.overlayMgr
def setDataVol(self, dataVol):
self._dataVol = dataVol
self._writeBegin = (0, 0, 0)
self._writeEnd = (dataVol.shape[1], dataVol.shape[2], dataVol.shape[3])
def setReadBounds(self, begin, end):
self._readBegin = begin
self._readEnd = end
def setWriteBounds(self, begin, end, shape):
self._writeBegin = begin
self._writeEnd = end
self._writeShape = shape
def __getitem__(self, args):
return self._dataVol._data[args]
def __setitem__(self, args, data):
self._dataVol._data[args] = data
def __getattr__(self, name):
if name == "dtype":
return self._dataVol._data.dtype
elif name == "shape":
return self._dataVol._data.shape
else:
raise AttributeError, name
def unLoadData(self):
# TODO: delete permanently here for better garbage collection
self._dataVol = None
self._data = None
def loadFromFile(self):
f = h5py.File(self.fileName, 'r')
g = f["volume"]
self.deserialize(g)
def serialize(self,
h5G,
destbegin=(0, 0, 0),
destend=(0, 0, 0),
srcbegin=(0, 0, 0),
srcend=(0, 0, 0),
destshape=(0, 0, 0)):
if destend != (0, 0, 0):
self._dataVol.serialize(h5G, destbegin, destend, srcbegin, srcend,
destshape)
elif self._writeEnd != (0, 0, 0):
destbegin = self._writeBegin
destend = self._writeEnd
srcbegin = self._readBegin
srcend = self._readEnd
destshape = self._writeShape
self._dataVol.serialize(h5G, "data", destbegin, destend, srcbegin,
srcend, destshape)
else:
self._dataVol.serialize(h5G)
for k in self.module.keys():
if hasattr(self.module[k], "serialize"):
print "serializing ", k
try:
self.module[k].serialize(h5G, destbegin, destend, srcbegin,
srcend, destshape)
except Exception as e:
print e
print traceback.print_exc()
print "couldn't serialize something"
def updateOverlays(self):
ov = overlayMgr.OverlayItem(self._dataVol._data,
color=QtGui.QColor(255, 255, 255),
alpha=1.0,
colorTable=None,
autoAdd=True,
autoVisible=True,
autoAlphaChannel=False,
min=0,
max=255)
self.overlayMgr["Raw Data"] = ov
def deserialize(self, h5G, offsets=(0, 0, 0), shape=(0, 0, 0)):
self._dataVol = DataAccessor.deserialize(h5G, "data", offsets, shape)
#load obsolete file format parts (pre version 0.5)
#and store them in the properties
#the responsible modules will take care of them
for k in self.module.keys():
if hasattr(self.module[k], "deserialize"):
print "Deserializing", k
self.module[k].deserialize(h5G, offsets, shape)
self.updateOverlays()
