def newImageVersion(self, oldimagedata, newimagedata, correct):
## store EMData to DB to prevent referencing errors
self.publish(newimagedata["scope"], database=True)
self.publish(newimagedata["camera"], database=True)
## convert CameraImageData to AcquisitionImageData
newimagedata = leginondata.AcquisitionImageData(initializer=newimagedata)
## then add stuff from old imagedata
newimagedata["preset"] = oldimagedata["preset"]
newimagedata["label"] = oldimagedata["label"]
newimagedata["target"] = oldimagedata["target"]
newimagedata["list"] = oldimagedata["list"]
newimagedata["emtarget"] = oldimagedata["emtarget"]
newimagedata["version"] = oldimagedata["version"] + 1
dim = newimagedata["camera"]["dimension"]
newimagedata["pixels"] = dim["x"] * dim["y"]
newimagedata["pixeltype"] = str(newimagedata["image"].dtype)
target = newimagedata["target"]
if target is not None and "grid" in target and target["grid"] is not None:
newimagedata["grid"] = target["grid"]
## set the 'filename' value
if newimagedata["label"] == "RCT":
rctacquisition.setImageFilename(newimagedata)
else:
acquisition.setImageFilename(newimagedata)
newimagedata.attachPixelSize()
self.logger.info("Publishing new version of image...")
self.publish(newimagedata, database=True, dbforce=True)
return newimagedata
def newImageVersion(self, oldimagedata, newimagedata, correct):
## store EMData to DB to prevent referencing errors
self.publish(newimagedata['scope'], database=True)
self.publish(newimagedata['camera'], database=True)
## convert CameraImageData to AcquisitionImageData
newimagedata = leginondata.AcquisitionImageData(initializer=newimagedata)
## then add stuff from old imagedata
newimagedata['preset'] = oldimagedata['preset']
newimagedata['label'] = oldimagedata['label']
newimagedata['target'] = oldimagedata['target']
newimagedata['list'] = oldimagedata['list']
newimagedata['emtarget'] = oldimagedata['emtarget']
newimagedata['version'] = oldimagedata['version'] + 1
dim = newimagedata['camera']['dimension']
newimagedata['pixels'] = dim['x'] * dim['y']
newimagedata['pixeltype'] = str(newimagedata['image'].dtype)
target = newimagedata['target']
if target is not None and 'grid' in target and target['grid'] is not None:
newimagedata['grid'] = target['grid']
## set the 'filename' value
if newimagedata['label'] == 'RCT':
rctacquisition.setImageFilename(newimagedata)
else:
acquisition.setImageFilename(newimagedata)
newimagedata.attachPixelSize()
self.logger.info('Publishing new version of image...')
self.publish(newimagedata, database=True, dbforce=True)
return newimagedata
def setImageFilename(imagedata, tiltnumber=None):
acquisition.setImageFilename(imagedata)
if tiltnumber is None:
tiltnumber = imagedata['tiltnumber']
if tiltnumber is not None:
imagedata['filename'] = imagedata['filename'] + '_%02d' % (
tiltnumber, )
def newImageVersion(self, oldimagedata, newimagedata, correct):
## store EMData to DB to prevent referencing errors
self.publish(newimagedata['scope'], database=True)
self.publish(newimagedata['camera'], database=True)
## convert CameraImageData to AcquisitionImageData
newimagedata = leginondata.AcquisitionImageData(initializer=newimagedata)
## then add stuff from old imagedata
newimagedata['preset'] = oldimagedata['preset']
newimagedata['label'] = oldimagedata['label']
newimagedata['target'] = oldimagedata['target']
newimagedata['list'] = oldimagedata['list']
newimagedata['emtarget'] = oldimagedata['emtarget']
newimagedata['version'] = oldimagedata['version'] + 1
dim = newimagedata['camera']['dimension']
newimagedata['pixels'] = dim['x'] * dim['y']
newimagedata['pixeltype'] = str(newimagedata['image'].dtype)
target = newimagedata['target']
if target is not None and 'grid' in target and target['grid'] is not None:
newimagedata['grid'] = target['grid']
## set the 'filename' value
if newimagedata['label'] == 'RCT':
rctacquisition.setImageFilename(newimagedata)
else:
acquisition.setImageFilename(newimagedata)
newimagedata.attachPixelSize()
self.logger.info('Publishing new version of image...')
self.publish(newimagedata, database=True, dbforce=True)
return newimagedata
def setImageFilename(self, imagedata, spot_x=None, spot_y=None):
acquisition.setImageFilename(imagedata)
if spot_x is None or spot_y is None:
spot_x = imagedata['spot_x']
spot_y = imagedata['spot_y']
if spot_x is not None and spot_y is not None:
imagedata['filename'] = imagedata['filename'] + '_%02d_%02d' % (spot_x, spot_y, )
else:
imagedata['filename'] = imagedata['filename'] + '_%02d_%02d' % (self.spotX, self.spotY, )
self.logger.info('Filename -> %s' % imagedata['filename'])
def setImageFilename(imagedata, tiltnumber=None, spot_x=None, spot_y=None):
acquisition.setImageFilename(imagedata)
if tiltnumber is None:
tiltnumber = imagedata['tiltnumber']
if tiltnumber is not None:
imagedata['filename'] = imagedata['filename'] + '_%02d' % (tiltnumber,)
if spot_x is None or spot_y is None:
spot_x = imagedata['spot_x']
spot_y = imagedata['spot_y']
if spot_x is not None and spot_y is not None:
imagedata['filename'] = imagedata['filename'] + '_%02d_%02d' % (spot_x, spot_y, )
def copyImage(self, oldimage):
imagedata = leginondata.AcquisitionImageData()
imagedata.update(oldimage)
version = self.recentImageVersion(oldimage)
imagedata['version'] = version + 1
imagedata['filename'] = None
imagedata['image'] = oldimage['image']
## set the 'filename' value
if imagedata['label'] == 'RCT':
rctacquisition.setImageFilename(imagedata)
else:
acquisition.setImageFilename(imagedata)
self.logger.info('Publishing new copied image...')
self.publish(imagedata, database=True)
return imagedata
def copyImage(self, oldimage):
imagedata = leginondata.AcquisitionImageData()
imagedata.update(oldimage)
version = self.recentImageVersion(oldimage)
imagedata['version'] = version + 1
imagedata['filename'] = None
imagedata['image'] = oldimage['image']
## set the 'filename' value
if imagedata['label'] == 'RCT':
rctacquisition.setImageFilename(imagedata)
else:
acquisition.setImageFilename(imagedata)
self.logger.info('Publishing new copied image...')
self.publish(imagedata, database=True)
return imagedata
def reacquire(self, targetdata):
oldimage = None
targetlist = targetdata['list']
tquery = leginondata.AcquisitionImageTargetData(session=self.session, list=targetlist, number=targetdata['number'], type=targetdata['type'])
aquery = leginondata.AcquisitionImageData(target=tquery)
results = aquery.query(readimages=False, results=1)
if len(results) > 0:
oldimage = results[0]
if oldimage is None:
print "can not find an image that is acquired with this target"
print targetdata.dbid
return None
oldemtarget = oldimage['emtarget']
movetype = oldemtarget['movetype']
try:
emtarget = self.targetToEMTargetData(targetdata,movetype)
except InvalidStagePosition:
self.logger.error('Invalid new emtarget')
return None
oldpresetdata = oldimage['preset']
presetname = oldpresetdata['name']
channel = int(oldimage['correction channel']==0)
self.presetsclient.toScope(presetname, emtarget, keep_shift=False)
targetdata = emtarget['target']
imagedata = self.acquireCorrectedCameraImageData(channel)
currentpresetdata = self.presetsclient.getCurrentPreset()
## convert CameraImageData to AcquisitionImageData
dim = imagedata['camera']['dimension']
pixels = dim['x'] * dim['y']
pixeltype = str(imagedata['image'].dtype)
## Fix me: Not sure what image list should go in here nor naming of the file
imagedata = leginondata.AcquisitionImageData(initializer=imagedata, preset=currentpresetdata, label=self.name, target=targetdata, list=oldimage['list'], emtarget=emtarget, pixels=pixels, pixeltype=pixeltype,grid=oldimage['grid'])
version = self.recentImageVersion(oldimage)
imagedata['version'] = version + 1
## set the 'filename' value
if imagedata['label'] == 'RCT':
rctacquisition.setImageFilename(imagedata)
else:
acquisition.setImageFilename(imagedata)
## store EMData to DB to prevent referencing errors
self.publish(imagedata['scope'], database=True)
self.publish(imagedata['camera'], database=True)
self.logger.info('Publishing new transformed image...')
self.publish(imagedata, database=True)
self.setImage(imagedata['image'], 'Image')
return imagedata
def setImageFilename(imagedata, tiltnumber=None): acquisition.setImageFilename(imagedata) if tiltnumber is None: tiltnumber = imagedata['tiltnumber'] if tiltnumber is not None: imagedata['filename'] = imagedata['filename'] + '_%02d' % (tiltnumber,)
currentpresetdata = self.presetsclient.getCurrentPreset()
## convert CameraImageData to AcquisitionImageData
dim = imagedata['camera']['dimension']
pixels = dim['x'] * dim['y']
pixeltype = str(imagedata['image'].dtype)
## Fix me: Not sure what image list should go in here nor naming of the file
# This does not include tilt series nor tilt number. If included,
# rct filenaming becomes corrupted
imagedata = leginondata.AcquisitionImageData(initializer=imagedata, preset=currentpresetdata, label=self.name, target=targetdata, list=oldimage['list'], emtarget=emtarget, pixels=pixels, pixeltype=pixeltype,grid=oldimage['grid'],mover=oldimage['mover'])
version = self.recentImageVersion(oldimage)
imagedata['version'] = version + 1
## set the 'filename' value
if imagedata['label'] == 'RCT':
rctacquisition.setImageFilename(imagedata)
else:
acquisition.setImageFilename(imagedata)
## store EMData to DB to prevent referencing errors
self.publish(imagedata['scope'], database=True)
self.publish(imagedata['camera'], database=True)
self.logger.info('Publishing new transformed image...')
self.publish(imagedata, database=True)
self.setImage(imagedata['image'], 'Image')
return imagedata
def _moveToLastFocusedStageZ(self):
'''
Set stage z to the height of an image acquired by the last focusing.
This should only be called from inside TrasnformManage
'''
self.moveToLastFocusedStageZ(self.target_to_transform)