def transformTargets(self,im1,im2,targets):
newtargets = []
shape = {}
shape['im1'] = im1['image'].shape
shape['im2'] = im2['image'].shape
im1scope = im1['scope']
im1camera = im1['camera']
im1trans = caltransformer.getTransformer(im1scope['tem'], im1camera['ccdcamera'], im1scope['high tension'], im1scope['magnification'], im1.timestamp)
im2scope = im2['scope']
im2camera = im2['camera']
im2trans = caltransformer.getTransformer(im2scope['tem'], im2camera['ccdcamera'], im2scope['high tension'], im2scope['magnification'], im2.timestamp)
c_lastnumber = self.lastTargetNumber(image=im1,
session=self.session)
c_number = c_lastnumber + 1
a_lastnumber = self.lastTargetNumber(image=im2,
session=self.session)
a_number = a_lastnumber + 1
for type in self.childtargetnames:
for targetdata in targets:
if targetdata['type'] == type:
drow = targetdata['delta row']
dcol = targetdata['delta column']
transformed_targetdata = self.newTargetForImage(im1, drow, dcol, type='transformed', list=self.childtargetlist, number=c_number)
self.publish(transformed_targetdata, database=True)
pixvect = {'row':drow,'col':dcol}
## get stage position of target on first image
bin = im1camera['binning']
stage0 = im1scope['stage position']
stage = im1trans.transform(pixvect, stage0, bin)
## get pixel position of stage position on second image
bin = im2camera['binning']
stage0 = im2scope['stage position']
pix = im2trans.itransform(stage, stage0, bin)
drow = pix['row']
dcol = pix['col']
if type == 'c_focus':
a_type = 'focus'
if type == 'c_acquisition':
a_type = 'acquisition'
a_targetdata = self.newTargetForImage(im2, drow, dcol, type=a_type, list=self.targetlist, number=a_number, fromtarget=transformed_targetdata)
self.publish(a_targetdata, database=True)
newtargets.append(a_targetdata)
c_number += 1
a_number += 1
return newtargets
def __init__(self, scope, camera, timestamp, fileref=None, rotation=0.0): self.scope = leginondata.ScopeEMData(initializer=scope) self.camera = leginondata.CameraEMData(initializer=camera) self.shape = self.camera['dimension']['y'], self.camera['dimension']['x'] self.fileref = fileref self.timestamp = timestamp self.trans = caltransformer.getTransformer(scope['tem'], camera['ccdcamera'], scope['high tension'], scope['magnification'], timestamp, rotation) self.newStage(scope['stage position'])
def __init__(self, scope, camera, timestamp, fileref=None, rotation=0.0):
self.scope = leginondata.ScopeEMData(initializer=scope)
self.camera = leginondata.CameraEMData(initializer=camera)
self.shape = self.camera['dimension']['y'], self.camera['dimension'][
'x']
self.fileref = fileref
self.timestamp = timestamp
self.trans = caltransformer.getTransformer(scope['tem'],
camera['ccdcamera'],
scope['high tension'],
scope['magnification'],
timestamp, rotation)
self.newStage(scope['stage position'])
def transformTargets(self, im1, im2, targets):
newtargets = []
shape = {}
shape['im1'] = im1['image'].shape
shape['im2'] = im2['image'].shape
im1scope = im1['scope']
im1camera = im1['camera']
im1trans = caltransformer.getTransformer(im1scope['tem'],
im1camera['ccdcamera'],
im1scope['high tension'],
im1scope['magnification'],
im1.timestamp)
im2scope = im2['scope']
im2camera = im2['camera']
im2trans = caltransformer.getTransformer(im2scope['tem'],
im2camera['ccdcamera'],
im2scope['high tension'],
im2scope['magnification'],
im2.timestamp)
c_lastnumber = self.lastTargetNumber(image=im1, session=self.session)
c_number = c_lastnumber + 1
a_lastnumber = self.lastTargetNumber(image=im2, session=self.session)
a_number = a_lastnumber + 1
for type in self.childtargetnames:
for targetdata in targets:
if targetdata['type'] == type:
drow = targetdata['delta row']
dcol = targetdata['delta column']
transformed_targetdata = self.newTargetForImage(
im1,
drow,
dcol,
type='transformed',
list=self.childtargetlist,
number=c_number)
self.publish(transformed_targetdata, database=True)
pixvect = {'row': drow, 'col': dcol}
## get stage position of target on first image
bin = im1camera['binning']
stage0 = im1scope['stage position']
stage = im1trans.transform(pixvect, stage0, bin)
## get pixel position of stage position on second image
bin = im2camera['binning']
stage0 = im2scope['stage position']
pix = im2trans.itransform(stage, stage0, bin)
drow = pix['row']
dcol = pix['col']
if type == 'c_focus':
a_type = 'focus'
if type == 'c_acquisition':
a_type = 'acquisition'
a_targetdata = self.newTargetForImage(
im2,
drow,
dcol,
type=a_type,
list=self.targetlist,
number=a_number,
fromtarget=transformed_targetdata)
self.publish(a_targetdata, database=True)
newtargets.append(a_targetdata)
c_number += 1
a_number += 1
return newtargets
def transformTargets(self, im1, im2, targets):
newtargets = []
shape = {}
shape["im1"] = im1["image"].shape
shape["im2"] = im2["image"].shape
im1scope = im1["scope"]
im1camera = im1["camera"]
im1trans = caltransformer.getTransformer(
im1scope["tem"], im1camera["ccdcamera"], im1scope["high tension"], im1scope["magnification"], im1.timestamp
)
im2scope = im2["scope"]
im2camera = im2["camera"]
im2trans = caltransformer.getTransformer(
im2scope["tem"], im2camera["ccdcamera"], im2scope["high tension"], im2scope["magnification"], im2.timestamp
)
c_lastnumber = self.lastTargetNumber(image=im1, session=self.session)
c_number = c_lastnumber + 1
a_lastnumber = self.lastTargetNumber(image=im2, session=self.session)
a_number = a_lastnumber + 1
for type in self.childtargetnames:
for targetdata in targets:
if targetdata["type"] == type:
drow = targetdata["delta row"]
dcol = targetdata["delta column"]
transformed_targetdata = self.newTargetForImage(
im1, drow, dcol, type="transformed", list=self.childtargetlist, number=c_number
)
self.publish(transformed_targetdata, database=True)
pixvect = {"row": drow, "col": dcol}
## get stage position of target on first image
bin = im1camera["binning"]
stage0 = im1scope["stage position"]
stage = im1trans.transform(pixvect, stage0, bin)
## get pixel position of stage position on second image
bin = im2camera["binning"]
stage0 = im2scope["stage position"]
pix = im2trans.itransform(stage, stage0, bin)
drow = pix["row"]
dcol = pix["col"]
if type == "c_focus":
a_type = "focus"
if type == "c_acquisition":
a_type = "acquisition"
a_targetdata = self.newTargetForImage(
im2,
drow,
dcol,
type=a_type,
list=self.targetlist,
number=a_number,
fromtarget=transformed_targetdata,
)
self.publish(a_targetdata, database=True)
newtargets.append(a_targetdata)
c_number += 1
a_number += 1
return newtargets