def showAssessedMask(self,imgfile,imgdata): self.filename = imgfile image = pyami.mrc.read(imgfile) sessiondata = self.params['sessionname'] maskassessname = self.params['checkMask'] mask,maskbin = apMask.makeInspectedMask(sessiondata,maskassessname,imgdata) overlay = apMask.overlayMask(image,mask) self.app.panel.setImage(overlay.astype(numpy.float32))
def displayCurrent(self):
imarray = numpy.zeros((2, 2))
while imarray.max() == 0:
currentname = self.files[self.currentindex]
self.logger.info('Displaying %s' % (currentname))
dir = self.maskdir
fullname = os.path.join(dir, currentname)
imarray = self.readPNG(fullname)
if imarray.max() == 0:
if self.forward:
if self.currentindex == len(self.files) - 1:
self.logger.info('End reached.')
return
else:
self.currentindex += 1
else:
if self.currentindex == 0:
self.logger.info('Beginning reached.')
return
else:
self.currentindex -= 1
if currentname.find('_mask') > -1:
alpha = 0.5
imgdata = self.images[self.currentindex]
parentimg = imgdata['image']
maskshape = imarray.shape
targets = apMask.getRegionsAsTargets(self.maskrundata, maskshape,
imgdata)
if targets is None or len(targets) == 0:
self.logger.warning('No Mask Regions in this Image')
keep = apDatabase.getImgAssessmentStatus(imgdata)
if keep == False:
self.logger.warning('Rejected Image, Mask Irelavent')
self.alltargets = targets[:]
self.setTargets(targets, 'Regions')
binning = parentimg.shape[0] / imarray.shape[0]
parentimg = imagefun.bin(parentimg, binning)
overlay = apMask.overlayMask(parentimg, imarray)
self.setImage(overlay, 'Mask')
imarray = parentimg
self.setImage(imarray, 'Image')
def displayCurrent(self):
imarray = numpy.zeros((2,2))
while imarray.max() == 0:
currentname = self.files[self.currentindex]
self.logger.info('Displaying %s' % (currentname))
dir = self.maskdir
fullname = os.path.join(dir, currentname)
imarray = self.readPNG(fullname)
if imarray.max() ==0:
if self.forward:
if self.currentindex == len(self.files)-1:
self.logger.info('End reached.')
return
else:
self.currentindex += 1
else:
if self.currentindex == 0:
self.logger.info('Beginning reached.')
return
else:
self.currentindex -= 1
if currentname.find('_mask') > -1:
alpha = 0.5
imgdata = self.images[self.currentindex]
parentimg = imgdata['image']
maskshape = imarray.shape
targets = apMask.getRegionsAsTargets(self.maskrundata,maskshape,imgdata)
if targets is None or len(targets)==0:
self.logger.warning('No Mask Regions in this Image')
keep = apDatabase.getImgAssessmentStatus(imgdata)
if keep == False:
self.logger.warning('Rejected Image, Mask Irelavent')
self.alltargets = targets[:]
self.setTargets(targets, 'Regions')
binning = parentimg.shape[0]/imarray.shape[0]
parentimg=imagefun.bin(parentimg,binning)
overlay = apMask.overlayMask(parentimg,imarray)
self.setImage(overlay, 'Mask')
imarray=parentimg
self.setImage(imarray, 'Image')
def onAdd(self, evt):
vertices = []
vertices = self.panel.getTargetPositions('Region to Remove')
# Write out vertices to mask file
def reversexy(coord):
clist=list(coord)
clist.reverse()
return tuple(clist)
vertices = map(reversexy,vertices)
polygonimg = leginon.polygon.filledPolygon(self.panel.imagedata.shape,vertices)
type(polygonimg)
self.panel.maskimg = self.panel.maskimg + polygonimg
overlay = apMask.overlayMask(self.panel.image,self.panel.maskimg)
self.panel.setImage(overlay.astype(numpy.float32))
self.panel.setTargets('Region to Remove', [])
def onAdd(self, evt):
vertices = []
vertices = self.panel.getTargetPositions('Region to Remove')
# Write out vertices to mask file
def reversexy(coord):
clist = list(coord)
clist.reverse()
return tuple(clist)
vertices = map(reversexy, vertices)
polygonimg = leginon.polygon.filledPolygon(self.panel.imagedata.shape,
vertices)
type(polygonimg)
self.panel.maskimg = self.panel.maskimg + polygonimg
overlay = apMask.overlayMask(self.panel.image, self.panel.maskimg)
self.panel.setImage(overlay.astype(numpy.float32))
self.panel.setTargets('Region to Remove', [])