def getImageList(self):
self.maskrundata, self.maskparamsdata = apMask.getMaskParamsByRunName(
self.settings['mask run'], self.session)
self.maskdir = os.path.join(self.maskrundata['path']['path'], "masks")
files = os.listdir(self.maskdir)
format = 'png'
assessrunname = self.settings['run']
goodfiles = []
for file in files:
ext = file.split('.')[-1]
if format == 'png' and ext in ('png', 'PNG'):
goodfiles.append(file)
self.assessrundata, exist = apMask.insertMaskAssessmentRun(
self.session, self.maskrundata, assessrunname)
if exist:
if self.settings['continueon']:
mode = 'continue'
else:
mode = 'overwrite'
self.logger.warning('Assessor Run exists, will %s' % (mode, ))
if mode == 'continue':
assessedmaskfiles = apMask.getAssessedMasks(
self.assessrundata, self.maskrundata)
for assessedmaskfile in assessedmaskfiles:
try:
aindex = goodfiles.index(assessedmaskfile)
del goodfiles[aindex]
except ValueError:
pass
if goodfiles:
goodfiles.sort()
self.images = []
self.files = []
for i, filename in enumerate(goodfiles):
imgdata = self.readParent(filename)
self.images.append(imgdata)
self.files.append(filename)
if self.noreject and apDatabase.getImgAssessmentStatus(
imgdata) == False:
self.files.pop()
self.images.pop()
else:
self.logger.error('No %s files in directory' % (format, ))
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 getImageList(self):
self.maskrundata,self.maskparamsdata = apMask.getMaskParamsByRunName(self.settings['mask run'],self.session)
self.maskdir=os.path.join(self.maskrundata['path']['path'],"masks")
files = os.listdir(self.maskdir)
format = 'png'
assessrunname = self.settings['run']
goodfiles = []
for file in files:
ext = file.split('.')[-1]
if format == 'png' and ext in ('png','PNG'):
goodfiles.append(file)
self.assessrundata,exist = apMask.insertMaskAssessmentRun(self.session,self.maskrundata,assessrunname)
if exist:
if self.settings['continueon']:
mode = 'continue'
else:
mode = 'overwrite'
self.logger.warning('Assessor Run exists, will %s' % (mode,))
if mode == 'continue':
assessedmaskfiles = apMask.getAssessedMasks(self.assessrundata,self.maskrundata)
for assessedmaskfile in assessedmaskfiles:
try:
aindex = goodfiles.index(assessedmaskfile)
del goodfiles[aindex]
except ValueError:
pass
if goodfiles:
goodfiles.sort()
self.images=[]
self.files=[]
for i,filename in enumerate(goodfiles):
imgdata = self.readParent(filename)
self.images.append(imgdata)
self.files.append(filename)
if self.noreject and apDatabase.getImgAssessmentStatus(imgdata)==False:
self.files.pop()
self.images.pop()
else:
self.logger.error('No %s files in directory' % (format,))
def processImage(self, imgdata):
### reset global value
self.imgassess = True
### get initial assessment
imgassess = apDatabase.getImgAssessmentStatus(imgdata)
if imgassess is False:
return
if imgassess is None:
imgassess = True
### hidden image
imgview = apDatabase.getImgViewerStatus(imgdata)
if imgview is False:
apDisplay.printColor(
"\nrejecting hidden image: " +
apDisplay.short(imgdata['filename']), "green")
self.imgassess = False
return
### tilt pair stuff
if imgassess is not False and self.params['notiltpairs'] is True:
imgassess = self.rejectTiltPairs(imgdata)
### picking stuff
if imgassess is not False and self.params['nopicks'] is True:
part = apParticle.getOneParticle(imgdata)
if not part:
apDisplay.printColor(
"\nrejecting unpicked image: " +
apDisplay.short(imgdata['filename']), "cyan")
imgassess = False
### ace stuff
if imgassess is not False:
imgassess = self.rejectAceInfo(imgdata)
### set global value
self.imgassess = imgassess
return
def processImage(self, imgdata):
### reset global value
self.imgassess = True
### get initial assessment
imgassess = apDatabase.getImgAssessmentStatus(imgdata)
if imgassess is False:
return
if imgassess is None:
imgassess = True
### hidden image
imgview = apDatabase.getImgViewerStatus(imgdata)
if imgview is False:
apDisplay.printColor("\nrejecting hidden image: "+apDisplay.short(imgdata['filename']), "green")
self.imgassess = False
return
### tilt pair stuff
if imgassess is not False and self.params['notiltpairs'] is True:
imgassess = self.rejectTiltPairs(imgdata)
### picking stuff
if imgassess is not False and self.params['nopicks'] is True:
part = apParticle.getOneParticle(imgdata)
if not part:
apDisplay.printColor("\nrejecting unpicked image: "+apDisplay.short(imgdata['filename']), "cyan")
imgassess = False
### ace stuff
if imgassess is not False:
imgassess = self.rejectAceInfo(imgdata)
### set global value
self.imgassess = imgassess
return
def processImage(self, imgdata):
### get initial assessment
self.imgassess = apDatabase.getImgAssessmentStatus(imgdata)
return
