def commitToDatabase(self, imgdata):
# if a kept mask was created in a previous mask run and the
# assess flag was used (basically combining the 2 runs) there is
# nothing new to commit.
if self.useAcceptedMask: return
sessiondata = imgdata['session']
rundir = self.params['rundir']
maskname = self.params['runname']
assessname = self.params['assessname']
bin = self.params['bin']
maskdir = os.path.join(rundir, "masks")
maskrundata, maskparamsdata = apMask.getMaskParamsByRunName(
maskname, sessiondata)
if not maskrundata:
apMask.insertManualMaskRun(sessiondata, rundir, maskname, bin)
maskrundata, maskparamsdata = apMask.getMaskParamsByRunName(
maskname, sessiondata)
try:
apParam.createDirectory(maskdir)
except:
apDisplay.printWarning('can not create mask directory')
massessrundata, exist = apMask.insertMaskAssessmentRun(
sessiondata, maskrundata, assessname)
mask = self.maskimg
maskfilename = imgdata['filename'] + '_mask.png'
image = self.image
labeled_regions, clabels = nd.label(mask)
testlog = [False, 0, ""]
infos = {}
infos, testlog = apCrud.getLabeledInfo(image, mask, labeled_regions,
range(1, clabels + 1), False,
infos, testlog)
offset = 1
for l1 in range(0, len(infos)):
l = l1 + offset
info = infos[l]
info.append(l)
regiondata = apMask.insertMaskRegion(maskrundata, imgdata, info)
print "Inserting mask region in database"
# PIL alpha channel read does not work
#apImage.arrayMaskToPngAlpha(mask, os.path.join(maskdir,maskfilename))
apImage.arrayMaskToPng(mask, os.path.join(maskdir, maskfilename))
allregiondata = apMask.getMaskRegions(maskrundata, imgdata)
for regiondata in allregiondata:
apMask.insertMaskAssessment(massessrundata, regiondata, 1)
print "Inserting mask assessment in database."
if self.assess != self.assessold and self.assess is not None:
#imageaccessor run is always named run1
apDatabase.insertImgAssessmentStatus(imgdata, 'run1', self.assess)
return
def commitToDatabase(self,imgdata):
# if a kept mask was created in a previous mask run and the
# assess flag was used (basically combining the 2 runs) there is
# nothing new to commit.
if self.useAcceptedMask: return
sessiondata = imgdata['session']
rundir = self.params['rundir']
maskname = self.params['runname']
assessname = self.params['assessname']
bin = self.params['bin']
maskdir=os.path.join(rundir,"masks")
maskrundata,maskparamsdata = apMask.getMaskParamsByRunName(maskname,sessiondata)
if not maskrundata:
apMask.insertManualMaskRun(sessiondata,rundir,maskname,bin)
maskrundata,maskparamsdata = apMask.getMaskParamsByRunName(maskname,sessiondata)
try:
apParam.createDirectory(maskdir)
except:
apDisplay.printWarning('can not create mask directory')
massessrundata,exist = apMask.insertMaskAssessmentRun(sessiondata,maskrundata,assessname)
mask = self.maskimg
maskfilename = imgdata['filename']+'_mask.png'
image = self.image
labeled_regions,clabels=nd.label(mask)
testlog = [False,0,""]
infos={}
infos,testlog=apCrud.getLabeledInfo(image,mask,labeled_regions,range(1,clabels+1),False,infos,testlog)
offset=1
for l1 in range(0,len(infos)):
l=l1+offset
info=infos[l]
info.append(l)
regiondata= apMask.insertMaskRegion(maskrundata,imgdata,info)
print "Inserting mask region in database"
# PIL alpha channel read does not work
#apImage.arrayMaskToPngAlpha(mask, os.path.join(maskdir,maskfilename))
apImage.arrayMaskToPng(mask, os.path.join(maskdir,maskfilename))
allregiondata = apMask.getMaskRegions(maskrundata,imgdata)
for regiondata in allregiondata:
apMask.insertMaskAssessment(massessrundata,regiondata,1)
print "Inserting mask assessment in database."
if self.assess != self.assessold and self.assess is not None:
#imageaccessor run is always named run1
apDatabase.insertImgAssessmentStatus(imgdata, 'run1', self.assess)
return
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 commitToDatabase(self, imgdata):
# if a kept mask was created in a previous mask run and the
# assess flag was used (basically combining the 2 runs) there is
# nothing new to commit.
if self.useAcceptedMask: return
sessiondata = imgdata['session']
rundir = self.params['rundir']
maskname = self.params['runname']
assessname = self.params['assessname']
bin = self.params['bin']
maskdir = os.path.join(rundir, "masks")
maskrundata, maskparamsdata = apMask.getMaskParamsByRunName(
maskname, sessiondata)
if not maskrundata:
apMask.insertManualMaskRun(sessiondata, rundir, maskname, bin)
maskrundata, maskparamsdata = apMask.getMaskParamsByRunName(
maskname, sessiondata)
massessrundata, exist = apMask.insertMaskAssessmentRun(
sessiondata, maskrundata, assessname)
mask = self.maskimg
maskfilename = imgdata['filename'] + '_mask.png'
image = self.image
labeled_regions, clabels = nd.label(mask)
testlog = [False, 0, ""]
infos = {}
infos, testlog = apCrud.getLabeledInfo(image, mask, labeled_regions,
range(1, clabels + 1), False,
infos, testlog)
offset = 1
for l1 in range(0, len(infos)):
l = l1 + offset
info = infos[l]
info.append(l)
regiondata = apMask.insertMaskRegion(maskrundata, imgdata, info)
print "Inserting mask region in database"
allregiondata = apMask.getMaskRegions(maskrundata, imgdata)
for regiondata in allregiondata:
apMask.insertMaskAssessment(massessrundata, regiondata, 1)
print "Inserting mask assessment in database."
return
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 commitToDatabase(self,imgdata):
# if a kept mask was created in a previous mask run and the
# assess flag was used (basically combining the 2 runs) there is
# nothing new to commit.
if self.useAcceptedMask: return
sessiondata = imgdata['session']
rundir = self.params['rundir']
maskname = self.params['runname']
assessname = self.params['assessname']
bin = self.params['bin']
maskdir=os.path.join(rundir,"masks")
maskrundata,maskparamsdata = apMask.getMaskParamsByRunName(maskname,sessiondata)
if not maskrundata:
apMask.insertManualMaskRun(sessiondata,rundir,maskname,bin)
maskrundata,maskparamsdata = apMask.getMaskParamsByRunName(maskname,sessiondata)
massessrundata,exist = apMask.insertMaskAssessmentRun(sessiondata,maskrundata,assessname)
mask = self.maskimg
maskfilename = imgdata['filename']+'_mask.png'
image = self.image
labeled_regions,clabels=nd.label(mask)
testlog = [False,0,""]
infos={}
infos,testlog=apCrud.getLabeledInfo(image,mask,labeled_regions,range(1,clabels+1),False,infos,testlog)
offset=1
for l1 in range(0,len(infos)):
l=l1+offset
info=infos[l]
info.append(l)
regiondata= apMask.insertMaskRegion(maskrundata,imgdata,info)
print "Inserting mask region in database"
allregiondata = apMask.getMaskRegions(maskrundata,imgdata)
for regiondata in allregiondata:
apMask.insertMaskAssessment(massessrundata,regiondata,1)
print "Inserting mask assessment in database."
return
def commitToDatabase(self, imgdata):
sessiondata = imgdata['session']
rundir = self.params['rundir']
maskname = self.params['runname']
assessname = self.params['runname']
bin = self.params['bin']
maskdir = os.path.join(rundir, "masks")
maskrundata, maskparamsdata = apMask.getMaskParamsByRunName(
maskname, sessiondata)
if not maskrundata:
apMask.insertManualMaskRun(sessiondata, rundir, maskname, bin)
maskrundata, maskparamsdata = apMask.getMaskParamsByRunName(
maskname, sessiondata)
try:
apParam.createDirectory(maskdir)
except:
apDisplay.printWarning('can not create mask directory')
massessrundata, exist = apMask.insertMaskAssessmentRun(
sessiondata, maskrundata, assessname)
# The mask file should only exist if the em_hole_finder found a region to mask.
# If it does not exist, do not insert anything to the DB.
if (os.path.exists(self.outfile)):
apDisplay.printMsg("Writing results to database: " +
time.asctime())
# Set black pixels to white and anything else to 0
img1 = Image.open(self.outfile)
img2 = Image.eval(img1, lambda px: 255 if px == 0 else 0)
# make sure the images have the same shape
imgshape = numpy.asarray(imgdata['image'].shape)
apDisplay.printMsg("MRC Image Shape:")
print imgshape
imgsize = imgshape[0] * imgshape[1]
apDisplay.printMsg("MRC Image Size:")
print imgsize
maskshape = numpy.shape(img2)
apDisplay.printMsg("Mask Image Shape:")
print maskshape
apDisplay.printMsg("resizing mask image with scale:")
scaleFactorx = float(imgshape[0]) / float(maskshape[0])
scaleFactory = float(imgshape[1]) / float(maskshape[1])
scale = scaleFactorx, scaleFactory
print scale
img3 = imagefun.scale(img2, scale)
maskshape = numpy.shape(img3)
apDisplay.printMsg("Mask Image Shape:")
print maskshape
#img3 = numpy.resize(img2, imgshape) # not working
img3path = self.outfile + "_tmp.jpg"
scipy.misc.imsave(img3path, img3)
labeled_regions, clabels = ndimage.label(img3)
testlog = [False, 0, ""]
infos = {}
apDisplay.printMsg("getting mask region info.")
infos, testlog = apCrud.getLabeledInfo(imgdata['image'], img3,
labeled_regions,
range(1, clabels + 1),
False, infos, testlog)
apDisplay.printMsg("inserting mask regions to DB.")
print len(infos)
area_max = imgsize * .9
offset = 1
for l1 in range(0, len(infos)):
l = l1 + offset
info = infos[l]
area = info[0]
print area
if (area > 400 and area < area_max):
apDisplay.printMsg("saving a region of size:")
print area
info.append(l)
regiondata = apMask.insertMaskRegion(
maskrundata, imgdata, info)
# Insert mask assessment regions. This keeps track of the mask regions that the user wants to reject.
allregiondata = apMask.getMaskRegions(maskrundata, imgdata)
for regiondata in allregiondata:
apMask.insertMaskAssessment(massessrundata, regiondata, True)
# if self.assess != self.assessold and self.assess is not None:
# #imageaccessor run is always named run1
# apDatabase.insertImgAssessmentStatus(imgdata, 'run1', self.assess)
return
def commitToDatabase(self,imgdata):
sessiondata = imgdata['session']
rundir = self.params['rundir']
maskname = self.params['runname']
assessname = self.params['runname']
bin = self.params['bin']
maskdir = os.path.join(rundir,"masks")
maskrundata,maskparamsdata = apMask.getMaskParamsByRunName(maskname,sessiondata)
if not maskrundata:
apMask.insertManualMaskRun(sessiondata,rundir,maskname,bin)
maskrundata,maskparamsdata = apMask.getMaskParamsByRunName(maskname,sessiondata)
try:
apParam.createDirectory(maskdir)
except:
apDisplay.printWarning('can not create mask directory')
massessrundata,exist = apMask.insertMaskAssessmentRun(sessiondata,maskrundata,assessname)
# The mask file should only exist if the em_hole_finder found a region to mask.
# If it does not exist, do not insert anything to the DB.
if ( os.path.exists(self.outfile) ):
apDisplay.printMsg("Writing results to database: " + time.asctime())
# Set black pixels to white and anything else to 0
img1 = Image.open(self.outfile)
img2 = Image.eval(img1, lambda px: 255 if px==0 else 0)
# make sure the images have the same shape
imgshape = numpy.asarray(imgdata['image'].shape)
apDisplay.printMsg("MRC Image Shape:")
print imgshape
imgsize = imgshape[0]*imgshape[1]
apDisplay.printMsg("MRC Image Size:")
print imgsize
maskshape = numpy.shape(img2)
apDisplay.printMsg("Mask Image Shape:")
print maskshape
apDisplay.printMsg("resizing mask image with scale:")
scaleFactorx = float(imgshape[0])/float(maskshape[0])
scaleFactory = float(imgshape[1])/float(maskshape[1])
scale = scaleFactorx, scaleFactory
print scale
img3 = imagefun.scale( img2, scale )
maskshape = numpy.shape(img3)
apDisplay.printMsg("Mask Image Shape:")
print maskshape
#img3 = numpy.resize(img2, imgshape) # not working
img3path = self.outfile + "_tmp.jpg"
scipy.misc.imsave(img3path, img3)
labeled_regions,clabels = ndimage.label(img3)
testlog = [False,0,""]
infos={}
apDisplay.printMsg("getting mask region info.")
infos,testlog = apCrud.getLabeledInfo( imgdata['image'], img3, labeled_regions, range(1,clabels+1), False, infos, testlog)
apDisplay.printMsg("inserting mask regions to DB.")
print len(infos)
area_max = imgsize*.9
offset = 1
for l1 in range(0,len(infos)):
l = l1 + offset
info = infos[l]
area=info[0]
print area
if (area > 400 and area < area_max):
apDisplay.printMsg("saving a region of size:")
print area
info.append(l)
regiondata = apMask.insertMaskRegion( maskrundata, imgdata, info )
# Insert mask assessment regions. This keeps track of the mask regions that the user wants to reject.
allregiondata = apMask.getMaskRegions(maskrundata,imgdata)
for regiondata in allregiondata:
apMask.insertMaskAssessment(massessrundata,regiondata,True)
# if self.assess != self.assessold and self.assess is not None:
# #imageaccessor run is always named run1
# apDatabase.insertImgAssessmentStatus(imgdata, 'run1', self.assess)
return