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 processImage(self,imgdata):
image = self.getImage(imgdata,self.params['bin'])
results=self.function(self.rundata, imgdata, image)
mask = results.pop('mask')
pngpath = os.path.join(self.params['rundir'],"masks")
apParam.createDirectory(pngpath,warning=False)
filepathname = os.path.join(self.params['rundir'],"masks",imgdata['filename']+"_mask.png")
if mask is not None:
# PIL alpha channel read does not work
#apImage.arrayMaskToPngAlpha(mask, filepathname)
apImage.arrayMaskToPng(mask, filepathname)
return results
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 processImage(self, imgdata):
image = self.getImage(imgdata, self.params['bin'])
results = self.function(self.rundata, imgdata, image)
mask = results.pop('mask')
pngpath = os.path.join(self.params['rundir'], "masks")
apParam.createDirectory(pngpath, warning=False)
filepathname = os.path.join(self.params['rundir'], "masks",
imgdata['filename'] + "_mask.png")
if mask is not None:
# PIL alpha channel read does not work
#apImage.arrayMaskToPngAlpha(mask, filepathname)
apImage.arrayMaskToPng(mask, filepathname)
return results
def commitToDatabase(self,imgdata): ''' Fake commitToDatabase for local file saving. In this case, the mask file is saved ''' rundir = self.params['rundir'] maskname = self.params['runname'] bin = self.params['bin'] maskdir=os.path.join(rundir,"masks") mask = self.maskimg maskfilename = imgdata['filename']+'_mask.png' labeled_regions,clabels=nd.label(mask) # PIL alpha channel read does not work #apImage.arrayMaskToPngAlpha(mask, os.path.join(maskdir,maskfilename)) apImage.arrayMaskToPng(mask, os.path.join(maskdir,maskfilename)) return
def commitToDatabase(self, imgdata):
'''
Fake commitToDatabase for local file saving.
In this case, the mask file is saved
'''
rundir = self.params['rundir']
maskname = self.params['runname']
bin = self.params['bin']
maskdir = os.path.join(rundir, "masks")
mask = self.maskimg
maskfilename = imgdata['filename'] + '_mask.png'
labeled_regions, clabels = nd.label(mask)
# PIL alpha channel read does not work
#apImage.arrayMaskToPngAlpha(mask, os.path.join(maskdir,maskfilename))
apImage.arrayMaskToPng(mask, os.path.join(maskdir, maskfilename))
return
