def OneKfold(i=0, datadict=None):
k = settings.options.kfolds
modelloc = TrainModel(idfold=i)
(train_set, test_set, valid_set) = GetSetupKfolds(settings.options.dbfile,
k, i)
sumscore = 0
sumscorefloat = 0
for idtest in test_set:
baseloc = '%s/%03d/%03d' % (settings.options.outdir, k, i)
imgloc = '%s/%s' % (settings.options.rootlocation,
datadict[idtest]['image'])
segloc = '%s/%s' % (settings.options.rootlocation,
datadict[idtest]['label'])
outloc = '%s/label-%04d.nii.gz' % (baseloc, idtest)
if settings.options.numepochs > 0 and (
settings.options.makepredictions
or settings.options.makedropoutmap):
if settings.options.makepredictions:
predseg, predfloat = PredictModel(model=modelloc,
image=imgloc,
outdir=outloc)
else:
predseg, predfloat = PredictDropout(model=modelloc,
image=imgloc,
outdir=outloc,
seg=segloc)
import settings
from settings import process_options, perform_setup
(options, args) = process_options()
IMG_DTYPE, SEG_DTYPE, _globalnpfile, _globalexpectedpixel, _nx, _ny = perform_setup(
options)
print('database file: %s ' % settings._globalnpfile)
from setupmodel import GetDataDictionary, BuildDB
from trainmodel import TrainModel
from predictmodel import PredictModel
from kfolds import OneKfold, Kfold
if options.builddb:
BuildDB()
if options.kfolds > 1:
if options.idfold > -1:
databaseinfo = GetDataDictionary(options.dbfile)
OneKfold(i=options.idfold, datadict=databaseinfo)
else:
Kfold()
if options.trainmodel and options.kfolds == 1: # no kfolds, i.e. k=1
TrainModel()
if options.predictmodel:
PredictModel()
if ((not options.builddb) and (not options.trainmodel)
and (not options.predictmodel) and (options.kfolds == 1)):
print("parser error")
import settings
from settings import process_options, perform_setup
(options, args) = process_options()
IMG_DTYPE, SEG_DTYPE, _globalnpfile, _globalexpectedpixel, _nx, _ny = perform_setup(
options)
print('database file: %s ' % settings._globalnpfile)
from setupmodel import GetDataDictionary, BuildDB
from trainmodel import TrainModel
from predictmodel import PredictModel
from kfolds import OneKfold, Kfold
if options.builddb:
BuildDB()
if options.kfolds > 1:
if options.idfold > -1:
databaseinfo = GetDataDictionary(options.dbfile)
OneKfold(i=options.idfold, datadict=databaseinfo)
else:
Kfold()
if options.trainmodel and options.kfolds == 1: # no kfolds, i.e. k=1
TrainModel()
if options.predictmodel:
segloc = options.predictimage.replace("volume", "segmentation")
PredictModel(seg=segloc)
if ((not options.builddb) and (not options.trainmodel)
and (not options.predictmodel) and (options.kfolds == 1)):
print("parser error")