def run_css(basedir,
region,
lr,
scale_method,
scale_factor,
cycles,
cyclesize,
Split,
dest_folder,
gpuid=0):
workdir = osp.join(basedir, region, dest_folder)
if osp.isdir(workdir):
shutil.rmtree(workdir)
os.mkdir(workdir)
labelset = ct.get_labelset(basedir, region)
imlist, imdict = ct.load_data(basedir, Split, labelset, region)
im_mean = bct.calculate_image_mean(imlist[::10])
for split in ['train', 'val']:
ct.write_split(basedir, workdir, region, split, labelset, scale_method,
scale_factor)
solver = bct.CaffeSolver(onlytrain=True)
solver.sp['base_lr'] = lr
solver.sp['lr_policy'] = '"fixed"'
#for f in ['test_net', 'test_iter', 'test_interval', 'test_initialization']:
# del solver.sp[f]
solver.write(osp.join(workdir, 'solver.prototxt'))
pyparams = pload(osp.join(workdir, 'valpyparams.pkl'))
cct.write_net(workdir,
im_mean,
len(labelset),
scaling_method=scale_method,
scaling_factor=scale_factor,
cropsize=224,
onlytrain=True)
shutil.copyfile(
osp.join(basedir, 'model_zoo/VGG_ILSVRC_16_layers.caffemodel'),
osp.join(basedir, workdir, 'vgg_initial.caffemodel'))
for i in range(cycles):
bct.run(workdir, gpuid=gpuid, nbr_iters=cyclesize, onlytrain=True)
_ = bct.classify_from_patchlist_wrapper(
imlist,
imdict,
pyparams,
workdir,
gpuid=gpuid,
save=True,
net_prototxt='trainnet.prototxt')
def find_best_iter(workdir, testtoken = 'predictions_using_snapshot_iter_*.caffemodel.p', accfcn = bmt.acc):
iterlist = []
bestacc = -1
for testname in glob.glob(osp.join(workdir, testtoken)):
[gtlist, estlist, scorelist] = bmt.pload(osp.join(workdir, testname))
acc = accfcn(estlist, gtlist)
iter_ = int(re.search('iter_([0-9]*).caffemodel.p', testname).group(1))
iterlist.append((iter_, acc))
if acc > bestacc:
bestiter = iter_
bestacc = acc
return bestiter, iterlist
def find_best_iter(workdir, testtoken="predictions_using_snapshot_iter_*.caffemodel.p", accfcn=bmt.acc):
iterlist = []
bestacc = -1
for testname in glob.glob(osp.join(workdir, testtoken)):
[gtlist, estlist, scorelist] = bmt.pload(osp.join(workdir, testname))
acc = accfcn(estlist, gtlist)
iter_ = int(re.search("iter_([0-9]*).caffemodel.p", testname).group(1))
iterlist.append((iter_, acc))
if acc > bestacc:
bestiter = iter_
bestacc = acc
return bestiter, iterlist
def classify_exp(basedir,
region,
expdir,
modeldir,
npoints=50,
gpuid=0,
force_rewrite=False):
bestiter, _ = cct.find_best_iter(modeldir)
caffemodel = 'snapshot_iter_{}.caffemodel'.format(bestiter)
net = bct.load_model(modeldir,
caffemodel,
gpuid=gpuid,
net_prototxt='trainnet.prototxt')
pyparams = pload(osp.join(modeldir, 'trainpyparams.pkl'))
labelset = ct.get_labelset(basedir, region)
indir_root = osp.join(basedir, region, 'data')
indir = osp.join(indir_root, expdir)
outdir = indir + '/coverages'
if not os.path.isdir(outdir):
os.makedirs(outdir)
imgs = glob.glob(indir + '/images/*.jpg')
print "Starting", indir, len(imgs)
for img in imgs:
imname = osp.basename(img)
covname = osp.join(outdir, imname + '.points.csv')
if osp.isfile(covname) and not force_rewrite:
continue
estlist, rows, cols = classify_image(img, pyparams, npoints, net)
f = open(covname, 'w')
f.write(imname + '\n')
f.write('row, col, labelcode\n')
for row, col, est in zip(rows, cols, estlist):
f.write('{}, {}, {}\n'.format(int(row), int(col), labelset[est]))
f.close()
print "Done", indir, len(imgs)
def classify_allexp(basedir,
modeldir,
region,
gpuid=0,
npoints=50,
force_rewrite=False):
"""
At the moment, this is using the net produced for test. Need to merge training and test-cell images to produce the deployment net
"""
bestiter, _ = cct.find_best_iter(modeldir)
caffemodel = 'snapshot_iter_{}.caffemodel'.format(bestiter)
net = bct.load_model(modeldir,
caffemodel,
gpuid=gpuid,
net_prototxt='deploy.prototxt')
pyparams = pload(osp.join(modeldir, 'deploytrainpyparams.pkl'))
labelset = ct.get_label(region)
indir_root = osp.join(basedir, region,
'data') ## Need ssh link this one to qcloud
for indir in glob.glob(indir_root + 'exp*'):
outdir = indir + '/coverages'
if not os.path.isdir(outdir):
os.makedirs(outdir)
imgs = glob.glob(indir + '/images/*.jpg')
print "Starting", indir, len(imgs)
for img in imgs:
imname = osp.basename(img)
covname = osp.join(outdir, imname + '.points.csv')
if osp.isfile(covname) and not force_rewrite:
continue
estlist, rows, cols = classify_image(img, pyparams, npoints, net)
f = open(covname, 'w')
f.write(imname + '\n')
f.write('row, col, labelcode\n')
for row, col, est in zip(rows, cols, estlist):
f.write('{}, {}, {}\n'.format(int(row), int(col),
labelset[est]))
f.close()
print "Done", indir, len(imgs)
def classify_test(basedir,
region,
test_folder,
modeldir,
gpuid=0,
force_rewrite=False,
height_cm=100):
'''
Run classification of test images using specific previously annotated points
'''
bestiter, _ = cct.find_best_iter(modeldir)
caffemodel = 'snapshot_iter_{}.caffemodel'.format(bestiter)
net = bct.load_model(modeldir,
caffemodel,
gpuid=gpuid,
net_prototxt='trainnet.prototxt')
pyparams = pload(osp.join(modeldir, 'trainpyparams.pkl'))
labelset = ct.get_labelset(basedir, region)
indir_root = osp.join(basedir, region)
indir = osp.join(indir_root, test_folder)
outdir = indir + '/coverages'
height_cm = 100
if not os.path.isdir(outdir):
os.makedirs(outdir)
# load test-data
imlist, imdict = ct.load_annotation_file(
osp.join(basedir, region, test_folder, 'annotations.csv'), labelset)
imlist = [
osp.join(basedir, region, test_folder, 'images', im) for im in imlist
]
for img in imlist:
transformer = bct.Transformer(pyparams['im_mean'])
imname = osp.basename(img)
covname = osp.join(outdir, imname + '.points.csv')
if osp.isfile(covname) and not force_rewrite:
continue
point_anns = []
rows = [y for y, _, _ in imdict[imname][0]]
cols = [y for _, y, _ in imdict[imname][0]]
for row, col in zip(rows, cols):
point_anns.append((int(row), int(col), 0))
# Resize & Crop
im = np.asarray(Image.open(img))
(im, scale) = ct.coral_image_resize(im, pyparams['scaling_method'],
pyparams['scaling_factor'],
height_cm)
patchlist = ct.crop_patch(im, pyparams['crop_size'], scale, point_anns,
height_cm)
# Classify
[estlist, _] = bct.classify_from_imlist(patchlist, net, transformer,
pyparams['batch_size'])
f = open(covname, 'w')
f.write(imname + '\n')
f.write('row, col, labelcode\n')
for row, col, est in zip(rows, cols, estlist):
f.write('{}, {}, {}\n'.format(int(row), int(col), labelset[est]))
f.close()
print "Done", indir, len(imlist)
def test_save_load(self):
a = {'field': 22, 'another_field': 'value'}
bmt.psave(a, osp.join(self.workdir, 'test.p'))
b = bmt.pload(osp.join(self.workdir, 'test.p'))
self.assertEqual(a, b)
def test_save_load(self):
a = {'field':22, 'another_field':'value'}
bmt.psave(a, osp.join(self.workdir, 'test.p'))
b = bmt.pload(osp.join(self.workdir, 'test.p'))
self.assertEqual(a, b)