/
cremiGP.py
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/
cremiGP.py
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import gp
import cPickle as pickle
import numpy as np
import os
HOMEDIR = '/n/home05/haehn/'
REGALDIR = '/n/regal/pfister_lab/haehn/'
DATADIR = HOMEDIR + 'data/CREMIGP/TEST/'
OUTDIR = REGALDIR + 'CREMIBIG/'
#
# load cnn
#
with open('nets/IPMLB_FULL_CREMI_FINAL.p', 'rb') as f:
cnn = pickle.load(f)
cnn.uuid = 'IPMLB'
#
# load data
#
input_image = []
input_prob = []
input_gold = []
input_rhoana = []
test_slices = range(75)# + range(25+20,50) + range(50+20,75)
for z in test_slices:
image, prob, gold, rhoana = gp.Util.read_cremi_section(os.path.expanduser('~/data/CREMIGP/TEST/'), z)
input_image.append(image)
input_prob.append(255.-prob)
input_gold.append(gold)
input_rhoana.append(rhoana)
original_mean_VI, original_median_VI, original_VI_s = gp.Legacy.VI(input_gold, input_rhoana)
# find merge errors, if we did not generate them before
# find merge errors, if we did not generate them before
merge_error_file = OUTDIR+'/merge_errors.p'
if os.path.exists(merge_error_file):
print 'Loading merge errors from file..'
with open(merge_error_file, 'rb') as f:
merge_errors = pickle.load(f)
print len(merge_errors), ' merge errors found.'
bigM_cremi_file = OUTDIR+'bigM_gp.p'
if os.path.exists(bigM_cremi_file):
print 'loading bigM'
with open(bigM_cremi_file, 'rb') as f:
bigM = pickle.load(f)
# else:
# print 'creating bigM'
# bigM = gp.Legacy.create_bigM_without_mask(cnn, input_image, input_prob, input_rhoana, verbose=True, max=1000000)
# with open(bigM_cremi_file, 'wb') as f:
# pickle.dump(bigM, f)
#
# run auto merge correction
#
cylinder_vi_95_file = OUTDIR + '/cremi_vi_00_w_merge_NEW.p'
merge_vis = OUTDIR + '/cremi_merge_auto00_vis.p'
split_vis = OUTDIR + '/cremi_split_auto00_vis.p'
merge_fixes = OUTDIR + '/cremi_merge_auto00_fixes.p'
split_fixes = OUTDIR + '/cremi_split_auto00_fixes.p'
output_95 = OUTDIR + '/cremi_auto00_output.p'
if os.path.exists(cylinder_vi_95_file):
print 'Loading merge errors p < .05 and split errors p > .00 from file..'
with open(cylinder_vi_95_file, 'rb') as f:
cylinder_vi_95 = pickle.load(f)
else:
#
# perform merge correction with p < .05
#
print 'Correcting merge errors with p < .05'
bigM_05, corrected_rhoana_05, cylinder_auto_merge_fixes, vi_s_per_step = gp.Legacy.perform_auto_merge_correction(cnn, bigM, input_image, input_prob, input_rhoana, merge_errors, .05, input_gold=input_gold)
print ' Mean VI improvement', original_mean_VI-gp.Legacy.VI(input_gold, corrected_rhoana_05)[0]
print ' Median VI improvement', original_median_VI-gp.Legacy.VI(input_gold, corrected_rhoana_05)[1]
with open(merge_vis, 'wb') as f:
pickle.dump(vi_s_per_step, f)
with open(merge_fixes, 'wb') as f:
pickle.dump(cylinder_auto_merge_fixes, f)
#
# run auto split correction
#
print 'Correcting split errors with p > .0'
bigM_cylinder_after_95, out_cylinder_volume_after_auto_95, cylinder_auto_fixes_95, cylinder_auto_vi_s_95, vi_s_per_step2 = gp.Legacy.splits_global_from_M_automatic(cnn, bigM_05, input_image, input_prob, corrected_rhoana_05, input_gold, sureness_threshold=.00)
cylinder_vi_95 = gp.Legacy.VI(input_gold, out_cylinder_volume_after_auto_95)
with open(cylinder_vi_95_file, 'wb') as f:
pickle.dump(cylinder_vi_95, f)
with open(split_vis, 'wb') as f:
pickle.dump(vi_s_per_step2, f)
with open(split_fixes, 'wb') as f:
pickle.dump(cylinder_auto_fixes_95, f)
with open(output_95, 'wb') as f:
pickle.dump(out_cylinder_volume_after_auto_95, f)
print ' Mean VI improvement', original_mean_VI-cylinder_vi_95[0]
print ' Median VI improvement', original_median_VI-cylinder_vi_95[1]
#
# run oracle merge correction
#
cylinder_vi_95_file = OUTDIR + '/cremi_vi_simuser_w_merge_NEW.p'
merge_vis = OUTDIR + '/cremi_merge_simuser_vis.p'
split_vis = OUTDIR + '/cremi_split_simuser_vis.p'
merge_fixes = OUTDIR + '/cremi_merge_simuser_fixes.p'
split_fixes = OUTDIR + '/cremi_split_simuser_fixes.p'
output_95 = OUTDIR + '/cremi_simuser_output.p'
if os.path.exists(cylinder_vi_95_file):
print 'Loading merge errors p < .05 and split errors p > .95 from file..'
with open(cylinder_vi_95_file, 'rb') as f:
cylinder_vi_95 = pickle.load(f)
else:
#
# perform merge correction with p < .05
#
print 'Correcting merge errors with oracle'
bigM_05, corrected_rhoana_05, cylinder_auto_merge_fixes, vi_s_per_step = gp.Legacy.perform_sim_user_merge_correction(cnn, bigM, input_image, input_prob, input_rhoana, input_gold, merge_errors)
print ' Mean VI improvement', original_mean_VI-gp.Legacy.VI(input_gold, corrected_rhoana_05)[0]
print ' Median VI improvement', original_median_VI-gp.Legacy.VI(input_gold, corrected_rhoana_05)[1]
with open(merge_vis, 'wb') as f:
pickle.dump(vi_s_per_step, f)
with open(merge_fixes, 'wb') as f:
pickle.dump(cylinder_auto_merge_fixes, f)
#
# run oracle split correction
#
print 'Correcting split errors with p > .95'
bigM_cylinder_after_95, out_cylinder_volume_after_auto_95, cylinder_auto_fixes_95, cylinder_auto_vi_s_95, vi_s_per_step2 = gp.Legacy.splits_global_from_M(cnn, bigM_05, input_image, input_prob, corrected_rhoana_05, input_gold, hours=-1)
cylinder_vi_95 = gp.Legacy.VI(input_gold, out_cylinder_volume_after_auto_95)
with open(cylinder_vi_95_file, 'wb') as f:
pickle.dump(cylinder_vi_95, f)
with open(split_vis, 'wb') as f:
pickle.dump(vi_s_per_step2, f)
with open(split_fixes, 'wb') as f:
pickle.dump(cylinder_auto_fixes_95, f)
with open(output_95, 'wb') as f:
pickle.dump(out_cylinder_volume_after_auto_95, f)
print ' Mean VI improvement', original_mean_VI-cylinder_vi_95[0]
print ' Median VI improvement', original_median_VI-cylinder_vi_95[1]
print 'All done.'