Example #1
0
    def run_svm_inference(self, test, w):
        logger.info('running inference on: {}'.format(test))

        outdir = self.dir_inf + test
        if not os.path.isdir(outdir):
            os.makedirs(outdir)

        ## segment test image with trained w
        def wwf(im, _w):
            ''' meta weight function'''
            data = 0
            for iwf, wf in enumerate(self.weight_functions.values()):
                ij, _data = wf(im)
                data += _w[iwf] * _data
            return ij, data

        ## load images and ground truth
        file_seg = self.dir_reg + test + 'seg.hdr'
        file_im = self.dir_reg + test + 'gray.hdr'
        im = io_analyze.load(file_im)
        seg = io_analyze.load(file_seg)
        seg.flat[~np.in1d(seg.ravel(), self.labelset)] = self.labelset[0]

        ## save image
        im = im / np.std(im)  # normalize image by variance

        ## prior
        anchor_api = BaseAnchorAPI(
            self.prior,
            anchor_weight=w[-1],
        )

        sol, y = rwsegment.segment(im,
                                   anchor_api,
                                   seeds=self.seeds,
                                   weight_function=lambda im: wwf(im, w),
                                   **self.rwparams_inf)

        np.save(outdir + 'y.test.npy', y)
        io_analyze.save(outdir + 'sol.test.hdr', sol.astype(np.int32))

        ## compute Dice coefficient
        dice = compute_dice_coef(sol, seg, labelset=self.labelset)
        np.savetxt(outdir + 'dice.test.txt',
                   np.c_[dice.keys(), dice.values()],
                   fmt='%d %.8f')

        ## inference compare with gold standard
        dice_gold = np.loadtxt(outdir + 'dice.gold.txt')
        y_gold = np.load(outdir + 'y.gold.npy')
        sol_gold = io_analyze.load(outdir + 'sol.gold.hdr')

        np.testing.assert_allclose(dice.values(),
                                   dict(dice_gold).values(),
                                   err_msg='FAIL: dice coef mismatch',
                                   atol=1e-8)
        np.testing.assert_allclose(y, y_gold, err_msg='FAIL: y mismatch')
        np.testing.assert_equal(sol, sol_gold, err_msg='FAIL: sol mismatch')

        print 'PASS: inference tests'
    def process_sample(self, test, fold=None):

        ## get prior
        prior, mask = load_or_compute_prior_and_mask(
            test, force_recompute=self.force_recompute_prior, pca=True, fold=fold
        )
        seeds = (-1) * mask
        mask = mask.astype(bool)

        ## load image
        file_name = config.dir_reg + test + "gray.hdr"
        logger.info("segmenting data: {}".format(file_name))
        im = io_analyze.load(file_name)
        file_gt = config.dir_reg + test + "seg.hdr"
        seg = io_analyze.load(file_gt)
        seg.flat[~np.in1d(seg, self.labelset)] = self.labelset[0]

        ## normalize image
        nim = im / np.std(im)

        ## init anchor_api
        anchor_api = MetaAnchor(
            prior=prior, prior_models=self.prior_models, prior_weights=self.prior_weights, image=nim
        )

        ## start segmenting
        # import ipdb; ipdb.set_trace()
        sol, impca = rwsegment_pca.segment(nim, anchor_api, seeds=seeds, labelset=self.labelset, **self.params)

        ## compute Dice coefficient per label
        dice = compute_dice_coef(sol, seg, labelset=self.labelset)
        logger.info("Dice: {}".format(dice))

        dice_pca = compute_dice_coef(impca, seg, labelset=self.labelset)
        logger.info("Dice pca only: {}".format(dice_pca))

        if not config.debug:
            if fold is not None:
                test_name = "f{}_{}".format(fold[0][:2], test)
            else:
                test_name = test
            outdir = config.dir_seg + "/{}/{}".format(self.model_name, test_name)

            logger.info("saving data in: {}".format(outdir))
            if not os.path.isdir(outdir):
                os.makedirs(outdir)

            io_analyze.save(outdir + "sol.hdr", sol.astype(np.int32))
            io_analyze.save(outdir + "solpca.hdr", impca.astype(np.int32))

            np.savetxt(outdir + "dice.txt", np.c_[dice.keys(), dice.values()], fmt="%d %.8f")
            np.savetxt(outdir + "dice_pca.txt", np.c_[dice.keys(), dice_pca.values()], fmt="%d %.8f")
def load_or_compute_prior_and_mask(test, force_recompute=False, pca=False, fold=None):
    if fold is not None:
        test_name = 'f{}_{}/'.format(fold[0][:2], test)
    else:
        test_name = test
        fold = [test]
     
    #import ipdb; ipdb.set_trace()
    labelset = np.asarray(config.labelset)
    if pca:
        outdir = config.dir_pca_prior + test_name
    else:
        outdir = config.dir_prior + test_name
    if not os.path.isdir(outdir):
        os.makedirs(outdir)
    
    ## load mask and prior
    prior = None
    file_mask  = outdir + 'mask.hdr'
    file_prior = outdir + 'prior.npz'
    file_U = outdir + 'eigenvectors.npy'
    file_segprior = outdir + 'segprior.hdr'
    file_entropymap = outdir + 'entropymap.hdr'
   
    if force_recompute or not (os.path.exists(file_prior) and os.path.exists(file_mask)):
        if pca:
            _prior, mask = load_or_compute_prior_and_mask(test, fold=fold)
            generator = rwsegment_pca_prior.PriorGenerator(labelset, mask=mask)
        else:
            generator = rwsegment_prior.PriorGenerator(labelset)
 
        ntrain = 0
        for train in config.vols:
            if train in fold: continue
            logger.debug('load training img: {}'.format(train))
            
            ## segmentation
            file_seg = config.dir_reg + test + train + 'regseg.hdr'
            seg = io_analyze.load(file_seg)
            
            ## image (for intensity prior)
            file_im = config.dir_reg + test + train + 'reggray.hdr'
            im = io_analyze.load(file_im)
            
            generator.add_training_data(seg,image=im, nrandom=5)
            ntrain += 1

        if not pca:
            from scipy import ndimage
            mask    = generator.get_mask()
            struct  = np.ones((7,)*mask.ndim)
            mask    = ndimage.binary_dilation(
                    mask.astype(bool),
                    structure=struct,
                    ).astype(bool)
         
                 
        prior = generator.get_prior(mask)
        #import ipdb; ipdb.set_trace()

        nlabel = len(labelset)
        segprior = np.zeros(mask.shape)
        segprior.flat[prior['imask']] = labelset[np.argmax(prior['data'],axis=0)]
            
        entropymap = np.zeros(mask.shape)
        entropymap.flat[prior['imask']] = np.sum(
            np.log(prior['data'] + 1e-10)*prior['data'],
            axis=0)
        entropymap = entropymap / np.log(nlabel) * 2**15
        
        if 'eigenvectors' in prior:
            U = prior.pop('eigenvectors')
            print 'size of U {}, dtype={}'.format(U.size, U.dtype)
            np.save(file_U, U)
            prior['eigenvectors'] = U
        np.savez(file_prior,**prior)
        
        io_analyze.save(file_mask, mask.astype(np.int32))
        io_analyze.save(file_segprior, segprior.astype(np.int32))
        #io_analyze.save(file_entropymap, entropymap.astype(np.int32))
        
    mask  = io_analyze.load(file_mask).astype(bool)
    prior = dict(np.load(file_prior))
    if pca:
        U = np.load(file_U)
        prior['eigenvectors'] = U
    return prior, mask
Example #4
0
def load_or_compute_prior_and_mask(test,
                                   force_recompute=False,
                                   pca=False,
                                   fold=None):
    if fold is not None:
        test_name = 'f{}_{}/'.format(fold[0][:2], test)
    else:
        test_name = test
        fold = [test]

    #import ipdb; ipdb.set_trace()
    labelset = np.asarray(config.labelset)
    if pca:
        outdir = config.dir_pca_prior + test_name
    else:
        outdir = config.dir_prior + test_name
    if not os.path.isdir(outdir):
        os.makedirs(outdir)

    ## load mask and prior
    prior = None
    file_mask = outdir + 'mask.hdr'
    file_prior = outdir + 'prior.npz'
    file_U = outdir + 'eigenvectors.npy'
    file_segprior = outdir + 'segprior.hdr'
    file_entropymap = outdir + 'entropymap.hdr'

    if force_recompute or not (os.path.exists(file_prior)
                               and os.path.exists(file_mask)):
        if pca:
            _prior, mask = load_or_compute_prior_and_mask(test, fold=fold)
            generator = rwsegment_pca_prior.PriorGenerator(labelset, mask=mask)
        else:
            generator = rwsegment_prior.PriorGenerator(labelset)

        ntrain = 0
        for train in config.vols:
            if train in fold: continue
            logger.debug('load training img: {}'.format(train))

            ## segmentation
            file_seg = config.dir_reg + test + train + 'regseg.hdr'
            seg = io_analyze.load(file_seg)

            ## image (for intensity prior)
            file_im = config.dir_reg + test + train + 'reggray.hdr'
            im = io_analyze.load(file_im)

            generator.add_training_data(seg, image=im, nrandom=5)
            ntrain += 1

        if not pca:
            from scipy import ndimage
            mask = generator.get_mask()
            struct = np.ones((7, ) * mask.ndim)
            mask = ndimage.binary_dilation(
                mask.astype(bool),
                structure=struct,
            ).astype(bool)

        prior = generator.get_prior(mask)
        #import ipdb; ipdb.set_trace()

        nlabel = len(labelset)
        segprior = np.zeros(mask.shape)
        segprior.flat[prior['imask']] = labelset[np.argmax(prior['data'],
                                                           axis=0)]

        entropymap = np.zeros(mask.shape)
        entropymap.flat[prior['imask']] = np.sum(
            np.log(prior['data'] + 1e-10) * prior['data'], axis=0)
        entropymap = entropymap / np.log(nlabel) * 2**15

        if 'eigenvectors' in prior:
            U = prior.pop('eigenvectors')
            print 'size of U {}, dtype={}'.format(U.size, U.dtype)
            np.save(file_U, U)
            prior['eigenvectors'] = U
        np.savez(file_prior, **prior)

        io_analyze.save(file_mask, mask.astype(np.int32))
        io_analyze.save(file_segprior, segprior.astype(np.int32))
        #io_analyze.save(file_entropymap, entropymap.astype(np.int32))

    mask = io_analyze.load(file_mask).astype(bool)
    prior = dict(np.load(file_prior))
    if pca:
        U = np.load(file_U)
        prior['eigenvectors'] = U
    return prior, mask
Example #5
0
    def process_sample(self, train, test):
        outdir = config.dir_work + 'autoseeds/' + config.basis + '/' + train + '/' + test
        logger.info('saving data in: {}'.format(outdir))
        if not os.path.isdir(outdir):
            os.makedirs(outdir)

        ## get prior
        from scipy import ndimage
        segtrain = io_analyze.load(config.dir_reg + test + train +
                                   '/regseg.hdr')
        segtrain.flat[~np.in1d(segtrain, self.labelset)] = self.labelset[0]
        struct = np.ones((10, ) * segtrain.ndim)
        mask = ndimage.binary_dilation(
            segtrain > 0,
            structure=struct,
        ).astype(bool)

        #prior, mask = load_or_compute_prior_and_mask(
        #    test,force_recompute=self.force_recompute_prior)
        #mask = mask.astype(bool)

        ## load image
        file_name = config.dir_reg + test + 'gray.hdr'
        logger.info('segmenting data: {}'.format(file_name))
        im = io_analyze.load(file_name).astype(float)
        file_gt = config.dir_reg + test + 'seg.hdr'
        seg = io_analyze.load(file_gt)
        seg.flat[~np.in1d(seg, self.labelset)] = self.labelset[0]

        ## normalize image
        nim = im / np.std(im)

        #orient_scores = self.load_or_compute_orientations(train,test, mask=mask)

        if 1:  #not os.path.isfile(outdir + 'points.npy'):

            from rwsegment import boundary_utils
            reload(boundary_utils)
            ## sample points
            points = boundary_utils.sample_points(im, self.step, mask=mask)
            points = points[mask[tuple(points.T)]]
            impoints = np.zeros(im.shape, dtype=int)
            impoints[tuple(points.T)] = np.arange(len(points)) + 1
            ipoints = np.where(impoints.ravel())[0]
            points = np.argwhere(impoints)
            np.save(outdir + 'points.npy', points)
            impoints[tuple(points.T)] = np.arange(len(points)) + 1

            ## set unary potentials from prior: array of unary costs
            nlabel = len(self.labelset)
            dist = self.distance_to_train(segtrain, points)
            T = 10.0
            prob_pts = np.exp(-(dist / T)**2) / np.c_[np.sum(
                np.exp(-(dist / T)**2), axis=1)]
            #prob = np.c_[np.ones(im.size), np.zeros((im.size, nlabel-1))]
            #prob[mask.ravel(),:] = prior['data'].T
            #prob_pts = prob[ipoints,:]
            np.save(outdir + 'prob_points.npy', prob_pts)

            ## binary potentials
            ## compute edges
            edges, edgev, labels = boundary_utils.get_edges(im,
                                                            points,
                                                            mask=mask)
            edges = np.sort(edges, axis=1)
            np.save(outdir + 'edges.npy', edges)

            ## get orientation hist
            orient_scores, hist = self.load_or_compute_orientations(train,
                                                                    test,
                                                                    mask=mask)

            ##classify edges
            vecs = points[edges[:, 1]] - points[edges[:, 0]]
            vecs = vecs / np.c_[np.sqrt(np.sum(vecs**2, axis=1))]
            scores = self.get_orient_scores(vecs)
            prob_orient = np.dot(scores, orient_scores)
            #prob_orient = prob_orient/np.c_[np.sum(prob_orient, axis=1)]
            np.save(outdir + 'prob_orient.npy', prob_orient)
            ''' 
            ## load classifier
            classifier = self.load_or_compute_classifier(train,test, mask=mask)
 
            ## extract profiles
            profiles,emap,dists = boundary_utils.get_profiles(nim, points, edges, rad=0)
   
            ## make features  
            x = boundary_utils.make_features(
                profiles, 
                size=self.sizex, 
                additional=[dists,edgev,edgev/dists],
                )
            
            ## classify
            cl, scores = classifier.classify(x)

            ## ground truth
            z = boundary_utils.is_boundary(points, edges, seg)

            logger.info('non boundary classification: {}%'\
                .format(np.sum((np.r_[z]==0)*(np.r_[cl]==0))/float(np.sum(np.r_[z]==0))*100))
            logger.info('boundary classification: {}%'\
                .format(np.sum((np.r_[z]==1)*(np.r_[cl]==1))/float(np.sum(np.r_[z]==1))*100))
            np.save(outdir + 'classified.npy', cl) 

            ## probabilities
            prob_edges = 1.  - scores/np.c_[np.sum(scores, axis=1)]
      
            ##save probs
            np.save(outdir + 'prob_edges.npy',prob_edges)
            '''
        else:
            points = np.load(outdir + 'points.npy')
            edges = np.load(outdir + 'edges.npy')
            cl = np.load(outdir + 'classified.npy')
            prob_pts = np.load(outdir + 'prob_points.npy')
            #prob_edges = np.load(outdir + 'prob_edges.npy')
            prob_orient = np.load(outdir + 'prob_orient.npy')

        ## make potentials
        unary = -np.log(prob_pts + 1e-10)
        #binary = - np.log(prob_edges + 1e-10)
        #thresh = (prob_orient.shape[1] - 1.0)/prob_orient.shape[1]
        thresh = (len(self.orients) - 1.0) / len(self.orients)
        orient_cost = -np.log(np.clip(prob_orient + thresh, 0, 1) +
                              1e-10) * 100
        orient_cost = np.clip(orient_cost, 0, 1e10)
        #import ipdb; ipdb.set_trace()

        ## solve MRF:
        import ipdb
        ipdb.set_trace()
        '''
        from rwsegment.mrf import fastPD
        class CostFunction(object):
            def __init__(self,**kwargs):
                self.binary = kwargs.pop('binary',0)
                self.orient_indices = kwargs.pop('orient_indices')
                self.orient_cost = kwargs.pop('orient_cost')

            def __call__(self,e,l1,l2):
                idpair = self.orient_indices[l1,l2]
                pair_cost = self.orient_cost[e,idpair]
                cost = (l1!=l2)*pair_cost
                #return (l1!=l2)*(1-cl[e])*0.1
                #return (l1!=l2)*self.binary[e,1]*0.1
                #y = l1!=l2
                #return self.binary[e, y]*pair_cost
                print e, l1, l2, cost
                return cost
 
        #sol, en = fastPD.fastPD_callback(unary, edges, cost_function(binary), debug=True)  
        cost_function = CostFunction(
            #binary=binary,
            orient_indices=self.orient_indices,
            orient_cost=orient_cost,
            )
        sol, en = fastPD.fastPD_callback(unary, edges, cost_function, debug=True)  
        '''
        wpairs = orient_cost
        from rwsegment.mrf import trw
        sol, en = trw.TRW_general(unary,
                                  edges,
                                  wpairs,
                                  niters=1000,
                                  verbose=True)

        labels = self.labelset[sol]
        imsol = np.ones(im.shape, dtype=np.int32) * 20
        imsol[tuple(points.T)] = labels
        io_analyze.save(outdir + 'imseeds.hdr', imsol)

        ## classify sol
        gtlabels = seg[tuple(points.T)]
        priorlabels = self.labelset[np.argmin(unary, axis=1)]

        err_prior = 1 - np.sum(gtlabels == priorlabels) / float(len(points))
        err = 1 - np.sum(gtlabels == labels) / float(len(points))

        logger.info('error in prior sol: {}%'.format(err_prior * 100))
        logger.info('error in sol: {}%'.format(err * 100))

        import ipdb
        ipdb.set_trace()

        ## start segmenting
        sol, y = rwsegment.segment(nim,
                                   seeds=seeds,
                                   labelset=self.labelset,
                                   weight_function=self.weight_function,
                                   **self.params)

        ## compute Dice coefficient per label
        dice = compute_dice_coef(sol, seg, labelset=self.labelset)
        logger.info('Dice: {}'.format(dice))

        if not config.debug:
            io_analyze.save(outdir + 'sol.hdr', sol.astype(np.int32))
            np.savetxt(outdir + 'dice.txt',
                       np.c_[dice.keys(), dice.values()],
                       fmt='%d %.8f')
 def run_svm_inference(self,test,w):
     logger.info('running inference on: {}'.format(test))
     
     outdir = self.dir_inf + test
     if not os.path.isdir(outdir):
         os.makedirs(outdir)
 
     ## segment test image with trained w
     def wwf(im,_w):    
         ''' meta weight function'''
         data = 0
         for iwf,wf in enumerate(self.weight_functions.values()):
             ij,_data = wf(im)
             data += _w[iwf]*_data
         return ij, data
     
     ## load images and ground truth
     file_seg = self.dir_reg + test + 'seg.hdr'
     file_im  = self.dir_reg + test + 'gray.hdr'
     im  = io_analyze.load(file_im)
     seg = io_analyze.load(file_seg)
     seg.flat[~np.in1d(seg.ravel(),self.labelset)] = self.labelset[0]
     
     ## save image
     im = im/np.std(im) # normalize image by variance
 
     ## prior
     anchor_api = BaseAnchorAPI(
         self.prior, 
         anchor_weight=w[-1],
         )
 
     sol,y = rwsegment.segment(
         im, 
         anchor_api, 
         seeds=self.seeds,
         weight_function=lambda im: wwf(im, w),
         **self.rwparams_inf
         )
     
     np.save(outdir + 'y.test.npy',y)        
     io_analyze.save(outdir + 'sol.test.hdr',sol.astype(np.int32))
     
     ## compute Dice coefficient
     dice = compute_dice_coef(sol, seg,labelset=self.labelset)
     np.savetxt(
         outdir + 'dice.test.txt', np.c_[dice.keys(),dice.values()],fmt='%d %.8f')
         
     ## inference compare with gold standard
     dice_gold = np.loadtxt(outdir + 'dice.gold.txt')
     y_gold    = np.load(outdir + 'y.gold.npy')        
     sol_gold  = io_analyze.load(outdir + 'sol.gold.hdr')
     
     np.testing.assert_allclose(
         dice.values(), 
         dict(dice_gold).values(), 
         err_msg='FAIL: dice coef mismatch',
         atol=1e-8)
     np.testing.assert_allclose(y, y_gold,  err_msg='FAIL: y mismatch')
     np.testing.assert_equal(sol, sol_gold, err_msg='FAIL: sol mismatch')
     
     print 'PASS: inference tests'
    def process_sample(self,test,fold=None):

        ## get prior
        prior, mask = load_or_compute_prior_and_mask(
            test,
            fold=fold,
            force_recompute=self.force_recompute_prior)
        seeds   = (-1)*mask
        
        ## load image
        file_name = config.dir_reg + test + 'gray.hdr'        
        logger.info('segmenting data: {}'.format(file_name))
        im      = io_analyze.load(file_name)
        file_gt = config.dir_reg + test + 'seg.hdr'
        seg     = io_analyze.load(file_gt)
        seg.flat[~np.in1d(seg, self.labelset)] = self.labelset[0]
        
           
        ## normalize image
        nim = im/np.std(im)
            
        ## init anchor_api
        anchor_api = MetaAnchor(
            prior=prior,
            prior_models=self.prior_models,
            prior_weights=self.prior_weights,
            image=nim,
            )
           
        ## start segmenting
        #import ipdb; ipdb.set_trace()
        sol,y = rwsegment.segment(
            nim, 
            anchor_api,
            seeds=seeds, 
            labelset=self.labelset, 
            weight_function=self.weight_function,
            **self.params
            )

        ## compute losses
        z = seg.ravel()==np.c_[self.labelset]
        flatmask = mask.ravel()*np.ones((len(self.labelset),1))
        
        ## loss 0 : 1 - Dice(y,z)
        loss0 = loss_functions.ideal_loss(z,y,mask=flatmask)
        logger.info('Tloss = {}'.format(loss0))
        
        ## loss2: squared difference with ztilde
        loss1 = loss_functions.anchor_loss(z,y,mask=flatmask)
        logger.info('SDloss = {}'.format(loss1))
        
        ## loss3: laplacian loss
        loss2 = loss_functions.laplacian_loss(z,y,mask=flatmask)
        logger.info('LAPloss = {}'.format(loss2))
 
        ## loss4: linear loss
        loss3 = loss_functions.linear_loss(z,y,mask=flatmask)
        logger.info('LINloss = {}'.format(loss3))
        
        ## compute Dice coefficient per label
        dice    = compute_dice_coef(sol, seg,labelset=self.labelset)
        logger.info('Dice: {}'.format(dice))
        
        if not config.debug:
            if fold is not None:
                test_name = 'f{}_{}'.format(fold[0][:2], test)
            else:
                test_name = test
            outdir = config.dir_seg + \
                '/{}/{}'.format(self.model_name,test_name)
            logger.info('saving data in: {}'.format(outdir))
            if not os.path.isdir(outdir):
                os.makedirs(outdir)
        
            f = open(outdir + 'losses.txt', 'w')
            f.write('ideal_loss\t{}\n'.format(loss0))
            f.write('anchor_loss\t{}\n'.format(loss1))
            f.write('laplacian_loss\t{}\n'.format(loss2))
            f.close()
            
            io_analyze.save(outdir + 'sol.hdr', sol.astype(np.int32)) 
            np.savetxt(
                outdir + 'dice.txt', np.c_[dice.keys(),dice.values()],fmt='%d %.8f')
    def compute_mean_segmentation(self, list):
        for test in list:
            file_gt = config.dir_reg + test + 'seg.hdr'
            seg     = io_analyze.load(file_gt)
            seg.flat[~np.in1d(seg, self.labelset)] = self.labelset[0]
           

            ## get prior
            prior, mask = load_or_compute_prior_and_mask(
                test,force_recompute=self.force_recompute_prior)
            mask = mask.astype(bool)            
           

            y = np.zeros((len(self.labelset),seg.size))
            y[:,0] = 1
            y.flat[prior['imask']] = prior['data']
 
            sol = np.zeros(seg.shape,dtype=np.int32)
            sol[mask] = self.labelset[np.argmax(prior['data'],axis=0)]

            ## compute losses
            z = seg.ravel()==np.c_[self.labelset]
            flatmask = mask.ravel()*np.ones((len(self.labelset),1))
 
            ## loss 0 : 1 - Dice(y,z)
            loss0 = loss_functions.ideal_loss(z,y,mask=flatmask)
            logger.info('Tloss = {}'.format(loss0))
            
            ## loss2: squared difference with ztilde
            #loss1 = loss_functions.anchor_loss(z,y,mask=flatmask)
            #logger.info('SDloss = {}'.format(loss1))
            
            ## loss3: laplacian loss
            #loss2 = loss_functions.laplacian_loss(z,y,mask=flatmask)
            #logger.info('LAPloss = {}'.format(loss2))
 
            ## loss4: linear loss
            #loss3 = loss_functions.linear_loss(z,y,mask=flatmask)
            #logger.info('LINloss = {}'.format(loss3))
            
            ## compute Dice coefficient per label
            dice    = compute_dice_coef(sol, seg,labelset=self.labelset)
            logger.info('Dice: {}'.format(dice))
            
            if not config.debug:
                outdir = config.dir_seg + \
                    '/{}/{}'.format('mean',test)
                logger.info('saving data in: {}'.format(outdir))
                if not os.path.isdir(outdir):
                    os.makedirs(outdir)
            
                #f = open(outdir + 'losses.txt', 'w')
                #f.write('ideal_loss\t{}\n'.format(loss0))
                #f.write('anchor_loss\t{}\n'.format(loss1))
                #f.write('laplacian_loss\t{}\n'.format(loss2))
                #f.close()
                
                io_analyze.save(outdir + 'sol.hdr', sol.astype(np.int32)) 

                np.savetxt(
                    outdir + 'dice.txt', np.c_[dice.keys(),dice.values()],fmt='%d %.8f')
Example #9
0
    def process_sample(self,train, test):
        outdir = config.dir_work + 'autoseeds/' + config.basis + '/' + train + '/' + test
        logger.info('saving data in: {}'.format(outdir))
        if not os.path.isdir(outdir):
            os.makedirs(outdir)
        
        ## get prior
        from scipy import ndimage
        segtrain = io_analyze.load(config.dir_reg + test + train + '/regseg.hdr')
        segtrain.flat[~np.in1d(segtrain, self.labelset)] = self.labelset[0]
        struct  = np.ones((10,)*segtrain.ndim)
        mask    = ndimage.binary_dilation(
                segtrain>0,
                structure=struct,
                ).astype(bool)
 
        #prior, mask = load_or_compute_prior_and_mask(
        #    test,force_recompute=self.force_recompute_prior)
        #mask = mask.astype(bool)

        ## load image
        file_name = config.dir_reg + test + 'gray.hdr'        
        logger.info('segmenting data: {}'.format(file_name))
        im      = io_analyze.load(file_name).astype(float)
        file_gt = config.dir_reg + test + 'seg.hdr'
        seg     = io_analyze.load(file_gt)
        seg.flat[~np.in1d(seg, self.labelset)] = self.labelset[0]
        
           
        ## normalize image
        nim = im/np.std(im)
     

        #orient_scores = self.load_or_compute_orientations(train,test, mask=mask)
 
        if 1:#not os.path.isfile(outdir + 'points.npy'):
  
            from rwsegment import boundary_utils
            reload(boundary_utils)
            ## sample points
            points = boundary_utils.sample_points(im, self.step,  mask=mask)
            points = points[mask[tuple(points.T)]]
            impoints = np.zeros(im.shape,dtype=int)
            impoints[tuple(points.T)] = np.arange(len(points)) + 1
            ipoints = np.where(impoints.ravel())[0]
            points = np.argwhere(impoints) 
            np.save(outdir + 'points.npy', points)
            impoints[tuple(points.T)] = np.arange(len(points)) + 1

            ## set unary potentials from prior: array of unary costs
            nlabel = len(self.labelset)
            dist = self.distance_to_train(segtrain, points)
            T = 10.0
            prob_pts = np.exp(-(dist/T)**2) / np.c_[np.sum(np.exp(-(dist/T)**2),axis=1)]
            #prob = np.c_[np.ones(im.size), np.zeros((im.size, nlabel-1))]
            #prob[mask.ravel(),:] = prior['data'].T
            #prob_pts = prob[ipoints,:]
            np.save(outdir + 'prob_points.npy', prob_pts) 
    
            ## binary potentials
            ## compute edges
            edges,edgev,labels = boundary_utils.get_edges(im, points,  mask=mask)
            edges = np.sort(edges,axis=1)
            np.save(outdir + 'edges.npy', edges)

            ## get orientation hist
            orient_scores,hist = self.load_or_compute_orientations(train,test, mask=mask)

            ##classify edges
            vecs = points[edges[:,1]] - points[edges[:,0]]
            vecs = vecs / np.c_[np.sqrt(np.sum(vecs**2,axis=1))] 
            scores = self.get_orient_scores(vecs)
            prob_orient = np.dot(scores, orient_scores)
            #prob_orient = prob_orient/np.c_[np.sum(prob_orient, axis=1)]
            np.save(outdir + 'prob_orient.npy', prob_orient) 

            ''' 
            ## load classifier
            classifier = self.load_or_compute_classifier(train,test, mask=mask)
 
            ## extract profiles
            profiles,emap,dists = boundary_utils.get_profiles(nim, points, edges, rad=0)
   
            ## make features  
            x = boundary_utils.make_features(
                profiles, 
                size=self.sizex, 
                additional=[dists,edgev,edgev/dists],
                )
            
            ## classify
            cl, scores = classifier.classify(x)

            ## ground truth
            z = boundary_utils.is_boundary(points, edges, seg)

            logger.info('non boundary classification: {}%'\
                .format(np.sum((np.r_[z]==0)*(np.r_[cl]==0))/float(np.sum(np.r_[z]==0))*100))
            logger.info('boundary classification: {}%'\
                .format(np.sum((np.r_[z]==1)*(np.r_[cl]==1))/float(np.sum(np.r_[z]==1))*100))
            np.save(outdir + 'classified.npy', cl) 

            ## probabilities
            prob_edges = 1.  - scores/np.c_[np.sum(scores, axis=1)]
      
            ##save probs
            np.save(outdir + 'prob_edges.npy',prob_edges)
            '''
        else:
            points     = np.load(outdir + 'points.npy')
            edges      = np.load(outdir + 'edges.npy')
            cl         = np.load(outdir + 'classified.npy') 
            prob_pts   = np.load(outdir + 'prob_points.npy')
            #prob_edges = np.load(outdir + 'prob_edges.npy')
            prob_orient = np.load(outdir + 'prob_orient.npy') 

        ## make potentials
        unary  = - np.log(prob_pts + 1e-10)
        #binary = - np.log(prob_edges + 1e-10)
        #thresh = (prob_orient.shape[1] - 1.0)/prob_orient.shape[1]
        thresh = (len(self.orients) - 1.0) / len(self.orients)
        orient_cost = - np.log(np.clip(prob_orient + thresh,0,1) + 1e-10)*100
        orient_cost = np.clip(orient_cost, 0, 1e10)
        #import ipdb; ipdb.set_trace()

        ## solve MRF:
        import ipdb; ipdb.set_trace()
        '''
        from rwsegment.mrf import fastPD
        class CostFunction(object):
            def __init__(self,**kwargs):
                self.binary = kwargs.pop('binary',0)
                self.orient_indices = kwargs.pop('orient_indices')
                self.orient_cost = kwargs.pop('orient_cost')

            def __call__(self,e,l1,l2):
                idpair = self.orient_indices[l1,l2]
                pair_cost = self.orient_cost[e,idpair]
                cost = (l1!=l2)*pair_cost
                #return (l1!=l2)*(1-cl[e])*0.1
                #return (l1!=l2)*self.binary[e,1]*0.1
                #y = l1!=l2
                #return self.binary[e, y]*pair_cost
                print e, l1, l2, cost
                return cost
 
        #sol, en = fastPD.fastPD_callback(unary, edges, cost_function(binary), debug=True)  
        cost_function = CostFunction(
            #binary=binary,
            orient_indices=self.orient_indices,
            orient_cost=orient_cost,
            )
        sol, en = fastPD.fastPD_callback(unary, edges, cost_function, debug=True)  
        '''
        wpairs = orient_cost
        from rwsegment.mrf import trw
        sol, en = trw.TRW_general(
            unary, edges, wpairs, niters=1000, verbose=True)

        labels = self.labelset[sol]
        imsol = np.ones(im.shape, dtype=np.int32)*20
        imsol[tuple(points.T)] = labels
        io_analyze.save(outdir + 'imseeds.hdr', imsol)

        ## classify sol
        gtlabels    = seg[tuple(points.T)]
        priorlabels = self.labelset[np.argmin(unary,axis=1)]

        err_prior = 1 - np.sum(gtlabels==priorlabels)/float(len(points))
        err       = 1 - np.sum(gtlabels==labels)/float(len(points))

        logger.info('error in prior sol: {}%'.format(err_prior*100))
        logger.info('error in sol: {}%'.format(err*100))

        import ipdb; ipdb.set_trace()

        ## start segmenting
        sol,y = rwsegment.segment(
            nim, 
            seeds=seeds, 
            labelset=self.labelset, 
            weight_function=self.weight_function,
            **self.params
            )

       
        ## compute Dice coefficient per label
        dice    = compute_dice_coef(sol, seg,labelset=self.labelset)
        logger.info('Dice: {}'.format(dice))
        
        if not config.debug:
            io_analyze.save(outdir + 'sol.hdr', sol.astype(np.int32))
            np.savetxt(
                outdir + 'dice.txt', np.c_[dice.keys(),dice.values()],fmt='%d %.8f')