Python numpy.argmax() Examples

def _cascade_evaluation(self, X_test, y_test):
        """ Evaluate the accuracy of the cascade using X and y.

        :param X_test: np.array
            Array containing the test input samples.
            Must be of the same shape as training data.

        :param y_test: np.array
            Test target values.

        :return: float
            the cascade accuracy.
        """
        casc_pred_prob = np.mean(self.cascade_forest(X_test), axis=0)
        casc_pred = np.argmax(casc_pred_prob, axis=1)
        casc_accuracy = accuracy_score(y_true=y_test, y_pred=casc_pred)
        print('Layer validation accuracy = {}'.format(casc_accuracy))

        return casc_accuracy 

def add(self, outputs, targets):
        outputs = to_numpy(outputs)
        targets = to_numpy(targets)

        if np.ndim(targets) == 2:
            targets = np.argmax(targets, 1)

        assert np.ndim(outputs) == 2, 'wrong output size (2D expected)'
        assert np.ndim(targets) == 1, 'wrong target size (1D or 2D expected)'
        assert targets.shape[0] == outputs.shape[0], 'number of outputs and targets do not match'

        top_k = self.top_k
        max_k = int(top_k[-1])

        predict = torch.from_numpy(outputs).topk(max_k, 1, True, True)[1].numpy()
        correct = (predict == targets[:, np.newaxis].repeat(predict.shape[1], 1))

        self.size += targets.shape[0]
        for k in top_k:
            self.corrects[k] += correct[:, :k].sum() 

def generate(self, src, sampled=False):
        dynet.renew_cg()

        embedding = self.embed_seq(src)
        encoding = self.encode_seq(embedding)[-1]

        w = dynet.parameter(self.decoder_w)
        b = dynet.parameter(self.decoder_b)

        s = self.dec_lstm.initial_state().add_input(encoding)

        out = []
        for _ in range(5*len(src)):
            out_vector = dynet.affine_transform([b, w, s.output()])
            probs = dynet.softmax(out_vector)
            selection = np.argmax(probs.value())
            out.append(self.tgt_vocab[selection])
            if out[-1].s == self.tgt_vocab.END_TOK: break
            embed_vector = self.tgt_lookup[selection]
            s = s.add_input(embed_vector)
        return out 

def gen_sent_on_topic(idxvocab, vocabxid, start_symbol, end_symbol, cf):
    output = codecs.open(args.gen_sent_on_topic, "w", "utf-8")
    topics, entropy = tm.get_topics(sess, topn=topn)
    with tf.variable_scope("model", reuse=True, initializer=initializer):
        mgen = LM(is_training=False, vocab_size=len(idxvocab), batch_size=1, num_steps=1, config=cf, \
            reuse_conv_variables=True)

    for t in range(cf.topic_number):
        output.write("\n" + "="*100 + "\n")
        output.write("Topic " +  str(t) + ":\n")
        output.write(" ".join([ idxvocab[item] for item in topics[t] ]) + "\n\n")

        output.write("\nSentence generation (greedy; argmax):" + "\n")
        s = mgen.generate_on_topic(sess, t, vocabxid[start_symbol], 0, cf.lm_sent_len+10, vocabxid[end_symbol])
        output.write("[0] " + " ".join([ idxvocab[item] for item in s ]) + "\n")
        
        for temp in gen_temps:
            output.write("\nSentence generation (random; temperature = " + str(temp) + "):\n")
            for i in xrange(gen_num):
                s = mgen.generate_on_topic(sess, t, vocabxid[start_symbol], temp, cf.lm_sent_len+10, \
                    vocabxid[end_symbol])
                output.write("[" + str(i) + "] " +  " ".join([ idxvocab[item] for item in s ]) + "\n") 

def write_predictions(self, inputs):
        '''
        Outputs predictions in a file named <model_name_prefix>.predictions.
        '''
        predictions = numpy.argmax(self.model.predict(inputs), axis=1)
        test_output_file = open("%s.predictions" % self.model_name_prefix, "w")
        for input_indices, prediction in zip(inputs, predictions):
            # The predictions are indices of words in padded sentences. We need to readjust them.
            padding_length = 0
            for index in input_indices:
                if numpy.all(index == 0):
                    padding_length += 1
                else:
                    break
            prediction = prediction - padding_length + 1  # +1 because the indices start at 1.
            print >>test_output_file, prediction 

def _infer_multiplets_from_observed(n_obs_multiplets, n_cells0, n_cells1):
        """ Given a number of observed multiplets and cell counts for two transcriptomes,
        infer the total number of multiplets (observed + unobserved) """

        if n_cells0 == 0 or n_cells1 == 0:
            return 0

        # Prior probability of a doublet given counts for each cell type (ignore N_cells > 2)
        p_obs_multiplet = 2*(float(n_cells0)/float(n_cells0+n_cells1))*(float(n_cells1)/float(n_cells0+n_cells1))

        # Brute force MLE of binomial n
        n_mle = 0
        if n_obs_multiplets > 0:
            likelihood = scipy.stats.binom.pmf(n_obs_multiplets, xrange(0, n_cells0 + n_cells1), p_obs_multiplet)
            n_mle = np.argmax(likelihood)
        return n_mle 

def has_tomatoes(self, im_path):
        # load the image
        im = Image.open(im_path)
        im = np.asarray(im, dtype=np.float32)
        im = self.prepare_image(im)

        # launch an inference with the image
        pred = self.sess.run(
            self.output_logits, feed_dict={
                self.img_feed: im.eval(
                    session=self.sess)})

        if np.argmax(pred) == 0:
            print("NOT a tomato ! (confidence : ", pred[0, 0], "%)")
        else:
            print("We have a tomato ! (confidence : ", pred[0, 1], "%)") 

def play(self, nb_rounds):
        img_saver = save_image()
        img_saver.next()

        game_cnt = it.count(1)
        for i in xrange(nb_rounds):
            game = self.game(width=self.width, height=self.height)
            screen, _ = game.next()
            img_saver.send(screen)
            frame_cnt = it.count()
            try:
                state = np.asarray([screen] * self.nb_frames)
                while True:
                    frame_cnt.next()
                    act_idx = np.argmax(
                        self.model.predict(state[np.newaxis]), axis=-1)[0]
                    screen, _ = game.send(self.actions[act_idx])
                    state = np.roll(state, 1, axis=0)
                    state[0] = screen
                    img_saver.send(screen)
            except StopIteration:
                print 'Saved %4i frames for game %3i' % (
                    frame_cnt.next(), game_cnt.next())
        img_saver.close() 

def test(self, input_path, output_path):
        if not self.load()[0]:
            raise Exception("No model is found, please train first")
            
        mean, std = self.sess.run([self.mean, self.std])
        
        images = np.empty((1, self.im_size[0], self.im_size[1], self.im_size[2], 1), dtype=np.float32)
        #labels = np.empty((1, self.im_size[0], self.im_size[1], self.im_size[2], self.nclass), dtype=np.float32)
        for f in input_path:
            images[0, ..., 0], read_info = read_testing_inputs(f, self.roi[0], self.im_size, output_path)
            probs = self.sess.run(self.probs, feed_dict = { self.images: (images - mean) / std,
                                                            self.is_training: True,
                                                            self.keep_prob: 1 })
            #print(self.roi[1] + os.path.basename(f) + ":" + str(dice))
            output_file = os.path.join(output_path, self.roi[1] + '_' + os.path.basename(f))
            f_h5 = h5py.File(output_file, 'w')
            if self.roi[0] < 0:
                f_h5['predictions'] = restore_labels(np.argmax(probs[0], 3), self.roi[0], read_info)
            else:
                f_h5['probs'] = restore_labels(probs[0, ..., 1], self.roi[0], read_info)
            f_h5.close() 

def __init__(self, channels=3, n_class=2, cost="cross_entropy", cost_kwargs={}, **kwargs):
        tf.reset_default_graph()
        
        self.n_class = n_class
        self.summaries = kwargs.get("summaries", True)
        
        self.x = tf.placeholder("float", shape=[None, None, None, channels])
        self.y = tf.placeholder("float", shape=[None, None, None, n_class])
        self.keep_prob = tf.placeholder(tf.float32) #dropout (keep probability)
        
        logits, self.variables, self.offset = create_conv_net(self.x, self.keep_prob, channels, n_class, **kwargs)
        
        self.cost = self._get_cost(logits, cost, cost_kwargs)
        
        self.gradients_node = tf.gradients(self.cost, self.variables)
         
        self.cross_entropy = tf.reduce_mean(cross_entropy(tf.reshape(self.y, [-1, n_class]),
                                                          tf.reshape(pixel_wise_softmax_2(logits), [-1, n_class])))
        
        self.predicter = pixel_wise_softmax_2(logits)
        self.correct_pred = tf.equal(tf.argmax(self.predicter, 3), tf.argmax(self.y, 3))
        self.accuracy = tf.reduce_mean(tf.cast(self.correct_pred, tf.float32)) 

def validate(model):
    dice_coefs = []
    for image_path, label_path in zip(df_val["image"], df_val["label"]):
        image = load_nifti(image_path)
        label = load_nifti(label_path)
        centers = [[], [], []]
        for img_len, len_out, center, n_tile in zip(image.shape, args.output_shape, centers, args.n_tiles):
            assert img_len < len_out * n_tile, "{} must be smaller than {} x {}".format(img_len, len_out, n_tile)
            stride = int((img_len - len_out) / (n_tile - 1))
            center.append(len_out / 2)
            for i in range(n_tile - 2):
                center.append(center[-1] + stride)
            center.append(img_len - len_out / 2)
        output = np.zeros((dataset["n_classes"],) + image.shape[:-1])
        for x, y, z in itertools.product(*centers):
            patch = crop_patch(image, [x, y, z], args.input_shape)
            patch = np.expand_dims(patch, 0)
            patch = xp.asarray(patch)
            slices_out = [slice(center - len_out / 2, center + len_out / 2) for len_out, center in zip(args.output_shape, [x, y, z])]
            slices_in = [slice((len_in - len_out) / 2, len_in - (len_in - len_out) / 2) for len_out, len_in, in zip(args.output_shape, args.input_shape)]
            output[slice(None), slices_out[0], slices_out[1], slices_out[2]] += chainer.cuda.to_cpu(model(patch).data[0, slice(None), slices_in[0], slices_in[1], slices_in[2]])
        y = np.argmax(output, axis=0).astype(np.int32)
        dice_coefs.append(dice_coefficients(y, label, labels=range(dataset["n_classes"])))
    dice_coefs = np.array(dice_coefs)
    return np.mean(dice_coefs, axis=0) 

def correct_for_multipol(pol):
    """
    Inputs are:
        pol, Suspected Multipolygon
    Takes the main polygon of a multipolygon.

    Typically used to solve the problem of non-overlapping polygons being substracted.

    """
    pol_type = pol.geom_type
    if pol_type == 'MultiPolygon':
        area = np.zeros(len(pol.geoms))
        for k, p in enumerate(pol.geoms):
            area[k] = p.area
        max_area_id = np.argmax(area)
        pol = pol.geoms[max_area_id]
    return pol 

def eval(flags):
    name = flags.pred_path
    yp = pd.read_csv(name)
    classes = len([i for i in yp.columns.values if 'class' in i])
    yp = yp[['class%d'%i for i in range(1,classes+1)]].values
    myDB = personalDB(flags,name="full")
    if "stage1" in name:
        y=myDB.data['test_variants_filter']['Class']-1
    else:
        myDB.get_split()
        va = myDB.split[flags.fold][1]
        y = np.argmax(myDB.y[va],axis=1)
    if np.max(y)>classes:
        y = np.argmax(to4c(onehot_encode(y)),axis=1)
    score = cross_entropy(y,yp)
    print(name,score,'\n') 

def eval(name,clip=False,bar=0.9):
    base = pd.read_csv('../input/stage1_solution_filtered.csv')
    base['Class'] = np.argmax(base[['class%d'%i for i in range(1,10)]].values,axis=1)
    sub = pd.read_csv(name)
    #sub = pd.merge(sub,base[['ID','Class']],on="ID",how='right')
    #print(sub.head())
    y = base['Class'].values
    yp = sub[['class%d'%i for i in range(1,10)]].values
    if clip:
        yp = np.clip(yp,(1.0-bar)/8,bar)
        yp = yp/np.sum(yp,axis=1).reshape([yp.shape[0],1])
    print(name,cross_entropy(y,yp),multiclass_log_loss(y,yp))
    for i in range(9):
        y1 = y[y==i]
        yp1 = yp[y==i]
        print(i,y1.shape,cross_entropy(y1,yp1),multiclass_log_loss(y1,yp1)) 

def post(self):
        if self.flags.task == "test_cnn_stage1":
            docs = self.DB.clean_doc['test_text_filter']
        elif self.flags.task == "test_cnn_stage2":
            docs = self.DB.clean_doc['stage2_test_text']
        else:
            self.mDB.get_split()
            docs = self.mDB.split[self.flags.fold][1]
        nrows = len(docs)
        p = np.zeros([nrows,9])
        for i in range(self.flags.epochs):
            if i==0:
                skiprows=None
            else:
                skiprows = nrows*i
            p = p + (pd.read_csv(self.flags.pred_path,header=None,nrows=nrows,skiprows=skiprows).values)
        p = p/self.flags.epochs
        if '_cv' in self.flags.task:
            from utils.np_utils.utils import cross_entropy
            y = np.argmax(self.mDB.y,axis=1)
            print("cross entropy", cross_entropy(y[self.mDB.split[self.flags.fold][1]],p))
        s = pd.DataFrame(p,columns=['class%d'%i for i in range(1,10)])
        s['ID'] = np.arange(nrows)+1
        s.to_csv(self.flags.pred_path.replace(".csv","_sub.csv"),index=False,float_format="%.5f") 

def cv(flags):
    X,y,Xt,yt,idx = build_feature(flags)
    
    params['verbose_eval'] = 10
    
    if '4c' in flags.task:
        y = np.argmax(to4c(onehot_encode(y)),axis=1)
        yt = np.argmax(to4c(onehot_encode(yt)),axis=1)
    params['num_class'] = np.max(y)+1
    model = xgb_model(params)
    print(X.shape,Xt.shape,y.shape,yt.shape)
    model.fit(X,y,Xt,yt,print_fscore=False)   
    yp = model.predict(Xt)
    s = pd.DataFrame(yp,columns=['class%d'%i for i in range(1,yp.shape[1]+1)])
    s['real'] = np.array(yt)
    s['ID'] = idx
    path = flags.data_path
    fold = flags.fold
    s.to_csv('%s/cv_%d.csv'%(path,fold),index=False)
    from utils.np_utils.utils import cross_entropy
    print(cross_entropy(yt,yp)) 

def sub(flags):
    X,y,Xt,_,_ = build_feature(flags)
    if '4c' in flags.task:
        y = np.argmax(to4c(onehot_encode(y)),axis=1)
    print(X.shape,Xt.shape,y.shape)
    params['num_class'] = np.max(y)+1
    params['num_round'] = 90 
    params["early_stopping_rounds"] = None
    params['verbose_eval'] = 100
    yp = np.zeros([Xt.shape[0],9])
    m = 5 if 'bag' in flags.task else 1
    for i in range(m):
        params['seed'] = i*9
        model = xgb_model(params)
        model.fit(X,y,print_fscore=False)
        tmp = model.predict(Xt)
        print(i,np.mean(tmp))
        yp += tmp
    yp/=m
    s = pd.DataFrame(yp,columns=["class%d"%i for i in range(1,yp.shape[1]+1)])
    s['ID'] = 1+np.arange(yp.shape[0])
    s.to_csv(flags.pred_path,index=False) 

def label_test_file(self):
    outfile = open("pred_vld.txt","w")
    prep_alfa = lambda X: pad_sequences(sequences=self.indexer.texts_to_sequences(X),
                                        maxlen=self.SentMaxLen)
    vld = json.loads(open('validation.json', 'r').read())
    for prem, hypo, label in zip(vld[0], vld[1], vld[2]):
      prem_pad, hypo_pad = prep_alfa([prem]), prep_alfa([hypo])
      ans = np.reshape(self.model.predict(x=[prem_pad, hypo_pad], batch_size = 1), -1)  # PREDICTION
      if np.argmax(ans) != label:
        outfile.write(prem + "\n" + hypo + "\n")
        outfile.write("Truth: " + self.rLabels[label] + "\n")
        outfile.write('Contradiction \t{:.1f}%\n'.format(float(ans[0]) * 100) +
                      'Neutral \t\t{:.1f}%\n'.format(float(ans[1]) * 100) +
                      'Entailment \t{:.1f}%\n'.format(float(ans[2]) * 100))
        outfile.write("-"*15 + "\n")
    outfile.close() 

def print_result(input,model,i2wi,maxlen_input):
    ans_partial = np.zeros((1,maxlen_input))
    ans_partial[0, 0] = BOS  #  the index of the symbol BOS (begin of sentence)
    for k in range(maxlen_input - 1):
        ye = model.predict([input, ans_partial])
        mp = np.argmax(ye)
        #print(mp,ans_partial)
        #ans_partial[0, 0:-1] = ans_partial[0, 1:]
        ans_partial[0, k+1] = mp
    text = []
    for k in ans_partial[0]:
        k = k.astype(int)
        w = i2w[k]
        text.append(w)
    return(" ".join(text))

# Función principal (interfaz con línea de comandos) 

def print_result(input,model,i2wi,maxlen_input):
    ans_partial = np.zeros((1,maxlen_input))
    ans_partial[0, 0] = BOS  #  the index of the symbol BOS (begin of sentence)
    for k in range(maxlen_input - 1):
        ye = model.predict([input, ans_partial])
        mp = np.argmax(ye)
        #print(mp,ans_partial)
        #ans_partial[0, 0:-1] = ans_partial[0, 1:]
        ans_partial[0, k+1] = mp
    text = []
    for k in ans_partial[0]:
        k = k.astype(int)
        w = i2w[k]
        text.append(w)
    return(" ".join(text))

# Función principal (interfaz con línea de comandos) 

def fit(self,X,verbose=False):
        ss =[]
        labels_list = []
        for i in xrange(self.n_repeat):
            od = self._create_detector(*self.ad_parms0, **self.ad_parms1)
            labels = self._train_clf(od, X, self.n_clusters,verbose=verbose)

            ss += [od.loglikelihood(X,labels)]

            labels_list += [labels]

        #print ss, labels

        self._detector_fit(X, np.array(labels_list[np.argmax(ss)]))

        self.clf_ = SklearnClassifier.clf(self)

        return self 

def sample(self, sess, chars, vocab, num, prime, temperature):
        state = self.cell.zero_state(1, tf.float32).eval()
        for char in prime[:-1]:
            x = np.zeros((1, 1))
            x[0, 0] = vocab[char]
            feed = {self.input_data: x, self.initial_state: state}
            [state] = sess.run([self.final_state], feed)

        def weighted_pick(a):
            a = a.astype(np.float64)
            a = a.clip(min=1e-20)
            a = np.log(a) / temperature
            a = np.exp(a) / (np.sum(np.exp(a)))
            return np.argmax(np.random.multinomial(1, a, 1))

        char = prime[-1]
        for n in range(num):
            x = np.zeros((1, 1))
            x[0, 0] = vocab[char]
            feed = {self.input_data: x, self.initial_state: state}
            [probs, state] = sess.run([self.probs, self.final_state], feed)
            p = probs[0]
            sample = weighted_pick(p)
            char = chars[sample]
            yield char 

def reset(self):
        """ Resets the state of the generator"""
        self.step = 0
        Y = np.argmax(self.Y,1)
        labels = np.unique(Y)
        idx = []
        smallest = len(Y)
        for i,label in enumerate(labels):
            where = np.where(Y==label)[0]
            if smallest > len(where): 
                self.slabel = i
                smallest = len(where)
            idx.append(where)
        self.idx = idx
        self.labels = labels
        self.n_per_class = int(self.batch_size // len(labels))
        self.n_batches = int(np.ceil((smallest//self.n_per_class)))+1
        self.update_probabilities() 

def __init__(self, X, Y, batch_size,cropsize=0, truncate=False, sequential=False,
                 random=True, val=False, class_weights=None):
        
        assert len(X) == len(Y), 'X and Y must be the same length {}!={}'.format(len(X),len(Y))
        if sequential: print('Using sequential mode')
        print ('starting normal generator')
        self.X = X
        self.Y = Y
        self.rnd_idx = np.arange(len(Y))
        self.Y_last_epoch = []
        self.val = val
        self.step = 0
        self.i = 0
        self.cropsize=cropsize
        self.truncate = truncate
        self.random = False if sequential or val else random
        self.batch_size = int(batch_size)
        self.sequential = sequential
        self.c_weights = class_weights if class_weights else dict(zip(np.unique(np.argmax(Y,1)),np.ones(len(np.argmax(Y,1)))))
        assert set(np.argmax(Y,1)) == set([int(x) for x in self.c_weights.keys()]), 'not all labels in class weights'
        self.n_batches = int(len(X)//batch_size if truncate else np.ceil(len(X)/batch_size))
        if self.random: self.randomize() 

def next_normal(self):
        x_batch = self.X[self.step*self.batch_size:(self.step+1)*self.batch_size]
        y_batch = self.Y[self.step*self.batch_size:(self.step+1)*self.batch_size]
        
        diff = len(x_batch[0]) - self.cropsize
        if self.cropsize!=0 and not self.val:
            start = np.random.choice(np.arange(0,diff+5,5), len(x_batch))
            x_batch = [x[start[i]:start[i]+self.cropsize,:] for i,x in enumerate(x_batch)]
        elif self.cropsize !=0 and self.val:
            x_batch = [x[diff//2:diff//2+self.cropsize] for i,x in enumerate(x_batch)]
            
        x_batch = np.array(x_batch, dtype=np.float32)
        y_batch = np.array(y_batch, dtype=np.int32)
        self.step+=1
        if self.val:
            self.Y_last_epoch.extend(y_batch)
            return x_batch # for validation generator, save the new y_labels
        else:
            weights = np.ones(len(y_batch))
            for t in np.unique(np.argmax(y_batch,1)):
                weights[np.argmax(y_batch,1)==t] = self.c_weights[t]
            return (x_batch,y_batch) 

def get_batch_idx(self, idx, **kwargs):
        if self.mode == 'train':
            new_idx = []
            # self.log.info('Label IDX: {}'.format(idx))
            if self.stats_provider is None:
                label_ids = [ii % self._real_size for ii in idx]
            else:
                # print idx, self.stats_provider.get_size()
                stats_batch = self.stats_provider.get_batch_idx(idx)
                label_ids = []
                for ii in xrange(len(idx)):
                    label_ids.append(np.argmax(stats_batch['y_gt'][ii]))

            for ii in label_ids:
                data_group = self.data_provider.label_idx[ii]
                num_ids = len(data_group)
                kk = int(np.floor(self.rnd.uniform(0, num_ids)))
                new_idx.append(data_group[kk])
        else:
            new_idx = idx
        return self.data_provider.get_batch_idx(new_idx) 

def listen(self, results):
        score_out = results['score_out']
        y_gt = results['y_gt']
        sort_idx = np.argsort(score_out, axis=-1)
        idx_gt = np.argmax(y_gt, axis=-1)
        correct = 0
        count = 0
        for kk, ii in enumerate(idx_gt):
            sort_idx_ = sort_idx[kk][::-1]
            for jj in sort_idx_[:self.top_k]:
                if ii == jj:
                    correct += 1
                    break
            count += 1
        # self.log.info('Correct {}/{}'.format(correct, count))
        self.correct += correct
        self.count += count
        self.step = int(results['step'])
        # self.log.info('Step {}'.format(self.step))
        pass 

def viterbi_decode(score, transition_params):
  """ Adapted from Tensorflow implementation.
  Decode the highest scoring sequence of tags outside of TensorFlow.
  This should only be used at test time.
  Args:
    score: A [seq_len, num_tags] matrix of unary potentials.
    transition_params: A [num_tags, num_tags] matrix of binary potentials.
  Returns:
    viterbi: A [seq_len] list of integers containing the highest scoring tag
        indicies.
    viterbi_score: A float containing the score for the Viterbi sequence.
  """
  trellis = numpy.zeros_like(score)
  backpointers = numpy.zeros_like(score, dtype=numpy.int32)
  trellis[0] = score[0]
  for t in range(1, score.shape[0]):
    v = numpy.expand_dims(trellis[t - 1], 1) + transition_params
    trellis[t] = score[t] + numpy.max(v, 0)
    backpointers[t] = numpy.argmax(v, 0)
  viterbi = [numpy.argmax(trellis[-1])]
  for bp in reversed(backpointers[1:]):
    viterbi.append(bp[viterbi[-1]])
  viterbi.reverse()
  viterbi_score = numpy.max(trellis[-1])
  return viterbi, viterbi_score 

def __init__(
        self,
        normalization_parameters,
        parameters,
    ):
        self._quantile_states = collections.deque(
            maxlen=parameters.action_budget.window_size
        )
        self._quantile = 100 - parameters.action_budget.action_limit
        self.quantile_value = 0
        self._limited_action = np.argmax(
            np.array(parameters.actions) ==
            parameters.action_budget.limited_action
        )
        self._discount_factor = parameters.rl.gamma
        self._quantile_update_rate = \
            parameters.action_budget.quantile_update_rate
        self._quantile_update_frequency = \
            parameters.action_budget.quantile_update_frequency
        self._update_counter = 0
        super(self.__class__,
              self).__init__(normalization_parameters, parameters)
        self._max_q = parameters.rl.maxq_learning 

def _build_policy(env, predictor, epsilon):
    eye = np.eye(env.num_states)
    q_values = predictor.predict(
        {str(i): eye[i]
         for i in range(env.num_states)}
    )
    policy_vector = [
        env.ACTIONS[np.argmax([q_values[action][i] for action in env.ACTIONS])]
        for i in range(env.num_states)
    ]

    def policy(state) -> str:
        if np.random.random() < epsilon:
            return np.random.choice(env.ACTIONS)
        else:
            return policy_vector[state]

    return policy 

def choose_action(d, c, q_table):

    global epsilon
    state_actions = q_table[d][c][:]

    # random move or no data recorded for this state yet
    if (np.random.uniform() < epsilon) or (np.sum(state_actions) == 0):
        
        action_chose = np.random.randint(n_actions)
    
        # decrease random moves over time to a minimum of 10%
        if epsilon >  0.1:
            epsilon *= 0.9
        
    else:
        action_chose = state_actions.argmax()
    
    return action_chose 

def choose_action(d, c, q_table):

    global epsilon
    state_actions = q_table[d][c][:]

    # random move or no data recorded for this state yet
    if (np.random.uniform() < epsilon) or (np.sum(state_actions) == 0):
        
        action_chose = np.random.randint(n_actions)
    
        # decrease random moves over time to a minimum of 10%
        if epsilon >  0.1: epsilon *= 0.9
    
    else:
        action_chose = state_actions.argmax()
    
    return action_chose 

def get_predicted_antecedents(self, antecedents, antecedent_scores):
        """
        Forms a list of predicted antecedent labels
        Args:
            antecedents: [] get from C++ function
            antecedent_scores: [num_mentions, max_ant + 1] output of fully-connected network
                that compute antecedent_scores

        Returns: a list of predicted antecedent labels

        """
        predicted_antecedents = []
        for i, index in enumerate(np.argmax(antecedent_scores, axis=1) - 1):
            if index < 0:
                predicted_antecedents.append(-1)
            else:
                predicted_antecedents.append(antecedents[i, index])
        return predicted_antecedents 

def adjust_prediction(self, probability, image):
        crf = dcrf.DenseCRF(np.prod(probability.shape), 2)
        # crf = dcrf.DenseCRF(np.prod(probability.shape), 1)

        binary_prob = np.stack((1 - probability, probability), axis=0)
        unary = unary_from_softmax(binary_prob)
        # unary = unary_from_softmax(np.expand_dims(probability, axis=0))
        crf.setUnaryEnergy(unary)

        # per dimension scale factors
        sdims = [self.sdims] * 3
        smooth = create_pairwise_gaussian(sdims=sdims, shape=probability.shape)
        crf.addPairwiseEnergy(smooth, compat=2)

        if self.schan:
            # per channel scale factors
            schan = [self.schan] * 6
            appearance = create_pairwise_bilateral(sdims=sdims, schan=schan, img=image, chdim=3)
            crf.addPairwiseEnergy(appearance, compat=2)

        result = crf.inference(self.iter)
        crf_prediction = np.argmax(result, axis=0).reshape(probability.shape).astype(np.float32)

        return crf_prediction 

def evaluate_performance(ladder, valid_loader, e, agg_cost_scaled, agg_supervised_cost_scaled,
                         agg_unsupervised_cost_scaled, args):
    correct = 0.
    total = 0.
    for batch_idx, (data, target) in enumerate(valid_loader):
        if args.cuda:
            data = data.cuda()
        data, target = Variable(data), Variable(target)
        output = ladder.forward_encoders_clean(data)
        # TODO: Do away with the below hack for GPU tensors.
        if args.cuda:
            output = output.cpu()
            target = target.cpu()
        output = output.data.numpy()
        preds = np.argmax(output, axis=1)
        target = target.data.numpy()
        correct += np.sum(target == preds)
        total += target.shape[0]

    print("Epoch:", e + 1, "\t",
          "Total Cost:", "{:.4f}".format(agg_cost_scaled), "\t",
          "Supervised Cost:", "{:.4f}".format(agg_supervised_cost_scaled), "\t",
          "Unsupervised Cost:", "{:.4f}".format(agg_unsupervised_cost_scaled), "\t",
          "Validation Accuracy:", correct / total) 

def extract_digits(self, image):
        """
        Extract digits from a binary image representing a sudoku
        :param image: binary image/sudoku
        :return: array of digits and their probabilities
        """
        prob = np.zeros(4, dtype=np.float32)
        digits = np.zeros((4, 9, 9), dtype=object)
        for i in range(4):
            labeled, features = label(image, structure=CROSS)
            objs = find_objects(labeled)
            for obj in objs:
                roi = image[obj]
                # center of bounding box
                cy = (obj[0].stop + obj[0].start) / 2
                cx = (obj[1].stop + obj[1].start) / 2
                dists = cdist([[cy, cx]], CENTROIDS, 'euclidean')
                pos = np.argmin(dists)
                cy, cx = pos % 9, pos / 9
                # 28x28 image, center relative to sudoku
                prediction = self.classifier.classify(morph(roi))
                if digits[i, cy, cx] is 0:
                    # Newly found digit
                    digits[i, cy, cx] = prediction
                    prob[i] += prediction[0, 0]
                elif prediction[0, 0] > digits[i, cy, cx][0, 0]:
                    # Overlapping! (noise), choose the most probable prediction
                    prob[i] -= digits[i, cy, cx][0, 0]
                    digits[i, cy, cx] = prediction
                    prob[i] += prediction[0, 0]
            image = np.rot90(image)
        logging.info(prob)
        return digits[np.argmax(prob)] 

def extract_digits(self, image):
        """
        Extract digits from a binary image representing a sudoku
        :param image: binary image/sudoku
        :return: array of digits and their probabilities
        """
        prob = np.zeros(4, dtype=np.float32)
        digits = np.zeros((4, 9, 9), dtype=object)
        for i in range(4):
            labeled, features = label(image, structure=CROSS)
            objs = find_objects(labeled)
            for obj in objs:
                roi = image[obj]
                # center of bounding box
                cy = (obj[0].stop + obj[0].start) / 2
                cx = (obj[1].stop + obj[1].start) / 2
                dists = cdist([[cy, cx]], CENTROIDS, 'euclidean')
                pos = np.argmin(dists)
                cy, cx = pos % 9, pos / 9
                # 28x28 image, center relative to sudoku
                prediction = self.classifier.classify(morph(roi))
                if digits[i, cy, cx] is 0:
                    # Newly found digit
                    digits[i, cy, cx] = prediction
                    prob[i] += prediction[0, 0]
                elif prediction[0, 0] > digits[i, cy, cx][0, 0]:
                    # Overlapping! (noise), choose the most probable prediction
                    prob[i] -= digits[i, cy, cx][0, 0]
                    digits[i, cy, cx] = prediction
                    prob[i] += prediction[0, 0]
            image = np.rot90(image)
        logging.info(prob)
        return digits[np.argmax(prob)] 

def predict(self, data):
        predictions = []
        for name in data:
            x = np.array([self.__parse_name(name)])
            prediction = self.__model.predict([x])
            predictions.append(self.__indexes_classes[np.argmax(prediction)])
        return predictions 

def binarize_predictions(array, task='binary.classification'):
    ''' Turn predictions into decisions {0,1} by selecting the class with largest 
    score for multiclass problems and thresholding at 0.5 for other cases.'''
    # add a very small random value as tie breaker (a bit bad because this changes the score every time)
    # so to make sure we get the same result every time, we seed it    
    #eps = 1e-15
    #np.random.seed(sum(array.shape))
    #array = array + eps*np.random.rand(array.shape[0],array.shape[1])
    bin_array = np.zeros(array.shape)
    if (task != 'multiclass.classification') or (array.shape[1]==1): 
        bin_array[array>=0.5] = 1
    else:        
        sample_num=array.shape[0]
        for i in range(sample_num):
            j = np.argmax(array[i,:])
            bin_array[i,j] = 1        
    return bin_array 

def run_epoch_doc(docs, labels, tags, tm, pad_id, cf):
    batches = int(math.ceil(float(len(docs))/cf.batch_size))
    accs = []
    for b in xrange(batches):
        d, y, m, t, num_docs = get_batch_doc(docs, labels, tags, b, cf.doc_len, cf.tag_len, cf.batch_size, pad_id)
        prob = sess.run(tm.sup_probs, {tm.doc:d, tm.label:y, tm.sup_mask: m, tm.tag: t})
        pred = np.argmax(prob, axis=1)
        accs.extend(pred[:num_docs] == y[:num_docs])

    print "\ntest classification accuracy = %.3f" % np.mean(accs) 

def gen_sent_on_doc(docs, tags, idxvocab, vocabxid, start_symbol, end_symbol, cf):
    topics, _ = tm.get_topics(sess, topn=topn)
    topics = [ " ".join([idxvocab[w] for w in t]) for t in topics ]
    doc_text = [ item.replace("\t", "\n") for item in codecs.open(args.input_doc, "r", "utf-8").readlines() ]
    output = codecs.open(args.gen_sent_on_doc, "w", "utf-8")
    with tf.variable_scope("model", reuse=True, initializer=initializer):
        mgen = LM(is_training=False, vocab_size=len(idxvocab), batch_size=1, num_steps=1, config=cf, \
            reuse_conv_variables=True)

    for d in range(len(docs)):
        output.write("\n" + "="*100 + "\n")
        output.write("Doc " +  str(d) +":\n")
        output.write(doc_text[d])

        doc, _, _, t, _ = get_batch_doc(docs, None, tags, d, cf.doc_len, cf.tag_len, 1, vocabxid[pad_symbol])
        best_topics, best_words = mgen.get_topics_on_doc(sess, doc, t, topn)
        
        output.write("\nRepresentative topics:\n")
        output.write("\n".join([ ("[%.3f] %s: %s" % (item[1],str(item[0]).zfill(3),topics[item[0]])) \
            for item in best_topics ]) + "\n")

        output.write("\nRepresentative words:\n")
        output.write("\n".join([ ("[%.3f] %s" % (item[1], idxvocab[item[0]])) for item in best_words ]) + "\n")

        output.write("\nSentence generation (greedy; argmax):" + "\n")
        s = mgen.generate_on_doc(sess, doc, t, vocabxid[start_symbol], 0, cf.lm_sent_len+10, vocabxid[end_symbol])
        output.write("[0] " + " ".join([ idxvocab[item] for item in s ]) + "\n")

        for temp in gen_temps:
            output.write("\nSentence generation (random; temperature = " + str(temp) + "):\n")

            for i in xrange(gen_num):
                s = mgen.generate_on_doc(sess, doc, t, vocabxid[start_symbol], temp, cf.lm_sent_len+10, \
                    vocabxid[end_symbol])
                output.write("[" + str(i) + "] " + " ".join([ idxvocab[item] for item in s ]) + "\n")
######
#main#
######

#load the vocabulary 

def sample(self, probs, temperature):
        if temperature == 0:
            return np.argmax(probs)

        probs = probs.astype(np.float64) #convert to float64 for higher precision
        probs = np.log(probs) / temperature
        probs = np.exp(probs) / math.fsum(np.exp(probs))
        return np.argmax(np.random.multinomial(1, probs, 1))

    #generate a sentence given conv_hidden 

def write_predictions(self, inputs):
        rev_label_map = {j: i for (i, j) in self.label_map.items()}
        predictions = numpy.argmax(self.model.predict(inputs), axis=1)
        test_output_file = open("%s.predictions" % self.model_name_prefix, "w")
        for prediction in predictions:
            print >>test_output_file, rev_label_map[prediction + 1] 

def test(self, inputs, targets):
        if not self.model:
            raise RuntimeError, "Model not trained!"
        metrics = self.model.evaluate(inputs, targets)
        print >>sys.stderr, "Test accuracy: %.4f" % (metrics[1])  # The first metric is loss.
        predictions = numpy.argmax(self.model.predict(inputs), axis=1)
        rev_label_map = {ind: label for label, ind in self.label_map.items()}
        predicted_labels = [rev_label_map[pred] for pred in predictions]
        return predicted_labels 

def calculate_assignments(self, assignment_weights):
        clusters = np.argmax(assignment_weights, axis=1)
        return clusters 

def calculate_roc(thresholds, embeddings1, embeddings2, actual_issame, nrof_folds=10):
    assert(embeddings1.shape[0] == embeddings2.shape[0])
    assert(embeddings1.shape[1] == embeddings2.shape[1])
    nrof_pairs = min(len(actual_issame), embeddings1.shape[0])
    nrof_thresholds = len(thresholds)
    k_fold = KFold(n_splits=nrof_folds, shuffle=False)
    
    tprs = np.zeros((nrof_folds,nrof_thresholds))
    fprs = np.zeros((nrof_folds,nrof_thresholds))
    accuracy = np.zeros((nrof_folds))
    
    diff = np.subtract(embeddings1, embeddings2)
    dist = np.sum(np.square(diff),1)
    indices = np.arange(nrof_pairs)
    
    for fold_idx, (train_set, test_set) in enumerate(k_fold.split(indices)):
        
        # Find the best threshold for the fold
        acc_train = np.zeros((nrof_thresholds))
        for threshold_idx, threshold in enumerate(thresholds):
            _, _, acc_train[threshold_idx] = calculate_accuracy(threshold, dist[train_set], actual_issame[train_set])
        best_threshold_index = np.argmax(acc_train)
        for threshold_idx, threshold in enumerate(thresholds):
            tprs[fold_idx,threshold_idx], fprs[fold_idx,threshold_idx], _ = calculate_accuracy(threshold, dist[test_set], actual_issame[test_set])
        _, _, accuracy[fold_idx] = calculate_accuracy(thresholds[best_threshold_index], dist[test_set], actual_issame[test_set])
          
    tpr = np.mean(tprs,0)
    fpr = np.mean(fprs,0)
    return tpr, fpr, accuracy 

def length_histogram(fqin, name):
    '''
    Create a histogram, and return the bin edges of the bin containing the most reads
    '''
    logging.info("Creating length histogram to find bin with most reads.")
    lengths = get_lengths(fqin)
    plt.hist(lengths, bins='auto')
    plt.savefig(name, format='png', dpi=100)
    plt.close("all")
    hist, bin_edges = np.histogram(lengths, bins='auto')
    maxindex = np.argmax(hist)
    return (bin_edges[maxindex], bin_edges[maxindex + 1]) 

def test_estimate_tree(num_edges):
    set_random_seed(0)
    E = num_edges
    V = 1 + E
    grid = make_complete_graph(V)
    K = grid.shape[1]
    edge_logits = np.random.random([K]) - 0.5
    edges = estimate_tree(grid, edge_logits)

    # Check size.
    assert len(edges) == E
    for v in range(V):
        assert any(v in edge for edge in edges)

    # Check optimality.
    edges = tuple(edges)
    if V < len(TREE_GENERATORS):
        all_trees = get_spanning_trees(V)
        assert edges in all_trees
        all_trees = list(all_trees)
        logits = []
        for tree in all_trees:
            logits.append(
                sum(edge_logits[find_complete_edge(u, v)] for (u, v) in tree))
        expected = all_trees[np.argmax(logits)]
        assert edges == expected 

def predict(self, X):
        """ Predict the class of unknown samples X.

        :param X: np.array
            Array containing the input samples.
            Must be of the same shape [n_samples, data] as the training inputs.

        :return: np.array
            1D array containing the predicted class for each input sample.
        """
        pred_proba = self.predict_proba(X=X)
        predictions = np.argmax(pred_proba, axis=1)

        return predictions 

def calculate_hit_at_one(predictions, actuals):
  """Performs a local (numpy) calculation of the hit at one.

  Args:
    predictions: Matrix containing the outputs of the model.
      Dimensions are 'batch' x 'num_classes'.
    actuals: Matrix containing the ground truth labels.
      Dimensions are 'batch' x 'num_classes'.

  Returns:
    float: The average hit at one across the entire batch.
  """
  top_prediction = numpy.argmax(predictions, 1)
  hits = actuals[numpy.arange(actuals.shape[0]), top_prediction]
  return numpy.average(hits)