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How to use test_run_list method in tempest

Best Python code snippet using tempest_python

kamitani_data_handler.py

Source:kamitani_data_handler.py

1from scipy.io import loadmat2import numpy as np3import pandas as pd4import sklearn.preprocessing5from sklearn import preprocessing6class kamitani_data_handler():7    """Generate batches for FMRI prediction8    frames_back - how many video frames to take before FMRI frame9    frames_forward - how many video frames to take after FMRI frame10    """11    def __init__(self, matlab_file ,test_img_csv = 'KamitaniData/imageID_test.csv',train_img_csv = 'KamitaniData/imageID_training.csv',voxel_spacing =3,log = 0 ):12        mat = loadmat(matlab_file)13        self.data = mat['dataSet'][:,3:]14        self.sample_meta = mat['dataSet'][:,:3]15        meta = mat['metaData']16        self.meta_keys = list(l[0] for l in meta[0][0][0][0])17        self.meta_desc = list(l[0] for l in meta[0][0][1][0])18        self.voxel_meta = np.nan_to_num(meta[0][0][2][:,3:])19        test_img_df = pd.read_csv(test_img_csv, header=None)20        train_img_df =pd.read_csv(train_img_csv, header=None)21        self.test_img_id = test_img_df[0].values22        self.train_img_id = train_img_df[0].values23        self.sample_type = {'train':1 , 'test':2 , 'test_imagine' : 3}24        self.voxel_spacing = voxel_spacing25        self.log = log26    def get_meta_field(self,field = 'DataType'):27        index = self.meta_keys.index(field)28        if(index <3): # 3 first keys are sample meta29            return self.sample_meta[:,index]30        else:31            return self.voxel_meta[index]32    def print_meta_desc(self):33        print(self.meta_desc)34    def get_labels(self, imag_data = 0,test_run_list = None):35        le = preprocessing.LabelEncoder()36        img_ids = self.get_meta_field('Label')37        type = self.get_meta_field('DataType')38        train = (type == self.sample_type['train'])39        test = (type == self.sample_type['test'])40        imag = (type == self.sample_type['test_imagine'])41        img_ids_train = img_ids[train]42        img_ids_test = img_ids[test]43        img_ids_imag = img_ids[imag]44        train_labels  = []45        test_labels  =  []46        imag_labels = []47        for id in img_ids_test:48            idx = (np.abs(id - self.test_img_id)).argmin()49            test_labels.append(idx)50        for id in img_ids_train:51            idx = (np.abs(id - self.train_img_id)).argmin()52            train_labels.append(idx)53        for id in img_ids_imag:54            idx = (np.abs(id - self.test_img_id)).argmin()55            imag_labels.append(idx)56        if (test_run_list is not None):57            run = self.get_meta_field('Run')58            test = (self.get_meta_field('DataType') == 2).astype(bool)59            run = run[test]60            select = np.in1d(run, test_run_list)61            test_labels = test_labels[select]62        #imag_labels = le.fit_transform(img_ids_imag)63        if(imag_data):64            return np.array(train_labels), np.array(test_labels), np.array(imag_labels)65        else:66            return np.array(train_labels),np.array(test_labels)67    def get_data(self,normalize =1 ,roi = 'ROI_VC',imag_data = 0,test_run_list = None):   # normalize 0-no, 1- per run , 2- train/test seperatly68        type = self.get_meta_field('DataType')69        train = (type == self.sample_type['train'])70        test = (type == self.sample_type['test'])71        test_imag = (type == self.sample_type['test_imagine'])72        test_all  = np.logical_or(test,test_imag)73        roi_select = self.get_meta_field(roi).astype(bool)74        data = self.data[:,roi_select]75        if(self.log ==1):76            data = np.log(1+np.abs(data))*np.sign(data)77        if(normalize==1):78            run = self.get_meta_field('Run').astype('int')-179            num_runs = np.max(run)+180            data_norm = np.zeros(data.shape)81            for r in range(num_runs):82                data_norm[r==run] = sklearn.preprocessing.scale(data[r==run])83            train_data = data_norm[train]84            test_data  = data_norm[test]85            test_all = data_norm[test_all]86            test_imag = data_norm[test_imag]87        else:88            train_data = data[train]89            test_data  =  data[test]90            if(normalize==2):91                train_data = sklearn.preprocessing.scale(train_data)92                test_data = sklearn.preprocessing.scale(test_data)93        if(self.log ==2):94            train_data = np.log(1+np.abs(train_data))*np.sign(train_data)95            test_data = np.log(1+np.abs(test_data))*np.sign(test_data)96            train_data = sklearn.preprocessing.scale(train_data)97            test_data = sklearn.preprocessing.scale(test_data)98        test_labels =  self.get_labels()[1]99        imag_labels = self.get_labels(1)[2]100        num_labels = max(test_labels)+1101        test_data_avg = np.zeros([num_labels,test_data.shape[1]])102        test_imag_avg = np.zeros([num_labels,test_data.shape[1]])103        if(test_run_list is not None):104            run = self.get_meta_field('Run')105            test = (self.get_meta_field('DataType') == 2).astype(bool)106            run = run[test]107            select = np.in1d(run, test_run_list)108            test_data = test_data[select,:]109            test_labels = test_labels[select]110        for i in range(num_labels):111            test_data_avg[i] = np.mean(test_data[test_labels==i],axis=0)112            test_imag_avg[i] = np.mean(test_imag[imag_labels == i], axis=0)113        if(imag_data):114            return train_data, test_data, test_data_avg,test_imag,test_imag_avg115        else:116            return train_data, test_data, test_data_avg117    def get_voxel_loc(self):118        x = self.get_meta_field('voxel_x')119        y = self.get_meta_field('voxel_y')120        z = self.get_meta_field('voxel_z')121        dim = [int(x.max() -x.min()+1),int(y.max() -y.min()+1), int(z.max() -z.min()+1)]...

main.py

Source:main.py

1from agent import *2training_eps=100003test_runs=54max_len=10005testing_steps=[]6ag=Agent()7for episode in range(training_eps):8  w=World(0,0)9  for step in range(max_len):10    a=ag.e_greedy(w.pos,w.vel)11    nextp,nextv,R=w.move(a)12    a_next=ag.e_greedy(nextp,nextv)13    ag.update(w.pos,w.vel,a,R,nextp,nextv,a_next)14    w.pos=nextp15    w.vel=nextv16    if(R==0):17      break18    elif(w.pos<=w.pmin):19      w.vel=0 # the car bumps to a stop 20  """21  running agent after each simulation22  multiple runs to get a better estimate of agent performance at this episode23  test_run_list stores the corresponding "test_run" number of values24  """25  test_run_list=[]26  for run in range(test_runs):27    w=World(0,0)28    for step in range(max_len):29      a=ag.greedy(w.pos,w.vel)30      nextp,nextv,R=w.move(a)31      a_next=ag.greedy(nextp,nextv)32      """33      The next command is required even in test case because the agent must learn to move in the environment every time it interacts with it. If it encounters a state upon which it is not trained well the agent would fail repeatedly across test runs unless we update it between runs.34      """35      ag.update(w.pos,w.vel,a,R,nextp,nextv,a_next) 36      w.pos=nextp37      w.vel=nextv38      if(R==0):39        break40      elif(w.pos<w.pmin):41        w.vel=042    test_run_list.append(step)43  testing_steps.append(mean(test_run_list))44  if(episode%1000==0):45    print('Done episode {}'.format(episode))    46# save agent47f='agent.sav'48file=open(f,'wb')49pickle.dump(ag,file)50file.close()51# plot peformance of agent with training episodes52plt.plot(range(1,1+len(testing_steps)),testing_steps,label='No. of steps')53plt.title('No. of steps to reach terminal states vs. training episodes')54plt.xlabel('Training Episodes')55plt.ylabel('No. of steps')56plt.legend()...

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