Python numpy.loadtxt() Examples

The following are 30 code examples of numpy.loadtxt(). You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example. You may also want to check out all available functions/classes of the module numpy , or try the search function .
Example #1
Source File: main.py    From transferlearning with MIT License 13 votes vote down vote up
def classify_1nn(data_train, data_test):
    '''
    Classification using 1NN
    Inputs: data_train, data_test: train and test csv file path
    Outputs: yprediction and accuracy
    '''
    from sklearn.neighbors import KNeighborsClassifier
    from sklearn.metrics import accuracy_score
    from sklearn.preprocessing import StandardScaler
    data = {'src': np.loadtxt(data_train, delimiter=','),
            'tar': np.loadtxt(data_test, delimiter=','),
            }
    Xs, Ys, Xt, Yt = data['src'][:, :-1], data['src'][:, -
                                                      1], data['tar'][:, :-1], data['tar'][:, -1]
    Xs = StandardScaler(with_mean=0, with_std=1).fit_transform(Xs)
    Xt = StandardScaler(with_mean=0, with_std=1).fit_transform(Xt)
    clf = KNeighborsClassifier(n_neighbors=1)
    clf.fit(Xs, Ys)
    ypred = clf.predict(Xt)
    acc = accuracy_score(y_true=Yt, y_pred=ypred)
    print('Acc: {:.4f}'.format(acc))
    return ypred, acc 
Example #2
Source File: utils.py    From pruning_yolov3 with GNU General Public License v3.0 7 votes vote down vote up
def plot_evolution_results(hyp):  # from utils.utils import *; plot_evolution_results(hyp)
    # Plot hyperparameter evolution results in evolve.txt
    x = np.loadtxt('evolve.txt', ndmin=2)
    f = fitness(x)
    weights = (f - f.min()) ** 2  # for weighted results
    fig = plt.figure(figsize=(12, 10))
    matplotlib.rc('font', **{'size': 8})
    for i, (k, v) in enumerate(hyp.items()):
        y = x[:, i + 5]
        # mu = (y * weights).sum() / weights.sum()  # best weighted result
        mu = y[f.argmax()]  # best single result
        plt.subplot(4, 5, i + 1)
        plt.plot(mu, f.max(), 'o', markersize=10)
        plt.plot(y, f, '.')
        plt.title('%s = %.3g' % (k, mu), fontdict={'size': 9})  # limit to 40 characters
        print('%15s: %.3g' % (k, mu))
    fig.tight_layout()
    plt.savefig('evolve.png', dpi=200) 
Example #3
Source File: m_phonons.py    From pyscf with Apache License 2.0 6 votes vote down vote up
def read_vibra_vectors(fname=None):
  """ Reads siesta.vectors file --- output of VIBRA utility """
  from io import StringIO   # StringIO behaves like a file object
  if fname is None: fname = 'siesta.vectors' 
  with open(fname, 'r') as content_file: content = content_file.readlines()
  
  na = -1
  na_prev = -1
  for i,l in enumerate(content):
    if 'Eigenmode (real part)' in l: l1 = i
    if 'Eigenmode (imaginary part)' in l: 
      na = i - l1 - 1
      if na!=na_prev and na_prev>0: raise RuntimeError('na!=na_prev')
      na_prev = na

  ma2xyz = list()
  m2e = list()
  for i,l in enumerate(content):
    if 'Frequency' in l: m2e.append(float(l.split()[2]))
    if 'Eigenmode (real part)' in l: ma2xyz.append(np.loadtxt(StringIO(''.join(str(k) for k in content[i+1:i+1+na]))))
  return np.array(m2e),np.array(ma2xyz) 
Example #4
Source File: test_0161_bse_h2b_spin1_uhf_cis.py    From pyscf with Apache License 2.0 6 votes vote down vote up
def test_161_bse_h2b_spin1_uhf_cis(self):
    """ This  """
    mol = gto.M(verbose=1,atom='B 0 0 0; H 0 0.489 1.074; H 0 0.489 -1.074',basis='cc-pvdz',spin=1)

    gto_mf = scf.UHF(mol)
    gto_mf.kernel()
    gto_td = tddft.TDHF(gto_mf)
    gto_td.nstates = 150
    gto_td.kernel()

    omegas = np.arange(0.0, 2.0, 0.01) + 1j*0.03
    p_ave = -polariz_freq_osc_strength(gto_td.e, gto_td.oscillator_strength(), omegas).imag
    data = np.array([omegas.real*HARTREE2EV, p_ave])
    np.savetxt('test_0161_bse_h2b_spin1_uhf_cis_pyscf.txt', data.T, fmt=['%f','%f'])
    #data_ref = np.loadtxt('test_0159_bse_h2b_uhf_cis_pyscf.txt-ref').T
    #self.assertTrue(np.allclose(data_ref, data, atol=1e-6, rtol=1e-3))
    
    nao_td  = bse_iter(mf=gto_mf, gto=mol, verbosity=0, xc_code='CIS')

    polariz = -nao_td.comp_polariz_inter_ave(omegas).imag
    data = np.array([omegas.real*HARTREE2EV, polariz])
    np.savetxt('test_0161_bse_h2b_spin1_uhf_cis_nao.txt', data.T, fmt=['%f','%f'])
    #data_ref = np.loadtxt('test_0161_bse_h2b_spin1_uhf_cis_nao.txt-ref').T
    #self.assertTrue(np.allclose(data_ref, data, atol=1e-6, rtol=1e-3)) 
Example #5
Source File: test_0091_tddft_x_zip_na20.py    From pyscf with Apache License 2.0 6 votes vote down vote up
def test_x_zip_feature_na20_chain(self):
    """ This a test for compression of the eigenvectos at higher energies """
    dname = dirname(abspath(__file__))
    siesd = dname+'/sodium_20'
    x = td_c(label='siesta', cd=siesd,x_zip=True, x_zip_emax=0.25,x_zip_eps=0.05,jcutoff=7,xc_code='RPA',nr=128, fermi_energy=-0.0913346431431985)
    
    eps = 0.005
    ww = np.arange(0.0, 0.5, eps/2.0)+1j*eps
    data = np.array([ww.real*27.2114, -x.comp_polariz_inter_ave(ww).imag])
    fname = 'na20_chain.tddft_iter_rpa.omega.inter.ave.x_zip.txt'
    np.savetxt(fname, data.T, fmt=['%f','%f'])
    #print(__file__, fname)
    data_ref = np.loadtxt(dname+'/'+fname+'-ref')
    #print('    x.rf0_ncalls ', x.rf0_ncalls)
    #print(' x.matvec_ncalls ', x.matvec_ncalls)
    self.assertTrue(np.allclose(data_ref,data.T, rtol=1.0e-1, atol=1e-06)) 
Example #6
Source File: test_0040_bse_rpa_nao.py    From pyscf with Apache License 2.0 6 votes vote down vote up
def test_0040_bse_rpa_nao(self):
    """ Compute polarization with RPA via 2-point non-local potentials (BSE solver)  """
    from timeit import default_timer as timer

    dname = os.path.dirname(os.path.abspath(__file__))
    bse = bse_iter(label='water', cd=dname, xc_code='RPA', verbosity=0)
    omegas = np.linspace(0.0,2.0,150)+1j*0.01
    #print(__name__, omegas.shape)
    
    pxx = np.zeros(len(omegas))
    for iw,omega in enumerate(omegas):
      for ixyz in range(1):
        dip = bse.dip_ab[ixyz]
        vab = bse.apply_l(dip, omega)
        pxx[iw] = pxx[iw] - (vab.imag*dip.reshape(-1)).sum()
        
    data = np.array([omegas.real*27.2114, pxx])
    np.savetxt('water.bse_iter_rpa.omega.inter.pxx.txt', data.T, fmt=['%f','%f'])
    data_ref = np.loadtxt(dname+'/water.bse_iter_rpa.omega.inter.pxx.txt-ref')
    #print('    bse.l0_ncalls ', bse.l0_ncalls)
    self.assertTrue(np.allclose(data_ref,data.T, rtol=1.0, atol=1e-05)) 
Example #7
Source File: generate_rotations.py    From pointnet-registration-framework with MIT License 6 votes vote down vote up
def get_datasets(args):

    cinfo = None
    if args.categoryfile:
        #categories = numpy.loadtxt(args.categoryfile, dtype=str, delimiter="\n").tolist()
        categories = [line.rstrip('\n') for line in open(args.categoryfile)]
        categories.sort()
        c_to_idx = {categories[i]: i for i in range(len(categories))}
        cinfo = (categories, c_to_idx)

    if args.dataset_type == 'modelnet':
        transform = torchvision.transforms.Compose([\
                ptlk.data.transforms.Mesh2Points(),\
                ptlk.data.transforms.OnUnitCube(),\
            ])

        testdata = ptlk.data.datasets.ModelNet(args.dataset_path, train=0, transform=transform, classinfo=cinfo)

    return testdata 
Example #8
Source File: test_0157_bse_h2o_rhf_cis.py    From pyscf with Apache License 2.0 6 votes vote down vote up
def test_157_bse_h2o_rhf_cis(self):
    """ This  """
    mol = gto.M(verbose=1,atom='O 0 0 0; H 0 0.489 1.074; H 0 0.489 -1.074',basis='cc-pvdz')

    gto_mf = scf.RHF(mol)
    gto_mf.kernel()
    gto_td = tddft.TDDFT(gto_mf)
    gto_td.nstates = 190
    gto_td.kernel()

    omegas = np.arange(0.0, 2.0, 0.01) + 1j*0.03
    p_ave = -polariz_freq_osc_strength(gto_td.e, gto_td.oscillator_strength(), omegas).imag
    data = np.array([omegas.real*HARTREE2EV, p_ave])
    np.savetxt('test_0157_bse_h2o_rhf_cis_pyscf.txt', data.T, fmt=['%f','%f'])
    data_ref = np.loadtxt('test_0157_bse_h2o_rhf_cis_pyscf.txt-ref').T
    self.assertTrue(np.allclose(data_ref, data, atol=1e-6, rtol=1e-3))
    
    nao_td  = bse_iter(mf=gto_mf, gto=mol, verbosity=0, xc_code='CIS')

    polariz = -nao_td.comp_polariz_inter_ave(omegas).imag
    data = np.array([omegas.real*HARTREE2EV, polariz])
    np.savetxt('test_0157_bse_h2o_rhf_cis_nao.txt', data.T, fmt=['%f','%f'])
    data_ref = np.loadtxt('test_0157_bse_h2o_rhf_cis_nao.txt-ref').T
    self.assertTrue(np.allclose(data_ref, data, atol=5e-5, rtol=5e-2), 
      msg="{}".format(abs(data_ref-data).sum()/data.size ) ) 
Example #9
Source File: test_0035_bse_nonin_nao.py    From pyscf with Apache License 2.0 6 votes vote down vote up
def test_bse_iter_nonin(self):
    """ Compute polarization with LDA TDDFT  """
    from timeit import default_timer as timer
    
    dname = os.path.dirname(os.path.abspath(__file__))
    bse = bse_iter(label='water', cd=dname, iter_broadening=1e-2, xc_code='RPA', verbosity=0)
    omegas = np.linspace(0.0,2.0,500)+1j*bse.eps
    
    pxx = np.zeros(len(omegas))
    for iw,omega in enumerate(omegas):
      for ixyz in range(1):
        vab = bse.apply_l0(bse.dip_ab[ixyz], omega)
        pxx[iw] = pxx[iw] - (vab.imag*bse.dip_ab[ixyz].reshape(-1)).sum()
        
    data = np.array([omegas.real*27.2114, pxx])
    np.savetxt('water.bse_iter_rpa.omega.nonin.pxx.txt', data.T, fmt=['%f','%f'])
    data_ref = np.loadtxt(dname+'/water.bse_iter_rpa.omega.nonin.pxx.txt-ref')
    #print('    bse.l0_ncalls ', bse.l0_ncalls)
    self.assertTrue(np.allclose(data_ref,data.T, rtol=1.0, atol=1e-05)) 
Example #10
Source File: DataManager.py    From Caffe-Python-Data-Layer with BSD 2-Clause "Simplified" License 6 votes vote down vote up
def load_all(self):
        """The function to load all data and labels

        Give:
        data: the list of raw data, needs to be decompressed
              (e.g., raw JPEG string)
        labels: numpy array, with each element is a string
        """
        start = time.time()
        print("Start Loading Data from BCF {}".format(
            'MEMORY' if self._bcf_mode == 'MEM' else 'FILE'))

        self._labels = np.loadtxt(self._label_fn).astype(str)

        if self._bcf.size() != self._labels.shape[0]:
            raise Exception("Number of samples in data"
                            "and labels are not equal")
        else:
            for idx in range(self._bcf.size()):
                datum_str = self._bcf.get(idx)
                self._data.append(datum_str)
        end = time.time()
        print("Loading {} samples Done: Time cost {} seconds".format(
            len(self._data), end - start))

        return self._data, self._labels 
Example #11
Source File: test_performance_indicator.py    From pymoo with Apache License 2.0 6 votes vote down vote up
def test_values_of_indicators(self):
        l = [
            (GD, "gd"),
            (IGD, "igd")
        ]
        folder = os.path.join(get_pymoo(), "tests", "performance_indicator")
        pf = np.loadtxt(os.path.join(folder, "performance_indicators.pf"))

        for indicator, ext in l:

            for i in range(1, 5):
                F = np.loadtxt(os.path.join(folder, "performance_indicators_%s.f" % i))

                val = indicator(pf).calc(F)
                correct = np.loadtxt(os.path.join(folder, "performance_indicators_%s.%s" % (i, ext)))
                self.assertTrue(correct == val) 
Example #12
Source File: test_0152_bse_h2b_uks_pz.py    From pyscf with Apache License 2.0 6 votes vote down vote up
def test_152_bse_h2b_uks_pz(self):
    """ This  """
    mol = gto.M(verbose=1,atom='B 0 0 0; H 0 0.489 1.074; H 0 0.489 -1.074',basis='cc-pvdz',spin=3)

    gto_mf = scf.UKS(mol)
    gto_mf.kernel()
    gto_td = tddft.TDDFT(gto_mf)
    gto_td.nstates = 190
    gto_td.kernel()

    omegas = np.arange(0.0, 2.0, 0.01) + 1j*0.03
    p_ave = -polariz_freq_osc_strength(gto_td.e, gto_td.oscillator_strength(), omegas).imag
    data = np.array([omegas.real*HARTREE2EV, p_ave])
    np.savetxt('test_0152_bse_h2b_uks_pz_pyscf.txt', data.T, fmt=['%f','%f'])
    data_ref = np.loadtxt('test_0152_bse_h2b_uks_pz_pyscf.txt-ref').T
    self.assertTrue(np.allclose(data_ref, data, atol=1e-6, rtol=1e-3))
    
    nao_td  = bse_iter(mf=gto_mf, gto=mol, verbosity=0)

    polariz = -nao_td.comp_polariz_inter_ave(omegas).imag
    data = np.array([omegas.real*HARTREE2EV, polariz])
    np.savetxt('test_0152_bse_h2b_uks_pz_nao.txt', data.T, fmt=['%f','%f'])
    data_ref = np.loadtxt('test_0152_bse_h2b_uks_pz_nao.txt-ref').T
    self.assertTrue(np.allclose(data_ref, data, atol=1e-6, rtol=1e-3)) 
Example #13
Source File: datasets.py    From discomll with Apache License 2.0 6 votes vote down vote up
def breastcancer_cont(replication=2):
    f = open(path + "breast_cancer_wisconsin_cont.txt", "r")
    data = np.loadtxt(f, delimiter=",", dtype=np.string0)
    x_train = np.array(data[:, range(0, 9)])
    y_train = np.array(data[:, 9])
    for j in range(replication - 1):
        x_train = np.vstack([x_train, data[:, range(0, 9)]])
        y_train = np.hstack([y_train, data[:, 9]])
    x_train = np.array(x_train, dtype=np.float)

    f = open(path + "breast_cancer_wisconsin_cont_test.txt")
    data = np.loadtxt(f, delimiter=",", dtype=np.string0)
    x_test = np.array(data[:, range(0, 9)])
    y_test = np.array(data[:, 9])
    for j in range(replication - 1):
        x_test = np.vstack([x_test, data[:, range(0, 9)]])
        y_test = np.hstack([y_test, data[:, 9]])
    x_test = np.array(x_test, dtype=np.float)

    return x_train, y_train, x_test, y_test 
Example #14
Source File: test_0162_bse_h2o_spin2_uhf_cis.py    From pyscf with Apache License 2.0 6 votes vote down vote up
def test_0162_bse_h2o_spin2_uhf_cis(self):
    """ This  """
    mol = gto.M(verbose=1,atom='O 0 0 0; H 0 0.489 1.074; H 0 0.489 -1.074',basis='cc-pvdz',spin=2)

    gto_mf = scf.UHF(mol)
    gto_mf.kernel()
    gto_td = tddft.TDDFT(gto_mf)
    gto_td.nstates = 190
    gto_td.kernel()

    omegas = np.arange(0.0, 2.0, 0.01) + 1j*0.03
    p_ave = -polariz_freq_osc_strength(gto_td.e, gto_td.oscillator_strength(), omegas).imag
    data = np.array([omegas.real*HARTREE2EV, p_ave])
    np.savetxt('test_0162_bse_h2o_spin2_uhf_cis_pyscf.txt', data.T, fmt=['%f','%f'])
    #data_ref = np.loadtxt('test_0162_bse_h2o_spin2_uhf_cis_pyscf.txt-ref').T
    #self.assertTrue(np.allclose(data_ref, data, atol=1e-6, rtol=1e-3))
    
    nao_td  = bse_iter(mf=gto_mf, gto=mol, verbosity=0, xc_code='CIS')

    polariz = -nao_td.comp_polariz_inter_ave(omegas).imag
    data = np.array([omegas.real*HARTREE2EV, polariz])
    np.savetxt('test_0162_bse_h2o_spin2_uhf_cis_nao.txt', data.T, fmt=['%f','%f'])
    #data_ref = np.loadtxt('test_0162_bse_h2o_spin2_uhf_cis_nao.txt-ref').T
    #self.assertTrue(np.allclose(data_ref, data, atol=1e-6, rtol=1e-3), \
    #  msg="{}".format(abs(data_ref-data).sum()/data.size)) 
Example #15
Source File: datasets.py    From discomll with Apache License 2.0 6 votes vote down vote up
def iris(replication=2):
    f = open(path + "iris.txt")
    data = np.loadtxt(f, delimiter=",", dtype=np.string0)
    x_train = np.array(data[:, range(0, 4)], dtype=np.float)
    y_train = data[:, 4]

    for j in range(replication - 1):
        x_train = np.vstack([x_train, data[:, range(0, 4)]])
        y_train = np.hstack([y_train, data[:, 4]])
    x_train = np.array(x_train, dtype=np.float)

    f = open(path + "iris_test.txt")
    data = np.loadtxt(f, delimiter=",", dtype=np.string0)
    x_test = np.array(data[:, range(0, 4)], dtype=np.float)
    y_test = data[:, 4]

    for j in range(replication - 1):
        x_test = np.vstack([x_test, data[:, range(0, 4)]])
        y_test = np.hstack([y_test, data[:, 4]])
    x_test = np.array(x_test, dtype=np.float)

    return x_train, y_train, x_test, y_test 
Example #16
Source File: datasets.py    From discomll with Apache License 2.0 6 votes vote down vote up
def regression_data():
    f = open(path + "regression_data1.txt")
    data = np.loadtxt(f, delimiter=",")
    x1 = np.insert(data[:, 0].reshape(len(data), 1), 0, np.ones(len(data)), axis=1)
    y1 = data[:, 1]
    f = open(path + "regression_data2.txt")
    data = np.loadtxt(f, delimiter=",")
    x2 = np.insert(data[:, 0].reshape(len(data), 1), 0, np.ones(len(data)), axis=1)
    y2 = data[:, 1]
    x1 = np.vstack((x1, x2))
    y1 = np.hstack((y1, y2))

    f = open(path + "regression_data_test1.txt")
    data = np.loadtxt(f, delimiter=",")
    x1_test = np.insert(data[:, 0].reshape(len(data), 1), 0, np.ones(len(data)), axis=1)
    y1_test = data[:, 1]
    f = open(path + "regression_data_test2.txt")
    data = np.loadtxt(f, delimiter=",")
    x2_test = np.insert(data[:, 0].reshape(len(data), 1), 0, np.ones(len(data)), axis=1)
    y2_test = data[:, 1]
    x1_test = np.vstack((x1_test, x2_test))
    y1_test = np.hstack((y1_test, y2_test))
    return x1, y1, x1_test, y1_test 
Example #17
Source File: script_preprocess_annoations_S3DIS.py    From DOTA_models with Apache License 2.0 6 votes vote down vote up
def collect_room(building_name, room_name):
  room_dir = os.path.join(DATA_DIR, 'Stanford3dDataset_v1.2', building_name,
                          room_name, 'Annotations')
  files = glob.glob1(room_dir, '*.txt')
  files = sorted(files, key=lambda s: s.lower())
  vertexs = []; colors = [];
  for f in files:
    file_name = os.path.join(room_dir, f)
    logging.info('  %s', file_name)
    a = np.loadtxt(file_name)
    vertex = a[:,:3]*1.
    color = a[:,3:]*1
    color = color.astype(np.uint8)
    vertexs.append(vertex)
    colors.append(color)
  files = [f.split('.')[0] for f in files]
  out = {'vertexs': vertexs, 'colors': colors, 'names': files}
  return out 
Example #18
Source File: tddft_iter.py    From pyscf with Apache License 2.0 6 votes vote down vote up
def load_kernel_method(self, kernel_fname, kernel_format="npy", kernel_path_hdf5=None, **kw):
      """ Loads from file and initializes .kernel field... Useful? Rewrite?"""
    
      if kernel_format == "npy":
          self.kernel = self.dtype(np.load(kernel_fname))
      elif kernel_format == "txt":
          self.kernel = np.loadtxt(kernel_fname, dtype=self.dtype)
      elif kernel_format == "hdf5":
          import h5py
          if kernel_path_hdf5 is None:
              raise ValueError("kernel_path_hdf5 not set while trying to read kernel from hdf5 file.")
          self.kernel = h5py.File(kernel_fname, "r")[kernel_path_hdf5].value
      else:
          raise ValueError("Wrong format for loading kernel, must be: npy, txt or hdf5, got " + kernel_format)

      if len(self.kernel.shape) > 1:
          raise ValueError("The kernel must be saved in packed format in order to be loaded!")
      
      assert self.nprod*(self.nprod+1)//2 == self.kernel.size, "wrong size for loaded kernel: %r %r "%(self.nprod*(self.nprod+1)//2, self.kernel.size)
      self.kernel_dim = self.nprod 
Example #19
Source File: Stark.py    From EXOSIMS with BSD 3-Clause "New" or "Revised" License 6 votes vote down vote up
def calcfbetaInput(self):
        # table 17 in Leinert et al. (1998)
        # Zodiacal Light brightness function of solar LON (rows) and LAT (columns)
        # values given in W m−2 sr−1 μm−1 for a wavelength of 500 nm
        path = os.path.split(inspect.getfile(self.__class__))[0]
        Izod = np.loadtxt(os.path.join(path, 'Leinert98_table17.txt'))*1e-8 # W/m2/sr/um
        # create data point coordinates
        lon_pts = np.array([0., 5, 10, 15, 20, 25, 30, 35, 40, 45, 60, 75, 90,
                105, 120, 135, 150, 165, 180]) # deg
        lat_pts = np.array([0., 5, 10, 15, 20, 25, 30, 45, 60, 75, 90]) # deg
        y_pts, x_pts = np.meshgrid(lat_pts, lon_pts)
        points = np.array(list(zip(np.concatenate(x_pts), np.concatenate(y_pts))))
        # create data values, normalized by (90,0) value
        z = Izod/Izod[12,0]
        values = z.reshape(z.size)
        return  points, values 
Example #20
Source File: m_dos_pdos_eigenvalues.py    From pyscf with Apache License 2.0 6 votes vote down vote up
def dosplot (filename = None, data = None, fermi = None):
    if (filename is not None): data = np.loadtxt(filename)
    elif (data is not None): data = data

    import matplotlib.pyplot as plt
    from matplotlib import rc
    plt.rc('text', usetex=True)
    plt.rc('font', family='serif')
    plt.plot(data.T[0], data.T[1], label='MF Spin-UP', linestyle=':',color='r')
    plt.fill_between(data.T[0], 0, data.T[1], facecolor='r',alpha=0.1, interpolate=True)
    plt.plot(data.T[0], data.T[2], label='QP Spin-UP',color='r')
    plt.fill_between(data.T[0], 0, data.T[2], facecolor='r',alpha=0.5, interpolate=True)
    plt.plot(data.T[0],-data.T[3], label='MF Spin-DN', linestyle=':',color='b')
    plt.fill_between(data.T[0], 0, -data.T[3], facecolor='b',alpha=0.1, interpolate=True)
    plt.plot(data.T[0],-data.T[4], label='QP Spin-DN',color='b')
    plt.fill_between(data.T[0], 0, -data.T[4], facecolor='b',alpha=0.5, interpolate=True)
    if (fermi!=None): plt.axvline(x=fermi ,color='k', linestyle='--') #label='Fermi Energy'
    plt.axhline(y=0,color='k')
    plt.title('Total DOS', fontsize=20)
    plt.xlabel('Energy (eV)', fontsize=15) 
    plt.ylabel('Density of States (electron/eV)', fontsize=15)
    plt.legend()
    plt.savefig("dos_eigen.svg", dpi=900)
    plt.show() 
Example #21
Source File: utils.py    From pruning_yolov3 with GNU General Public License v3.0 6 votes vote down vote up
def print_mutation(hyp, results, bucket=''):
    # Print mutation results to evolve.txt (for use with train.py --evolve)
    a = '%10s' * len(hyp) % tuple(hyp.keys())  # hyperparam keys
    b = '%10.3g' * len(hyp) % tuple(hyp.values())  # hyperparam values
    c = '%10.3g' * len(results) % results  # results (P, R, mAP, F1, test_loss)
    print('\n%s\n%s\nEvolved fitness: %s\n' % (a, b, c))

    if bucket:
        os.system('gsutil cp gs://%s/evolve.txt .' % bucket)  # download evolve.txt

    with open('evolve.txt', 'a') as f:  # append result
        f.write(c + b + '\n')
    x = np.unique(np.loadtxt('evolve.txt', ndmin=2), axis=0)  # load unique rows
    np.savetxt('evolve.txt', x[np.argsort(-fitness(x))], '%10.3g')  # save sort by fitness

    if bucket:
        os.system('gsutil cp evolve.txt gs://%s' % bucket)  # upload evolve.txt 
Example #22
Source File: utils.py    From pruning_yolov3 with GNU General Public License v3.0 6 votes vote down vote up
def plot_results(start=0, stop=0):  # from utils.utils import *; plot_results()
    # Plot training results files 'results*.txt'
    fig, ax = plt.subplots(2, 5, figsize=(14, 7))
    ax = ax.ravel()
    s = ['GIoU', 'Objectness', 'Classification', 'Precision', 'Recall',
         'val GIoU', 'val Objectness', 'val Classification', 'mAP', 'F1']
    for f in sorted(glob.glob('results*.txt') + glob.glob('../../Downloads/results*.txt')):
        results = np.loadtxt(f, usecols=[2, 3, 4, 8, 9, 12, 13, 14, 10, 11], ndmin=2).T
        n = results.shape[1]  # number of rows
        x = range(start, min(stop, n) if stop else n)
        for i in range(10):
            y = results[i, x]
            if i in [0, 1, 2, 5, 6, 7]:
                y[y == 0] = np.nan  # dont show zero loss values
            ax[i].plot(x, y, marker='.', label=f.replace('.txt', ''))
            ax[i].set_title(s[i])
            if i in [5, 6, 7]:  # share train and val loss y axes
                ax[i].get_shared_y_axes().join(ax[i], ax[i - 5])

    fig.tight_layout()
    ax[1].legend()
    fig.savefig('results.png', dpi=200) 
Example #23
Source File: utils.py    From pruning_yolov3 with GNU General Public License v3.0 6 votes vote down vote up
def plot_results_overlay(start=0, stop=0):  # from utils.utils import *; plot_results_overlay()
    # Plot training results files 'results*.txt', overlaying train and val losses
    s = ['train', 'train', 'train', 'Precision', 'mAP', 'val', 'val', 'val', 'Recall', 'F1']  # legends
    t = ['GIoU', 'Objectness', 'Classification', 'P-R', 'mAP-F1']  # titles
    for f in sorted(glob.glob('results*.txt') + glob.glob('../../Downloads/results*.txt')):
        results = np.loadtxt(f, usecols=[2, 3, 4, 8, 9, 12, 13, 14, 10, 11], ndmin=2).T
        n = results.shape[1]  # number of rows
        x = range(start, min(stop, n) if stop else n)
        fig, ax = plt.subplots(1, 5, figsize=(14, 3.5))
        ax = ax.ravel()
        for i in range(5):
            for j in [i, i + 5]:
                y = results[j, x]
                if i in [0, 1, 2]:
                    y[y == 0] = np.nan  # dont show zero loss values
                ax[i].plot(x, y, marker='.', label=s[j])
            ax[i].set_title(t[i])
            ax[i].legend()
            ax[i].set_ylabel(f) if i == 0 else None  # add filename
        fig.tight_layout()
        fig.savefig(f.replace('.txt', '.png'), dpi=200) 
Example #24
Source File: data_io.py    From Kaggler with MIT License 6 votes vote down vote up
def load_csv(path):
    """Load data from a CSV file.

    Args:
        path (str): A path to the CSV format file containing data.
        dense (boolean): An optional variable indicating if the return matrix
                         should be dense.  By default, it is false.

    Returns:
        Data matrix X and target vector y
    """

    with open(path) as f:
        line = f.readline().strip()

    X = np.loadtxt(path, delimiter=',',
                   skiprows=0 if is_number(line.split(',')[0]) else 1)

    y = np.array(X[:, 0]).flatten()
    X = X[:, 1:]

    return X, y 
Example #25
Source File: test_topfarm.py    From TOPFARM with GNU Affero General Public License v3.0 6 votes vote down vote up
def test_2x3(self):
        # Loading the water depth map
        dat = loadtxt('data/WaterDepth1.dat')
        X, Y = meshgrid(linspace(0., 1000., 50), linspace(0., 1000., 50))
        depth = array(zip(X.flatten(), Y.flatten(), dat.flatten()))
        borders = array([[200, 200], [150, 500], [200, 800], [600, 900], [700, 700], [900, 500], [800, 200], [500, 100], [200, 200]])
        baseline = array([[587.5, 223.07692308], [525., 346.15384615], [837.5, 530.76923077], [525., 530.76923077], [525., 838.46153846], [837.5, 469.23076923]])

        wt_desc = WTDescFromWTG('data/V80-2MW-offshore.wtg').wt_desc
        wt_layout = GenericWindFarmTurbineLayout([WTPC(wt_desc=wt_desc, position=pos) for pos in baseline])

        t = Topfarm(
            baseline_layout = wt_layout,
            borders = borders,
            depth_map = depth,
            dist_WT_D = 5.0,
            distribution='spiral',
            wind_speeds=[4., 8., 20.],
            wind_directions=linspace(0., 360., 36)[:-1]
        )

        t.run()

        self.fail('make save function')
        t.save() 
Example #26
Source File: datasets.py    From discomll with Apache License 2.0 6 votes vote down vote up
def breastcancer_disc(replication=2):
    f = open(path + "breast_cancer_wisconsin_disc.txt")
    data = np.loadtxt(f, delimiter=",")
    x_train = data[:, range(1, 10)]
    y_train = data[:, 10]
    for j in range(replication - 1):
        x_train = np.vstack([x_train, data[:, range(1, 10)]])
        y_train = np.hstack([y_train, data[:, 10]])

    f = open(path + "breast_cancer_wisconsin_disc_test.txt")
    data = np.loadtxt(f, delimiter=",")
    x_test = data[:, range(1, 10)]
    y_test = data[:, 10]
    for j in range(replication - 1):
        x_test = np.vstack([x_test, data[:, range(1, 10)]])
        y_test = np.hstack([y_test, data[:, 10]])

    return x_train, y_train, x_test, y_test 
Example #27
Source File: test_problems_dascmop.py    From pymoo with Apache License 2.0 5 votes vote down vote up
def load(name, diff):
    path = os.path.join(os.path.dirname(os.path.realpath(__file__)), "resources", "DASCMOP", str(diff))
    X = np.loadtxt(os.path.join(path, "%s.x" % name))
    F = np.loadtxt(os.path.join(path, "%s.f" % name))
    CV = np.loadtxt(os.path.join(path, "%s.cv" % name))[:, None]
    return X, F, -CV 
Example #28
Source File: test_ctaea.py    From pymoo with Apache License 2.0 5 votes vote down vote up
def setUpClass(cls):
        cls.ref_dirs = np.loadtxt(path_to_test_resources('ctaea', 'weights.txt'))
        cls.evaluator = Evaluator() 
Example #29
Source File: test_decomposition.py    From pymoo with Apache License 2.0 5 votes vote down vote up
def test_perp_dist(self):
        np.random.seed(1)
        F = np.random.random((100, 3))
        weights = np.random.random((10, 3))

        D = PerpendicularDistance(_type="python").do(F, weights, _type="many_to_many")
        np.testing.assert_allclose(D, np.loadtxt(path_to_test_resources("perp_dist")))

        D = PerpendicularDistance(_type="cython").do(F, weights, _type="many_to_many")
        np.testing.assert_allclose(D, np.loadtxt(path_to_test_resources("perp_dist"))) 
Example #30
Source File: m_dos_pdos_eigenvalues.py    From pyscf with Apache License 2.0 5 votes vote down vote up
def pdosplot (filename = None, data = None, size = None,  fermi = None):
    if (filename is not None): data = np.loadtxt(filename).T
    elif (data is not None): data = data
    if (size is None): print('Please give number of resolved angular momentum!')
    if (fermi is None): print ('Please give fermi energy')


    import matplotlib.pyplot as plt
    from matplotlib import rc
    plt.rc('text', usetex=True)
    plt.rc('font', family='serif')
    orb_name = ['$s$','$p$','$d$','$f$','$g$','$h$','$i$','$k$']
    orb_colo = ['r','g','b','y','k','m','c','w']
    for i, (n,c) in enumerate(zip(orb_name[0:size],orb_colo[0:size])):
        #GW_spin_UP
        plt.plot(data[0], data[i+1], label='QP- '+n,color=c)
        plt.fill_between(data[0], 0, data[i+1], facecolor=c, alpha=0.5, interpolate=True)
        #MF_spin_UP
        plt.plot(data[0], data[i+size+1], label='MF- '+n, linestyle=':',color=c)
        plt.fill_between(data[0], 0, data[i+size+1], facecolor=c, alpha=0.1, interpolate=True)
        #GW_spin_DN
        plt.plot(data[0], -data[i+2*size+1], label='_nolegend_',color=c)
        plt.fill_between(data[0], 0, -data[i+2*size+1], facecolor=c, alpha=0.5, interpolate=True)
        #MF_spin_DN
        plt.plot(data[0], -data[i+3*size+1], label='_nolegend_', linestyle=':',color=c)
        plt.fill_between(data[0], 0, -data[i+3*size+1], facecolor=c, alpha=0.1, interpolate=True)
    plt.axvline(x=fermi, color='k', linestyle='--') #label='Fermi Energy'
    plt.axhline(y=0,color='k')
    plt.title('PDOS', fontsize=20)
    plt.xlabel('Energy (eV)', fontsize=15) 
    plt.ylabel('Projected Density of States (electron/eV)', fontsize=15)
    plt.legend()
    plt.savefig("pdos.svg", dpi=900)
    plt.show()