Python numpy.sort方法代码示例

# 需要导入模块: import numpy [as 别名]
# 或者: from numpy import sort [as 别名]
def read_cpg_profiles(filenames, log=None, *args, **kwargs):
    """Read methylation profiles.

    Input files can be gzip compressed.

    Returns
    -------
    dict
        `dict (key, value)`, where `key` is the output name and `value` the CpG
        table.
    """

    cpg_profiles = OrderedDict()
    for filename in filenames:
        if log:
            log(filename)
        #cpg_file = dat.GzipFile(filename, 'r')
        cpg_file = get_fh(filename, 'r')
        output_name = split_ext(filename)
        cpg_profile = dat.read_cpg_profile(cpg_file, sort=True, *args, **kwargs)
        cpg_profiles[output_name] = cpg_profile
        cpg_file.close()
    return cpg_profiles 

# 需要导入模块: import numpy [as 别名]
# 或者: from numpy import sort [as 别名]
def map_values(values, pos, target_pos, dtype=None, nan=dat.CPG_NAN):
    """Maps `values` array at positions `pos` to `target_pos`.

    Inserts `nan` for uncovered positions.
    """
    assert len(values) == len(pos)
    assert np.all(pos == np.sort(pos))
    assert np.all(target_pos == np.sort(target_pos))

    values = values.ravel()
    pos = pos.ravel()
    target_pos = target_pos.ravel()
    idx = np.in1d(pos, target_pos)
    pos = pos[idx]
    values = values[idx]
    if not dtype:
        dtype = values.dtype
    target_values = np.empty(len(target_pos), dtype=dtype)
    target_values.fill(nan)
    idx = np.in1d(target_pos, pos).nonzero()[0]
    assert len(idx) == len(values)
    assert np.all(target_pos[idx] == pos)
    target_values[idx] = values
    return target_values 

# 需要导入模块: import numpy [as 别名]
# 或者: from numpy import sort [as 别名]
def map_cpg_tables(cpg_tables, chromo, chromo_pos):
    """Maps values from cpg_tables to `chromo_pos`.

    Positions in `cpg_tables` for `chromo`  must be a subset of `chromo_pos`.
    Inserts `dat.CPG_NAN` for uncovered positions.
    """
    chromo_pos.sort()
    mapped_tables = OrderedDict()
    for name, cpg_table in six.iteritems(cpg_tables):
        cpg_table = cpg_table.loc[cpg_table.chromo == chromo]
        cpg_table = cpg_table.sort_values('pos')
        mapped_table = map_values(cpg_table.value.values,
                                  cpg_table.pos.values,
                                  chromo_pos)
        assert len(mapped_table) == len(chromo_pos)
        mapped_tables[name] = mapped_table
    return mapped_tables 

# 需要导入模块: import numpy [as 别名]
# 或者: from numpy import sort [as 别名]
def add_exon(self, chrom, strand, start, stop):
        if strand != self.strand or chrom != self.chrom:
            print("The exon has different chrom or strand to the transcript.")
            return
        _exon = np.array([start, stop], "int").reshape(1, 2)
        self.exons = np.append(self.exons, _exon, axis=0)
        self.exons = np.sort(self.exons, axis=0)
        self.tranL += abs(int(stop) - int(start) + 1)
        self.exonNum += 1

        self.seglen = np.zeros(self.exons.shape[0] * 2 - 1, "int")
        self.seglen[0] = self.exons[0, 1] - self.exons[0, 0] + 1
        for i in range(1, self.exons.shape[0]):
            self.seglen[i * 2 - 1] = self.exons[i, 0] - self.exons[i - 1, 1] - 1
            self.seglen[i * 2] = self.exons[i, 1] - self.exons[i, 0] + 1

        if ["-", "-1", "0", 0, -1].count(self.strand) > 0:
            self.seglen = self.seglen[::-1] 

# 需要导入模块: import numpy [as 别名]
# 或者: from numpy import sort [as 别名]
def add_exon(self, chrom, strand, start, stop):
        if strand != self.strand or chrom != self.chrom:
            print("The exon has different chrom or strand to the transcript.")
            return
        _exon = np.array([start, stop], "int").reshape(1,2)
        self.exons = np.append(self.exons, _exon, axis=0)
        self.exons = np.sort(self.exons, axis=0)
        self.tranL += abs(int(stop) - int(start) + 1)
        self.exonNum += 1


        self.seglen = np.zeros(self.exons.shape[0] * 2 - 1, "int")
        self.seglen[0] = self.exons[0,1]-self.exons[0,0] + 1
        for i in range(1, self.exons.shape[0]):
            self.seglen[i*2-1] = self.exons[i,0]-self.exons[i-1,1] - 1
            self.seglen[i*2] = self.exons[i,1]-self.exons[i,0] + 1

        if ["-","-1","0",0,-1].count(self.strand) > 0:
            self.seglen = self.seglen[::-1] 

# 需要导入模块: import numpy [as 别名]
# 或者: from numpy import sort [as 别名]
def test_convert_to_normalized_and_back(self):
    coordinates = np.random.uniform(size=(100, 4))
    coordinates = np.round(np.sort(coordinates) * 200)
    coordinates[:, 2:4] += 1
    coordinates[99, :] = [0, 0, 201, 201]
    img = tf.ones((128, 202, 202, 3))

    boxlist = box_list.BoxList(tf.constant(coordinates, tf.float32))
    boxlist = box_list_ops.to_normalized_coordinates(boxlist,
                                                     tf.shape(img)[1],
                                                     tf.shape(img)[2])
    boxlist = box_list_ops.to_absolute_coordinates(boxlist,
                                                   tf.shape(img)[1],
                                                   tf.shape(img)[2])

    with self.test_session() as sess:
      out = sess.run(boxlist.get())
      self.assertAllClose(out, coordinates) 

# 需要导入模块: import numpy [as 别名]
# 或者: from numpy import sort [as 别名]
def test_convert_to_absolute_and_back(self):
    coordinates = np.random.uniform(size=(100, 4))
    coordinates = np.sort(coordinates)
    coordinates[99, :] = [0, 0, 1, 1]
    img = tf.ones((128, 202, 202, 3))

    boxlist = box_list.BoxList(tf.constant(coordinates, tf.float32))
    boxlist = box_list_ops.to_absolute_coordinates(boxlist,
                                                   tf.shape(img)[1],
                                                   tf.shape(img)[2])
    boxlist = box_list_ops.to_normalized_coordinates(boxlist,
                                                     tf.shape(img)[1],
                                                     tf.shape(img)[2])

    with self.test_session() as sess:
      out = sess.run(boxlist.get())
      self.assertAllClose(out, coordinates) 

# 需要导入模块: import numpy [as 别名]
# 或者: from numpy import sort [as 别名]
def test_all_columns_accounted_for(self):
    # Note: deliberately setting to small number so not always
    # all possibilities appear (matched, unmatched, ignored)
    num_matches = 10
    match_results = tf.random_uniform(
        [num_matches], minval=-2, maxval=5, dtype=tf.int32)
    match = matcher.Match(match_results)
    matched_column_indices = match.matched_column_indices()
    unmatched_column_indices = match.unmatched_column_indices()
    ignored_column_indices = match.ignored_column_indices()
    with self.test_session() as sess:
      matched, unmatched, ignored = sess.run([
          matched_column_indices, unmatched_column_indices,
          ignored_column_indices
      ])
      all_indices = np.hstack((matched, unmatched, ignored))
      all_indices_sorted = np.sort(all_indices)
      self.assertAllEqual(all_indices_sorted,
                          np.arange(num_matches, dtype=np.int32)) 

# 需要导入模块: import numpy [as 别名]
# 或者: from numpy import sort [as 别名]
def test_honor_arange(self):
        """
        Tests that the input range for semi-major axis is properly set.
        """

        exclude_setrange = ['EarthTwinHabZone1', 'EarthTwinHabZone2', 'JupiterTwin',
                            'AlbedoByRadiusDulzPlavchan', 'DulzPlavchan', 'EarthTwinHabZone1SDET',
                            'EarthTwinHabZone3', 'EarthTwinHabZoneSDET']

        arangein = np.sort(np.random.rand(2)*10.0)
        
        for mod in self.allmods:
            if mod.__name__ not in exclude_setrange:
                with RedirectStreams(stdout=self.dev_null):
                    obj = mod(arange = arangein,**self.spec)

                #test that the correct input arange is used
                self.assertTrue(obj.arange[0].value == arangein[0],'sma low bound set failed for %s'%mod.__name__)
                self.assertTrue(obj.arange[1].value == arangein[1],'sma high bound set failed for %s'%mod.__name__)

                # test that an incorrect input arange is corrected
                with RedirectStreams(stdout=self.dev_null):
                    obj = mod(arange=arangein[::-1], **self.spec)
                self.assertTrue(obj.arange[0].value == arangein.min(), 'sma low bound set failed for %s' % mod.__name__)
                self.assertTrue(obj.arange[1].value == arangein.max(), 'sma high bound set failed for %s' % mod.__name__) 

# 需要导入模块: import numpy [as 别名]
# 或者: from numpy import sort [as 别名]
def test_revise_update(self):
        """
        Ensure that target completeness update revisions are appropriately sized
        """
    
        for mod in self.allmods:
            if 'revise_updates' not in mod.__dict__:
                continue

            with RedirectStreams(stdout=self.dev_null):
                obj = mod(**copy.deepcopy(self.spec))
                obj.gen_update(self.TL)

            ind = np.sort(np.random.choice(self.TL.nStars,size=int(self.TL.nStars/2.0),replace=False))
            obj.revise_updates(ind)

            self.assertTrue(obj.updates.shape == (len(ind),5),"Updates array improperly resized for %s"%mod.__name__) 

# 需要导入模块: import numpy [as 别名]
# 或者: from numpy import sort [as 别名]
def train_model(self):
        minibatch = random.sample(self.memory, self.batch_size)
        state_stack = [mini[0] for mini in minibatch]
        next_state_stack = [mini[1] for mini in minibatch]
        action_stack = [mini[2] for mini in minibatch]
        reward_stack = [mini[3] for mini in minibatch]
        done_stack = [mini[4] for mini in minibatch]
        done_stack = [int(i) for i in done_stack]
        onehotaction = np.zeros([self.batch_size, self.output_size])
        for i, j in zip(onehotaction, action_stack):
            i[j] = 1
        action_stack = np.stack(onehotaction)

        Q_next_state = self.sess.run(self.target_network, feed_dict={self.targetNet.input: next_state_stack})
        next_action = np.argmax(np.mean(Q_next_state, axis=2), axis=1)
        Q_next_state_next_action = [Q_next_state[i, action, :] for i, action in enumerate(next_action)]
        Q_next_state_next_action = np.sort(Q_next_state_next_action)
        T_theta = [np.ones(self.num_support) * reward if done else reward + self.gamma * Q for reward, Q, done in
                    zip(reward_stack, Q_next_state_next_action, done_stack)]
        _, l = self.sess.run([self.train_op, self.loss],
                                feed_dict={self.mainNet.input: state_stack, self.action: action_stack, self.Y: T_theta})
        return l 

# 需要导入模块: import numpy [as 别名]
# 或者: from numpy import sort [as 别名]
def map_onto_unit_simplex(rnd, method):
    n_points, n_dim = rnd.shape

    if method == "sum":
        ret = rnd / rnd.sum(axis=1)[:, None]

    elif method == "kraemer":
        M = sys.maxsize

        rnd *= M
        rnd = rnd[:, :n_dim - 1]
        rnd = np.column_stack([np.zeros(n_points), rnd, np.full(n_points, M)])

        rnd = np.sort(rnd, axis=1)

        ret = np.full((n_points, n_dim), np.nan)
        for i in range(1, n_dim + 1):
            ret[:, i - 1] = rnd[:, i] - rnd[:, i - 1]
        ret /= M

    else:
        raise Exception("Invalid unit simplex mapping!")

    return ret 

# 需要导入模块: import numpy [as 别名]
# 或者: from numpy import sort [as 别名]
def order_crossover_contributed_no_shift(x1, x2, seq=None):
    assert len(x1) == len(x2)

    if seq is not None:
        start, end = seq
    else:
        start, end = np.sort(np.random.choice(len(x1), 2, replace=False))

    y1 = x1.copy()
    y2 = x2.copy()
    # build y1 and y2
    segment1 = set(y1[start:end])
    segment2 = set(y2[start:end])
    I = np.concatenate((np.arange(0, start), np.arange(end, len(x1))))

    # find elements in x2 that are not in segment1
    y1[I] = [y for y in x2 if y not in segment1]
    # find elements in x1 that are not in segment2
    y2[I] = [y for y in x1 if y not in segment2]

    return y1, y2 

# 需要导入模块: import numpy [as 别名]
# 或者: from numpy import sort [as 别名]
def diagonalize(a, b, nroots=4):
    a_aa, a_ab, a_bb = a
    b_aa, b_ab, b_bb = b
    nocc_a, nvir_a, nocc_b, nvir_b = a_ab.shape
    a_aa = a_aa.reshape((nocc_a*nvir_a,nocc_a*nvir_a))
    a_ab = a_ab.reshape((nocc_a*nvir_a,nocc_b*nvir_b))
    a_bb = a_bb.reshape((nocc_b*nvir_b,nocc_b*nvir_b))
    b_aa = b_aa.reshape((nocc_a*nvir_a,nocc_a*nvir_a))
    b_ab = b_ab.reshape((nocc_a*nvir_a,nocc_b*nvir_b))
    b_bb = b_bb.reshape((nocc_b*nvir_b,nocc_b*nvir_b))
    a = numpy.bmat([[ a_aa  , a_ab],
                    [ a_ab.T, a_bb]])
    b = numpy.bmat([[ b_aa  , b_ab],
                    [ b_ab.T, b_bb]])
    e = numpy.linalg.eig(numpy.bmat([[a        , b       ],
                                     [-b.conj(),-a.conj()]]))[0]
    lowest_e = numpy.sort(e[e.real > 0].real)[:nroots]
    return lowest_e 

# 需要导入模块: import numpy [as 别名]
# 或者: from numpy import sort [as 别名]
def dynamic_occ_(mf, tol=1e-3):
    assert(isinstance(mf, hf.RHF))
    old_get_occ = mf.get_occ
    def get_occ(mo_energy, mo_coeff=None):
        mol = mf.mol
        nocc = mol.nelectron // 2
        sort_mo_energy = numpy.sort(mo_energy)
        lumo = sort_mo_energy[nocc]
        if abs(sort_mo_energy[nocc-1] - lumo) < tol:
            mo_occ = numpy.zeros_like(mo_energy)
            mo_occ[mo_energy<lumo] = 2
            lst = abs(mo_energy - lumo) < tol
            mo_occ[lst] = 0
            logger.warn(mf, 'set charge = %d', mol.charge+int(lst.sum())*2)
            logger.info(mf, 'HOMO = %.12g  LUMO = %.12g',
                        sort_mo_energy[nocc-1], sort_mo_energy[nocc])
            logger.debug(mf, '  mo_energy = %s', sort_mo_energy)
        else:
            mo_occ = old_get_occ(mo_energy, mo_coeff)
        return mo_occ
    mf.get_occ = get_occ
    return mf