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#! /usr/bin/python
# -*- coding: utf8 -*-
import logging
import tensorflow as tf
import numbers
from tensorflow.python.framework import ops
from tensorflow.python.ops import standard_ops
## Cost Functions
def cross_entropy(output, target, name=None):
"""It is a softmax cross-entropy operation, returns the TensorFlow expression of cross-entropy of two distributions, implement
softmax internally. See ``tf.nn.sparse_softmax_cross_entropy_with_logits``.
Parameters
----------
output : Tensorflow variable
A distribution with shape: [batch_size, n_feature].
target : Tensorflow variable
A batch of index with shape: [batch_size, ].
name : string
Name of this loss.
Examples
--------
>>> ce = tl.cost.cross_entropy(y_logits, y_target_logits, 'my_loss')
References
-----------
- About cross-entropy: `wiki <https://en.wikipedia.org/wiki/Cross_entropy>`_.\n
- The code is borrowed from: `here <https://en.wikipedia.org/wiki/Cross_entropy>`_.
"""
# try: # old
# return tf.reduce_mean(tf.nn.sparse_softmax_cross_entropy_with_logits(logits=output, targets=target))
# except: # TF 1.0
assert name is not None, "Please give a unique name to tl.cost.cross_entropy for TF1.0+"
return tf.reduce_mean(tf.nn.sparse_softmax_cross_entropy_with_logits(labels=target, logits=output, name=name))
def sigmoid_cross_entropy(output, target, name=None):
"""It is a sigmoid cross-entropy operation, see ``tf.nn.sigmoid_cross_entropy_with_logits``.
"""
# try: # TF 1.0
return tf.reduce_mean(tf.nn.sigmoid_cross_entropy_with_logits(labels=target, logits=output, name=name))
# except:
# return tf.reduce_mean(tf.nn.sigmoid_cross_entropy_with_logits(logits=output, targets=target))
def binary_cross_entropy(output, target, epsilon=1e-8, name='bce_loss'):
"""Computes binary cross entropy given `output`.
For brevity, let `x = output`, `z = target`. The binary cross entropy loss is
loss(x, z) = - sum_i (x[i] * log(z[i]) + (1 - x[i]) * log(1 - z[i]))
Parameters
----------
output : tensor of type `float32` or `float64`.
target : tensor of the same type and shape as `output`.
epsilon : float
A small value to avoid output is zero.
name : string
An optional name to attach to this layer.
References
-----------
- `DRAW <https://github.com/ericjang/draw/blob/master/draw.py#L73>`_
"""
# from tensorflow.python.framework import ops
# with ops.op_scope([output, target], name, "bce_loss") as name:
# output = ops.convert_to_tensor(output, name="preds")
# target = ops.convert_to_tensor(targets, name="target")
with tf.name_scope(name):
return tf.reduce_mean(tf.reduce_sum(-(target * tf.log(output + epsilon) +
(1. - target) * tf.log(1. - output + epsilon)), axis=1))
def mean_squared_error(output, target, is_mean=False):
"""Return the TensorFlow expression of mean-square-error of two distributions.
Parameters
----------
output : 2D or 4D tensor.
target : 2D or 4D tensor.
is_mean : boolean, if True, use ``tf.reduce_mean`` to compute the loss of one data, otherwise, use ``tf.reduce_sum`` (default).
References
------------
- `Wiki Mean Squared Error <https://en.wikipedia.org/wiki/Mean_squared_error>`_
"""
with tf.name_scope("mean_squared_error_loss"):
if output.get_shape().ndims == 2: # [batch_size, n_feature]
if is_mean:
mse = tf.reduce_mean(tf.reduce_mean(tf.squared_difference(output, target), 1))
else:
mse = tf.reduce_mean(tf.reduce_sum(tf.squared_difference(output, target), 1))
elif output.get_shape().ndims == 4: # [batch_size, w, h, c]
if is_mean:
mse = tf.reduce_mean(tf.reduce_mean(tf.squared_difference(output, target), [1, 2, 3]))
else:
mse = tf.reduce_mean(tf.reduce_sum(tf.squared_difference(output, target), [1, 2, 3]))
return mse
def normalized_mean_square_error(output, target):
"""Return the TensorFlow expression of normalized mean-square-error of two distributions.
Parameters
----------
output : 2D or 4D tensor.
target : 2D or 4D tensor.
"""
with tf.name_scope("mean_squared_error_loss"):
if output.get_shape().ndims == 2: # [batch_size, n_feature]
nmse_a = tf.sqrt(tf.reduce_sum(tf.squared_difference(output, target), axis=1))
nmse_b = tf.sqrt(tf.reduce_sum(tf.square(target), axis=1))
elif output.get_shape().ndims == 4: # [batch_size, w, h, c]
nmse_a = tf.sqrt(tf.reduce_sum(tf.squared_difference(output, target), axis=[1,2,3]))
nmse_b = tf.sqrt(tf.reduce_sum(tf.square(target), axis=[1,2,3]))
nmse = tf.reduce_mean(nmse_a / nmse_b)
return nmse
def dice_coe(output, target, loss_type='jaccard', axis=[1,2,3], smooth=1e-5):
"""Soft dice (Sørensen or Jaccard) coefficient for comparing the similarity
of two batch of data, usually be used for binary image segmentation
i.e. labels are binary. The coefficient between 0 to 1, 1 means totally match.
Parameters
-----------
output : tensor
A distribution with shape: [batch_size, ....], (any dimensions).
target : tensor
A distribution with shape: [batch_size, ....], (any dimensions).
loss_type : string
``jaccard`` or ``sorensen``, default is ``jaccard``.
axis : list of integer
All dimensions are reduced, default ``[1,2,3]``.
smooth : float
This small value will be added to the numerator and denominator.
If both output and target are empty, it makes sure dice is 1.
If either output or target are empty (all pixels are background), dice = ```smooth/(small_value + smooth)``,
then if smooth is very small, dice close to 0 (even the image values lower than the threshold),
so in this case, higher smooth can have a higher dice.
Examples
---------
>>> outputs = tl.act.pixel_wise_softmax(network.outputs)
>>> dice_loss = 1 - tl.cost.dice_coe(outputs, y_)
References
-----------
- `Wiki-Dice <https://en.wikipedia.org/wiki/Sørensen–Dice_coefficient>`_
"""
inse = tf.reduce_sum(output * target, axis=axis)
if loss_type == 'jaccard':
l = tf.reduce_sum(output * output, axis=axis)
r = tf.reduce_sum(target * target, axis=axis)
elif loss_type == 'sorensen':
l = tf.reduce_sum(output, axis=axis)
r = tf.reduce_sum(target, axis=axis)
else:
raise Exception("Unknow loss_type")
## old axis=[0,1,2,3]
# dice = 2 * (inse) / (l + r)
# epsilon = 1e-5
# dice = tf.clip_by_value(dice, 0, 1.0-epsilon) # if all empty, dice = 1
## new haodong
dice = (2. * inse + smooth) / (l + r + smooth)
##
dice = tf.reduce_mean(dice)
return dice
def dice_hard_coe(output, target, threshold=0.5, axis=[1,2,3], smooth=1e-5):
"""Non-differentiable Sørensen–Dice coefficient for comparing the similarity
of two batch of data, usually be used for binary image segmentation i.e. labels are binary.
The coefficient between 0 to 1, 1 if totally match.
Parameters
-----------
output : tensor
A distribution with shape: [batch_size, ....], (any dimensions).
target : tensor
A distribution with shape: [batch_size, ....], (any dimensions).
threshold : float
The threshold value to be true.
axis : list of integer
All dimensions are reduced, default ``[1,2,3]``.
smooth : float
This small value will be added to the numerator and denominator, see ``dice_coe``.
References
-----------
- `Wiki-Dice <https://en.wikipedia.org/wiki/Sørensen–Dice_coefficient>`_
"""
output = tf.cast(output > threshold, dtype=tf.float32)
target = tf.cast(target > threshold, dtype=tf.float32)
inse = tf.reduce_sum(tf.multiply(output, target), axis=axis)
l = tf.reduce_sum(output, axis=axis)
r = tf.reduce_sum(target, axis=axis)
## old axis=[0,1,2,3]
# hard_dice = 2 * (inse) / (l + r)
# epsilon = 1e-5
# hard_dice = tf.clip_by_value(hard_dice, 0, 1.0-epsilon)
## new haodong
hard_dice = (2. * inse + smooth) / (l + r + smooth)
##
hard_dice = tf.reduce_mean(hard_dice)
return hard_dice
def iou_coe(output, target, threshold=0.5, axis=[1,2,3], smooth=1e-5):
"""Non-differentiable Intersection over Union (IoU) for comparing the
similarity of two batch of data, usually be used for evaluating binary image segmentation.
The coefficient between 0 to 1, 1 means totally match.
Parameters
-----------
output : tensor
A distribution with shape: [batch_size, ....], (any dimensions).
target : tensor
A distribution with shape: [batch_size, ....], (any dimensions).
threshold : float
The threshold value to be true.
axis : list of integer
All dimensions are reduced, default ``[1,2,3]``.
smooth : float
This small value will be added to the numerator and denominator, see ``dice_coe``.
Notes
------
- IoU cannot be used as training loss, people usually use dice coefficient for training, IoU and hard-dice for evaluating.
"""
pre = tf.cast(output > threshold, dtype=tf.float32)
truth = tf.cast(target > threshold, dtype=tf.float32)
inse = tf.reduce_sum(tf.multiply(pre, truth), axis=axis) # AND
union = tf.reduce_sum(tf.cast(tf.add(pre, truth)>= 1, dtype=tf.float32), axis=axis) # OR
## old axis=[0,1,2,3]
# epsilon = 1e-5
# batch_iou = inse / (union + epsilon)
## new haodong
batch_iou = (inse + smooth) / (union + smooth)
iou = tf.reduce_mean(batch_iou)
return iou#, pre, truth, inse, union
# ## test soft/hard dice and iou
# import numpy as np
# y = np.zeros((1,10,10,1))
# # y[0,0:5,0:5]=1.0
# o = np.zeros((1,10,10,1))
# # o[:,:,:,:] = 0 # what we want: dice=0 iou=0 OK
# # o[0,0:2,0:2]=0.3 # what we want: dice larger iou=0 OK
# # o[0,0:2,0:2]=0.6 # what we want: dice larger iou small OK
# # o[0,0:3,0:3]=0.6 # what we want: dice larger iou larger OK
# # o[0,0:3,0:3]=1 # what we want: dice larger iou same OK
# # o[0,0:5,0:5]=1 # what we want: dice=1 iou=1 OK
# # o[0,0:5,0:5]=0.3 # what we want: dice smaller iou=0 OK
# # o[0,0:5,0:5]=1e-2 # what we want: dice≈0 iou=0 OK
# # o[0,8:10,8:10]=1.0 # what we want: dice=0 iou=0 OK
# # o[0,8:10,8:10]=1e-10 # what we want: dice=0 iou=0 OK
# # y[:,:,:,:] = o[:,:,:,:] = 0 # what we want: dice=1 iou=1 OK
# ## why in u-net, dice=1 hard-dice=1 iou=1 exist?? print bug?
#
# d = dice_coe(o, y, 'jaccard', smooth=1.)
# hd = dice_hard_coe(o, y, smooth=1e-5)
# i = iou_coe(o, y, smooth=1e-5)
# sess = tf.Session(config=tf.ConfigProto(allow_soft_placement=True))
# # sess.run(tf.local_variables_initializer())
# print(sess.run([d,hd,i]))
# # p, t, i, u = sess.run([pre, truth, inse, union])
# # import pprint
# # pprint.pprint(((y>0.5)*(o>0.5)).astype(int).tolist())
# # pprint.pprint(p.tolist())
# # pprint.pprint(t.tolist())
# # pprint.pprint(i)
# # pprint.pprint(u)
# exit()
def cross_entropy_seq(logits, target_seqs, batch_size=None):#, batch_size=1, num_steps=None):
"""Returns the expression of cross-entropy of two sequences, implement
softmax internally. Normally be used for Fixed Length RNN outputs.
Parameters
----------
logits : Tensorflow variable
2D tensor, ``network.outputs``, [batch_size*n_steps (n_examples), number of output units]
target_seqs : Tensorflow variable
target : 2D tensor [batch_size, n_steps], if the number of step is dynamic, please use ``cross_entropy_seq_with_mask`` instead.
batch_size : None or int.
If not None, the return cost will be divided by batch_size.
Examples
--------
>>> see PTB tutorial for more details
>>> input_data = tf.placeholder(tf.int32, [batch_size, num_steps])
>>> targets = tf.placeholder(tf.int32, [batch_size, num_steps])
>>> cost = tl.cost.cross_entropy_seq(network.outputs, targets)
"""
# try: # TF 1.0
sequence_loss_by_example_fn = tf.contrib.legacy_seq2seq.sequence_loss_by_example
# except:
# sequence_loss_by_example_fn = tf.nn.seq2seq.sequence_loss_by_example
loss = sequence_loss_by_example_fn(
[logits],
[tf.reshape(target_seqs, [-1])],
[tf.ones_like(tf.reshape(target_seqs, [-1]), dtype=tf.float32)])
# [tf.ones([batch_size * num_steps])])
cost = tf.reduce_sum(loss) #/ batch_size
if batch_size is not None:
cost = cost / batch_size
return cost
def cross_entropy_seq_with_mask(logits, target_seqs, input_mask, return_details=False, name=None):
"""Returns the expression of cross-entropy of two sequences, implement
softmax internally. Normally be used for Dynamic RNN outputs.
Parameters
-----------
logits : network identity outputs
2D tensor, ``network.outputs``, [batch_size, number of output units].
target_seqs : int of tensor, like word ID.
[batch_size, ?]
input_mask : the mask to compute loss
The same size with target_seqs, normally 0 and 1.
return_details : boolean
- If False (default), only returns the loss.
- If True, returns the loss, losses, weights and targets (reshape to one vetcor).
Examples
--------
- see Image Captioning Example.
"""
targets = tf.reshape(target_seqs, [-1]) # to one vector
weights = tf.to_float(tf.reshape(input_mask, [-1])) # to one vector like targets
losses = tf.nn.sparse_softmax_cross_entropy_with_logits(logits=logits, labels=targets, name=name) * weights
#losses = tf.reduce_mean(tf.nn.sparse_softmax_cross_entropy_with_logits(logits=logits, labels=targets, name=name)) # for TF1.0 and others
# try: ## TF1.0
loss = tf.divide(tf.reduce_sum(losses), # loss from mask. reduce_sum before element-wise mul with mask !!
tf.reduce_sum(weights),
name="seq_loss_with_mask")
# except: ## TF0.12
# loss = tf.div(tf.reduce_sum(losses), # loss from mask. reduce_sum before element-wise mul with mask !!
# tf.reduce_sum(weights),
# name="seq_loss_with_mask")
if return_details:
return loss, losses, weights, targets
else:
return loss
def cosine_similarity(v1, v2):
"""Cosine similarity [-1, 1], `wiki <https://en.wikipedia.org/wiki/Cosine_similarity>`_.
Parameters
-----------
v1, v2 : tensor of [batch_size, n_feature], with the same number of features.
Returns
-----------
a tensor of [batch_size, ]
"""
# try: ## TF1.0
cost = tf.reduce_sum(tf.multiply(v1, v2), 1) / (tf.sqrt(tf.reduce_sum(tf.multiply(v1, v1), 1)) * tf.sqrt(tf.reduce_sum(tf.multiply(v2, v2), 1)))
# except: ## TF0.12
# cost = tf.reduce_sum(tf.mul(v1, v2), reduction_indices=1) / (tf.sqrt(tf.reduce_sum(tf.mul(v1, v1), reduction_indices=1)) * tf.sqrt(tf.reduce_sum(tf.mul(v2, v2), reduction_indices=1)))
return cost
## Regularization Functions
def li_regularizer(scale, scope=None):
"""li regularization removes the neurons of previous layer, `i` represents `inputs`.\n
Returns a function that can be used to apply group li regularization to weights.\n
The implementation follows `TensorFlow contrib <https://github.com/tensorflow/tensorflow/blob/master/tensorflow/contrib/layers/python/layers/regularizers.py>`_.
Parameters
----------
scale : float
A scalar multiplier `Tensor`. 0.0 disables the regularizer.
scope: An optional scope name for TF12+.
Returns
--------
A function with signature `li(weights, name=None)` that apply Li regularization.
Raises
------
ValueError : if scale is outside of the range [0.0, 1.0] or if scale is not a float.
"""
import numbers
from tensorflow.python.framework import ops
from tensorflow.python.ops import standard_ops
# from tensorflow.python.platform import tf_logging as logging
if isinstance(scale, numbers.Integral):
raise ValueError('scale cannot be an integer: %s' % scale)
if isinstance(scale, numbers.Real):
if scale < 0.:
raise ValueError('Setting a scale less than 0 on a regularizer: %g' %
scale)
if scale >= 1.:
raise ValueError('Setting a scale greater than 1 on a regularizer: %g' %
scale)
if scale == 0.:
logging.info('Scale of 0 disables regularizer.')
return lambda _, name=None: None
def li(weights, name=None):
"""Applies li regularization to weights."""
with tf.name_scope('li_regularizer') as scope:
my_scale = ops.convert_to_tensor(scale,
dtype=weights.dtype.base_dtype,
name='scale')
# if tf.__version__ <= '0.12':
# standard_ops_fn = standard_ops.mul
# else:
standard_ops_fn = standard_ops.multiply
return standard_ops_fn(
my_scale,
standard_ops.reduce_sum(standard_ops.sqrt(standard_ops.reduce_sum(tf.square(weights), 1))),
name=scope)
return li
def lo_regularizer(scale, scope=None):
"""lo regularization removes the neurons of current layer, `o` represents `outputs`\n
Returns a function that can be used to apply group lo regularization to weights.\n
The implementation follows `TensorFlow contrib <https://github.com/tensorflow/tensorflow/blob/master/tensorflow/contrib/layers/python/layers/regularizers.py>`_.
Parameters
----------
scale : float
A scalar multiplier `Tensor`. 0.0 disables the regularizer.
scope: An optional scope name for TF12+.
Returns
-------
A function with signature `lo(weights, name=None)` that apply Lo regularization.
Raises
------
ValueError : If scale is outside of the range [0.0, 1.0] or if scale is not a float.
"""
import numbers
from tensorflow.python.framework import ops
from tensorflow.python.ops import standard_ops
# from tensorflow.python.platform import tf_logging as logging
if isinstance(scale, numbers.Integral):
raise ValueError('scale cannot be an integer: %s' % scale)
if isinstance(scale, numbers.Real):
if scale < 0.:
raise ValueError('Setting a scale less than 0 on a regularizer: %g' %
scale)
if scale >= 1.:
raise ValueError('Setting a scale greater than 1 on a regularizer: %g' %
scale)
if scale == 0.:
logging.info('Scale of 0 disables regularizer.')
return lambda _, name=None: None
def lo(weights, name='lo_regularizer'):
"""Applies group column regularization to weights."""
with tf.name_scope(name) as scope:
my_scale = ops.convert_to_tensor(scale,
dtype=weights.dtype.base_dtype,
name='scale')
# if tf.__version__ <= '0.12':
# standard_ops_fn = standard_ops.mul
# else:
standard_ops_fn = standard_ops.multiply
return standard_ops_fn(
my_scale,
standard_ops.reduce_sum(standard_ops.sqrt(standard_ops.reduce_sum(tf.square(weights), 0))),
name=scope)
return lo
def maxnorm_regularizer(scale=1.0, scope=None):
"""Max-norm regularization returns a function that can be used
to apply max-norm regularization to weights.
About max-norm: `wiki <https://en.wikipedia.org/wiki/Matrix_norm#Max_norm>`_.\n
The implementation follows `TensorFlow contrib <https://github.com/tensorflow/tensorflow/blob/master/tensorflow/contrib/layers/python/layers/regularizers.py>`_.
Parameters
----------
scale : float
A scalar multiplier `Tensor`. 0.0 disables the regularizer.
scope: An optional scope name.
Returns
---------
A function with signature `mn(weights, name=None)` that apply Lo regularization.
Raises
--------
ValueError : If scale is outside of the range [0.0, 1.0] or if scale is not a float.
"""
import numbers
from tensorflow.python.framework import ops
from tensorflow.python.ops import standard_ops
if isinstance(scale, numbers.Integral):
raise ValueError('scale cannot be an integer: %s' % scale)
if isinstance(scale, numbers.Real):
if scale < 0.:
raise ValueError('Setting a scale less than 0 on a regularizer: %g' %
scale)
# if scale >= 1.:
# raise ValueError('Setting a scale greater than 1 on a regularizer: %g' %
# scale)
if scale == 0.:
logging.info('Scale of 0 disables regularizer.')
return lambda _, name=None: None
def mn(weights, name='max_regularizer'):
"""Applies max-norm regularization to weights."""
with tf.name_scope(name) as scope:
my_scale = ops.convert_to_tensor(scale,
dtype=weights.dtype.base_dtype,
name='scale')
# if tf.__version__ <= '0.12':
# standard_ops_fn = standard_ops.mul
# else:
standard_ops_fn = standard_ops.multiply
return standard_ops_fn(my_scale, standard_ops.reduce_max(standard_ops.abs(weights)), name=scope)
return mn
def maxnorm_o_regularizer(scale, scope):
"""Max-norm output regularization removes the neurons of current layer.\n
Returns a function that can be used to apply max-norm regularization to each column of weight matrix.\n
The implementation follows `TensorFlow contrib <https://github.com/tensorflow/tensorflow/blob/master/tensorflow/contrib/layers/python/layers/regularizers.py>`_.
Parameters
----------
scale : float
A scalar multiplier `Tensor`. 0.0 disables the regularizer.
scope: An optional scope name.
Returns
---------
A function with signature `mn_o(weights, name=None)` that apply Lo regularization.
Raises
---------
ValueError : If scale is outside of the range [0.0, 1.0] or if scale is not a float.
"""
import numbers
from tensorflow.python.framework import ops
from tensorflow.python.ops import standard_ops
if isinstance(scale, numbers.Integral):
raise ValueError('scale cannot be an integer: %s' % scale)
if isinstance(scale, numbers.Real):
if scale < 0.:
raise ValueError('Setting a scale less than 0 on a regularizer: %g' %
scale)
# if scale >= 1.:
# raise ValueError('Setting a scale greater than 1 on a regularizer: %g' %
# scale)
if scale == 0.:
logging.info('Scale of 0 disables regularizer.')
return lambda _, name=None: None
def mn_o(weights, name='maxnorm_o_regularizer'):
"""Applies max-norm regularization to weights."""
with tf.name_scope(name) as scope:
my_scale = ops.convert_to_tensor(scale,
dtype=weights.dtype.base_dtype,
name='scale')
if tf.__version__ <= '0.12':
standard_ops_fn = standard_ops.mul
else:
standard_ops_fn = standard_ops.multiply
return standard_ops_fn(my_scale, standard_ops.reduce_sum(standard_ops.reduce_max(standard_ops.abs(weights), 0)), name=scope)
return mn_o
def maxnorm_i_regularizer(scale, scope=None):
"""Max-norm input regularization removes the neurons of previous layer.\n
Returns a function that can be used to apply max-norm regularization to each row of weight matrix.\n
The implementation follows `TensorFlow contrib <https://github.com/tensorflow/tensorflow/blob/master/tensorflow/contrib/layers/python/layers/regularizers.py>`_.
Parameters
----------
scale : float
A scalar multiplier `Tensor`. 0.0 disables the regularizer.
scope: An optional scope name.
Returns
---------
A function with signature `mn_i(weights, name=None)` that apply Lo regularization.
Raises
---------
ValueError : If scale is outside of the range [0.0, 1.0] or if scale is not a float.
"""
import numbers
from tensorflow.python.framework import ops
from tensorflow.python.ops import standard_ops
if isinstance(scale, numbers.Integral):
raise ValueError('scale cannot be an integer: %s' % scale)
if isinstance(scale, numbers.Real):
if scale < 0.:
raise ValueError('Setting a scale less than 0 on a regularizer: %g' %
scale)
# if scale >= 1.:
# raise ValueError('Setting a scale greater than 1 on a regularizer: %g' %
# scale)
if scale == 0.:
logging.info('Scale of 0 disables regularizer.')
return lambda _, name=None: None
def mn_i(weights, name='maxnorm_i_regularizer'):
"""Applies max-norm regularization to weights."""
with tf.name_scope(name) as scope:
my_scale = ops.convert_to_tensor(scale,
dtype=weights.dtype.base_dtype,
name='scale')
if tf.__version__ <= '0.12':
standard_ops_fn = standard_ops.mul
else:
standard_ops_fn = standard_ops.multiply
return standard_ops_fn(my_scale, standard_ops.reduce_sum(standard_ops.reduce_max(standard_ops.abs(weights), 1)), name=scope)
return mn_i
#