From 6e4d208ab7862d77ba386516950ec8aa94c7d4aa Mon Sep 17 00:00:00 2001
From: Baptiste Bauvin <baptiste.bauvin@lis-lab.fr>
Date: Tue, 3 Sep 2019 16:10:09 -0400
Subject: [PATCH] ECMLJ_expes
---
.../MonoMultiViewClassifiers/ExecClassif.py | 17 +-
.../Monoview/Additions/BoostUtils.py | 2 +-
.../Monoview/Additions/CBBoostUtils.py | 20 +-
.../Monoview/Additions/CGDescUtils.py | 40 +-
.../Monoview/Additions/_custom_criterion.pyx | 621 +++++++++++++++++-
.../Monoview/ExecClassifMonoView.py | 4 +-
.../Monoview/ExportResults.py | 12 +-
.../Monoview/MonoviewUtils.py | 2 +-
.../MonoviewClassifiers/AdaboostPregen.py | 1 +
.../Multiview/ExecMultiview.py | 4 +-
.../ResultAnalysis.py | 6 +-
.../utils/GetMultiviewDb.py | 47 +-
.../utils/HyperParameterSearch.py | 2 +-
.../utils/execution.py | 2 +-
14 files changed, 711 insertions(+), 69 deletions(-)
diff --git a/multiview_platform/MonoMultiViewClassifiers/ExecClassif.py b/multiview_platform/MonoMultiViewClassifiers/ExecClassif.py
index e75934e9..bcc03aed 100644
--- a/multiview_platform/MonoMultiViewClassifiers/ExecClassif.py
+++ b/multiview_platform/MonoMultiViewClassifiers/ExecClassif.py
@@ -9,6 +9,7 @@ import matplotlib
import itertools
import numpy as np
from joblib import Parallel, delayed
+from sklearn.tree import DecisionTreeClassifier
matplotlib.use(
'Agg') # Anti-Grain Geometry C++ library to make a raster (pixel) image of the figure
@@ -183,15 +184,23 @@ def gen_multiple_kwargs_combinations(clKWARGS):
keys = clKWARGS.keys()
kwargs_combination = [dict((key, value) for key, value in zip(keys, values))
for values in values_cartesian_prod]
- return kwargs_combination
+
+ reduce_dict = {DecisionTreeClassifier: "DT", }
+ reduced_listed_values = [
+ [_ if type(_) not in reduce_dict else reduce_dict[type(_)] for _ in
+ list_] for list_ in listed_values]
+ reduced_values_cartesian_prod = [_ for _ in itertools.product(*reduced_listed_values)]
+ reduced_kwargs_combination = [dict((key, value) for key, value in zip(keys, values))
+ for values in reduced_values_cartesian_prod]
+ return kwargs_combination, reduced_kwargs_combination
def gen_multiple_args_dictionnaries(nbClass, kwargsInit,
classifier, viewName, viewIndex):
- multiple_kwargs_list = gen_multiple_kwargs_combinations(kwargsInit[classifier + "KWARGSInit"])
+ multiple_kwargs_list, reduced_multiple_kwargs_list = gen_multiple_kwargs_combinations(kwargsInit[classifier + "KWARGSInit"])
multiple_kwargs_dict = dict(
- (classifier+"_"+"_".join(map(str,list(dictionary.values()))), dictionary)
- for dictionary in multiple_kwargs_list)
+ (classifier+"_"+"_".join(map(str,list(reduced_dictionary.values()))), dictionary)
+ for reduced_dictionary, dictionary in zip(reduced_multiple_kwargs_list, multiple_kwargs_list ))
args_dictionnaries = [{
"args": {classifier_name + "KWARGS": arguments,
"feat": viewName,
diff --git a/multiview_platform/MonoMultiViewClassifiers/Monoview/Additions/BoostUtils.py b/multiview_platform/MonoMultiViewClassifiers/Monoview/Additions/BoostUtils.py
index 5573f626..10f034b7 100644
--- a/multiview_platform/MonoMultiViewClassifiers/Monoview/Additions/BoostUtils.py
+++ b/multiview_platform/MonoMultiViewClassifiers/Monoview/Additions/BoostUtils.py
@@ -851,7 +851,7 @@ def get_accuracy_graph(plotted_data, classifier_name, file_name,
# plt.tight_layout()
else:
ax.legend((scat,), (name,))
- f.savefig(file_name)
+ f.savefig(file_name, transparent=True)
plt.close()
diff --git a/multiview_platform/MonoMultiViewClassifiers/Monoview/Additions/CBBoostUtils.py b/multiview_platform/MonoMultiViewClassifiers/Monoview/Additions/CBBoostUtils.py
index 3187fc8f..38b3ab87 100644
--- a/multiview_platform/MonoMultiViewClassifiers/Monoview/Additions/CBBoostUtils.py
+++ b/multiview_platform/MonoMultiViewClassifiers/Monoview/Additions/CBBoostUtils.py
@@ -17,11 +17,11 @@ from ... import Metrics
# Used for CBBoost
class CBBoostClassifier(BaseEstimator, ClassifierMixin, BaseBoost):
- def __init__(self, n_max_iterations=None, estimators_generator=None,
- random_state=42, self_complemented=True, twice_the_same=False,
- random_start=True, n_stumps=1, c_bound_sol=True,
- plotted_metric=Metrics.zero_one_loss, save_train_data=True,
- test_graph=True, mincq_tracking=True):
+ def __init__(self, n_max_iterations=100, estimators_generator="Stumps",
+ random_state=42, self_complemented=True, twice_the_same=True,
+ random_start=False, n_stumps=1, c_bound_sol=True,
+ plotted_metric=Metrics.zero_one_loss, save_train_data=False,
+ test_graph=True, mincq_tracking=False):
super(CBBoostClassifier, self).__init__()
r"""
@@ -240,16 +240,6 @@ class CBBoostClassifier(BaseEstimator, ClassifierMixin, BaseBoost):
self.new_voter = self.classification_matrix[:, new_voter_index].reshape(
(self.n_total_examples, 1))
- # def choose_new_voter(self, y_kernel_matrix, formatted_y):
- # """Used to choose the voter according to the specified criterion (margin or C-Bound"""
- # if self.c_bound_choice:
- # sol, new_voter_index = self._find_new_voter(y_kernel_matrix,
- # formatted_y)
- # else:
- # new_voter_index, sol = self._find_best_weighted_margin(
- # y_kernel_matrix)
- # return sol, new_voter_index
-
def init_boosting(self, m, y, y_kernel_matrix):
"""THis initialization corressponds to the first round of boosting with equal weights for each examples and the voter chosen by it's margin."""
diff --git a/multiview_platform/MonoMultiViewClassifiers/Monoview/Additions/CGDescUtils.py b/multiview_platform/MonoMultiViewClassifiers/Monoview/Additions/CGDescUtils.py
index cfc5765a..0fbc8b08 100644
--- a/multiview_platform/MonoMultiViewClassifiers/Monoview/Additions/CGDescUtils.py
+++ b/multiview_platform/MonoMultiViewClassifiers/Monoview/Additions/CGDescUtils.py
@@ -22,7 +22,7 @@ class ColumnGenerationClassifierQar(BaseEstimator, ClassifierMixin, BaseBoost):
c_bound_choice=True, random_start=True,
n_stumps=1, use_r=True, c_bound_sol=True,
plotted_metric=Metrics.zero_one_loss, save_train_data=True,
- test_graph=True, mincq_tracking=True):
+ test_graph=True, mincq_tracking=False):
super(ColumnGenerationClassifierQar, self).__init__()
r"""
@@ -104,15 +104,15 @@ class ColumnGenerationClassifierQar(BaseEstimator, ClassifierMixin, BaseBoost):
# Print dynamically the step and the error of the current classifier
self.it = k
- print(
- "Resp. bound : {}, {}; {}/{}, eps :{}, ".format(
- self.respected_bound,
- self.bounds[-1] > self.train_metrics[-1],
- k + 2,
- self.n_max_iterations,
- self.voter_perfs[-1],
- ),
- end="\r")
+ # print(
+ # "Resp. bound : {}, {}; {}/{}, eps :{}, ".format(
+ # self.respected_bound,
+ # self.bounds[-1] > self.train_metrics[-1],
+ # k + 2,
+ # self.n_max_iterations,
+ # self.voter_perfs[-1],
+ # ),
+ # end="\r")
sol, new_voter_index = self.choose_new_voter(y_kernel_matrix,
formatted_y)
if type(sol) == str:
@@ -132,8 +132,8 @@ class ColumnGenerationClassifierQar(BaseEstimator, ClassifierMixin, BaseBoost):
self.raw_weights = self.weights_
self.y_train = formatted_y
- print(self.classification_matrix)
- print(self.weights_, self.break_cause)
+ # print(self.classification_matrix)
+ # print(self.weights_, self.break_cause)
self.weights_ = np.array(self.weights_)
self.weights_ /= np.sum(self.weights_)
@@ -451,11 +451,26 @@ class ColumnGenerationClassifierQar(BaseEstimator, ClassifierMixin, BaseBoost):
self.A2s = np.sum(weighted_hypothesis, axis=0) ** 2
self.A1s = np.sum(weighted_hypothesis, axis=0) * margin_old * 2
self.A0 = margin_old ** 2
+ import matplotlib.pyplot as plt
+ # plt.plot(self.A2s * 0.5 * self.B1s / m**3)
+ # plt.plot(np.array([margin_old/m for _ in range(len(self.A2s))]))
+ # plt.savefig("try.png")
+
+ # print("C2 < 0 :", np.where(np.array([margin_old/m for _ in range(len(self.A2s))]) < np.sqrt(self.A2s) * 0.5 * self.B1s / m**2)[0])
+ # print("C1 < 0 :", np.where(np.array([margin_old ** 2 / m for _ in range(
+ # len(self.A2s))]) < self.A2s * self.B0 / m ** 2)[0])
+ # print("Double root:", np.where((0.5 * self.B1s / m)**2 * m > self.B0)[0])
+
C2s = (self.A1s * self.B2 - self.A2s * self.B1s)
+ # print("Wrong C2 :" , np.where(C2s < 0)[0].shape, bad_margins.shape)
C1s = 2 * (self.A0 * self.B2 - self.A2s * self.B0)
+ # print("Wrong C2 :", np.where(C1s < 0)[0].shape, bad_margins.shape)
C0s = self.A0 * self.B1s - self.A1s * self.B0
+ # print(np.where(C2s==0))
+ # print(self.chosen_columns_)
+
sols = np.zeros(C0s.shape) - 3
# sols[np.where(C2s == 0)[0]] = C0s[np.where(C2s == 0)[0]] / C1s[np.where(C2s == 0)[0]]
sols[np.where(C2s != 0)[0]] = (-C1s[np.where(C2s != 0)[0]] + np.sqrt(
@@ -469,7 +484,6 @@ class ColumnGenerationClassifierQar(BaseEstimator, ClassifierMixin, BaseBoost):
return "No more pertinent voters", 0
else:
best_hyp_index = np.argmin(masked_c_bounds)
-
self.c_bounds.append(masked_c_bounds[best_hyp_index])
self.margins.append(math.sqrt(self.A2s[best_hyp_index] / m))
self.disagreements.append(0.5 * self.B1s[best_hyp_index] / m)
diff --git a/multiview_platform/MonoMultiViewClassifiers/Monoview/Additions/_custom_criterion.pyx b/multiview_platform/MonoMultiViewClassifiers/Monoview/Additions/_custom_criterion.pyx
index 8e50ea22..f6deb43e 100644
--- a/multiview_platform/MonoMultiViewClassifiers/Monoview/Additions/_custom_criterion.pyx
+++ b/multiview_platform/MonoMultiViewClassifiers/Monoview/Additions/_custom_criterion.pyx
@@ -1,3 +1,11 @@
+from sklearn.tree._criterion import ClassificationCriterion
+
+class Cbound(ClassificationCriterion):
+ def node_impurity(self):
+ pass
+
+
+
# # cython: cdivision=True
# # cython: boundscheck=False
# # cython: wraparound=False
@@ -14,6 +22,22 @@
# # Jacob Schreiber <jmschreiber91@gmail.com>
# # Nelson Liu <nelson@nelsonliu.me>
# #
+# # License: BSD 3 clause# cython: cdivision=True
+# # cython: boundscheck=False
+# # cython: wraparound=False
+#
+# # Authors: Gilles Louppe <g.louppe@gmail.com>
+# # Peter Prettenhofer <peter.prettenhofer@gmail.com>
+# # Brian Holt <bdholt1@gmail.com>
+# # Noel Dawe <noel@dawe.me>
+# # Satrajit Gosh <satrajit.ghosh@gmail.com>
+# # Lars Buitinck
+# # Arnaud Joly <arnaud.v.joly@gmail.com>
+# # Joel Nothman <joel.nothman@gmail.com>
+# # Fares Hedayati <fares.hedayati@gmail.com>
+# # Jacob Schreiber <jmschreiber91@gmail.com>
+# # Nelson Liu <nelson@nelsonliu.me>
+# #
# # License: BSD 3 clause
#
# calloc
@@ -76,7 +100,602 @@
# cdef
#
#
-# class CustomCriterion:
+# class CustomCriterion(Criterion):
+# """Interface for impurity criteria.
+# This object stores methods on how to calculate how good a split is using
+# different metrics.
+# """
+#
+# def __dealloc__(self):
+# """Destructor."""
+#
+# free(self.sum_total)
+# free(self.sum_left)
+# free(self.sum_right)
+#
+# def __getstate__(self):
+# return {}
+#
+# def __setstate__(self, d):
+# pass
+#
+# cdef
+# int
+# init(self, DOUBLE_t * y, SIZE_t
+# y_stride, DOUBLE_t * sample_weight,
+# double
+# weighted_n_samples, SIZE_t * samples, SIZE_t
+# start,
+# SIZE_t
+# end) nogil except -1:
+# """Placeholder for a method which will initialize the criterion.
+# Returns -1 in case of failure to allocate memory (and raise MemoryError)
+# or 0 otherwise.
+# Parameters
+# ----------
+# y : array-like, dtype=DOUBLE_t
+# y is a buffer that can store values for n_outputs target variables
+# y_stride : SIZE_t
+# y_stride is used to index the kth output value as follows:
+# y[i, k] = y[i * y_stride + k]
+# sample_weight : array-like, dtype=DOUBLE_t
+# The weight of each sample
+# weighted_n_samples : DOUBLE_t
+# The total weight of the samples being considered
+# samples : array-like, dtype=DOUBLE_t
+# Indices of the samples in X and y, where samples[start:end]
+# correspond to the samples in this node
+# start : SIZE_t
+# The first sample to be used on this node
+# end : SIZE_t
+# The last sample used on this node
+# """
+#
+# pass
+# #
+# # cdef int reset(self) nogil except -1:
+# # """Reset the criterion at pos=start.
+# # This method must be implemented by the subclass.
+# # """
+# #
+# # pass
+# #
+# # cdef int reverse_reset(self) nogil except -1:
+# # """Reset the criterion at pos=end.
+# # This method must be implemented by the subclass.
+# # """
+# # pass
+# #
+# # cdef int update(self, SIZE_t new_pos) nogil except -1:
+# # """Updated statistics by moving samples[pos:new_pos] to the left child.
+# # This updates the collected statistics by moving samples[pos:new_pos]
+# # from the right child to the left child. It must be implemented by
+# # the subclass.
+# # Parameters
+# # ----------
+# # new_pos : SIZE_t
+# # New starting index position of the samples in the right child
+# # """
+# #
+# # pass
+# #
+# # cdef double node_impurity(self) nogil:
+# # """Placeholder for calculating the impurity of the node.
+# # Placeholder for a method which will evaluate the impurity of
+# # the current node, i.e. the impurity of samples[start:end]. This is the
+# # primary function of the criterion class.
+# # """
+# #
+# # pass
+# #
+# # cdef void children_impurity(self, double* impurity_left,
+# # double* impurity_right) nogil:
+# # """Placeholder for calculating the impurity of children.
+# # Placeholder for a method which evaluates the impurity in
+# # children nodes, i.e. the impurity of samples[start:pos] + the impurity
+# # of samples[pos:end].
+# # Parameters
+# # ----------
+# # impurity_left : double pointer
+# # The memory address where the impurity of the left child should be
+# # stored.
+# # impurity_right : double pointer
+# # The memory address where the impurity of the right child should be
+# # stored
+# # """
+# #
+# # pass
+# #
+# # cdef void node_value(self, double* dest) nogil:
+# # """Placeholder for storing the node value.
+# # Placeholder for a method which will compute the node value
+# # of samples[start:end] and save the value into dest.
+# # Parameters
+# # ----------
+# # dest : double pointer
+# # The memory address where the node value should be stored.
+# # """
+# #
+# # pass
+# #
+# # cdef double proxy_impurity_improvement(self) nogil:
+# # """Compute a proxy of the impurity reduction
+# # This method is used to speed up the search for the best split.
+# # It is a proxy quantity such that the split that maximizes this value
+# # also maximizes the impurity improvement. It neglects all constant terms
+# # of the impurity decrease for a given split.
+# # The absolute impurity improvement is only computed by the
+# # impurity_improvement method once the best split has been found.
+# # """
+# # cdef double impurity_left
+# # cdef double impurity_right
+# # self.children_impurity(&impurity_left, &impurity_right)
+# #
+# # return (- self.weighted_n_right * impurity_right
+# # - self.weighted_n_left * impurity_left)
+# #
+# # cdef double impurity_improvement(self, double impurity) nogil:
+# # """Compute the improvement in impurity
+# # This method computes the improvement in impurity when a split occurs.
+# # The weighted impurity improvement equation is the following:
+# # N_t / N * (impurity - N_t_R / N_t * right_impurity
+# # - N_t_L / N_t * left_impurity)
+# # where N is the total number of samples, N_t is the number of samples
+# # at the current node, N_t_L is the number of samples in the left child,
+# # and N_t_R is the number of samples in the right child,
+# # Parameters
+# # ----------
+# # impurity : double
+# # The initial impurity of the node before the split
+# # Return
+# # ------
+# # double : improvement in impurity after the split occurs
+# # """
+# #
+# # cdef double impurity_left
+# # cdef double impurity_right
+# #
+# # self.children_impurity(&impurity_left, &impurity_right)
+# #
+# # return ((self.weighted_n_node_samples / self.weighted_n_samples) *
+# # (impurity - (self.weighted_n_right /
+# # self.weighted_n_node_samples * impurity_right)
+# # - (self.weighted_n_left /
+# # self.weighted_n_node_samples * impurity_left)))
+# #
+# #
+# # cdef class CustomClassificationCriterion(Criterion):
+# # """Abstract criterion for classification."""
+# #
+# # def __cinit__(self, SIZE_t n_outputs,
+# # np.ndarray[SIZE_t, ndim=1] n_classes):
+# # """Initialize attributes for this criterion.
+# # Parameters
+# # ----------
+# # n_outputs : SIZE_t
+# # The number of targets, the dimensionality of the prediction
+# # n_classes : numpy.ndarray, dtype=SIZE_t
+# # The number of unique classes in each target
+# # """
+# #
+# # self.y = NULL
+# # self.y_stride = 0
+# # self.sample_weight = NULL
+# #
+# # self.samples = NULL
+# # self.start = 0
+# # self.pos = 0
+# # self.end = 0
+# #
+# # self.n_outputs = n_outputs
+# # self.n_samples = 0
+# # self.n_node_samples = 0
+# # self.weighted_n_node_samples = 0.0
+# # self.weighted_n_left = 0.0
+# # self.weighted_n_right = 0.0
+# #
+# # # Count labels for each output
+# # self.sum_total = NULL
+# # self.sum_left = NULL
+# # self.sum_right = NULL
+# # self.n_classes = NULL
+# #
+# # safe_realloc(&self.n_classes, n_outputs)
+# #
+# # cdef SIZE_t k = 0
+# # cdef SIZE_t sum_stride = 0
+# #
+# # # For each target, set the number of unique classes in that target,
+# # # and also compute the maximal stride of all targets
+# # for k in range(n_outputs):
+# # self.n_classes[k] = n_classes[k]
+# #
+# # if n_classes[k] > sum_stride:
+# # sum_stride = n_classes[k]
+# #
+# # self.sum_stride = sum_stride
+# #
+# # cdef SIZE_t n_elements = n_outputs * sum_stride
+# # self.sum_total = <double*> calloc(n_elements, sizeof(double))
+# # self.sum_left = <double*> calloc(n_elements, sizeof(double))
+# # self.sum_right = <double*> calloc(n_elements, sizeof(double))
+# #
+# # if (self.sum_total == NULL or
+# # self.sum_left == NULL or
+# # self.sum_right == NULL):
+# # raise MemoryError()
+# #
+# # def __dealloc__(self):
+# # """Destructor."""
+# # free(self.n_classes)
+# #
+# # def __reduce__(self):
+# # return (type(self),
+# # (self.n_outputs,
+# # sizet_ptr_to_ndarray(self.n_classes, self.n_outputs)),
+# # self.__getstate__())
+# #
+# # cdef int init(self, DOUBLE_t* y, SIZE_t y_stride,
+# # DOUBLE_t* sample_weight, double weighted_n_samples,
+# # SIZE_t* samples, SIZE_t start, SIZE_t end) nogil except -1:
+# # """Initialize the criterion at node samples[start:end] and
+# # children samples[start:start] and samples[start:end].
+# # Returns -1 in case of failure to allocate memory (and raise MemoryError)
+# # or 0 otherwise.
+# # Parameters
+# # ----------
+# # y : array-like, dtype=DOUBLE_t
+# # The target stored as a buffer for memory efficiency
+# # y_stride : SIZE_t
+# # The stride between elements in the buffer, important if there
+# # are multiple targets (multi-output)
+# # sample_weight : array-like, dtype=DTYPE_t
+# # The weight of each sample
+# # weighted_n_samples : SIZE_t
+# # The total weight of all samples
+# # samples : array-like, dtype=SIZE_t
+# # A mask on the samples, showing which ones we want to use
+# # start : SIZE_t
+# # The first sample to use in the mask
+# # end : SIZE_t
+# # The last sample to use in the mask
+# # """
+# #
+# # self.y = y
+# # self.y_stride = y_stride
+# # self.sample_weight = sample_weight
+# # self.samples = samples
+# # self.start = start
+# # self.end = end
+# # self.n_node_samples = end - start
+# # self.weighted_n_samples = weighted_n_samples
+# # self.weighted_n_node_samples = 0.0
+# #
+# # cdef SIZE_t* n_classes = self.n_classes
+# # cdef double* sum_total = self.sum_total
+# #
+# # cdef SIZE_t i
+# # cdef SIZE_t p
+# # cdef SIZE_t k
+# # cdef SIZE_t c
+# # cdef DOUBLE_t w = 1.0
+# # cdef SIZE_t offset = 0
+# #
+# # for k in range(self.n_outputs):
+# # memset(sum_total + offset, 0, n_classes[k] * sizeof(double))
+# # offset += self.sum_stride
+# #
+# # for p in range(start, end):
+# # i = samples[p]
+# #
+# # # w is originally set to be 1.0, meaning that if no sample weights
+# # # are given, the default weight of each sample is 1.0
+# # if sample_weight != NULL:
+# # w = sample_weight[i]
+# #
+# # # Count weighted class frequency for each target
+# # for k in range(self.n_outputs):
+# # c = <SIZE_t> y[i * y_stride + k]
+# # sum_total[k * self.sum_stride + c] += w
+# #
+# # self.weighted_n_node_samples += w
+# #
+# # # Reset to pos=start
+# # self.reset()
+# # return 0
+# #
+# # cdef int reset(self) nogil except -1:
+# # """Reset the criterion at pos=start
+# # Returns -1 in case of failure to allocate memory (and raise MemoryError)
+# # or 0 otherwise.
+# # """
+# # self.pos = self.start
+# #
+# # self.weighted_n_left = 0.0
+# # self.weighted_n_right = self.weighted_n_node_samples
+# #
+# # cdef double* sum_total = self.sum_total
+# # cdef double* sum_left = self.sum_left
+# # cdef double* sum_right = self.sum_right
+# #
+# # cdef SIZE_t* n_classes = self.n_classes
+# # cdef SIZE_t k
+# #
+# # for k in range(self.n_outputs):
+# # memset(sum_left, 0, n_classes[k] * sizeof(double))
+# # memcpy(sum_right, sum_total, n_classes[k] * sizeof(double))
+# #
+# # sum_total += self.sum_stride
+# # sum_left += self.sum_stride
+# # sum_right += self.sum_stride
+# # return 0
+# #
+# # cdef int reverse_reset(self) nogil except -1:
+# # """Reset the criterion at pos=end
+# # Returns -1 in case of failure to allocate memory (and raise MemoryError)
+# # or 0 otherwise.
+# # """
+# # self.pos = self.end
+# #
+# # self.weighted_n_left = self.weighted_n_node_samples
+# # self.weighted_n_right = 0.0
+# #
+# # cdef double* sum_total = self.sum_total
+# # cdef double* sum_left = self.sum_left
+# # cdef double* sum_right = self.sum_right
+# #
+# # cdef SIZE_t* n_classes = self.n_classes
+# # cdef SIZE_t k
+# #
+# # for k in range(self.n_outputs):
+# # memset(sum_right, 0, n_classes[k] * sizeof(double))
+# # memcpy(sum_left, sum_total, n_classes[k] * sizeof(double))
+# #
+# # sum_total += self.sum_stride
+# # sum_left += self.sum_stride
+# # sum_right += self.sum_stride
+# # return 0
+# #
+# # cdef int update(self, SIZE_t new_pos) nogil except -1:
+# # """Updated statistics by moving samples[pos:new_pos] to the left child.
+# # Returns -1 in case of failure to allocate memory (and raise MemoryError)
+# # or 0 otherwise.
+# # Parameters
+# # ----------
+# # new_pos : SIZE_t
+# # The new ending position for which to move samples from the right
+# # child to the left child.
+# # """
+# # cdef DOUBLE_t* y = self.y
+# # cdef SIZE_t pos = self.pos
+# # cdef SIZE_t end = self.end
+# #
+# # cdef double* sum_left = self.sum_left
+# # cdef double* sum_right = self.sum_right
+# # cdef double* sum_total = self.sum_total
+# #
+# # cdef SIZE_t* n_classes = self.n_classes
+# # cdef SIZE_t* samples = self.samples
+# # cdef DOUBLE_t* sample_weight = self.sample_weight
+# #
+# # cdef SIZE_t i
+# # cdef SIZE_t p
+# # cdef SIZE_t k
+# # cdef SIZE_t c
+# # cdef SIZE_t label_index
+# # cdef DOUBLE_t w = 1.0
+# #
+# # # Update statistics up to new_pos
+# # #
+# # # Given that
+# # # sum_left[x] + sum_right[x] = sum_total[x]
+# # # and that sum_total is known, we are going to update
+# # # sum_left from the direction that require the least amount
+# # # of computations, i.e. from pos to new_pos or from end to new_po.
+# #
+# # if (new_pos - pos) <= (end - new_pos):
+# # for p in range(pos, new_pos):
+# # i = samples[p]
+# #
+# # if sample_weight != NULL:
+# # w = sample_weight[i]
+# #
+# # for k in range(self.n_outputs):
+# # label_index = (k * self.sum_stride +
+# # <SIZE_t> y[i * self.y_stride + k])
+# # sum_left[label_index] += w
+# #
+# # self.weighted_n_left += w
+# #
+# # else:
+# # self.reverse_reset()
+# #
+# # for p in range(end - 1, new_pos - 1, -1):
+# # i = samples[p]
+# #
+# # if sample_weight != NULL:
+# # w = sample_weight[i]
+# #
+# # for k in range(self.n_outputs):
+# # label_index = (k * self.sum_stride +
+# # <SIZE_t> y[i * self.y_stride + k])
+# # sum_left[label_index] -= w
+# #
+# # self.weighted_n_left -= w
+# #
+# # # Update right part statistics
+# # self.weighted_n_right = self.weighted_n_node_samples - self.weighted_n_left
+# # for k in range(self.n_outputs):
+# # for c in range(n_classes[k]):
+# # sum_right[c] = sum_total[c] - sum_left[c]
+# #
+# # sum_right += self.sum_stride
+# # sum_left += self.sum_stride
+# # sum_total += self.sum_stride
+# #
+# # self.pos = new_pos
+# # return 0
+# #
+# # cdef double node_impurity(self) nogil:
+# # pass
+# #
+# # cdef void children_impurity(self, double* impurity_left,
+# # double* impurity_right) nogil:
+# # pass
+# #
+# # cdef void node_value(self, double* dest) nogil:
+# # """Compute the node value of samples[start:end] and save it into dest.
+# # Parameters
+# # ----------
+# # dest : double pointer
+# # The memory address which we will save the node value into.
+# # """
+# #
+# # cdef double* sum_total = self.sum_total
+# # cdef SIZE_t* n_classes = self.n_classes
+# # cdef SIZE_t k
+# #
+# # for k in range(self.n_outputs):
+# # memcpy(dest, sum_total, n_classes[k] * sizeof(double))
+# # dest += self.sum_stride
+# # sum_total += self.sum_stride
+# #
+# # cdef class CCriterion(CustomClassificationCriterion):
+# # r"""Cross Entropy impurity criterion.
+# # This handles cases where the target is a classification taking values
+# # 0, 1, ... K-2, K-1. If node m represents a region Rm with Nm observations,
+# # then let
+# # count_k = 1 / Nm \sum_{x_i in Rm} I(yi = k)
+# # be the proportion of class k observations in node m.
+# # The cross-entropy is then defined as
+# # cross-entropy = -\sum_{k=0}^{K-1} count_k log(count_k)
+# # """
+# #
+# # cdef double node_impurity(self) nogil:
+# # """Evaluate the impurity of the current node, i.e. the impurity of
+# # samples[start:end], using the cross-entropy criterion."""
+# #
+# # # cdef SIZE_t* n_classes = self.n_classes
+# # # cdef double* sum_total = self.sum_total
+# # # cdef double entropy = 0.0
+# # # cdef double count_k
+# # # cdef SIZE_t k
+# # # cdef SIZE_t c
+# # #
+# # # for k in range(self.n_outputs):
+# # # for c in range(n_classes[k]):
+# # # count_k = sum_total[c]
+# # # if count_k > 0.0:
+# # # count_k /= self.weighted_n_node_samples
+# # # entropy -= count_k * log(count_k)
+# # #
+# # # sum_total += self.sum_stride
+# #
+# # return 1.0
+# #
+# # cdef void children_impurity(self, double* impurity_left,
+# # double* impurity_right) nogil:
+# # """Evaluate the impurity in children nodes
+# # i.e. the impurity of the left child (samples[start:pos]) and the
+# # impurity the right child (samples[pos:end]).
+# # Parameters
+# # ----------
+# # impurity_left : double pointer
+# # The memory address to save the impurity of the left node
+# # impurity_right : double pointer
+# # The memory address to save the impurity of the right node
+# # """
+# #
+# # # cdef SIZE_t* n_classes = self.n_classes
+# # # cdef double* sum_left = self.sum_left
+# # # cdef double* sum_right = self.sum_right
+# # # cdef double entropy_left = 0.0
+# # # cdef double entropy_right = 0.0
+# # # cdef double count_k
+# # # cdef SIZE_t k
+# # # cdef SIZE_t c
+# # #
+# # # for k in range(self.n_outputs):
+# # # for c in range(n_classes[k]):
+# # # count_k = sum_left[c]
+# # # if count_k > 0.0:
+# # # count_k /= self.weighted_n_left
+# # # entropy_left -= count_k * log(count_k)
+# # #
+# # # count_k = sum_right[c]
+# # # if count_k > 0.0:
+# # # count_k /= self.weighted_n_right
+# # # entropy_right -= count_k * log(count_k)
+# # #
+# # # sum_left += self.sum_stride
+# # # sum_right += self.sum_stride
+# # #
+# # # impurity_left[0] = entropy_left / self.n_outputs
+# # # impurity_right[0] = entropy_right / self.n_outputs
+#
+#
+# calloc
+#
+# free
+#
+# memcpy
+#
+# memset
+#
+# fabs
+#
+# malloc
+#
+# realloc
+# # from libc.math cimport log as ln
+#
+# import numpy as np
+# from sklearn.tree import Crit
+#
+# cimport
+# numpy as np
+# np.import_array()
+# # from sklearn.tree._criterion cimport Criterion, ClassificationCriterion
+#
+# cdef
+# realloc_ptr
+# safe_realloc(realloc_ptr * p, size_t
+# nelems) nogil except *:
+# # sizeof(realloc_ptr[0]) would be more like idiomatic C, but causes Cython
+# # 0.20.1 to crash.
+# cdef
+# size_t
+# nbytes = nelems * sizeof(p[0][0])
+# if nbytes / sizeof(p[0][0]) != nelems:
+# # Overflow in the multiplication
+# with gil:
+# raise MemoryError("could not allocate (%d * %d) bytes"
+# % (nelems, sizeof(p[0][0])))
+# cdef
+# realloc_ptr
+# tmp = < realloc_ptr > realloc(p[0], nbytes)
+# if tmp == NULL:
+# with gil:
+# raise MemoryError("could not allocate %d bytes" % nbytes)
+# p[0] = tmp
+# return tmp # for
+#
+# cdef
+# inline
+# np.ndarray
+# sizet_ptr_to_ndarray(SIZE_t * data, SIZE_t
+# size):
+# """Return copied data as 1D numpy array of intp's."""
+# cdef
+# np.npy_intp
+# shape[1]
+# shape[0] = < np.npy_intp > size
+# return np.PyArray_SimpleNewFromData(1, shape, np.NPY_INTP, data).copy()
+#
+# cdef
+#
+#
+# class CustomCriterion(Criterion):
# """Interface for impurity criteria.
# This object stores methods on how to calculate how good a split is using
# different metrics.
diff --git a/multiview_platform/MonoMultiViewClassifiers/Monoview/ExecClassifMonoView.py b/multiview_platform/MonoMultiViewClassifiers/Monoview/ExecClassifMonoView.py
index a1fcab81..0e689085 100644
--- a/multiview_platform/MonoMultiViewClassifiers/Monoview/ExecClassifMonoView.py
+++ b/multiview_platform/MonoMultiViewClassifiers/Monoview/ExecClassifMonoView.py
@@ -222,11 +222,11 @@ def saveResults(stringAnalysis, outputFileName, full_labels_pred, y_train_pred,
testFileName = outputFileName + imageName + "-" + str(
i) + ".png"
if not os.path.isfile(testFileName):
- imagesAnalysis[imageName].savefig(testFileName)
+ imagesAnalysis[imageName].savefig(testFileName, transparent=True)
break
imagesAnalysis[imageName].savefig(
- outputFileName + imageName + '.png')
+ outputFileName + imageName + '.png', transparent=True)
if __name__ == '__main__':
diff --git a/multiview_platform/MonoMultiViewClassifiers/Monoview/ExportResults.py b/multiview_platform/MonoMultiViewClassifiers/Monoview/ExportResults.py
index ba1a9088..086080ee 100644
--- a/multiview_platform/MonoMultiViewClassifiers/Monoview/ExportResults.py
+++ b/multiview_platform/MonoMultiViewClassifiers/Monoview/ExportResults.py
@@ -135,11 +135,11 @@ def showScoreTime(directory, filename, store, resScore, resTime, rangeX,
for i in range(1, 20):
testFileName = filename + "-" + str(i) + ".png"
if not os.path.isfile(directory + testFileName):
- plt.savefig(directory + testFileName)
+ plt.savefig(directory + testFileName, transparent=True)
break
else:
- plt.savefig(file)
+ plt.savefig(file, transparent=True)
else:
plt.show()
@@ -180,11 +180,11 @@ def showResults(directory, filename, db, feat, score):
for i in range(1, 20):
testFileName = filename + "-" + str(i) + ".png"
if not os.path.isfile(directory + testFileName):
- plt.savefig(directory + testFileName)
+ plt.savefig(directory + testFileName, transparent=True)
break
else:
- plt.savefig(file)
+ plt.savefig(file, transparent=True)
plt.close()
@@ -262,11 +262,11 @@ def plot_confusion_matrix(directory, filename, df_confusion,
for i in range(1, 20):
testFileName = filename + "-" + str(i) + ".png"
if not os.path.isfile(directory + testFileName):
- plt.savefig(directory + testFileName)
+ plt.savefig(directory + testFileName, transparent=True)
break
else:
- plt.savefig(file)
+ plt.savefig(file, transparent=True)
plt.close()
diff --git a/multiview_platform/MonoMultiViewClassifiers/Monoview/MonoviewUtils.py b/multiview_platform/MonoMultiViewClassifiers/Monoview/MonoviewUtils.py
index daa2fff7..1d6c4129 100644
--- a/multiview_platform/MonoMultiViewClassifiers/Monoview/MonoviewUtils.py
+++ b/multiview_platform/MonoMultiViewClassifiers/Monoview/MonoviewUtils.py
@@ -190,7 +190,7 @@ class BaseMonoviewClassifier(object):
ax.yaxis.set_major_formatter(formatter)
plt.bar(x, featureImportancesSorted)
plt.title("Importance depending on feature")
- fig.savefig(directory + "feature_importances.png")
+ fig.savefig(directory + "feature_importances.png", transparent=True)
plt.close()
featuresImportancesDict = dict((featureIndex, featureImportance)
for featureIndex, featureImportance in
diff --git a/multiview_platform/MonoMultiViewClassifiers/MonoviewClassifiers/AdaboostPregen.py b/multiview_platform/MonoMultiViewClassifiers/MonoviewClassifiers/AdaboostPregen.py
index 6e70dc9d..9df79130 100644
--- a/multiview_platform/MonoMultiViewClassifiers/MonoviewClassifiers/AdaboostPregen.py
+++ b/multiview_platform/MonoMultiViewClassifiers/MonoviewClassifiers/AdaboostPregen.py
@@ -55,6 +55,7 @@ class AdaboostPregen(AdaBoostClassifier, BaseMonoviewClassifier,
self.metrics = np.array(
[self.plotted_metric.score(change_label_to_zero(pred), y) for pred
in self.staged_predict(pregen_X)])
+
self.bounds = np.array([np.prod(
np.sqrt(1 - 4 * np.square(0.5 - self.estimator_errors_[:i + 1])))
for i in
diff --git a/multiview_platform/MonoMultiViewClassifiers/Multiview/ExecMultiview.py b/multiview_platform/MonoMultiViewClassifiers/Multiview/ExecMultiview.py
index a8b97339..54cd4e85 100644
--- a/multiview_platform/MonoMultiViewClassifiers/Multiview/ExecMultiview.py
+++ b/multiview_platform/MonoMultiViewClassifiers/Multiview/ExecMultiview.py
@@ -69,11 +69,11 @@ def saveResults(LABELS_DICTIONARY, stringAnalysis, views, classifierModule,
testFileName = outputFileName + imageName + "-" + str(
i) + ".png"
if not os.path.isfile(testFileName):
- imagesAnalysis[imageName].savefig(testFileName)
+ imagesAnalysis[imageName].savefig(testFileName, transparent=True)
break
imagesAnalysis[imageName].savefig(
- outputFileName + imageName + '.png')
+ outputFileName + imageName + '.png', transparent=True)
def ExecMultiview_multicore(directory, coreIndex, name, learningRate, nbFolds,
diff --git a/multiview_platform/MonoMultiViewClassifiers/ResultAnalysis.py b/multiview_platform/MonoMultiViewClassifiers/ResultAnalysis.py
index 34fb2ad5..22ba5ec0 100644
--- a/multiview_platform/MonoMultiViewClassifiers/ResultAnalysis.py
+++ b/multiview_platform/MonoMultiViewClassifiers/ResultAnalysis.py
@@ -249,7 +249,7 @@ def plotMetricScores(trainScores, testScores, names, nbResults, metricName,
plt.tight_layout()
except:
pass
- f.savefig(fileName + '.png')
+ f.savefig(fileName + '.png', transparent=True)
plt.close()
import pandas as pd
if train_STDs is None:
@@ -377,7 +377,7 @@ def publish2Dplot(data, classifiersNames, nbClassifiers, nbExamples, nbCopies,
cbar = fig.colorbar(cax, ticks=[-100 * statsIter / 2, 0, statsIter])
cbar.ax.set_yticklabels(['Unseen', 'Always Wrong', 'Always Right'])
fig.tight_layout()
- fig.savefig(fileName + "error_analysis_2D.png", bbox_inches="tight")
+ fig.savefig(fileName + "error_analysis_2D.png", bbox_inches="tight", transparent=True)
plt.close()
@@ -405,7 +405,7 @@ def publishErrorsBarPlot(errorOnExamples, nbClassifiers, nbExamples, fileName):
plt.bar(x, errorOnExamples)
plt.ylim([0, nbClassifiers])
plt.title("Number of classifiers that failed to classify each example")
- fig.savefig(fileName + "error_analysis_bar.png")
+ fig.savefig(fileName + "error_analysis_bar.png", transparent=True)
plt.close()
diff --git a/multiview_platform/MonoMultiViewClassifiers/utils/GetMultiviewDb.py b/multiview_platform/MonoMultiViewClassifiers/utils/GetMultiviewDb.py
index 1bfa4f92..c60796db 100644
--- a/multiview_platform/MonoMultiViewClassifiers/utils/GetMultiviewDb.py
+++ b/multiview_platform/MonoMultiViewClassifiers/utils/GetMultiviewDb.py
@@ -333,25 +333,26 @@ def filterViews(datasetFile, temp_dataset, views, usedIndices):
for viewIndex in range(datasetFile.get("Metadata").attrs["nbView"]):
copyhdf5Dataset(datasetFile, temp_dataset, "View" + str(viewIndex),
"View" + str(viewIndex), usedIndices)
- for askedViewName in views:
- for viewIndex in range(datasetFile.get("Metadata").attrs["nbView"]):
- viewName = datasetFile.get("View" + str(viewIndex)).attrs["name"]
- if type(viewName) == bytes:
- viewName = viewName.decode("utf-8")
- if viewName == askedViewName:
- copyhdf5Dataset(datasetFile, temp_dataset,
- "View" + str(viewIndex),
- "View" + str(newViewIndex), usedIndices)
- newViewName = \
- temp_dataset.get("View" + str(newViewIndex)).attrs["name"]
- if type(newViewName) == bytes:
- temp_dataset.get("View" + str(newViewIndex)).attrs[
- "name"] = newViewName.decode("utf-8")
-
- newViewIndex += 1
- else:
- pass
- temp_dataset.get("Metadata").attrs["nbView"] = len(views)
+ else:
+ for askedViewName in views:
+ for viewIndex in range(datasetFile.get("Metadata").attrs["nbView"]):
+ viewName = datasetFile.get("View" + str(viewIndex)).attrs["name"]
+ if type(viewName) == bytes:
+ viewName = viewName.decode("utf-8")
+ if viewName == askedViewName:
+ copyhdf5Dataset(datasetFile, temp_dataset,
+ "View" + str(viewIndex),
+ "View" + str(newViewIndex), usedIndices)
+ newViewName = \
+ temp_dataset.get("View" + str(newViewIndex)).attrs["name"]
+ if type(newViewName) == bytes:
+ temp_dataset.get("View" + str(newViewIndex)).attrs[
+ "name"] = newViewName.decode("utf-8")
+
+ newViewIndex += 1
+ else:
+ pass
+ temp_dataset.get("Metadata").attrs["nbView"] = len(views)
def copyhdf5Dataset(sourceDataFile, destinationDataFile, sourceDatasetName,
@@ -447,6 +448,14 @@ def add_gaussian_noise(dataset_file, random_state, path_f, dataset_name,
view_limits[:, 0], noised_data)
noised_data = np.where(noised_data > view_limits[:, 1],
view_limits[:, 1], noised_data)
+ # import matplotlib.pyplot as plt
+ # plt.imshow(noised_data[1,:].reshape((28,28)))
+ # plt.savefig("plif.png")
+ # lower_contrast = view_dset.value[1,:].reshape((28,28))/10
+ # print(np.max(lower_contrast))
+ # plt.imshow(lower_contrast.astype(int))
+ # plt.savefig("plif2.png")
+ # quit()
noisy_dataset[view_name][...] = noised_data
# final_shape = noised_data.shape
return noisy_dataset, dataset_name + "_noised"
diff --git a/multiview_platform/MonoMultiViewClassifiers/utils/HyperParameterSearch.py b/multiview_platform/MonoMultiViewClassifiers/utils/HyperParameterSearch.py
index 84e03d89..08b23063 100644
--- a/multiview_platform/MonoMultiViewClassifiers/utils/HyperParameterSearch.py
+++ b/multiview_platform/MonoMultiViewClassifiers/utils/HyperParameterSearch.py
@@ -146,7 +146,7 @@ def genHeatMaps(params, scoresArray, outputFileName):
plt.yticks(np.arange(len(paramArray2Set)), paramArray2Set, rotation=45)
plt.title('Validation metric')
plt.savefig(
- outputFileName + "heat_map-" + paramName1 + "-" + paramName2 + ".png")
+ outputFileName + "heat_map-" + paramName1 + "-" + paramName2 + ".png", transparent=True)
plt.close()
# nohup python ~/dev/git/spearmint/spearmint/main.py . &
diff --git a/multiview_platform/MonoMultiViewClassifiers/utils/execution.py b/multiview_platform/MonoMultiViewClassifiers/utils/execution.py
index ad2b75e7..92b96cbf 100644
--- a/multiview_platform/MonoMultiViewClassifiers/utils/execution.py
+++ b/multiview_platform/MonoMultiViewClassifiers/utils/execution.py
@@ -848,7 +848,6 @@ def genSplits(labels, splitRatio, statsIterRandomStates):
random_state=randomState,
test_size=splitRatio)
folds = foldsObj.split(indices, labels)
- print(indices)
for fold in folds:
train_fold, test_fold = fold
trainIndices = indices[train_fold]
@@ -907,6 +906,7 @@ def initViews(DATASET, argViews):
Names of all the available views in the dataset.
"""
NB_VIEW = DATASET.get("Metadata").attrs["nbView"]
+ print(NB_VIEW)
if argViews != [""]:
allowedViews = argViews
allViews = [str(DATASET.get("View" + str(viewIndex)).attrs["name"])
--
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