diff --git a/.gitignore b/.gitignore
index 7a6d303a1256cba62a5d540e2acb74a4fab4b124..db4f192195f18ddead21ddf6e973c87286d03ca2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,4 +6,6 @@ demo/tutorials/.ipy*
demo/tutorials/supplementary_material/demo.hdf5
demo/tutorials/supplementary_material/tuto.hdf5
demo/tutorials/supplementary_material/report.md
-demo/tutorials/supplementary_material/tuto/
\ No newline at end of file
+demo/tutorials/supplementary_material/tuto/
+.idea*
+_static
\ No newline at end of file
diff --git a/.idea/.gitignore b/.idea/.gitignore
deleted file mode 100644
index 0e40fe8f57160b43f9ea8e200b1a5d9f91f4aed9..0000000000000000000000000000000000000000
--- a/.idea/.gitignore
+++ /dev/null
@@ -1,3 +0,0 @@
-
-# Default ignored files
-/workspace.xml
\ No newline at end of file
diff --git a/.idea/misc.xml b/.idea/misc.xml
deleted file mode 100644
index 3c2c013aca5383a4194378b8fe233d5f04daa7b8..0000000000000000000000000000000000000000
--- a/.idea/misc.xml
+++ /dev/null
@@ -1,7 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
- <component name="JavaScriptSettings">
- <option name="languageLevel" value="ES6" />
- </component>
- <component name="ProjectRootManager" version="2" languageLevel="JDK_12" default="false" project-jdk-name="Python 3.6 (develop)" project-jdk-type="Python SDK" />
-</project>
\ No newline at end of file
diff --git a/.idea/modules.xml b/.idea/modules.xml
deleted file mode 100644
index 6164328c76fbdf70a112333535f10474e6703fd0..0000000000000000000000000000000000000000
--- a/.idea/modules.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
- <component name="ProjectModuleManager">
- <modules>
- <module fileurl="file://$PROJECT_DIR$/.idea/multiview_generator.iml" filepath="$PROJECT_DIR$/.idea/multiview_generator.iml" />
- </modules>
- </component>
-</project>
\ No newline at end of file
diff --git a/.idea/multiview_generator.iml b/.idea/multiview_generator.iml
deleted file mode 100644
index b6d61efc59564f86c4cca889b90b0289fe871ca5..0000000000000000000000000000000000000000
--- a/.idea/multiview_generator.iml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module type="JAVA_MODULE" version="4">
- <component name="NewModuleRootManager">
- <content url="file://$MODULE_DIR$" />
- <orderEntry type="jdk" jdkName="Python 3.6 (develop)" jdkType="Python SDK" />
- <orderEntry type="sourceFolder" forTests="false" />
- <orderEntry type="library" name="R User Library" level="project" />
- <orderEntry type="library" name="R Skeletons" level="application" />
- </component>
-</module>
\ No newline at end of file
diff --git a/.idea/vcs.xml b/.idea/vcs.xml
deleted file mode 100644
index 35eb1ddfbbc029bcab630581847471d7f238ec53..0000000000000000000000000000000000000000
--- a/.idea/vcs.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
- <component name="VcsDirectoryMappings">
- <mapping directory="" vcs="Git" />
- </component>
-</project>
\ No newline at end of file
diff --git a/_static/fig_rec.png b/_static/fig_rec.png
deleted file mode 100644
index 8b1dde52ecc5797568e18ec7dd5efe9ddb01a54e..0000000000000000000000000000000000000000
Binary files a/_static/fig_rec.png and /dev/null differ
diff --git a/multiview_generator/base.py b/multiview_generator/base.py
index f616c4a5ee5a76406714ec2600fe90bec1a1f442..ca6180ee6a01db81f7bb36924e1031cefa7af4d7 100644
--- a/multiview_generator/base.py
+++ b/multiview_generator/base.py
@@ -64,7 +64,7 @@ class MultiViewSubProblemsGenerator:
complementarity_level=3,
mutual_error=0.0, name="generated_dataset", config_file=None,
sub_problem_type="base", sub_problem_configurations=None,
- **kwargs):
+ min_rndm_val=-1, max_rndm_val=1, **kwargs):
if config_file is not None:
args = get_config_from_file(config_file)
@@ -76,6 +76,8 @@ class MultiViewSubProblemsGenerator:
self.n_classes = n_classes
self.n_views = n_views
self.name = name
+ self.min_rndm_val = min_rndm_val
+ self.max_rndm_val = max_rndm_val
self.n_features = format_array(n_features, n_views, type_needed=int)
self.redundancy = format_array(redundancy, n_classes,
type_needed=float).reshape(
@@ -263,72 +265,72 @@ class MultiViewSubProblemsGenerator:
label_indice in label_indices]
self.dt_error[:, view_index] = np.array(loss)
- def _find_rows_cols(self):
- rows=1
- cols=1
- if self.n_views == 4:
- rows = 2
- cols = 2
- if self.n_views>1:
- for i in range(self.n_views):
- if rows*cols < i+1:
- if cols < 4*rows:
- cols+=1
- else:
- rows+=1
- return rows, cols
-
- def _get_pca(self, n_components=2, output_path='.'):
- pca = PCA(n_components=n_components)
- import plotly.graph_objects as go
- from plotly.subplots import make_subplots
- rows, cols = self._find_rows_cols()
- fig = make_subplots(rows=rows, cols=cols,
- subplot_titles=["View{}".format(view_index)
- for view_index
- in range(self.n_views)],
- specs=[[{'type': 'scatter'} for _ in range(cols) ]
- for _ in range(rows)])
- row = 1
- col = 1
- import plotly.express as px
- for view_index, view_data in enumerate(self.dataset):
- if self.n_features[view_index]>n_components:
- pca.fit(view_data)
- reducted_data = pca.transform(view_data)
- elif self.n_features[view_index] ==1:
- reducted_data = np.transpose(np.array([view_data, view_data]))[0, :, :]
- else:
- reducted_data = view_data
- fig.add_trace(
- go.Scatter(
- x=reducted_data[:, 0],
- y=reducted_data[:, 1],
- text=self.sample_ids,
- mode='markers', marker=dict(
- size=3, # set color to an array/list of desired values
- color=self.y,
- colorscale=["red", "blue", "black", "green", "orange", "purple"],
- opacity=0.8
- ), ),
- row=row, col=col)
- col += 1
- if col > cols:
- col = 1
- row += 1
- fig.update_shapes(dict(xref='x', yref='y'))
- plotly.offline.plot(fig, filename=os.path.join(output_path, self.name+"_fig_pca.html"), auto_open=False)
+ # def _find_rows_cols(self):
+ # rows=1
+ # cols=1
+ # if self.n_views == 4:
+ # rows = 2
+ # cols = 2
+ # if self.n_views>1:
+ # for i in range(self.n_views):
+ # if rows*cols < i+1:
+ # if cols < 4*rows:
+ # cols+=1
+ # else:
+ # rows+=1
+ # return rows, cols
+
+ # def _get_pca(self, n_components=2, output_path='.'):
+ # pca = PCA(n_components=n_components)
+ # import plotly.graph_objects as go
+ # from plotly.subplots import make_subplots
+ # rows, cols = self._find_rows_cols()
+ # fig = make_subplots(rows=rows, cols=cols,
+ # subplot_titles=["View{}".format(view_index)
+ # for view_index
+ # in range(self.n_views)],
+ # specs=[[{'type': 'scatter'} for _ in range(cols) ]
+ # for _ in range(rows)])
+ # row = 1
+ # col = 1
+ # import plotly.express as px
+ # for view_index, view_data in enumerate(self.dataset):
+ # if self.n_features[view_index]>n_components:
+ # pca.fit(view_data)
+ # reducted_data = pca.transform(view_data)
+ # elif self.n_features[view_index] ==1:
+ # reducted_data = np.transpose(np.array([view_data, view_data]))[0, :, :]
+ # else:
+ # reducted_data = view_data
+ # fig.add_trace(
+ # go.Scatter(
+ # x=reducted_data[:, 0],
+ # y=reducted_data[:, 1],
+ # text=self.sample_ids,
+ # mode='markers', marker=dict(
+ # size=3, # set color to an array/list of desired values
+ # color=self.y,
+ # colorscale=["red", "blue", "black", "green", "orange", "purple"],
+ # opacity=0.8
+ # ), ),
+ # row=row, col=col)
+ # col += 1
+ # if col > cols:
+ # col = 1
+ # row += 1
+ # fig.update_shapes(dict(xref='x', yref='y'))
+ # plotly.offline.plot(fig, filename=os.path.join(output_path, self.name+"_fig_pca.html"), auto_open=False)
def gen_view_report(self, view_index):
view_string = "\n\n### View "+str(view_index+1)
view_string+=self._sub_problem_generators[view_index].gen_report()
return view_string
- def _get_generator_report(self, view_index, doc_type=".md"):
- if self.sub_problem_types[view_index] in ["make_classification", "base"]:
- return "[`make_classification`](https://scikit-learn.org/stable/modules/generated/sklearn.datasets.make_classification.html)"
- elif self.sub_problem_types[view_index]in ["gaussian", "make_gaussian_quantiles"]:
- return "[`make_gaussian_quantiles`](https://scikit-learn.org/stable/modules/generated/sklearn.datasets.make_gaussian_quantiles.html#sklearn.datasets.make_gaussian_quantiles)"
+ # def _get_generator_report(self, view_index, doc_type=".md"):
+ # if self.sub_problem_types[view_index] in ["make_classification", "base"]:
+ # return "[`make_classification`](https://scikit-learn.org/stable/modules/generated/sklearn.datasets.make_classification.html)"
+ # elif self.sub_problem_types[view_index]in ["gaussian", "make_gaussian_quantiles"]:
+ # return "[`make_gaussian_quantiles`](https://scikit-learn.org/stable/modules/generated/sklearn.datasets.make_gaussian_quantiles.html#sklearn.datasets.make_gaussian_quantiles)"
def _init_base_arguments(self):
self.n_samples_per_class = (
diff --git a/multiview_generator/gaussian_classes.py b/multiview_generator/gaussian_classes.py
index 2a6dbdcb180ce123914e275d2b4936e2233745c5..23b7a3001448809dcdd5a39170e1bd19d698a1b5 100644
--- a/multiview_generator/gaussian_classes.py
+++ b/multiview_generator/gaussian_classes.py
@@ -19,8 +19,8 @@ class MultiViewGaussianSubProblemsGenerator(MultiViewSubProblemsGenerator):
complementarity_level=3,
mutual_error=0.01, name="generated_dataset", config_file=None,
sub_problem_type="base", sub_problem_configurations=None,
- sub_problem_generators="StumpsGenerator", random_vertices=False
- , **kwargs):
+ sub_problem_generators="StumpsGenerator", random_vertices=False,
+ min_rndm_val=-1, max_rndm_val=1, **kwargs):
"""
:param random_state: int or np.random.RandomState object to fix the
@@ -66,6 +66,8 @@ class MultiViewGaussianSubProblemsGenerator(MultiViewSubProblemsGenerator):
config_file=config_file,
sub_problem_type=sub_problem_type,
sub_problem_configurations=sub_problem_configurations,
+ min_rndm_val=min_rndm_val,
+ max_rndm_val=max_rndm_val,
**kwargs)
self.random_vertices = format_array(random_vertices, n_views, bool)
self.sub_problem_generators = format_array(sub_problem_generators, n_views, str)
@@ -273,8 +275,13 @@ class MultiViewGaussianSubProblemsGenerator(MultiViewSubProblemsGenerator):
self.n_samples = np.sum(self.n_samples_per_class)
self.n_complem =np.zeros(self.n_classes)
self.n_max_features = np.max(self.n_features)
- self.generated_data = self.rs.uniform(low=-self.latent_size_mult, high=self.latent_size_mult, size=(self.n_views, self.n_classes, self.n_max_samples, self.n_max_features))
- self.descriptions = np.zeros((self.n_views, self.n_classes, self.n_max_samples,))
+ self.generated_data = self.rs.uniform(low=-self.min_rndm_val,
+ high=self.max_rndm_val,
+ size=(self.n_views, self.n_classes,
+ self.n_max_samples,
+ self.n_max_features))
+ self.descriptions = np.zeros((self.n_views, self.n_classes,
+ self.n_max_samples,))
self.n_total_samples = np.sum(self.n_samples_per_class)
sample_indices = np.arange(int(np.sum(self.n_samples_per_class)))
self.rs.shuffle(sample_indices)
diff --git a/multiview_generator/sub_problems.py b/multiview_generator/sub_problems.py
index b08c7f347c280785fa7a345449b6aaf5690d58b6..e464b8ab97ba7797f15e3c54b17a2ceca3b582c2 100644
--- a/multiview_generator/sub_problems.py
+++ b/multiview_generator/sub_problems.py
@@ -120,7 +120,7 @@ class StumpsGenerator(BaseSubProblem):
return DecisionTreeClassifier(max_depth=math.ceil(math.log2(self.n_classes)))
-class TreesGenerator(BaseSubProblem):
+class TreesGenerator(BaseSubProblem): # pragma: no cover
""" Work in progress : Similar generator as StumpsGenerator, but that
generates several blobs per class """
diff --git a/multiview_generator/tests/test_gaussian_classes.py b/multiview_generator/tests/test_gaussian_classes.py
index 8dc472287f75c3a9534452462afaf53f7328168a..4890343f5588af8a1f0d4dc8879987c7e0190f66 100644
--- a/multiview_generator/tests/test_gaussian_classes.py
+++ b/multiview_generator/tests/test_gaussian_classes.py
@@ -1,7 +1,24 @@
import unittest
+import os
from ..gaussian_classes import MultiViewGaussianSubProblemsGenerator
+tmp_path = os.path.join(
+ os.path.dirname(
+ os.path.abspath(__file__)),
+ "tmp_tests", "")
+
+def rm_tmp(path=tmp_path):
+ try:
+ for file_name in os.listdir(path):
+ if os.path.isdir(os.path.join(path, file_name)):
+ rm_tmp(os.path.join(path, file_name))
+ else:
+ os.remove(os.path.join(path, file_name))
+ os.rmdir(path)
+ except BaseException:
+ pass
+
class Test_MultiViewGaussianSubProblemsGenerator(unittest.TestCase):
@classmethod
@@ -13,4 +30,25 @@ class Test_MultiViewGaussianSubProblemsGenerator(unittest.TestCase):
pass
def test_simple(self):
+ gene = MultiViewGaussianSubProblemsGenerator(sub_problem_generators=["StumpsGenerator",
+ "RingsGenerator",
+ "StumpsGenerator",
+ "RingsGenerator"])
+ data, labels = gene.generate_multi_view_dataset()
+
+ def test_report(self):
+ gene = MultiViewGaussianSubProblemsGenerator(sub_problem_generators=["StumpsGenerator",
+ "RingsGenerator",
+ "StumpsGenerator",
+ "RingsGenerator"])
+ data, labels = gene.generate_multi_view_dataset()
+ rep = gene.gen_report(save=False)
+
+ def test_save(self):
gene = MultiViewGaussianSubProblemsGenerator()
+ data, labels = gene.generate_multi_view_dataset()
+ rm_tmp()
+ os.mkdir(tmp_path)
+ gene.to_hdf5_mc(tmp_path)
+ rep = gene.gen_report(output_path=tmp_path, save=True)
+ rm_tmp()
\ No newline at end of file
diff --git a/multiview_generator/tests/test_multiple_sub_problems.py b/multiview_generator/tests/test_multiple_sub_problems.py
deleted file mode 100644
index e2ce0c3cc3997271862b76cd4fe75a631dd5e725..0000000000000000000000000000000000000000
--- a/multiview_generator/tests/test_multiple_sub_problems.py
+++ /dev/null
@@ -1,19 +0,0 @@
-# import unittest
-# import numpy as np
-#
-# from ..multiple_sub_problems import MultiViewSubProblemsGenerator
-#
-#
-# class Test_MultiViewSubProblemsGenerator(unittest.TestCase):
-#
-# @classmethod
-# def setUpClass(cls):
-# pass
-#
-# @classmethod
-# def tearDownClass(cls):
-# pass
-#
-# def test_simple(self):
-# gene = MultiViewSubProblemsGenerator()
-