From 68b6e3f3d641cd4a1e86f08bff96e417cc17ac59 Mon Sep 17 00:00:00 2001
From: takeshimeonerespect <m.takenouchi@fujitsu.com>
Date: Fri, 31 Jan 2020 08:08:43 +0100
Subject: timedelay added on fork

---
 src/python/CMakeLists.txt                 |  5 +++
 src/python/doc/point_cloud.rst            |  7 ++++
 src/python/gudhi/point_cloud/timedelay.py | 56 +++++++++++++++++++++++++++++++
 src/python/test/test_point_cloud.py       | 35 +++++++++++++++++++
 4 files changed, 103 insertions(+)
 create mode 100644 src/python/gudhi/point_cloud/timedelay.py
 create mode 100755 src/python/test/test_point_cloud.py

(limited to 'src')

diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index b558d4c4..b23ec8a9 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -52,6 +52,7 @@ if(PYTHONINTERP_FOUND)
     # Modules that should not be auto-imported in __init__.py
     set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'representations', ")
     set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'wasserstein', ")
+    set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'point_cloud', ")
 
     add_gudhi_debug_info("Python version ${PYTHON_VERSION_STRING}")
     add_gudhi_debug_info("Cython version ${CYTHON_VERSION}")
@@ -221,6 +222,7 @@ endif(CGAL_FOUND)
     file(COPY "gudhi/persistence_graphical_tools.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi")
     file(COPY "gudhi/representations" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi/")
     file(COPY "gudhi/wasserstein.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi")
+    file(COPY "gudhi/point_cloud" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi")
 
     add_custom_command(
         OUTPUT gudhi.so
@@ -399,6 +401,9 @@ endif(CGAL_FOUND)
       add_gudhi_py_test(test_representations)
     endif()
 
+    # Point cloud
+    add_gudhi_py_test(test_point_cloud)
+
     # Documentation generation is available through sphinx - requires all modules
     if(SPHINX_PATH)
       if(MATPLOTLIB_FOUND)
diff --git a/src/python/doc/point_cloud.rst b/src/python/doc/point_cloud.rst
index d668428a..55c74ff3 100644
--- a/src/python/doc/point_cloud.rst
+++ b/src/python/doc/point_cloud.rst
@@ -20,3 +20,10 @@ Subsampling
    :members:
    :special-members:
    :show-inheritance:
+
+TimeDelayEmbedding
+------------------
+
+.. autoclass:: gudhi.point_cloud.timedelay.TimeDelayEmbedding
+   :members:
+
diff --git a/src/python/gudhi/point_cloud/timedelay.py b/src/python/gudhi/point_cloud/timedelay.py
new file mode 100644
index 00000000..5c7ba542
--- /dev/null
+++ b/src/python/gudhi/point_cloud/timedelay.py
@@ -0,0 +1,56 @@
+import numpy as np
+
+class TimeDelayEmbedding:
+    """Point cloud transformation class.
+
+    Embeds time-series data in the R^d according to Takens' Embedding Theorem
+    and obtains the coordinates of each point.
+
+    Parameters
+    ----------
+    dim : int, optional (default=3)
+        `d` of R^d to be embedded.
+
+    delay : int, optional (default=1)
+        Time-Delay embedding.
+
+    skip : int, optional (default=1)
+        How often to skip embedded points.
+
+    """
+    def __init__(self, dim=3, delay=1, skip=1):
+        self._dim = dim
+        self._delay = delay
+        self._skip = skip
+
+    def __call__(self, *args, **kwargs):
+        return self.transform(*args, **kwargs)
+
+    def _transform(self, ts):
+        """Guts of transform method."""
+        return ts[
+            np.add.outer(
+                np.arange(0, len(ts)-self._delay*(self._dim-1), self._skip),
+                np.arange(0, self._dim*self._delay, self._delay))
+        ]
+
+    def transform(self, ts):
+        """Transform method.
+
+        Parameters
+        ----------
+        ts : list[float] or list[list[float]]
+            A single or multiple time-series data.
+
+        Returns
+        -------
+        point clouds : list[list[float, float, float]] or list[list[list[float, float, float]]]
+            Makes point cloud every a single time-series data.
+        """
+        ndts = np.array(ts)
+        if ndts.ndim == 1:
+            # for single.
+            return self._transform(ndts).tolist()
+        else:
+            # for multiple.
+            return np.apply_along_axis(self._transform, 1, ndts).tolist()
diff --git a/src/python/test/test_point_cloud.py b/src/python/test/test_point_cloud.py
new file mode 100755
index 00000000..2ee0c1fb
--- /dev/null
+++ b/src/python/test/test_point_cloud.py
@@ -0,0 +1,35 @@
+from gudhi.point_cloud.timedelay import TimeDelayEmbedding
+
+def test_normal():
+    # Sample array
+    ts = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
+    # Normal case.
+    prep = TimeDelayEmbedding()
+    attractor = prep(ts)
+    assert (attractor[0] == [1, 2, 3])
+    assert (attractor[1] == [2, 3, 4])
+    assert (attractor[2] == [3, 4, 5])
+    assert (attractor[3] == [4, 5, 6])
+    assert (attractor[4] == [5, 6, 7])
+    assert (attractor[5] == [6, 7, 8])
+    assert (attractor[6] == [7, 8, 9])
+    assert (attractor[7] == [8, 9, 10])
+    # Delay = 3
+    prep = TimeDelayEmbedding(delay=3)
+    attractor = prep(ts)
+    assert (attractor[0] == [1, 4, 7])
+    assert (attractor[1] == [2, 5, 8])
+    assert (attractor[2] == [3, 6, 9])
+    assert (attractor[3] == [4, 7, 10])
+    # Skip = 3
+    prep = TimeDelayEmbedding(skip=3)
+    attractor = prep(ts)
+    assert (attractor[0] == [1, 2, 3])
+    assert (attractor[1] == [4, 5, 6])
+    assert (attractor[2] == [7, 8, 9])
+    # Delay = 2 / Skip = 2
+    prep = TimeDelayEmbedding(delay=2, skip=2)
+    attractor = prep(ts)
+    assert (attractor[0] == [1, 3, 5])
+    assert (attractor[1] == [3, 5, 7])
+    assert (attractor[2] == [5, 7, 9])
-- 
cgit v1.2.3


From d6afaa8300daa6204282a7d34df6bea33ea59fd2 Mon Sep 17 00:00:00 2001
From: takeshimeonerespect
 <58589594+takeshimeonerespect@users.noreply.github.com>
Date: Mon, 3 Feb 2020 14:13:52 +0900
Subject: Update timedelay.py

---
 src/python/gudhi/point_cloud/timedelay.py | 8 ++++++++
 1 file changed, 8 insertions(+)

(limited to 'src')

diff --git a/src/python/gudhi/point_cloud/timedelay.py b/src/python/gudhi/point_cloud/timedelay.py
index 5c7ba542..f283916d 100644
--- a/src/python/gudhi/point_cloud/timedelay.py
+++ b/src/python/gudhi/point_cloud/timedelay.py
@@ -1,3 +1,11 @@
+# This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+# See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
+# Author(s):       Martin Royer, Yuichi Ike, Masatoshi Takenouchi
+#
+# Copyright (C) 2020 Inria, Copyright (C) 2020 Fujitsu Laboratories Ltd.
+# Modification(s):
+#   - YYYY/MM Author: Description of the modification
+
 import numpy as np
 
 class TimeDelayEmbedding:
-- 
cgit v1.2.3


From eded147ffffe5b7143cad19ecd134fb7a63991a3 Mon Sep 17 00:00:00 2001
From: takenouchi <m.takenouchi@fujitsu.com>
Date: Tue, 4 Feb 2020 14:08:19 +0900
Subject: change a file name

---
 src/python/test/test_time_delay.py | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)
 create mode 100755 src/python/test/test_time_delay.py

(limited to 'src')

diff --git a/src/python/test/test_time_delay.py b/src/python/test/test_time_delay.py
new file mode 100755
index 00000000..2ee0c1fb
--- /dev/null
+++ b/src/python/test/test_time_delay.py
@@ -0,0 +1,35 @@
+from gudhi.point_cloud.timedelay import TimeDelayEmbedding
+
+def test_normal():
+    # Sample array
+    ts = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
+    # Normal case.
+    prep = TimeDelayEmbedding()
+    attractor = prep(ts)
+    assert (attractor[0] == [1, 2, 3])
+    assert (attractor[1] == [2, 3, 4])
+    assert (attractor[2] == [3, 4, 5])
+    assert (attractor[3] == [4, 5, 6])
+    assert (attractor[4] == [5, 6, 7])
+    assert (attractor[5] == [6, 7, 8])
+    assert (attractor[6] == [7, 8, 9])
+    assert (attractor[7] == [8, 9, 10])
+    # Delay = 3
+    prep = TimeDelayEmbedding(delay=3)
+    attractor = prep(ts)
+    assert (attractor[0] == [1, 4, 7])
+    assert (attractor[1] == [2, 5, 8])
+    assert (attractor[2] == [3, 6, 9])
+    assert (attractor[3] == [4, 7, 10])
+    # Skip = 3
+    prep = TimeDelayEmbedding(skip=3)
+    attractor = prep(ts)
+    assert (attractor[0] == [1, 2, 3])
+    assert (attractor[1] == [4, 5, 6])
+    assert (attractor[2] == [7, 8, 9])
+    # Delay = 2 / Skip = 2
+    prep = TimeDelayEmbedding(delay=2, skip=2)
+    attractor = prep(ts)
+    assert (attractor[0] == [1, 3, 5])
+    assert (attractor[1] == [3, 5, 7])
+    assert (attractor[2] == [5, 7, 9])
-- 
cgit v1.2.3


From 5ddb724824798fe194a66285e29ea4c5cc2713e2 Mon Sep 17 00:00:00 2001
From: takeshimeonerespect <m.takenouchi@fujitsu.com>
Date: Tue, 4 Feb 2020 14:24:27 +0900
Subject: Delete test_point_cloud.py

---
 src/python/test/test_point_cloud.py | 35 -----------------------------------
 1 file changed, 35 deletions(-)
 delete mode 100755 src/python/test/test_point_cloud.py

(limited to 'src')

diff --git a/src/python/test/test_point_cloud.py b/src/python/test/test_point_cloud.py
deleted file mode 100755
index 2ee0c1fb..00000000
--- a/src/python/test/test_point_cloud.py
+++ /dev/null
@@ -1,35 +0,0 @@
-from gudhi.point_cloud.timedelay import TimeDelayEmbedding
-
-def test_normal():
-    # Sample array
-    ts = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
-    # Normal case.
-    prep = TimeDelayEmbedding()
-    attractor = prep(ts)
-    assert (attractor[0] == [1, 2, 3])
-    assert (attractor[1] == [2, 3, 4])
-    assert (attractor[2] == [3, 4, 5])
-    assert (attractor[3] == [4, 5, 6])
-    assert (attractor[4] == [5, 6, 7])
-    assert (attractor[5] == [6, 7, 8])
-    assert (attractor[6] == [7, 8, 9])
-    assert (attractor[7] == [8, 9, 10])
-    # Delay = 3
-    prep = TimeDelayEmbedding(delay=3)
-    attractor = prep(ts)
-    assert (attractor[0] == [1, 4, 7])
-    assert (attractor[1] == [2, 5, 8])
-    assert (attractor[2] == [3, 6, 9])
-    assert (attractor[3] == [4, 7, 10])
-    # Skip = 3
-    prep = TimeDelayEmbedding(skip=3)
-    attractor = prep(ts)
-    assert (attractor[0] == [1, 2, 3])
-    assert (attractor[1] == [4, 5, 6])
-    assert (attractor[2] == [7, 8, 9])
-    # Delay = 2 / Skip = 2
-    prep = TimeDelayEmbedding(delay=2, skip=2)
-    attractor = prep(ts)
-    assert (attractor[0] == [1, 3, 5])
-    assert (attractor[1] == [3, 5, 7])
-    assert (attractor[2] == [5, 7, 9])
-- 
cgit v1.2.3


From 596355344e6205d02110e38a0cb7e0a94e8dbd27 Mon Sep 17 00:00:00 2001
From: takenouchi <m.takenouchi@fujitsu.com>
Date: Thu, 6 Feb 2020 16:00:47 +0900
Subject: modify CMakeLists.txt

---
 src/python/CMakeLists.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'src')

diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index b23ec8a9..798e2907 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -401,8 +401,8 @@ endif(CGAL_FOUND)
       add_gudhi_py_test(test_representations)
     endif()
 
-    # Point cloud
-    add_gudhi_py_test(test_point_cloud)
+    # Time Delay
+    add_gudhi_py_test(test_time_delay)
 
     # Documentation generation is available through sphinx - requires all modules
     if(SPHINX_PATH)
-- 
cgit v1.2.3


From a6a4f375822cf3e2ca1866d78472e4350140ddbc Mon Sep 17 00:00:00 2001
From: mtakenouchi <m.takenouchi@jp.fujitsu.com>
Date: Fri, 14 Feb 2020 11:02:56 +0900
Subject: Add __init__.py

---
 src/python/gudhi/point_cloud/__init__.py | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 src/python/gudhi/point_cloud/__init__.py

(limited to 'src')

diff --git a/src/python/gudhi/point_cloud/__init__.py b/src/python/gudhi/point_cloud/__init__.py
new file mode 100644
index 00000000..e69de29b
-- 
cgit v1.2.3


From 9cc9e1cf3cd9ea42908324d410ef68fa12e8e832 Mon Sep 17 00:00:00 2001
From: mtakenouchi <m.takenouchi@jp.fujitsu.com>
Date: Fri, 14 Feb 2020 11:08:50 +0900
Subject: Update timedelay.py

---
 src/python/gudhi/point_cloud/timedelay.py | 66 ++++++++++++++++++++++---------
 1 file changed, 48 insertions(+), 18 deletions(-)

(limited to 'src')

diff --git a/src/python/gudhi/point_cloud/timedelay.py b/src/python/gudhi/point_cloud/timedelay.py
index f283916d..d899da67 100644
--- a/src/python/gudhi/point_cloud/timedelay.py
+++ b/src/python/gudhi/point_cloud/timedelay.py
@@ -10,30 +10,55 @@ import numpy as np
 
 class TimeDelayEmbedding:
     """Point cloud transformation class.
-
     Embeds time-series data in the R^d according to Takens' Embedding Theorem
     and obtains the coordinates of each point.
-
     Parameters
     ----------
     dim : int, optional (default=3)
         `d` of R^d to be embedded.
-
     delay : int, optional (default=1)
         Time-Delay embedding.
-
     skip : int, optional (default=1)
         How often to skip embedded points.
-
+        Given delay=3 and skip=2, an point cloud which is obtained by embedding 
+        a single time-series data into R^3 is as follows.
+        
+    .. code-block:: none
+    
+    time-series = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
+    point clouds = [[1, 4, 7], 
+                    [3, 6, 9]]
+                   
     """
     def __init__(self, dim=3, delay=1, skip=1):
         self._dim = dim
         self._delay = delay
         self._skip = skip
 
-    def __call__(self, *args, **kwargs):
-        return self.transform(*args, **kwargs)
+    def __call__(self, ts):
+        """Transform method for single time-series data.
+        Parameters
+        ----------
+        ts : list[float]
+            A single time-series data.
+        Returns
+        -------
+        point clouds : list[list[float, float, float]]
+            Makes point cloud every a single time-series data.
+        Raises
+        -------
+        TypeError
+            If the parameter's type does not match the desired type.
+        """
+        ndts = np.array(ts)
+        if ndts.ndim == 1:
+            return self._transform(ndts)
+        else:
+            raise TypeError("Expects 1-dimensional array.")
 
+    def fit(self, ts, y=None):
+        return self
+    
     def _transform(self, ts):
         """Guts of transform method."""
         return ts[
@@ -43,22 +68,27 @@ class TimeDelayEmbedding:
         ]
 
     def transform(self, ts):
-        """Transform method.
-
+        """Transform method for multiple time-series data.
         Parameters
         ----------
-        ts : list[float] or list[list[float]]
-            A single or multiple time-series data.
-
+        ts : list[list[float]]
+            Multiple time-series data.
+        Attributes
+        ----------
+        ndts : 
+             The ndts means that all time series need to have exactly 
+             the same size. 
         Returns
         -------
-        point clouds : list[list[float, float, float]] or list[list[list[float, float, float]]]
+        point clouds : list[list[list[float, float, float]]]
             Makes point cloud every a single time-series data.
+        Raises
+        -------
+        TypeError
+            If the parameter's type does not match the desired type.
         """
         ndts = np.array(ts)
-        if ndts.ndim == 1:
-            # for single.
-            return self._transform(ndts).tolist()
+        if ndts.ndim == 2:
+            return np.apply_along_axis(self._transform, 1, ndts)
         else:
-            # for multiple.
-            return np.apply_along_axis(self._transform, 1, ndts).tolist()
+            raise TypeError("Expects 2-dimensional array.")
-- 
cgit v1.2.3


From 2253fd03bb49aea455309f6d633a6edeb2362d79 Mon Sep 17 00:00:00 2001
From: mtakenouchi <m.takenouchi@jp.fujitsu.com>
Date: Fri, 14 Feb 2020 17:52:07 +0900
Subject: Update test_time_delay.py

---
 src/python/test/test_time_delay.py | 36 ++++++++++++++++++------------------
 1 file changed, 18 insertions(+), 18 deletions(-)

(limited to 'src')

diff --git a/src/python/test/test_time_delay.py b/src/python/test/test_time_delay.py
index 2ee0c1fb..d2ffbf40 100755
--- a/src/python/test/test_time_delay.py
+++ b/src/python/test/test_time_delay.py
@@ -6,30 +6,30 @@ def test_normal():
     # Normal case.
     prep = TimeDelayEmbedding()
     attractor = prep(ts)
-    assert (attractor[0] == [1, 2, 3])
-    assert (attractor[1] == [2, 3, 4])
-    assert (attractor[2] == [3, 4, 5])
-    assert (attractor[3] == [4, 5, 6])
-    assert (attractor[4] == [5, 6, 7])
-    assert (attractor[5] == [6, 7, 8])
-    assert (attractor[6] == [7, 8, 9])
-    assert (attractor[7] == [8, 9, 10])
+    assert (attractor[0] == np.array[1, 2, 3])
+    assert (attractor[1] == np.array[2, 3, 4])
+    assert (attractor[2] == np.array[3, 4, 5])
+    assert (attractor[3] == np.array[4, 5, 6])
+    assert (attractor[4] == np.array[5, 6, 7])
+    assert (attractor[5] == np.array[6, 7, 8])
+    assert (attractor[6] == np.array[7, 8, 9])
+    assert (attractor[7] == np.array[8, 9, 10])
     # Delay = 3
     prep = TimeDelayEmbedding(delay=3)
     attractor = prep(ts)
-    assert (attractor[0] == [1, 4, 7])
-    assert (attractor[1] == [2, 5, 8])
-    assert (attractor[2] == [3, 6, 9])
-    assert (attractor[3] == [4, 7, 10])
+    assert (attractor[0] == np.array[1, 4, 7])
+    assert (attractor[1] == np.array[2, 5, 8])
+    assert (attractor[2] == np.array[3, 6, 9])
+    assert (attractor[3] == np.array[4, 7, 10])
     # Skip = 3
     prep = TimeDelayEmbedding(skip=3)
     attractor = prep(ts)
-    assert (attractor[0] == [1, 2, 3])
-    assert (attractor[1] == [4, 5, 6])
-    assert (attractor[2] == [7, 8, 9])
+    assert (attractor[0] == np.array[1, 2, 3])
+    assert (attractor[1] == np.array[4, 5, 6])
+    assert (attractor[2] == np.array[7, 8, 9])
     # Delay = 2 / Skip = 2
     prep = TimeDelayEmbedding(delay=2, skip=2)
     attractor = prep(ts)
-    assert (attractor[0] == [1, 3, 5])
-    assert (attractor[1] == [3, 5, 7])
-    assert (attractor[2] == [5, 7, 9])
+    assert (attractor[0] == np.array[1, 3, 5])
+    assert (attractor[1] == np.array[3, 5, 7])
+    assert (attractor[2] == np.array[5, 7, 9])
-- 
cgit v1.2.3


From f58a4120b70487aede3cb4e81fbb15171e34fa37 Mon Sep 17 00:00:00 2001
From: mtakenouchi <m.takenouchi@jp.fujitsu.com>
Date: Fri, 14 Feb 2020 18:24:18 +0900
Subject: Update test_time_delay.py

---
 src/python/test/test_time_delay.py | 36 ++++++++++++++++++------------------
 1 file changed, 18 insertions(+), 18 deletions(-)

(limited to 'src')

diff --git a/src/python/test/test_time_delay.py b/src/python/test/test_time_delay.py
index d2ffbf40..1cdf56f9 100755
--- a/src/python/test/test_time_delay.py
+++ b/src/python/test/test_time_delay.py
@@ -6,30 +6,30 @@ def test_normal():
     # Normal case.
     prep = TimeDelayEmbedding()
     attractor = prep(ts)
-    assert (attractor[0] == np.array[1, 2, 3])
-    assert (attractor[1] == np.array[2, 3, 4])
-    assert (attractor[2] == np.array[3, 4, 5])
-    assert (attractor[3] == np.array[4, 5, 6])
-    assert (attractor[4] == np.array[5, 6, 7])
-    assert (attractor[5] == np.array[6, 7, 8])
-    assert (attractor[6] == np.array[7, 8, 9])
-    assert (attractor[7] == np.array[8, 9, 10])
+    assert (attractor[0] == np.array([1, 2, 3]))
+    assert (attractor[1] == np.array([2, 3, 4]))
+    assert (attractor[2] == np.array([3, 4, 5]))
+    assert (attractor[3] == np.array([4, 5, 6]))
+    assert (attractor[4] == np.array([5, 6, 7]))
+    assert (attractor[5] == np.array([6, 7, 8]))
+    assert (attractor[6] == np.array([7, 8, 9]))
+    assert (attractor[7] == np.array([8, 9, 10]))
     # Delay = 3
     prep = TimeDelayEmbedding(delay=3)
     attractor = prep(ts)
-    assert (attractor[0] == np.array[1, 4, 7])
-    assert (attractor[1] == np.array[2, 5, 8])
-    assert (attractor[2] == np.array[3, 6, 9])
-    assert (attractor[3] == np.array[4, 7, 10])
+    assert (attractor[0] == np.array([1, 4, 7]))
+    assert (attractor[1] == np.array([2, 5, 8]))
+    assert (attractor[2] == np.array([3, 6, 9]))
+    assert (attractor[3] == np.array([4, 7, 10]))
     # Skip = 3
     prep = TimeDelayEmbedding(skip=3)
     attractor = prep(ts)
-    assert (attractor[0] == np.array[1, 2, 3])
-    assert (attractor[1] == np.array[4, 5, 6])
-    assert (attractor[2] == np.array[7, 8, 9])
+    assert (attractor[0] == np.array([1, 2, 3]))
+    assert (attractor[1] == np.array([4, 5, 6]))
+    assert (attractor[2] == np.array([7, 8, 9]))
     # Delay = 2 / Skip = 2
     prep = TimeDelayEmbedding(delay=2, skip=2)
     attractor = prep(ts)
-    assert (attractor[0] == np.array[1, 3, 5])
-    assert (attractor[1] == np.array[3, 5, 7])
-    assert (attractor[2] == np.array[5, 7, 9])
+    assert (attractor[0] == np.array([1, 3, 5]))
+    assert (attractor[1] == np.array([3, 5, 7]))
+    assert (attractor[2] == np.array([5, 7, 9]))
-- 
cgit v1.2.3


From 1c0f48fb26bb2e606dfe0a22e62618357686e2c2 Mon Sep 17 00:00:00 2001
From: mtakenouchi <m.takenouchi@jp.fujitsu.com>
Date: Fri, 14 Feb 2020 18:49:27 +0900
Subject: Update test_time_delay.py

---
 src/python/test/test_time_delay.py | 1 +
 1 file changed, 1 insertion(+)

(limited to 'src')

diff --git a/src/python/test/test_time_delay.py b/src/python/test/test_time_delay.py
index 1cdf56f9..3b586ad2 100755
--- a/src/python/test/test_time_delay.py
+++ b/src/python/test/test_time_delay.py
@@ -1,4 +1,5 @@
 from gudhi.point_cloud.timedelay import TimeDelayEmbedding
+import numpy as np
 
 def test_normal():
     # Sample array
-- 
cgit v1.2.3


From 39873c0cf43ca7352dddeab8c1cc6a3fc40a2e58 Mon Sep 17 00:00:00 2001
From: mtakenouchi <m.takenouchi@jp.fujitsu.com>
Date: Fri, 14 Feb 2020 19:08:50 +0900
Subject: Update test_time_delay.py

---
 src/python/test/test_time_delay.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'src')

diff --git a/src/python/test/test_time_delay.py b/src/python/test/test_time_delay.py
index 3b586ad2..7b6562a5 100755
--- a/src/python/test/test_time_delay.py
+++ b/src/python/test/test_time_delay.py
@@ -7,7 +7,8 @@ def test_normal():
     # Normal case.
     prep = TimeDelayEmbedding()
     attractor = prep(ts)
-    assert (attractor[0] == np.array([1, 2, 3]))
+    assert (attractor[0] == np.array([1, 2, 3])
+            print(attractor[0].all()))
     assert (attractor[1] == np.array([2, 3, 4]))
     assert (attractor[2] == np.array([3, 4, 5]))
     assert (attractor[3] == np.array([4, 5, 6]))
-- 
cgit v1.2.3


From 7c6966ee9821aaeb60d282616445a47071ac1fee Mon Sep 17 00:00:00 2001
From: mtakenouchi <m.takenouchi@jp.fujitsu.com>
Date: Fri, 14 Feb 2020 19:20:25 +0900
Subject: Update test_time_delay.py

---
 src/python/test/test_time_delay.py | 37 ++++++++++++++++++-------------------
 1 file changed, 18 insertions(+), 19 deletions(-)

(limited to 'src')

diff --git a/src/python/test/test_time_delay.py b/src/python/test/test_time_delay.py
index 7b6562a5..f652fc88 100755
--- a/src/python/test/test_time_delay.py
+++ b/src/python/test/test_time_delay.py
@@ -7,31 +7,30 @@ def test_normal():
     # Normal case.
     prep = TimeDelayEmbedding()
     attractor = prep(ts)
-    assert (attractor[0] == np.array([1, 2, 3])
-            print(attractor[0].all()))
-    assert (attractor[1] == np.array([2, 3, 4]))
-    assert (attractor[2] == np.array([3, 4, 5]))
-    assert (attractor[3] == np.array([4, 5, 6]))
-    assert (attractor[4] == np.array([5, 6, 7]))
-    assert (attractor[5] == np.array([6, 7, 8]))
-    assert (attractor[6] == np.array([7, 8, 9]))
-    assert (attractor[7] == np.array([8, 9, 10]))
+    assert (attractor[0].all() == np.array([1, 2, 3]))
+    assert (attractor[1].all() == np.array([2, 3, 4]))
+    assert (attractor[2].all() == np.array([3, 4, 5]))
+    assert (attractor[3].all() == np.array([4, 5, 6]))
+    assert (attractor[4].all() == np.array([5, 6, 7]))
+    assert (attractor[5].all() == np.array([6, 7, 8]))
+    assert (attractor[6].all() == np.array([7, 8, 9]))
+    assert (attractor[7].all() == np.array([8, 9, 10]))
     # Delay = 3
     prep = TimeDelayEmbedding(delay=3)
     attractor = prep(ts)
-    assert (attractor[0] == np.array([1, 4, 7]))
-    assert (attractor[1] == np.array([2, 5, 8]))
-    assert (attractor[2] == np.array([3, 6, 9]))
-    assert (attractor[3] == np.array([4, 7, 10]))
+    assert (attractor[0].all() == np.array([1, 4, 7]))
+    assert (attractor[1].all() == np.array([2, 5, 8]))
+    assert (attractor[2].all() == np.array([3, 6, 9]))
+    assert (attractor[3].all() == np.array([4, 7, 10]))
     # Skip = 3
     prep = TimeDelayEmbedding(skip=3)
     attractor = prep(ts)
-    assert (attractor[0] == np.array([1, 2, 3]))
-    assert (attractor[1] == np.array([4, 5, 6]))
-    assert (attractor[2] == np.array([7, 8, 9]))
+    assert (attractor[0].all() == np.array([1, 2, 3]))
+    assert (attractor[1].all() == np.array([4, 5, 6]))
+    assert (attractor[2].all() == np.array([7, 8, 9]))
     # Delay = 2 / Skip = 2
     prep = TimeDelayEmbedding(delay=2, skip=2)
     attractor = prep(ts)
-    assert (attractor[0] == np.array([1, 3, 5]))
-    assert (attractor[1] == np.array([3, 5, 7]))
-    assert (attractor[2] == np.array([5, 7, 9]))
+    assert (attractor[0].all() == np.array([1, 3, 5]))
+    assert (attractor[1].all() == np.array([3, 5, 7]))
+    assert (attractor[2].all() == np.array([5, 7, 9]))
-- 
cgit v1.2.3


From 5023aa0ff30474a96783152844e7fb0ed52e0c98 Mon Sep 17 00:00:00 2001
From: mtakenouchi <m.takenouchi@jp.fujitsu.com>
Date: Fri, 14 Feb 2020 20:25:14 +0900
Subject: Update test_time_delay.py

---
 src/python/test/test_time_delay.py | 36 ++++++++++++++++++------------------
 1 file changed, 18 insertions(+), 18 deletions(-)

(limited to 'src')

diff --git a/src/python/test/test_time_delay.py b/src/python/test/test_time_delay.py
index f652fc88..5464a185 100755
--- a/src/python/test/test_time_delay.py
+++ b/src/python/test/test_time_delay.py
@@ -7,30 +7,30 @@ def test_normal():
     # Normal case.
     prep = TimeDelayEmbedding()
     attractor = prep(ts)
-    assert (attractor[0].all() == np.array([1, 2, 3]))
-    assert (attractor[1].all() == np.array([2, 3, 4]))
-    assert (attractor[2].all() == np.array([3, 4, 5]))
-    assert (attractor[3].all() == np.array([4, 5, 6]))
-    assert (attractor[4].all() == np.array([5, 6, 7]))
-    assert (attractor[5].all() == np.array([6, 7, 8]))
-    assert (attractor[6].all() == np.array([7, 8, 9]))
-    assert (attractor[7].all() == np.array([8, 9, 10]))
+    assert (attractor[0] == np.array([1, 2, 3])).all()
+    assert (attractor[1] == np.array([2, 3, 4])).all()
+    assert (attractor[2] == np.array([3, 4, 5])).all()
+    assert (attractor[3] == np.array([4, 5, 6])).all()
+    assert (attractor[4] == np.array([5, 6, 7])).all()
+    assert (attractor[5] == np.array([6, 7, 8])).all()
+    assert (attractor[6] == np.array([7, 8, 9])).all()
+    assert (attractor[7] == np.array([8, 9, 10])).all()
     # Delay = 3
     prep = TimeDelayEmbedding(delay=3)
     attractor = prep(ts)
-    assert (attractor[0].all() == np.array([1, 4, 7]))
-    assert (attractor[1].all() == np.array([2, 5, 8]))
-    assert (attractor[2].all() == np.array([3, 6, 9]))
-    assert (attractor[3].all() == np.array([4, 7, 10]))
+    assert (attractor[0] == np.array([1, 4, 7])).all()
+    assert (attractor[1] == np.array([2, 5, 8])).all()
+    assert (attractor[2] == np.array([3, 6, 9])).all()
+    assert (attractor[3] == np.array([4, 7, 10])).all()
     # Skip = 3
     prep = TimeDelayEmbedding(skip=3)
     attractor = prep(ts)
-    assert (attractor[0].all() == np.array([1, 2, 3]))
-    assert (attractor[1].all() == np.array([4, 5, 6]))
-    assert (attractor[2].all() == np.array([7, 8, 9]))
+    assert (attractor[0] == np.array([1, 2, 3])).all()
+    assert (attractor[1] == np.array([4, 5, 6])).all()
+    assert (attractor[2] == np.array([7, 8, 9])).all()
     # Delay = 2 / Skip = 2
     prep = TimeDelayEmbedding(delay=2, skip=2)
     attractor = prep(ts)
-    assert (attractor[0].all() == np.array([1, 3, 5]))
-    assert (attractor[1].all() == np.array([3, 5, 7]))
-    assert (attractor[2].all() == np.array([5, 7, 9]))
+    assert (attractor[0] == np.array([1, 3, 5])).all()
+    assert (attractor[1] == np.array([3, 5, 7])).all()
+    assert (attractor[2] == np.array([5, 7, 9])).all()
-- 
cgit v1.2.3


From 80d84e5d8f9a24de745d23f7d721ea3e62217ff4 Mon Sep 17 00:00:00 2001
From: mtakenouchi <m.takenouchi@jp.fujitsu.com>
Date: Wed, 19 Feb 2020 12:32:00 +0900
Subject: Update timedelay.py

---
 src/python/gudhi/point_cloud/timedelay.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'src')

diff --git a/src/python/gudhi/point_cloud/timedelay.py b/src/python/gudhi/point_cloud/timedelay.py
index d899da67..6ad87cdc 100644
--- a/src/python/gudhi/point_cloud/timedelay.py
+++ b/src/python/gudhi/point_cloud/timedelay.py
@@ -43,7 +43,7 @@ class TimeDelayEmbedding:
             A single time-series data.
         Returns
         -------
-        point clouds : list[list[float, float, float]]
+        point clouds : list of n x 2 numpy arrays
             Makes point cloud every a single time-series data.
         Raises
         -------
@@ -80,7 +80,7 @@ class TimeDelayEmbedding:
              the same size. 
         Returns
         -------
-        point clouds : list[list[list[float, float, float]]]
+        point clouds : list of n x 3 numpy arrays
             Makes point cloud every a single time-series data.
         Raises
         -------
-- 
cgit v1.2.3


From 88964b4ff10798d6d9c3d0a342c004ee6b8b1496 Mon Sep 17 00:00:00 2001
From: mtakenouchi <m.takenouchi@jp.fujitsu.com>
Date: Tue, 25 Feb 2020 13:21:55 +0900
Subject: Update timedelay.py

---
 src/python/gudhi/point_cloud/timedelay.py | 89 +++++++++++++++----------------
 1 file changed, 44 insertions(+), 45 deletions(-)

(limited to 'src')

diff --git a/src/python/gudhi/point_cloud/timedelay.py b/src/python/gudhi/point_cloud/timedelay.py
index 6ad87cdc..d7a1dab7 100644
--- a/src/python/gudhi/point_cloud/timedelay.py
+++ b/src/python/gudhi/point_cloud/timedelay.py
@@ -8,10 +8,12 @@
 
 import numpy as np
 
+
 class TimeDelayEmbedding:
     """Point cloud transformation class.
     Embeds time-series data in the R^d according to Takens' Embedding Theorem
     and obtains the coordinates of each point.
+
     Parameters
     ----------
     dim : int, optional (default=3)
@@ -20,16 +22,27 @@ class TimeDelayEmbedding:
         Time-Delay embedding.
     skip : int, optional (default=1)
         How often to skip embedded points.
-        Given delay=3 and skip=2, an point cloud which is obtained by embedding 
-        a single time-series data into R^3 is as follows.
-        
-    .. code-block:: none
-    
-    time-series = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
-    point clouds = [[1, 4, 7], 
-                    [3, 6, 9]]
-                   
+
+    Example
+    -------
+
+    Given delay=3 and skip=2, a point cloud which is obtained by embedding
+    a scalar time-series into R^3 is as follows::
+
+        time-series = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
+        point cloud = [[1, 4, 7],
+                       [3, 6, 9]]
+
+    Given delay=1 and skip=1, a point cloud which is obtained by embedding
+    a 2D vector time-series data into R^4 is as follows::
+
+        time-series = [[0, 1], [2, 3], [4, 5], [6, 7], [8, 9]]
+        point cloud = [[0, 1, 2, 3],
+                       [2, 3, 4, 5],
+                       [4, 5, 6, 7],
+                       [6, 7, 8, 9]]
     """
+
     def __init__(self, dim=3, delay=1, skip=1):
         self._dim = dim
         self._delay = delay
@@ -39,56 +52,42 @@ class TimeDelayEmbedding:
         """Transform method for single time-series data.
         Parameters
         ----------
-        ts : list[float]
-            A single time-series data.
+        ts : Iterable[float] or Iterable[Iterable[float]]
+            A single time-series data, with scalar or vector values.
+
         Returns
         -------
-        point clouds : list of n x 2 numpy arrays
-            Makes point cloud every a single time-series data.
-        Raises
-        -------
-        TypeError
-            If the parameter's type does not match the desired type.
+        point cloud : n x dim numpy arrays
+            Makes point cloud from a single time-series data.
         """
-        ndts = np.array(ts)
-        if ndts.ndim == 1:
-            return self._transform(ndts)
-        else:
-            raise TypeError("Expects 1-dimensional array.")
+        return self._transform(np.array(ts))
 
     def fit(self, ts, y=None):
         return self
     
     def _transform(self, ts):
         """Guts of transform method."""
-        return ts[
-            np.add.outer(
-                np.arange(0, len(ts)-self._delay*(self._dim-1), self._skip),
-                np.arange(0, self._dim*self._delay, self._delay))
-        ]
+        if ts.ndim == 1:
+            repeat = self._dim
+        else:
+            assert self._dim % ts.shape[1] == 0
+            repeat = self._dim // ts.shape[1]
+        end = len(ts) - self._delay * (repeat - 1)
+        short = np.arange(0, end, self._skip)
+        vertical = np.arange(0, repeat * self._delay, self._delay)
+        return ts[np.add.outer(short, vertical)].reshape(len(short), -1)
 
     def transform(self, ts):
         """Transform method for multiple time-series data.
+
         Parameters
         ----------
-        ts : list[list[float]]
-            Multiple time-series data.
-        Attributes
-        ----------
-        ndts : 
-             The ndts means that all time series need to have exactly 
-             the same size. 
+        ts : Iterable[Iterable[float]] or Iterable[Iterable[Iterable[float]]]
+            Multiple time-series data, with scalar or vector values.
+
         Returns
         -------
-        point clouds : list of n x 3 numpy arrays
-            Makes point cloud every a single time-series data.
-        Raises
-        -------
-        TypeError
-            If the parameter's type does not match the desired type.
+        point clouds : list of n x dim numpy arrays
+            Makes point cloud from each time-series data.
         """
-        ndts = np.array(ts)
-        if ndts.ndim == 2:
-            return np.apply_along_axis(self._transform, 1, ndts)
-        else:
-            raise TypeError("Expects 2-dimensional array.")
+        return [self._transform(np.array(s)) for s in ts]
-- 
cgit v1.2.3


From 66c96498b994fea1fcaa6877121023410f4209f9 Mon Sep 17 00:00:00 2001
From: mtakenouchi <m.takenouchi@jp.fujitsu.com>
Date: Tue, 25 Feb 2020 13:24:48 +0900
Subject: Update test_time_delay.py

---
 src/python/test/test_time_delay.py | 51 ++++++++++++++++++++++----------------
 1 file changed, 29 insertions(+), 22 deletions(-)

(limited to 'src')

diff --git a/src/python/test/test_time_delay.py b/src/python/test/test_time_delay.py
index 5464a185..1ead9bca 100755
--- a/src/python/test/test_time_delay.py
+++ b/src/python/test/test_time_delay.py
@@ -1,36 +1,43 @@
 from gudhi.point_cloud.timedelay import TimeDelayEmbedding
 import numpy as np
 
+
 def test_normal():
     # Sample array
     ts = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
     # Normal case.
     prep = TimeDelayEmbedding()
-    attractor = prep(ts)
-    assert (attractor[0] == np.array([1, 2, 3])).all()
-    assert (attractor[1] == np.array([2, 3, 4])).all()
-    assert (attractor[2] == np.array([3, 4, 5])).all()
-    assert (attractor[3] == np.array([4, 5, 6])).all()
-    assert (attractor[4] == np.array([5, 6, 7])).all()
-    assert (attractor[5] == np.array([6, 7, 8])).all()
-    assert (attractor[6] == np.array([7, 8, 9])).all()
-    assert (attractor[7] == np.array([8, 9, 10])).all()
+    pointclouds = prep(ts)
+    assert (pointclouds[0] == np.array([1, 2, 3])).all()
+    assert (pointclouds[1] == np.array([2, 3, 4])).all()
+    assert (pointclouds[2] == np.array([3, 4, 5])).all()
+    assert (pointclouds[3] == np.array([4, 5, 6])).all()
+    assert (pointclouds[4] == np.array([5, 6, 7])).all()
+    assert (pointclouds[5] == np.array([6, 7, 8])).all()
+    assert (pointclouds[6] == np.array([7, 8, 9])).all()
+    assert (pointclouds[7] == np.array([8, 9, 10])).all()
     # Delay = 3
     prep = TimeDelayEmbedding(delay=3)
-    attractor = prep(ts)
-    assert (attractor[0] == np.array([1, 4, 7])).all()
-    assert (attractor[1] == np.array([2, 5, 8])).all()
-    assert (attractor[2] == np.array([3, 6, 9])).all()
-    assert (attractor[3] == np.array([4, 7, 10])).all()
+    pointclouds = prep(ts)
+    assert (pointclouds[0] == np.array([1, 4, 7])).all()
+    assert (pointclouds[1] == np.array([2, 5, 8])).all()
+    assert (pointclouds[2] == np.array([3, 6, 9])).all()
+    assert (pointclouds[3] == np.array([4, 7, 10])).all()
     # Skip = 3
     prep = TimeDelayEmbedding(skip=3)
-    attractor = prep(ts)
-    assert (attractor[0] == np.array([1, 2, 3])).all()
-    assert (attractor[1] == np.array([4, 5, 6])).all()
-    assert (attractor[2] == np.array([7, 8, 9])).all()
+    pointclouds = prep(ts)
+    assert (pointclouds[0] == np.array([1, 2, 3])).all()
+    assert (pointclouds[1] == np.array([4, 5, 6])).all()
+    assert (pointclouds[2] == np.array([7, 8, 9])).all()
     # Delay = 2 / Skip = 2
     prep = TimeDelayEmbedding(delay=2, skip=2)
-    attractor = prep(ts)
-    assert (attractor[0] == np.array([1, 3, 5])).all()
-    assert (attractor[1] == np.array([3, 5, 7])).all()
-    assert (attractor[2] == np.array([5, 7, 9])).all()
+    pointclouds = prep(ts)
+    assert (pointclouds[0] == np.array([1, 3, 5])).all()
+    assert (pointclouds[1] == np.array([3, 5, 7])).all()
+    assert (pointclouds[2] == np.array([5, 7, 9])).all()
+
+    # Vector series
+    ts = np.arange(0, 10).reshape(-1, 2)
+    prep = TimeDelayEmbedding(dim=4)
+    prep.fit([ts])
+    assert (prep.transform([ts])[0] == [[0, 1, 2, 3], [2, 3, 4, 5], [4, 5, 6, 7], [6, 7, 8, 9]]).all()
-- 
cgit v1.2.3


From a74ec878560bbe5fa340b2650ca9c16471b685af Mon Sep 17 00:00:00 2001
From: mtakenouchi <m.takenouchi@jp.fujitsu.com>
Date: Tue, 25 Feb 2020 13:27:03 +0900
Subject: Update point_cloud.rst

---
 src/python/doc/point_cloud.rst | 1 +
 1 file changed, 1 insertion(+)

(limited to 'src')

diff --git a/src/python/doc/point_cloud.rst b/src/python/doc/point_cloud.rst
index 55c74ff3..c0d4b303 100644
--- a/src/python/doc/point_cloud.rst
+++ b/src/python/doc/point_cloud.rst
@@ -26,4 +26,5 @@ TimeDelayEmbedding
 
 .. autoclass:: gudhi.point_cloud.timedelay.TimeDelayEmbedding
    :members:
+   :special-members: __call__
 
-- 
cgit v1.2.3


From f25d0f86fcd4ac9ab2939b2919d7a66df8b21269 Mon Sep 17 00:00:00 2001
From: mtakenouchi <m.takenouchi@jp.fujitsu.com>
Date: Tue, 25 Feb 2020 16:35:41 +0900
Subject: Update timedelay.py

---
 src/python/gudhi/point_cloud/timedelay.py | 1 +
 1 file changed, 1 insertion(+)

(limited to 'src')

diff --git a/src/python/gudhi/point_cloud/timedelay.py b/src/python/gudhi/point_cloud/timedelay.py
index d7a1dab7..576f4386 100644
--- a/src/python/gudhi/point_cloud/timedelay.py
+++ b/src/python/gudhi/point_cloud/timedelay.py
@@ -50,6 +50,7 @@ class TimeDelayEmbedding:
 
     def __call__(self, ts):
         """Transform method for single time-series data.
+
         Parameters
         ----------
         ts : Iterable[float] or Iterable[Iterable[float]]
-- 
cgit v1.2.3


From 2c1edeb7fd241c8718a22618438b482704703b4a Mon Sep 17 00:00:00 2001
From: mtakenouchi <m.takenouchi@jp.fujitsu.com>
Date: Tue, 25 Feb 2020 17:46:28 +0900
Subject: Update timedelay.py

---
 src/python/gudhi/point_cloud/timedelay.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'src')

diff --git a/src/python/gudhi/point_cloud/timedelay.py b/src/python/gudhi/point_cloud/timedelay.py
index 576f4386..f01df442 100644
--- a/src/python/gudhi/point_cloud/timedelay.py
+++ b/src/python/gudhi/point_cloud/timedelay.py
@@ -11,8 +11,9 @@ import numpy as np
 
 class TimeDelayEmbedding:
     """Point cloud transformation class.
-    Embeds time-series data in the R^d according to Takens' Embedding Theorem
-    and obtains the coordinates of each point.
+    Embeds time-series data in the R^d according to [Takens' Embedding Theorem]
+    (https://en.wikipedia.org/wiki/Takens%27s_theorem) and obtains the 
+    coordinates of each point.
 
     Parameters
     ----------
-- 
cgit v1.2.3