From 0701157102b321cf38802530937d8e6f1b8632af Mon Sep 17 00:00:00 2001
From: Adam Fekete <adam.fekete@kcl.ac.uk>
Date: Tue, 24 Jan 2017 15:22:00 +0000
Subject: [PATCH] adding datamodel class and future version of GP

---
 .../ML_of_Forces/DataModel/ForceConfs.py      | 90 +++++++++++++++++++
 .../ML_of_Forces/DataModel/__init__.py        |  3 +
 .../ML_of_Forces/DataModel/baseclasses.py     |  5 ++
 .../GP/Extensions/BeakerSupport.py            |  1 +
 .../GP/Extensions/PlotlySupport.py            | 36 ++++++++
 .../ML_of_Forces/GP/Extensions/__init__.py    |  0
 python-module/ML_of_Forces/GP/GPVec.py        | 42 +++++++++
 .../ML_of_Forces/GP/Optimizer/__init__.py     |  0
 python-module/ML_of_Forces/GP/__init__.py     |  4 +
 python-module/ML_of_Forces/GP/baseclass.py    | 22 +++++
 .../ML_of_Forces/GP/feature/__init__.py       |  2 +
 .../ML_of_Forces/GP/feature/cov_mat.py        | 13 +++
 .../ML_of_Forces/GP/kernels/__init__.py       | 11 +++
 python-module/ML_of_Forces/GP/kernels/id.py   |  7 ++
 .../ML_of_Forces/GP/tools/__init__.py         |  9 ++
 15 files changed, 245 insertions(+)
 create mode 100644 python-module/ML_of_Forces/DataModel/ForceConfs.py
 create mode 100644 python-module/ML_of_Forces/DataModel/__init__.py
 create mode 100644 python-module/ML_of_Forces/DataModel/baseclasses.py
 create mode 100644 python-module/ML_of_Forces/GP/Extensions/BeakerSupport.py
 create mode 100644 python-module/ML_of_Forces/GP/Extensions/PlotlySupport.py
 create mode 100644 python-module/ML_of_Forces/GP/Extensions/__init__.py
 create mode 100644 python-module/ML_of_Forces/GP/GPVec.py
 create mode 100644 python-module/ML_of_Forces/GP/Optimizer/__init__.py
 create mode 100644 python-module/ML_of_Forces/GP/__init__.py
 create mode 100644 python-module/ML_of_Forces/GP/baseclass.py
 create mode 100644 python-module/ML_of_Forces/GP/feature/__init__.py
 create mode 100644 python-module/ML_of_Forces/GP/feature/cov_mat.py
 create mode 100644 python-module/ML_of_Forces/GP/kernels/__init__.py
 create mode 100644 python-module/ML_of_Forces/GP/kernels/id.py
 create mode 100644 python-module/ML_of_Forces/GP/tools/__init__.py

diff --git a/python-module/ML_of_Forces/DataModel/ForceConfs.py b/python-module/ML_of_Forces/DataModel/ForceConfs.py
new file mode 100644
index 0000000..cad83b5
--- /dev/null
+++ b/python-module/ML_of_Forces/DataModel/ForceConfs.py
@@ -0,0 +1,90 @@
+from DataModel.baseclasses import DataModel
+from collections import namedtuple
+import numpy as np
+
+
+### Subsampling from big database ###
+
+### Spliting database in training/testing sets ###
+
+
+class ForceConfs(DataModel):
+
+    def __init__(self, confs=[], force=[]):
+        """
+
+        :param force: array of forces
+        :type force: np.array
+        :param confs: array of configurations
+        """
+        assert len(confs) == len(force)
+
+        self.confs = confs
+        self.force = force
+
+    def __str__(self):
+
+        out = 'ForceConfs model\n' + \
+              '       # of configuration: {}\n'.format(len(self.confs)) +\
+              '  range of configurations: mean={2}, min={0}, max={1}\n'.format(*self.range())
+
+        return out
+
+    def __len__(self):
+        """
+
+        :return: length of the forces/configurations
+        """
+        return len(self.confs)
+
+    def range(self):
+
+        """
+        Determine the minimum and maximum length for a given list of configurations
+        :return: namedtuple('LengthRange', ['min', 'max', 'mean'])
+        """
+        lengths = [len(conf) for conf in self.confs]
+
+        LengthRange = namedtuple('LengthRange', ['min', 'max', 'mean'])
+        return LengthRange(min=np.min(lengths), max=np.max(lengths), mean=np.mean(lengths))
+
+        # return np.min(lengths), np.max(lengths), np.mean(lengths)
+
+    def read_json_data(self, filename):
+        import json
+
+        with open(filename, 'r') as jsonfile:
+            data = json.load(jsonfile)['data']
+
+        self.confs = [timestep['confs'] for timestep in data]
+        self.force = [timestep['force'] for timestep in data]
+
+        self.confs = np.asarray(self.confs)
+        self.force = np.asarray(self.force)
+
+
+    def subsampling(self, train: int = 0, test: int = 0, random: bool = True) -> None:
+
+        self.nsample = train + test
+
+        if random:
+            inds = range(len(self))
+            inds = np.random.choice(inds, size=self.nsample, replace=False)
+
+        self.train_confs = self.confs[inds[0:train]]
+        self.train_force = self.force[inds[train:]]
+
+
+if __name__ == '__main__':
+
+    filename = '../Data/Si_TB_300K.json'
+
+    data = ForceConfs()
+    data.read_json_data(filename)
+    print(data)
+
+    data.subsampling(40,10)
+
+    print(len(data.train_confs))
+    print(len(data.train_force))
+    print('END')
diff --git a/python-module/ML_of_Forces/DataModel/__init__.py b/python-module/ML_of_Forces/DataModel/__init__.py
new file mode 100644
index 0000000..9dd5dd5
--- /dev/null
+++ b/python-module/ML_of_Forces/DataModel/__init__.py
@@ -0,0 +1,3 @@
+from .ForceConfs import ForceConfs
+
+__all__ = ["ForceConfs"]
\ No newline at end of file
diff --git a/python-module/ML_of_Forces/DataModel/baseclasses.py b/python-module/ML_of_Forces/DataModel/baseclasses.py
new file mode 100644
index 0000000..a7d6986
--- /dev/null
+++ b/python-module/ML_of_Forces/DataModel/baseclasses.py
@@ -0,0 +1,5 @@
+from abc import ABCMeta
+
+
+class DataModel(metaclass=ABCMeta):
+    pass
diff --git a/python-module/ML_of_Forces/GP/Extensions/BeakerSupport.py b/python-module/ML_of_Forces/GP/Extensions/BeakerSupport.py
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/python-module/ML_of_Forces/GP/Extensions/BeakerSupport.py
@@ -0,0 +1 @@
+
diff --git a/python-module/ML_of_Forces/GP/Extensions/PlotlySupport.py b/python-module/ML_of_Forces/GP/Extensions/PlotlySupport.py
new file mode 100644
index 0000000..632bef1
--- /dev/null
+++ b/python-module/ML_of_Forces/GP/Extensions/PlotlySupport.py
@@ -0,0 +1,36 @@
+# from bokeh.plotting import figure, output_file, show
+# output_file("test.html")
+# p = figure()
+# p.line([1, 2, 3, 4, 5], [6, 7, 2, 4, 5], line_width=2)
+# show(p)
+
+
+# from plotly import __version__
+#
+# from plotly.offline import download_plotlyjs, init_notebook_mode, plot, iplot
+#
+# print(__version__) # requires version >= 1.9.0
+#
+# from plotly.graph_objs import Scatter, Figure, Layout
+#
+# plot([Scatter(x=[1, 2, 3], y=[3, 1, 6])])
+
+#
+#
+# import plotly
+# from plotly.graph_objs import Scatter, Layout
+#
+# plotly.offline.plot({
+#     "data": [Scatter(x=[1, 2, 3, 4], y=[4, 3, 2, 1])],
+#     "layout": Layout(title="hello world")
+# })
+
+import plotly
+from plotly.graph_objs import Scatter, Layout
+
+plotly.offline.init_notebook_mode()
+
+plotly.offline.iplot({
+    "data": [Scatter(x=[1, 2, 3, 4], y=[4, 3, 2, 1])],
+    "layout": Layout(title="hello world")
+})
\ No newline at end of file
diff --git a/python-module/ML_of_Forces/GP/Extensions/__init__.py b/python-module/ML_of_Forces/GP/Extensions/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/python-module/ML_of_Forces/GP/GPVec.py b/python-module/ML_of_Forces/GP/GPVec.py
new file mode 100644
index 0000000..bb794f6
--- /dev/null
+++ b/python-module/ML_of_Forces/GP/GPVec.py
@@ -0,0 +1,42 @@
+from .baseclass import GaussianProcess
+
+from typing import Optional
+from typing import Union, List, Dict
+
+
+class GPVec(GaussianProcess):
+
+    def __init__(self,
+                 kernel: Optional[str] = None,
+                 datamodel=None):
+
+        """
+        sdfdsfdf
+        :param kernel: Hello
+        :type kernel: Optional[str]
+        :param datamodel:
+        """
+
+
+        super().__init__()
+        self.datamodel = datamodel  # type: Optional[str]
+        self.kernel = kernel    # kernel functions
+
+        pass
+
+    def fit(self, X, Y):
+        pass
+
+    def predict(self): pass
+
+    # def __repr__(self):
+    #     return "%s(%r)" % (self.__class__, self.__dict__)
+
+    def __str__(self):
+
+        out = 'GaussianProcess:\n' +\
+              '  datamodel: {}\n'.format(self.datamodel) +\
+              '  kernel: {}\n'.format(self.kernel)
+        return out
+
+
diff --git a/python-module/ML_of_Forces/GP/Optimizer/__init__.py b/python-module/ML_of_Forces/GP/Optimizer/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/python-module/ML_of_Forces/GP/__init__.py b/python-module/ML_of_Forces/GP/__init__.py
new file mode 100644
index 0000000..b862cc4
--- /dev/null
+++ b/python-module/ML_of_Forces/GP/__init__.py
@@ -0,0 +1,4 @@
+from .GPVec import GPVec
+
+
+__all__=['GPVec']
\ No newline at end of file
diff --git a/python-module/ML_of_Forces/GP/baseclass.py b/python-module/ML_of_Forces/GP/baseclass.py
new file mode 100644
index 0000000..64886e8
--- /dev/null
+++ b/python-module/ML_of_Forces/GP/baseclass.py
@@ -0,0 +1,22 @@
+from abc import ABCMeta, abstractmethod, abstractproperty
+
+
+class GaussianProcess(metaclass=ABCMeta):
+
+
+    # @abstractproperty
+    # def kernel(self): pass
+
+    @abstractmethod
+    def fit(self): pass
+
+    @abstractmethod
+    def predict(self): pass
+
+
+
+class Kernel(metaclass=ABCMeta):
+    pass
+
+class FeatureSpace(metaclass=ABCMeta):
+    pass
diff --git a/python-module/ML_of_Forces/GP/feature/__init__.py b/python-module/ML_of_Forces/GP/feature/__init__.py
new file mode 100644
index 0000000..139597f
--- /dev/null
+++ b/python-module/ML_of_Forces/GP/feature/__init__.py
@@ -0,0 +1,2 @@
+
+
diff --git a/python-module/ML_of_Forces/GP/feature/cov_mat.py b/python-module/ML_of_Forces/GP/feature/cov_mat.py
new file mode 100644
index 0000000..c2fac9a
--- /dev/null
+++ b/python-module/ML_of_Forces/GP/feature/cov_mat.py
@@ -0,0 +1,13 @@
+from GP.baseclass import FeatureSpace
+
+
+class cov_mat(FeatureSpace):
+
+    pass
+
+
+if __name__ == '__main__':
+
+    m = cov_mat()
+
+    print(m)
\ No newline at end of file
diff --git a/python-module/ML_of_Forces/GP/kernels/__init__.py b/python-module/ML_of_Forces/GP/kernels/__init__.py
new file mode 100644
index 0000000..b0e4ad0
--- /dev/null
+++ b/python-module/ML_of_Forces/GP/kernels/__init__.py
@@ -0,0 +1,11 @@
+
+from .id import id
+
+
+__all__ = ['id']
+
+
+
+
+if __name__ == '__main__':
+    pass
diff --git a/python-module/ML_of_Forces/GP/kernels/id.py b/python-module/ML_of_Forces/GP/kernels/id.py
new file mode 100644
index 0000000..db8db88
--- /dev/null
+++ b/python-module/ML_of_Forces/GP/kernels/id.py
@@ -0,0 +1,7 @@
+from GP.baseclass import Kernel
+
+
+class id(Kernel):
+
+    def __call__(self, *args, **kwargs):
+        return 1.0
diff --git a/python-module/ML_of_Forces/GP/tools/__init__.py b/python-module/ML_of_Forces/GP/tools/__init__.py
new file mode 100644
index 0000000..a5700ee
--- /dev/null
+++ b/python-module/ML_of_Forces/GP/tools/__init__.py
@@ -0,0 +1,9 @@
+import json
+
+
+def read_json_data(filename):
+
+    with open(filename, 'r') as jsonfile:
+        data = json.load(jsonfile)
+
+    return data['data']
-- 
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