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Posted to dev@systemml.apache.org by GitBox <gi...@apache.org> on 2020/06/15 09:51:55 UTC
[GitHub] [systemml] juliale-15 opened a new pull request #975: Extend the Python API
juliale-15 opened a new pull request #975:
URL: https://github.com/apache/systemml/pull/975
Extend the Python API by
- Trigonometric Built-In Functions such as sin, cos, tan etc
- Other Build-In Functions: reverse, transpose, order
- Linear Algebra Built-In Functions: Cholesky
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[GitHub] [systemml] juliale-15 commented on pull request #975: Extend the Python API
Posted by GitBox <gi...@apache.org>.
juliale-15 commented on pull request #975:
URL: https://github.com/apache/systemml/pull/975#issuecomment-645926669
> Hi Juliale!
>
> Great job, ⭐ i like the addition, and nice to see that you also consider the invalid input cases!
> I have a few comments to be addressed but nothing major.
>
> Question. How did you like the new test setup?
Great! I like it it is more readable now :)
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[GitHub] [systemml] Baunsgaard commented on a change in pull request #975: Extend the Python API
Posted by GitBox <gi...@apache.org>.
Baunsgaard commented on a change in pull request #975:
URL: https://github.com/apache/systemml/pull/975#discussion_r441434083
##########
File path: src/main/python/systemds/matrix/data_gen.py
##########
@@ -102,3 +105,70 @@ def rand(sds_context: SystemDSContext, rows: int, cols: int,
named_input_nodes['seed'] = seed
return OperationNode(sds_context, 'rand', [], named_input_nodes=named_input_nodes)
+
+
+def rev(sds_context: 'SystemDSContext', X: Matrix) -> 'OperationNode':
+ """ Reverses the rows in a matrix
+
+ :param sds_context: SystemDS context
+ :param X: Input matrix
+ :return: reversed matrix
+ """
+ X._check_matrix_op()
+ return OperationNode(sds_context, 'rev', [X])
+
+
+def order(sds_context: 'SystemDSContext', X: Matrix, by: int = 1, decreasing: bool = False, index_return: bool = False) -> 'OperationNode':
+ """ Sort by a column of the matrix X in increasing/decreasing order and returns either the index or data
+
+ :param sds_context: SystemDS context
+ :param X: Input matrix
+ :param by: Column number
+ :param decreasing: If true the matrix will be sorted in decreasing order
+ :param index_return: If true, theindex numbers will be returned
+ :return: sorted matrix
+ """
+ X._check_matrix_op()
+
+ cols = X._np_array.shape[1]
+ if by > cols:
+ raise IndexError("Index {i} is out of bounds for axis 1 with size {c}".format(i=by, c=cols))
+
+ named_input_nodes = {'target': X, 'by': by, 'decreasing': str(decreasing).upper(), 'index.return': str(index_return).upper()}
+
+ return OperationNode(sds_context, 'order', [], named_input_nodes=named_input_nodes)
+
+
+def t(sds_context: 'SystemDSContext', X: Matrix) -> 'OperationNode':
+ """ Transposes the input matrix
+
+ :param sds_context: SystemDS context
+ :param X: Input matrix
+ :return: transposed matrix
+ """
+ X._check_matrix_op()
+ return OperationNode(sds_context, 't', [X])
+
+
+def cholesky(sds_context: 'SystemDSContext', X: Matrix) -> 'OperationNode':
+ """ Computes the Cholesky decomposition of a symmetric, positive definite matrix
+
+ :param sds_context: SystemDS context
+ :param X: Input matrix
+ :return: Cholesky decomposition
+ """
+ X._check_matrix_op()
+
+ # check square dimension
+ if X._np_array.shape[0] != X._np_array.shape[1]:
+ raise ValueError("Last 2 dimensions of the array must be square")
+
+ # check if mat is positive definite
+ if not np.all(np.linalg.eigvals(X._np_array)>0):
+ raise ValueError("Matrix is not positive definite")
+
+ # check if mat is symmetric
+ if not np.allclose(X._np_array, X._np_array.transpose()):
+ raise ValueError("Matrix is not symmetric")
Review comment:
The system have changed alittle, so that it should be possible to catch these exceptions.
once `compute()` is called. But i don't expect to be able to use it here in this operations content. Therefore, i suggest to still just have a flag, that specifies unsafe, that simply skips these checks.
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[GitHub] [systemml] Baunsgaard commented on a change in pull request #975: Extend the Python API
Posted by GitBox <gi...@apache.org>.
Baunsgaard commented on a change in pull request #975:
URL: https://github.com/apache/systemml/pull/975#discussion_r442164461
##########
File path: src/main/python/systemds/matrix/data_gen.py
##########
@@ -102,3 +105,70 @@ def rand(sds_context: SystemDSContext, rows: int, cols: int,
named_input_nodes['seed'] = seed
return OperationNode(sds_context, 'rand', [], named_input_nodes=named_input_nodes)
+
+
+def rev(sds_context: 'SystemDSContext', X: Matrix) -> 'OperationNode':
+ """ Reverses the rows in a matrix
+
+ :param sds_context: SystemDS context
+ :param X: Input matrix
+ :return: reversed matrix
+ """
+ X._check_matrix_op()
+ return OperationNode(sds_context, 'rev', [X])
+
+
+def order(sds_context: 'SystemDSContext', X: Matrix, by: int = 1, decreasing: bool = False, index_return: bool = False) -> 'OperationNode':
+ """ Sort by a column of the matrix X in increasing/decreasing order and returns either the index or data
+
+ :param sds_context: SystemDS context
+ :param X: Input matrix
+ :param by: Column number
+ :param decreasing: If true the matrix will be sorted in decreasing order
+ :param index_return: If true, theindex numbers will be returned
+ :return: sorted matrix
+ """
+ X._check_matrix_op()
+
+ cols = X._np_array.shape[1]
+ if by > cols:
+ raise IndexError("Index {i} is out of bounds for axis 1 with size {c}".format(i=by, c=cols))
+
+ named_input_nodes = {'target': X, 'by': by, 'decreasing': str(decreasing).upper(), 'index.return': str(index_return).upper()}
+
+ return OperationNode(sds_context, 'order', [], named_input_nodes=named_input_nodes)
+
+
+def t(sds_context: 'SystemDSContext', X: Matrix) -> 'OperationNode':
+ """ Transposes the input matrix
+
+ :param sds_context: SystemDS context
+ :param X: Input matrix
+ :return: transposed matrix
+ """
+ X._check_matrix_op()
+ return OperationNode(sds_context, 't', [X])
+
+
+def cholesky(sds_context: 'SystemDSContext', X: Matrix) -> 'OperationNode':
+ """ Computes the Cholesky decomposition of a symmetric, positive definite matrix
+
+ :param sds_context: SystemDS context
+ :param X: Input matrix
+ :return: Cholesky decomposition
+ """
+ X._check_matrix_op()
+
+ # check square dimension
+ if X._np_array.shape[0] != X._np_array.shape[1]:
+ raise ValueError("Last 2 dimensions of the array must be square")
+
+ # check if mat is positive definite
+ if not np.all(np.linalg.eigvals(X._np_array)>0):
+ raise ValueError("Matrix is not positive definite")
+
+ # check if mat is symmetric
+ if not np.allclose(X._np_array, X._np_array.transpose()):
+ raise ValueError("Matrix is not symmetric")
Review comment:
Something along the lines of:
```python
def cholesky(sds_context: SystemDSContext, X: Matrix, safe: boolean = false) -> OperationNode:
```
But then again + old comments it becomes:
```python
def cholesky(safe: boolean = false) -> OperationNode:
```
if you move the operations into the matrix object
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[GitHub] [systemml] Baunsgaard commented on a change in pull request #975: Extend the Python API
Posted by GitBox <gi...@apache.org>.
Baunsgaard commented on a change in pull request #975:
URL: https://github.com/apache/systemml/pull/975#discussion_r440771496
##########
File path: src/main/python/systemds/matrix/data_gen.py
##########
@@ -29,6 +29,8 @@
from systemds.operator import OperationNode
from systemds.context import SystemDSContext
+from systemds.matrix import Matrix
+import numpy as np
def full(sds_context: SystemDSContext, shape: Tuple[int, int], value: Union[float, int]) -> OperationNode:
Review comment:
Also if you want to, then maybe change these data_gen functions to return matrix Objects, not Operation nods.
##########
File path: src/main/python/systemds/matrix/data_gen.py
##########
@@ -19,7 +19,7 @@
#
# -------------------------------------------------------------
-__all__ = ['full', 'seq', 'rand']
+__all__ = ['full', 'seq', 'rand', 'rev', 'order', 't', 'cholesky']
Review comment:
This file contains methods for data generation, not for operations.
I think it would be nice if you could move the `rev` `order` `t` and `cholesky` to the matrix.py object. thereby removing the need and potential error associated with calling these functions with an SystemDSContext.
##########
File path: src/main/python/systemds/matrix/data_gen.py
##########
@@ -102,3 +105,70 @@ def rand(sds_context: SystemDSContext, rows: int, cols: int,
named_input_nodes['seed'] = seed
return OperationNode(sds_context, 'rand', [], named_input_nodes=named_input_nodes)
+
+
+def rev(sds_context: 'SystemDSContext', X: Matrix) -> 'OperationNode':
+ """ Reverses the rows in a matrix
+
+ :param sds_context: SystemDS context
+ :param X: Input matrix
+ :return: reversed matrix
+ """
+ X._check_matrix_op()
+ return OperationNode(sds_context, 'rev', [X])
+
+
+def order(sds_context: 'SystemDSContext', X: Matrix, by: int = 1, decreasing: bool = False, index_return: bool = False) -> 'OperationNode':
+ """ Sort by a column of the matrix X in increasing/decreasing order and returns either the index or data
+
+ :param sds_context: SystemDS context
+ :param X: Input matrix
+ :param by: Column number
+ :param decreasing: If true the matrix will be sorted in decreasing order
+ :param index_return: If true, theindex numbers will be returned
+ :return: sorted matrix
+ """
+ X._check_matrix_op()
+
+ cols = X._np_array.shape[1]
+ if by > cols:
+ raise IndexError("Index {i} is out of bounds for axis 1 with size {c}".format(i=by, c=cols))
+
+ named_input_nodes = {'target': X, 'by': by, 'decreasing': str(decreasing).upper(), 'index.return': str(index_return).upper()}
+
+ return OperationNode(sds_context, 'order', [], named_input_nodes=named_input_nodes)
+
+
+def t(sds_context: 'SystemDSContext', X: Matrix) -> 'OperationNode':
+ """ Transposes the input matrix
+
+ :param sds_context: SystemDS context
+ :param X: Input matrix
+ :return: transposed matrix
+ """
+ X._check_matrix_op()
+ return OperationNode(sds_context, 't', [X])
+
+
+def cholesky(sds_context: 'SystemDSContext', X: Matrix) -> 'OperationNode':
+ """ Computes the Cholesky decomposition of a symmetric, positive definite matrix
+
+ :param sds_context: SystemDS context
+ :param X: Input matrix
+ :return: Cholesky decomposition
+ """
+ X._check_matrix_op()
+
+ # check square dimension
+ if X._np_array.shape[0] != X._np_array.shape[1]:
+ raise ValueError("Last 2 dimensions of the array must be square")
+
+ # check if mat is positive definite
+ if not np.all(np.linalg.eigvals(X._np_array)>0):
+ raise ValueError("Matrix is not positive definite")
+
+ # check if mat is symmetric
+ if not np.allclose(X._np_array, X._np_array.transpose()):
+ raise ValueError("Matrix is not symmetric")
Review comment:
I like the checks, but the complexity of these operations grow in size of X. (except for the first check).
This makes the overall performance of the operation slow, maybe we add an optional flag saying unsafe, that skip these checks?
##########
File path: src/main/python/systemds/matrix/data_gen.py
##########
@@ -102,3 +105,70 @@ def rand(sds_context: SystemDSContext, rows: int, cols: int,
named_input_nodes['seed'] = seed
return OperationNode(sds_context, 'rand', [], named_input_nodes=named_input_nodes)
+
+
+def rev(sds_context: 'SystemDSContext', X: Matrix) -> 'OperationNode':
Review comment:
In the Methods, i would appreciate if the syntax is:
` def rev(sds_context: SystemDSContext, X: Matrix) -> OperationNode:`
Since it allows the system to complain earlier about missing imports and such not resulting in a potential runtime error.
##########
File path: src/main/python/tests/test_matrix_cholesky.py
##########
@@ -0,0 +1,75 @@
+# -------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements. See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership. The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied. See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+# -------------------------------------------------------------
+
+import unittest
+
+import numpy as np
+from systemds.context import SystemDSContext
+from systemds.matrix.data_gen import cholesky
+from systemds.matrix import Matrix
+
+np.random.seed(7)
+shape = np.random.randint(1, 100)
+A = np.random.rand(shape, shape)
+# set A = MM^T and A is a positive definite matrix
+A = np.matmul(A, A.transpose())
+
+m1 = -np.random.rand(shape, shape)
+m2 = np.asarray([[4, 9], [1, 4]])
+m3 = np.random.rand(shape, shape + 1)
+
+class TestCholesky(unittest.TestCase):
+
+ sds: SystemDSContext = None
+
+ @classmethod
+ def setUpClass(cls):
+ cls.sds = SystemDSContext()
+
+ @classmethod
+ def tearDownClass(cls):
+ cls.sds.close()
+
+ def test_basic1(self):
+ L = cholesky(self.sds, Matrix(self.sds, A)).compute()
+ self.assertTrue(np.allclose(L, np.linalg.cholesky(A)))
+
+ def test_basic2(self):
+ L = cholesky(self.sds, Matrix(self.sds, A)).compute()
+ # L * L.H = A
+ self.assertTrue(np.allclose(A, np.dot(L, L.T.conj())))
+
+ def test_pos_def(self):
+ with self.assertRaises(ValueError) as context:
+ cholesky(self.sds, Matrix(self.sds, m1)).compute()
+
+ def test_symmetric_matrix(self):
+ np.linalg.cholesky(m2)
+ with self.assertRaises(ValueError) as context:
+ cholesky(self.sds, Matrix(self.sds, m2)).compute()
+
+ def test_asymetric_dim(self):
+ with self.assertRaises(ValueError) as context:
+ cholesky(self.sds, Matrix(self.sds, m3)).compute()
+
+
+if __name__ == "__main__":
+ unittest.main(exit=False)
Review comment:
If you want to make git happy, then add a single newline in the end of the files.
##########
File path: src/main/python/tests/test_matrix_reverse.py
##########
@@ -0,0 +1,68 @@
+# -------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements. See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership. The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied. See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+# -------------------------------------------------------------
+import math
+import os
+import random
+import sys
+import unittest
+
+import numpy as np
+from systemds.context import SystemDSContext
+from systemds.matrix.data_gen import rev
+from systemds.matrix import Matrix
+
+np.random.seed(7)
+
+shape = (random.randrange(1, 25), random.randrange(1, 25))
+m = np.random.rand(shape[0], shape[1])
+mx = np.random.rand(1, shape[1])
+my = np.random.rand(shape[0], 1)
+
+class TestReverse(unittest.TestCase):
+
+ sds: SystemDSContext = None
+
+ @classmethod
+ def setUpClass(cls):
+ cls.sds = SystemDSContext()
+
+ @classmethod
+ def tearDownClass(cls):
+ cls.sds.close()
+
+ def test_basic(self):
+ r = rev(self.sds, Matrix(self.sds, m)).compute()
Review comment:
Just a single example of the syntax i think would be great:
`r = Matrix(self.sds, m).rev().compute()`
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[GitHub] [systemml] juliale-15 commented on a change in pull request #975: Extend the Python API
Posted by GitBox <gi...@apache.org>.
juliale-15 commented on a change in pull request #975:
URL: https://github.com/apache/systemml/pull/975#discussion_r442124998
##########
File path: src/main/python/systemds/matrix/data_gen.py
##########
@@ -102,3 +105,70 @@ def rand(sds_context: SystemDSContext, rows: int, cols: int,
named_input_nodes['seed'] = seed
return OperationNode(sds_context, 'rand', [], named_input_nodes=named_input_nodes)
+
+
+def rev(sds_context: 'SystemDSContext', X: Matrix) -> 'OperationNode':
+ """ Reverses the rows in a matrix
+
+ :param sds_context: SystemDS context
+ :param X: Input matrix
+ :return: reversed matrix
+ """
+ X._check_matrix_op()
+ return OperationNode(sds_context, 'rev', [X])
+
+
+def order(sds_context: 'SystemDSContext', X: Matrix, by: int = 1, decreasing: bool = False, index_return: bool = False) -> 'OperationNode':
+ """ Sort by a column of the matrix X in increasing/decreasing order and returns either the index or data
+
+ :param sds_context: SystemDS context
+ :param X: Input matrix
+ :param by: Column number
+ :param decreasing: If true the matrix will be sorted in decreasing order
+ :param index_return: If true, theindex numbers will be returned
+ :return: sorted matrix
+ """
+ X._check_matrix_op()
+
+ cols = X._np_array.shape[1]
+ if by > cols:
+ raise IndexError("Index {i} is out of bounds for axis 1 with size {c}".format(i=by, c=cols))
+
+ named_input_nodes = {'target': X, 'by': by, 'decreasing': str(decreasing).upper(), 'index.return': str(index_return).upper()}
+
+ return OperationNode(sds_context, 'order', [], named_input_nodes=named_input_nodes)
+
+
+def t(sds_context: 'SystemDSContext', X: Matrix) -> 'OperationNode':
+ """ Transposes the input matrix
+
+ :param sds_context: SystemDS context
+ :param X: Input matrix
+ :return: transposed matrix
+ """
+ X._check_matrix_op()
+ return OperationNode(sds_context, 't', [X])
+
+
+def cholesky(sds_context: 'SystemDSContext', X: Matrix) -> 'OperationNode':
+ """ Computes the Cholesky decomposition of a symmetric, positive definite matrix
+
+ :param sds_context: SystemDS context
+ :param X: Input matrix
+ :return: Cholesky decomposition
+ """
+ X._check_matrix_op()
+
+ # check square dimension
+ if X._np_array.shape[0] != X._np_array.shape[1]:
+ raise ValueError("Last 2 dimensions of the array must be square")
+
+ # check if mat is positive definite
+ if not np.all(np.linalg.eigvals(X._np_array)>0):
+ raise ValueError("Matrix is not positive definite")
+
+ # check if mat is symmetric
+ if not np.allclose(X._np_array, X._np_array.transpose()):
+ raise ValueError("Matrix is not symmetric")
Review comment:
Can you specify what you meant by using a flag unsafe? I could just put a warning into this function saying it is unsafe to use such a matrix and just let the program continue even if the user violates the conditions. Did you mean something like this?
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[GitHub] [systemml] Baunsgaard commented on pull request #975: Extend the Python API
Posted by GitBox <gi...@apache.org>.
Baunsgaard commented on pull request #975:
URL: https://github.com/apache/systemml/pull/975#issuecomment-648032616
Hi @juliale-15,
Thank you for your PR :+1: , while merging I only updated the documentation.
I hope you feel motivated to commit more to Open Source and SystemDS in the future!
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[GitHub] [systemml] juliale-15 commented on a change in pull request #975: Extend the Python API
Posted by GitBox <gi...@apache.org>.
juliale-15 commented on a change in pull request #975:
URL: https://github.com/apache/systemml/pull/975#discussion_r441426528
##########
File path: src/main/python/systemds/matrix/data_gen.py
##########
@@ -102,3 +105,70 @@ def rand(sds_context: SystemDSContext, rows: int, cols: int,
named_input_nodes['seed'] = seed
return OperationNode(sds_context, 'rand', [], named_input_nodes=named_input_nodes)
+
+
+def rev(sds_context: 'SystemDSContext', X: Matrix) -> 'OperationNode':
+ """ Reverses the rows in a matrix
+
+ :param sds_context: SystemDS context
+ :param X: Input matrix
+ :return: reversed matrix
+ """
+ X._check_matrix_op()
+ return OperationNode(sds_context, 'rev', [X])
+
+
+def order(sds_context: 'SystemDSContext', X: Matrix, by: int = 1, decreasing: bool = False, index_return: bool = False) -> 'OperationNode':
+ """ Sort by a column of the matrix X in increasing/decreasing order and returns either the index or data
+
+ :param sds_context: SystemDS context
+ :param X: Input matrix
+ :param by: Column number
+ :param decreasing: If true the matrix will be sorted in decreasing order
+ :param index_return: If true, theindex numbers will be returned
+ :return: sorted matrix
+ """
+ X._check_matrix_op()
+
+ cols = X._np_array.shape[1]
+ if by > cols:
+ raise IndexError("Index {i} is out of bounds for axis 1 with size {c}".format(i=by, c=cols))
+
+ named_input_nodes = {'target': X, 'by': by, 'decreasing': str(decreasing).upper(), 'index.return': str(index_return).upper()}
+
+ return OperationNode(sds_context, 'order', [], named_input_nodes=named_input_nodes)
+
+
+def t(sds_context: 'SystemDSContext', X: Matrix) -> 'OperationNode':
+ """ Transposes the input matrix
+
+ :param sds_context: SystemDS context
+ :param X: Input matrix
+ :return: transposed matrix
+ """
+ X._check_matrix_op()
+ return OperationNode(sds_context, 't', [X])
+
+
+def cholesky(sds_context: 'SystemDSContext', X: Matrix) -> 'OperationNode':
+ """ Computes the Cholesky decomposition of a symmetric, positive definite matrix
+
+ :param sds_context: SystemDS context
+ :param X: Input matrix
+ :return: Cholesky decomposition
+ """
+ X._check_matrix_op()
+
+ # check square dimension
+ if X._np_array.shape[0] != X._np_array.shape[1]:
+ raise ValueError("Last 2 dimensions of the array must be square")
+
+ # check if mat is positive definite
+ if not np.all(np.linalg.eigvals(X._np_array)>0):
+ raise ValueError("Matrix is not positive definite")
+
+ # check if mat is symmetric
+ if not np.allclose(X._np_array, X._np_array.transpose()):
+ raise ValueError("Matrix is not symmetric")
Review comment:
Ah ok I get your point, but I'm not sure how to catch these two scenarios (positive definite, symmetric) without these check since SystemDS will throw an exception which is not easily readable after calling `compute()`.
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[GitHub] [systemml] asfgit closed pull request #975: Extend the Python API
Posted by GitBox <gi...@apache.org>.
asfgit closed pull request #975:
URL: https://github.com/apache/systemml/pull/975
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