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baunsgaard pushed a commit to branch main
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The following commit(s) were added to refs/heads/main by this push:
new 4434eeb [SYSTEMDS-3202] Python slice selection of rows and cols
4434eeb is described below
commit 4434eeba465fecc6295d63a3f33ef47cfaa4f642
Author: baunsgaard <baunsga...@tugraz.at>
AuthorDate: Fri Nov 5 15:09:42 2021 +0100
[SYSTEMDS-3202] Python slice selection of rows and cols
This commit adds slice arguments to python to allow slicing a
selection of rows or columns for both matrix and frame:
X = sds.from_numpy(a)
getCols 1 and 2:
b = X[:,[1,2]]
getRows 3,5
b = X[[3,5]]
This fits to the python numpy specification.
Closes #1438
---
src/main/python/systemds/operator/nodes/frame.py | 37 +++++++--
src/main/python/systemds/operator/nodes/matrix.py | 43 ++++++++---
src/main/python/systemds/script_building/script.py | 4 +-
src/main/python/systemds/utils/helpers.py | 18 +++--
src/main/python/tests/frame/test_slice.py | 87 ++++++++++++++++++++++
src/main/python/tests/matrix/test_slice.py | 81 ++++++++++++++++++++
src/main/python/tests/matrix/test_split.py | 2 +-
7 files changed, 250 insertions(+), 22 deletions(-)
diff --git a/src/main/python/systemds/operator/nodes/frame.py
b/src/main/python/systemds/operator/nodes/frame.py
index efa75b0..a609929 100644
--- a/src/main/python/systemds/operator/nodes/frame.py
+++ b/src/main/python/systemds/operator/nodes/frame.py
@@ -28,12 +28,12 @@ from typing import (TYPE_CHECKING, Dict, Iterable,
Optional, Sequence, Tuple,
import numpy as np
import pandas as pd
from py4j.java_gateway import JavaObject, JVMView
-from systemds.operator import Matrix, MultiReturn, OperationNode
+from systemds.operator import Matrix, MultiReturn, OperationNode, Scalar
from systemds.script_building.dag import DAGNode, OutputType
from systemds.utils.consts import VALID_INPUT_TYPES
from systemds.utils.converters import (frame_block_to_pandas,
pandas_to_frame_block)
-from systemds.utils.helpers import get_slice_string
+from systemds.utils.helpers import check_is_empty_slice,
check_no_less_than_zero, get_slice_string
if TYPE_CHECKING:
# to avoid cyclic dependencies during runtime
@@ -73,7 +73,7 @@ class Frame(OperationNode):
code_line = code_line.format(file_name=var_name)
return code_line
- def compute(self, verbose: bool = False, lineage: bool = False) ->
Union[pd.DataFrame]:
+ def compute(self, verbose: bool = False, lineage: bool = False) ->
pd.DataFrame:
if self._is_pandas():
if verbose:
print("[Pandas Frame - No Compilation necessary]")
@@ -139,6 +139,33 @@ class Frame(OperationNode):
def __str__(self):
return "FrameNode"
+ def nRow(self) -> 'Scalar':
+ return Scalar(self.sds_context, 'nrow', [self])
+
+ def nCol(self) -> 'Scalar':
+ return Scalar(self.sds_context, 'ncol', [self])
+
def __getitem__(self, i) -> 'Frame':
- sliceIns = get_slice_string(i)
- return Frame(self.sds_context, '', [self, sliceIns], brackets=True)
+ if isinstance(i, tuple) and len(i) > 2:
+ raise ValueError("Maximum of two dimensions are allowed")
+ elif isinstance(i, list):
+ check_no_less_than_zero(i)
+ slice = self.sds_context.from_numpy(np.array(i)) + 1
+ select = Matrix(self.sds_context, "table",
+ [slice, 1, self.nRow(), 1])
+ ret = Frame(self.sds_context, "removeEmpty", [], {
+ 'target': self, 'margin': '"rows"', 'select': select})
+ return ret
+ elif isinstance(i, tuple) and isinstance(i[0], list) and
isinstance(i[1], list):
+ raise NotImplementedError("double slicing is not supported yet")
+ elif isinstance(i, tuple) and check_is_empty_slice(i[0]) and
isinstance(i[1], list):
+ check_no_less_than_zero(i[1])
+ slice = self.sds_context.from_numpy(np.array(i[1])) + 1
+ select = Matrix(self.sds_context, "table",
+ [slice, 1, self.nCol(), 1])
+ ret = Frame(self.sds_context, "removeEmpty", [], {
+ 'target': self, 'margin': '"cols"', 'select': select})
+ return ret
+ else:
+ sliceIns = get_slice_string(i)
+ return Frame(self.sds_context, '', [self, sliceIns], brackets=True)
diff --git a/src/main/python/systemds/operator/nodes/matrix.py
b/src/main/python/systemds/operator/nodes/matrix.py
index 9def246..6816245 100644
--- a/src/main/python/systemds/operator/nodes/matrix.py
+++ b/src/main/python/systemds/operator/nodes/matrix.py
@@ -21,25 +21,23 @@
__all__ = ["Matrix"]
-import os
-from typing import (TYPE_CHECKING, Dict, Iterable, Optional, Sequence, Tuple,
- Union)
+from typing import TYPE_CHECKING, Dict, Iterable, Sequence, Union
import numpy as np
-from py4j.java_gateway import JavaObject, JVMView
+from py4j.java_gateway import JavaObject
from systemds.operator import OperationNode, Scalar
from systemds.script_building.dag import OutputType
from systemds.utils.consts import (BINARY_OPERATIONS, VALID_ARITHMETIC_TYPES,
VALID_INPUT_TYPES)
from systemds.utils.converters import (matrix_block_to_numpy,
numpy_to_matrix_block)
-from systemds.utils.helpers import get_slice_string
+from systemds.utils.helpers import check_is_empty_slice,
check_no_less_than_zero, get_slice_string
class Matrix(OperationNode):
_np_array: np.array
- def __init__(self, sds_context: 'SystemDSContext', operation: str,
+ def __init__(self, sds_context, operation: str,
unnamed_input_nodes: Union[str,
Iterable[VALID_INPUT_TYPES]] =
None,
named_input_nodes: Dict[str, VALID_INPUT_TYPES] = None,
@@ -68,7 +66,7 @@ class Matrix(OperationNode):
code_line = code_line.format(file_name=var_name)
return code_line
- def compute(self, verbose: bool = False, lineage: bool = False) ->
Union[np.array]:
+ def compute(self, verbose: bool = False, lineage: bool = False) ->
np.array:
if self._is_numpy():
if verbose:
print('[Numpy Array - No Compilation necessary]')
@@ -154,9 +152,36 @@ class Matrix(OperationNode):
def __matmul__(self, other: 'Matrix') -> 'Matrix':
return Matrix(self.sds_context, '%*%', [self, other])
+ def nRow(self) -> 'Scalar':
+ return Scalar(self.sds_context, 'nrow', [self])
+
+ def nCol(self) -> 'Scalar':
+ return Scalar(self.sds_context, 'ncol', [self])
+
def __getitem__(self, i):
- sliceIns = get_slice_string(i)
- return Matrix(self.sds_context, '', [self, sliceIns], brackets=True)
+ if isinstance(i, tuple) and len(i) > 2:
+ raise ValueError("Maximum of two dimensions are allowed")
+ elif isinstance(i, list):
+ check_no_less_than_zero(i)
+ slice = self.sds_context.from_numpy(np.array(i)) + 1
+ select = Matrix(self.sds_context, "table",
+ [slice, 1, self.nRow(), 1])
+ ret = Matrix(self.sds_context, "removeEmpty", [], {
+ 'target': self, 'margin': '"rows"', 'select': select})
+ return ret
+ elif isinstance(i, tuple) and isinstance(i[0], list) and
isinstance(i[1], list):
+ raise NotImplementedError("double slicing is not supported yet")
+ elif isinstance(i, tuple) and check_is_empty_slice(i[0]) and
isinstance(i[1], list):
+ check_no_less_than_zero(i[1])
+ slice = self.sds_context.from_numpy(np.array(i[1])) + 1
+ select = Matrix(self.sds_context, "table",
+ [slice, 1, self.nCol(), 1])
+ ret = Matrix(self.sds_context, "removeEmpty", [], {
+ 'target': self, 'margin': '"cols"', 'select': select})
+ return ret
+ else:
+ sliceIns = get_slice_string(i)
+ return Matrix(self.sds_context, '', [self, sliceIns],
brackets=True)
def sum(self, axis: int = None) -> 'OperationNode':
"""Calculate sum of matrix.
diff --git a/src/main/python/systemds/script_building/script.py
b/src/main/python/systemds/script_building/script.py
index 313c6b9..06753ab 100644
--- a/src/main/python/systemds/script_building/script.py
+++ b/src/main/python/systemds/script_building/script.py
@@ -81,7 +81,7 @@ class DMLScript:
ret = self.prepared_script.executeScript()
return ret
except Py4JNetworkError:
- exception_str = "Py4JNetworkError: no connection to JVM, most
likely due to previous crash"
+ exception_str = "Py4JNetworkError: no connection to JVM, most
likely due to previous crash or closed JVM from calls to close()"
trace_back_limit = 0
except Exception as e:
exception_str = str(e)
@@ -111,7 +111,7 @@ class DMLScript:
return ret, traces
except Py4JNetworkError:
- exception_str = "Py4JNetworkError: no connection to JVM, most
likely due to previous crash"
+ exception_str = "Py4JNetworkError: no connection to JVM, most
likely due to previous crash or closed JVM from calls to close()"
trace_back_limit = 0
except Exception as e:
exception_str = str(e)
diff --git a/src/main/python/systemds/utils/helpers.py
b/src/main/python/systemds/utils/helpers.py
index 83ca596..b25ac65 100644
--- a/src/main/python/systemds/utils/helpers.py
+++ b/src/main/python/systemds/utils/helpers.py
@@ -51,12 +51,10 @@ def get_module_dir() -> os.PathLike:
def get_slice_string(i):
+ if isinstance(i, list):
+ raise ValueError("Not Supported list query")
if isinstance(i, tuple):
- if len(i) > 2:
- raise ValueError(
- f'Invalid number of dimensions to slice {len(i)}, Only 2
dimensions allowed')
- else:
- return f'{get_slice_string(i[0])},{get_slice_string(i[1])}'
+ return f'{get_slice_string(i[0])},{get_slice_string(i[1])}'
elif isinstance(i, slice):
if i.step:
raise ValueError("Invalid to slice with step in systemds")
@@ -71,3 +69,13 @@ def get_slice_string(i):
# + 1 since R and systemDS is 1 indexed.
sliceIns = i+1
return sliceIns
+
+
+def check_is_empty_slice(i):
+ return isinstance(i, slice) and i.start == None and i.stop == None and
i.step == None
+
+
+def check_no_less_than_zero(i: list):
+ for x in i:
+ if(x < 0):
+ raise ValueError("Negative index not supported in systemds")
diff --git a/src/main/python/tests/frame/test_slice.py
b/src/main/python/tests/frame/test_slice.py
new file mode 100644
index 0000000..0bb5a31
--- /dev/null
+++ b/src/main/python/tests/frame/test_slice.py
@@ -0,0 +1,87 @@
+# -------------------------------------------------------------
+#
+# 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
+import pandas as pd
+from systemds.context import SystemDSContext
+
+df = pd.DataFrame(
+ {
+ "col1": ["col1_hello_3", "col1_world_3", "col1_hello_3"],
+ "col2": [6, 7, 8],
+ "col3": [0.6, 0.7, 0.8],
+ }
+)
+
+
+class TestFederatedAggFn(unittest.TestCase):
+
+ sds: SystemDSContext = None
+
+ @classmethod
+ def setUpClass(cls):
+ cls.sds = SystemDSContext()
+
+ @classmethod
+ def tearDownClass(cls):
+ cls.sds.close()
+
+ def test_setup(self):
+ sm = self.sds.from_pandas(df)
+ sr = sm.compute()
+ self.assertTrue(isinstance(sr, pd.DataFrame))
+ e = df
+ self.assertTrue((e.values == sr.values).all())
+
+ def test_slice_first_third_row(self):
+ sm = self.sds.from_pandas(df)[[0, 2]]
+ sr = sm.compute()
+ e = df.loc[[0, 2]]
+ self.assertTrue((e.values == sr.values).all())
+
+ def test_slice_single_row(self):
+ sm = self.sds.from_pandas(df)[[1]]
+ sr = sm.compute()
+ e = df.loc[[1]]
+ self.assertTrue((e.values == sr.values).all())
+
+ def test_slice_last_row(self):
+ with self.assertRaises(ValueError):
+ self.sds.from_pandas(df)[[-1]]
+
+ # https://issues.apache.org/jira/browse/SYSTEMDS-3203
+ # def test_slice_first_third_col(self):
+ # sm = self.sds.from_pandas(df)[:, [0, 2]]
+ # sr = sm.compute()
+ # e = df.loc[:, [0, 2]]
+ # self.assertTrue((e.values == sr.values).all())
+
+ # def test_slice_single_col(self):
+ # sm = self.sds.from_pandas(df)[:, [1]]
+ # sr = sm.compute()
+ # e = df.loc[:, [1]]
+ # self.assertTrue((e.values == sr.values).all())
+
+ def test_slice_row_col_both(self):
+ with self.assertRaises(NotImplementedError):
+ self.sds.from_pandas(df)[[1, 2], [0, 2]]
diff --git a/src/main/python/tests/matrix/test_slice.py
b/src/main/python/tests/matrix/test_slice.py
new file mode 100644
index 0000000..bb988a6
--- /dev/null
+++ b/src/main/python/tests/matrix/test_slice.py
@@ -0,0 +1,81 @@
+# -------------------------------------------------------------
+#
+# 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
+
+# Seed the randomness.
+np.random.seed(7)
+
+m = np.random.rand(3, 4)
+
+
+class TestFederatedAggFn(unittest.TestCase):
+
+ sds: SystemDSContext = None
+
+ @classmethod
+ def setUpClass(cls):
+ cls.sds = SystemDSContext()
+
+ @classmethod
+ def tearDownClass(cls):
+ cls.sds.close()
+
+ def test_setup(self):
+ sm = self.sds.from_numpy(m)
+ sr = sm.compute()
+ e = m
+ self.assertTrue(np.allclose(e, sr))
+
+ def test_slice_first_third_row(self):
+ sm = self.sds.from_numpy(m)[[0, 2]]
+ sr = sm.compute()
+ e = m[[0, 2]]
+ self.assertTrue(np.allclose(e, sr))
+
+ def test_slice_single_row(self):
+ sm = self.sds.from_numpy(m)[[1]]
+ sr = sm.compute()
+ e = m[[1]]
+ self.assertTrue(np.allclose(e, sr))
+
+ def test_slice_last_row(self):
+ with self.assertRaises(ValueError):
+ self.sds.from_numpy(m)[[-1]]
+
+ def test_slice_first_third_col(self):
+ sm = self.sds.from_numpy(m)[:, [0, 2]]
+ sr = sm.compute()
+ e = m[:, [0, 2]]
+ self.assertTrue(np.allclose(e, sr))
+
+ def test_slice_single_col(self):
+ sm = self.sds.from_numpy(m)[:, [1]]
+ sr = sm.compute()
+ e = m[:, [1]]
+ self.assertTrue(np.allclose(e, sr))
+
+ def test_slice_row_col_both(self):
+ with self.assertRaises(NotImplementedError):
+ self.sds.from_numpy(m)[[1, 2], [0, 3]]
diff --git a/src/main/python/tests/matrix/test_split.py
b/src/main/python/tests/matrix/test_split.py
index 7c92353..2920821 100644
--- a/src/main/python/tests/matrix/test_split.py
+++ b/src/main/python/tests/matrix/test_split.py
@@ -26,7 +26,7 @@ import numpy as np
from systemds.context import SystemDSContext
from systemds.operator.algorithm import split
-# Seed the random ness.
+# Seed the randomness.
np.random.seed(7)
class TestOrder(unittest.TestCase):
