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new 889db1fe42 [SYSTEMDS-3701] New Python API for multimodal data
alignment (scuro)
889db1fe42 is described below
commit 889db1fe422976152705b14f0caf74494abd98dd
Author: Christina Dionysio <[email protected]>
AuthorDate: Mon Jun 3 09:42:24 2024 +0200
[SYSTEMDS-3701] New Python API for multimodal data alignment (scuro)
Closes #2023.
---
src/main/python/systemds/__init__.py | 3 +-
src/main/python/systemds/{ => scuro}/__init__.py | 6 ---
.../systemds/{ => scuro/aligner}/__init__.py | 6 ---
.../python/systemds/scuro/aligner/alignment.py | 45 ++++++++++++++++++++++
.../aligner/alignment_strategy.py} | 22 +++++++++--
.../aligner/similarity_measures.py} | 16 ++++++--
.../python/systemds/{__init__.py => scuro/main.py} | 21 ++++++++--
.../systemds/{ => scuro/modality}/__init__.py | 6 ---
.../modality/aligned_modality.py} | 15 ++++++--
.../{__init__.py => scuro/modality/modality.py} | 22 +++++++++--
.../modality/representation.py} | 16 +++++---
.../modality/video_modality.py} | 31 +++++++++++++--
12 files changed, 160 insertions(+), 49 deletions(-)
diff --git a/src/main/python/systemds/__init__.py
b/src/main/python/systemds/__init__.py
index 27d7425566..e0f485df79 100644
--- a/src/main/python/systemds/__init__.py
+++ b/src/main/python/systemds/__init__.py
@@ -22,5 +22,6 @@
from systemds import context
from systemds import operator
from systemds import examples
+from systemds import scuro
-__all__ = ["context", "operator", "examples"]
+__all__ = ["context", "operator", "examples", "scuro"]
diff --git a/src/main/python/systemds/__init__.py
b/src/main/python/systemds/scuro/__init__.py
similarity index 87%
copy from src/main/python/systemds/__init__.py
copy to src/main/python/systemds/scuro/__init__.py
index 27d7425566..e66abb4646 100644
--- a/src/main/python/systemds/__init__.py
+++ b/src/main/python/systemds/scuro/__init__.py
@@ -18,9 +18,3 @@
# under the License.
#
# -------------------------------------------------------------
-
-from systemds import context
-from systemds import operator
-from systemds import examples
-
-__all__ = ["context", "operator", "examples"]
diff --git a/src/main/python/systemds/__init__.py
b/src/main/python/systemds/scuro/aligner/__init__.py
similarity index 87%
copy from src/main/python/systemds/__init__.py
copy to src/main/python/systemds/scuro/aligner/__init__.py
index 27d7425566..e66abb4646 100644
--- a/src/main/python/systemds/__init__.py
+++ b/src/main/python/systemds/scuro/aligner/__init__.py
@@ -18,9 +18,3 @@
# under the License.
#
# -------------------------------------------------------------
-
-from systemds import context
-from systemds import operator
-from systemds import examples
-
-__all__ = ["context", "operator", "examples"]
diff --git a/src/main/python/systemds/scuro/aligner/alignment.py
b/src/main/python/systemds/scuro/aligner/alignment.py
new file mode 100644
index 0000000000..0e89cdf9e8
--- /dev/null
+++ b/src/main/python/systemds/scuro/aligner/alignment.py
@@ -0,0 +1,45 @@
+# -------------------------------------------------------------
+#
+# 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.
+#
+# -------------------------------------------------------------
+from aligner.alignment_strategy import AlignmentStrategy
+from modality.aligned_modality import AlignedModality
+from modality.modality import Modality
+from modality.representation import Representation
+from aligner.similarity_measures import Measure
+
+
+class Alignment:
+ def __init__(self, modality_a: Modality, modality_b: Modality, strategy:
AlignmentStrategy,
+ similarity_measure: Measure):
+ """
+ Defines the core of the library where the alignment of two modalities
is performed
+ :param modality_a: first modality
+ :param modality_b: second modality
+ :param strategy: the alignment strategy used in the alignment process
+ :param similarity_measure: the similarity measure used to check the
score of the alignment
+ """
+ self.modality_a = modality_a
+ self.modality_b = modality_b
+ self.strategy = strategy
+ self.similarity_measure = similarity_measure
+
+ def align_modalities(self) -> Modality:
+ return AlignedModality(Representation())
+
\ No newline at end of file
diff --git a/src/main/python/systemds/__init__.py
b/src/main/python/systemds/scuro/aligner/alignment_strategy.py
similarity index 65%
copy from src/main/python/systemds/__init__.py
copy to src/main/python/systemds/scuro/aligner/alignment_strategy.py
index 27d7425566..70d88ee8a8 100644
--- a/src/main/python/systemds/__init__.py
+++ b/src/main/python/systemds/scuro/aligner/alignment_strategy.py
@@ -18,9 +18,23 @@
# under the License.
#
# -------------------------------------------------------------
+from aligner.similarity_measures import Measure
-from systemds import context
-from systemds import operator
-from systemds import examples
-__all__ = ["context", "operator", "examples"]
+class AlignmentStrategy:
+ def __init__(self):
+ pass
+
+ def align_chunk(self, chunk_a, chunk_b, similarity_measure: Measure):
+ raise 'Not implemented error'
+
+
+class ChunkedCrossCorrelation(AlignmentStrategy):
+ def __init__(self):
+ super().__init__()
+
+ def align_chunk(self, chunk_a, chunk_b, similarity_measure: Measure):
+ raise 'Not implemented error'
+
+
+# TODO: Add additional alignment methods
diff --git a/src/main/python/systemds/__init__.py
b/src/main/python/systemds/scuro/aligner/similarity_measures.py
similarity index 85%
copy from src/main/python/systemds/__init__.py
copy to src/main/python/systemds/scuro/aligner/similarity_measures.py
index 27d7425566..31f8ed50c1 100644
--- a/src/main/python/systemds/__init__.py
+++ b/src/main/python/systemds/scuro/aligner/similarity_measures.py
@@ -18,9 +18,17 @@
# under the License.
#
# -------------------------------------------------------------
+class Measure:
+ pass
-from systemds import context
-from systemds import operator
-from systemds import examples
-__all__ = ["context", "operator", "examples"]
+class EuclideanDistance(Measure):
+ pass
+
+
+class CosineSimilarity(Measure):
+ pass
+
+
+class PearsonCorrelation(Measure):
+ pass
diff --git a/src/main/python/systemds/__init__.py
b/src/main/python/systemds/scuro/main.py
similarity index 52%
copy from src/main/python/systemds/__init__.py
copy to src/main/python/systemds/scuro/main.py
index 27d7425566..9a6349568c 100644
--- a/src/main/python/systemds/__init__.py
+++ b/src/main/python/systemds/scuro/main.py
@@ -18,9 +18,22 @@
# under the License.
#
# -------------------------------------------------------------
+from aligner.alignment import Alignment
+from aligner.alignment_strategy import ChunkedCrossCorrelation
+from modality.representation import PixelRepresentation
+from modality.video_modality import VideoModality
+from aligner.similarity_measures import CosineSimilarity
-from systemds import context
-from systemds import operator
-from systemds import examples
+# Setup modalities
+file_path_a = ''
+file_path_b = ''
+representation_a = PixelRepresentation() # Concrete Representation
+representation_b = PixelRepresentation() # Concrete Representation
+modality_a = VideoModality(file_path_a, representation_a)
+modality_b = VideoModality(file_path_b, representation_b)
-__all__ = ["context", "operator", "examples"]
+# Align modalities
+alignment_strategy = ChunkedCrossCorrelation() # Concrete Alignment Strategy
+similarity_measure = CosineSimilarity()
+aligner = Alignment(modality_a, modality_b, alignment_strategy,
similarity_measure)
+aligned_modality = aligner.align_modalities()
diff --git a/src/main/python/systemds/__init__.py
b/src/main/python/systemds/scuro/modality/__init__.py
similarity index 87%
copy from src/main/python/systemds/__init__.py
copy to src/main/python/systemds/scuro/modality/__init__.py
index 27d7425566..e66abb4646 100644
--- a/src/main/python/systemds/__init__.py
+++ b/src/main/python/systemds/scuro/modality/__init__.py
@@ -18,9 +18,3 @@
# under the License.
#
# -------------------------------------------------------------
-
-from systemds import context
-from systemds import operator
-from systemds import examples
-
-__all__ = ["context", "operator", "examples"]
diff --git a/src/main/python/systemds/__init__.py
b/src/main/python/systemds/scuro/modality/aligned_modality.py
similarity index 64%
copy from src/main/python/systemds/__init__.py
copy to src/main/python/systemds/scuro/modality/aligned_modality.py
index 27d7425566..ef6a102472 100644
--- a/src/main/python/systemds/__init__.py
+++ b/src/main/python/systemds/scuro/modality/aligned_modality.py
@@ -18,9 +18,16 @@
# under the License.
#
# -------------------------------------------------------------
+from modality.modality import Modality
+from modality.representation import Representation
-from systemds import context
-from systemds import operator
-from systemds import examples
-__all__ = ["context", "operator", "examples"]
+class AlignedModality(Modality):
+ def __init__(self, representation: Representation):
+ """
+ Defines the modality that is created during the alignment process
+ :param representation: The representation for the aligned modality
+ (made up of the #columns from the modalities
that are being aligned)
+ """
+ super().__init__(representation)
+
\ No newline at end of file
diff --git a/src/main/python/systemds/__init__.py
b/src/main/python/systemds/scuro/modality/modality.py
similarity index 57%
copy from src/main/python/systemds/__init__.py
copy to src/main/python/systemds/scuro/modality/modality.py
index 27d7425566..d82ac3e989 100644
--- a/src/main/python/systemds/__init__.py
+++ b/src/main/python/systemds/scuro/modality/modality.py
@@ -19,8 +19,22 @@
#
# -------------------------------------------------------------
-from systemds import context
-from systemds import operator
-from systemds import examples
+from modality.representation import Representation
-__all__ = ["context", "operator", "examples"]
+
+class Modality:
+
+ def __init__(self, representation: Representation, start_index: int = 0):
+ """
+ Defines the modality that is to be aligned
+ :param representation: Specifies how the data should be represented
for a specific modality
+ :param start_index: Defines the first index used for the alignment
+ """
+ self.representation = representation
+ self.start_index = start_index
+
+ def read_chunk(self):
+ """
+ Extracts a data chunk of the modality according to the window size
specified in params
+ """
+ raise NotImplementedError
diff --git a/src/main/python/systemds/__init__.py
b/src/main/python/systemds/scuro/modality/representation.py
similarity index 84%
copy from src/main/python/systemds/__init__.py
copy to src/main/python/systemds/scuro/modality/representation.py
index 27d7425566..cdf9bf9e93 100644
--- a/src/main/python/systemds/__init__.py
+++ b/src/main/python/systemds/scuro/modality/representation.py
@@ -18,9 +18,13 @@
# under the License.
#
# -------------------------------------------------------------
-
-from systemds import context
-from systemds import operator
-from systemds import examples
-
-__all__ = ["context", "operator", "examples"]
+class Representation:
+ def __init__(self):
+ pass
+
+
+class PixelRepresentation(Representation):
+ def __init__(self):
+ super().__init__()
+
+
\ No newline at end of file
diff --git a/src/main/python/systemds/__init__.py
b/src/main/python/systemds/scuro/modality/video_modality.py
similarity index 50%
copy from src/main/python/systemds/__init__.py
copy to src/main/python/systemds/scuro/modality/video_modality.py
index 27d7425566..04ed24cf7c 100644
--- a/src/main/python/systemds/__init__.py
+++ b/src/main/python/systemds/scuro/modality/video_modality.py
@@ -18,9 +18,32 @@
# under the License.
#
# -------------------------------------------------------------
+import os
-from systemds import context
-from systemds import operator
-from systemds import examples
+from modality.modality import Modality
+from modality.representation import Representation
-__all__ = ["context", "operator", "examples"]
+
+class VideoModality(Modality):
+ def __init__(self, file_path: str, representation: Representation,
start_index: int = 0):
+ super().__init__(representation, start_index)
+ self.file_path = file_path
+
+ def file_sanity_check(self):
+ """
+ Checks if the file can be found is not empty
+ """
+ try:
+ file_size = os.path.getsize(self.file_path)
+ except:
+ raise (f"Error: File {0} not found!".format(self.file_path))
+
+ if file_size == 0:
+ raise ("File {0} is empty".format(self.file_path))
+
+ def read_chunk(self):
+ # Read chunk (self.params.window_size)
+ # self.representation.apply_representation()
+ # additional preprocessing?
+ # return numpy array
+ pass
