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new readers and schemas for reduced data storage in db #437

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new readers and schemas for reduced data storage in db #437

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b54e1c3
new readers and schemas for reduced data storage in db
jkbhagatio Oct 10, 2024
d6cf52f
updated tests
jkbhagatio Oct 10, 2024
f12e359
cleaned up linting for ruff
jkbhagatio Oct 10, 2024
daf6224
updated pandas and changed S to s lmao
jkbhagatio Oct 10, 2024
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21 changes: 1 addition & 20 deletions aeon/io/reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,7 @@
from dotmap import DotMap

from aeon import util
from aeon.io.api import aeon as aeon_time
from aeon.io.api import chunk, chunk_key
from aeon.io.api import chunk_key
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_SECONDS_PER_TICK = 32e-6
_payloadtypes = {
Expand Down Expand Up @@ -187,24 +186,6 @@ class Encoder(Harp):
def __init__(self, pattern):
super().__init__(pattern, columns=["angle", "intensity"])

def read(self, file, downsample=True):
"""Reads encoder data from the specified Harp binary file.

By default the encoder data is downsampled to 50Hz. Setting downsample to
False or None can be used to force the raw data to be returned.
"""
data = super().read(file)
if downsample is True:
# resample requires a DatetimeIndex so we convert early
data.index = aeon_time(data.index)

first_index = data.first_valid_index()
if first_index is not None:
# since data is absolute angular position we decimate by taking first of each bin
chunk_origin = chunk(first_index)
data = data.resample("20ms", origin=chunk_origin).first()
return data


class Position(Harp):
"""Extract 2D position tracking data for a specific camera.
Expand Down
204 changes: 204 additions & 0 deletions aeon/schema/ingestion_schemas.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,204 @@
"""Aeon experiment schemas for DataJoint database ingestion."""

from os import PathLike

import pandas as pd
from dotmap import DotMap

import aeon.schema.core as stream
from aeon.io import reader
from aeon.io.api import aeon as aeon_time
from aeon.schema import foraging, octagon, social_01, social_02, social_03
from aeon.schema.foraging import DepletionFunction, Feeder
from aeon.schema.streams import Device, Stream, StreamGroup


# Define new readers
class _Encoder(reader.Encoder):
"""A version of the encoder reader that can downsample the data."""

def read(self, file: PathLike[str], sr_hz: int = 50) -> pd.DataFrame:
"""Reads encoder data from the specified Harp binary file."""
data = super().read(file)
data.index = aeon_time(data.index)
first_index = data.first_valid_index()
if first_index is not None:
data = data.resample(f"{1/sr_hz}S").first() # take first sample in each resampled bin
return data
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class _Video(reader.Video):
"""A version of the video reader that drops columns that can be recreated from data and metadata."""

def read(self, file: PathLike[str], drop_cols=None) -> pd.DataFrame:
"""Reads video metadata from the specified file."""
drop_cols = ["hw_counter", "_frame", "_path", "_epoch"] if drop_cols is None else drop_cols
data = pd.read_csv(file, header=0, names=self._rawcolumns)
data.drop(columns=drop_cols, errors="ignore", inplace=True)
data.set_index("time", inplace=True)
return data
Comment on lines +33 to +39
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Image description CodeRabbit

In the read method of the _Video class, you are dropping columns from the DataFrame without checking if they exist. This could lead to errors if one or more of the specified columns are not present in the DataFrame. Consider adding a check to ensure that only existing columns are dropped.

-        data.drop(columns=drop_cols, errors="ignore", inplace=True)
+        drop_cols = [col for col in drop_cols if col in data.columns]
+        data.drop(columns=drop_cols, inplace=True)



# Define new streams and stream groups
class Video(Stream):
"""Video frame metadata."""

def __init__(self, pattern):
super().__init__(_Video(f"{pattern}_*"))


class Encoder(Stream):
"""Wheel magnetic encoder data."""

def __init__(self, pattern):
super().__init__(_Encoder(f"{pattern}_90_*"))
Comment on lines +46 to +54
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Image description CodeRabbit

The __init__ methods in the Video and Encoder classes are hardcoding the pattern for file matching. This reduces the flexibility of these classes and makes them less reusable. Consider passing the pattern as an argument to the __init__ method instead.

-    def __init__(self, pattern):
-        super().__init__(_Video(f"{pattern}_*"))
+    def __init__(self, pattern, file_pattern):
+        super().__init__(_Video(f"{pattern}_{file_pattern}"))

-    def __init__(self, pattern):
-        super().__init__(_Encoder(f"{pattern}_90_*"))
+    def __init__(self, pattern, file_pattern):
+        super().__init__(_Encoder(f"{pattern}_{file_pattern}"))



class Patch(StreamGroup):
"""Data streams for a patch."""

def __init__(self, pattern):
super().__init__(pattern, DepletionFunction, Encoder, Feeder)
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# Define schemas
octagon01 = DotMap(
[
Device("Metadata", stream.Metadata),
Device("CameraTop", Video, stream.Position),
Device("CameraColorTop", Video),
Device("ExperimentalMetadata", stream.SubjectState),
Device("Photodiode", octagon.Photodiode),
Device("OSC", octagon.OSC),
Device("TaskLogic", octagon.TaskLogic),
Device("Wall1", octagon.Wall),
Device("Wall2", octagon.Wall),
Device("Wall3", octagon.Wall),
Device("Wall4", octagon.Wall),
Device("Wall5", octagon.Wall),
Device("Wall6", octagon.Wall),
Device("Wall7", octagon.Wall),
Device("Wall8", octagon.Wall),
]
)

exp01 = DotMap(
[
Device("SessionData", foraging.SessionData),
Device("FrameTop", Video, stream.Position),
Device("FrameEast", Video),
Device("FrameGate", Video),
Device("FrameNorth", Video),
Device("FramePatch1", Video),
Device("FramePatch2", Video),
Device("FrameSouth", Video),
Device("FrameWest", Video),
Device("Patch1", foraging.DepletionFunction, stream.Encoder, foraging.Feeder),
Device("Patch2", foraging.DepletionFunction, stream.Encoder, foraging.Feeder),
]
)

exp02 = DotMap(
[
Device("Metadata", stream.Metadata),
Device("ExperimentalMetadata", stream.Environment, stream.MessageLog),
Device("CameraTop", Video, stream.Position, foraging.Region),
Device("CameraEast", Video),
Device("CameraNest", Video),
Device("CameraNorth", Video),
Device("CameraPatch1", Video),
Device("CameraPatch2", Video),
Device("CameraSouth", Video),
Device("CameraWest", Video),
Device("Nest", foraging.Weight),
Device("Patch1", Patch),
Device("Patch2", Patch),
]
)

social01 = DotMap(
[
Device("Metadata", stream.Metadata),
Device("Environment", social_02.Environment, social_02.SubjectData),
Device("CameraTop", Video, social_01.Pose),
Device("CameraNorth", Video),
Device("CameraSouth", Video),
Device("CameraEast", Video),
Device("CameraWest", Video),
Device("CameraPatch1", Video),
Device("CameraPatch2", Video),
Device("CameraPatch3", Video),
Device("CameraNest", Video),
Device("Nest", social_02.WeightRaw, social_02.WeightFiltered),
Device("Patch1", Patch),
Device("Patch2", Patch),
Device("Patch3", Patch),
Device("RfidGate", social_01.RfidEvents),
Device("RfidNest1", social_01.RfidEvents),
Device("RfidNest2", social_01.RfidEvents),
Device("RfidPatch1", social_01.RfidEvents),
Device("RfidPatch2", social_01.RfidEvents),
Device("RfidPatch3", social_01.RfidEvents),
]
)


social02 = DotMap(
[
Device("Metadata", stream.Metadata),
Device("Environment", social_02.Environment, social_02.SubjectData),
Device("CameraTop", Video, social_02.Pose),
Device("CameraNorth", Video),
Device("CameraSouth", Video),
Device("CameraEast", Video),
Device("CameraWest", Video),
Device("CameraPatch1", Video),
Device("CameraPatch2", Video),
Device("CameraPatch3", Video),
Device("CameraNest", Video),
Device("Nest", social_02.WeightRaw, social_02.WeightFiltered),
Device("Patch1", Patch),
Device("Patch2", Patch),
Device("Patch3", Patch),
Device("GateRfid", social_02.RfidEvents),
Device("NestRfid1", social_02.RfidEvents),
Device("NestRfid2", social_02.RfidEvents),
Device("Patch1Rfid", social_02.RfidEvents),
Device("Patch2Rfid", social_02.RfidEvents),
Device("Patch3Rfid", social_02.RfidEvents),
]
)


social03 = DotMap(
[
Device("Metadata", stream.Metadata),
Device("Environment", social_02.Environment, social_02.SubjectData),
Device("CameraTop", Video, social_03.Pose),
Device("CameraNorth", Video),
Device("CameraSouth", Video),
Device("CameraEast", Video),
Device("CameraWest", Video),
Device("CameraNest", Video),
Device("CameraPatch1", Video),
Device("CameraPatch2", Video),
Device("CameraPatch3", Video),
Device("Nest", social_02.WeightRaw, social_02.WeightFiltered),
Device("Patch1", Patch),
Device("Patch2", Patch),
Device("Patch3", Patch),
Device("PatchDummy1", Patch),
Device("NestRfid1", social_02.RfidEvents),
Device("NestRfid2", social_02.RfidEvents),
Device("GateRfid", social_02.RfidEvents),
Device("GateEastRfid", social_02.RfidEvents),
Device("GateWestRfid", social_02.RfidEvents),
Device("Patch1Rfid", social_02.RfidEvents),
Device("Patch2Rfid", social_02.RfidEvents),
Device("Patch3Rfid", social_02.RfidEvents),
Device("PatchDummy1Rfid", social_02.RfidEvents),
]
)


__all__ = ["octagon01", "exp01", "exp02", "social01", "social02", "social03"]
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Image description CodeRabbit

The __all__ variable is used to specify the public interface of a module. However, it's not clear from this code whether all the items listed in __all__ are intended to be part of the public interface. Please ensure that only those items that should be accessible when importing the module using from module import * are included in __all__.

-__all__ = ["octagon01", "exp01", "exp02", "social01", "social02", "social03"]
+__all__ = ["intended_public_interface_item1", "intended_public_interface_item2", ...]

13 changes: 7 additions & 6 deletions tests/io/test_api.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@

import aeon
from aeon.schema.schemas import exp02
from aeon.schema.ingestion_schemas import social03

nonmonotonic_path = Path(__file__).parent.parent / "data" / "nonmonotonic"
monotonic_path = Path(__file__).parent.parent / "data" / "monotonic"
Expand All @@ -14,15 +15,15 @@
@mark.api
def test_load_start_only():
data = aeon.load(
nonmonotonic_path, exp02.Patch2.Encoder, start=pd.Timestamp("2022-06-06T13:00:49"), downsample=None
nonmonotonic_path, exp02.Patch2.Encoder, start=pd.Timestamp("2022-06-06T13:00:49")
)
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Image description CodeRabbit

In the function test_load_start_only(), there's no error handling for the case when the data loading fails and returns an empty dataset. This could lead to a misleading test result. Consider adding an explicit check for this scenario.

    data = aeon.load(
       nonmonotonic_path, exp02.Patch2.Encoder, start=pd.Timestamp("2022-06-06T13:00:49")
    )
+    assert data is not None, "Data loading failed"
    assert len(data) > 0

assert len(data) > 0


@mark.api
def test_load_end_only():
data = aeon.load(
nonmonotonic_path, exp02.Patch2.Encoder, end=pd.Timestamp("2022-06-06T13:00:49"), downsample=None
nonmonotonic_path, exp02.Patch2.Encoder, end=pd.Timestamp("2022-06-06T13:00:49")
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)
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Image description CodeRabbit

Similar to the previous comment, in the function test_load_end_only(), there's no error handling for the case when the data loading fails and returns an empty dataset. This could lead to a misleading test result. Consider adding an explicit check for this scenario.

    data = aeon.load(
       nonmonotonic_path, exp02.Patch2.Encoder, end=pd.Timestamp("2022-06-06T13:00:49")
    )
+    assert data is not None, "Data loading failed"
    assert len(data) > 0

assert len(data) > 0

Expand All @@ -35,22 +36,22 @@ def test_load_filter_nonchunked():

@mark.api
def test_load_monotonic():
data = aeon.load(monotonic_path, exp02.Patch2.Encoder, downsample=None)
data = aeon.load(monotonic_path, exp02.Patch2.Encoder)
assert len(data) > 0
assert data.index.is_monotonic_increasing


@mark.api
def test_load_nonmonotonic():
data = aeon.load(nonmonotonic_path, exp02.Patch2.Encoder, downsample=None)
data = aeon.load(nonmonotonic_path, exp02.Patch2.Encoder)
assert not data.index.is_monotonic_increasing


@mark.api
def test_load_encoder_with_downsampling():
DOWNSAMPLE_PERIOD = 0.02
data = aeon.load(monotonic_path, exp02.Patch2.Encoder, downsample=True)
raw_data = aeon.load(monotonic_path, exp02.Patch2.Encoder, downsample=None)
data = aeon.load(monotonic_path, social03.Patch2.Encoder)
raw_data = aeon.load(monotonic_path, exp02.Patch2.Encoder)
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Image description CodeRabbit

In the function test_load_encoder_with_downsampling(), the variable DOWNSAMPLE_PERIOD is defined but not used in the subsequent code. This can lead to confusion and should be removed if not necessary.

- DOWNSAMPLE_PERIOD = 0.02

Also, similar to previous comments, there's no error handling for the case when the data loading fails and returns an empty dataset. This could lead to a misleading test result. Consider adding an explicit check for this scenario.

    data = aeon.load(monotonic_path, social03.Patch2.Encoder)
+    assert data is not None, "Data loading failed"
    raw_data = aeon.load(monotonic_path, exp02.Patch2.Encoder)
+    assert raw_data is not None, "Raw data loading failed"


# Check that the length of the downsampled data is less than the raw data
assert len(data) < len(raw_data)
Expand Down
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