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Improve TimeSeries wrong orientation message #638

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198cf6a
improve time series message
h-mayorquin Nov 25, 2025
d7d9bd9
fix tests to correspond to the new change
h-mayorquin Nov 25, 2025
b00a233
improve text
h-mayorquin Nov 25, 2025
24ed800
add changelog
h-mayorquin Nov 25, 2025
3a682da
Merge branch 'dev' into improve_data_orientation_msg
h-mayorquin Nov 25, 2025
7a98792
correct test message
h-mayorquin Nov 26, 2025
e48240a
restore
h-mayorquin Nov 26, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -5,6 +5,7 @@

### Improvements
* Added documentation to API and CLI docs on how to use the dandi config option. [#624](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/624)
* Improved `check_data_orientation` error message to include the TimeSeries name, current shape, and a suggestion for transposing the data. [#1430](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/1430)
* Dropped Python 3.9 and middle Python versions (3.11, 3.12) from CI; now testing only Python 3.10 and 3.13. [#632](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/632)
* Updated macOS CI runner from `macos-13` to `macos-latest`. [#639](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/639)

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5 changes: 5 additions & 0 deletions pyproject.toml
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Expand Up @@ -134,3 +134,8 @@ known-first-party = ["nwbinspector"]
skip = '.git*,*.pdf,*.css'
check-hidden = true
ignore-words-list = 'assertin'

[dependency-groups]
dev = [
"pytest>=8.4.2",
]
8 changes: 6 additions & 2 deletions src/nwbinspector/checks/_time_series.py
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Expand Up @@ -56,10 +56,14 @@ def check_data_orientation(time_series: TimeSeries) -> Optional[InspectorMessage
return None

if any(np.array(data_shape[1:]) > data_shape[0]):
longest_axis = int(np.argmax(data_shape))
return InspectorMessage(
message=(
"Data may be in the wrong orientation. Time should be in the first dimension, and is usually the "
"longest dimension. Here, another dimension is longer."
f"Data may be in the wrong orientation. "
f"Time should be in the first dimension, and is usually the longest dimension. "
f"Here, another dimension is longer. "
f"Current shape: {data_shape}. "
f"Suggestion: Transpose your data so the first dimension is {data_shape[longest_axis]}."
),
)

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2 changes: 1 addition & 1 deletion tests/expected_reports/true_nwbinspector_default_report_hdf5.txt
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Expand Up @@ -16,7 +16,7 @@ Found 5 issues over 2 files:
===========

0.0 ./testing0.hdf5.nwb: check_data_orientation - 'SpatialSeries' object at location '/processing/behavior/Position/my_spatial_series'
Message: Data may be in the wrong orientation. Time should be in the first dimension, and is usually the longest dimension. Here, another dimension is longer.
Message: Data may be in the wrong orientation. Time should be in the first dimension, and is usually the longest dimension. Here, another dimension is longer. Current shape: (2, 3). Suggestion: Transpose your data so the first dimension is 3.

0.1 ./testing0.hdf5.nwb: check_timestamps_match_first_dimension - 'TimeSeries' object at location '/acquisition/test_time_series_3'
Message: The length of the first dimension of data (4) does not match the length of timestamps (3).
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2 changes: 1 addition & 1 deletion tests/expected_reports/true_nwbinspector_default_report_zarr.txt
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Expand Up @@ -16,7 +16,7 @@ Found 5 issues over 2 files:
===========

0.0 ./testing0.nwb.zarr: check_data_orientation - 'SpatialSeries' object at location '/processing/behavior/Position/my_spatial_series'
Message: Data may be in the wrong orientation. Time should be in the first dimension, and is usually the longest dimension. Here, another dimension is longer.
Message: Data may be in the wrong orientation. Time should be in the first dimension, and is usually the longest dimension. Here, another dimension is longer. Current shape: (2, 3). Suggestion: Transpose your data so the first dimension is 3.

0.1 ./testing0.nwb.zarr: check_timestamps_match_first_dimension - 'TimeSeries' object at location '/acquisition/test_time_series_3'
Message: The length of the first dimension of data (4) does not match the length of timestamps (3).
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4 changes: 2 additions & 2 deletions tests/expected_reports/true_nwbinspector_report_with_dandi_config_hdf5.txt
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Expand Up @@ -30,7 +30,7 @@ Found 10 issues over 2 files:
Message: TimeSeries appears to have a constant sampling rate. Consider specifying starting_time=1.2 and rate=0.5 instead of timestamps.

1.4 ./testing0.hdf5.nwb: check_data_orientation - 'SpatialSeries' object at location '/processing/behavior/Position/my_spatial_series'
Message: Data may be in the wrong orientation. Time should be in the first dimension, and is usually the longest dimension. Here, another dimension is longer.
Message: Data may be in the wrong orientation. Time should be in the first dimension, and is usually the longest dimension. Here, another dimension is longer. Current shape: (2, 3). Suggestion: Transpose your data so the first dimension is 3.

1.5 ./testing0.hdf5.nwb: check_missing_unit - 'TimeSeries' object at location '/acquisition/test_time_series_3'
Message: Missing text for attribute 'unit'. Please specify the scientific unit of the 'data'.
Expand All @@ -42,4 +42,4 @@ Found 10 issues over 2 files:
Message: Missing text for attribute 'unit'. Please specify the scientific unit of the 'data'.

1.8 ./testing1.hdf5.nwb: check_data_orientation - 'TimeSeries' object at location '/acquisition/my_spatial_series'
Message: Data may be in the wrong orientation. Time should be in the first dimension, and is usually the longest dimension. Here, another dimension is longer.
Message: Data may be in the wrong orientation. Time should be in the first dimension, and is usually the longest dimension. Here, another dimension is longer. Current shape: (2, 3). Suggestion: Transpose your data so the first dimension is 3.
4 changes: 2 additions & 2 deletions tests/expected_reports/true_nwbinspector_report_with_dandi_config_zarr.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ Found 10 issues over 2 files:
Message: TimeSeries appears to have a constant sampling rate. Consider specifying starting_time=1.2 and rate=0.5 instead of timestamps.

1.4 ./testing0.nwb.zarr: check_data_orientation - 'SpatialSeries' object at location '/processing/behavior/Position/my_spatial_series'
Message: Data may be in the wrong orientation. Time should be in the first dimension, and is usually the longest dimension. Here, another dimension is longer.
Message: Data may be in the wrong orientation. Time should be in the first dimension, and is usually the longest dimension. Here, another dimension is longer. Current shape: (2, 3). Suggestion: Transpose your data so the first dimension is 3.

1.5 ./testing0.nwb.zarr: check_missing_unit - 'TimeSeries' object at location '/acquisition/test_time_series_3'
Message: Missing text for attribute 'unit'. Please specify the scientific unit of the 'data'.
Expand All @@ -42,4 +42,4 @@ Found 10 issues over 2 files:
Message: Missing text for attribute 'unit'. Please specify the scientific unit of the 'data'.

1.8 ./testing1.nwb.zarr: check_data_orientation - 'TimeSeries' object at location '/acquisition/my_spatial_series'
Message: Data may be in the wrong orientation. Time should be in the first dimension, and is usually the longest dimension. Here, another dimension is longer.
Message: Data may be in the wrong orientation. Time should be in the first dimension, and is usually the longest dimension. Here, another dimension is longer. Current shape: (2, 3). Suggestion: Transpose your data so the first dimension is 3.
46 changes: 33 additions & 13 deletions tests/test_inspector.py
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Expand Up @@ -240,8 +240,11 @@ def test_inspect_all(self):
),
InspectorMessage(
message=(
"Data may be in the wrong orientation. Time should be in the first dimension, and is usually "
"the longest dimension. Here, another dimension is longer."
"Data may be in the wrong orientation. "
"Time should be in the first dimension, and is usually the longest dimension. "
"Here, another dimension is longer. "
"Current shape: (2, 3). "
"Suggestion: Transpose your data so the first dimension is 3."
),
importance=Importance.CRITICAL,
severity=Severity.LOW,
Expand Down Expand Up @@ -312,8 +315,11 @@ def test_inspect_all_parallel(self):
),
InspectorMessage(
message=(
"Data may be in the wrong orientation. Time should be in the first dimension, and is usually "
"the longest dimension. Here, another dimension is longer."
"Data may be in the wrong orientation. "
"Time should be in the first dimension, and is usually the longest dimension. "
"Here, another dimension is longer. "
"Current shape: (2, 3). "
"Suggestion: Transpose your data so the first dimension is 3."
),
importance=Importance.CRITICAL,
severity=Severity.LOW,
Expand Down Expand Up @@ -388,8 +394,11 @@ def test_inspect_nwbfile(self):
),
InspectorMessage(
message=(
"Data may be in the wrong orientation. Time should be in the first dimension, and is usually the "
"longest dimension. Here, another dimension is longer."
"Data may be in the wrong orientation. "
"Time should be in the first dimension, and is usually the longest dimension. "
"Here, another dimension is longer. "
"Current shape: (2, 3). "
"Suggestion: Transpose your data so the first dimension is 3."
),
importance=Importance.CRITICAL,
check_function_name="check_data_orientation",
Expand Down Expand Up @@ -422,8 +431,11 @@ def test_inspect_nwbfile_importance_threshold_as_importance(self):
true_results = [
InspectorMessage(
message=(
"Data may be in the wrong orientation. Time should be in the first dimension, and is "
"usually the longest dimension. Here, another dimension is longer."
"Data may be in the wrong orientation. "
"Time should be in the first dimension, and is usually the longest dimension. "
"Here, another dimension is longer. "
"Current shape: (2, 3). "
"Suggestion: Transpose your data so the first dimension is 3."
),
importance=Importance.CRITICAL,
check_function_name="check_data_orientation",
Expand Down Expand Up @@ -456,8 +468,11 @@ def test_inspect_nwbfile_importance_threshold_as_string(self):
true_results = [
InspectorMessage(
message=(
"Data may be in the wrong orientation. Time should be in the first dimension, and is "
"usually the longest dimension. Here, another dimension is longer."
"Data may be in the wrong orientation. "
"Time should be in the first dimension, and is usually the longest dimension. "
"Here, another dimension is longer. "
"Current shape: (2, 3). "
"Suggestion: Transpose your data so the first dimension is 3."
),
importance=Importance.CRITICAL,
check_function_name="check_data_orientation",
Expand Down Expand Up @@ -622,7 +637,9 @@ def test_inspect_nwbfile_dandi_config(self):
message=(
"Data may be in the wrong orientation. "
"Time should be in the first dimension, and is usually the longest dimension. "
"Here, another dimension is longer."
"Here, another dimension is longer. "
"Current shape: (2, 3). "
"Suggestion: Transpose your data so the first dimension is 3."
),
importance=Importance.BEST_PRACTICE_VIOLATION, # Normally CRITICAL, now a BEST_PRACTICE_VIOLATION
check_function_name="check_data_orientation",
Expand Down Expand Up @@ -777,8 +794,11 @@ def test_inspect_nwbfile_dandi_config_violation_and_above_entire_registry(self):
),
InspectorMessage(
message=(
"Data may be in the wrong orientation. Time should be in the first dimension, "
"and is usually the longest dimension. Here, another dimension is longer."
"Data may be in the wrong orientation. "
"Time should be in the first dimension, and is usually the longest dimension. "
"Here, another dimension is longer. "
"Current shape: (2, 3). "
"Suggestion: Transpose your data so the first dimension is 3."
),
importance=Importance.BEST_PRACTICE_VIOLATION,
severity=Severity.LOW,
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4 changes: 3 additions & 1 deletion tests/unit_tests/test_time_series.py
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Expand Up @@ -68,7 +68,9 @@ def test_check_data_orientation():
message=(
"Data may be in the wrong orientation. "
"Time should be in the first dimension, and is usually the longest dimension. "
"Here, another dimension is longer."
"Here, another dimension is longer. "
"Current shape: (2, 100). "
"Suggestion: Transpose your data so the first dimension is 100."
),
importance=Importance.CRITICAL,
check_function_name="check_data_orientation",
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