Use NWBInspector when testing livescript tutorials #618
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- Add note about why dimension of SpatialSeries data is transposed wrt the type specification - Fix typos
- Add explanation of why arrays are transposed relative to the type documentation - Fix dimension order of AbstractFeatureSeries
ehennestad
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Nov 5, 2024
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| position_data = [linspace(0, 10, 50); linspace(0, 8, 50)]; % 2 x nT array | ||
| %% | ||
| % In <https://neurodatawithoutborders.github.io/matnwb/doc/+types/+core/SpatialSeries.html | ||
| % |SpatialSeries|> data, the first dimension is always time (in seconds), the | ||
| % second dimension represents the x, y position. <https://neurodatawithoutborders.github.io/matnwb/doc/+types/+core/SpatialSeries.html | ||
| % second dimension represents the x, y position. However, as described in the | ||
| % <https://neurodatawithoutborders.github.io/matnwb/tutorials/html/dimensionMapNoDataPipes.html | ||
| % dimensionMapNoDataPipes> tutorial, when a MATLAB array is exported to HDF5, | ||
| % the array is transposed. Therefore, in order to correctly export the data, in | ||
| % MATLAB the last dimension of an array should be time. <https://neurodatawithoutborders.github.io/matnwb/doc/+types/+core/SpatialSeries.html |
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@bendichter Can you confirm that this change to the text makes this section more consistent?
ehennestad
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Nov 5, 2024
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| % Image data can be stored either in the HDF5 file or as an external image file. | ||
| % For this tutorial, we will use fake image data with shape of |('RGB', 'y', 'x', | ||
| % 'time') = (200, 50, 50, 3)|. As in all <https://neurodatawithoutborders.github.io/matnwb/doc/+types/+core/TimeSeries.html | ||
| % For this tutorial, we will use fake image data with shape of |('time', 'x', | ||
| % 'y', 'RGB') = (200, 50, 50, 3)|. As in all <https://neurodatawithoutborders.github.io/matnwb/doc/+types/+core/TimeSeries.html | ||
| % |*TimeSeries*|>, the first dimension is time. The second and third dimensions | ||
| % represent x and y. The fourth dimension represents the RGB value (length of | ||
| % 3) for color images. | ||
| % 3) for color images. *Please note*: As described in the <https://neurodatawithoutborders.github.io/matnwb/tutorials/html/dimensionMapNoDataPipes.html | ||
| % dimensionMapNoDataPipes> tutorial, when a MATLAB array is exported to HDF5, | ||
| % the array is transposed. Therefore, in order to correctly export the data, we | ||
| % will need to create a transposed array, where the dimensions are in reverse | ||
| % order compared to the type specification. |
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@bendichter Same here
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## master #618 +/- ##
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+ Coverage 90.80% 90.84% +0.04%
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Files 107 107
Lines 4774 4774
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+ Hits 4335 4337 +2
+ Misses 439 437 -2 ☔ View full report in Codecov by Sentry. |
- Simplifies the reading of nwb files using pynwb in TutorialTest
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Fix #484
Motivation
More robust testing of NWB files created by tutorials
Checklist
fix #XXwhereXXis the issue number?