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Add distance summary plots #48

Merged
merged 9 commits into from
Dec 6, 2023
Merged

Add distance summary plots #48

merged 9 commits into from
Dec 6, 2023

Commits on Dec 6, 2023

  1. Fix README spelling

    @kaitj
    kaitj committed Dec 6, 2023
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  2. Add MNI coordinates into resource templates

    @kaitj
    kaitj committed Dec 6, 2023
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  3. Add connectome summary plotting functionality 

    This commit adds the functionality to generate a summary plot of AFID
distances on a connectome using nilearn.plotting to do so. In doing so,
a complete set of AfidSet distances are provided as an argument, and
coloured based on their distance from "expected" (ground-truth).

Approporiate unit tests are also added in to make sure plots are generated
and of the correct type. During development, generated plots were visually
assessed to ensure generated plots are as expected.

Note: a `pyright: ignore` has been temporarily added to line 230 in
plotting.py until other plot_types are implemented in order to bypass
the pyright error being thrown.
    @kaitj
    kaitj committed Dec 6, 2023
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  4. Add histogram summary plotting functionality 

    This commit adds the functionality to generate a summary histogram plot
of AFID distances using `plotly`. In doing so, an optional argument has
been added - `afid_labels` for labelling the histogram. If not provided,
`afid_labels`, indices are used to label the histogram.

Appropriate unit tests are also added. During development, generated
plots were visually assessed.

Note: `pyright: ignore` have been added where `afid_labels` is not
expected to be None.

Also added type stubs for plotly.
    @kaitj
    kaitj committed Dec 6, 2023
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  5. Take actual value of distances (instead of abs) 

    Knowing if the "distance" is negative can provide some insight - this is
mostly for plotting distances along specific spatial components (e.g. x,
y, z).

These distances will be automatically set in the histogram and upcoming
scatter plots. For the connectome plot, the minimum node value is set by
either taking the smallest value (if negative) or 0 (if positive).
    @kaitj
    kaitj committed Dec 6, 2023
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  6. Add scatter summary plotting functionality 

    This commit adds functionality to generate a summary scatter plot of
AFID distances using `plotly`. Similar to generating a histogram plot,
this also makes use of the new `afid_labels` argument to label the
markers. If not porvided, indices are used to label the scatter plot.

Appropriate unit tests are alos added, with generated plots visually
assessed during development.
    @kaitj
    kaitj committed Dec 6, 2023
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  7. Enable multicore testing, update test durations

    @kaitj
    kaitj committed Dec 6, 2023
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  8. Add callable helper for slow data generation 

    Some tests may fail a HealthCheck due to slow data generation - namely
any tests that try to generate an entire AfidSet. This commit adds a
function to the helpers that disables this check.
    @kaitj
    kaitj committed Dec 6, 2023
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  9. Fix test errors 

    This commit adds the slow_generation decorator where appropriate to
disable the health checks for tests where data generation is slow.
Additionally, delete the view that is created from plot_ortho for memory
considerations (`close()` is not a valid command for these views).
    @kaitj
    kaitj committed Dec 6, 2023
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