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Plotting fix for CBU nodes #413

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Plotting fix for CBU nodes #413

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64849f5
First attempt at fix
neukym Nov 25, 2024
0ff3857
Adds ability to try with the next available number of buffer
neukym Nov 26, 2024
631436f
Merge branch 'main' into plotting-fix-for-CBU-nodes
neukym Nov 30, 2024
844e3ad
fix #416
young-x-skyee Dec 1, 2024
ef2196f
fix #417
young-x-skyee Dec 1, 2024
e2eb5f6
Enhanced legend display function
young-x-skyee Dec 1, 2024
b103e01
Using higher precision for threshold p-valus
young-x-skyee Dec 5, 2024
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12 changes: 7 additions & 5 deletions kymata/plot/plot.py
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Original file line number Diff line number Diff line change
Expand Up @@ -165,7 +165,7 @@ def _hexel_minimap_data(expression_set: HexelExpressionSet,
best_transforms_left, best_transforms_right = expression_set.best_transforms()
best_transforms_left = best_transforms_left[best_transforms_left[COL_LOGP_VALUE] < alpha_logp]
best_transforms_right = best_transforms_right[best_transforms_right[COL_LOGP_VALUE] < alpha_logp]
if minimap_latency_range is not None or (None, None):
if minimap_latency_range is not None and not (None, None):
# Filter the dataframe to keep rows where 'latency' is within the range
best_transforms_left = best_transforms_left[(best_transforms_left['latency'] >= minimap_latency_range[0]) &
(best_transforms_left['latency'] <= minimap_latency_range[1])]
Expand Down Expand Up @@ -503,8 +503,10 @@ def expression_plot(

sidak_corrected_alpha = 1 - (
(1 - alpha)
** (1 / (2 * len(expression_set.latencies) * n_channels * len(show_only)))
)
** np.float128(1 / (2
* len(expression_set.latencies)
* n_channels
* len(show_only))))

sidak_corrected_alpha = p_to_logp(sidak_corrected_alpha)

Expand Down Expand Up @@ -734,7 +736,7 @@ def _custom_label(transform_name):
if show_legend:
split_legend_at_n_transforms = 15
legend_n_col = 2 if len(custom_handles) > split_legend_at_n_transforms else 1
if hidden_transforms_in_legend and len(not_shown) > 0:
if hidden_transforms_in_legend and len(not_shown) > 0 and legend_display is None:
if len(not_shown) > split_legend_at_n_transforms:
legend_n_col = 2
# Plot dummy legend for other transforms which are included in model selection but not plotted
Expand Down Expand Up @@ -770,7 +772,7 @@ def _custom_label(transform_name):
)
legends.append(top_legend)

__reposition_axes_for_legends(fig, legends)
__reposition_axes_for_legends(fig, legends)

__add_text_annotations(axes_names, top_ax, bottom_ax, fig, paired_axes, ylim)

Expand Down
12 changes: 12 additions & 0 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -48,12 +48,24 @@ h5io = "^0.1.9"
mkdocs-material = "^9.5.24"
mkdocstrings = {extras = ["python"], version = "^0.25.1"}
twine = "^5.1.1"
ipywidgets = "^8.1.5"
ipyevents = "^2.0.2"
cairocffi = "^1.7.1"
vtk = "^9.3.1"
pyqt5 = "^5.15.11"
vtk-osmesa = "^9.3.1"
mesa = "^3.0.3"

[tool.poetry.dev-dependencies]
pytest = "^8.3.2"
ipdb = "^0.13.13"
ruff = "^0.5.6"

[[tool.poetry.source]]
name = "vtk-osmesa"
url = "https://wheels.vtk.org"
priority = "supplemental"

[build-system]
requires = ["poetry-core>=1.0.0"]
build-backend = "poetry.core.masonry.api"
6 changes: 4 additions & 2 deletions submit_gridsearch.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -21,11 +21,13 @@ ARG=${args[$SLURM_ARRAY_TASK_ID - 1]}
module load apptainer
apptainer exec \
-B /imaging/projects/cbu/kymata/ \
/imaging/local/software/singularity_images/python/python_3.11.7-slim.sif \
/imaging/local/software/singularity_images/ubuntu/ubuntu_22.04.5.sif \
bash -c \
" cd /imaging/projects/cbu/kymata/analyses/andy/kymata-core/ ; \
export VENV_PATH=~/poetry/ ; \
\$VENV_PATH/bin/poetry run python -m kymata.invokers.run_gridsearch \
export PYVISTA_OFF_SCREEN=true ;
export PYVISTA_USE_IPYVTK=true ;
xvfb-run -a \$VENV_PATH/bin/poetry run python -m kymata.invokers.run_gridsearch \
--config dataset4.yaml \
--input-stream auditory \
--transform-path 'predicted_function_contours/GMSloudness/stimulisig' \
Expand Down