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Bugfix and Speedup for render_labels #38

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Merged
merged 4 commits into from
Apr 4, 2023
Merged

Bugfix and Speedup for render_labels #38

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7772f9b
bugfix and speedup
timtreis Apr 4, 2023
0a0d058
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 4, 2023
62a9658
typo
timtreis Apr 4, 2023
2ae241c
merge
timtreis Apr 4, 2023
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14 changes: 11 additions & 3 deletions src/spatialdata_plot/pl/basic.py
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Original file line number Diff line number Diff line change
Expand Up @@ -666,11 +666,18 @@ def show(
# If any of the previous conditions are not met, generate random
# colors for each cell id

N_DISTINCT_FOR_RANDOM = 30

if sdata.table is not None:
# annoying case since number of cells in labels can be
# different from number of cells in table. So we just use
# the index and randomise colours for it

# add fake column for limiting the amount of different colors
sdata.table.obs["fake"] = np.random.randint(
0, N_DISTINCT_FOR_RANDOM, sdata.table.obs.shape[0]
)

# has a table, so it has a region key
region_key = _get_region_key(sdata)

Expand All @@ -681,7 +688,7 @@ def show(
region_key = _get_region_key(sdata)
instance_key = _get_instance_key(sdata)
params["instance_key"] = instance_key
params["color_key"] = instance_key
params["color_key"] = "fake"
params["add_legend"] = False
# TODO(ttreis) log the decision not to display a legend

Expand All @@ -693,7 +700,7 @@ def show(
cell_ids_per_label = {}
for key in list(sdata.labels.keys()):
cell_ids_per_label[key] = sdata.labels[key].values.max()

print(cell_ids_per_label)
region_key = "tmp_label_id"
instance_key = "tmp_cell_id"
params["instance_key"] = instance_key
Expand All @@ -708,10 +715,11 @@ def show(
}
)

tmp_table["fake"] = np.random.randint(0, N_DISTINCT_FOR_RANDOM, len(tmp_table))
distinct_cells = max(list(cell_ids_per_label.values()))

if sdata.table is not None:
print("Plotting a lot of cells with random colors, might take a while...")
# print("Plotting a lot of cells with random colors, might take a while...")
sdata.table.uns[f"{instance_key}_colors"] = _get_random_hex_colors(distinct_cells)

elif sdata.table is None:
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2 changes: 2 additions & 0 deletions src/spatialdata_plot/pl/render.py
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Original file line number Diff line number Diff line change
Expand Up @@ -161,7 +161,9 @@ def _render_labels(
ax.set_ylim(extent["y"][0], extent["y"][1])

for group in groups:
# Getting cell ids belonging to group and casting them to int for later numpy comparisons
vaid_cell_ids = table[table[params["color_key"]] == group][params["instance_key"]].values
vaid_cell_ids = [int(id) for id in vaid_cell_ids]

# define all out-of-group cells as background
in_group_mask = segmentation.copy()
Expand Down