10000 fix: blob.py 2d intensities shape and pd.concat instead of append by shachafl · Pull Request #2064 · spacetx/starfish · GitHub
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fix: blob.py 2d intensities shape and pd.concat instead of append #2064

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Merged
merged 1 commit into from
Apr 16, 2025
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fix: blob.py 2d intensities shape and pd.concat instead of append #2064

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6 changes: 3 additions & 3 deletions starfish/core/spots/FindSpots/blob.py
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Original file line number Diff line number Diff line change
Expand Up @@ -148,7 +148,7 @@ def image_to_spots(
y_inds = fitted_blobs_array[:, 0].astype(int)
x_inds = fitted_blobs_array[:, 1].astype(int)
radius = np.round(fitted_blobs_array[:, 2] * np.sqrt(2))
intensities = data_image[tuple([y_inds, x_inds])]
intensities = data_image[tuple([z_inds, y_inds, x_inds])]

# construct dataframe
spot_data = pd.DataFrame(
Expand Down Expand Up @@ -215,8 +215,8 @@ def run(
spot_attributes_list[i][1]['z']
r = spot_attributes_list[i][1][Axes.ROUND]
ch = spot_attributes_list[i][1][Axes.CH]
merged_z_tables[(r, ch)] = merged_z_tables[(r, ch)].append(
spot_attributes_list[i][0].spot_attrs.data)
merged_z_tables[(r, ch)] = pd.concat(
[merged_z_tables[(r, ch)], spot_attributes_list[i][0].spot_attrs.data])
new = []
r_chs = sorted([*merged_z_tables])
selectors = list(image_stack._iter_axes({Axes.ROUND, Axes.CH}))
Expand Down
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