bug-fix: quantification was done on object bounding-box instead of object mask

afrendeiro · afrendeiro · commit 48bd3e947988 · 2021-12-22T10:57:20.000-05:00
diff --git a/imc/ops/quant.py b/imc/ops/quant.py
@@ -79,7 +79,7 @@ def quantify_cell_intensity(
     res = np.zeros((n_cells, n_channels), dtype=int if red_func == "sum" else float)
     for channel in np.arange(stack.shape[0])[channel_include & ~channel_exclude]:
         res[:, channel] = [
-            getattr(x.intensity_image, red_func)()
+            getattr(x.intensity_image[x.image], red_func)()
             for x in skimage.measure.regionprops(mask, stack[channel])
         ]
     return pd.DataFrame(res, index=cells[1:]).rename_axis(index="obj_id")

Original file line number	Diff line number	Diff line change
`@@ -79,7 +79,7 @@ def quantify_cell_intensity(`
`79`	`79`	`res = np.zeros((n_cells, n_channels), dtype=int if red_func == "sum" else float)`
`80`	`80`	`for channel in np.arange(stack.shape[0])[channel_include & ~channel_exclude]:`
`81`	`81`	`res[:, channel] = [`
`82`		`- getattr(x.intensity_image, red_func)()`
	`82`	`+ getattr(x.intensity_image[x.image], red_func)()`
`83`	`83`	`for x in skimage.measure.regionprops(mask, stack[channel])`
`84`	`84`	`]`
`85`	`85`	`return pd.DataFrame(res, index=cells[1:]).rename_axis(index="obj_id")`