From 2f6342fb662b8cd08ab70224a393e0dee8d8f3b2 Mon Sep 17 00:00:00 2001 From: shachafl Date: Thu, 15 May 2025 22:54:40 -0400 Subject: [PATCH] fix: index shift correction for blob detection in 2d tiles --- starfish/core/spots/FindSpots/blob.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/starfish/core/spots/FindSpots/blob.py b/starfish/core/spots/FindSpots/blob.py index 93d548da..c747f9aa 100644 --- a/starfish/core/spots/FindSpots/blob.py +++ b/starfish/core/spots/FindSpots/blob.py @@ -137,18 +137,18 @@ def image_to_spots( # measure intensities data_image = np.asarray(data_image) - if self.is_volume: + if fitted_blobs_array.shape[1] == 4: z_inds = fitted_blobs_array[:, 0].astype(int) y_inds = fitted_blobs_array[:, 1].astype(int) x_inds = fitted_blobs_array[:, 2].astype(int) radius = np.round(fitted_blobs_array[:, 3] * np.sqrt(3)) intensities = data_image[tuple([z_inds, y_inds, x_inds])] - else: + elif fitted_blobs_array.shape[1] == 3: z_inds = np.asarray([0 for x in range(len(fitted_blobs_array))]) 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([z_inds, y_inds, x_inds])] + intensities = data_image[tuple([y_inds, x_inds])] # construct dataframe spot_data = pd.DataFrame(