From bcfb26f7c81bf9b8b907c32e2efadcbfbfdc3df7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <amuoz@ed.ac.uk>
Date: Tue, 9 Aug 2022 11:45:03 +0100
Subject: [PATCH] fix(extractor, imView): Update Cells import
---
aliby/utils/imageViewer.py | 2 +-
extraction/core/extractor.py | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/aliby/utils/imageViewer.py b/aliby/utils/imageViewer.py
index 59ea0734..de766d8b 100644
--- a/aliby/utils/imageViewer.py
+++ b/aliby/utils/imageViewer.py
@@ -23,7 +23,7 @@ import matplotlib.pyplot as plt
import numpy as np
import seaborn as sns
import yaml
-from agora.io.cells import CellsLinear as Cells
+from agora.io.cells import Cells
from agora.io.writer import load_attributes
from PIL import Image
from skimage.morphology import dilation
diff --git a/extraction/core/extractor.py b/extraction/core/extractor.py
index 285cb772..6d5a4510 100644
--- a/extraction/core/extractor.py
+++ b/extraction/core/extractor.py
@@ -6,7 +6,7 @@ import h5py
import numpy as np
import pandas as pd
from agora.abc import ParametersABC, ProcessABC
-from agora.io.cells import CellsLinear
+from agora.io.cells import Cells
from agora.io.writer import Writer, load_attributes
from aliby.tile.tiler import Tiler
@@ -338,7 +338,7 @@ class Extractor(ProcessABC):
ch_tree = {ch: v for ch, v in tree.items() if ch != "general"}
tree_chs = (*ch_tree,)
- cells = CellsLinear(self.local)
+ cells = Cells(self.local)
# labels
if labels is None:
--
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