From ecef1146d83076ee561c19d4d0d3efaaefe4470d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <amuoz@ed.ac.uk>
Date: Mon, 21 Feb 2022 15:56:30 +0000
Subject: [PATCH] add support for CellsLinear
---
extraction/core/extractor.py | 9 ++-------
1 file changed, 2 insertions(+), 7 deletions(-)
diff --git a/extraction/core/extractor.py b/extraction/core/extractor.py
index b3418224..e36bf2bb 100644
--- a/extraction/core/extractor.py
+++ b/extraction/core/extractor.py
@@ -27,7 +27,7 @@ from extraction.core.functions.utils import depth
from agora.abc import ProcessABC, ParametersABC
from agora.io.writer import Writer, load_attributes
-from agora.io.cells import Cells
+from agora.io.cells import CellsLinear
from aliby.tile.tiler import Tiler
import matplotlib.pyplot as plt
@@ -127,10 +127,6 @@ class Extractor(ProcessABC):
def from_img(cls, parameters: ExtractorParameters, store: str, img_meta: tuple):
return cls(parameters, store=store, tiler=Tiler(*img_meta))
- # @classmethod
- # def from_store(cls, parameters: ExtractorParameters, store: str, img_meta: tuple):
- # return cls(parameters, store=store, tiler=Tiler(*img_meta))
-
@property
def channels(self):
if not hasattr(self, "_channels"):
@@ -324,7 +320,7 @@ class Extractor(ProcessABC):
ch_tree = {ch: v for ch, v in tree.items() if ch != "general"}
tree_chs = (*ch_tree,)
- cells = Cells.hdf(self.local)
+ cells = CellsLinear(self.local)
# labels
if labels is None:
@@ -421,7 +417,6 @@ class Extractor(ProcessABC):
"""
Returns the image from a correct source, either raw or bgsub
-
:channel: str name of channel to get
:img: ndarray (trap_id, channel, tp, tile_size, tile_size, n_zstacks) of standard channels
:channels: List of channels
--
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