From 4faa3698a57371a3c1901e64bb77e110dc000742 Mon Sep 17 00:00:00 2001 From: Simon Warchol Date: Thu, 27 Oct 2022 17:35:29 -0400 Subject: [PATCH] Adding handling for un-pyramided tiff --- minerva_analysis/server/models/data_model.py | 3 +++ minerva_analysis/server/routes/import_routes.py | 2 -- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/minerva_analysis/server/models/data_model.py b/minerva_analysis/server/models/data_model.py index a0014cf6e..7dd902eb9 100644 --- a/minerva_analysis/server/models/data_model.py +++ b/minerva_analysis/server/models/data_model.py @@ -1431,6 +1431,9 @@ def convertOmeTiff(filePath, channelFilePath=None, dataDirectory=None, isLabelIm if isinstance(channels, zarr.Array): channel_info['maxLevel'] = 1 chunks = channels.chunks + if chunks[1] == 1 or chunks[2] == 1: + chunks = [1, channels.shape[1], channels.shape[2]] + channel_info['channels'] = channels.shape[0] shape = channels.shape else: channel_info['maxLevel'] = len(channels) diff --git a/minerva_analysis/server/routes/import_routes.py b/minerva_analysis/server/routes/import_routes.py index 4e544d829..4154ba262 100644 --- a/minerva_analysis/server/routes/import_routes.py +++ b/minerva_analysis/server/routes/import_routes.py @@ -462,8 +462,6 @@ def save_config(): for name in datasets: data_model.load_datasource(name, reload=True) - # Create Embedding - data_model.create_embedding(datasets) resp = jsonify(success=True) return resp