From ae0175c73216f337f10e9bab264643786cfb704d Mon Sep 17 00:00:00 2001 From: DenisSch Date: Wed, 8 Apr 2020 15:43:58 -0400 Subject: [PATCH] Now the CSV file needs to have the discussed structure as stated #60 in micro-nf --- SingleCellDataExtraction.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/SingleCellDataExtraction.py b/SingleCellDataExtraction.py index 947886a..1cb6b07 100644 --- a/SingleCellDataExtraction.py +++ b/SingleCellDataExtraction.py @@ -166,11 +166,10 @@ def ExtractSingleCells(mask,image,channel_names,output): output = Path(output) #Read the channels names - channel_names_loaded = pd.read_csv(channel_names,header=None) - #Add a column index for ease - channel_names_loaded.columns = ["marker"] + channel_names_loaded = pd.read_csv(channel_names) #Convert the channel names to a list - channel_names_loaded = list(channel_names_loaded.marker.values) + channel_names_loaded_list = list(channel_names_loaded.marker_name) + #Check for unique marker names -- create new list to store new names channel_names_loaded_checked = [] for idx,val in enumerate(channel_names_loaded):