fix Morphology_main.py keyerror:has_ruler

hdr-bgnn · Jun 10, 2022 · 3341b10 · 3341b10
1 parent 21074f7
commit 3341b10
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Showing 4 changed files with 3 additions and 4 deletions.
diff --git a/SLURM_Snake_v2 b/SLURM_Snake_v2
@@ -41,7 +41,6 @@ snakemake \
     --cores $SLURM_NTASKS \
     --snakefile $SNAKEFILE \
     --use-singularity \
-    --use-conda \
     --directory $WORKDIR \
     --config list=$REAL_INPUTCSV
 

diff --git a/Scripts/Merge_files/Merge_files_main.py b/Scripts/Merge_files/Merge_files_main.py
diff --git a/Scripts/Morphology/Morphology_main.py b/Scripts/Morphology/Morphology_main.py
@@ -18,7 +18,7 @@ def get_scale(metadata_file):
     data = json.load(f)
     first_value = list(data.values())[0]
 
-    if first_value['ruler']==True :
+    if first_value['has_ruler']==True :
 
         scale = round(first_value['scale'],3)
         unit = first_value['unit']

diff --git a/Snakefile b/Snakefile
@@ -50,7 +50,7 @@ rule Cropped_image:
     output:'Cropped/{image}_cropped.jpg'
     singularity:
         'docker://ghcr.io/hdr-bgnn/bgnn_snakemake/crop_morph:0.0.10'
-    shell: 'Crop_image_main.py.py {input.image} {input.metadata} {output}'
+    shell: 'Crop_image_main.py {input.image} {input.metadata} {output}'
 
 rule Segmentation:
     input: 'Cropped/{image}_cropped.jpg'
@@ -62,7 +62,7 @@ rule Segmentation:
 
 rule Morphological_analysis:
     input:
-        image = 'Segmented/{image}_segmented.png'
+        image = 'Segmented/{image}_segmented.png',
         metadata = 'Metadata/{image}.json'
         #name = '{image}'
     output: