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Skip QC if label file is empty #61

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merged 4 commits into from
Sep 15, 2023
Merged

Skip QC if label file is empty #61

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b5d49ad
Check if label file is empty (i.e., no lesion was drawn in MS patient…
valosekj Aug 21, 2023
d2833ed
Switch from print to logging
valosekj Aug 21, 2023
b481504
Skip QC only for sct_label_utils, sct_label_vertebrae, and sct_detect…
valosekj Sep 14, 2023
8adb172
Change python version from 3.8.17 to 3.8.18 to prevent CI failing
valosekj Sep 14, 2023
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2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ jobs:
- name: Install Python 3
uses: actions/setup-python@v1
with:
python-version: 3.8.17
python-version: 3.8.18

- name: Install dependencies
run: |
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14 changes: 14 additions & 0 deletions manual_correction.py
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Expand Up @@ -22,6 +22,7 @@
import glob
import json
import os
import logging
import sys
import shutil
from textwrap import dedent
Expand All @@ -31,6 +32,9 @@

import utils

import numpy as np
import nibabel as nib


def get_parser():
"""
Expand Down Expand Up @@ -581,6 +585,16 @@ def generate_qc(fname, fname_label, task, fname_qc, subject, config_file, qc_les
:param suffix_dict: dictionary of suffixes
:return:
"""
# Not all sct_qc -p functions support empty label files. Check if the label file is empty and skip QC if so.
# Context: https://github.com/spinalcordtoolbox/manual-correction/issues/60#issuecomment-1720280352
skip_qc_list = ['FILES_LABEL', 'FILES_COMPRESSION', 'FILES_PMJ', 'FILES_CENTERLINE']
if task in skip_qc_list:
img_label = nib.load(fname_label)
data_label = img_label.get_fdata()
if np.sum(data_label) == 0:
logging.warning(f"File {fname_label} is empty. Skipping QC.\n")
return

# Lesion QC needs also SC segmentation for cropping
if task == 'FILES_LESION':
# Construct SC segmentation file name
Expand Down
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