Spaces:
Sleeping
Sleeping
File size: 5,135 Bytes
0506a57 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 |
#!/bin/bash
# Aeon Model Test Script
# This script runs the Aeon cancer subtype prediction model on test slides
# for reproducibility and validation.
set -e # Exit on error
# Configuration
TEST_SAMPLES_FILE="test_slides/test_samples.json"
RESULTS_DIR="test_slides/results"
LOG_DIR="test_slides/logs"
SEGMENTATION_CONFIG="Biopsy"
NUM_WORKERS=4
# Colors for output
GREEN='\033[0;32m'
YELLOW='\033[1;33m'
RED='\033[0;31m'
NC='\033[0m' # No Color
echo "========================================="
echo "Aeon Model Test Suite"
echo "========================================="
echo ""
# Create directories
mkdir -p "${RESULTS_DIR}"
mkdir -p "${LOG_DIR}"
# Check if test samples file exists
if [ ! -f "${TEST_SAMPLES_FILE}" ]; then
echo -e "${RED}Error: Test samples file not found: ${TEST_SAMPLES_FILE}${NC}"
exit 1
fi
# Read test samples
echo "Reading test samples from ${TEST_SAMPLES_FILE}..."
SLIDE_IDS=$(python3 -c "
import json
with open('${TEST_SAMPLES_FILE}') as f:
samples = json.load(f)
for sample in samples:
slide_id = sample.get('slide_id') or sample.get('image_id')
print(slide_id)
")
# Count slides
NUM_SLIDES=$(echo "${SLIDE_IDS}" | wc -l)
echo -e "${GREEN}Found ${NUM_SLIDES} test slides${NC}"
echo ""
# Process each slide
CURRENT=0
PASSED=0
FAILED=0
for SLIDE_ID in ${SLIDE_IDS}; do
CURRENT=$((CURRENT + 1))
echo "========================================="
echo -e "${YELLOW}Processing slide ${CURRENT}/${NUM_SLIDES}: ${SLIDE_ID}${NC}"
echo "========================================="
# Get slide metadata
METADATA=$(python3 -c "
import json
with open('${TEST_SAMPLES_FILE}') as f:
samples = json.load(f)
for sample in samples:
slide_id = sample.get('slide_id') or sample.get('image_id')
if slide_id == '${SLIDE_ID}':
cancer_subtype = sample.get('cancer_subtype') or sample.get('cancer_type')
print(f\"{cancer_subtype}|{sample['site_type']}|{sample['sex']}|{sample['tissue_site']}\")
break
")
IFS='|' read -r CANCER_SUBTYPE SITE_TYPE SEX TISSUE_SITE <<< "${METADATA}"
echo "Ground Truth:"
echo " Cancer Subtype: ${CANCER_SUBTYPE}"
echo " Site Type: ${SITE_TYPE}"
echo " Sex: ${SEX}"
echo " Tissue Site: ${TISSUE_SITE}"
echo ""
# Find slide file
SLIDE_FILE=$(find test_slides -name "${SLIDE_ID}.svs" -o -name "${SLIDE_ID}.tiff" -o -name "${SLIDE_ID}.ndpi" 2>/dev/null | head -1)
if [ -z "${SLIDE_FILE}" ]; then
echo -e "${RED}Error: Slide file not found for ${SLIDE_ID}${NC}"
FAILED=$((FAILED + 1))
continue
fi
echo "Slide file: ${SLIDE_FILE}"
echo ""
# Run Mosaic pipeline with Aeon inference
LOG_FILE="${LOG_DIR}/${SLIDE_ID}_aeon_test.log"
echo "Running Mosaic pipeline..."
if uv run python -m mosaic.cli \
--input-slide "${SLIDE_FILE}" \
--output-dir "${RESULTS_DIR}/${SLIDE_ID}" \
--cancer-subtype "Unknown" \
--site-type "${SITE_TYPE}" \
--sex "${SEX}" \
--tissue-site "${TISSUE_SITE}" \
--segmentation-config "${SEGMENTATION_CONFIG}" \
--num-workers "${NUM_WORKERS}" \
> "${LOG_FILE}" 2>&1; then
# Check if results exist
AEON_RESULTS="${RESULTS_DIR}/${SLIDE_ID}/${SLIDE_ID}_aeon_results.csv"
if [ -f "${AEON_RESULTS}" ]; then
# Extract prediction
PREDICTION=$(python3 -c "
import pandas as pd
df = pd.read_csv('${AEON_RESULTS}')
if not df.empty:
print(f\"{df.iloc[0]['Cancer Subtype']}|{df.iloc[0]['Confidence']:.4f}\")
")
IFS='|' read -r PRED_SUBTYPE CONFIDENCE <<< "${PREDICTION}"
echo ""
echo "Aeon Prediction:"
echo " Predicted: ${PRED_SUBTYPE}"
echo " Confidence: ${CONFIDENCE}"
echo ""
# Check if prediction matches ground truth
if [ "${PRED_SUBTYPE}" == "${CANCER_SUBTYPE}" ]; then
echo -e "${GREEN}✓ PASS: Prediction matches ground truth${NC}"
PASSED=$((PASSED + 1))
else
echo -e "${RED}✗ FAIL: Prediction does not match ground truth${NC}"
echo " Expected: ${CANCER_SUBTYPE}"
echo " Got: ${PRED_SUBTYPE}"
FAILED=$((FAILED + 1))
fi
else
echo -e "${RED}✗ FAIL: Aeon results file not found${NC}"
FAILED=$((FAILED + 1))
fi
else
echo -e "${RED}✗ FAIL: Mosaic pipeline failed${NC}"
echo "Check log file: ${LOG_FILE}"
FAILED=$((FAILED + 1))
fi
echo ""
done
# Summary
echo "========================================="
echo "Test Summary"
echo "========================================="
echo "Total slides: ${NUM_SLIDES}"
echo -e "${GREEN}Passed: ${PASSED}${NC}"
if [ ${FAILED} -gt 0 ]; then
echo -e "${RED}Failed: ${FAILED}${NC}"
else
echo "Failed: ${FAILED}"
fi
echo ""
if [ ${FAILED} -eq 0 ]; then
echo -e "${GREEN}All tests passed!${NC}"
exit 0
else
echo -e "${RED}Some tests failed. Check logs in ${LOG_DIR}${NC}"
exit 1
fi
|