Untitled

keselyoleren

Jun 30th, 2025

263

Never

Add comment

Not a member of Pastebin yet? Sign Up, it unlocks many cool features!

Python 6.21 KB | None | 0 0

raw download clone embed print report

import openslide
import boto3
from io import BytesIO
from slugify import slugify
import json
import os
import glob
class SVSFileProcessor:
def __init__(self, svs_file_path, file_name, aws_access_key, aws_secret_key, s3_bucket_name, s3_region):
self.svs_file_path = svs_file_path
self.original_filename = os.path.basename(svs_file_path)
self.s3_bucket_name = s3_bucket_name
self.s3_region = s3_region
self.safe_file_name = slugify(file_name)
self.s3_client = None
self.wsi = None
# Initialize S3 client
try:
self.s3_client = boto3.client(
's3',
aws_access_key_id=aws_access_key,
aws_secret_access_key=aws_secret_key,
region_name=self.s3_region
)
except Exception as e:
print(f"Kesalahan Kredensial AWS: {str(e)}")
# Open the SVS file
try:
self.wsi = openslide.OpenSlide(self.svs_file_path)
print(f"File SVS '{self.original_filename}' berhasil dibuka.")
except openslide.OpenSlideError as e:
print(f"Gagal membuka file SVS '{self.original_filename}': {e}")
def extract_properties(self):
if not self.wsi:
return []
data = []
try:
properties = self.wsi.properties
for key, value in properties.items():
# Clean up key for better compatibility (e.g., in JSON)
clean_key = key.replace(' ', '-').replace('.', '-')
data.append({clean_key: str(value)})
except Exception as e:
print(f"Terjadi kesalahan saat mengekstrak properti: {e}")
return data
def generate_and_upload_thumbnail(self, thumb_size=(256, 256)):
if not self.wsi or not self.s3_client:
print("Tidak dapat membuat thumbnail. File SVS atau klien S3 tidak diinisialisasi.")
return None
try:
thumb_image = self.wsi.get_thumbnail(thumb_size)
thumb_buffer = BytesIO()
thumb_image.save(thumb_buffer, "PNG")
thumb_buffer.seek(0)
s3_key = f"thumbnails/{self.safe_file_name}_thumb.png"
print(f"Mengunggah thumbnail ke bucket S3 '{self.s3_bucket_name}' dengan key '{s3_key}'...")
self.s3_client.upload_fileobj(
thumb_buffer,
self.s3_bucket_name,
s3_key,
)
s3_url = f"https://{self.s3_bucket_name}.s3.{self.s3_region}.amazonaws.com/{s3_key}"
print(f"Thumbnail berhasil diunggah. URL: {s3_url}")
return s3_url
except Exception as e:
print(f"Gagal mengunggah thumbnail: {e}")
return None
def process_file(self):
if not self.wsi:
return {
"filename": self.original_filename,
"properties": [],
"thumbnail": None,
"error": "File SVS tidak dapat dibaca atau rusak."
}
properties_data = self.extract_properties()
thumbnail_url = self.generate_and_upload_thumbnail()
return {
"filename": self.original_filename,
"properties": properties_data,
"thumbnail": thumbnail_url
}
def __del__(self):
if self.wsi:
self.wsi.close()
def process_svs_batch(directory_path, aws_access_key, aws_secret_key, s3_bucket_name, s3_region):
search_pattern = os.path.join(directory_path, '*.svs')
file_paths = glob.glob(search_pattern)
if not file_paths:
print(f"Peringatan: Tidak ada file .svs yang ditemukan di '{directory_path}'")
return json.dumps([], indent=4)
print(f"Ditemukan {len(file_paths)} file .svs untuk diproses.")
all_results = []
for file_path in file_paths:
print("\n" + "="*20 + f" Memproses {os.path.basename(file_path)} " + "="*20)
file_name_base = os.path.splitext(os.path.basename(file_path))[0]
processor = SVSFileProcessor(
svs_file_path=file_path,
file_name=file_name_base,
aws_access_key=aws_access_key,
aws_secret_key=aws_secret_key,
s3_bucket_name=s3_bucket_name,
s3_region=s3_region
)
result = processor.process_file()
all_results.append(result)
return json.dumps(all_results, indent=4)
# --- CONTOH PENGGUNAAN ---
if __name__ == '__main__':
SVS_DIRECTORY = input("Masukkan path lengkap ke direktori yang berisi file .svs .tiff \n contoh /Users/f/keselyoleren/neurabot/product/data/slide : ")
AWS_ACCESS_KEY_ID = os.environ.get('AWS_ACCESS_KEY_ID', 'AKIA5XSKJQZJZCKNAUKI')
AWS_SECRET_ACCESS_KEY = os.environ.get('AWS_SECRET_ACCESS_KEY', '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')
S3_BUCKET = os.environ.get('S3_BUCKET', 'mylab-production')
S3_REGION = os.environ.get('S3_REGION', 'ap-southeast-3')
if not os.path.isdir(SVS_DIRECTORY):
print("="*50)
print(f"Error: Direktori tidak ditemukan di '{SVS_DIRECTORY}'")
print("Harap jalankan kembali skrip dan masukkan path folder yang benar.")
print("Contoh /Users/f/keselyoleren/neurabot/product/data/slide")
print("="*50)
elif 'YOUR_AWS' in AWS_ACCESS_KEY_ID or 'your-s3' in S3_BUCKET:
print("="*50)
print(f"Peringatan: Kredensial AWS atau nama bucket belum diatur.")
print("Harap perbarui variabel kredensial AWS atau atur melalui environment variables.")
print("="*50)
else:
json_output = process_svs_batch(
directory_path=SVS_DIRECTORY,
aws_access_key=AWS_ACCESS_KEY_ID,
aws_secret_key=AWS_SECRET_ACCESS_KEY,
s3_bucket_name=S3_BUCKET,
s3_region=S3_REGION
)
output_filename = 'svs_metadata_output.json'
print(f"\n\n--- HASIL OUTPUT JSON GABUNGAN ---")
print(f"Menyimpan hasil ke file '{output_filename}'...")
with open(output_filename, 'w') as f:
f.write(json_output)
print("Selesai.")

Add Comment

Please, Sign In to add comment