mirror of
https://github.com/ClovertaTheTrilobita/cellpose-web.git
synced 2026-04-01 23:14:50 +00:00
95 lines
3.6 KiB
Python
95 lines
3.6 KiB
Python
import os
|
||
from PIL import Image
|
||
import numpy as np
|
||
import datetime
|
||
import time
|
||
from omegaconf import OmegaConf
|
||
from pathlib import Path
|
||
|
||
CONFIG_PATH = Path(__file__).parent / "config.yaml"
|
||
cfg = OmegaConf.load(CONFIG_PATH)
|
||
cfg.data.root_dir = str((CONFIG_PATH.parent / cfg.data.root_dir).resolve())
|
||
BASE_DIR = cfg.data.root_dir
|
||
UPLOAD_DIR = cfg.data.upload_dir
|
||
OUTPUT_DIR = cfg.data.run.output_dir
|
||
OUTPUT_TEST_DIR = cfg.data.run.test_output_dir
|
||
MODELS_DIR = str((CONFIG_PATH.parent / cfg.model.save_dir).resolve())
|
||
os.makedirs(MODELS_DIR, exist_ok=True)
|
||
os.environ["CELLPOSE_LOCAL_MODELS_PATH"] = MODELS_DIR
|
||
|
||
from cellpose import models, plot
|
||
from cellpose.io import imread, save_masks
|
||
|
||
class Cprun:
|
||
|
||
@classmethod
|
||
def run_test(cls):
|
||
model = models.CellposeModel(gpu=True)
|
||
files = ['test_tif/img.png']
|
||
imgs = [imread(f) for f in files]
|
||
masks, flows, styles = model.eval(
|
||
imgs, flow_threshold=0.4, cellprob_threshold=0.0
|
||
)
|
||
for i, m in enumerate(masks):
|
||
print(
|
||
f"[{i}] mask max={int(getattr(m, 'max', lambda: 0)()) if hasattr(m, 'max') else int(np.max(m))}, unique={np.unique(m)[:5]} ..."
|
||
)
|
||
|
||
ts = datetime.datetime.now().strftime("%Y-%m-%d-%H-%M-%S") + f"-{int(time.time()*1000)%1000:03d}"
|
||
outdir = os.path.join(OUTPUT_TEST_DIR, ts)
|
||
os.makedirs(outdir, exist_ok=True) # 自动创建目录
|
||
for img, mask, flow, name in zip(imgs, masks, flows, files):
|
||
base = os.path.join(outdir, os.path.splitext(os.path.basename(name))[0])
|
||
#使用内置绘图生成蒙版
|
||
out = base + "_output"
|
||
save_masks(imgs, mask, flow, out, tif=True)
|
||
|
||
# 用 plot 生成彩色叠加图（不依赖 skimage）
|
||
rgb = plot.image_to_rgb(img, channels=[0, 0]) # 原图转 RGB
|
||
over = plot.mask_overlay(rgb, masks=mask, colors=None) # 叠加彩色实例
|
||
Image.fromarray(over).save(base + "_overlay.png")
|
||
|
||
@classmethod
|
||
async def run(cls,
|
||
images: list[str] | str | None = None,
|
||
time: str | None = None,
|
||
model: str = "cpsam",
|
||
diameter: float | None = None,
|
||
flow_threshold: float = 0.4,
|
||
cellprob_threshold: float = 0.0, ):
|
||
|
||
if time is None:
|
||
return [False, "No time received"]
|
||
|
||
if images is None:
|
||
return [False, "No images received"]
|
||
|
||
message = [f"Using {model} model"]
|
||
|
||
model = models.CellposeModel(gpu=True, model_type=model)
|
||
files = images
|
||
imgs = [imread(f) for f in files]
|
||
masks, flows, styles = model.eval(
|
||
imgs,
|
||
flow_threshold=flow_threshold,
|
||
cellprob_threshold=cellprob_threshold,
|
||
diameter=diameter
|
||
)
|
||
|
||
ts = time
|
||
outdir = os.path.join(OUTPUT_DIR, ts)
|
||
os.makedirs(outdir, exist_ok=True) # 自动创建目录
|
||
for img, mask, flow, name in zip(imgs, masks, flows, files):
|
||
base = os.path.join(outdir, os.path.splitext(os.path.basename(name))[0])
|
||
# 使用内置绘图生成蒙版
|
||
out = base + "_output"
|
||
save_masks(imgs, mask, flow, out, tif=True)
|
||
|
||
# 用 plot 生成彩色叠加图（不依赖 skimage）
|
||
rgb = plot.image_to_rgb(img, channels=[0, 0]) # 原图转 RGB
|
||
over = plot.mask_overlay(rgb, masks=mask, colors=None) # 叠加彩色实例
|
||
Image.fromarray(over).save(base + "_overlay.png")
|
||
|
||
message.append(f"Output saved to: {outdir}")
|
||
message.append(outdir)
|
||
return [True, message]
|