comparison cp_segmentation.py @ 2:e5370bb71633 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/cellpose commit 5846f23282167df28e6cc00e1bda31523b66b5b4

1:1857781df226

import argparse
import json
import os
import warnings

import matplotlib.pyplot as plt
import numpy as np
import skimage.io
from cellpose import models, plot, transforms


def main(inputs, img_path, img_format, output_dir):
    """
    Parameter

2:e5370bb71633

import argparse
import json
import os
import warnings

# Make sure, that `MKL_NUM_THREADS` is set to 1, to ensure reproducibility:
# https://forum.image.sc/t/reproducibility-how-we-spent-years-building-containers-and-then-mkl-decided-to-screw-our-results/109599
if str(os.environ['MKL_NUM_THREADS']) != '1':
    warnings.warn('MKL_NUM_THREADS must be set to 1 to ensure reproducibility, and will be adjusted accordingly for now.')
    os.environ['MKL_NUM_THREADS'] = '1'

# Load the remaining packages *after* adjusting `MKL_NUM_THREADS` (this likely necessary for it to take effect)
import matplotlib.pyplot as plt
import numpy as np
import skimage.io
import torch
from cellpose import models, plot, transforms

# Apply PyTorch guidelines for reproducibility
torch.backends.cudnn.benchmark = True
torch.backends.cudnn.deterministic = True
torch.manual_seed(0)


def main(inputs, img_path, img_format, output_dir):
    """
    Parameter