kaczmarj

// groovy script to measure running time of wsinfer
import groovy.time.TimeCategory

qupath.ext.wsinfer.ui.WSInferPrefs.deviceProperty().setValue("cpu");
selectAnnotations()
def timeStart = new Date()
qupath.ext.wsinfer.WSInfer.runInference("kaczmarj/breast-tumor-resnet34.tcga-brca")
def timeStop = new Date()
duration = TimeCategory.minus(timeStop, timeStart)
println duration

kaczmarj

kaczmarj

"""Repair the TIFF metadata for images where XResolution and YResolution contain MPP.

This script updates the following tags:
- ResolutionUnit --> to centimeter
- XResolution --> from mppx to pixels per centimeter in x dimension
- YResolution --> from mppy to pixels per centimeter in y dimension
"""

import argparse
from pathlib import Path

kaczmarj

"""Example torch Dataset for loading whole slide image patches on the fly."""

from pathlib import Path

import large_image
import pandas as pd
import torch


class PatchDataset(torch.utils.data.Dataset):

kaczmarj

BootStrap: docker
From: debian:bookworm-slim

%post
    apt update -qq
    apt install --yes inkscape
    rm -rf /var/lib/apt/lists/*

%runscript
    inkscape "$@"

kaczmarj

conda create --name MYNAME -c pytorch -c conda-forge pytorch torchvision torchaudio cudatoolkit=11.3 openslide openslide-python

kaczmarj

#!/bin/bash
#
#$ -cwd
#$ -q gpu_ded.q
#$ -w e
#$ -l gpu=1
#$ -l m_mem_free=32G
#
# To run this script, first create a file with each command you want to run. Each
# command must be on a separate line.

kaczmarj

#!/usr/bin/env bash

set -u

echo "Searching for nodes with available GPUs..."

for suffix in {001..010}; do
	remote="gpu${suffix}"
	ssh "$remote" nvidia-smi | grep -q "No running processes found"
	if [ $? -eq 0 ]; then

kaczmarj

How to use ColabFold on Elzar

This guide demonstrates how to use Sergey's ColabFold notebooks on Cold Spring Harbor's Elzar cluster. The instructions can also be extended to any cluster that has a GPU and Singularity installed.

These instructions were only tested with Jakub Kaczmarzyk's AlphaFold2_advanced_notcolab.ipynb notebook, which is a minor modification of Sergey's original AlphaFold2_advanced.ipynb notebook. Even Amber relaxation is tested.

❗❗❗IMPORTANT: after finishing your work, be sure to terminate the GPU process. To do this, you can shutdown the jupyter notebook (this is not equivalent to closing the tab, you need to go to Kernel->Shutdown). And quit the singularity process as well. Exit the qrsh job when you are finished.

kaczmarj

def to_png_with_metadata(img, path, **meta_kwds):
    """Write a PIL image to PNG with associated metadata.

    Parameters
    ----------
    img : PIL.Image.Image
        Image to write.
    path : str, pathlib.Path
        Save the image to this path. The extension '.png' is added
        if it is not present.