thomasaarholt

module load CUDA/11.0 CMake/3.21.1-GCCcore-11.2.0 Boost/1.74.0-GCC-10.2.0

pip install lightgbm --install-option=--gpu

# If running from notebook, ensure that the following contains Boost:
# import os
# os.environ["LD_LIBRARY_PATH"].split(":")

thomasaarholt

# must not use gcc version > 10
module load CUDA/11.0 CMake/3.21.1-GCCcore-11.2.0

# Clone with recursive! Otherwise you get dmlc error later on!
git clone --recursive https://github.com/dmlc/xgboost
cd xgboost/python-package

# clean out any old build files that may break things if try to recompile
rm -rf build

thomasaarholt

# From a directory with a Dockerfile
# Example Dockerfile with "Dockerfile" as filename
FROM python:3.10-slim-buster
RUN pip install numpy


# Then, run the following

docker build -t your_image_name .

thomasaarholt

from matplotlib.colors import LinearSegmentedColormap

def black_to_color(high_color: tuple, low_color: tuple = (0,0,0), name: str = "my_color", steps=256):
    "Get linear colormap from one rgb color to another, defaulting from black"
    
    r1,g1,b1 = low_color
    r2,g2,b2 = high_color
    
    cdict = {
        'red':    [(0.0,  r1, r1),

thomasaarholt

cat /root/.jupyter/lab/user-settings/@jupyterlab/notebook-extension/tracker.jupyterlab-settings
{
    // Notebook
    // @jupyterlab/notebook-extension:tracker
    // Notebook settings.
    // **************************************

    // Code Cell Configuration
    // The configuration for all code cells.
    "codeCellConfig": {

thomasaarholt

if docker info > /dev/null 2>&1; then 
    : # pass
else 
    echo "Docker Daemon is not running. Please open it and retry."
    exit -1
fi

thomasaarholt

import numpy as np
import dask.array as da

x = da.random.random((120,500,500), chunks=(40, 500, 500)) # 80 MB chunks
X = x.compute()

@da.as_gufunc(signature="(n,n)->(n,n)", output_dtypes=float, vectorize=True)
def gufunc(x):
    return np.linalg.inv(x)

thomasaarholt

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
/var/folders/yt/z22_f0896l74f8gs3_20vc_00000gn/T/ipykernel_88946/1449311839.py in <module>
      7     return np.linalg.inv(x)
      8 
----> 9 y = gufoo(b)

~/mambaforge/envs/py/lib/python3.9/site-packages/dask/array/gufunc.py in __call__(self, *args, **kwargs)
    659 
    660     def __call__(self, *args, **kwargs):

thomasaarholt

def bilinear_interpolate(img, points, clipped_nan=True):
    """Bilinearly interpolate points from an image using NumPy or CuPy

    Args:
        img: Image of shape (Y, X) to interpolate from.
        points: array of shape (2, N) of (y, x) coordinates
        clipped_nan: If True, the value of coordinates outside the image shape 
            are set to nan. Otherwise they are clipped to the image edge.

    Returns:

thomasaarholt

def bilinear_binning(points, intensities, subpixel=1, gaussian_blur=False):
    """Bilinear weighting of points onto a grid.
    Extent of grid given by min and max of points in each dimension
    points should be an array of shape (N, 2)
    intensity should be an array of shape (N,)
    subpixel will increase the gridsize by its factor
    gaussian_blur: blur the binned intensity and weighting images before they are divided, avoiding divide-by-zero warnings
    
    TODO: Give a known grid as input
    """