Graeme Winter graeme-winter
graeme-winter
/ extract.py
Created
September 11, 2024 08:24
Tool to extract raw data from NeXus formatted HDF5 files to "raw" memory mapped data files
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| import os | |
| import sys | |
| import tqdm | |
| import hdf5plugin | |
| import h5py | |
| def extract(nxs, template, start=None, end=None): |
graeme-winter
/ simple_dispersion.cc
Created
June 27, 2024 13:52
Simple dispersion spot finding implementation in C++
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| #include <vector> | |
| int dispersion_filter(std::vector<uint16_t> &image_in, | |
| std::vector<uint16_t> &mask_out, | |
| int NY, int NX) { | |
| int32_t knl = 3; | |
| float sigma_b = 6.0f, sigma_s = 3.0f; | |
| std::vector<uint32_t> im(NY * NX); |
graeme-winter
/ make_shoeboxes.py
Last active
April 11, 2024 09:31
Script to take predictions, add some fixed shoebox size and then extract to shoeboxes.refl
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| # to get to the starting point: | |
| # | |
| # dials.import ~/data/i04_bag_training/*gz | |
| # dials.find_spots imported.expt | |
| # dials.index imported.expt strong.refl | |
| # dials.refine indexed.* | |
| # dials.predict refined.expt | |
| # | |
| # then | |
| # |
graeme-winter
/ unbitshufflelz4.py
Created
April 3, 2024 05:37
Manually unpack bitshuffle / lz4 data in Python
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| # Proof of work is computing the sha1 hash of the uncompressed and unshuffled | |
| # data and comparing with the result of doing the operation on the h5py | |
| # extracted data | |
| import binascii | |
| import hashlib | |
| import struct | |
| import sys | |
| import lz4.block |
graeme-winter
/ jpg_mp4.py
Created
September 23, 2023 06:27
JPG sequence conversion to MP4 - N.B. set up for monochrome, includes overlay with time
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| import sys | |
| import os | |
| import numpy as np | |
| from PIL import Image, ImageFont, ImageDraw | |
| import cv2 | |
| def main(file_template, start, end): | |
| font = ImageFont.truetype("FreeMono.ttf", 32) |
graeme-winter
/ quilt.py
Created
May 14, 2023 18:48
Quilt combination generator - ensure each 3x3 block contains a unique permutation of 5 coloured pieces
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| import random | |
| # FIXME fill in numbers of each unique piece here | |
| tiles = { | |
| "a": 10, | |
| "b": 10, | |
| "c": 10, | |
| "d": 10, | |
| "e": 10, |
graeme-winter
/ reciprocal_xyz.py
Created
May 9, 2023 09:09
Map strong spots to reciprocal space and print x, y, z positions
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| # Print reciprocal space positions from DIALS strong reflections | |
| # after spot finding | |
| # | |
| # Usage: | |
| # | |
| # dials.import (data) | |
| # dials.find_spots imported.expt | |
| # dials.python reciprocal_xyz.py strong.refl imported.expt | |
| # | |
| # Prints long list of x, y, z positions |
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| /home/graeme/git/rp2040-explore/asm/blink/build/blink.elf: file format elf32-littlearm | |
| Sections: | |
| Idx Name Size VMA LMA File off Algn | |
| 0 .boot2 00000100 10000000 10000000 00001000 2**0 | |
| CONTENTS, ALLOC, LOAD, READONLY, CODE | |
| 1 .text 00001fd0 10000100 10000100 00001100 2**4 | |
| CONTENTS, ALLOC, LOAD, READONLY, CODE | |
| 2 .rodata 000000b8 100020d0 100020d0 000030d0 2**2 |
graeme-winter
/ fetch-7085897.sh
Created
February 24, 2023 11:25
Shell script to download i24 multi-crystal data for a dials tutorial from Zenodo
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| for filename in ins11_b200_1_000001.h5 ins11_b200_1_master.h5 ins11_b200_1_meta.h5 ins11_b200_1.nxs ins11_b295_1_000001.h5 ins11_b295_1_master.h5 ins11_b295_1_meta.h5 ins11_b295_1.nxs ins11_b299_1_000001.h5 ins11_b299_1_master.h5 ins11_b299_1_meta.h5 ins11_b299_1.nxs ins11_b302_1_000001.h5 ins11_b302_1_master.h5 ins11_b302_1_meta.h5 ins11_b302_1.nxs ins11_b365_1_000001.h5 ins11_b365_1_master.h5 ins11_b365_1_meta.h5 ins11_b365_1.nxs ins11_b391_1_000001.h5 ins11_b391_1_master.h5 ins11_b391_1_meta.h5 ins11_b391_1.nxs ins11_b453_1_000001.h5 ins11_b453_1_master.h5 ins11_b453_1_meta.h5 ins11_b453_1.nxs ins11_b474_1_000001.h5 ins11_b474_1_master.h5 ins11_b474_1_meta.h5 ins11_b474_1.nxs ins11_b487_1_000001.h5 ins11_b487_1_master.h5 ins11_b487_1_meta.h5 ins11_b487_1.nxs ins11_b508_1_000001.h5 ins11_b508_1_master.h5 ins11_b508_1_meta.h5 ins11_b508_1.nxs ins11_b566_1_000001.h5 ins11_b566_1_master.h5 ins11_b566_1_meta.h5 ins11_b566_1.nxs ins11_b616_1_000001.h5 ins11_b616_1_master.h5 ins11_b616_1_meta.h5 ins11_b616_1.nxs |
graeme-winter
/ movify.py
Created
June 11, 2022 05:07
Python script to make movie from stack of jpeg images
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| import sys | |
| import os | |
| import numpy as np | |
| from PIL import Image, ImageFont, ImageDraw | |
| import cv2 | |
| def main(file_template, start=0, end=100000): |
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