Skip to content

Instantly share code, notes, and snippets.

View xulman's full-sized avatar

Vladimír Ulman xulman

29 followers · 3 following
View GitHub Profile
@xulman
xulman / progresive_writing.md
Created September 18, 2026 23:19
progresive writing in ome-zarr-fiji-java

This is the original wording of the progresive writing issue #132 before I re-edited that issue in favour of (hopefully) more comprehensive version.

The goal: Progressive writing

This issue aims to outline/frame how progressive writing could be implemented. The subject of the writing for now shall be the PyramidContents, a holder of lazily-loaded pixel data (images) at decreasing spatial resolutions (pyramids), with a couple of additional metadata such as transforms, axes information, or display settings.

Progressive writing means here that

@xulman
xulman / S3.md
Last active August 18, 2026 09:43
Using AWS Profiles for (full) accessing non-AWS and not only public-open S3 stores

The native AWS Command Line Interface has built-in support for accessing S3 stores, including means to provide authentication keys and endpoints urls. And so does the Python and Java libraries.

Here, I'd like to remind of the shorthand parameter --profile and especially of its companion environment variable AWS_PROFILE that works

  • in conjunction with ~/.aws/config and ~/.aws/credentials files,
@xulman
xulman / instanseg-vlado.py
Created January 29, 2025 09:53
InstanSeg API to create, train, save, and use own models on own data
import numpy as np
import torch
from instanseg.scripts.train import instanseg_training
from instanseg.utils.model_loader import load_model as original_load_model
from instanseg import inference_class as IS
device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu")
print(f"Will use: {device}")
@xulman
xulman / gist:31e8d251e0c4f4334968faf63c8507cf
Last active March 4, 2024 14:39
testing new folder-DnD in ImageJ2/Fiji
================================================================================================
variant for
a) near future (when image-legacy master makes it into scijava/parent-pom)
b) for apps that harvest an image their own way (here somehow from a given folder)
================================================================================================
git clone git@github.com:xulman/imagej-legacy.git
cd imagej-legacy
mvn -Dmaven.test.skip=true clean install
cd ..
@xulman
xulman / BdvIoPlugin.java
Created February 6, 2022 12:31
drag&drop handler of BDV's xml (should be part of BDV-core distro)
package cz.ulman.dnd;
import org.scijava.Priority;
import org.scijava.io.IOService;
import org.scijava.io.location.FileLocation;
import org.scijava.io.location.Location;
import org.scijava.plugin.Plugin;
import org.scijava.io.IOPlugin;
import org.scijava.io.AbstractIOPlugin;
@xulman
xulman / MastodonIoPlugin.java
Created February 5, 2022 19:53
starting Mastodon with Drag&Drop onto Fiji window
package cz.ulman.dnd;
import org.scijava.plugin.Plugin;
import org.scijava.io.IOPlugin;
import org.scijava.io.AbstractIOPlugin;
import org.scijava.io.location.FileLocation;
import org.scijava.io.location.Location;
import java.io.IOException;
import java.util.ArrayList;
@xulman
xulman / gist:23f08764fe76cc6b95d70bce36fc3788
Created March 24, 2021 16:08
C++ example code how to submit http comm using the Poco project
$ more *.*
::::::::::::::
CMakeLists.txt
::::::::::::::
cmake_minimum_required (VERSION 3.5)
project (poco-VladoClientTest)
find_package (Poco REQUIRED Net)
add_executable (clientTest main.cpp)
@xulman
xulman / gist:07fbaa26108cc5fa90568f805005513e
Last active March 7, 2021 17:34
How to compile EmbryoGen on IT4I's supercomputers
# plan:
# -----
# 1) get EmbryoGen source code
# 2) set up the environment
# a) with: module add git, then GCC/10.2.0, CMake, OpenMPI/4.0.5-GCC-10.2.0
# b) calling a script from EmbryoGen's repo
# 3) download, compile and install locally all necessary libs
# 4) setup & compile EmbryoGen
@xulman
xulman / gist:b47b789daef93f7431e0db55dec3b450
Created February 25, 2021 08:51
How to compile CBIA's viewer4d on a Linux system
The official web page : https://cbia.fi.muni.cz/software/viewer4d/main.html
with the offical howto: https://cbia.fi.muni.cz/software/viewer4d/main-compiling.html
(with official DL-page: https://cbia.fi.muni.cz/software/viewer4d/main-download.html)
install into your OS the following packages:
i3dlibs, glew-devel, wxWidgets-devel, gcc, cmake
i3dlibs : https://cbia.fi.muni.cz/software/i3d-library.html
glew-devel: reported working with version 2.1
@xulman
xulman / gist:f4b80081a461e39a961654ce63dec23b
Created February 3, 2021 09:27
start 20 MitoGens
# create 20 runX folders
for i in `seq 1 20`; do mkdir -p run${i}; done
# submit 20 jobs, each in its own folder
for i in `seq 1 20`; do
cd run${i}
. /some/path/to/qsub/script mitogen params.....
cd ..
done