prerakmody / slurm-status.sh

Created March 28, 2025 11:37

SLURM Management

	#!/bin/bash

	# Function to check the status of a service
	check_service_status() {
	local service=$1
	while true; do
	sudo systemctl status "$service" --no-pager
	if [ $? -eq 0 ]; then
	break
	fi

prerakmody / gping.md

Created March 28, 2025 08:48

Windows Powershell

1 - Install gping

1.1 - Sample command

prerakmody / uv-monai-torchsummary.py

Last active January 18, 2025 15:50

UV - fast Python package installer and resolver

	"""
	>> pip install uv # OR https://docs.astral.sh/uv/getting-started/installation/
	>> uv run -p 3.11 uv-monai-torchsummary.py
	"""

	# /// script
	# requires-python = ">=3.11"
	# dependencies = [
	# "monai==1.3.2",
	# "torchsummary==1.5.1",

prerakmody / dicomweb.json

Created October 28, 2024 09:32

Orthanc config JSONs

	{
	"DicomWeb" :
	{
	"Enable" : true, // Whether DICOMweb support is enabled
	"Root" : "/dicom-web/", // Root URI of the DICOMweb API (for QIDO-RS, STOW-RS and WADO-RS)
	"EnableWado" : true, // Whether WADO-URI (aka. WADO) support is enabled
	"WadoRoot" : "/wado", // Root URI of the WADO-URI (aka. WADO) API
	"Host" : "localhost:8042", // Hard-codes the name of the host for subsequent WADO-RS requests
	"Ssl" : false, // Whether HTTPS should be used for subsequent WADO-RS requests
	"Servers" : {

prerakmody / getContourScribbleForBinarySlice.py

Last active October 27, 2024 16:33

Scribble Generation (in an auto segmentation editing scenario)

	import skimage
	import skimage.morphology
	import voxynth as voxynth # https://github.com/dalcalab/voxynth
	import numpy as np
	import matplotlib.pyplot as plt

	def getContourScribbleForBinarySlice(mask, show=False):
	"""
	Params
	------

prerakmody / dataloaderCompare.py

Last active June 1, 2024 14:12

TORCH MULTIPROCESSING

prerakmody / svlsTensorflow.py

Created April 19, 2024 09:42

Stochasticaly Varying Spatial Smoothing (SVLS)

	def get_svls_filter_3d(kernel_size=3, sigma=1, verbose=False):
	"""
	Ref: https://github.com/mobarakol/SVLS/blob/main/svls.py (pytorch)
	- Alternative (for gauss kernel): https://gist.github.com/blzq/c87d42f45a8c5a53f5b393e27b1f5319

	Note: group parameter in Conv3D is giving an issue in tf==2.10.0 on Unix
	- "tensorflow/compiler/xla/service/gpu/nvptx_compiler.cc:453] ptxas returned an error during compilation of ptx to sass: 'INTERNAL: Failed to launch ptxas'"
	"""

	try:

prerakmody / loadCTInCornerstone.html

Created January 24, 2024 10:51

Cornerstone.js for loading a folder of .dcm files


	<!DOCTYPE html>
	<html>
	<head>
	<script src="https://cdnjs.cloudflare.com/ajax/libs/hammer.js/2.0.8/hammer.min.js"></script>

	<script src="https://unpkg.com/cornerstone-core/dist/cornerstone.js"></script> <!-- cornerstone-core - 2.6.1 - 2021-11-19 -->
	<script src="https://unpkg.com/cornerstone-tools/dist/cornerstoneTools.js"></script> <!-- cornerstone-tools - 6.0.10 - 2023-07-21 -->
	<script src="https://unpkg.com/cornerstone-math/dist/cornerstoneMath.js"></script> <!-- cornerstone-math - 0.1.10 - 2022-06-09 -->

prerakmody / ct-rtdose-plot.py

Last active January 17, 2025 00:40

DICOM (CT and RTDOSE) mapping in matplotlib

	"""
	Step 1 - Read Dose and CT .dcm files
	Step 2 - Resample dose to CT
	Step 3 - Plot
	"""
	import pdb
	import pydicom
	import traceback
	import numpy as np
	import SimpleITK as sitk

prerakmody / copyPlan.py

Last active July 13, 2023 09:12

Raystation - Dual Arc Beam

	import connect

	RS_CHECK_PREFIX = '_'
	RS_STR_TRANSLATE_OBJ = { ord(' ') : ord('_') , ord('(') : ord('_') , ord(')') : ord('_') , ord('-') : ord('_') , ord('+') : ord('_') , ord('<') : ord('_') , ord('>') : ord('_') }
	KEYNAME_PATIENT = 'Patient'

	def checkForRTPlan(case, planName):
	exists = False
	if RS_CHECK_PREFIX + str(planName).translate(RS_STR_TRANSLATE_OBJ) in dir(case.TreatmentPlans):
	exists = True