Ilkay Isik ilkayisik

Learning and coding, mostly in Python, R

ilkayisik / convert_image.py

Created January 24, 2022 14:02

convert_image.py

ilkayisik / conda_env_share

Last active August 31, 2024 00:38

Sharing a conda environment

	# Exporting the environment.yml file

	# Activate the environment to export:
	conda activate myenv

	# go to the directory where you want the newly created .yml file to be
	cd /Users/ilkayisik/Desktop/

	# Export your active environment to a new file
	conda env export > environment.yml

ilkayisik / square_matrix_from_vector.py

Last active February 19, 2021 10:40

two ways of making a square matrix from a vector

	'''make square matrix from vector'''

	import numpy as np
	nr_elems = 253
	vals = np.random.rand(nr_elems)

	# first method using scipy distance:
	from scipy.spatial import distance
	vals_square_1 = distance.squareform(vals)

ilkayisik / rsync_cmd.sh

Created April 18, 2020 15:44

command to sync external hard disk to local

	# local to external hd
	rsync -azP --delete /Users/ilkay.isik/project_folder_temp/fc_content/MRI_data/lscp_data /Volumes/ilkay_iMAC

	# external hd to local
	rsync -azP --delete /Volumes/ilkay_iMAC /Users/ilkay.isik/project_folder_temp/fc_content/MRI_data/lscp_data

ilkayisik / make_gif_with_image_magick.sh

Created March 31, 2020 14:40

	cd /path
	convert -delay 50 -loop 0 cope6*.png cope6_gif.gif

ilkayisik / jn_notebook_themes.txt

Last active March 29, 2020 10:21

	# favorite jupyter notebook themes
	#https://github.com/dunovank/jupyter-themes

	# light
	jt -r # restore default theme
	jt -t grade3 -f roboto -fs 12 -ofs 11 -cellw 90% -lineh 130 -T -N
	jupyter notebook


	# dark can also be onedork

ilkayisik / t2p_matlab.m

Created February 4, 2020 15:37

1 - cdf('t', tval, df)

ilkayisik / remove_elements_starts_with.py

Created February 3, 2020 16:36

remove list element that starts with a certain expression

	labels = ['pericalc','FFA','MT','comb_a','comb_b']
	comb_ind = [labels.index(l) for l in labels if l.startswith('comb')]
	len_comb = len(comb_ind)
	arr = np.arange(len(labels))
	arr = list(arr[~np.isin(arr, comb_ind)])
	labels = [i for j, i in enumerate(labels) if j in arr]

ilkayisik / index_fourdim_array.py

Created February 1, 2020 19:12

	mask = np.zeros([18, 18, 1, 4])
	for i in range(mask.shape[3]):
	mask[:, :, 0, :] = ipl_mask
	no_mask = np.zeros_like(mask)


	k = 0
	mask_all_sub = np.zeros_like(four_dim_array)
	for s, sub in enumerate(sub_list):
	if sub in missing_roi_sub:

ilkayisik / bash_read_pipe_withawk.sh

Last active January 28, 2020 11:58

Example script containing several important operations in bash

	#!/bin/bash
	# How to skip the first line while using read,
	# how to check a value and increment based on the value of another variable,
	# pipe a value from bash to awk to parse the line and get the value as a variable to use in another bash command

	PREVCINDEX=99999
	i=1 # skip the first line (part 1)
	while read LINE
	do
	test $i -eq 1 && ((i=i+1)) && continue # skip the first line (part 2)