gireeshkbogu

	steps
2020-02-01 00:00:00	0
2020-02-01 00:01:00	0
2020-02-01 00:02:00	0
2020-02-01 00:03:00	0
2020-02-01 00:04:00	0
2020-02-01 00:05:00	0
2020-02-01 00:06:00	0
2020-02-01 00:07:00	0
2020-02-01 00:08:00	0

gireeshkbogu

Subject	datetime	Type	Count
User1	4/16/20 15:00	A1	1
User2	3/28/20 13:00	A1	1
User3	4/29/20 15:00	A1	1
User4	5/2/20 9:00	A1	1
User5	2/19/20 18:00	A1	1
User6	4/20/20 16:00	A1	1
User7	5/4/20 20:00	A1	1
User8	4/4/20 16:00	A1	1
User9	4/5/20 8:00	A1	1

gireeshkbogu

# source: https://pypi.org/project/med2image/
# https://stackoverflow.com/questions/29640641/how-to-convert-nii-format-file-into-2d-image

# requirements
#pip3 install pydicom
#pip3 install med2image
#pip3 install pudb
#pip3 install pfmisc

#$1 = input.nii

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for filename in *.jpg; do mv "$filename" "prefix_$filename"; done;

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import sys
import os
from PIL import Image
import shutil
import numpy as np


mask_dir = "/Users/gireeshbogu/Downloads/MSNYD_8_22_17/MSNYD_8_22_17__AB_AXT1_fl2d_inopp_mbh_15/masks_machine/"
new_mask_dir = "/Users/gireeshbogu/Downloads/MSNYD_8_22_17__AB_AXT1_fl2d_inopp_mbh_15_masks/"
if not os.path.exists(new_mask_dir):

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# identify images with at least one mask (sum of all pixels > 0) and copy them to a new folder
# usage: script.py mask_dir new_mask_dir

import sys
import os
from PIL import Image
import shutil
import pandas as pd
import numpy as np

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from glob import glob                                                           
import cv2 
jpgs = glob('./*.jpg')

for image in jpgs:
    img = cv2.imread(image)
    cv2.imwrite(image[:-3] + 'png', img)

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# Simulate Omics style data for ML

import uuid
import itertools


features = 700
subjects = 40

columns_list = []

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