Gireesh Bogu gireeshkbogu
gireeshkbogu
/ segmentation_brain_MRI_using_PyTorch.ipynb
Created
October 3, 2019 04:47
source: https://pytorch.org/hub/mateuszbuda_brain-segmentation-pytorch_unet/
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
gireeshkbogu
/ segmentation_kits2019_using_fastai_test_version.ipynb
Last active
October 9, 2019 22:01
segmentation_kits2019_using_fastai_test_version
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
gireeshkbogu
/ simulate_data.sh
Last active
April 5, 2020 14:01
Simulate Omics style data for Machine Learning programs
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # Simulate Omics style data for ML | |
| import uuid | |
| import itertools | |
| features = 700 | |
| subjects = 40 | |
| columns_list = [] |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| from glob import glob | |
| import cv2 | |
| jpgs = glob('./*.jpg') | |
| for image in jpgs: | |
| img = cv2.imread(image) | |
| cv2.imwrite(image[:-3] + 'png', img) |
gireeshkbogu
/ mask_filter.py
Last active
April 8, 2020 19:03
Filter images with at least one mask (sum of all pixels > 0) and copy them to a new folder
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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 |
gireeshkbogu
/ mask_class_names_modifier.py
Created
April 5, 2020 13:41
Changes the unordered class names of multiple image masks in a give folder
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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): |
gireeshkbogu
/ add_prefix_to_filenames.sh
Created
April 8, 2020 19:32
Adds a prefix to multiple file names
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| for filename in *.jpg; do mv "$filename" "prefix_$filename"; done; |
gireeshkbogu
/ nii_to_png.sh
Last active
April 11, 2020 21:40
Converts .nii format to .jpg or .png format
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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 |
gireeshkbogu
/ reproducible.examples.txt
Created
June 3, 2020 19:26
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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
/ test.txt
Last active
June 11, 2020 15:10
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 |