The following are instructions for user to label and annotate timestamps of Four Chamber View (4CV) and Ejection Fraction (EF) of ultrasound echocardiography datasets.
1.1 Download datasets from the filezilla server which are located at /01NVb/01NVb/Group 1-ECHO + LUS.
It is suggested that you create a path for datasets as showing below:
cd /media/$USER/vitaluskcl/datasets/echocardiography/videos-echo-annotated-33-subjects/ ## change path
mkdir -p 01NVb-003-072/T1 ## participant name and T1 for day 01
Then you can download the following files from filezilla:
/01NVb/01NVb/Group 1-ECHO + LUS/01NVb-003-070/T1/01NVb-003-072-1 echo.mp4
/01NVb/01NVb/Group 1-ECHO + LUS/01NVb-003-070/T2/01NVb-003-072-2 echo.mp4
/01NVb/01NVb/Group 1-ECHO + LUS/01NVb-003-070/T3/01NVb-003-072-3 echo.mp4
1.2 Save files in your local machine. For instance, files are organised as follows where "mx19@sie113-lap" is the username with machine name:
mx19@sie133-lap:/media/mx19/vitaluskcl/datasets/echocardiography/videos-echo-annotated-33-subjects$ tree -s
.
├── [ 32768] 01NVb-003-040
│ ├── [ 32768] T1
│ │ ├── [ 1070] 01nvb-003-040-1-4cv.json
│ │ └── [ 985197916] 01NVb-003-040-1 echo.mp4
│ ├── [ 32768] T2
│ │ ├── [ 990] 01nvb-003-040-2-4cv.json
│ │ └── [ 1378718854] 01NVb-003-040-2 echo.mp4
│ └── [ 32768] T3
├── [ 32768] 01NVb-003-041
│ ├── [ 32768] T1
│ │ ├── [ 990] 01nvb-003-041-1-4cv.json
│ │ └── [ 1146822377] 01NVb-003-041-1 echo.mp4
│ ├── [ 32768] T2
│ │ ├── [ 990] 01nvb-003-041-2-4cv.json
│ │ └── [ 654004200] 01NVb-003-041-2 echo.mp4
│ └── [ 32768] T3
│ ├── [ 1148] 01nvb-003-041-3-4cv.json
│ ├── [ 106323225] 01NVb-003-041-3 echo cont_mp4_
│ └── [ 621610199] 01NVb-003-041-3 echo.mp4
├── [ 32768] 01NVb-003-042
│ ├── [ 32768] T1
│ │ ├── [ 906] 01nvb-003-042-1-4cv.json
│ │ └── [ 1169134134] 01NVb-003-042-1 echo.mp4
│ ├── [ 32768] T2
│ │ ├── [ 906] 01nvb-003-042-2-4cv.json
│ │ └── [ 725567484] 01NVb-003-042-2 echo.mp4
│ └── [ 32768] T3
│ ├── [ 1072] 01nvb-003-042-3-4cv.json
│ └── [ 809756791] 01NVb-003-042-3 echo.mp4
2.1 Open the VIA software in your favorite internet web-browser (tested in firefox-92.0 (64-bit) in Ubuntu20.04).
2.2 Open json files are saved in this repository and are located at:
mx19@sie133-lap:/media/mx19/vitaluskcl/datasets/echocardiography/videos-echo-annotated-33-subjects/01NVb-003-052/T1$ ls -lr
total 930976
-rw-r--r-- 1 mx19 mx19 953257316 Jan 26 2022 '01NVb-003-052-1 echo.mp4'
-rw-r--r-- 1 mx19 mx19 990 Aug 12 15:29 01NVb-003-052-1-4CV.json
NOTE you can bookmark the path of your files in 'nautiulus', file browsers, to have a quicker accessibility to the files.
2.3 Select paths of video files and verify annotations.
NOTE you can bookmark the path of your files in 'nautiulus', file browsers, to have a quicker accessibility to the files.
2.4 Verify annotations
With your mouse scroll the time line of the video to verify annotation(s).
2.5 Save annotations in json files and only leave two json files (last most updates files).
NOTE you can bookmark the path of your files in 'nautiulus', file browsers, to have a quicker accessibility to the files.
See README in json_files path for further details.
Run validation-of-4cv-labels.ipynb, see further documentations here.