PALMS

Platform for Analysis and Labeling of Medical Time Series
This software features the following pubication: https://www.mdpi.com/1424-8220/20/24/7302/htm

Fiducials annotation: https://vimeo.com/490142964

Partitions annotation: https://vimeo.com/490143050

Quality annotation

LICENSE

Copyright (c) 2020 Stichting imec Nederland ([email protected])
https://www.imec-int.com/en/imec-the-netherlands
@license GPL-3.0+ http://spdx.org/licenses/GPL-3.0+
See COPYING, README.

ATTRIBUTION

This software includes (modified) third party open source software components distributed under the MIT license:
./gui/display_panel.py,
./gui/model.py,
./gui/plot_area.py,
./gui/rendering.py,
./gui/tracking.py,
./gui/view_table.py,
./gui/viewer.py
For license text see ./gui/LICENSE.txt

This software includes (modified) third party open source software components distributed under the MIT license:
./utils/QRSDetectorOffline.py
See license in the source code.

This software makes use of the GPL-3.0+ licensed PyQt library (Riverbank Computing Limited).
For more info see https://www.riverbankcomputing.com/static/Docs/PyQt5/

The two example data files (see Examples below) contain raw data from:

• IEEE TBME Respiratory Rate Benchmark data set: http://www.capnobase.org/database/pulse-oximeter-ieee-tbme-benchmark/
• BIDMC PPG and Respiration Dataset: https://physionet.org/content/bidmc/1.0.0/

HOW TO START USING THE TOOL

A) Using source code:
1.1 Install Python 3.6 from https://www.python.org/ftp/python/3.6.8/python-3.6.8-amd64.exe as Admin and add Python to the PATH
1.2 (advised) create a separate virtual environment in the root folder of the project: https://www.jetbrains.com/help/pycharm/creating-virtual-environment.html
1.3 Install required packages: pip install -r requirements.txt
1.4 Run the tool: python __main__.py

B) Using portable (executable) version:
1.1 PALMS.exe and required dependencies for portable execution of the software is available in !portable\

2. A pop-up window with available databases will appear (see also Examples below)
3. Select a database and a file to annotate

EXAMPLES

PALMS is provided with 2 ready-to-run examples for annotating:

• PPG peak and foot (see logic\databases\EXAMPLE_PPG.py)
• respiration signal fiducials (see logic\databases\EXAMPLE_RESPIRATION.py)

Small data chunks for these examples to work are stored in docs\examples\

PALMS also provides a configuration file logic\databases\ECG_Physionet2011.py to make possible ECG quality annotation of Physionet data. In order to run this example one has to download some datafiles from the corresponding Physionet database and place them into docs\examples\examples_Physionet2011\

DOCUMENTATION

User_manual (may be outdated): docs\user_manual.pdf
Demo video (may be outdated):

1. Browse: https://vimeo.com/490143111
2. Annotation: https://vimeo.com/490142964
3. Partitions: https://vimeo.com/490143050

Instructions for creating new database-configurations: logic\databases\EXAMPLE_...

HOW TO CREATE AN EXECUTABLE VERSION OF THE TOOL

Portable version allows someone without even Python installed to use the software.

1. Execute in the console: pyinstaller --onefile --name PALMS main.py
2. Modify PALMS.spec created in the root to add non-python files necessary to run the app:
   2.1 Add the following block of code:
     ...
     added_files = [
       ("docs\examples", "docs\examples" ),
       ("docs\user_manual.pdf","docs"),
       ("gui\LICENSE.txt", "gui"),
       ("config\shortcuts.json","config"),
       ("config\icons\PALMS.png","config\icons"),
       ("config\AnnotationConfig","config\AnnotationConfig"),
       ("config\EpochConfig","config\EpochConfig"),
       ("logic\databases\EXAMPLE_PPG.py","logic\databases"),
       ("logic\databases\EXAMPLE_RESPIRATION.py","logic\databases")
       ]
     ...
   2.2 Below find a line 'datas=[],' and assign:
     datas = added_files
     ...

2.3 including ("config\shortcuts.json","config") will make shortcuts fixed, won't be possible to change in portable version. Omitting this will require a config\shortcuts.json to be near executable when running (or default is used)
3. Execute in the console: pyinstaller --onefile PALMS.spec
4. PALMS.exe is ready in dist\
5. In order PALMS.exe to work and find all necessary files it should be given to an annotator-expert in the following folder with accordingly configured newDatabase.py. (PALMS.exe will contain all necessary dependencies to show examples)

annotation_task\
  |-- data_folder\
    |-- file_to_annotate
  |-- PALMS.exe
  |-- newDatabase.py (contains newDatabase class, see EXAMPLES)
  |-- config.json