extra space

README.md

@@ -1,61 +1,36 @@
-# app-detect-alpha-peak
-Detect individual alpha peak in MEG signals.
+# Find frequency peak of PSD data
 
-# app-detect-alpha-peak documentation
+[![Abcdspec-compliant](https://img.shields.io/badge/ABCD_Spec-v1.1-green.svg)](https://github.com/brain-life/abcd-spec)
+[![Run on Brainlife.io](https://img.shields.io/badge/Brainlife-bl.app.531-blue.svg)](https://doi.org/10.25663/brainlife.app.531)
 
-1) Detect alpha peak frequency for each channel and for the mean over all channels
+## Documentation
+
+Detects peak frequency of PSD for each channel on a given bandwith
+
+1) Detect peak frequency for each channel for a given bandwith
 2) Input file is:
-    * a `.csv` file containing the Power Spectral Densities
+    * a `.tsv` file containing the signal PSD, Power Spectral Densities
 5) Ouput files are:
-    * a `.csv` file containing the alpha peak frequency for each channel and the mean over all channels,
-    * plot of the mean Power Spectral density over all channels,
-    * plot of the mean Power Spectral density for each channel.
+    * a `.tsv` file containing the peak frequency for each channel
+    * a plot with the distribution of all peak frequencies across channels
+    * a plot the PSD frequency peak for each channel (peak found in the psd)
 
-### Authors
-- [Aurore Bussalb](aurore.bussalb@icm-institute.org)
+## Authors
+- [Guiomar Niso](guiomar.niso@ctb.upm.es), Instituto Cajal, CSIC, Spain
 
-### Contributors
-- [Aurore Bussalb](aurore.bussalb@icm-institute.org)
-- [Maximilien Chaumon](maximilien.chaumon@icm-institute.org)
+## Citations
+We kindly ask that you cite the following articles when publishing papers and code using this app. 
 
-### Funding Acknowledgement
-brainlife.io is publicly funded and for the sustainability of the project it is helpful to Acknowledge the use of the platform. We kindly ask that you acknowledge the funding below in your code and publications. Copy and past the following lines into your repository when using this code.
+1. **brainlife. io: A decentralized and open source cloud platform to support neuroscience research**. Hayashi, S., Caron, B. A., et al. & Pestilli, F. (2023). ArXiv. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10274934/
+
+## Funding Acknowledgement
+brainlife.io is publicly funded and for the sustainability of the project we kindly ask that you acknowledge the following funding sources:
 
 [![NSF-BCS-1734853](https://img.shields.io/badge/NSF_BCS-1734853-blue.svg)](https://nsf.gov/awardsearch/showAward?AWD_ID=1734853)
 [![NSF-BCS-1636893](https://img.shields.io/badge/NSF_BCS-1636893-blue.svg)](https://nsf.gov/awardsearch/showAward?AWD_ID=1636893)
 [![NSF-ACI-1916518](https://img.shields.io/badge/NSF_ACI-1916518-blue.svg)](https://nsf.gov/awardsearch/showAward?AWD_ID=1916518)
 [![NSF-IIS-1912270](https://img.shields.io/badge/NSF_IIS-1912270-blue.svg)](https://nsf.gov/awardsearch/showAward?AWD_ID=1912270)
-[![NIH-NIBIB-R01EB029272](https://img.shields.io/badge/NIH_NIBIB-R01EB029272-green.svg)](https://grantome.com/grant/NIH/R01-EB029272-01)
-
-### Citations
-1. Avesani, P., McPherson, B., Hayashi, S. et al. The open diffusion data derivatives, brain data upcycling via integrated publishing of derivatives and reproducible open cloud services. Sci Data 6, 69 (2019). [https://doi.org/10.1038/s41597-019-0073-y](https://doi.org/10.1038/s41597-019-0073-y)
-
-## Running the App 
-
-### On Brainlife.io
-
-This App is still private on Brainlife.io.
-
-### Running Locally (on your machine)
-
-1. git clone this repo
-2. Inside the cloned directory, create `config.json` with the same keys as in `config.json.example` but with paths to your input 
-   files and values of the input parameters. For instance:
-
-```json
-{
-  "fif": "rest1-raw.fif"
-}
-```
-
-3. Launch the App by executing `main`
-
-```bash
-./main
-```
-
-## Output
-
-The output files are a `.csv` file and two plots in `.png`.
+[![NIH-NIBIB-R01EB030896](https://img.shields.io/badge/NIH_NIBIB-R01EB030896-green.svg)](https://grantome.com/grant/NIH/R01-EB030896-01)
 
 
+#### MIT Copyright (c) 2021 brainlife.io The University of Texas at Austin and Indiana University

main

@@ -8,32 +8,36 @@
 #
 # This is the main file run by the brainlife.io orchestration system
 #
-# Author: Franco Pestilli
+# Author: Guiomar Niso, Aurore Bussalb
 
 
 set -e
 set -x
 
 # Make output directories
 mkdir -p out_dir
+mkdir -p out_figs
 
 # Run the actual python code
-singularity exec docker://brainlife/mne:0.23dev python3 detect_alpha_peak.py
+singularity exec docker://brainlife/mne:0.23dev python3 main.py
 
 # Store PSD plot with alpha peak on product.json
 cat << EOF > product.json
 {
     "brainlife": [
-       { 
-           "type": "image/png", 
-	   "name": "Alpha peak on mean spectrum",
-           "base64": "$(base64 -w 0 out_dir/psd_mean.png)"
-       },
-       { 
-           "type": "image/png", 
-	   "name": "Power spectrum for all channels",
-           "base64": "$(base64 -w 0 out_dir/psd_channels.png)"
-       }
-]
+        { 
+            "type": "image/png", 
+	        "name": "Peak frequencies",
+            "base64": "$(base64 -w 0 out_figs/hist_peak_frequency.png)"
+        },
+        { 
+            "type": "image/png", 
+	        "name": "Power spectrum for all channels",
+            "base64": "$(base64 -w 0 out_figs/psd_allchannels.png)"
+        }
+    ]
 }
+
 EOF
+
+