Last modified by robing on 2022/03/25 09:55
From version 79.1
edited by robing
on 2020/05/25 22:10
Change comment: There is no comment for this version
To version 73.1
edited by denker
on 2020/05/08 15:19
Change comment: There is no comment for this version

Summary

Details

Page properties
Author
... ... @@ -1,1 +1,1 @@
1 -XWiki.robing
1 +XWiki.denker
Content
... ... @@ -78,8 +78,6 @@
78 78  
79 79  === ii) Local execution ===
80 80  
81 -//tested only with Linux!//
82 -
83 83  * **Get the code**
84 84  The source code of the pipeline is available via Github: [[INM-6/wavescalephant>>https://github.com/INM-6/wavescalephant]] and can be cloned to your machine ([[how to get started with Github>>https://guides.github.com/activities/hello-world/]]).
85 85  
... ... @@ -88,10 +88,6 @@
88 88  In the wavescalephant git repository, there is an environment file ([[pipeline/environment.yaml>>https://drive.ebrains.eu/smart-link/1a0b15bb-be87-46ee-b838-4734bc320d20/]]) specifying the required packages and versions. To build the environment, we recommend using conda ([[how to get started with conda>>https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html]]).
89 89  ##conda env create ~-~-file environment.yaml
90 90  conda activate wavescalephant_env##
91 -
92 -Make sure that neo and elephant were installed as their Github development version, and if necessary add them manually to the environment.
93 -##pip install git+https:~/~/github.com/NeuralEnsemble/elephant.git
94 -pip install git+https:~/~/github.com/NeuralEnsemble/python-neo.git##
95 95  
96 96  )))
97 97  * **Edit the settings**
... ... @@ -119,20 +119,8 @@
119 119  
120 120  All results are stored in the path specified in the //settings.py// file. The folder structure reflects the structuring of the pipeline into stages and blocks. All intermediate results are stored as //.nix// files using the [[Neo data format>>https://neo.readthedocs.io/en/stable/]] and can be loaded with ##neo.NixIO('/path/to/file.nix').read_block()##. Additionally, most blocks produce a figure, and each stage a report file, to give an overview of the execution log, parameters, intermediate results, and to help with debugging. The final stage (//stage05_wave_characterization//) stores the results as[[ //pandas.DataFrames//>>https://pandas.pydata.org/]] in //.csv// files, separately for each measure as well as in a combined dataframe for all measures.
121 121  
122 -**Examples of the output figures (for IDIBAPS dataset)**
116 +== Outlook ==
123 123  
124 -* Stage 01 - [[example signal traces and metadata>>https://drive.ebrains.eu/smart-link/cf2fa914-260d-4d61-a2da-03ea07b7f9be/]]
125 -* Stage 02 - [[background substraction>>https://drive.ebrains.eu/smart-link/586d2f3c-591b-4dfb-94ee-8c0e28050dc4/]]
126 -* Stage 02 - [[logMUA estimation>>https://drive.ebrains.eu/smart-link/c92e4b0c-0938-44e8-9f8d-00522796b2fd/]]
127 -* Stage 02 - [[processed signal trace>>https://drive.ebrains.eu/smart-link/26ed27c6-de56-4b48-a57b-f70aab629197/]]
128 -* Stage 03 - [[amplitude distribution>>https://drive.ebrains.eu/smart-link/8ba80293-ba75-4a37-8a8f-05d44cf6f65c/]]
129 -* Stage 03 - [[UP state detection>>https://drive.ebrains.eu/smart-link/ab172be0-178e-4153-a3e6-b4bace32dd50/]]
130 -* Stage 04 - [[trigger clustering>>https://drive.ebrains.eu/smart-link/4a1f0169-8b43-49ce-80c8-f2fa0f4d50d3/]]
131 -* Stage 05 - [[planar velocities>>https://drive.ebrains.eu/smart-link/f4de8073-cb40-47a7-bc82-f97d36dbae25/]]
132 -* Stage 05 - [[directionality>>https://drive.ebrains.eu/smart-link/5485032d-0121-4cde-9ea2-3e0af3f12178/]]
133 -
134 -=== Outlook ===
135 -
136 136  * Using the **KnowledgeGraph API **to insert data directly from the Knowledge Graph into the pipeline and also register and store the corresponding results as Analysis Objects. Such Analysis Objects are to incorporate **Provenance Tracking, **using [[fairgraph>>https://github.com/HumanBrainProject/fairgraph]],** **to record the details of the processing and analysis steps.
137 137  * Adding support for the pipeline to make use of **HPC** resources when running on the collab.
138 138  * Further extending the available **methods** to address a wider variety of analysis objectives and support the processing of other datatypes. Additional documentation and guides should also make it easier for non-developers to contribute new method blocks.
Collaboratory.Apps.Collab.Code.CollabClass[0]
Public
... ... @@ -1,1 +1,1 @@
1 -Yes
1 +No
XWiki.XWikiRights[3]
Allow/Deny
... ... @@ -1,1 +1,0 @@
1 -Allow
Levels
... ... @@ -1,1 +1,0 @@
1 -view
Users
... ... @@ -1,1 +1,0 @@
1 -XWiki.XWikiGuest
XWiki.XWikiRights[4]
Allow/Deny
... ... @@ -1,1 +1,0 @@
1 -Allow
Groups
... ... @@ -1,1 +1,0 @@
1 -XWiki.XWikiAllGroup
Levels
... ... @@ -1,1 +1,0 @@
1 -view