From e62ccde0b85a61c69daec68195da2a6b93f4d068 Mon Sep 17 00:00:00 2001
From: thorstenwagner <twa1@posteo.de>
Date: Tue, 5 Dec 2023 15:31:27 +0100
Subject: [PATCH 1/3] add small training tutorial

---
 docs/developer/devs.rst | 21 ++++++++++++++++++++-
 1 file changed, 20 insertions(+), 1 deletion(-)

diff --git a/docs/developer/devs.rst b/docs/developer/devs.rst
index a16b8e1..4413a05 100644
--- a/docs/developer/devs.rst
+++ b/docs/developer/devs.rst
@@ -32,11 +32,30 @@ Now you are in principle set to train your network (see ``How to train TomoTwin`
 How to train TomoTwin
 *********************
 
+Here we describe how to train the SiameseNet (bad name, as it is actually a tripletnetwork). Hardwarewise, 12GB of GPU memory should be enough.
+
+1. Download training and validation data
+
 Training and validation set can be found here:
 
 https://zenodo.org/record/6637456
 
-More will follow soon :-)
+Download and untar training and validation data.
+
+2. Download siamese network config
+
+You find the configuration file here:
+https://github.com/MPI-Dortmund/tomotwin-cryoet/blob/main/resources/configs/config_siamese.json
+
+
+3. Start the training
+
+
+ .. prompt:: bash $
+
+    tomotwin_train.py -v path/train/volumes/ --validvolumes path/valid/volumes/ -o out_train -nc path/to/siamese_network.json --epochs 300
+
+
 
 
 How to evaluate TomoTwin

From a025b58c5c18fdd64064d01d8384802aefcef396 Mon Sep 17 00:00:00 2001
From: thorstenwagner <twa1@posteo.de>
Date: Tue, 5 Dec 2023 15:49:55 +0100
Subject: [PATCH 2/3] make it pretty

---
 docs/developer/devs.rst | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/docs/developer/devs.rst b/docs/developer/devs.rst
index 4413a05..e4d47a5 100644
--- a/docs/developer/devs.rst
+++ b/docs/developer/devs.rst
@@ -35,6 +35,7 @@ How to train TomoTwin
 Here we describe how to train the SiameseNet (bad name, as it is actually a tripletnetwork). Hardwarewise, 12GB of GPU memory should be enough.
 
 1. Download training and validation data
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Training and validation set can be found here:
 
@@ -43,19 +44,20 @@ https://zenodo.org/record/6637456
 Download and untar training and validation data.
 
 2. Download siamese network config
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 You find the configuration file here:
-https://github.com/MPI-Dortmund/tomotwin-cryoet/blob/main/resources/configs/config_siamese.json
 
+https://github.com/MPI-Dortmund/tomotwin-cryoet/blob/main/resources/configs/config_siamese.json
 
 3. Start the training
+^^^^^^^^^^^^^^^^^^^^^
 
+To run it on one GPU do:
 
  .. prompt:: bash $
 
-    tomotwin_train.py -v path/train/volumes/ --validvolumes path/valid/volumes/ -o out_train -nc path/to/siamese_network.json --epochs 300
-
-
+    CUDA_VISIBLE_DEVICES=0 tomotwin_train.py -v path/train/volumes/ --validvolumes path/valid/volumes/ -o out_train -nc path/to/siamese_network.json --epochs 300
 
 
 How to evaluate TomoTwin

From 2196b8165263f85cebcac7cb1a5fd3346a284639 Mon Sep 17 00:00:00 2001
From: thorstenwagner <twa1@posteo.de>
Date: Tue, 5 Dec 2023 15:53:00 +0100
Subject: [PATCH 3/3] make it pretty

---
 docs/developer/devs.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/developer/devs.rst b/docs/developer/devs.rst
index e4d47a5..a2728b0 100644
--- a/docs/developer/devs.rst
+++ b/docs/developer/devs.rst
@@ -53,7 +53,7 @@ https://github.com/MPI-Dortmund/tomotwin-cryoet/blob/main/resources/configs/conf
 3. Start the training
 ^^^^^^^^^^^^^^^^^^^^^
 
-To run it on one GPU do:
+To run it on one GPU for 300 epochs do:
 
  .. prompt:: bash $