From 25cb2478ba850ac2cfb3b22324eda62dc3149fb9 Mon Sep 17 00:00:00 2001
From: EuanPyle <euanpyle@gmail.com>
Date: Mon, 5 Sep 2022 16:10:58 +0100
Subject: [PATCH] Update sample jsons and README

---
 README.md           | 23 ++++++++++++++---------
 predict_config.json |  7 ++++---
 train_config.json   |  5 +++--
 3 files changed, 21 insertions(+), 14 deletions(-)

diff --git a/README.md b/README.md
index 0393e70..09fc35d 100644
--- a/README.md
+++ b/README.md
@@ -97,7 +97,8 @@ Create an empty file called `train_config.json`, copy-paste the following templa
   "unet_n_first": 16,
   "learning_rate": 0.0004,
   "model_name": "model_name",
-  "path": "./"
+  "path": "./",
+  "gpu_id": 0
 }
 ```
 
@@ -112,6 +113,7 @@ Create an empty file called `train_config.json`, copy-paste the following templa
 * `"learning_rate"`: Learning rate of the model training.
 * `"model_name"`: Name of the model.
 * `"path"`: Output path for the model.
+* `"gpu_id"`: This is optional. Provide the GPU ID(s) of the GPUs you wish to use.
 
 #### Run Training:
 To run the training we run the following command:
@@ -123,21 +125,24 @@ You will find a `.tar.gz` file in the directory you specified as `path`. This yo
 Create an empty file called `predict_config.json`, copy-paste the following template and fill it in.
 ```
 {
-  "path": "path/to/your/model.tar.gz",
-  "even": "/path/to/even/tomos/",
-  "odd": "/path/to/odd/tomos/",
-  "n_tiles": [1, 1, 1],
-  "output": "/path/to/output/folder/",
-  "overwrite": false
+  "path": "path/to/your/model/model_name.tar.gz",
+  "even": "/path/to/even.rec",
+  "odd": "/path/to/odd.rec",
+  "n_tiles": [1,1,1],
+  "output": "denoised.rec",
+  "overwrite": False,
+  "gpu_id": 0
 }
 ```
 
 #### Parameters:
 * `"path"`: Path to your model file.
-* `"even"`: Path to directory with even tomograms or a specific even tomogram.
-* `"odd"`: Path to directory with odd tomograms or a specific odd tomogram.
+* `"even"`: Path to directory with even tomograms or a specific even tomogram or a list of specific even tomograms.
+* `"odd"`: Path to directory with odd tomograms or a specific odd tomogram or a list of specific odd tomograms in the same order as the even tomograms.
 * `"n_tiles"`: Initial tiles per dimension. Gets increased if the tiles do not fit on the GPU.
 * `"output"`: Path where the denoised tomograms will be written.
+* `"overwrite"`: Allow previous files to be overwritten.
+* `"gpu_id"`: This is optional. Provide the GPU ID(s) of the GPUs you wish to use.
 
 #### Run Prediction:
 To run the training we run the following command:
diff --git a/predict_config.json b/predict_config.json
index 65318fb..4449f73 100644
--- a/predict_config.json
+++ b/predict_config.json
@@ -1,8 +1,9 @@
 {
-  "model_name": "model_name",
-  "path": "./",
+  "path": "path/to/your/model/model_name.tar.gz",
   "even": "/path/to/even.rec",
   "odd": "/path/to/odd.rec",
   "n_tiles": [1,1,1],
-  "output_name": "denoised.rec"
+  "output": "denoised.rec",
+  "overwrite": False,
+  "gpu_id": 0
 }
diff --git a/train_config.json b/train_config.json
index ffe55c5..cbbfb4e 100644
--- a/train_config.json
+++ b/train_config.json
@@ -8,5 +8,6 @@
   "unet_n_first": 16,
   "learning_rate": 0.0004,
   "model_name": "model_name",
-  "path": "./"
-}
\ No newline at end of file
+  "path": "./",
+  "gpu_id": 0
+}