p7ayfu77 · bgilsrud · Sep 17, 2022
diff --git a/.gitignore b/.gitignore
@@ -18,8 +18,5 @@ htmlcov/
 .coverage*
 *.npz
 *.tif*
-*.hdf5
-*.h5
 *.zip
 *.tfevents.*
-config.json
diff --git a/README.md b/README.md
@@ -12,7 +12,7 @@ Please see the documentation at http://csbdeep.bioimagecomputing.com/doc/.
 
 You will need a few things to get started:
 
-1. An NVIDIA GPU and relevant CUDA libraries installed - great video guide here [Install Tensorflow GPU and PyTorch in Windows 10 - Generalized method](https://www.youtube.com/watch?v=86Mq-h8tazc)
+1. An NVIDIA GPU is recommended and relevant CUDA libraries installed - great video guide here [Install Tensorflow GPU and PyTorch in Windows 10 - Generalized method](https://www.youtube.com/watch?v=86Mq-h8tazc). Astro CSBDeep can be run using only a CPU but it may be slow.
 2. Python 3 installed
 3. Create and venv environment preferabley named `.venv` by running `python -m venv .venv` and activating it `.venv\Scripts\activate`
 3. Install the pip3 requirement found in the `requirements.txt` file by running `pip3 install -r requirements.txt`
@@ -61,6 +61,15 @@ Open up the notebook `AstroNoise2Noise.ipynb` and configure the same python inte
 
 Happy coding and clear skies!
 
+## Running on linux
+```
+python3 -m venv .venv
+. .venv/bin/activate
+pip install -r requirements.txt
+python3 ./astrodenoisypygui.py
+```
+When the gui loads, select the denoise model v0.4.0-01. 
+
 ## Contributors
 
 Want to say a big thank you to the CSBDeep team who provided their framework along with great examples to get started.
@@ -70,4 +79,4 @@ To date, further much appreciated thanks go to contributions from:
 * Michael Kitange - ongoing validation and contributions to code
 * JimmyTheChicken#2719 - STF Tone Mapping Algorithm
 
-More to come!
+More to come!
diff --git a/models/v0.4.0-01/config.json b/models/v0.4.0-01/config.json
@@ -0,0 +1 @@
+{"n_dim": 2, "axes": "YXC", "n_channel_in": 1, "n_channel_out": 1, "train_checkpoint": "weights_best.h5", "train_checkpoint_last": "weights_last.h5", "train_checkpoint_epoch": "weights_now.h5", "probabilistic": false, "unet_residual": true, "unet_n_depth": 4, "unet_kern_size": 3, "unet_n_first": 32, "unet_last_activation": "linear", "unet_input_shape": [null, null, 1], "train_loss": "hdr2", "train_epochs": 30, "train_steps_per_epoch": 75, "train_learning_rate": 0.0004, "train_batch_size": 128, "train_tensorboard": true, "train_reduce_lr": {"factor": 0.5, "patience": 10, "min_delta": 0}}
diff --git a/models/v0.4.0-01/weights_best.h5 b/models/v0.4.0-01/weights_best.h5
diff --git a/requirements.txt b/requirements.txt
@@ -1,5 +1,5 @@
-tensorflow-gpu==2.7.0
-keras==2.7.0
+tensorflow-gpu==2.8.0
+keras==2.8.0
 jupyter==1.0.0
 tensorboard==2.8.0
 astropy==5.0.1
@@ -9,4 +9,7 @@ tqdm==4.62.3
 six==1.16.0
 numpy==1.22.1
 numexpr==2.8.1
-imagecodecs==2022.2.22
+imagecodecs==2022.2.22
+kivy==2.1.0
+protobuf==3.20.0
+scipy==1.9.1
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		{"n_dim": 2, "axes": "YXC", "n_channel_in": 1, "n_channel_out": 1, "train_checkpoint": "weights_best.h5", "train_checkpoint_last": "weights_last.h5", "train_checkpoint_epoch": "weights_now.h5", "probabilistic": false, "unet_residual": true, "unet_n_depth": 4, "unet_kern_size": 3, "unet_n_first": 32, "unet_last_activation": "linear", "unet_input_shape": [null, null, 1], "train_loss": "hdr2", "train_epochs": 30, "train_steps_per_epoch": 75, "train_learning_rate": 0.0004, "train_batch_size": 128, "train_tensorboard": true, "train_reduce_lr": {"factor": 0.5, "patience": 10, "min_delta": 0}}