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Part 2: GAN for image translation #7

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f81e155
init commit
Tonks684 Jul 17, 2024
296fcf3
setup changes
Tonks684 Jul 17, 2024
0931e99
Update README.md
Tonks684 Jul 18, 2024
e550fe7
setup fixes
Tonks684 Jul 18, 2024
6a28ea9
Merge branch 'main' of github.com:Tonks684/dlmbl_material into main
Tonks684 Jul 18, 2024
ce19ee2
added instance evaluation
Tonks684 Jul 18, 2024
479958a
add svg as well as pdf
Tonks684 Jul 19, 2024
fd724ae
final tweeks
Tonks684 Jul 19, 2024
e5dc3d3
Merge branch 'main' of github.com:Tonks684/dlmbl_material
Tonks684 Jul 19, 2024
3a752a1
solution notebook
Tonks684 Jul 19, 2024
d18df70
Add files via upload
Tonks684 Jul 19, 2024
1a4995c
Add files via upload
Tonks684 Jul 19, 2024
f8b778c
working solution
Tonks684 Jul 19, 2024
e7f5105
Merge branch 'main' of github.com:Tonks684/dlmbl_material into main
Tonks684 Jul 19, 2024
76e5860
solution changes
Tonks684 Jul 19, 2024
4450193
setup
Tonks684 Jul 19, 2024
61aee93
debug
Tonks684 Jul 19, 2024
6ea3d47
final part
Tonks684 Jul 19, 2024
6c88f65
solution
Tonks684 Jul 19, 2024
d01d565
solution
Tonks684 Jul 22, 2024
b76d6d1
jpg fixes
Tonks684 Jul 22, 2024
3afdc58
solution updates
Tonks684 Jul 22, 2024
61a62cf
solution tweeks
Tonks684 Jul 22, 2024
ff24757
visualise samples
Tonks684 Jul 22, 2024
611e085
sample animation
Tonks684 Jul 23, 2024
9202b4d
notebooks
Tonks684 Jul 23, 2024
00db3b1
new yml
Tonks684 Jul 23, 2024
c9fecfc
import bugs
Tonks684 Jul 23, 2024
1533c60
setup
Tonks684 Jul 23, 2024
33f3857
Update README.md
Tonks684 Jul 23, 2024
dbaae06
setup
Tonks684 Jul 23, 2024
ca00752
Update README.md
Tonks684 Jul 23, 2024
d73145c
workign setup.sh
Tonks684 Jul 23, 2024
de5c0e9
setup windows to linux
Tonks684 Jul 23, 2024
4a93d82
setup windows to linux
Tonks684 Jul 23, 2024
721dd72
Merge pull request #1 from Tonks684/master
Tonks684 Jul 23, 2024
8323d2f
Update setup.sh
Tonks684 Jul 23, 2024
7715149
Merge pull request #2 from Tonks684/Tonks684-patch-1
Tonks684 Jul 23, 2024
8209a81
solution
Tonks684 Jul 23, 2024
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Merge pull request #3 from Tonks684/master
Tonks684 Jul 23, 2024
0d33bb5
Update README.md
Tonks684 Jul 23, 2024
3824c66
changes before meeting 250724
Tonks684 Jul 23, 2024
bc555a1
solution updates
Tonks684 Jul 23, 2024
f1f9f37
Merge pull request #4 from Tonks684/master
Tonks684 Jul 23, 2024
91f5da9
Add files via upload
Tonks684 Jul 24, 2024
6cbb8cc
solution updates
Tonks684 Jul 24, 2024
f2a1c94
Merge pull request #5 from Tonks684/master
Tonks684 Jul 24, 2024
1c2d3c9
initial commit to open a PR by modifying the setup.sh
edyoshikun Aug 2, 2024
d92d5ed
modifying setup to work with the same conda env as part 1.
edyoshikun Aug 2, 2024
c8846b9
making relative paths and attemptint to run code.
edyoshikun Aug 2, 2024
33a529a
dummy test
Tonks684 Aug 8, 2024
a92104c
download weights, tensorboards and dataset
Tonks684 Aug 9, 2024
d9ba83c
load env, dl weights, tensorboards, dataset
Tonks684 Aug 9, 2024
509c4b0
load env, dl weights, tensorboards, dataset
Tonks684 Aug 9, 2024
e75cb8c
load env, dl weights, tensorboards, dataset
Tonks684 Aug 9, 2024
9de0694
ignore previous commits. This is the latest setup.sh which works for …
Tonks684 Aug 9, 2024
e00afc1
should be able to train and load a pretrained model
Tonks684 Aug 9, 2024
3fa1a6c
initial commit to open a PR by modifying the setup.sh
edyoshikun Aug 2, 2024
a6fa01f
modifying setup to work with the same conda env as part 1.
edyoshikun Aug 2, 2024
a81f1dd
making relative paths and attemptint to run code.
edyoshikun Aug 2, 2024
2a03429
same file structure as part_1
edyoshikun Aug 12, 2024
cb00d7b
Merge branch 'part_2' into dlmbl-part2
edyoshikun Aug 12, 2024
90caab2
cleanup to match part_1
edyoshikun Aug 12, 2024
c455dd1
adding changes to the setup.sh from Sam's prev commit
edyoshikun Aug 12, 2024
0ce77bd
adding dominate
edyoshikun Aug 12, 2024
bce118c
fixing paths. the pix2pix code needs to get some fixed to run this.
edyoshikun Aug 12, 2024
ad31793
taken out content from notebook and added to readme. Also added in in…
Tonks684 Aug 15, 2024
2b6134d
updated to add required packages to 06_image_translation (part1 env)
Tonks684 Aug 15, 2024
fdf6031
numerous updates
Tonks684 Aug 15, 2024
e8caeaa
Merge pull request #8 from dlmbl/pr-7
Tonks684 Aug 15, 2024
20bc2f2
- setup had hardcoded variables to Sam's home.
edyoshikun Aug 19, 2024
5d2f531
commented out unecessary dependencies
edyoshikun Aug 19, 2024
a0b7286
mean_average_precision fix and visualise instance metrics
Tonks684 Aug 19, 2024
c4ec0f6
Merge branch 'dlmbl-part2' of github.com:dlmbl/image_translation into…
Tonks684 Aug 19, 2024
795f17b
integration with part1, download data and pretrained files
Tonks684 Aug 20, 2024
138178d
tested e2e with no bugs on dlmbl node
Tonks684 Aug 20, 2024
0385528
fixing typo on the setup.sh
edyoshikun Aug 21, 2024
44a45a5
adding conda deactivate to setup
edyoshikun Aug 21, 2024
73394b8
- increasing the batch size
edyoshikun Aug 21, 2024
ff09462
- adding ziwen's comments on readme
edyoshikun Aug 23, 2024
eabdd4f
updates based on Ziwen comments
Tonks684 Aug 24, 2024
c521985
Ziwens updates
Tonks684 Aug 24, 2024
3b02cb0
removing merge conflicts
Tonks684 Aug 24, 2024
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37 changes: 5 additions & 32 deletions README.md
Original file line number Diff line number Diff line change
@@ -1,34 +1,7 @@
# Exercise 4: Image translation
## Setup
# Exercise 6: Image translation

Make sure that you are inside of the `image_translation` folder by using the `cd` command to change directories if needed.
This exercise is split into two parts:
- Virtual staining with a regression approach using a UNet [part_1](./part_1/)
- Virtual staining with an generative approach using a GAN [part_2](./part_2/)

Make sure that you can use mamba to switch environments.

```bash
mamba init
```

**Close your shell, and login again.**

Run the setup script to create the environment for this exercise and download the dataset.
```bash
sh setup.sh
```
Activate your environment
```bash
mamba activate 04_image_translation
```

Launch a jupyter environment

```
jupyter notebook
```

...and continue with the instructions in the notebook.

If 04_image_translation is not available as a kernel in jupyter, run
```
python -m ipykernel install --user --name=04_image_translation
```
Look into the directory for the part you will be working on (i.e `part_1` or `part_2`) for further installation and 'how to run' instructions.
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