Add a script to automatically update all demo figures/ visualisations

[s-sd]

Subject of the feature

A script to automatically update all demo figures/ visualisations. Any time a number of demos are changed (e.g. a checkpoints are updated), all the visualisations/ figures need to be updated. Currently this needs to be done manually, so a script can help to update all using the single script.

What are you trying to do and how would you want to do it differently?

Add a script which automatically generated visualisations for all demos.

Is it something you currently you cannot do?

Yes

Is this related to an issue/problem?

There was a need to update all figures in PR #602

Has the feature been requested before? If yes, please provide a link to the issue.

No

If the feature request is approved, would you be willing to submit a PR? (Help can be
provided if you need assistance submitting a PR)

Yes

[s-sd]

@mathpluscode I'll just test my script and make a few modification and then add. Where would you suggest to add this?

[mathpluscode]

@mathpluscode I'll just test my script and make a few modification and then add. Where would you suggest to add this?

under demos/ maybe? so you can name as update_visualization.py or whatever you like XD.

[NMontanaBrown]

Is this related to #626 ? EDIT: No it is unlikely.

However, @s-sd can you please make your issue description more informative?

It says: "A script to automatically update demo figures/ visualisations" - why is this necessary? I went in and read #602, the models are being updated with registry... I assume we are going to be modifying the provided models? Can you add your reasoning to the issue description?

[mathpluscode]

Also,

Is this related to #626 ? EDIT: No it is unlikely.

However, @s-sd can you please make your issue description more informative?

It says: "A script to automatically update demo figures/ visualisations" - why is this necessary? I went in and read #602, the models are being updated with registry... I assume we are going to be modifying the provided models? Can you add your reasoning to the issue description?

When the checkpoint files for prediction changes due to

• we change the model structure (like i did in Issue #557: refactoring models #602)
• we update the model config or ckpts (like all recent updates)

we need to update the visualization images correspondingly

[mathpluscode]

btw, @s-sd the visualization.png are now under demos/xxxx/logs_predict/ directly, not related to a specific prediction run, I suggest to store it inside the folder same as other nifti files, what do you think

[s-sd]

Is this related to #626 ? EDIT: No it is unlikely.

However, @s-sd can you please make your issue description more informative?

It says: "A script to automatically update demo figures/ visualisations" - why is this necessary? I went in and read #602, the models are being updated with registry... I assume we are going to be modifying the provided models? Can you add your reasoning to the issue description?

@NMontanaBrown updated the description.

btw, @s-sd the visualization.png are now under demos/xxxx/logs_predict/ directly, not related to a specific prediction run, I suggest to store it inside the folder same as other nifti files, what do you think

@mathpluscode good point. Will change this.

@YipengHu @mathpluscode I'll add the labels where they're available as mentioned in Issue #621. The order should be image then corresponding label then image then label and so on or all images first then all labels?

[mathpluscode]

Is this related to #626 ? EDIT: No it is unlikely.

However, @s-sd can you please make your issue description more informative?

It says: "A script to automatically update demo figures/ visualisations" - why is this necessary? I went in and read #602, the models are being updated with registry... I assume we are going to be modifying the provided models? Can you add your reasoning to the issue description?

@NMontanaBrown updated the description.

btw, @s-sd the visualization.png are now under demos/xxxx/logs_predict/ directly, not related to a specific prediction run, I suggest to store it inside the folder same as other nifti files, what do you think

@mathpluscode good point. Will change this.

@YipengHu @mathpluscode I'll add the labels where they're available as mentioned in Issue #621. The order should be image then corresponding label then image then label and so on or all images first then all labels?

OH, regarding the labels, be careful that some data have multiple labels....
Actually, we can choose to show one label only! and for the order I guess columns can be

1. moving_image
2. fixed_image
3. pred_fixed_image
4. moving_label
5. fixed_label
6. pred_fixed_label
7. DDF if applicable
8. DVF if applicable

[mathpluscode]

another point, for now you call demo_data to download the latest checkpoint, but the data script handle more than checkpoint, so it takes lots of time for downloading data. should we use parser to provide a "download checkpoint only" mode?

[s-sd]

another point, for now you call demo_data to download the latest checkpoint, but the data script handle more than checkpoint, so it takes lots of time for downloading data. should we use parser to provide a "download checkpoint only" mode?

@mathpluscode On one hand if people do not already have the data downloaded and we use the "download checkpoint only" mode in the update_vis.py script then to run it successfully, the user would have to first run all demo_data.py scripts separately. But on the other hand, if data is already downloaded then it saves a lot of time. So I am not completely sure which would be best. Up to you, feel free to create a new issue and assign to me if you think that we need it and I'll add the checkpoint only mode.

[mathpluscode]

another point, for now you call demo_data to download the latest checkpoint, but the data script handle more than checkpoint, so it takes lots of time for downloading data. should we use parser to provide a "download checkpoint only" mode?

@mathpluscode On one hand if people do not already have the data downloaded and we use the "download checkpoint only" mode in the update_vis.py script then to run it successfully, the user would have to first run all demo_data.py scripts separately. But on the other hand, if data is already downloaded then it saves a lot of time. So I am not completely sure which would be best. Up to you, feel free to create a new issue and assign to me if you think that we need it and I'll add the checkpoint only mode.

Oh I see, then it should be more like, in data script, we skip the downloading if the file exists? Emmm but here we removed the downloaded files lol.... ok leave this for another ticket.