Add depth map estimation bundle

[franklinwk]

Add depth map estimation bundle based on: https://github.com/SNRLab/Visually_Navigated_Bronchoscopy

[yiheng-wang-nv]

Hi @franklinwk , thanks for posting this ticket. May I know that will you contribute this bundle? If meeting any questions during the developing, feel free to ask here.

[dbericat]

@jjomier ^^

[franklinwk]

I have the metadata and models set up, but I'm having some issue figuring out the inference configuration and what from it is needed (dataset directory? data list?).

https://github.com/franklinwk/model-zoo/tree/dev/models/bronchoscopic_depthmap_estimation

[dbericat]

@wyli @Nic-Ma is there anyone from the core dev team that can help @franklinwk finish his first MONAI CAI Bundle?

It's the first case coming from MONAI Stream. Visually Navigated Bronchoscopy for depth pose estimation using a 3cGAN. Really cool use case. :)

[yiheng-wang-nv]

Hi @franklinwk , please refer to: https://github.com/Project-MONAI/model-zoo/blob/dev/CONTRIBUTING.md#preferred-files-and-keys

In inference config file (if exists), please include the following keys: bundle_root (root directory of your bundle), device (required device), network_def (definition of the network components), inferer, and if there are any output files, the directory key should be defined as output_dir (click here for instance).

[yiheng-wang-nv]

for the branch you forked, could you submit a draft PR, thus it's easier to review (and help to debug if needed)? Thanks in advance!

[franklinwk]

I've created a draft PR: https://github.com/Project-MONAI/model-zoo/pull/447

My main issue is how to set up inference.json, especially network_def when the model wasn't originally made using MONAI. I'm also unsure how to describe the data format to describe grayscale data.

[yiheng-wang-nv]

Hi @franklinwk ,

especially network_def when the model wasn't originally made using MONAI If the model can be used via pip install, like from external import mymodel, you can write the config like:

"network_def": {
"_target_": "external.mymodel",

This bundle is an actual example.

how to describe the data format to describe grayscale data

May I know that what is the input shape and what is the value range of the data?