Merge branch 'main' into improve-slides

data/models/README.md

@@ -1,23 +1,31 @@
-# Data
+# Models
 
 ## `onnx` models
 
 ### Trained models
-ColonSegNet-07112023-2359.onnx (20MB or 20,067,028) Model was create with > colon_seg_net_test.ipynb Open In Colab
 
+| Model (Size)  | Download | Notebook |
+| -- |-- | -- |
+| ColonSegNet-07112023-2359.onnx (20MB or 20,067,028) | [:link:](TOADD) | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1s-eKu6QjaV54jva_ylG1VxwCj1B8nwJ3) |
+| Add Your model (copy and paste this line) | [:link:](TOADD) | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/TOADD) |
+
+
+### Examples to download models in your local machine
+* ColonSegNet-07112023-2359.onnx
 ```
 wget https://raw.githubusercontent.com/SciKit-Surgery/cmicHACKS2/main/data/ColonSegNet-07112023-2359.onnx
 ```
 
-### Original model
+* Original model
 ```
 wget --content-disposition 'https://api.ngc.nvidia.com/v2/resources/org/nvidia/team/clara-holoscan/holoscan_colonoscopy_sample_data/20230222/files?redirect=true&path=colon.onnx' -O colon.onnx
 ```
 
 ```
 wget --content-disposition 'https://api.ngc.nvidia.com/v2/resources/org/nvidia/team/clara-holoscan/holoscan_colonoscopy_sample_data/20230222/files?redirect=true&path=colon_exam_720x576.mp4' -O colon_exam_720x576.mp4
 ```
-* References 
+
+## References 
 https://catalog.ngc.nvidia.com/orgs/nvidia/teams/clara-holoscan/resources/holoscan_colonoscopy_sample_data/files
 
 

data/polyp-dataset/README.md

@@ -1,16 +1,19 @@
 # Kvasir-SEG dataset
 > The Kvasir-SEG dataset (size 46.2 MB) contains 1000 polyp images and their corresponding ground truth from the Kvasir Dataset v2. The resolution of the images contained in Kvasir-SEG varies from 332x487 to 1920x1072 pixels. The images and its corresponding masks are stored in two separate folders with the same filename. The image files are encoded using JPEG compression, and online browsing is facilitated. The bounding box (coordinate points) for the corresponding images are stored in a JSON file. https://datasets.simula.no/downloads/kvasir-seg.zip
 
+
 ```
 wget https://datasets.simula.no/downloads/kvasir-seg.zip #(45M)
+unzip kvasir-seg.zip
+rm kvasir-seg.zip
 ```
 
 ## Converting images to video 
-
 ```
 cd data/polyp-dataset/Kvasir-SEG/images
-ffmpeg -framerate 1 -pattern_type glob -i 'ck*.jpg' -c:v libx264 ../../out.mp4
+ffmpeg -framerate 1 -pattern_type glob -i 'Kvasir-SEG/images/ck*.jpg' -c:v libx264 out.mp4
 ```
 
 
+## References 
 https://stackoverflow.com/questions/22965569/convert-from-jpg-to-mp4-by-ffmpeg  

program/day-one/README.md

@@ -22,6 +22,15 @@ git clone [email protected]:SciKit-Surgery/cmicHACKS2.git   ##using password-protec
       E --> F[Close Bug Issue]
 ```
 
+4. Rebasing your branch with the latest changes of main 
+```
+git checkout main
+git pull origin main
+git checkout RB
+git rebase main
+git push --force origin RB
+```
+
 ## 13:00 - 15:00 > Get familiar with your data
 > Get familiar with your data (download data, label data, etc.)
 
@@ -42,6 +51,7 @@ https://datasets.simula.no/downloads/kvasir-seg.zip
 ![fig](ml-pipeline.png)
 
 * Train segmentation models > [colon_seg_net_train.ipynb](colon_seg_net_train.ipynb) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1s-eKu6QjaV54jva_ylG1VxwCj1B8nwJ3)    
+* Add your model and notebook [here](../../data/models/README.md#onnx-models)
 
 ## References