updates notebooks, virtual env and few other minor changes (#15)

.gitignore

@@ -10,6 +10,7 @@
 **/test**.avi.csv
 **/testvideo*
 **/basicvideo.*
+**/raw.githubusercontent.com
 
 ## temporal TeX files
 **/*.aux
@@ -28,5 +29,9 @@
 **/*.out
 **/main.pdf
 
+## temp models
+**/best_model.h5
+**/best_transforer_model.h5
+
 ## others
 *.ipynb_checkpoints

dependencies/README.md

@@ -11,14 +11,17 @@ $ mamba activate ai-surg-skills-VE
 $ python package_versions.py 
 
 
-python: 3.8.16 | packaged by conda-forge | (default, Feb  1 2023, 16:01:55) 
-[GCC 11.3.0]
-opencv: 4.7.0
+2023-07-19 01:32:02.612388: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  SSE4.1 SSE4.2 AVX AVX2 AVX_VNNI FMA
+To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
+2023-07-19 01:32:02.772598: I tensorflow/core/util/port.cc:104] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable `TF_ENABLE_ONEDNN_OPTS=0`.
+python: 3.10.12 | packaged by conda-forge | (main, Jun 23 2023, 22:40:32) [GCC 12.3.0]
+opencv: 4.8.0
 torch: 2.0.0.post200
 torch cuda_is_available: True
 torch cuda version: 11.2
 torch cuda.device_count  1
-PIL version: 9.5.0
+PIL version: 10.0.0
+Tensorflow version: 2.11.1
 
 ```
 

dependencies/packages_versions.py

@@ -9,6 +9,7 @@
 #import plotly
 import PIL
 #import pandas
+import tensorflow as tf
 
 print(f'python: {sys.version}')
 print(f'opencv: {cv2.__version__}')
@@ -22,3 +23,4 @@
 #print(f'plotly version: {plotly.__version__}')
 print(f'PIL version: {PIL.__version__}')
 #print(f'pandas version: {pandas.__version__}')
+print(f'Tensorflow version: {tf.__version__}')

dependencies/ve.yml

@@ -1,13 +1,13 @@
 ## USAGE
-## conda update --all                           ## UPDATE ALL base PACKAGES
-## conda list -n *VE # show list of installed packages
-## conda env create -f *ve.yml   		    ## INSTALL
-## conda env update --file *ve.yml --prune  	## UPDATE
-## conda activate *VE   			            ## ACTIVATE
-## conda remove -n *VE --all			        ## REMOVE
+## mamba update --all                           ## UPDATE ALL base PACKAGES
+## mamba list -n *VE # show list of installed packages
+## mamba env create -f *ve.yml   		    ## INSTALL
+## mamba env update --file *ve.yml --prune  	## UPDATE
+## mamba activate *VE   			            ## ACTIVATE
+## mamba remove -n *VE --all			        ## REMOVE
 
 ## QUICK TEST OF THE AVAILABILITY OF CUDA
-## conda activate *VE
+## mamba activate ai-surg-skills-VE
 ## python
 ## import torch
 ## torch.cuda.is_available()
@@ -31,3 +31,4 @@ dependencies:
      - scikit-image
      - notebook
      - thread6 #from threading import Thread
+     - pydot

scripts/README.md

@@ -1 +1,9 @@
 # Scripts
+
+
+1. Running notebooks
+```
+cd $HOME/repositories/in2research2023/scripts
+mamba activate ai-surg-skills-VE && jupyter notebook --browser=firefox
+```
+