resolving readme issue; updated tests.sh

Former-commit-id: 37ae3ca092a709f420a503584103457db6840785
spoonsso · Jan 25, 2021 · 696b4d8 · 696b4d8
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diff --git a/README.md b/README.md
@@ -34,33 +34,19 @@ cd dannce
 
 2. If you do not already have it, install [Anaconda](https://www.anaconda.com/products/individual).
 
-<<<<<<< HEAD
 3. Set up a new Anaconda environment with the following configuration: \
-=======
-2. Set up a new Anaconda environment with the following configuration: \
->>>>>>> sampleID_fix
 `conda create -n dannce python=3.7 cudatoolkit=10.1 cudnn ffmpeg`
 
 4. Activate the new Anaconda environment: \
 `conda activate dannce`
 
-<<<<<<< HEAD
 5. Install PyTorch: \
 `conda install pytorch=1.7 -c pytorch`
 
 6. Update setuptools: \
 `pip install -U setuptools`
 
 7. Install DANNCE with the included setup script from within the base repository directory: \
-=======
-4. Install PyTorch: \
-`conda install pytorch=1.7 -c pytorch`
-
-5. Update setuptools: \
-`pip install -U setuptools`
-
-6. Install DANNCE with the included setup script from within the base repository directory: \
->>>>>>> sampleID_fix
 `pip install -e .`
 
 Then you should be ready to try the quickstart demo! \

diff --git a/setup.py b/setup.py
@@ -13,11 +13,7 @@
         "scikit-image",
         "matplotlib",
         "opencv-python",
-<<<<<<< HEAD
         "tensorflow==2.3.1",
-=======
-        "tensorflow==2.3.0",
->>>>>>> sampleID_fix
         "torch",
         "numpy==1.18"
     ],
@@ -29,4 +25,4 @@
             "com-predict = dannce.cli:com_predict_cli",
         ]
     },
-)
+)
diff --git a/tests/tests.sh b/tests/tests.sh
@@ -22,56 +22,56 @@ python setup.py install
 
 cd tests/configs
 
-# echo "Testing COMfinder training"
-# com-train config_com_mousetest.yaml --com-finetune-weights=../../demo/markerless_mouse_1/COM/weights/
+echo "Testing COMfinder training"
+com-train config_com_mousetest.yaml --com-finetune-weights=../../demo/markerless_mouse_1/COM/weights/
 
-# echo "Testing COMfinder training w/ mono"
-# com-train config_com_mousetest.yaml --mono=True
+echo "Testing COMfinder training w/ mono"
+com-train config_com_mousetest.yaml --mono=True
 
-# echo "Testing COMfinder prediction"
-# com-predict config_com_mousetest.yaml
-# python ../compare_predictions.py ../touchstones/COM3D_undistorted_masternn.mat ../../demo/markerless_mouse_1/COM/predict_test/com3d.mat 0.001
+echo "Testing COMfinder prediction"
+com-predict config_com_mousetest.yaml
+python ../compare_predictions.py ../touchstones/COM3D_undistorted_masternn.mat ../../demo/markerless_mouse_1/COM/predict_test/com3d.mat 0.001
 
-# echo "Testing COMfinder prediction, 3 cams"
-# #cp ./label3d_temp_dannce_3cam.mat ./alabel3d_temp_dannce.mat
-# com-predict config_com_mousetest.yaml --downfac=4
+echo "Testing COMfinder prediction, 3 cams"
+#cp ./label3d_temp_dannce_3cam.mat ./alabel3d_temp_dannce.mat
+com-predict config_com_mousetest.yaml --downfac=4
 
 echo "Testing COMfinder prediction, 5 cams"
 cp ./label3d_temp_dannce_5cam.mat ./alabel3d_temp_dannce.mat
 com-predict config_com_mousetest.yaml --downfac=2
 
-# echo "Testing DANNCE training, finetune_MAX"
-# dannce-train config_mousetest.yaml --net-type=MAX --dannce-finetune-weights=../../demo/markerless_mouse_1/DANNCE/weights/weights.rat.MAX/
+echo "Testing DANNCE training, finetune_MAX"
+dannce-train config_mousetest.yaml --net-type=MAX --dannce-finetune-weights=../../demo/markerless_mouse_1/DANNCE/weights/weights.rat.MAX/
 
-# echo "Testing DANNCE training, finetune_AVG"
-# dannce-train config_mousetest.yaml --net-type=AVG --dannce-finetune-weights=../../demo/markerless_mouse_1/DANNCE/weights/
+echo "Testing DANNCE training, finetune_AVG"
+dannce-train config_mousetest.yaml --net-type=AVG --dannce-finetune-weights=../../demo/markerless_mouse_1/DANNCE/weights/
 
-# echo "Testing DANNCE training, AVG net from scratch"
-# dannce-train config_mousetest.yaml --net=unet3d_big_expectedvalue --train-mode=new --n-channels-out=22
+echo "Testing DANNCE training, AVG net from scratch"
+dannce-train config_mousetest.yaml --net=unet3d_big_expectedvalue --train-mode=new --n-channels-out=22
 
-# echo "Testing DANNCE training, MAX net from scratch"
-# dannce-train config_mousetest.yaml --net=unet3d_big --train-mode=new --n-channels-out=22
+echo "Testing DANNCE training, MAX net from scratch"
+dannce-train config_mousetest.yaml --net=unet3d_big --train-mode=new --n-channels-out=22
 
-# echo "Testing DANNCE training, AVG net continued"
-# dannce-train config_mousetest.yaml --net-type=AVG --train-mode=continued --dannce-finetune-weights=../../demo/markerless_mouse_1/DANNCE/train_results/AVG/
+echo "Testing DANNCE training, AVG net continued"
+dannce-train config_mousetest.yaml --net-type=AVG --train-mode=continued --dannce-finetune-weights=../../demo/markerless_mouse_1/DANNCE/train_results/AVG/
 
-# echo "Testing DANNCE training, MAX net continued"
-# dannce-train config_mousetest.yaml --net=finetune_MAX --train-mode=continued --dannce-finetune-weights=../../demo/markerless_mouse_1/DANNCE/train_results/
+echo "Testing DANNCE training, MAX net continued"
+dannce-train config_mousetest.yaml --net=finetune_MAX --train-mode=continued --dannce-finetune-weights=../../demo/markerless_mouse_1/DANNCE/train_results/
 
-# echo "Testing DANNCE training, AVG MONO from scratch"
-# dannce-train config_mousetest.yaml --net-type=AVG --train-mode=new --net=unet3d_big_expectedvalue --mono=True --n-channels-out=22
+echo "Testing DANNCE training, AVG MONO from scratch"
+dannce-train config_mousetest.yaml --net-type=AVG --train-mode=new --net=unet3d_big_expectedvalue --mono=True --n-channels-out=22
 
-# echo "Testing DANNCE training, AVG MONO from scratch w/ augmentation"
-# dannce-train config_mousetest.yaml --net-type=AVG --train-mode=new --net=unet3d_big_expectedvalue --mono=True --n-channels-out=22 --augment-brightness=True --augment-continuous-rotation=True --augment-hue=True
+echo "Testing DANNCE training, AVG MONO from scratch w/ augmentation"
+dannce-train config_mousetest.yaml --net-type=AVG --train-mode=new --net=unet3d_big_expectedvalue --mono=True --n-channels-out=22 --augment-brightness=True --augment-continuous-rotation=True --augment-hue=True
 
-# echo "Testing DANNCE training, AVG MONO finetune"
-# dannce-train config_mousetest.yaml --net-type=AVG --mono=True --dannce-finetune-weights=../../demo/markerless_mouse_1/DANNCE/weights/weights.rat.AVG.MONO/
+echo "Testing DANNCE training, AVG MONO finetune"
+dannce-train config_mousetest.yaml --net-type=AVG --mono=True --dannce-finetune-weights=../../demo/markerless_mouse_1/DANNCE/weights/weights.rat.AVG.MONO/
 
-# echo "Testing DANNCE training, AVG MONO finetune"
-# dannce-train config_mousetest.yaml --net-type=AVG --mono=True --dannce-finetune-weights=../../demo/markerless_mouse_1/DANNCE/weights/weights.rat.AVG.MONO/ --drop-landmark=[5,7]
+echo "Testing DANNCE training, AVG MONO finetune"
+dannce-train config_mousetest.yaml --net-type=AVG --mono=True --dannce-finetune-weights=../../demo/markerless_mouse_1/DANNCE/weights/weights.rat.AVG.MONO/ --drop-landmark=[5,7]
 
-# echo "Testing DANNCE prediction, MONO"
-# dannce-predict config_mousetest.yaml --net-type=AVG --dannce-predict-model=../../demo/markerless_mouse_1/DANNCE/train_test/fullmodel_weights/fullmodel_end.hdf5 --mono=True
+echo "Testing DANNCE prediction, MONO"
+dannce-predict config_mousetest.yaml --net-type=AVG --dannce-predict-model=../../demo/markerless_mouse_1/DANNCE/train_test/fullmodel_weights/fullmodel_end.hdf5 --mono=True
 
 # 32 NVOX --------- 
 #MONO
@@ -94,14 +94,14 @@ com-predict config_com_mousetest.yaml --downfac=2
 
 # -----------
 
-# cp ./label3d_temp_dannce.mat ./alabel3d_temp_dannce.mat
-# echo "Testing DANNCE AVG prediction"
-# dannce-predict config_mousetest.yaml --net-type=AVG
-# python ../compare_predictions.py ../touchstones/save_data_AVG_torch_nearest.mat ../../demo/markerless_mouse_1/DANNCE/predict_test/save_data_AVG0.mat 0.001
+cp ./label3d_temp_dannce.mat ./alabel3d_temp_dannce.mat
+echo "Testing DANNCE AVG prediction"
+dannce-predict config_mousetest.yaml --net-type=AVG
+python ../compare_predictions.py ../touchstones/save_data_AVG_torch_nearest.mat ../../demo/markerless_mouse_1/DANNCE/predict_test/save_data_AVG0.mat 0.001
 
-# echo "Testing DANNCE MAX prediction"
-# dannce-predict config_mousetest.yaml --net-type=MAX --expval=False --dannce-predict-model=../../demo/markerless_mouse_1/DANNCE/train_results/weights.12000-0.00014.hdf5
-# python ../compare_predictions.py ../touchstones/save_data_MAX_torchnearest_newtfroutine.mat ../../demo/markerless_mouse_1/DANNCE/predict_test/save_data_MAX0.mat 0.001
+echo "Testing DANNCE MAX prediction"
+dannce-predict config_mousetest.yaml --net-type=MAX --expval=False --dannce-predict-model=../../demo/markerless_mouse_1/DANNCE/train_results/weights.12000-0.00014.hdf5
+python ../compare_predictions.py ../touchstones/save_data_MAX_torchnearest_newtfroutine.mat ../../demo/markerless_mouse_1/DANNCE/predict_test/save_data_MAX0.mat 0.001
 
 
 echo "PASSED WITHOUT ERROR"