Merge pull request #188 from KMarshallX:marshall-patch-1031-2

minor changes

documentation/tta_readme.md

@@ -11,7 +11,7 @@ mkdir ./pretrained_models/
 Download the pre-trained model from osf:
 
 ```bash
-osf -p abk4p fetch /osfstorage/pretrained_models/manual_ep1000_0925 ./pretrained_models/manual_ep1000_0925
+osf -p abk4p fetch /osfstorage/pretrained_models/manual_ep1000_1029 ./pretrained_models/manual_ep1000_1029
 ```
 
 

notebooks/Module_Prediction.ipynb

@@ -19,9 +19,9 @@
     "cd ./../saved_models/\n",
     "\n",
     "# Each line of code below corresponds to a pre-trained model provide by us\n",
-    "osf -p abk4p fetch /pretrained_models/manual_ep5000_0621\n",
-    "osf -p abk4p fetch /pretrained_models/om1_ep5000_0711\n",
-    "osf -p abk4p fetch /pretrained_models/om2_ep5000_0711\n",
+    "osf -p abk4p fetch /pretrained_models/manual_ep1000_1029\n",
+    "osf -p abk4p fetch /pretrained_models/om1_ep1000_1029\n",
+    "osf -p abk4p fetch /pretrained_models/om2_ep1000_1029\n",
     "```\n"
    ]
   },
@@ -42,7 +42,7 @@
     "import os\n",
     "os.chdir('./../saved_models/')\n",
     "\n",
-    "!osf -p abk4p fetch /pretrained_models/manual_ep1000_0925 ./test_model\n",
+    "!osf -p abk4p fetch /pretrained_models/manual_ep1000_1029 ./test_model\n",
     "# !osf -p abk4p fetch /pretrained_models/om1_ep1000_1029 ./test_model\n",
     "# !osf -p abk4p fetch /pretrained_models/om2_ep1000_1029 ./test_model"
    ]

notebooks/Module_TestTimeAdaptation.ipynb

@@ -19,7 +19,7 @@
     "cd ./../saved_models/\n",
     "\n",
     "# Each line of code below corresponds to a pre-trained model provide by us\n",
-    "osf -p abk4p fetch /pretrained_models/manual_ep1000_0925\n",
+    "osf -p abk4p fetch /pretrained_models/manual_ep1000_1029\n",
     "osf -p abk4p fetch /pretrained_models/om1_ep1000_1029\n",
     "osf -p abk4p fetch /pretrained_models/om2_ep1000_1029\n",
     "```\n"
@@ -42,7 +42,7 @@
     "import os\n",
     "os.chdir('./../saved_models/')\n",
     "\n",
-    "!osf -p abk4p fetch /pretrained_models/manual_ep1000_0925 ./test_model\n",
+    "!osf -p abk4p fetch /pretrained_models/manual_ep1000_1029 ./test_model\n",
     "# !osf -p abk4p fetch /pretrained_models/om1_ep1000_1029\n",
     "# !osf -p abk4p fetch /pretrained_models/om2_ep1000_1029"
    ]

tests/test_prediction_module.sh

@@ -41,7 +41,7 @@ mkdir ./pretrained_models/
 pip install osfclient
 osf -p nr6gc fetch /osfstorage/twoEchoTOF/raw/GRE_3D_400um_TR20_FA18_TE7p5_14_sli52_FCY_GMP_BW200_32.nii ./data/images/sub-001.nii
 #pretrained model download
-osf -p abk4p fetch /osfstorage/pretrained_models/manual_ep1000_0925 ./pretrained_models/manual_ep1000_0925
+osf -p abk4p fetch /osfstorage/pretrained_models/manual_ep1000_1029 ./pretrained_models/manual_ep1000_1029
 osf -p abk4p fetch /osfstorage/pretrained_models/om1_ep1000_1029 ./pretrained_models/om1_ep1000_1029
 osf -p abk4p fetch /osfstorage/pretrained_models/om2_ep1000_1029 ./pretrained_models/om2_ep1000_1029
 
@@ -55,7 +55,7 @@ echo "Path to output: "$path_to_output""
 path_to_preprocessed_images="./data/preprocessed_imgs/"
 echo "Path to preprocessed images: "$path_to_preprocessed_images""
 
-path_to_pretrained_model="./pretrained_models/manual_ep1000_0925"
+path_to_pretrained_model="./pretrained_models/manual_ep1000_1029"
 echo "Path to pretrained model: "$path_to_pretrained_model""
 
 echo "[DEBUG]: testing prediction module without preprocessing:"

tests/test_tta_module.sh

@@ -59,7 +59,7 @@ echo "Path to proxy labels: "$path_to_proxy_labels""
 path_to_preprocessed_images="./data/preprocessed_imgs/"
 echo "Path to preprocessed images: "$path_to_preprocessed_images""
 
-path_to_pretrained_model="./pretrained_models/manual_ep1000_0925"
+path_to_pretrained_model="./pretrained_models/manual_ep1000_1029"
 echo "Path to pretrained model: "$path_to_pretrained_model""
 
 n_epochs=5