Merge pull request #3 from pohl-michel/cmig_revision

Cmig revision

Author: pohl-michel

.gitattributes

@@ -1,4 +1,7 @@
-*.fig binary
+# end of lines
+*.py text eol=lf
+
+# binary files*.fig binary
 *.mat binary
 *.mdl binary diff merge=mlAutoMerge
 *.mdlp binary
@@ -26,3 +29,7 @@
 *.pdf binary
 *.png binary
 *.xlsx binary
+
+# To help for code review
+*.IMA linguist-generated=true
+*.dcm linguist-generated=true

.gitignore

@@ -6,6 +6,14 @@
 !/Image_prediction/input_imgs/2D images/3. sq sl010 sag Xcs=80/
 !/Image_prediction/input_imgs/2D images/4. sq sl014 sag Xcs=165/
 !/Image_prediction/input_imgs/2D images/5. sq sl014 sag Xcs=95/
+!/Image_prediction/input_imgs/2D images/2020-11-10_KS81_Nav_Pur_1/
+!/Image_prediction/input_imgs/2D images/2020-11-12_QN76_Nav_Pur_1/
+!/Image_prediction/input_imgs/2D images/2020-11-17_CS31_Nav_Pur_2/
+!/Image_prediction/input_imgs/2D images/2020-11-17_JY02_Nav_Pur_2/
+!/Image_prediction/input_imgs/2D images/2020-11-23_ON65_Nav_Pur_2/
+!/Image_prediction/input_imgs/2D images/2020-11-23_PS11_Nav_Pur_1/
+!/Image_prediction/input_imgs/2D images/2020-11-25_II29_Nav_Pur_1/
+!/Image_prediction/input_imgs/2D images/2020-11-26_NE38_Nav_Pur_1/
 
 # Ignoring txt files inside the "2D images" subdireectory
 /Image_prediction/input_imgs/2D images/*.txt
@@ -30,6 +38,9 @@ create_4Dmri_dataset_spec-file.txt
 /Time_series_forecasting/c. Prediction results (images)
 /Time_series_forecasting/d. RNN variables (temp)
 /Time_series_forecasting/e. Log txt files
+/Time_series_forecasting/models/*
+!/Time_series_forecasting/models/training_with_eth_dataset/
+!/Time_series_forecasting/models/training_with_magdeburg_dataset/
 
 # Excluding gifs inside the visualisation folder except a few ones
 /Image_prediction/visualization/*.gif
@@ -42,3 +53,9 @@ create_4Dmri_dataset_spec-file.txt
 *.bak
 *.asv
 *.jpg
+
+# Ignore Python bytecode
+__pycache__/
+*.pyc
+*.pyo
+*.pyd

.prettierrc

@@ -0,0 +1,3 @@
+{
+    "tabWidth": 4
+}

.pylintrc

@@ -0,0 +1,2 @@
+[TYPECHECK]
+generated-members=torch.*

.vscode/extensions.json

@@ -0,0 +1,11 @@
+{
+    "recommendations": [
+        "gimly81.matlab",
+        "ms-python.python",
+        "ms-toolsai.jupyter",
+        "eamodio.gitlens",
+        "ms-vscode-remote.remote-wsl",
+        "ms-python.black-formatter",
+        "esbenp.prettier-vscode"
+    ]
+}

.vscode/launch.json

@@ -0,0 +1,17 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Population Transformer Test",
+            "type": "debugpy",
+            "request": "launch",
+            "module": "other_prediction_functions.train_population_transformer",
+            "cwd": "${workspaceFolder}/Time_series_forecasting",
+            "args": ["--tuning", "--gpu", "--njobs", "1"],
+            "console": "integratedTerminal"
+        }
+    ]
+}

.vscode/settings.json

@@ -0,0 +1,17 @@
+{
+    "[python]":{
+        "editor.formatOnType": false,
+        "editor.defaultFormatter": "ms-python.black-formatter",
+        "editor.formatOnSave": true,
+    },
+    "[notebook]":{
+        "editor.defaultFormatter": "ms-python.black-formatter",
+    },
+    "notebook.formatOnSave.enabled": true,
+    "[json]":{
+        "editor.defaultFormatter": "esbenp.prettier-vscode",
+        "editor.formatOnSave": true,
+        "editor.tabSize": 4
+    },
+    "editor.rulers": [120]
+}

Image_prediction/1. Optical flow calculation/compute_2Dof.m

@@ -1,4 +1,4 @@
-function eval_OF_results = compute_2Dof( OF_par, im_par, path_par)
+function eval_OF_results = compute_2Dof( OF_par, im_par, path_par, eval_OF_results)
 % Computes the optical flow (OF) between t = 1 and im_par.nb_im,
 % and saves the result in a mat file.
 % The optical flow is saved rather than returned as an output.
@@ -9,6 +9,9 @@
 % Version : v1.1
 % License : 3-clause BSD License
 
+    if nargin < 4
+        eval_OF_results = struct();
+    end
 
     fprintf('OPTICAL FLOW CALCULATION \n');
     fid = 1; % screen display

Image_prediction/2. Optical flow evaluation/analyze_OF_param_influence.m

@@ -1,4 +1,4 @@
-function analyze_OF_param_influence( rms_error_all_seq, OFeval_par, beh_par, path_par)
+function analyze_OF_param_influence( rms_error_all_seq, OFeval_par, beh_par, path_par, nb_optim_imgs)
 % Returns information about the influence of each hyper-parameter set in the grid search on the DVF accuracy in a txt file.
 %
 % Possible steps to improve the code:
@@ -139,8 +139,8 @@ function analyze_OF_param_influence( rms_error_all_seq, OFeval_par, beh_par, pat
         else
             fprintf(fid, 'evaluation in the entire image \n');
         end
-        fprintf(fid, '\n');
-        
+        fprintf(fid, 'optimization using the first %d images\n', nb_optim_imgs);
+        fprintf(fid, '\n');        
     end
 
     fprintf(fid, 'Lines : Parameter variation \n'); 

Image_prediction/2. Optical flow evaluation/write_OFhyperpar_optim_log_file.m

@@ -28,6 +28,7 @@ function write_OFhyperpar_optim_log_file( beh_par, OFeval_par, path_par, im_par,
     else
         fprintf(fid, 'evaluation in the entire image \n');
     end
+    fprintf(fid, 'optimization using the first %d images\n', im_par.nb_im);
     fprintf(fid, '\n');
 
     fprintf(fid, 'Gradient method : %s \n', OFeval_par.grad_meth_str);