Removed completed TODOs.

DG_Approximation.py

@@ -15,16 +15,16 @@ TODO: Ask whether all quadratures depend on freely chosen num_nodes
 TODO: Contemplate saving training data for each IC separately
 TODO: Contemplate removing TrainingDataGenerator class
 TODO: Ask why no fine mesh is used for calculate_coarse_projection()
+TODO: Contemplate keeping Theoretical threshold over all degrees (only p)
 
 Urgent:
-TODO: Investigate self-referencing in classes -> Done
-TODO: Apply self-referencing in Mesh -> Done
-TODO: Refactor random_stencil() -> Done
-TODO: Fix bug applying wrong boundary condition when generating ANN
-    training data -> Done
-TODO: Find errors in centering for ANN training -> Done
-TODO: Remove stencil_length as instance variable -> Done
-TODO: Note down TCD adjustment TODOs -> Done
+TODO: Change heaviside random to uniform(-100, 100)
+TODO: Adjust Heaviside to have non-symmetric values (left- and right_value)
+TODO: Rename 'adjustment' to 'shift'
+TODO: Induce shift in IC class
+TODO: Give option to set discontinuity to cell boundary
+TODO: Fix typo in LinearAbsolute
+TODO: Introduce middle_factor for two-sided Heaviside
 TODO: Adapt TCD from Soraya
     (Dropbox->...->TEST_troubled-cell-detector->Troubled_Cell_Detector)
 TODO: Move plot_approximation_results() into plotting script
@@ -38,6 +38,8 @@ TODO: Check whether 'projection' is always a ndarray
 TODO: Force input_size for each ANN model to be stencil length
 
 Critical, but not urgent:
+TODO: Introduce env files for each SM rule
+TODO: Add images to report
 TODO: Add verbose output
 TODO: Outsource scripts into separate directory
 TODO: Check whether all instance variables are sensible

Troubled_Cell_Detector.py

@@ -2,14 +2,19 @@
 """
 @author: Laura C. Kühle, Soraya Terrab (sorayaterrab)
 
-TODO: Add TC condition to only flag cell if left-adjacent one is flagged as
-    well
-TODO: Determine max_value for Theoretical only over 0th degree (?)
-TODO: Introduce Adjusted Outer Fence method in Boxplot using global_mean
-TODO: Introduce overlapping cell for adjacent folds in Boxplot
-TODO: Introduce lower extreme outliers in Boxplot
 TODO: Adjust TCs for wavelet detectors (sliding window over all cells instead
     of every second)
+TODO: Introduce Adjusted Outer Fence method in Boxplot using global_mean
+TODO: Introduce overlapping cell for adjacent folds in Boxplot
+TODO: Introduce lower/upper extreme outliers in Boxplot
+    (each cell is also checked for neighboring domains if existing)
+TODO: Determine max_value for Theoretical only over highest degree
+TODO: Check if indexing in wavelets is correct
+TODO: Extract fold computing from TC checking
+TODO: Add ThresholdDetector
+TODO: Add TC condition to only flag cell if left-adjacent one is flagged as
+    well (remove this condition)
+TODO: Check coarse_projection calculation for indexing errors
 TODO: Adjust Boxplot approach (adjacent cells, outer fence, etc.)
 TODO: Give detailed description of wavelet detection