Codacy warning fixes

examples/ROOT_files/ROOT_STIR_consistency/DebugScripts/debug_consistency_with_root.py

@@ -124,7 +124,7 @@ def point_cloud_3D_all(dict_of_data_handlers):
     """
     generates a single plot with pointclouds of generated LOR-positions, original source-positions and tolerance-whiskers for all sources
     Args:
-        dict_of_data_handlers (dictionary containing objects of type ROOTConsistencyDataHandler): dictionary of objects containing all relevant data for the plot
+        dict_of_data_handlers (dict[int, ROOTConsistencyDataHandler]): dictionary of objects containing all relevant data for the plot
     """
 
     fig = plt.figure(figsize=(10, 10))

examples/ROOT_files/ROOT_STIR_consistency/README.md

@@ -1,65 +1,57 @@
 # TOF consistency checks for STIR
+
 ## Authors: Elise Emond & Robert Twyman
 
-Copyright (C) 2022, University College London
-  This file is part of STIR.
+Copyright (C) 2022, 2024 University College London
+This file is part of STIR.
 SPDX-License-Identifier: Apache-2.0
 See STIR/LICENSE.txt for details
 
-These files were included to :
-* Test non-TOF ROOT and STIR consistency, particularly the rotation.
-* Test the TOF STIR implementation is correct.
+These files are included to :
+
+- Test non-TOF ROOT and STIR consistency, particularly the rotation.
+- Test the TOF STIR implementation is correct.
 
-See src/recon_test/test_consistency_with_GATE.cxx. This test is run
-automatically when using ctest.
+See src/recon_test/test_consistency_with_GATE.cxx. This test is run automatically when using ctest.
 
-Directories
------
+## Directories
 
 - `SourceFiles/`: Contains 8 `generate_image` parameter files and GATE macro files for the emission source positions. One pair of files for each simulation.
 - `Gate_macros/`: Contains the GATE macro files for generating the data.
 - `DebugScripts/`: Contains scripts for better understanding the tests.
 
-
-FILES
-----
+## FILES
 
 - `README.md`: This file.
 - `root_header_test_template.hroot`: Template file for generating root header files for each of the test list mode data files that are generated by GATE.
 - `run_pretest_script.sh`: The main script for generating the data (requires GATE). This script runs GATE simulations for each test emission and generates the root header files for them.
 
+---
 
-______
+## Methodology
 
-Methodology
-----
- 1. Get the ROOT data: either
-     - Run `./run_pretest_script.sh` in the terminal to generate the ROOT files (requires Gate) for different point sources, or
-    - Download the ROOT data and proceed without Gate simulation. This is done
-    by ctest when the STIR build was configured with `DOWNLOAD_ZENODO_TEST_DATA=ON`.
-
- 2. Run the STIR test: `src/recon_test/test_consistency_with_GATE` (Best via ctest).
-    This test should tell you whether it failed or not by testing if the LOR passes by, 
-    or close to, the original point source position.
- 3. Run the python scripts in `DebugScripts` to better understand errors and to give a more in-depth analysis.
+1.  Get the ROOT data: either
+    - Run `./run_pretest_script.sh` in the terminal to generate the ROOT files (requires Gate) for different point sources, or
+    - Download the ROOT data and proceed without Gate simulation. This is done by ctest when the STIR build was configured with `DOWNLOAD_ZENODO_TEST_DATA=ON`.
+2.  Run the STIR test: `src/recon_test/test_consistency_with_GATE` (Best via ctest). This test should tell you whether it failed or not by testing if the LOR passes by, or close to, the original point source position.
+3.  Run the python scripts in `DebugScripts` to better understand errors and to give a more in-depth analysis.
 
+---
 
-_____
+## SOURCE POSITION CONFIGURATION
 
-SOURCE POSITION CONFIGURATION
------
 In GATE coordinates (`mm`), the point sources positions are as follows:
 
-| ID | x | y | z | comment |
-| :---: | :---: | :----: | :---: | :---: |
-| **1** | 0 | 0 | 0 | center scanner |
-| **2** | 190 | 0 | 0 | +x |
-| **3** | 0 | 190 | 0 | +y  |
-| **4** | 95 | 95 | 0 | +x +y |
-| **5** | 0 | 0 | 70 | +z | 
-| **6** | 190 | 0 | 70 | +x +z |
-| **7** | 0 | 190 | 70 |  +y +z |
-| **8** | 95 | 95 | 70 |  +x +y +z |
+|  ID   |  x  |  y  |  z  |    comment     |
+| :---: | :-: | :-: | :-: | :------------: |
+| **1** |  0  |  0  |  0  | center scanner |
+| **2** | 190 |  0  |  0  |       +x       |
+| **3** |  0  | 190 |  0  |       +y       |
+| **4** | 95  | 95  |  0  |     +x +y      |
+| **5** |  0  |  0  | 70  |       +z       |
+| **6** | 190 |  0  | 70  |     +x +z      |
+| **7** |  0  | 190 | 70  |     +y +z      |
+| **8** | 95  | 95  | 70  |    +x +y +z    |
 
 _Note_: The activity of testIDs 5-8 are 10x that of 1-4 because of the large z-shift.
 
@@ -70,9 +62,8 @@ This is given by:
 
 ```
 stir_z = (L-d)/2 + gate_z
-``` 
+```
 
 where `L` is the scanner z-length (`157.16 mm`) and `d = 6.54mm` is the distance between rings .
 For the data currently used in this test, `(L-d)/2 = 75.31mm`.
-There are no translations in x or y. 
-
+There are no translations in x or y.

src/recon_test/test_consistency_with_GATE.cxx

@@ -164,7 +164,7 @@ class GATEConsistencyTests : public RunTests
   //! The number of nonTOF LORs that failed the closest approach test.
   int num_failed_nonTOF_lor_events = 0;
   //! The threshold distance for the closest approach test.
-  double nonTOF_distance_threshold;
+  double nonTOF_distance_threshold = 0.f;
 
   /// TOF VARIABLES
   //! A vector to store the coordinates of the maximum voxels for each LOR.
@@ -226,7 +226,7 @@ setup()
   num_events_tested = 0;
 
   // Find threshold for failure
-  nonTOF_distance_threshold = 1.5 * norm(grid_spacing); // Using norm(grid_spacing) as a nonTOF_distance_threshold
+  nonTOF_distance_threshold = 1.5 * norm(grid_spacing);
   {
     // With the default files, we found that 3.3*norm(grid_spacing) is a reasonable limit.
     // We try to generalise this to other data (although it will likely need further