RetinaNet model augmented

.gitignore

@@ -2,6 +2,19 @@ src/data-coco/*
 src/data-yolo/*
 src/data_axondeepseg_sem/*
 src/runs
+src/output
+
+src/train_figures
+src/output_predictions
+
+src/retinaNet/wandb/*
+src/retinaNet/output
+src/retinaNet/constants/__pycache__
+src/retinaNet/__pycache__
+
+src/__pycache__
+src/constants/__pycache__
+src/.DS_Store
 
 detectron2/*
 venv/*

README.md

@@ -2,14 +2,15 @@
 
 This project focuses on preprocessing and segmenting axons and myelin from microscopy images stored in the BIDS format. It leverages OpenCV for image manipulation and is designed to work with object detection models like YOLO or RetinaNet.
 
-## Features
-
+## Overview
+### General:
 * Loads BIDS-formatted microscopy images.
 * Automatically adjusts pixel values based on metadata.
 * Resizes and pads images to fit object detection model input sizes.
 * Addinded
 * Includes a `utils.py` file with helper functions for easy preprocessing.
 
+
 ## Getting Started
 
 ### Prerequisites
@@ -35,6 +36,12 @@ This project focuses on preprocessing and segmenting axons and myelin from micro
 
 ### Running scripts
    ```bash
+### Old yolo model:
    cd src
    python preprocessing.py
    python yolo_train.py
+
+### Specific script for RetinaNet model:
+   ```bash
+   cd src
+   python -m retinaNet.retinaNet_train

requirements.txt

@@ -7,4 +7,5 @@ pandas
 scikit-image
 ultralytics
 tqdm
-scikit-learn
+scikit-learn
+wandb

src/constants/data_constants.py

@@ -1 +1,6 @@
-SEM_DATASET_URL = "https://github.com/axondeepseg/data_axondeepseg_sem"
+SEM_DATASET_URL = "https://github.com/axondeepseg/data_axondeepseg_sem"
+
+SEM_DATA_NAME = "data_axondeepseg_sem"
+TEM_DATA_NAME = "data_axondeepseg_tem"
+SEM = "sem"
+TEM = "tem"

src/data_sem_split.json

@@ -0,0 +1,14 @@
+{
+    "train": [
+      "sub-rat3_sample-data10.png",
+      "sub-rat3_sample-data11.png",
+      "sub-rat2_sample-data5.png",
+      "sub-rat8_sample-V915.png",
+      "sub-rat5_sample-data14.png",
+      "sub-rat4_sample-data12.png",
+      "sub-rat6_sample-data15.png",
+      "sub-rat7_sample-Maxo03img60.png"
+    ],
+    "val": ["sub-rat3_sample-data9.png"],
+    "test": ["sub-rat1_sample-data1.png"]
+}

src/data_tem_split.json

@@ -0,0 +1,166 @@
+{
+    "train": [
+        "sub-nyuMouse26_sample-0007.png",
+        "sub-nyuMouse11_sample-0005.png",
+        "sub-nyuMouse12_sample-0005.png",
+        "sub-nyuMouse15_sample-0005.png",
+        "sub-nyuMouse34_sample-0008.png",
+        "sub-nyuMouse35_sample-0009.png",
+        "sub-nyuMouse36_sample-0004.png",
+        "sub-nyuMouse12_sample-0010.png",
+        "sub-nyuMouse09_sample-0008.png",
+        "sub-nyuMouse36_sample-0005.png",
+        "sub-nyuMouse30_sample-0001.png",
+        "sub-nyuMouse12_sample-0003.png",
+        "sub-nyuMouse31_sample-0001.png",
+        "sub-nyuMouse27_sample-0004.png",
+        "sub-nyuMouse33_sample-0009.png",
+        "sub-nyuMouse07_sample-0008.png",
+        "sub-nyuMouse11_sample-0004.png",
+        "sub-nyuMouse29_sample-0001.png",
+        "sub-nyuMouse14_sample-0005.png",
+        "sub-nyuMouse28_sample-0004.png",
+        "sub-nyuMouse12_sample-0002.png",
+        "sub-nyuMouse33_sample-0005.png",
+        "sub-nyuMouse33_sample-0004.png",
+        "sub-nyuMouse26_sample-0003.png",
+        "sub-nyuMouse28_sample-0008.png",
+        "sub-nyuMouse09_sample-0003.png",
+        "sub-nyuMouse11_sample-0008.png",
+        "sub-nyuMouse35_sample-0002.png",
+        "sub-nyuMouse12_sample-0004.png",
+        "sub-nyuMouse29_sample-0005.png",
+        "sub-nyuMouse27_sample-0002.png",
+        "sub-nyuMouse13_sample-0003.png",
+        "sub-nyuMouse32_sample-0002.png",
+        "sub-nyuMouse14_sample-0001.png",
+        "sub-nyuMouse14_sample-0002.png",
+        "sub-nyuMouse12_sample-0011.png",
+        "sub-nyuMouse32_sample-0006.png",
+        "sub-nyuMouse25_sample-0004.png",
+        "sub-nyuMouse30_sample-0005.png",
+        "sub-nyuMouse36_sample-0008.png",
+        "sub-nyuMouse14_sample-0003.png",
+        "sub-nyuMouse26_sample-0001.png",
+        "sub-nyuMouse13_sample-0002.png",
+        "sub-nyuMouse09_sample-0001.png",
+        "sub-nyuMouse31_sample-0002.png",
+        "sub-nyuMouse13_sample-0006.png",
+        "sub-nyuMouse15_sample-0002.png",
+        "sub-nyuMouse30_sample-0004.png",
+        "sub-nyuMouse10_sample-0001.png",
+        "sub-nyuMouse33_sample-0006.png",
+        "sub-nyuMouse25_sample-0001.png",
+        "sub-nyuMouse25_sample-0005.png",
+        "sub-nyuMouse35_sample-0005.png",
+        "sub-nyuMouse29_sample-0004.png",
+        "sub-nyuMouse30_sample-0003.png",
+        "sub-nyuMouse34_sample-0005.png",
+        "sub-nyuMouse27_sample-0005.png",
+        "sub-nyuMouse14_sample-0004.png",
+        "sub-nyuMouse13_sample-0007.png",
+        "sub-nyuMouse29_sample-0002.png",
+        "sub-nyuMouse28_sample-0001.png",
+        "sub-nyuMouse13_sample-0004.png",
+        "sub-nyuMouse36_sample-0001.png",
+        "sub-nyuMouse29_sample-0009.png",
+        "sub-nyuMouse25_sample-0008.png",
+        "sub-nyuMouse32_sample-0009.png",
+        "sub-nyuMouse10_sample-0003.png",
+        "sub-nyuMouse33_sample-0002.png",
+        "sub-nyuMouse27_sample-0008.png",
+        "sub-nyuMouse36_sample-0003.png",
+        "sub-nyuMouse15_sample-0007.png",
+        "sub-nyuMouse13_sample-0008.png",
+        "sub-nyuMouse34_sample-0004.png",
+        "sub-nyuMouse15_sample-0006.png",
+        "sub-nyuMouse15_sample-0008.png",
+        "sub-nyuMouse26_sample-0004.png",
+        "sub-nyuMouse09_sample-0006.png",
+        "sub-nyuMouse33_sample-0003.png",
+        "sub-nyuMouse30_sample-0002.png",
+        "sub-nyuMouse33_sample-0001.png",
+        "sub-nyuMouse27_sample-0006.png",
+        "sub-nyuMouse27_sample-0007.png",
+        "sub-nyuMouse07_sample-0007.png",
+        "sub-nyuMouse32_sample-0005.png",
+        "sub-nyuMouse25_sample-0006.png",
+        "sub-nyuMouse32_sample-0007.png",
+        "sub-nyuMouse32_sample-0004.png",
+        "sub-nyuMouse28_sample-0009.png",
+        "sub-nyuMouse35_sample-0007.png",
+        "sub-nyuMouse10_sample-0006.png",
+        "sub-nyuMouse07_sample-0001.png",
+        "sub-nyuMouse09_sample-0004.png",
+        "sub-nyuMouse34_sample-0009.png",
+        "sub-nyuMouse32_sample-0003.png",
+        "sub-nyuMouse09_sample-0005.png",
+        "sub-nyuMouse10_sample-0007.png",
+        "sub-nyuMouse32_sample-0001.png",
+        "sub-nyuMouse31_sample-0006.png",
+        "sub-nyuMouse34_sample-0001.png",
+        "sub-nyuMouse13_sample-0005.png",
+        "sub-nyuMouse28_sample-0002.png",
+        "sub-nyuMouse11_sample-0006.png",
+        "sub-nyuMouse26_sample-0005.png",
+        "sub-nyuMouse12_sample-0009.png",
+        "sub-nyuMouse14_sample-0008.png",
+        "sub-nyuMouse30_sample-0009.png",
+        "sub-nyuMouse28_sample-0006.png",
+        "sub-nyuMouse36_sample-0007.png",
+        "sub-nyuMouse35_sample-0001.png",
+        "sub-nyuMouse26_sample-0008.png",
+        "sub-nyuMouse27_sample-0003.png",
+        "sub-nyuMouse10_sample-0002.png",
+        "sub-nyuMouse36_sample-0006.png",
+        "sub-nyuMouse26_sample-0006.png",
+        "sub-nyuMouse30_sample-0008.png",
+        "sub-nyuMouse15_sample-0004.png",
+        "sub-nyuMouse07_sample-0005.png",
+        "sub-nyuMouse31_sample-0003.png",
+        "sub-nyuMouse34_sample-0003.png",
+        "sub-nyuMouse14_sample-0006.png",
+        "sub-nyuMouse30_sample-0006.png",
+        "sub-nyuMouse35_sample-0006.png",
+        "sub-nyuMouse31_sample-0009.png",
+        "sub-nyuMouse10_sample-0005.png",
+        "sub-nyuMouse33_sample-0008.png",
+        "sub-nyuMouse10_sample-0008.png"
+    ],
+    "val": [
+        "sub-nyuMouse29_sample-0007.png",
+        "sub-nyuMouse27_sample-0001.png",
+        "sub-nyuMouse09_sample-0002.png",
+        "sub-nyuMouse14_sample-0007.png",
+        "sub-nyuMouse11_sample-0001.png",
+        "sub-nyuMouse28_sample-0003.png",
+        "sub-nyuMouse26_sample-0002.png",
+        "sub-nyuMouse31_sample-0004.png",
+        "sub-nyuMouse11_sample-0002.png",
+        "sub-nyuMouse11_sample-0007.png",
+        "sub-nyuMouse29_sample-0006.png",
+        "sub-nyuMouse07_sample-0006.png",
+        "sub-nyuMouse34_sample-0002.png",
+        "sub-nyuMouse13_sample-0001.png",
+        "sub-nyuMouse09_sample-0007.png",
+        "sub-nyuMouse07_sample-0002.png"
+    ],
+    "test": [
+        "sub-nyuMouse15_sample-0003.png",
+        "sub-nyuMouse31_sample-0005.png",
+        "sub-nyuMouse35_sample-0003.png",
+        "sub-nyuMouse28_sample-0005.png",
+        "sub-nyuMouse11_sample-0003.png",
+        "sub-nyuMouse10_sample-0004.png",
+        "sub-nyuMouse25_sample-0003.png",
+        "sub-nyuMouse29_sample-0003.png",
+        "sub-nyuMouse15_sample-0001.png",
+        "sub-nyuMouse07_sample-0004.png",
+        "sub-nyuMouse12_sample-0008.png",
+        "sub-nyuMouse36_sample-0002.png",
+        "sub-nyuMouse35_sample-0004.png",
+        "sub-nyuMouse07_sample-0003.png",
+        "sub-nyuMouse31_sample-0007.png",
+        "sub-nyuMouse34_sample-0006.png"
+    ]
+}