first commit

README.md

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+# Horticultural Temporal Fruit Monitoring via 3D Instance Segmentation and Re-Identification using Point Clouds
+
+```
+python3.8 -m venv venv
+source venv/bin/activate
+pip install -r requirements.txt
+```
+
+### Install MinkowskiEngine
+
+If you don't have it, it's better to install ninja to compile MinkowskiEngine
+```
+pip install ninja
+```
+
+```
+git clone https://github.com/NVIDIA/MinkowskiEngine.git
+cd MinkowskiEngine
+python setup.py install
+```
+
+## Instance Segmentation
+```
+export PYTHONPATH=$(realpath instance_segmentation)
+cd instance_segmentation/mink_pan
+python scripts/run_full_row.py --modelpath {PATH_TO_MODEL}
+```
+
+## Re-Identification
+```
+cd re_identification
+python3 associate.py --data {PATH_TO_DATA_FOLDER} --iou 0.05 
+python3 extractor.py --data {PATH_TO_DATA_FOLDER} --iou 0.05
+python3 train.py --data {PATH_TO_DATA_FOLDER} --iou 0.05 --mode testinst
+```
+
+
+## Visualize Results
+```
+visualize entire test set in 2D
+python3 visualize_clouds.py --data {PATH_TO_DATA_FOLDER} --iou 0.05
+
+visualize entire test set in 2D
+python3 visualize_clouds3D.py --data {PATH_TO_DATA_FOLDER} --iou 0.05
+
+```

instance_segmentation/mink_pan/config/backbone.yaml

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+BACKBONE:
+    DIMENSION: 3
+    INPUT_DIM: 6 # coords + rgb
+    CR: 1 # channel ratio, change feature dimensions
+    CHANNELS: [32, 32, 64, 128, 256, 256, 128, 96, 96]
+    RESOLUTION: 0.0005

instance_segmentation/mink_pan/config/model.yaml

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+EXPERIMENT:
+    ID: mink_panoptic
+
+TRAIN:
+    LR: 0.02
+    MAX_EPOCH: 100
+    BATCH_SIZE: 2
+    BATCH_ACC: 4
+    NUM_WORKERS: 6
+    N_GPUS: -1
+    FREEZE_MODULES: []
+    #FREEZE_MODULES: ['BACKBONE','SEM_HEAD','INS_HEAD']
+    AUG: True
+    SUBSAMPLE: True
+
+MODEL:
+    DATASET: STRAWBERRIES
+
+POST:
+    ALG: MEANSHIFT #HDBSCAN, MEANSHIFT
+    BANDWIDTH: 0.01 #Meanshift
+    MIN_CLUSTER: 5 #hdbscan #10 for nuscenes
+
+LOSS:
+    SEM:
+        WEIGHTS: [2,6] #Ce, Lovasz
+
+STRAWBERRIES:
+    PATH: /home/fusy/Documents/strawberries/DeployStrawberries/data #data/kitti
+    CONFIG: datasets/strawberries.yaml
+    NUM_CLASSES: 2 #Get from yaml
+    IGNORE_LABEL: -1
+    SPACE: # coord limits
+        [[-48.0,48.0],[-48.0,48.0],[-4.0,1.5]]
+    MIN_VOLUME_SPACE: [3,'-pi',-3]
+    MAX_VOLUME_SPACE: [50,'pi',1.5]
+    MINI: False
+    SUB_NUM_POINTS: 400000
+
+KITTI:
+    PATH: data/kitti
+    CONFIG: datasets/semantic-kitti.yaml
+    NUM_CLASSES: 20 #Get from yaml
+    IGNORE_LABEL: 0
+    SPACE: # coord limits
+        [[-48.0,48.0],[-48.0,48.0],[-4.0,1.5]]
+    MIN_VOLUME_SPACE: [3,'-pi',-3]
+    MAX_VOLUME_SPACE: [50,'pi',1.5]
+    MINI: False
+    SUB_NUM_POINTS: 80000
+
+NUSCENES:
+    PATH: data/nuscenes
+    CONFIG: datasets/semantic-nuscenes.yaml
+    NUM_CLASSES: 17 #Get from yaml
+    IGNORE_LABEL: 0
+    SPACE: # coord limits
+        [[-50.0,50.0],[-50.0,50.0],[-5.0,3]]
+    MIN_VOLUME_SPACE: [0,'-pi',-5]
+    MAX_VOLUME_SPACE: [50,'pi',3]
+    MINI: False
+    SUB_NUM_POINTS: 50000