Merge pull request #83 from Gregor-Mendel-Institute/development

Fixing minor bugs

.github/workflows/container.yml

@@ -6,6 +6,7 @@ on:
         - master
       tags:
         - '*'
+
 env:
   REGISTRY_USER: treeringgenomics
   IMAGE_REGISTRY: quay.io

.gitignore

@@ -3,14 +3,14 @@ data
 datasets
 RUNID
 model_eval
+Quercus_retraining
 laptop_debug.sh
 cluster_debug.sh
 laptop_docker_test.sh
 laptop_singularity_test.sh
 trg-imageprocessing_master.sif
 image-processing_master.sif
 
-
 Dockerfile_with_Cracks
 Docker_commands
 TRG-process.def

CoreProcessingPipelineScripts/CNN/Mask_RCNN/Dockerfile

@@ -8,9 +8,9 @@ RUN micromamba install -y -n base wget -f /home/mambauser/environment.yml && mic
 
 ARG MAMBA_DOCKERFILE_ACTIVATE=1
 
-RUN wget https://data.swarts.gmi.oeaw.ac.at/treeringcrackscomb2_onlyring20210121T1457/mask_rcnn_treeringcrackscomb2_onlyring_0186.h5
+RUN wget https://data.swarts.gmi.oeaw.ac.at/treeringcrackscomb2_onlycracks20210121T2224/mask_rcnn_treeringcrackscomb2_onlycracks_0522.h5 && wget https://data.swarts.gmi.oeaw.ac.at/treeringcrackscomb2_onlyring20210121T1457/mask_rcnn_treeringcrackscomb2_onlyring_0186.h5
 
 ENV PATH "/home/mambauser/postprocessing:$MAMBA_ROOT_PREFIX/bin:$PATH"
 ENV PYTHONPATH "/home/mambauser:$PYTHONPATH"
 
-ENTRYPOINT ["postprocessingCracksRings.py", "--weightRing", "/home/mambauser/mask_rcnn_treeringcrackscomb2_onlyring_0186.h5"]
+ENTRYPOINT ["postprocessingCracksRings.py", "--weightRing", "/home/mambauser/mask_rcnn_treeringcrackscomb2_onlyring_0186.h5", "--weightCrack", "/home/mambauser/mask_rcnn_treeringcrackscomb2_onlycracks_0522.h5"]

CoreProcessingPipelineScripts/CNN/Mask_RCNN/environment.yml

@@ -1,5 +1,7 @@
 name: TreeRingCNN
 channels:
+  - pytorch
+  - nvidia
   - conda-forge
   - defaults
 dependencies:
@@ -11,7 +13,7 @@ dependencies:
   - blas=1.0=mkl
   - bzip2=1.0.8=h7b6447c_0
   - c-ares=1.15.0=h7b6447c_1001
-  - ca-certificates=2021.10.26=h06a4308_2
+  - ca-certificates=2023.01.10=h06a4308_0
   - cairo=1.14.12=h8948797_3
   - certifi=2021.5.30=py36h06a4308_0
   - cloudpickle=1.2.2=py_0
@@ -69,6 +71,8 @@ dependencies:
   - libvpx=1.7.0=h439df22_0
   - libxcb=1.13=h1bed415_1
   - libxml2=2.9.9=hea5a465_1
+  - libxslt=1.1.33=h7d1a2b0_0
+  - lxml=4.5.1=py36hefd8a0e_0
   - markdown=3.1.1=py36_0
   - matplotlib=3.2.1=0
   - matplotlib-base=3.2.1=py36hef1b27d_0
@@ -82,7 +86,7 @@ dependencies:
   - numpy-base=1.17.2=py36hde5b4d6_0
   - olefile=0.46=py36_0
   - opencv=3.4.2=py36h6fd60c2_1
-  - openssl=1.1.1m=h7f8727e_0
+  - openssl=1.1.1t=h7f8727e_0
   - pandas=0.25.3=py36he6710b0_0
   - parso=0.6.0=py_0
   - pcre=8.43=he6710b0_0

CoreProcessingPipelineScripts/CNN/Mask_RCNN/mrcnn/model.py

@@ -2350,7 +2350,7 @@ def train(self, train_dataset, val_dataset, learning_rate, epochs, layers,
                 keras.callbacks.TensorBoard(log_dir=self.log_dir,
                                             histogram_freq=0, write_graph=True, write_images=False),
                 keras.callbacks.ModelCheckpoint(self.checkpoint_path,
-                                                verbose=0, save_weights_only=True),
+                                                verbose=0, monitor='val_mrcnn_mask_loss', save_weights_only=True),
             ]
 
         # Add custom callbacks to the list

CoreProcessingPipelineScripts/CNN/Mask_RCNN/postprocessing/TRACE_Quercus_detect.sh

@@ -0,0 +1,20 @@
+#!/usr/bin/env bash
+
+#SBATCH --nodes=1
+#SBATCH --partition=g
+#SBATCH --gres=gpu:RTX:1
+#SBATCH --mem=64G
+#SBATCH --qos=medium
+#SBATCH --time=00-20:00:00
+#SBATCH --output=TRACE_QuercusWeights.stdout
+
+ml load anaconda3/2019.03
+source activate ~/.conda/envs/TreeRingCNN
+
+~/.conda/envs/TreeRingCNN/bin/python3 postprocessingCracksRings.py \
+  --dpi=13039 \
+  --run_ID=TRACE_QuercusWeight_detect \
+  --input=/groups/swarts/lab/TRACE_2023_posterData/TRACE_multispec_dendroelev_adjusted \
+  --weightRing=/groups/swarts/user/miroslav.polacek/TRG_development0/TRG-ImageProcessing/CoreProcessingPipelineScripts/CNN/Mask_RCNN/postprocessing/logs/retrainedrings20230427T2201/mask_rcnn_retrainedrings_0184.h5 \
+  --output_folder=/groups/swarts/lab/TRACE_2023_posterData/CNN_output \
+  --print_detections=yes \

CoreProcessingPipelineScripts/CNN/Mask_RCNN/postprocessing/TRACE_multispec_detect.sh

@@ -0,0 +1,20 @@
+#!/usr/bin/env bash
+
+#SBATCH --nodes=1
+#SBATCH --partition=g
+#SBATCH --gres=gpu:RTX:1
+#SBATCH --mem=32G
+#SBATCH --qos=medium
+#SBATCH --time=00-20:00:00
+#SBATCH --output=TRACE_multispec.stdout
+
+ml load anaconda3/2019.03
+source activate ~/.conda/envs/TreeRingCNN
+
+~/.conda/envs/TreeRingCNN/bin/python3 postprocessingCracksRings.py \
+  --dpi=13039 \
+  --run_ID=TRACE_multispec_detect \
+  --input=/groups/swarts/lab/TRACE_2023_posterData/TRACE_multispec_dendroelev_adjusted \
+  --weightRing=/groups/swarts/lab/ImageProcessingPipeline/TRG-ImageProcessing/CoreProcessingPipelineScripts/CNN/Mask_RCNN/logs/treeringcrackscomb2_onlyring20210121T1457/mask_rcnn_treeringcrackscomb2_onlyring_0186.h5 \
+  --output_folder=/groups/swarts/lab/TRACE_2023_posterData/CNN_output \
+  --print_detections=yes \

CoreProcessingPipelineScripts/CNN/Mask_RCNN/postprocessing/cluster_time_images.sh

@@ -6,14 +6,14 @@
 #SBATCH --mem=32G
 #SBATCH --qos=medium
 #SBATCH --time=00-20:00:00
-#SBATCH --output=Time_images.stdout
+#SBATCH --output=Time_images_TF1.stdout
 
 ml load anaconda3/2019.03
 source activate ~/.conda/envs/TreeRingCNN
 
 ~/.conda/envs/TreeRingCNN/bin/python3 postprocessingCracksRings.py \
   --dpi=13039 \
-  --run_ID=Image_time_test_debug \
+  --run_ID=Inference_time_test_TF1 \
   --input=/groups/swarts/lab/DendroImages/CNN_test/AlexPOS/MEECNNPaperTreeringSupplementalInfo/Tiffs \
-  --weightRing=/users/miroslav.polacek/TRG_testing/TRG-ImageProcessing/CoreProcessingPipelineScripts/CNN/Mask_RCNN/logs/onlyring/mask_rcnn_treeringcrackscomb2_onlyring_0186.h5 \
-  --output_folder=/users/miroslav.polacek/Time_results \
+  --weightRing=/groups/swarts/lab/ImageProcessingPipeline/TRG-ImageProcessing/CoreProcessingPipelineScripts/CNN/Mask_RCNN/logs/treeringcrackscomb2_onlyring20210121T1457/mask_rcnn_treeringcrackscomb2_onlyring_0186.h5 \
+  --output_folder=../output \