V0.1.2

AUTHORS.md

@@ -9,14 +9,16 @@ Contributors  (sorted alphabetically)
 -------------------------------------
 To contributors: please add your name to the list when you submit a patch to the project.
 
+* Yazeed Alaudah
 * Ashish Bhatia
+* Sharat Chikkerur
 * Daniel Ciborowski
 * George Iordanescu
 * Ilia Karmanov
 * Max Kaznady
 * Vanja Paunic
 * Mathew Salvaris
-
+* Wee Hyong Tok
 
 ## How to be a contributor to the repository
 This project welcomes contributions and suggestions.  Most contributions require you to agree to a

NOTICE.txt

@@ -1949,7 +1949,7 @@ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 
 -------------------------------------------------------------------
 
-olivesgatech/facies_classification_benchmark 12102683a1ae78f8fbc953823c35a43b151194b3 - MIT
+yalaudah/facies_classification_benchmark 12102683a1ae78f8fbc953823c35a43b151194b3 - MIT
 Copyright (c) 2017 Meet Pragnesh Shah
 
 Copyright (c) 2010-2018 Benjamin Peterson

cgmanifest.json

@@ -3,7 +3,7 @@
       "component": { 
        "type": "git", 
        "git": { 
-         "repositoryUrl": "https://github.com/olivesgatech/facies_classification_benchmark", 
+         "repositoryUrl": "https://github.com/yalaudah/facies_classification_benchmark", 
          "commitHash": "12102683a1ae78f8fbc953823c35a43b151194b3" 
          }
        },

contrib/experiments/interpretation/dutchf3_patch/distributed/configs/hrnet.yaml

@@ -0,0 +1,103 @@
+CUDNN:
+  BENCHMARK: true
+  DETERMINISTIC: false
+  ENABLED: true
+GPUS: (0,)
+OUTPUT_DIR: 'output' 
+LOG_DIR: 'log'
+WORKERS: 4
+PRINT_FREQ: 10
+LOG_CONFIG: logging.conf
+SEED: 2019
+OPENCV_BORDER_CONSTANT: 0
+
+
+DATASET:
+  NUM_CLASSES: 6
+  ROOT: /mnt/dutchf3
+  CLASS_WEIGHTS: [0.7151, 0.8811, 0.5156, 0.9346, 0.9683, 0.9852]
+
+
+MODEL:
+  NAME: seg_hrnet
+  IN_CHANNELS: 3
+  PRETRAINED: '/mnt/hrnet_pretrained/image_classification/hrnetv2_w48_imagenet_pretrained.pth'
+  EXTRA:
+    FINAL_CONV_KERNEL: 1
+    STAGE2:
+      NUM_MODULES: 1
+      NUM_BRANCHES: 2
+      BLOCK: BASIC
+      NUM_BLOCKS:
+      - 4
+      - 4
+      NUM_CHANNELS:
+      - 48
+      - 96
+      FUSE_METHOD: SUM
+    STAGE3:
+      NUM_MODULES: 4
+      NUM_BRANCHES: 3
+      BLOCK: BASIC
+      NUM_BLOCKS:
+      - 4
+      - 4
+      - 4
+      NUM_CHANNELS:
+      - 48
+      - 96
+      - 192
+      FUSE_METHOD: SUM
+    STAGE4:
+      NUM_MODULES: 3
+      NUM_BRANCHES: 4
+      BLOCK: BASIC
+      NUM_BLOCKS:
+      - 4
+      - 4
+      - 4
+      - 4
+      NUM_CHANNELS:
+      - 48
+      - 96
+      - 192
+      - 384
+      FUSE_METHOD: SUM
+
+TRAIN:
+  BATCH_SIZE_PER_GPU: 16
+  BEGIN_EPOCH: 0
+  END_EPOCH: 300
+  MIN_LR: 0.001
+  MAX_LR: 0.02
+  MOMENTUM: 0.9
+  WEIGHT_DECAY: 0.0001
+  SNAPSHOTS: 5
+  AUGMENTATION: True
+  DEPTH: "section" #"patch" # Options are none, patch, and section
+  STRIDE: 50
+  PATCH_SIZE: 100
+  AUGMENTATIONS:
+    RESIZE:
+      HEIGHT: 200
+      WIDTH: 200
+    PAD:
+      HEIGHT: 256
+      WIDTH: 256
+  MEAN: 0.0009997 # 0.0009996710808862074
+  STD: 0.20977 # 0.20976548783479299 
+  MODEL_DIR: "models"
+
+
+VALIDATION:
+  BATCH_SIZE_PER_GPU: 32
+
+TEST: 
+  MODEL_PATH: "/data/home/mat/repos/DeepSeismic/interpretation/experiments/segmentation/dutchf3/local/output/mat/exp/ccb7206b41dc7411609705e49d9f4c2d74c6eb88/seg_hrnet/Aug30_141919/models/seg_hrnet_running_model_18.pth"
+  TEST_STRIDE: 10
+  SPLIT: 'Both' # Can be Both, Test1, Test2
+  INLINE: True
+  CROSSLINE: True
+  POST_PROCESSING: 
+    SIZE: 128 # 
+    CROP_PIXELS: 14 # Number of pixels to crop top, bottom, left and right

contrib/experiments/interpretation/dutchf3_patch/distributed/configs/patch_deconvnet.yaml

@@ -0,0 +1,59 @@
+CUDNN:
+  BENCHMARK: true
+  DETERMINISTIC: false
+  ENABLED: true
+GPUS: (0,)
+OUTPUT_DIR: 'output'
+LOG_DIR: 'log'
+WORKERS: 4
+PRINT_FREQ: 10
+LOG_CONFIG: logging.conf
+SEED: 2019
+
+DATASET:
+  NUM_CLASSES: 6
+  ROOT: /mnt/dutchf3
+  CLASS_WEIGHTS: [0.7151, 0.8811, 0.5156, 0.9346, 0.9683, 0.9852]
+
+MODEL:
+  NAME: patch_deconvnet_skip
+  IN_CHANNELS: 1
+
+
+TRAIN:
+  BATCH_SIZE_PER_GPU: 64
+  BEGIN_EPOCH: 0
+  END_EPOCH: 300
+  MIN_LR: 0.001
+  MAX_LR: 0.02
+  MOMENTUM: 0.9
+  WEIGHT_DECAY: 0.0001
+  SNAPSHOTS: 5
+  AUGMENTATION: True
+  DEPTH: "none" #"patch" # Options are none, patch, and section
+  STRIDE: 50
+  PATCH_SIZE: 99
+  AUGMENTATIONS:
+    RESIZE:
+      HEIGHT: 99
+      WIDTH: 99
+    PAD:
+      HEIGHT: 99
+      WIDTH: 99
+  MEAN: 0.0009997 # 0.0009996710808862074
+  STD: 0.20977 # 0.20976548783479299 
+  MODEL_DIR: "models"
+
+VALIDATION:
+  BATCH_SIZE_PER_GPU: 512
+
+TEST: 
+  MODEL_PATH: ""
+  TEST_STRIDE: 10
+  SPLIT: 'Both' # Can be Both, Test1, Test2
+  INLINE: True
+  CROSSLINE: True
+  POST_PROCESSING: 
+    SIZE: 99 # 
+    CROP_PIXELS: 0 # Number of pixels to crop top, bottom, left and right
+

contrib/experiments/interpretation/dutchf3_patch/distributed/configs/patch_deconvnet_skip.yaml

@@ -0,0 +1,59 @@
+CUDNN:
+  BENCHMARK: true
+  DETERMINISTIC: false
+  ENABLED: true
+GPUS: (0,)
+OUTPUT_DIR: 'output'
+LOG_DIR: 'log'
+WORKERS: 4
+PRINT_FREQ: 10
+LOG_CONFIG: logging.conf
+SEED: 2019
+
+DATASET:
+  NUM_CLASSES: 6
+  ROOT: /mnt/dutchf3
+  CLASS_WEIGHTS: [0.7151, 0.8811, 0.5156, 0.9346, 0.9683, 0.9852]
+
+MODEL:
+  NAME: patch_deconvnet_skip
+  IN_CHANNELS: 1
+
+
+TRAIN:
+  BATCH_SIZE_PER_GPU: 64
+  BEGIN_EPOCH: 0
+  END_EPOCH: 300
+  MIN_LR: 0.001
+  MAX_LR: 0.02
+  MOMENTUM: 0.9
+  WEIGHT_DECAY: 0.0001
+  SNAPSHOTS: 5
+  AUGMENTATION: True
+  DEPTH: "none" #"patch" # Options are none, patch, and section
+  STRIDE: 50
+  PATCH_SIZE: 99
+  AUGMENTATIONS:
+    RESIZE:
+      HEIGHT: 99
+      WIDTH: 99
+    PAD:
+      HEIGHT: 99
+      WIDTH: 99
+  MEAN: 0.0009997 # 0.0009996710808862074
+  STD: 0.20977 # 0.20976548783479299 
+  MODEL_DIR: "models"
+
+VALIDATION:
+  BATCH_SIZE_PER_GPU: 512
+
+TEST: 
+  MODEL_PATH: ""
+  TEST_STRIDE: 10
+  SPLIT: 'Both' # Can be Both, Test1, Test2
+  INLINE: True
+  CROSSLINE: True
+  POST_PROCESSING: 
+    SIZE: 99 # 
+    CROP_PIXELS: 0 # Number of pixels to crop top, bottom, left and right
+

contrib/experiments/interpretation/dutchf3_patch/distributed/configs/seresnet_unet.yaml

@@ -0,0 +1,59 @@
+CUDNN:
+  BENCHMARK: true
+  DETERMINISTIC: false
+  ENABLED: true
+GPUS: (0,)
+OUTPUT_DIR: 'output' 
+LOG_DIR: 'log'
+WORKERS: 4
+PRINT_FREQ: 10
+LOG_CONFIG: logging.conf
+SEED: 2019
+
+
+DATASET:
+  NUM_CLASSES: 6
+  ROOT: /mnt/dutchf3
+  CLASS_WEIGHTS: [0.7151, 0.8811, 0.5156, 0.9346, 0.9683, 0.9852]
+
+MODEL:
+  NAME: resnet_unet
+  IN_CHANNELS: 3
+
+TRAIN:
+  BATCH_SIZE_PER_GPU: 16
+  BEGIN_EPOCH: 0
+  END_EPOCH: 300
+  MIN_LR: 0.001
+  MAX_LR: 0.02
+  MOMENTUM: 0.9
+  WEIGHT_DECAY: 0.0001
+  SNAPSHOTS: 5
+  AUGMENTATION: True
+  DEPTH: "section" # Options are none, patch, and section
+  STRIDE: 50
+  PATCH_SIZE: 100
+  AUGMENTATIONS:
+    RESIZE:
+      HEIGHT: 200
+      WIDTH: 200
+    PAD:
+      HEIGHT: 256
+      WIDTH: 256
+  MEAN: 0.0009997 # 0.0009996710808862074
+  STD: 0.20977 # 0.20976548783479299 
+  MODEL_DIR: "models"
+
+
+VALIDATION:
+  BATCH_SIZE_PER_GPU: 32
+
+TEST:
+  MODEL_PATH: "/data/home/mat/repos/DeepSeismic/interpretation/experiments/segmentation/dutchf3/local/output/mat/exp/dc2e2d20b7f6d508beb779ffff37c77d0139e588/resnet_unet/Sep01_125513/models/resnet_unet_snapshot1model_52.pth"
+  TEST_STRIDE: 10
+  SPLIT: 'Both' # Can be Both, Test1, Test2
+  INLINE: True
+  CROSSLINE: True
+  POST_PROCESSING: 
+    SIZE: 128 
+    CROP_PIXELS: 14 # Number of pixels to crop top, bottom, left and right

contrib/experiments/interpretation/dutchf3_patch/distributed/configs/unet.yaml

@@ -0,0 +1,63 @@
+# UNet configuration
+
+CUDNN:
+  BENCHMARK: true
+  DETERMINISTIC: false
+  ENABLED: true
+GPUS: (0,)
+OUTPUT_DIR: 'output' 
+LOG_DIR: 'log'
+WORKERS: 4
+PRINT_FREQ: 10
+LOG_CONFIG: logging.conf
+SEED: 2019
+
+
+DATASET:
+  NUM_CLASSES: 6
+  ROOT: /mnt/dutchf3
+  CLASS_WEIGHTS: [0.7151, 0.8811, 0.5156, 0.9346, 0.9683, 0.9852]
+
+MODEL:
+  NAME: resnet_unet
+  IN_CHANNELS: 3
+
+
+TRAIN:
+  BATCH_SIZE_PER_GPU: 16
+  BEGIN_EPOCH: 0
+  END_EPOCH: 300
+  MIN_LR: 0.001
+  MAX_LR: 0.02
+  MOMENTUM: 0.9
+  WEIGHT_DECAY: 0.0001
+  SNAPSHOTS: 5
+  AUGMENTATION: True
+  DEPTH: "section" # Options are none, patch, and section
+  STRIDE: 50
+  PATCH_SIZE: 100
+  AUGMENTATIONS:
+    RESIZE:
+      HEIGHT: 200
+      WIDTH: 200
+    PAD:
+      HEIGHT: 256
+      WIDTH: 256
+  MEAN: 0.0009997 # 0.0009996710808862074
+  STD: 0.20977 # 0.20976548783479299 
+  MODEL_DIR: "models"
+
+
+VALIDATION:
+  BATCH_SIZE_PER_GPU: 32
+
+TEST:
+  MODEL_PATH: ""
+  TEST_STRIDE: 10
+  SPLIT: 'Both' # Can be Both, Test1, Test2
+  INLINE: True
+  CROSSLINE: True
+  POST_PROCESSING: 
+    SIZE: 128 
+    CROP_PIXELS: 14 # Number of pixels to crop top, bottom, left and right
+