added content from OSF

also cleaned up some OSX meta-data such as .DS_STORE or __MACOSX hidden files
axondeepseg · Jun 14, 2021 · 8434a65 · 8434a65
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diff --git a/__test_files__/__test_16b_file__/raw/data1/image.tif b/__test_files__/__test_16b_file__/raw/data1/image.tif
diff --git a/__test_files__/__test_16b_file__/raw/data1/mask.tif b/__test_files__/__test_16b_file__/raw/data1/mask.tif
diff --git a/__test_files__/__test_16b_file__/raw/data1/pixel_size_in_micrometer.txt b/__test_files__/__test_16b_file__/raw/data1/pixel_size_in_micrometer.txt
@@ -0,0 +1 @@
+0.00136
diff --git a/__test_files__/__test_demo_files__/__prediction_only__/image_seg-axonmyelin.png b/__test_files__/__test_demo_files__/__prediction_only__/image_seg-axonmyelin.png
diff --git a/__test_files__/__test_demo_files__/image.png b/__test_files__/__test_demo_files__/image.png
diff --git a/__test_files__/__test_demo_files__/image_seg-axon.png b/__test_files__/__test_demo_files__/image_seg-axon.png
diff --git a/__test_files__/__test_demo_files__/image_seg-axonmyelin.png b/__test_files__/__test_demo_files__/image_seg-axonmyelin.png
diff --git a/__test_files__/__test_demo_files__/image_seg-myelin.png b/__test_files__/__test_demo_files__/image_seg-myelin.png
diff --git a/__test_files__/__test_demo_files__/mask.png b/__test_files__/__test_demo_files__/mask.png
diff --git a/__test_files__/__test_demo_files__/pixel_size_in_micrometer.txt b/__test_files__/__test_demo_files__/pixel_size_in_micrometer.txt
@@ -0,0 +1 @@
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diff --git a/__test_files__/__test_model__/Model/checkpoint b/__test_files__/__test_model__/Model/checkpoint
@@ -0,0 +1,2 @@
+model_checkpoint_path: "/Users/mathieuboudreau/neuropoly/github/axondeepseg/test/__test_files__/__test_training_files__/Model/model.ckpt"
+all_model_checkpoint_paths: "/Users/mathieuboudreau/neuropoly/github/axondeepseg/test/__test_files__/__test_training_files__/Model/model.ckpt"
diff --git a/__test_files__/__test_model__/Model/config_network.json b/__test_files__/__test_model__/Model/config_network.json
@@ -0,0 +1,77 @@
+{
+  "n_classes": 3,
+  "thresholds": [
+    0,
+    0.2,
+    0.8
+  ],
+  "trainingset_patchsize": 256,
+  "trainingset": "SEM_3c_256",
+  "batch_size": 2,
+  "save_epoch_freq": 1,
+  "depth": 2,
+  "convolution_per_layer": [
+    2,
+    2
+  ],
+  "size_of_convolutions_per_layer": [
+    [
+      3,
+      3
+    ],
+    [
+      3,
+      3
+    ]
+  ],
+  "features_per_convolution": [
+    [
+      [
+        1,
+        5
+      ],
+      [
+        5,
+        5
+      ]
+    ],
+    [
+      [
+        5,
+        10
+      ],
+      [
+        10,
+        10
+      ]
+    ]
+  ],
+  "downsampling": "maxpooling",
+  "dropout": 0.75,
+  "learning_rate": 0.001,
+  "learning_rate_decay_activate": true,
+  "learning_rate_decay_period": 4,
+  "learning_rate_decay_type": "polynomial",
+  "learning_rate_decay_rate": 0.99,
+  "batch_norm_activate": true,
+  "batch_norm_decay_decay_activate": true,
+  "batch_norm_decay_starting_decay": 0.7,
+  "batch_norm_decay_ending_decay": 0.9,
+  "batch_norm_decay_decay_period": 16000,
+  "weighted_cost-activate": true,
+  "weighted_cost-balanced_activate": true,
+  "weighted_cost-balanced_weights": [
+    1.1,
+    1,
+    1.3
+  ],
+  "weighted_cost-boundaries_sigma": 2,
+  "weighted_cost-boundaries_activate": false,
+  "da-type": "all",
+  "da-2-random_rotation-activate": false,
+  "da-5-noise_addition-activate": false,
+  "da-3-elastic-activate": true,
+  "da-0-shifting-activate": true,
+  "da-4-flipping-activate": true,
+  "da-1-rescaling-activate": false
+}
diff --git a/__test_files__/__test_model__/Model/evolution.pkl b/__test_files__/__test_model__/Model/evolution.pkl
diff --git a/__test_files__/__test_model__/Model/evolution_stats.pkl b/__test_files__/__test_model__/Model/evolution_stats.pkl
diff --git a/__test_files__/__test_model__/Model/model.ckpt.data-00000-of-00001 b/__test_files__/__test_model__/Model/model.ckpt.data-00000-of-00001
diff --git a/__test_files__/__test_model__/Model/model.ckpt.index b/__test_files__/__test_model__/Model/model.ckpt.index
diff --git a/__test_files__/__test_model__/Model/model.ckpt.meta b/__test_files__/__test_model__/Model/model.ckpt.meta
diff --git a/__test_files__/__test_model__/Model/report.txt b/__test_files__/__test_model__/Model/report.txt
@@ -0,0 +1,21 @@
+
+
+---Savings---
+ Model saved in : /Users/mathieuboudreau/neuropoly/github/axondeepseg/test/__test_files__/__test_training_files__/Model
+
+---PARAMETERS---
+learning_rate : 0.001; 
+ batch_size :  2;
+ depth :  2;
+ epoch_size: 2;
+ dropout :  0.75;
+ (if model restored) restored_model :None
+5763
+
+
+---Intermediary results---
+
+----
+ Last epoch: 1
+ Accuracy: 0.2949371337890625;
+ Loss: 1.1041648387908936;
diff --git a/__test_files__/__test_patch_files__/raw/data1/image.png b/__test_files__/__test_patch_files__/raw/data1/image.png
diff --git a/__test_files__/__test_patch_files__/raw/data1/mask.png b/__test_files__/__test_patch_files__/raw/data1/mask.png
diff --git a/__test_files__/__test_patch_files__/raw/data1/pixel_size_in_micrometer.txt b/__test_files__/__test_patch_files__/raw/data1/pixel_size_in_micrometer.txt
@@ -0,0 +1 @@
+0.07
diff --git a/__test_files__/__test_patch_files__/raw/data2/image.png b/__test_files__/__test_patch_files__/raw/data2/image.png
diff --git a/__test_files__/__test_patch_files__/raw/data2/mask.png b/__test_files__/__test_patch_files__/raw/data2/mask.png
diff --git a/__test_files__/__test_patch_files__/raw/data2/pixel_size_in_micrometer.txt b/__test_files__/__test_patch_files__/raw/data2/pixel_size_in_micrometer.txt
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+
diff --git a/__test_files__/__test_postprocessing_files__/after_flood_fill.png b/__test_files__/__test_postprocessing_files__/after_flood_fill.png
diff --git a/__test_files__/__test_postprocessing_files__/before_flood_fill.png b/__test_files__/__test_postprocessing_files__/before_flood_fill.png
diff --git a/__test_files__/__test_postprocessing_files__/test_numbers_image.png b/__test_files__/__test_postprocessing_files__/test_numbers_image.png
diff --git a/__test_files__/__test_segment_files__/image.png b/__test_files__/__test_segment_files__/image.png
diff --git a/__test_files__/__test_segment_files__/image_2.png b/__test_files__/__test_segment_files__/image_2.png
diff --git a/__test_files__/__test_segment_files_with_pixel_size__/image.png b/__test_files__/__test_segment_files_with_pixel_size__/image.png
diff --git a/__test_files__/__test_segment_files_with_pixel_size__/image_2.png b/__test_files__/__test_segment_files_with_pixel_size__/image_2.png
diff --git a/__test_files__/__test_segment_files_with_pixel_size__/pixel_size_in_micrometer.txt b/__test_files__/__test_segment_files_with_pixel_size__/pixel_size_in_micrometer.txt
@@ -0,0 +1,2 @@
+0.37
+
diff --git a/__test_files__/__test_simulated_axons__/pixel_size_in_micrometer.txt b/__test_files__/__test_simulated_axons__/pixel_size_in_micrometer.txt
@@ -0,0 +1 @@
+1
diff --git a/__test_files__/__test_training_files__/Testing/data1/image.png b/__test_files__/__test_training_files__/Testing/data1/image.png
diff --git a/__test_files__/__test_training_files__/Testing/data1/mask.png b/__test_files__/__test_training_files__/Testing/data1/mask.png
diff --git a/__test_files__/__test_training_files__/Testing/data1/pixel_size_in_micrometer.txt b/__test_files__/__test_training_files__/Testing/data1/pixel_size_in_micrometer.txt
@@ -0,0 +1,2 @@
+0.37
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diff --git a/__test_files__/__test_training_files__/Train/image_0.png b/__test_files__/__test_training_files__/Train/image_0.png
diff --git a/__test_files__/__test_training_files__/Train/image_1.png b/__test_files__/__test_training_files__/Train/image_1.png
diff --git a/__test_files__/__test_training_files__/Train/mask_0.png b/__test_files__/__test_training_files__/Train/mask_0.png
diff --git a/__test_files__/__test_training_files__/Train/mask_1.png b/__test_files__/__test_training_files__/Train/mask_1.png
diff --git a/__test_files__/__test_training_files__/Validation/image_0.png b/__test_files__/__test_training_files__/Validation/image_0.png
diff --git a/__test_files__/__test_training_files__/Validation/image_1.png b/__test_files__/__test_training_files__/Validation/image_1.png
diff --git a/__test_files__/__test_training_files__/Validation/mask_0.png b/__test_files__/__test_training_files__/Validation/mask_0.png
diff --git a/__test_files__/__test_training_files__/Validation/mask_1.png b/__test_files__/__test_training_files__/Validation/mask_1.png
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		model_checkpoint_path: "/Users/mathieuboudreau/neuropoly/github/axondeepseg/test/__test_files__/__test_training_files__/Model/model.ckpt"
		all_model_checkpoint_paths: "/Users/mathieuboudreau/neuropoly/github/axondeepseg/test/__test_files__/__test_training_files__/Model/model.ckpt"