Merge pull request #61 from henrypinkard/main

Supplementary figs and dir for github pages
Waller-Lab · Oct 21, 2024 · 3e73f63 · 3e73f63
2 parents b83c11b + 3759bac
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diff --git a/figure_making/animations/tree_figure.ipynb b/figure_making/animations/tree_figure.ipynb
@@ -1754,6 +1754,108 @@
     "video_output_path = '/home/hpinkard_waller/data/trees/animation.mp4'\n",
     "os.system(f'ffmpeg -y -framerate 20 -i {output_dir}/frame_%03d.png -vf \"scale=ceil(iw/2)*2:ceil(ih/2)*2\" -vcodec libx264 -crf 23 -pix_fmt yuv420p {video_output_path}')\n"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/tmp/ipykernel_216680/1253613364.py:82: DeprecationWarning: ANTIALIAS is deprecated and will be removed in Pillow 10 (2023-07-01). Use LANCZOS or Resampling.LANCZOS instead.\n",
+      "  montage_image = montage_image.resize((1920, 1080), Image.ANTIALIAS)\n"
+     ]
+    }
+   ],
+   "source": [
+    "import numpy as np\n",
+    "from PIL import Image\n",
+    "from scipy.ndimage import gaussian_filter\n",
+    "import os\n",
+    "\n",
+    "# Function to add Gaussian noise to an image\n",
+    "def add_noise(image, gaussian_sigma):\n",
+    "    noise = np.random.normal(0, gaussian_sigma, image.shape)\n",
+    "    noisy_image = image + noise\n",
+    "    return noisy_image\n",
+    "\n",
+    "# Function to apply Gaussian blur to each channel of an image\n",
+    "def blur_each_channel(image, sigma):\n",
+    "    blurred_image = np.zeros_like(image)\n",
+    "    for channel in range(3):  # Assuming RGB image\n",
+    "        blurred_image[:, :, channel] = gaussian_filter(\n",
+    "            image[:, :, channel], sigma=sigma, mode='reflect'\n",
+    "        )\n",
+    "    return blurred_image\n",
+    "\n",
+    "# Parameters\n",
+    "shape = (220, 220)  # Resize shape for each tree image\n",
+    "grid_size = (8, 8)  # Grid size (rows, columns)\n",
+    "min_blur = 0        # Minimum blur level\n",
+    "max_blur = 13      # Maximum blur level\n",
+    "min_noise = 0       # Minimum noise level\n",
+    "max_noise = 120     # Maximum noise level\n",
+    "\n",
+    "# Directories (update these paths as needed)\n",
+    "tree_dir = '/home/hpinkard_waller/data/trees/high_res'\n",
+    "output_path = '/home/hpinkard_waller/data/trees/montage.png'\n",
+    "\n",
+    "# Load tree images\n",
+    "trees = []\n",
+    "for name in os.listdir(tree_dir):\n",
+    "    img_path = os.path.join(tree_dir, name)\n",
+    "    img = Image.open(img_path).resize(shape)\n",
+    "    trees.append(np.array(img))\n",
+    "\n",
+    "# Generate the montage image\n",
+    "row_images = []\n",
+    "for y in range(grid_size[0]):  # Rows\n",
+    "    col_images = []\n",
+    "    for x in range(grid_size[1]):  # Columns\n",
+    "        # Generate random blur and noise levels within limits\n",
+    "        blur_sigma = np.random.uniform(min_blur, max_blur)\n",
+    "        noise_sigma = np.random.uniform(min_noise, max_noise)\n",
+    "\n",
+    "        # Pick a random tree image\n",
+    "        img = trees[np.random.randint(len(trees))]\n",
+    "\n",
+    "        # Apply blur and noise\n",
+    "        blurred_img = blur_each_channel(img, blur_sigma)\n",
+    "        noisy_img = add_noise(blurred_img, gaussian_sigma=noise_sigma)\n",
+    "        noisy_img = np.clip(noisy_img, 0, 255).astype(np.uint8)\n",
+    "        col_images.append(noisy_img)\n",
+    "\n",
+    "    # Concatenate images horizontally\n",
+    "    row_image = np.hstack(col_images)\n",
+    "    row_images.append(row_image)\n",
+    "\n",
+    "# Concatenate images vertically to form the grid\n",
+    "montage_image = np.vstack(row_images)\n",
+    "\n",
+    "# Crop to 16:9 aspect ratio and resize to 1920x1080\n",
+    "h, w = montage_image.shape[:2]\n",
+    "target_aspect_ratio = 16 / 9\n",
+    "current_aspect_ratio = w / h\n",
+    "\n",
+    "if current_aspect_ratio > target_aspect_ratio:\n",
+    "    # Crop width\n",
+    "    new_w = int(h * target_aspect_ratio)\n",
+    "    start_w = (w - new_w) // 2\n",
+    "    montage_image = montage_image[:, start_w:start_w + new_w]\n",
+    "elif current_aspect_ratio < target_aspect_ratio:\n",
+    "    # Crop height\n",
+    "    new_h = int(w / target_aspect_ratio)\n",
+    "    start_h = (h - new_h) // 2\n",
+    "    montage_image = montage_image[start_h:start_h + new_h, :]\n",
+    "\n",
+    "montage_image = Image.fromarray(montage_image)\n",
+    "montage_image = montage_image.resize((1920, 1080), Image.ANTIALIAS)\n",
+    "\n",
+    "# Save the final montage image\n",
+    "montage_image.save(output_path)\n"
+   ]
   }
  ],
  "metadata": {
@@ -1763,7 +1865,15 @@
    "name": "python3"
   },
   "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
    "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
    "version": "3.10.6"
   }
  },

diff --git a/figure_making/bayer_figure.ipynb b/figure_making/bayer_figure.ipynb
diff --git a/led_array/phenotyping_experiments/compute_mi_and_phenotyping_performance.py b/led_array/phenotyping_experiments/compute_mi_and_phenotyping_performance.py
@@ -60,7 +60,7 @@ def compute_nlls(model, test_dataset, max_num, markers):
     return np.array(negative_log_likelihoods), np.array(marker_indices)
 
 
-def estimate_mi(model_name, config, patch_size, num_images=5000, num_patches=10000, test_set_fraction=0.1, confidence=0.9):
+def estimate_mi(model_name, config, patch_size, num_images=5000, num_patches=10000, test_set_fraction=0.1, confidence=0.95):
     saving_name = f'{model_name}_{patch_size}patch_mi_estimates'
 
     # # check if already cached
@@ -94,7 +94,7 @@ def estimate_mi(model_name, config, patch_size, num_images=5000, num_patches=100
     pixel_cnn = PixelCNN()
     # stationary_gp = StationaryGaussianProcess(noisy_patches)
 
-    pixel_cnn.fit(noisy_patches, verbose=False, max_epochs=500, patience=100)
+    pixel_cnn.fit(noisy_patches, verbose=False, max_epochs=1000, patience=300)
     # stationary_gp.fit(noisy_patches, verbose=False)
 
 

diff --git a/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_0.yaml b/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_0.yaml
@@ -43,7 +43,7 @@ patch_size: 40
 saving_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/
 train_script_path: /home/hpinkard_waller/GitRepos/EncodingInformation/led_array/phenotyping_experiments/compute_mi_and_phenotyping_performance.py
 training:
-  attempt_number: 7
+  attempt_number: 8
   elapsed: 0
   start_date: '2023-12-13'
   tensorboard_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_0/tensorboard/
diff --git a/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_1.yaml b/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_1.yaml
@@ -43,7 +43,7 @@ patch_size: 40
 saving_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/
 train_script_path: /home/hpinkard_waller/GitRepos/EncodingInformation/led_array/phenotyping_experiments/compute_mi_and_phenotyping_performance.py
 training:
-  attempt_number: 8
+  attempt_number: 9
   elapsed: 0
   start_date: '2023-12-13'
   tensorboard_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_1/tensorboard/
diff --git a/...nfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_10.yaml b/...nfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_10.yaml
@@ -43,7 +43,7 @@ patch_size: 40
 saving_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/
 train_script_path: /home/hpinkard_waller/GitRepos/EncodingInformation/led_array/phenotyping_experiments/compute_mi_and_phenotyping_performance.py
 training:
-  attempt_number: 9
+  attempt_number: 10
   elapsed: 0
   start_date: '2023-12-13'
   tensorboard_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_10/tensorboard/
diff --git a/..._Brightfield_150photons_replicate_11.yaml → ..._Brightfield_150photons_replicate_11.yaml b/..._Brightfield_150photons_replicate_11.yaml → ..._Brightfield_150photons_replicate_11.yaml
@@ -43,7 +43,7 @@ patch_size: 40
 saving_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/
 train_script_path: /home/hpinkard_waller/GitRepos/EncodingInformation/led_array/phenotyping_experiments/compute_mi_and_phenotyping_performance.py
 training:
-  attempt_number: 1
+  attempt_number: 4
   elapsed: 0
   start_date: '2023-12-13'
-  tensorboard_dir: /home/hpinkard_waller/models/template/tensorboard/
+  tensorboard_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_11/tensorboard/
diff --git a/..._Brightfield_150photons_replicate_12.yaml → ..._Brightfield_150photons_replicate_12.yaml b/..._Brightfield_150photons_replicate_12.yaml → ..._Brightfield_150photons_replicate_12.yaml
@@ -43,7 +43,7 @@ patch_size: 40
 saving_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/
 train_script_path: /home/hpinkard_waller/GitRepos/EncodingInformation/led_array/phenotyping_experiments/compute_mi_and_phenotyping_performance.py
 training:
-  attempt_number: 1
+  attempt_number: 3
   elapsed: 0
   start_date: '2023-12-13'
-  tensorboard_dir: /home/hpinkard_waller/models/template/tensorboard/
+  tensorboard_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_12/tensorboard/
diff --git a/..._Brightfield_150photons_replicate_13.yaml → ..._Brightfield_150photons_replicate_13.yaml b/..._Brightfield_150photons_replicate_13.yaml → ..._Brightfield_150photons_replicate_13.yaml
@@ -43,7 +43,7 @@ patch_size: 40
 saving_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/
 train_script_path: /home/hpinkard_waller/GitRepos/EncodingInformation/led_array/phenotyping_experiments/compute_mi_and_phenotyping_performance.py
 training:
-  attempt_number: 1
+  attempt_number: 4
   elapsed: 0
   start_date: '2023-12-13'
-  tensorboard_dir: /home/hpinkard_waller/models/template/tensorboard/
+  tensorboard_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_13/tensorboard/
diff --git a/..._Brightfield_150photons_replicate_14.yaml → ..._Brightfield_150photons_replicate_14.yaml b/..._Brightfield_150photons_replicate_14.yaml → ..._Brightfield_150photons_replicate_14.yaml
@@ -43,7 +43,7 @@ patch_size: 40
 saving_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/
 train_script_path: /home/hpinkard_waller/GitRepos/EncodingInformation/led_array/phenotyping_experiments/compute_mi_and_phenotyping_performance.py
 training:
-  attempt_number: 1
+  attempt_number: 3
   elapsed: 0
   start_date: '2023-12-13'
-  tensorboard_dir: /home/hpinkard_waller/models/template/tensorboard/
+  tensorboard_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_14/tensorboard/
diff --git a/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_2.yaml b/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_2.yaml
@@ -43,7 +43,7 @@ patch_size: 40
 saving_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/
 train_script_path: /home/hpinkard_waller/GitRepos/EncodingInformation/led_array/phenotyping_experiments/compute_mi_and_phenotyping_performance.py
 training:
-  attempt_number: 6
+  attempt_number: 7
   elapsed: 0
   start_date: '2023-12-13'
   tensorboard_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_2/tensorboard/
diff --git a/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_3.yaml b/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_3.yaml
@@ -43,7 +43,7 @@ patch_size: 40
 saving_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/
 train_script_path: /home/hpinkard_waller/GitRepos/EncodingInformation/led_array/phenotyping_experiments/compute_mi_and_phenotyping_performance.py
 training:
-  attempt_number: 9
+  attempt_number: 10
   elapsed: 0
   start_date: '2023-12-13'
   tensorboard_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_3/tensorboard/
diff --git a/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_4.yaml b/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_4.yaml
@@ -43,7 +43,7 @@ patch_size: 40
 saving_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/
 train_script_path: /home/hpinkard_waller/GitRepos/EncodingInformation/led_array/phenotyping_experiments/compute_mi_and_phenotyping_performance.py
 training:
-  attempt_number: 6
+  attempt_number: 7
   elapsed: 0
   start_date: '2023-12-13'
   tensorboard_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_4/tensorboard/
diff --git a/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_5.yaml b/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_5.yaml
@@ -43,7 +43,7 @@ patch_size: 40
 saving_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/
 train_script_path: /home/hpinkard_waller/GitRepos/EncodingInformation/led_array/phenotyping_experiments/compute_mi_and_phenotyping_performance.py
 training:
-  attempt_number: 9
+  attempt_number: 10
   elapsed: 0
   start_date: '2023-12-13'
   tensorboard_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_5/tensorboard/
diff --git a/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_6.yaml b/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_6.yaml
@@ -43,7 +43,7 @@ patch_size: 40
 saving_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/
 train_script_path: /home/hpinkard_waller/GitRepos/EncodingInformation/led_array/phenotyping_experiments/compute_mi_and_phenotyping_performance.py
 training:
-  attempt_number: 6
+  attempt_number: 7
   elapsed: 0
   start_date: '2023-12-13'
   tensorboard_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_6/tensorboard/
diff --git a/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_7.yaml b/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_7.yaml
@@ -43,7 +43,7 @@ patch_size: 40
 saving_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/
 train_script_path: /home/hpinkard_waller/GitRepos/EncodingInformation/led_array/phenotyping_experiments/compute_mi_and_phenotyping_performance.py
 training:
-  attempt_number: 7
+  attempt_number: 10
   elapsed: 0
   start_date: '2023-12-13'
   tensorboard_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_7/tensorboard/
diff --git a/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_8.yaml b/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_8.yaml
@@ -43,7 +43,7 @@ patch_size: 40
 saving_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/
 train_script_path: /home/hpinkard_waller/GitRepos/EncodingInformation/led_array/phenotyping_experiments/compute_mi_and_phenotyping_performance.py
 training:
-  attempt_number: 6
+  attempt_number: 7
   elapsed: 0
   start_date: '2023-12-13'
   tensorboard_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_8/tensorboard/
diff --git a/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_9.yaml b/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_9.yaml
@@ -43,7 +43,7 @@ patch_size: 40
 saving_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/
 train_script_path: /home/hpinkard_waller/GitRepos/EncodingInformation/led_array/phenotyping_experiments/compute_mi_and_phenotyping_performance.py
 training:
-  attempt_number: 6
+  attempt_number: 7
   elapsed: 0
   start_date: '2023-12-13'
   tensorboard_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/Analysis_Synthetic_Noise_v10_Brightfield_150photons_replicate_9/tensorboard/
diff --git a/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_450photons_replicate_0.yaml b/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_450photons_replicate_0.yaml
@@ -43,7 +43,7 @@ patch_size: 40
 saving_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/
 train_script_path: /home/hpinkard_waller/GitRepos/EncodingInformation/led_array/phenotyping_experiments/compute_mi_and_phenotyping_performance.py
 training:
-  attempt_number: 7
+  attempt_number: 8
   elapsed: 0
   start_date: '2023-12-13'
   tensorboard_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/Analysis_Synthetic_Noise_v10_Brightfield_450photons_replicate_0/tensorboard/
diff --git a/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_450photons_replicate_1.yaml b/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_450photons_replicate_1.yaml
@@ -43,7 +43,7 @@ patch_size: 40
 saving_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/
 train_script_path: /home/hpinkard_waller/GitRepos/EncodingInformation/led_array/phenotyping_experiments/compute_mi_and_phenotyping_performance.py
 training:
-  attempt_number: 6
+  attempt_number: 7
   elapsed: 0
   start_date: '2023-12-13'
   tensorboard_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/Analysis_Synthetic_Noise_v10_Brightfield_450photons_replicate_1/tensorboard/
diff --git a/...nfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_450photons_replicate_10.yaml b/...nfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_450photons_replicate_10.yaml
@@ -43,7 +43,7 @@ patch_size: 40
 saving_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/
 train_script_path: /home/hpinkard_waller/GitRepos/EncodingInformation/led_array/phenotyping_experiments/compute_mi_and_phenotyping_performance.py
 training:
-  attempt_number: 8
+  attempt_number: 9
   elapsed: 0
   start_date: '2023-12-13'
   tensorboard_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/Analysis_Synthetic_Noise_v10_Brightfield_450photons_replicate_10/tensorboard/
diff --git a/..._Brightfield_450photons_replicate_11.yaml → ..._Brightfield_450photons_replicate_11.yaml b/..._Brightfield_450photons_replicate_11.yaml → ..._Brightfield_450photons_replicate_11.yaml
@@ -43,7 +43,7 @@ patch_size: 40
 saving_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/
 train_script_path: /home/hpinkard_waller/GitRepos/EncodingInformation/led_array/phenotyping_experiments/compute_mi_and_phenotyping_performance.py
 training:
-  attempt_number: 1
+  attempt_number: 4
   elapsed: 0
   start_date: '2023-12-13'
-  tensorboard_dir: /home/hpinkard_waller/models/template/tensorboard/
+  tensorboard_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/Analysis_Synthetic_Noise_v10_Brightfield_450photons_replicate_11/tensorboard/
diff --git a/..._Brightfield_450photons_replicate_12.yaml → ..._Brightfield_450photons_replicate_12.yaml b/..._Brightfield_450photons_replicate_12.yaml → ..._Brightfield_450photons_replicate_12.yaml
@@ -43,7 +43,7 @@ patch_size: 40
 saving_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/
 train_script_path: /home/hpinkard_waller/GitRepos/EncodingInformation/led_array/phenotyping_experiments/compute_mi_and_phenotyping_performance.py
 training:
-  attempt_number: 1
+  attempt_number: 3
   elapsed: 0
   start_date: '2023-12-13'
-  tensorboard_dir: /home/hpinkard_waller/models/template/tensorboard/
+  tensorboard_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/Analysis_Synthetic_Noise_v10_Brightfield_450photons_replicate_12/tensorboard/
diff --git a/..._Brightfield_450photons_replicate_13.yaml → ..._Brightfield_450photons_replicate_13.yaml b/..._Brightfield_450photons_replicate_13.yaml → ..._Brightfield_450photons_replicate_13.yaml
@@ -43,7 +43,7 @@ patch_size: 40
 saving_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/
 train_script_path: /home/hpinkard_waller/GitRepos/EncodingInformation/led_array/phenotyping_experiments/compute_mi_and_phenotyping_performance.py
 training:
-  attempt_number: 1
+  attempt_number: 5
   elapsed: 0
   start_date: '2023-12-13'
-  tensorboard_dir: /home/hpinkard_waller/models/template/tensorboard/
+  tensorboard_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/Analysis_Synthetic_Noise_v10_Brightfield_450photons_replicate_13/tensorboard/
diff --git a/..._Brightfield_450photons_replicate_14.yaml → ..._Brightfield_450photons_replicate_14.yaml b/..._Brightfield_450photons_replicate_14.yaml → ..._Brightfield_450photons_replicate_14.yaml
@@ -43,7 +43,7 @@ patch_size: 40
 saving_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/
 train_script_path: /home/hpinkard_waller/GitRepos/EncodingInformation/led_array/phenotyping_experiments/compute_mi_and_phenotyping_performance.py
 training:
-  attempt_number: 1
+  attempt_number: 3
   elapsed: 0
   start_date: '2023-12-13'
-  tensorboard_dir: /home/hpinkard_waller/models/template/tensorboard/
+  tensorboard_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/Analysis_Synthetic_Noise_v10_Brightfield_450photons_replicate_14/tensorboard/
diff --git a/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_450photons_replicate_2.yaml b/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_450photons_replicate_2.yaml
@@ -43,7 +43,7 @@ patch_size: 40
 saving_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/
 train_script_path: /home/hpinkard_waller/GitRepos/EncodingInformation/led_array/phenotyping_experiments/compute_mi_and_phenotyping_performance.py
 training:
-  attempt_number: 7
+  attempt_number: 10
   elapsed: 0
   start_date: '2023-12-13'
   tensorboard_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/Analysis_Synthetic_Noise_v10_Brightfield_450photons_replicate_2/tensorboard/
diff --git a/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_450photons_replicate_3.yaml b/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_450photons_replicate_3.yaml
@@ -43,7 +43,7 @@ patch_size: 40
 saving_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/
 train_script_path: /home/hpinkard_waller/GitRepos/EncodingInformation/led_array/phenotyping_experiments/compute_mi_and_phenotyping_performance.py
 training:
-  attempt_number: 8
+  attempt_number: 9
   elapsed: 0
   start_date: '2023-12-13'
   tensorboard_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/Analysis_Synthetic_Noise_v10_Brightfield_450photons_replicate_3/tensorboard/
diff --git a/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_450photons_replicate_4.yaml b/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_450photons_replicate_4.yaml
@@ -43,7 +43,7 @@ patch_size: 40
 saving_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/
 train_script_path: /home/hpinkard_waller/GitRepos/EncodingInformation/led_array/phenotyping_experiments/compute_mi_and_phenotyping_performance.py
 training:
-  attempt_number: 6
+  attempt_number: 7
   elapsed: 0
   start_date: '2023-12-13'
   tensorboard_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/Analysis_Synthetic_Noise_v10_Brightfield_450photons_replicate_4/tensorboard/
diff --git a/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_450photons_replicate_5.yaml b/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_450photons_replicate_5.yaml
@@ -43,7 +43,7 @@ patch_size: 40
 saving_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/
 train_script_path: /home/hpinkard_waller/GitRepos/EncodingInformation/led_array/phenotyping_experiments/compute_mi_and_phenotyping_performance.py
 training:
-  attempt_number: 6
+  attempt_number: 10
   elapsed: 0
   start_date: '2023-12-13'
   tensorboard_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/Analysis_Synthetic_Noise_v10_Brightfield_450photons_replicate_5/tensorboard/
diff --git a/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_450photons_replicate_6.yaml b/...onfig_files/complete/Analysis_Synthetic_Noise_v10_Brightfield_450photons_replicate_6.yaml
@@ -43,7 +43,7 @@ patch_size: 40
 saving_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/
 train_script_path: /home/hpinkard_waller/GitRepos/EncodingInformation/led_array/phenotyping_experiments/compute_mi_and_phenotyping_performance.py
 training:
-  attempt_number: 6
+  attempt_number: 7
   elapsed: 0
   start_date: '2023-12-13'
   tensorboard_dir: /home/hpinkard_waller/models/Synthetic_Noise_v10/Analysis_Synthetic_Noise_v10_Brightfield_450photons_replicate_6/tensorboard/