Merge remote-tracking branch 'origin/master'

Author: WenChentao

CellTracker/stardistwrapper.py

@@ -50,14 +50,14 @@ def load_2d_slices_at_time(images_path: str | dict, t: int, do_normalize: bool =
         slice_paths_at_t = sorted(glob(images_path % t))
         if len(slice_paths_at_t) == 0:
             raise FileNotFoundError(f"No image at time {t} was found")
-        x = np.array([np.array(Image.open(img)) for img in slice_paths_at_t])
+        x = imread(slice_paths_at_t)
     elif isinstance(images_path, dict):
         file_extension = os.path.splitext(images_path["h5_file"])[1]
         assert file_extension in [".h5", ".hdf5"], "Currently only TIFF sequences or HDF5 dataset are supported"
 
         import h5py
         with h5py.File(images_path["h5_file"], 'r') as f:
-            x = f[images_path["dset"]][t - 1, images_path["channel"], :, :, :]
+            x = f["default"][t - 1, images_path["channel"], :, :, :]
     else:
         raise ValueError("image_paths should be a str for TIFF sequences or dict for HDF5 dataset")
 

Examples/use_stardist/track_stardist_single_mode-h5.ipynb

@@ -100,18 +100,18 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "2023-09-26 14:40:01.505383: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:937] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero\n",
-      "2023-09-26 14:40:01.510975: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:937] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero\n",
-      "2023-09-26 14:40:01.511674: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:937] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero\n",
-      "2023-09-26 14:40:01.512420: I tensorflow/core/platform/cpu_feature_guard.cc:142] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  AVX2 AVX512F FMA\n",
+      "2024-01-09 13:52:38.479539: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:937] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero\n",
+      "2024-01-09 13:52:38.482970: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:937] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero\n",
+      "2024-01-09 13:52:38.483351: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:937] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero\n",
+      "2024-01-09 13:52:38.483869: I tensorflow/core/platform/cpu_feature_guard.cc:142] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  AVX2 AVX512F FMA\n",
       "To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.\n",
-      "2023-09-26 14:40:01.512820: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:937] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero\n",
-      "2023-09-26 14:40:01.513241: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:937] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero\n",
-      "2023-09-26 14:40:01.513648: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:937] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero\n",
-      "2023-09-26 14:40:01.748405: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:937] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero\n",
-      "2023-09-26 14:40:01.748815: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:937] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero\n",
-      "2023-09-26 14:40:01.749180: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:937] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero\n",
-      "2023-09-26 14:40:01.749544: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1510] Created device /job:localhost/replica:0/task:0/device:GPU:0 with 10035 MB memory:  -> device: 0, name: NVIDIA GeForce RTX 3080 Ti, pci bus id: 0000:01:00.0, compute capability: 8.6\n"
+      "2024-01-09 13:52:38.484683: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:937] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero\n",
+      "2024-01-09 13:52:38.485084: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:937] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero\n",
+      "2024-01-09 13:52:38.485460: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:937] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero\n",
+      "2024-01-09 13:52:38.740138: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:937] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero\n",
+      "2024-01-09 13:52:38.740558: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:937] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero\n",
+      "2024-01-09 13:52:38.740921: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:937] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero\n",
+      "2024-01-09 13:52:38.741269: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1510] Created device /job:localhost/replica:0/task:0/device:GPU:0 with 10035 MB memory:  -> device: 0, name: NVIDIA GeForce RTX 3080 Ti, pci bus id: 0000:01:00.0, compute capability: 8.6\n"
      ]
     }
    ],
@@ -151,8 +151,8 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "2023-09-26 14:40:02.335379: I tensorflow/compiler/mlir/mlir_graph_optimization_pass.cc:185] None of the MLIR Optimization Passes are enabled (registered 2)\n",
-      "2023-09-26 14:40:02.928110: I tensorflow/stream_executor/cuda/cuda_dnn.cc:369] Loaded cuDNN version 8101\n"
+      "2024-01-09 13:52:39.321889: I tensorflow/compiler/mlir/mlir_graph_optimization_pass.cc:185] None of the MLIR Optimization Passes are enabled (registered 2)\n",
+      "2024-01-09 13:52:39.873823: I tensorflow/stream_executor/cuda/cuda_dnn.cc:369] Loaded cuDNN version 8101\n"
      ]
     },
     {
@@ -170,8 +170,7 @@
    ],
    "source": [
     "path_results = \"./mikami_test/\"\n",
-    "path_raw_images = {\"h5_file\":\"./mikami_test/virtual_array.h5\",\n",
-    "                   \"dset\": \"raw_images\",\n",
+    "path_raw_images = {\"h5_file\":\"/home/wen/BIG_DATA_1/Mikami_free_moving_worm/20231218/raw_gzip.h5\",\n",
     "                   \"channel\": 0}\n",
     "\n",
     "# Load raw image at vol 1\n",