auto download

Author: ErinWeisbart

dockerfiles/RunCellpose_CellposeOmnipose/Makefile

@@ -1,4 +1,4 @@
-NAME ?= runcellpose_omnipose_no_pretrained
+NAME ?= runcellpose_omnipose_with_pretrained
 TAG ?= 1.0.2
 REPO ?= cellprofiler
 IMG := $(REPO)/$(NAME):$(TAG)

dockerfiles/RunCellpose_CellposeOmnipose/download_cellpose_models.py

@@ -0,0 +1,35 @@
+import cellpose
+import cellpose_omni
+from cellpose.models import MODEL_NAMES
+
+for m in ["cyto", "nuclei", "cyto2"]:
+    model = cellpose.models.Cellpose(gpu=True, model_type=m)
+    if model in ("cyto", "nuclei", "cyto2"):
+        size_model_name =  cellpose.models.size_model_path(model)
+
+import urllib.request
+import zipfile
+import os
+
+url = "https://files.osf.io/v1/resources/xmury/providers/osfstorage/646d978ef4be380b5362bb64/?zip="
+filename = "omnipose_models.zip"
+
+try:
+    urllib.request.urlretrieve(url, filename)
+    print(f"File downloaded successfully to {filename}")
+except Exception as e:
+    print(f"Error downloading file: {e}")
+
+destination_directory = os.path.expanduser("~/.cellpose/models/")
+
+# Create the destination directory if it doesn't already exist
+os.makedirs(destination_directory, exist_ok=True)
+
+try:
+    # Open the zip file in read mode ('r')
+    with zipfile.ZipFile(filename, 'r') as zip_ref:
+        print(f"Extracting all contents of '{filename}' to '{destination_directory}'...")
+        # Extract all the contents to the specified directory
+        zip_ref.extractall(destination_directory)
+except Exception as e:
+    print(f"An unexpected error occurred: {e}")