Fix api docker (#10)

tuke307 · web-flow · commit a8aa4e89b179 · 2025-02-15T01:41:55.000+01:00
* bump: update tree-disk-pith version to 0.1.5

* refactor: move directory creation and model downloads to main execution context

* refactor: remove unused method parameter from detect_pith function

* feat: add checks to skip model download if already exists

* chore: update .dockerignore to exclude environment files

* feat: add volume mappings for models, input, and output directories in compose.yml

* refactor: remove root_dir argument and related validations from CLI and config

* refactor: convert output_dir to string and update EndPoints reference in postprocessing

* docs: remove root directory option from README

* feat: support platform-specific devernay binaries for Linux and macOS

* refactor: disable debug mode in test cases for treediskrings
diff --git a/compose.yml b/compose.yml
@@ -8,3 +8,7 @@ services:
       - ./tree-disk-api/.env.production.local
     ports:
       - 3001:3100
+    volumes:
+      - ./tree-disk-api/models:/app/models
+      - ./tree-disk-api/input:/app/input
+      - ./tree-disk-api/output:/app/output
diff --git a/tree-disk-api/.dockerignore b/tree-disk-api/.dockerignore
@@ -33,4 +33,8 @@ docker.compose.yml
 output/
 input/
 tests/
-models/
+models/
+
+# env
+.env
+.env.*
diff --git a/tree-disk-api/poetry.lock b/tree-disk-api/poetry.lock
diff --git a/tree-disk-api/pyproject.toml b/tree-disk-api/pyproject.toml
@@ -14,7 +14,7 @@ uvicorn = "^0.32.0"
 gunicorn = "^23.0.0"
 python-multipart = "^0.0.17"
 tree-disk-segmentation = "^0.1.3"
-tree-disk-pith = "^0.1.4"
+tree-disk-pith = "^0.1.5"
 tree-disk-rings = "^0.4.7" 
 gdown = "^5.2.0"
 python-dotenv = "^1.0.1"
diff --git a/tree-disk-api/src/api/endpoints/pith.py b/tree-disk-api/src/api/endpoints/pith.py
@@ -43,7 +43,6 @@ async def detect_pith(
         input_image=path,
         model_path=YOLO_MODEL_PATH,
         output_dir=OUTPUT_DIR,
-        method="apd_dl",
         save_results=SAVE_RESULTS,
         debug=DEBUG,
     )
diff --git a/tree-disk-api/src/config/preparation.py b/tree-disk-api/src/config/preparation.py
@@ -15,6 +15,12 @@ def download_u2net_model():
     """
     Download the model from Google Drive.
     """
+    if U2NET_MODEL_PATH.exists():
+        logger.info(
+            f"U2NET model already exists at {U2NET_MODEL_PATH}, skipping download."
+        )
+        return
+
     file_id = "10HXfiEMT4QapiRXMSSEJEAViRmRmSDUW"
     url = f"https://drive.google.com/uc?id={file_id}"
 
@@ -27,6 +33,12 @@ def download_yolo_model():
     """
     Download the model from Google Drive.
     """
+    if YOLO_MODEL_PATH.exists():
+        logger.info(
+            f"YOLO model already exists at {YOLO_MODEL_PATH}, skipping download."
+        )
+        return
+
     file_id = "1_-dDH4DNiL8wbgiPWPaNqne7kbJyZc8z"
     url = f"https://drive.google.com/uc?id={file_id}"
 
@@ -44,6 +56,8 @@ def create_dirs():
     MODEL_PATH.mkdir(parents=True, exist_ok=True)
 
 
-create_dirs()
-download_u2net_model()
-download_yolo_model()
+if __name__ == "__main__":
+    # When running this file directly, create dirs and download models.
+    create_dirs()
+    download_u2net_model()
+    download_yolo_model()
diff --git a/tree-disk-api/src/main.py b/tree-disk-api/src/main.py
@@ -5,6 +5,7 @@
 import uvicorn
 import logging
 
+from .config.preparation import create_dirs
 from .config.settings import DEBUG, log_settings
 from .api.router import router
 
@@ -22,6 +23,8 @@ async def lifespan(app: FastAPI):
     # print all settings in debug
     log_settings()
 
+    create_dirs()
+
     yield
 
 
diff --git a/tree-disk-rings/README.md b/tree-disk-rings/README.md
@@ -71,7 +71,6 @@ tree-disk-rings \
 | `--cx` | int | Yes | - | Pith x-coordinate |
 | `--cy` | int | Yes | - | Pith y-coordinate |
 | `--output_dir` | str | No | `./output` | Output directory path |
-| `--root` | str | No | Current dir | Root directory of the repository |
 | `--sigma` | float | No | 3.0 | Gaussian kernel parameter for edge detection |
 | `--th_low` | float | No | 5.0 | Low threshold for gradient magnitude |
 | `--th_high` | float | No | 20.0 | High threshold for gradient magnitude |
@@ -105,5 +104,5 @@ pytest
 
 3. Compile the external C code:
 ```bash
-cd ./externas/devernay_1.0 && make clean && make
+cd ./externals/devernay_1.0 && make clean && make
 ```
diff --git a/tree-disk-rings/pyproject.toml b/tree-disk-rings/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "tree-disk-rings"
-version = "0.4.7"
+version = "0.4.8"
 description = "A package for tree disk rings detection in images"
 authors = ["Tony <tonymeissner70@gmail.com>"]
 license = "MIT"
@@ -11,7 +11,8 @@ keywords = ["tree", "rings", "image processing"]
 packages = [{ include = "treediskrings", from = "src" }]
 
 include = [
-    "src/treediskrings/externals/devernay.out",
+    "src/treediskrings/externals/linux/devernay.out",
+    "src/treediskrings/externals/macos/devernay.out",
 ]
 
 [tool.poetry.dependencies]
diff --git a/tree-disk-rings/src/treediskrings/cli.py b/tree-disk-rings/src/treediskrings/cli.py
@@ -25,12 +25,6 @@ def parse_arguments() -> argparse.Namespace:
     parser.add_argument(
         "--output_dir", default="./output", help="Output directory", metavar="DIR"
     )
-    parser.add_argument(
-        "--root_dir",
-        default="./",
-        help="Root directory of the repository",
-        metavar="DIR",
-    )
     parser.add_argument(
         "--sigma",
         type=float,
@@ -106,7 +100,6 @@ def main():
     # Configure settings from CLI arguments
     configure(
         input_image=args.input_image,
-        root_dir=args.root_dir,
         output_dir=args.output_dir,
         cx=args.cx,
         cy=args.cy,
diff --git a/tree-disk-rings/src/treediskrings/config.py b/tree-disk-rings/src/treediskrings/config.py
@@ -26,9 +26,6 @@ class Config:
     output_dir: Path = Path("./output/")
     """Directory where results and debug information will be saved."""
 
-    root_dir: Path = Path("./")
-    """Root directory of the project."""
-
     # -------------- Image Processing Parameters ----------------
 
     cx: Optional[int] = None
@@ -87,17 +84,8 @@ def __post_init__(self):
 
     def _validate_and_set_paths(self):
         """Validate and set all path-related fields."""
-        # Validate root directory
-        root_path = Path(self.root_dir).resolve()
-        if not root_path.exists():
-            raise ValueError(f"Root directory does not exist: {root_path}")
-        self.root_dir = root_path
-
         # Set up output directory
         output_path = Path(self.output_dir)
-        if not output_path.is_absolute():
-            output_path = root_path / output_path
-
         try:
             self.output_dir = ensure_directory(output_path, clear=self.clear_output)
         except PermissionError:
@@ -110,8 +98,6 @@ def _validate_and_set_paths(self):
         # Validate input image if provided
         if self.input_image:
             input_path = Path(self.input_image)
-            if not input_path.is_absolute():
-                input_path = root_path / input_path
 
             if not input_path.exists():
                 raise ValueError(f"Input image file does not exist: {input_path}")
diff --git a/tree-disk-rings/src/treediskrings/detection/canny_devernay_edge_detector.py b/tree-disk-rings/src/treediskrings/detection/canny_devernay_edge_detector.py
@@ -1,30 +1,50 @@
 import os
 from pathlib import Path
 from typing import Dict, List, Tuple
+from venv import logger
 
 import cv2
 import numpy as np
 import pandas as pd
 from importlib import resources
+import sys
 
 from ..config import config
 
 
 def get_devernay_path() -> str:
-    """Get the absolute path to the devernay binary."""
-    package = "treediskrings.externals"
-
-    # Get the path to the resource file
-    devernay_path = str(resources.files(package) / "devernay.out")
-
-    # Ensure the file exists and is executable
-    if not os.path.isfile(devernay_path):
-        raise FileNotFoundError(f"Binary not found at {devernay_path}")
-
-    # Make sure it's executable
-    os.chmod(devernay_path, 0o755)
-
-    return devernay_path
+    """Get the absolute path to the appropriate devernay binary based on the platform."""
+    base_package = "treediskrings.externals"
+
+    # Determine subdirectory and binary name based on platform
+    if sys.platform.startswith("linux"):
+        subdir = "linux"
+        binary_name = "devernay.out"
+    elif sys.platform == "darwin":
+        subdir = "macos"
+        binary_name = "devernay.out"
+    elif sys.platform == "win32":
+        logger.warning(
+            "Windows platform detected. Devernay binary not supported on Windows."
+        )
+        # subdir = "windows"
+        # binary_name = "devernay.exe"
+    else:
+        raise RuntimeError(f"Unsupported platform: {sys.platform}")
+
+    # Construct the path to the binary using the resources API
+    binary_path = resources.files(base_package) / subdir / binary_name
+    binary_path = str(binary_path)  # Convert to string if needed by os functions
+
+    # Ensure the file exists
+    if not os.path.isfile(binary_path):
+        raise FileNotFoundError(f"Binary not found at {binary_path}")
+
+    # Make sure it's executable (skip on Windows)
+    if sys.platform != "win32":
+        os.chmod(binary_path, 0o755)
+
+    return binary_path
 
 
 def load_curves(output_txt: Path) -> np.ndarray:
diff --git a/tree-disk-rings/src/treediskrings/externals/linux/__init__.py b/tree-disk-rings/src/treediskrings/externals/linux/__init__.py
diff --git a/tree-disk-rings/src/treediskrings/externals/linux/devernay.out b/tree-disk-rings/src/treediskrings/externals/linux/devernay.out
diff --git a/tree-disk-rings/src/treediskrings/externals/macos/__init__.py b/tree-disk-rings/src/treediskrings/externals/macos/__init__.py
diff --git a/tree-disk-rings/src/treediskrings/externals/macos/devernay.out b/tree-disk-rings/src/treediskrings/externals/macos/devernay.out
diff --git a/tree-disk-rings/src/treediskrings/processing/postprocessing.py b/tree-disk-rings/src/treediskrings/processing/postprocessing.py
@@ -1196,7 +1196,9 @@ def postprocessing(l_ch_c, l_nodes_c, img_pre):
     iteracion = [0]
 
     while True:
-        ctx = ChainContext(l_ch_p, idx_start, save_path=config.output_dir, img=img_pre)
+        ctx = ChainContext(
+            l_ch_p, idx_start, save_path=str(config.output_dir), img=img_pre
+        )
 
         while len(ctx.completed_chains) > 0:
             #  l_within_chains, inward_ring and outward_ring are attributes of ctx which are updated in next line
@@ -1281,7 +1283,7 @@ def complete_chains_if_required(ch_p):
     for chain in chain_list:
         if chain.is_closed() and chain.size < chain.nr:
             inward_chain, outward_chain, _ = get_inward_and_outward_visible_chains(
-                chain_list, chain, EndPoints.A
+                chain_list, chain, EndPoints.A.value
             )
             if inward_chain is not None and outward_chain is not None:
                 complete_chain_using_2_support_ring(inward_chain, outward_chain, chain)
diff --git a/tree-disk-rings/tests/test_treediskrings.py b/tree-disk-rings/tests/test_treediskrings.py
@@ -18,7 +18,7 @@ def test_treediskringss_without_save():
         cx=1204,
         cy=1264,
         save_results=False,
-        debug=True,
+        debug=False,
     )
 
     # Run the detector
@@ -47,7 +47,7 @@ def test_treediskrings_with_save():
         cx=1204,
         cy=1264,
         save_results=True,
-        debug=True,
+        debug=False,
     )
 
     # Run the detector

-Original file line number
+Diff line change
 output/
 input/
 tests/
 -models/
 +models/
++
 +# env
 +.env
 +.env.*
Original file line number	Diff line number	Diff line change
`@@ -43,7 +43,6 @@ async def detect_pith(`
`43`	`43`	`input_image=path,`
`44`	`44`	`model_path=YOLO_MODEL_PATH,`
`45`	`45`	`output_dir=OUTPUT_DIR,`
`46`		`- method="apd_dl",`
`47`	`46`	`save_results=SAVE_RESULTS,`
`48`	`47`	`debug=DEBUG,`
`49`	`48`	`)`