cleanup in ignores, docker file and minor adjustments

Author: DocMinus

.dockerignore

@@ -6,19 +6,20 @@
 **/.vs
 **/.conda
 /.temp/*
-**/.env
-**/.venv
+**/.env/
+**/.venv/
 **/env/
 **/venv/
 **/.git
-**/lightning_logs
+optional_standalone_no_server/
 
 Makefile
 win_make.bat
 README.md
 gnurff*.*
 tmp.txt
 Dockerfile*
+requirements_mac.txt
 *.yaml
 *.yml
 .git

.gitignore

@@ -13,7 +13,6 @@
 **/venv
 /.temp
 
-**/optional_standalone_no_server
 
 # installer files
 **/*egg-info
@@ -41,15 +40,16 @@ gnurff*.py
 gnurff*.txt
 
 # Image files
-# allow images for examples to be uploaded to the repo
-# *.png
-# *.emf
-# *.gif
-# *.svg
-# *.jpg
-# *.jpeg
-# *.bmp
-
+*.png
+*.emf
+*.gif
+*.svg
+*.jpg
+*.jpeg
+*.bmp
+# keep these two for demo purposes
+!not_structure.gif
+!structure.png
 
 # macOS system files
 .DS_Store

Dockerfile

@@ -3,9 +3,8 @@
 FROM python:3.11.9-slim
 RUN apt-get update && \
     apt-get install -y build-essential libgl1-mesa-glx libglib2.0-0 curl && \
-    rm -rf /var/lib/apt/lists/*
-
-RUN pip install --upgrade pip
+    rm -rf /var/lib/apt/lists/* && \
+    pip install --upgrade pip
 
 # Keeps Python from buffering stdout and stderr to avoid situations where
 # the application crashes without emitting any logs due to buffering.
@@ -18,15 +17,15 @@ COPY . /app
 # Install any needed packages specified in requirements.txt
 RUN pip install --trusted-host pypi.python.org --no-cache-dir -r requirements.txt
 # add the adapted decimer image classifier and decimerapi packages
-RUN python -m pip install /app/packages/decimer_ic
+# RUN python -m pip install /app/packages/decimer_ic
 
 # To avoid redownloading the model every time the container is started; needs mounting when running the container
 RUN mkdir -p /home/appuser/.data/DECIMER-V2
 
 # Add a non-root user to run the app
-RUN adduser --disabled-password --gecos '' appuser
-RUN chown -R appuser:appuser /app
-RUN chown -R appuser:appuser /home/appuser/.data
+RUN adduser --disabled-password --gecos '' appuser \
+    && chown -R appuser:appuser /app \
+    && chown -R appuser:appuser /home/appuser/.data
 USER appuser
 
 # open port to listen to requests from outside

Makefile

@@ -7,27 +7,27 @@ DOCKER_USER = DocMinus
 all: buildx tag push
 
 build:
-	@echo -e "\n------------------------------------"
+	@echo "\n------------------------------------"
 	@echo "Building the image $(IMAGE_NAME):"
 	docker build -t $(IMAGE_NAME) .
 	@echo "------------------------------------\n"
 	@echo "Use 'docker-compose up -d' to start the container"
 
 buildx:
-	@echo -e "\n------------------------------------"
+	@echo "\n------------------------------------"
 	@echo "Building the image $(IMAGE_NAME):"
 	docker buildx build --platform linux/amd64,linux/arm64 -t $(IMAGE_NAME) .
 	@echo "------------------------------------\n"
 	@echo "Use 'docker-compose up -d' to start the container"
 
 tag: 
-	@echo -e "\n------------------------------------"
+	@echo "\n------------------------------------"
 	@echo "Tagging the image $(IMAGE_NAME):"
 	docker tag $(IMAGE_NAME) $(IMAGE_NAME):latest
 	@echo "------------------------------------\n"
 
 push: tag
-	@echo -e "\n------------------------------------"
+	@echo "\n------------------------------------"
 	@echo "Pushing the image $(IMAGE_NAME):"
 	docker push $(DOCKER_USER)/$(IMAGE_NAME):latest
 	@echo "------------------------------------\n"

README.md

@@ -74,11 +74,21 @@ conda activate decimerserver
 
 ## Usage
 ### Docker
-`docker-compose up -d` to start the API server, ´docker-compose down´ to stop. <br>
+Edit the compose file for it to use the correct image, depending if you build it yourself or if you pulled it from dockerhub, then:<br>
+To start:
+```shell
+docker-compose up -d
+```
+And to stop:
+```shell
+docker-compose down 
+```
 (depending on your install it might be ´docker compose (space, no -))´.<br>
 
 ### Local (non docker) server version
-`python decimer_server.py`<br>
+```shell
+python decimer_server.py
+```
 
 ### Example usage
 The server runs on localhost:8099. This can be changed to ip-address:portnumber if you want to run another machine (or cloud even).<br>

decimer_exampel.py

@@ -4,26 +4,27 @@
 
 license: MIT
 Copyright (c) 2024 DocMinus
-V0.3.1 - updated example code
+V0.3.1b - updated example code
 2024-12-23
 
 """
 
 from pathlib import Path
+
 from decimerapi.decimerapi import DecimerAPI
 
 
 def main():
     decimer_api = DecimerAPI()  # using default host locahost on port 8099
     print(decimer_api.server_status())
 
-    current_file_path = Path(__file__).resolve()
-    input_image = current_file_path.parents[0] / "structure.png"
+    current_directory = Path(__file__).resolve()
+    input_image = current_directory.parents[0] / "structure.png"
     # both string or path can be used
     # input_image = r"/Users/a/dev/DecimerAPI/structure.png"
     smiles = decimer_api.call_image2smiles(input_image, hand_drawn=False)
     print(smiles)
-    input_image = current_file_path.parents[0] / "not_structure.gif"
+    input_image = current_directory.parents[0] / "not_structure.gif"
     smiles = decimer_api.call_image2smiles(input_image, hand_drawn=False)
     print(smiles)
 

docker-compose.yml

@@ -3,7 +3,7 @@
 services:
   decimer_api:
     image: docker.io/docminus/decimer_api:latest # for dockerhub image
-    # image: decimer_api:latest  # for locally built image
+    #image: decimer_api:latest # for locally built image
     container_name: decimerapi
     ports:
       - "8099:8099"

optional_standalone_no_server/decimer_standalone_no_server.py

@@ -4,20 +4,24 @@
 
 license: MIT
 Copyright (c) 2024 DocMinus
-V0.2.0 - following the decimer_server.py version
+V0.2.1 - following the decimer_server.py version
 
 Main difference: aside from no server, imagepath is used directly instead of base64 encoding
 
 !beware: this version does not check for large image sizes or correct file types as the server version together with the API does
 !It also doesn't support emf files as the use of the API would, but is in principle possible.
+!Remember: startup time may be long due to model loading
 
-2024-12-22
+2024-12-22 / 2025-01-15
 """
 
+from pathlib import Path
+
 from DECIMER.decimer import *
 from decimer_image_classifier import DecimerImageClassifier
 
 decimer_classifier = DecimerImageClassifier()
+IC_TRESHOLD: float = 0.3
 
 
 def _getdecimersmiles(
@@ -45,7 +49,7 @@ def _getdecimersmiles(
 
 
 def predict_smiles(
-    image_path: str, is_hand_drawn: bool = False, classify_image: bool = True
+    image_name: str, is_hand_drawn: bool = False, classify_image: bool = True
 ) -> str:
     """
     This function reads the image file from the provided path and does the conversion to SMILES.
@@ -56,13 +60,13 @@ def predict_smiles(
     """
 
     if classify_image:
-        if decimer_classifier.get_classifier_score(image_path) < 0.3:
-            decoded_image = config.decode_image(image_path)
+        if decimer_classifier.get_classifier_score(image_name) < IC_TRESHOLD:
+            decoded_image = config.decode_image(image_name)
             smiles = _getdecimersmiles(decoded_image, is_hand_drawn)
             if smiles is not None:
                 return smiles
     else:
-        decoded_image = config.decode_image(image_path)
+        decoded_image = config.decode_image(image_name)
         smiles = _getdecimersmiles(decoded_image, is_hand_drawn)
         if smiles is not None:
             return smiles
@@ -71,8 +75,11 @@ def predict_smiles(
 
 
 def main():
+    current_directory = Path(__file__).resolve()
+    # 1 for folder level above (0 for same level)
+    input_image = str(current_directory.parents[1] / "structure.png")
     smiles = predict_smiles(
-        "/Users/a/dev/DecimerAPI/structure.png",
+        input_image,
         is_hand_drawn=False,
         classify_image=True,
     )

requirements.txt

@@ -2,6 +2,6 @@ uvicorn==0.32.1
 fastapi==0.115.5
 python-multipart==0.0.19
 decimer==2.7.1
+./packages/decimer_ic
 # matplotlib==3.9.3 # only required for decimer classifier training
 ./packages/decimerapi
-./packages/decimer_ic

requirements_mac.txt

@@ -4,6 +4,6 @@ python-multipart==0.0.19
 decimer==2.7.1
 tensorflow-macos==2.15.0
 tensorflow-metal==1.1.0
+./packages/decimer_ic
 # matplotlib==3.9.3 # only required for decimer classifier training
 ./packages/decimerapi
-./packages/decimer_ic