Added fathom_net_crop tool

pyproject.toml

@@ -3,86 +3,78 @@ requires = ["hatchling"]
 build-backend = "hatchling.build"
 
 [tool.hatch.build.targets.wheel]
-packages = ["src/DD_tools"]
+packages = ["src/TreeOfLife_toolbox"]
 
 [project]
-name = "DD_tools"
+name = "TreeOfLife_toolbox"
 dynamic = ["version"]
 authors = [
     { name = "Andrey Kopanev", email = "kopanev.1@osu.edu" },
     { name = "Elizabeth G. Campolongo", email = "e.campolongo479@gmail.com" },
     { name = "Matthew J. Thompson", email = "thompson.m.j@outlook.com" },
 ]
-description = "A tool for downloading files from a list of URLs in parallel."
+description = "A tool for processing datasets that was downloaded using the distributed-downloader package."
 readme = "README.md"
-requires-python = ">=3.8"
+requires-python = ">=3.10, <3.12"
 classifiers = [
+    "Development Status :: 4 - Beta",
     "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
     "License :: OSI Approved :: MIT License",
     "Operating System :: OS Independent",
 ]
 dependencies = [
     "attrs",
     "brotli",
-    "certifi",
-    "charset-normalizer",
     "cramjam",
     "cython",
-    "exceptiongroup",
     "fsspec",
-    "hatchling",
-    "idna",
     "inflate64",
-    "iniconfig",
-    "mpi4py < 4",
+    "mpi4py",
     "multivolumefile",
-    "numpy",
     "opencv-python",
-    "packaging",
     "pandas",
     "pathspec",
     "pillow",
-    "pip",
-    "pluggy",
     "psutil",
-    "py4j",
     "pyarrow",
     "pybcj",
     "pycryptodomex",
     "pyppmd",
     "pyspark",
-    "pytest",
-    "python-dateutil",
     "python-dotenv",
-    "pytz",
     "pyyaml",
     "pyzstd",
     "requests",
     "setuptools",
-    "six",
     "texttable",
-    "tomli",
     "trove-classifiers",
     "typing-extensions",
-    "tzdata",
-    "urllib3",
     "wheel"
 ]
 
 [project.optional-dependencies]
-dev = ["pytest"]
+dev = [
+    "pytest",
+    "ruff"
+]
 
 keywords = [
     "parallel",
     "distributed",
-    "download",
     "url",
+    "mpi-applications",
+    "dataset-generation",
 ]
 
 [project.urls]
 Homepage = "https://github.com/Imageomics/distributed-downloader"
 Repository = "https://github.com/Imageomics/distributed-downloader.git"
 "Bug Tracker" = "https://github.com/Imageomics/distributed-downloader/issues"
 
+[project.scripts]
+tree_of_life_toolbox = "TreeOfLife_toolbox.main.main:main"
+
 [tool.hatch.version]
-path = "src/DD_tools/main/__about__.py"
+path = "src/TreeOfLife_toolbox/main/__about__.py"

scripts/tools_filter.slurm

@@ -19,11 +19,10 @@ executor_memory="64G"
 module load spark/3.4.1
 module load miniconda3/23.3.1-py310
 source "${REPO_ROOT}/.venv/bin/activate"
-export PYTHONPATH=${PYTHONPATH}:"${REPO_ROOT}/src":"${REPO_ROOT}/distributed-downloader"
 
 pbs-spark-submit \
     --driver-memory $driver_memory \
     --executor-memory $executor_memory \
-    "${REPO_ROOT}/src/distributed_downloader/tools/filter.py" \
+    "${TOOLBOX_PATH}/main/filter.py" \
     "${tool_name}" \
     > "${logs_dir}/tool_filter.log"

scripts/tools_scheduler.slurm

@@ -19,7 +19,6 @@ module load miniconda3/23.3.1-py310
 source "${REPO_ROOT}/.venv/bin/activate"
 export PYARROW_IGNORE_TIMEZONE=1
 export I_MPI_JOB_RESPECT_PROCESS_PLACEMENT=0
-export PYTHONPATH=${PYTHONPATH}:"${REPO_ROOT}/src":"${REPO_ROOT}/distributed-downloader"
 
 srun \
   --mpi=pmi2 \
@@ -28,4 +27,4 @@ srun \
   --cpus-per-task=1 \
   --mem=0 \
   --output="${logs_dir}/tool_scheduler.log" \
-  python "${REPO_ROOT}/src/distributed_downloader/tools/scheduler.py" "${tool_name}"
+  python "${TOOLBOX_PATH}/main/scheduler.py" "${tool_name}"

scripts/tools_verifier.slurm

@@ -19,7 +19,6 @@ module load miniconda3/23.3.1-py310
 source "${REPO_ROOT}/.venv/bin/activate"
 export PYARROW_IGNORE_TIMEZONE=1
 export I_MPI_JOB_RESPECT_PROCESS_PLACEMENT=0
-export PYTHONPATH=${PYTHONPATH}:"${REPO_ROOT}/src":"${REPO_ROOT}/distributed-downloader"
 
 srun \
   --mpi=pmi2 \
@@ -28,4 +27,4 @@ srun \
   --cpus-per-task=1 \
   --mem=0 \
   --output="${logs_dir}/tool_verifier.log" \
-  python "${REPO_ROOT}/src/distributed_downloader/tools/verification.py" "${tool_name}"
+  python "${TOOLBOX_PATH}/main/verification.py" "${tool_name}"

scripts/tools_worker.slurm

@@ -19,7 +19,6 @@ module load miniconda3/23.3.1-py310
 source "${REPO_ROOT}/.venv/bin/activate"
 export PYARROW_IGNORE_TIMEZONE=1
 export I_MPI_JOB_RESPECT_PROCESS_PLACEMENT=0
-export PYTHONPATH=${PYTHONPATH}:"${REPO_ROOT}/src":"${REPO_ROOT}/distributed-downloader"
 
 srun \
   --mpi=pmi2 \
@@ -28,4 +27,4 @@ srun \
   --cpus-per-task="$TOOLS_CPU_PER_WORKER" \
   --mem=0 \
   --output="${logs_dir}/tool_worker-%2t.log" \
-  python "${REPO_ROOT}/src/distributed_downloader/tools/runner.py" "${tool_name}"
+  python "${TOOLBOX_PATH}/main/runner.py" "${tool_name}"

src/TreeOfLife_toolbox/__init__.py

@@ -0,0 +1 @@
+from TreeOfLife_toolbox import fathom_net_crop

src/TreeOfLife_toolbox/fathom_net_crop/README.md

@@ -0,0 +1,64 @@
+# FathomNet Image Cropping Tool
+
+This tool is used to crop images from the FathomNet dataset using the bounding box coordinates provided in an external
+CSV file. The cropping operation extracts regions of interest from full-sized images and preserves them as separate
+image entries with updated metadata.
+
+## How It Works
+
+The tool consists of three main components:
+
+1. **FathomnetCropFilter**: Identifies all valid image partitions in the dataset that can be processed. Creates a simple
+   list of server/partition pairs for the scheduler.
+
+2. **FathomnetCropScheduleCreation**: Creates a processing schedule by distributing server/partition pairs across
+   available worker nodes to balance the workload.
+
+3. **FathomnetCropRunner**: Performs the actual image cropping operation by:
+    - Loading images that have corresponding bounding box entries
+    - Cropping each image according to the specified coordinates (x, y, width, height)
+    - Computing new hash values and metadata for the cropped images
+    - Saving the results in a structure that mirrors the original dataset
+
+## Required Configuration
+
+Add these fields to your configuration file:
+
+- `bb_csv_path`: Path to the CSV file containing the bounding box information with columns:
+    - `image_uuid`: UUID of the original image
+    - `bb_uuid`: UUID for the bounding box entry
+    - `tol_uuid`: UUID to be assigned to the cropped image
+    - `x`, `y`: Top-left coordinates of the bounding box
+    - `width`, `height`: Dimensions of the bounding box
+
+- `image_crop_path`: Path where the cropped images will be stored
+
+## Pre-conditions
+
+- The source image directory follows the distributed-downloader structure:
+  ```
+  <path_to_output_folder>/<images_folder>/
+  ├── server_name=<server1>
+  │   ├── partition_id=<id>
+  │   │   ├── successes.parquet
+  │   │   ├── errors.parquet
+  │   │   └── completed
+  │   └── partition_id=<id2>
+  │       ├── ...
+  └── server_name=<server2>
+      └── ...
+  ```
+- The bounding box CSV file exists and contains the required columns
+- The original images are stored in parquet files with binary image data and metadata
+- Images with multi-channel RGB data (3 channels)
+
+## Post-conditions
+
+- Cropped images are saved in the specified output path using the same directory structure as the source
+- Each cropped image has:
+    - Updated UUID and source_id based on values from the bounding box CSV
+    - Updated resized_size reflecting the dimensions of the cropped region
+    - New hashsum_resized value calculated from the cropped image data
+- If a bounding box extends beyond the image boundaries, it will be automatically clipped to fit within the image
+- All original metadata is preserved, except for fields that needed to be updated due to cropping
+- A verification structure is created to track which server/partition pairs have been successfully processed

src/TreeOfLife_toolbox/fathom_net_crop/__init__.py

@@ -0,0 +1,5 @@
+from .classes import (
+    FathomnetCropFilter,
+    FathomnetCropScheduleCreation,
+    FathomnetCropRunner,
+)