From 71dc02b47b66dd7421dbdaba8e5ad52a53202fdf Mon Sep 17 00:00:00 2001
From: David Humphrey <david.andrew.humphrey@gmail.com>
Date: Sat, 14 Oct 2023 11:07:07 -0400
Subject: [PATCH] Create a proper setup system for others to use

---
 .gitattributes                 |     3 +-
 .gitignore                     |     9 +-
 .vscode/extensions.json        |     3 +-
 README.md                      |    28 +
 megadetector_detector.py       |     4 +-
 pixi.lock                      | 10864 +++++++++++++++++++++++++++++++
 pixi.toml                      |    26 +
 requirements.apple-silicon.txt |     2 +
 requirements.txt               |     2 +
 yolo_fish_detector.py          |     4 +-
 10 files changed, 10933 insertions(+), 12 deletions(-)
 create mode 100644 pixi.lock
 create mode 100644 pixi.toml
 create mode 100644 requirements.apple-silicon.txt
 create mode 100644 requirements.txt

diff --git a/.gitattributes b/.gitattributes
index 2db6bda..22cbe20 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -1,5 +1,6 @@
 # Project specific information for git
 # telling it we always use Unix line endings
-
 # Auto detect text files and perform LF normalization
 * text=auto
+# We store our ONNX models in git-lfs
+*.onnx filter=lfs diff=lfs merge=lfs -text
diff --git a/.gitignore b/.gitignore
index 929a098..c002899 100644
--- a/.gitignore
+++ b/.gitignore
@@ -154,11 +154,8 @@ cython_debug/
 # Ignore video files
 video/
 
-# Ignore the yolo-fish model because it is too large
-yolov4_1_3_608_608_static.onnx
-
-# Ignore the megadetector model because it is to large
-md_v5a_1_3_640_640_static.onnx
-
 # Ignore Mac Finder files
 .DS_Store
+
+# Ingnore the .pixi/ folder for dependencies
+.pixi/
diff --git a/.vscode/extensions.json b/.vscode/extensions.json
index fb04c96..f7d8fbf 100644
--- a/.vscode/extensions.json
+++ b/.vscode/extensions.json
@@ -1,6 +1,7 @@
 {
   "recommendations": [
     "streetsidesoftware.code-spell-checker",
-    "ms-python.black-formatter"
+    "ms-python.black-formatter",
+    "charliermarsh.ruff",
   ]
 }
diff --git a/README.md b/README.md
index 6e081e5..3c1b900 100644
--- a/README.md
+++ b/README.md
@@ -1,2 +1,30 @@
 # Automated Camera Trapping Identification and Organization Network (ACTION)
 
+## Setup
+
+Action is written in Python and requires a number of dependencies and large machine learning models (~778M) to be installed and downloaded.
+
+The easiest way to use it is with the [pixi](https://prefix.dev/docs/pixi/overview) package manager.  Pixi installs everything you need into a local `.pixi` folder (i.e., at the root of the project), without needing to modify your system.
+
+1. [Clone](https://github.com/humphrem/action.git) this repo using `git`
+2. [Install pixi](https://prefix.dev/docs/pixi/overview#installation)
+3. Start a terminal and navigate to the root of the Action project folder, `cd action`
+4. Enter the command `pixi run setup` to download, install, and setup everything you'll need
+
+## Using Action
+
+### Pixi Shell
+
+Each time you want to use Action, you need to open a terminal and navigate to the Action folder, then start a shell with `pixi`:
+
+```sh
+pixi shell
+```
+
+This will make all of the dependencies installed with `pixi run setup` available.
+
+You can exit the pixi shell by using:
+
+```sh
+exit
+```
diff --git a/megadetector_detector.py b/megadetector_detector.py
index aa3fa4b..de068f7 100644
--- a/megadetector_detector.py
+++ b/megadetector_detector.py
@@ -10,8 +10,8 @@
 
 from base_detector import BaseDetector
 
-# The Megadetector ONNX model should be in the same directory as this file
-megadetector_model_path = "md_v5a_1_3_640_640_static.onnx"
+# The Megadetector ONNX model should be in the ./models directory and needs to be pulled with git-lfs
+megadetector_model_path = "models/md_v5a_1_3_640_640_static.onnx"
 # Input images should be 640 x 640
 megadetector_image_width = 640
 megadetector_image_height = 640
diff --git a/pixi.lock b/pixi.lock
new file mode 100644
index 0000000..0dc757c
--- /dev/null
+++ b/pixi.lock
@@ -0,0 +1,10864 @@
+metadata:
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+    win-64: e90c2ee71ad70fc0a1c8302029533a7d1498f2bffcd0eaa8d2934700e775dc1d
+    osx-64: e90c2ee71ad70fc0a1c8302029533a7d1498f2bffcd0eaa8d2934700e775dc1d
+  channels:
+  - url: https://conda.anaconda.org/conda-forge/
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+  - osx-64
+  - osx-arm64
+  - win-64
+  sources: []
+  time_metadata: null
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+  inputs_metadata: null
+  custom_metadata: null
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+- name: libopenvino-paddle-frontend
+  version: 2023.1.0
+  manager: conda
+  platform: linux-64
+  dependencies:
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+    libgcc-ng: '>=12'
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+  dependencies:
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+    libgcc-ng: '>=12'
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+    ncurses: '>=6.3,<7.0a0'
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+  optional: false
+  category: main
+  build: h9e318b2_1
+  arch: x86_64
+  subdir: osx-64
+  build_number: 1
+  license: GPL-3.0-only
+  license_family: GPL
+  size: 255870
+  timestamp: 1679532707590
+- name: libsqlite
+  version: 3.43.2
+  manager: conda
+  platform: osx-64
+  dependencies:
+    libzlib: '>=1.2.13,<1.3.0a0'
+  url: https://conda.anaconda.org/conda-forge/osx-64/libsqlite-3.43.2-h92b6c6a_0.conda
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+    sha256: e0ba6181738d5250213576167935a97dc3ee581032f716dd4e2acbc817c763dc
+  optional: false
+  category: main
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+  subdir: osx-64
+  build_number: 0
+  license: Unlicense
+  size: 885196
+  timestamp: 1696959083399
+- name: tk
+  version: 8.6.13
+  manager: conda
+  platform: osx-64
+  dependencies:
+    libzlib: '>=1.2.13,<1.3.0a0'
+  url: https://conda.anaconda.org/conda-forge/osx-64/tk-8.6.13-hef22860_0.conda
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+  optional: false
+  category: main
+  build: hef22860_0
+  arch: x86_64
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diff --git a/pixi.toml b/pixi.toml
new file mode 100644
index 0000000..00ce0b1
--- /dev/null
+++ b/pixi.toml
@@ -0,0 +1,26 @@
+[project]
+name = "action"
+version = "0.1.0"
+description = "Automated Camera Trapping Identification and Organization Network (ACTION)"
+repository = "https://github.com/humphrem/action"
+authors = [ "Morgan Humphrey", "David Humphrey"]
+channels = ["conda-forge"]
+platforms = ["win-64", "linux-64", "osx-64", "osx-arm64"]
+
+[tasks]
+install-requirements = "pip install -r requirements.txt"
+download-models = "git lfs pull"
+setup = {depends_on=["install-requirements", "download-models"]}
+
+[target.osx-arm64.tasks]
+# On macOS ARM we use a different ONNX Runtime optimized for Apple Silicon
+install-requirements = "pip install -r requirements.apple-silicon.txt"
+
+[dependencies]
+python = "3.11.0.*"
+ffmpeg = "6.0.0.*"
+pip = "23.2.1.*"
+git-lfs = "3.4.0.*"
+git = "2.42.0.*"
+numpy = "1.26.0.*"
+opencv = "4.8.1.*"
diff --git a/requirements.apple-silicon.txt b/requirements.apple-silicon.txt
new file mode 100644
index 0000000..b8a13b3
--- /dev/null
+++ b/requirements.apple-silicon.txt
@@ -0,0 +1,2 @@
+opencv-python==4.8.1.78
+onnxruntime-silicon==1.16.0
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000..66b2956
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,2 @@
+opencv-python==4.8.1.78
+onnxruntime==1.16.1
diff --git a/yolo_fish_detector.py b/yolo_fish_detector.py
index ef91075..1c545aa 100644
--- a/yolo_fish_detector.py
+++ b/yolo_fish_detector.py
@@ -13,8 +13,8 @@
 # https://github.com/Tianxiaomo/pytorch-YOLOv4/blob/master/License.txt
 
 
-# The YOLO-Fish ONNX model should be in the same directory as this file
-yolo_fish_model_path = "yolov4_1_3_608_608_static.onnx"
+# The YOLO-Fish ONNX model should be in the ./models directory and needs to be pulled with git-lfs
+yolo_fish_model_path = "models/yolov4_1_3_608_608_static.onnx"
 # Input images should be 608 x 608
 yolo_fish_image_width = 608
 yolo_fish_image_height = 608