mo-image-identifier:基于图像的蘑菇识别

### *Tools for doing image-based mushroom identification* - [**@github.com**](https://github.com/Jesssullivan/image-identifer) <br> - [**@github.io**](https://jesssullivan.github.io/image-identifer/) <br> ***Overview:*** - [**Setup**](#setup) <br> - [**Artifacts**](#artifacts) <br> - [**Preprocess**](#preprocess) <br> - [**Artifacts**](#artifacts) <br> - [**Train**](#train) <br> - [**Structures**](#structures) <br> - [**Notes**](#notes) <br> - - - <h4 id="setup"> </h4> ### *Setup:* ``` # venv: python3 -m venv mushroomobserver_venv source mushroomobserver_venv/bin/activate pip3 install -r requirements.txt ``` <h4 id="artifacts"> </h4> |***Artifacts:***|[*train.tgz*](https://mo.columbari.us/static/train.tgz)|[*test.tgz*](https://mo.columbari.us/static/test.tgz)| |---|---|---| |[*images.tgz*](https://mo.columbari.us/static/images.tgz) |[*images.json*](https://mo.columbari.us/static/images.json)|[*gbif.zip*](https://mo.columbari.us/static/gbif.zip)| - - - <h4 id="preprocess"> </h4> ### *Preprocess:* ``` python3 preprocess ``` - Fetches & saves off gbif archive to `./static/` - Checks the archive, tries loading it into memory etc - Fetches Leaflet Annotator binary & licenses from [JessSullivan/MerlinAI-Interpreters](https://github.com/Jesssullivan/MerlinAI-Interpreters); Need to commit annotator *(as of 03/16/21)*, still fussing with a version for Mushroom Observer - Generates an `images.json` file from the 500 assets selected by Joe & Nathan - Downloads, organizes the 500 selected assets from *images.mushroomoberver.org* at `./static/images/<category>/<id>.jpg` - writes out images archive - More or less randomly divvies up testing & training image sets - writes out example testing/training archives; (while training it'll probably be easier to resample directly from images.tgz from keras) ### *Train:* ``` python3 train ``` - Fetches, divvies & shuffles train / validation sets from within Keras using archive available at [*mo.columbari.us/static/images.tgz*](https://mo.columbari.us/static/images.tgz) - More or less running Google's demo transfer learning training script in [`train/training_v1.py`](train/training_v1.py) as of *03/17/21*, still need to bring in training operations and whatnot from merlin_ai/ repo --> experiment with Danish Mycology Society's ImageNet v4 notes ***Google Colab:*** - [@gvanhorn38](https://github.com/gvanhorn38/) pointed out Google Colabs's neat Juptyer notebook service will train models for free if things are small enough- I have no idea what the limits are- fiddle with their [***intro to image classification on Google Colab here***](https://colab.research.google.com/github/tensorflow/docs/blob/master/site/en/tutorials/images/classification.ipynb), its super cool! ***Jupyter:*** - One may also open and run notebooks locally like this: - [rendered pdf version available over here](train/notebook/training_v1.pdf) - rename ipython notebook: ``` cp train/notebook/training_v1.ipynb.bak train/notebook/training_v1.ipynb ``` - launch jupyter: ``` jupyter notebook ``` - or without authentication: ``` jupyter notebook --ip='*' --NotebookApp.token='' --NotebookApp.password='' ``` - - - <h4 id="structures"> </h4> ### *Structures:* - *Leaflet Annotator `images.json` Structure:* - **id**: *taxonID* The MO taxon id - **category_id**: The binomen defined in the `./static/sample_select_assets.csv`; for directories and URIs this is converted to snake case. - **url**: Temporary elastic ip address this asset will be available from, just to reduce any excessive / redundant traffic to *images.mushroomobserver.org* - **src**: *imageURL* The asset's source URL form Mushroom Observer ``` [{ "id": "12326", "category_id": "Peltula euploca", "url": "https://mo.columbari.us/static/images/peltula_euploca/290214.jpg" "src": "https://images.mushroomobserver.org/640/290214.jpg" }] ``` - *Selected asset directory structure:* ``` ├── static ├── gbif.zip ├── images | ... │   └── peltula_euploca │   ├── 290214.jpg │   ... │   └── 522128.jpg │   ... ├── images.json ├── images.tgz ├── js │   ├── leaflet.annotation.js │   └── leaflet.annotation.js.LICENSE.txt └── sample_select_assets.csv ... ``` - - - <h4 id="notes"> </h4> #### *Notes:* *...Progress:* <br/> | ... | *51%*, ...a ways to go... | |---|---| |  |  | *Fiddling with the archive:* - `MODwca.gbif[1].id`: Integer: This is the Mushroom Observer taxon id, e.g. - `https://mushroomobserver.org/13` - `https://images.mushroomobserver.org/640/13.jpg` - `MODwca.gbif[1].data:`: Dictionary: DWCA row data, e.g. - `MODwca.gbif[1].data['http://rs.gbif.org/terms/1.0/gbifID']` = `13` - `MODwca.gbif[1].data['http://rs.tdwg.org/dwc/terms/recordedBy']` = `Nathan Wilson`