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PlantVillage Image Classification Tutorial

Using AlexNet on Caffe to solve the PlantVillage image classification problem.

Environment

This tutorial is built around Caffe, and the instructions to install caffe can be found at : http://caffe.berkeleyvision.org/installation.html

Given that we will be using a Transfer Learning based approach, the requirement of a GPU is not strict, and all the instructions will work perfectly well on any modern and general purpose laptop or desktop. If you do not have a GPU on your laptop or desktop, make sure to build Caffe in CPU only mode.

Unfortunately Windows is not officially supported by Caffe, but there are a few unofficial Windows ports of Caffe listed on the above mentioned installation page. Instructions for Windows users to replicate this tutorial will be added soon.

After you have installed Caffe, make sure to set the $CAFFE_ROOT environment variable, as it is referenced numerous times in the following sections when calling caffe specific scripts. It should point to the root directory of your caffe source folder. You can set it by

export CAFFE_ROOT=<path_to_your_caffe_source_folder>

Data

The data for the PlantVillage Classification Challenge can be obtained at : https://www.crowdai.org/challenges/1/dataset_files

After logging in on the above page, you can download the Training Data and the Test Data and you should have the corresponding crowdai_train.tar and crowdai_test.tar files. For replicability of all the instructions across the whole tutorial, we would encourage you to create a folder at /home/<your_user_name>/plantvillage and save both of these files inside this newly created folder. Then you can extract both these files by :

    cd /home/<your_user_name>/plantvillage
    tar xvf crowdai_train.tar
    tar xvf crowdai_test.tar

Validation Set

To be able to get an estimate of how well the model if performing across the whole training, we will take a small subset of the training set and consider it as out validation set. We can do this by using the following python script:

    #!/usr/bin/env python

    # Note: this script needs to be present at
    #   /home/<your_user_name>/plantvillage/create_distribution.py
    # and executed from within the
    #   /home/<your_user_name>/plantvillage/
    # directory

    import glob
    import os
    import random
    import shutil

    TRAIN_PERCENTAGE = 70

    TRAIN_SET = []
    VAL_SET = []

    #Distribute the files into Training and Validation sets
    for _image in glob.glob("crowdai/*/*"):
        className = _image.split("/")[-2]

        # Some fileNames contain spaces, which creates some incompatibility with a preprocessing script shipped with caffe
        # Hence we replace all spaces in the filename with _
        newFileName = _image.split("/")[-1]
        newFileName = newFileName.replace(" ", "_")
        newFilePath = "crowdai/"+className+"/"+newFileName
        shutil.move(_image, newFilePath)

        if random.randint(0,100) < TRAIN_PERCENTAGE:
            TRAIN_SET.append((newFilePath, className.split("_")[-1]))
        else:
            VAL_SET.append((newFilePath, className.split("_")[-1]))

    #Write the distribution into a separate text files
    try:
        os.mkdir("lmdb")
    except:
        pass

    f = open("lmdb/train.txt", "w")
        for _entry in TRAIN_SET:
    f.write(_entry[0]+" "+_entry[1]+"\n")
    f.close()

    f = open("lmdb/val.txt", "w")
    for _entry in VAL_SET:
    f.write(_entry[0]+" "+_entry[1]+"\n")
    f.close()

This can then be executed by :

    cd /home/<your_user_name>/plantvillage
    python create_distribution.py

At the end of its execution, it will create a folder named lmdb with two text files by the name train.txt and val.txt. Each line in these two text files, correspond to the path to a single image and its corresponding class, and we randomly use ~70% of the available labelled data as the training set and the rest as the validation set. The distribution can be changed simply by changing the TRAIN_PERCENTAGE variable in the above script.

Preprocessing

As we are trying to fine-tune an AlexNet model, we will have to use input images of the exact same size as was used to train the said model. AlexNet was trained on images of size 256x256 pixels with randomized/central crop of 227x227 pixels which was eventually fed into the network. As the images in our dataset have varied image sizes, we will "squash" them all to 256x256 pixels before we feed into the adapted AlexNet architecture that we want to fine-tune. Apart from that, instead of having to deal with all images straight from the disk, we will store them in LMDB which is a high performance embedded transactional database. While Caffe does supports reading images directly from the disk, using LMDB as the datastore has quite significant performance gains.

Caffe ships with a utility to quickly convert images on disk into LMDB. To convert our training and validation sets, we will need to do :

    cd /home/<your_user_name>/plantvillage

    $CAFFE_ROOT/build/tools/convert_imageset \
         --resize_height 256 \
         --resize_width 256 \
         --shuffle \
         /home/<your_user_name>/plantvillage/ \
         lmdb/train.txt \
         lmdb/train_lmdb

    $CAFFE_ROOT/build/tools/convert_imageset \
        --resize_height 256 \
        --resize_width 256 \
        --shuffle \
        /home/<your_user_name>/plantvillage/ \
        lmdb/val.txt \
        lmdb/val_lmdb

which should spit out something along these lines : http://pastebin.com/ptymwZDm

A quick guide to some other features of the convert_imageset utility can be found here.

Then finally we compute the image mean for the training set which will be used later during both the training and prediction.

cd /home/<your_user_name>/plantvillage
$CAFFE_ROOT/build/tools/compute_image_mean lmdb/train_lmdb lmdb/mean.binaryproto

NOTE: $CAFFE_ROOT is the environment variable which should point to your caffe installation root. If the bin folder of your Caffe installation is in your system path, you can also simply try convert_imageset instead of $CAFFE_ROOT/build/tools/convert_imageset and compute_image_mean instead of $CAFFE_ROOT/build/tools/compute_image_mean