RSGISLib Keras Image Chips Classification

These functions are first attempts and connecting spatial image data with window based (convolutional) neural networks. These functions and other will be developed as our research and understanding of these methods move forward.

The application is similar to the RSGISLib classification modules. However, custom functions have been created to extract image training data and you need to keep in mind some of things about the network structure to fit to the shape/order of the data extracted.

Get Sample Data

Training data is defined using a raster image where for each pixel defined as the training data for a given class a window centred on that pixel will be extracted.

If that raster is already available then you can use the rsgislib.imageutils.extractChipZoneImageBandValues2HDF function to extract the training data to a HDF5 file:

import rsgislib.imageutils

chip_h_size = 5

imgBandInfo = []
imgBandInfo.append(rsgislib.imageutils.ImageBandInfo('sen2_refl_img.kea', 'sen2', [7,9,3]))

mangrove_train_pxls_img = 'mangrove_sample_pxls.kea'
mangrove_train_chips_h5 = 'mangrove_sample_chips.h5'
rsgislib.imageutils.extractChipZoneImageBandValues2HDF(imgBandInfo, mangrove_train_pxls_img, 1, chip_h_size, mangrove_train_chips_h5)


The chip_h_size is half the size of the chip extracted. The chip size will always be an odd size, for example an input value of 5 will result in an output chip size of 11. A value of 10 a chip size of 21.

If vector layers are being used to define the training data then the helper function rsgislib.classification.get_class_training_chips_data can be used:

import rsgislib.classification
import rsgislib.imageutils

chip_h_size = 5

mangrove_samples = 'class_samples_mangrove.h5'
other_samples = 'class_samples_other.h5'
water_samples = 'class_samples_water.h5'

classVecSampleInfo = []
classVecSampleInfo.append(rsgislib.classification.ClassVecSamplesInfoObj(id=1, classname="Mangrove", vecfile="class_samples_mangrove.geojson", veclyr="class_samples_mangrove", fileH5=mangrove_samples))
classVecSampleInfo.append(rsgislib.classification.ClassVecSamplesInfoObj(id=2, classname="Other", vecfile="class_samples_other.geojson", veclyr="class_samples_other", fileH5=other_samples))
classVecSampleInfo.append(rsgislib.classification.ClassVecSamplesInfoObj(id=3, classname="Water", vecfile="class_samples_water.geojson", veclyr="class_samples_water", fileH5=water_samples))

imgBandInfo = []
imgBandInfo.append(rsgislib.imageutils.ImageBandInfo('sen2_refl_img.kea', 'sen2', [7,9,3]))

tmp_path = './tmp'

rsgislib.classification.get_class_training_chips_data(imgBandInfo, classVecSampleInfo, chip_h_size, tmp_path)

To split those input samples into training, validation and training data then the rsgislib.classification.split_chip_sample_train_valid_test function is used:

mangrove_samples_train = 'class_samples_mangrove_train.h5'
mangrove_samples_valid = 'class_samples_mangrove_valid.h5'
mangrove_samples_test = 'class_samples_mangrove_test.h5'
rsgislib.classification.split_chip_sample_train_valid_test(mangrove_samples, mangrove_samples_train, mangrove_samples_valid, mangrove_samples_test, 1000, 1000, 5000)

other_samples_train = 'class_samples_other_train.h5'
other_samples_valid = 'class_samples_other_valid.h5'
other_samples_test = 'class_samples_other_test.h5'
rsgislib.classification.split_chip_sample_train_valid_test(other_samples, other_samples_train, other_samples_valid, other_samples_test, 1000, 1000, 5000)

water_samples_train = 'class_samples_water_train.h5'
water_samples_valid = 'class_samples_water_valid.h5'
water_samples_test = 'class_samples_water_test.h5'
rsgislib.classification.split_chip_sample_train_valid_test(water_samples, water_samples_train, water_samples_valid, water_samples_test, 1000, 1000, 5000)

Training Classifer

First you need to define a classifier using Keras:

import keras.optimizers
import keras.losses
from keras.models import Sequential
from keras.layers import Dense, Conv2D, MaxPooling2D, Dropout, Flatten, Activation

# input_shape: [n_bands, chip_size, chip_size]
# chip_size = (chip_h_size * 2) + 1
# data_format must be 'channels_first' (i.e., bands first)

cls_mdl = Sequential()
cls_mdl.add(Conv2D(filters=32, kernel_size=(3,3), strides=(1,1), padding='same', input_shape=[3, 11, 11], data_format='channels_first'))
cls_mdl.add(MaxPooling2D(pool_size=(2,2), strides=1))
# The final layer must be the same size as the number of classes and use a softmax activation.
cls_mdl.add(Dense(3, activation='softmax'))

cls_mdl.compile(optimizer=keras.optimizers.Adam(), loss=keras.losses.categorical_crossentropy, metrics=['accuracy'])

The classification model can then be trained, note this can take a lot of time (hours/days) and it might be recommended that you have your system setup so Keras/Tensorflow can use the GPU for processing:

import rsgislib.classification.classkeraschips

clsinfodict = dict()
clsinfodict['Mangroves'] = rsgislib.classification.ClassInfoObj(id=0, out_id=1, trainfileH5=mangroves_samples_train, testfileH5=mangroves_samples_test, validfileH5=mangroves_samples_valid, red=0, green=255, blue=0)
clsinfodict['Other'] = rsgislib.classification.ClassInfoObj(id=1, out_id=2, trainfileH5=other_samples_train, testfileH5=other_samples_test, validfileH5=other_samples_valid, red=100, green=100, blue=100)
clsinfodict['Water'] = rsgislib.classification.ClassInfoObj(id=2, out_id=3, trainfileH5=water_samples_train, testfileH5=water_samples_test, validfileH5=water_samples_valid, red=0, green=0, blue=255)

out_mdl_file = 'basic_chip_mdl.h5'

rsgislib.classification.classkeraschips.train_keras_chips_pixel_classifier(cls_mdl, clsinfodict, out_mdl_file)

Apply Classifier

The following code allows you to re-opening the model you have trained, it would be common for the training phase to take a long period of time (hours, even days!!) so you will likely have separate training and application scripts:

from keras.models import load_model
cls_mdl = load_model('basic_chip_mdl.h5')

Apply the classifier to scene:

img_mask = 'mangrove_habitat_img.kea'
out_cls_img = 'class_out_img.kea'
rsgislib.classification.classkeraspxl.apply_keras_pixel_classifier(clsinfodict, cls_mdl, img_mask, 1, imgs_info, chip_h_size, out_cls_img, 'KEA')

Training Functions

rsgislib.classification.classkeraschips.train_keras_chips_pixel_classifier(cls_mdl, cls_info_dict, out_mdl_file=None, train_epochs=5, train_batch_size=32)

A function which trains a neural network defined using the keras API for the classification of remotely sensed data. A dict of class information, as ClassInfoObj objects, is defined with the training data.

This function requires that tensorflow and keras modules to be installed.

  • out_mdl_file – The output model which can be loaded to perform a classification.

  • cls_info_dict – dict (key is string with class name) of ClassInfoObj objects defining the training data.

  • out_mdl_file – A file path to save the trained model as a hdf5 file. If None then ignored.

  • train_epochs – The number of epochs to use for training

  • train_batch_size – The batch size to use for training.

Classify Functions

rsgislib.classification.classkeraschips.apply_keras_chips_pixel_classifier(class_train_info, keras_cls_mdl, in_img_mask, img_mask_val, img_file_info, chip_size, out_class_img, norm_function=None, gdalformat='KEA', class_clr_names=True)

This function applies a trained single pixel keras model to an image. The function train_keras_pixel_classifier can be used to train such as model. The output image will contain the hard membership of the predicted class.

  • class_train_info – dict (where the key is the class name) of rsgislib.classification.ClassInfoObj objects which will be used to train the classifier (i.e., train_keras_pixel_classifier()), provide pixel value id and RGB class values.

  • keras_cls_mdl – a trained keras model object, with a input dimensions equivlent to the number of image bands specified in the imgFileInfo input and output layer which provides an output array of the length of the number of classes.

  • in_img_mask – is an image file providing a mask to specify where should be classified. Simplest mask is all the valid data regions (rsgislib.imageutils.gen_valid_mask)

  • img_mask_val – the pixel value within the imgMask to limit the region to which the classification is applied. Can be used to create a heirachical classification.

  • img_file_info – a list of rsgislib.imageutils.ImageBandInfo objects (also used within rsgislib.zonalstats.extract_zone_img_band_values_to_hdf) to identify which images and bands are to be used for the classification so it adheres to the training data.

  • out_class_img – Output image which will contain the hard classification.

  • norm_function – Normalisation function to apply before running classification

  • chip_size – is the chip size to be extracted.

  • gdalformat – is the output image format - all GDAL supported formats are supported.

  • class_clr_names – default is True and therefore a colour table will the colours specified in ClassInfoObj and a class_names (from classTrainInfo) column will be added to the output file.

rsgislib.classification.classkeraschips.train_keras_chips_ref_classifier(cls_mdl, train_data_file, valid_data_file, test_data_file, n_classes, out_mdl_file=None, train_epochs=5, train_batch_size=32)

A function which trains a neural network defined using the keras API for the classification of remotely sensed data.

This function requires that tensorflow and keras modules to be installed.

  • cls_mdl – The Keras model which has already been defined.

  • train_data_file – a HDF5 file with training data (needs to have elements /DATA/DATA and /DATA/REF)

  • valid_data_file – a HDF5 file with validation data (needs to have elements /DATA/DATA and /DATA/REF)

  • test_data_file – a HDF5 file with testing data (needs to have elements /DATA/DATA and /DATA/REF)

  • n_classes – integer specifying the number of classes within the system

  • out_mdl_file – A file path to save the trained model as a hdf5 file. If None then ignored.

  • train_epochs – The number of epochs to use for training

  • train_batch_size – The batch size to use for training.