def main(args):
# parse arguments
model_path = args.path
save = args.save
# ============= LOAD MODEL AND PREPROCESSING CONFIGURATION ================
# load model and info
model, info, _ = utils.load_model_HDF5(model_path)
# set parameters
input_directory = info["data"]["input_directory"]
architecture = info["model"]["architecture"]
loss = info["model"]["loss"]
rescale = info["preprocessing"]["rescale"]
shape = info["preprocessing"]["shape"]
color_mode = info["preprocessing"]["color_mode"]
vmin = info["preprocessing"]["vmin"]
vmax = info["preprocessing"]["vmax"]
nb_validation_images = info["data"]["nb_validation_images"]
# =================== LOAD VALIDATION PARAMETERS =========================
model_dir_name = os.path.basename(str(Path(model_path).parent))
finetune_dir = os.path.join(
os.getcwd(),
"results",
input_directory,
architecture,
loss,
model_dir_name,
"finetuning",
)
subdirs = os.listdir(finetune_dir)
for subdir in subdirs:
logger.info("testing with finetuning parameters from \n{}...".format(
os.path.join(finetune_dir, subdir)))
try:
with open(
os.path.join(finetune_dir, subdir,
"finetuning_result.json"), "r") as read_file:
validation_result = json.load(read_file)
except FileNotFoundError:
logger.warning("run finetune.py before testing.\nexiting script.")
sys.exit()
min_area = validation_result["best_min_area"]
threshold = validation_result["best_threshold"]
method = validation_result["method"]
dtype = validation_result["dtype"]
# ====================== PREPROCESS TEST IMAGES ==========================
# get the correct preprocessing function
preprocessing_function = get_preprocessing_function(architecture)
# initialize preprocessor
preprocessor = Preprocessor(
input_directory=input_directory,
rescale=rescale,
shape=shape,
color_mode=color_mode,
preprocessing_function=preprocessing_function,
)
# get test generator
nb_test_images = preprocessor.get_total_number_test_images()
test_generator = preprocessor.get_test_generator(
batch_size=nb_test_images, shuffle=False)
# retrieve test images from generator
imgs_test_input = test_generator.next()[0]
# retrieve test image names
filenames = test_generator.filenames
# predict on test images
imgs_test_pred = model.predict(imgs_test_input)
# instantiate TensorImages object
tensor_test = postprocessing.TensorImages(
imgs_input=imgs_test_input,
imgs_pred=imgs_test_pred,
vmin=vmin,
vmax=vmax,
method=method,
dtype=dtype,
filenames=filenames,
)
# ====================== CLASSIFICATION ==========================
# retrieve ground truth
y_true = get_true_classes(filenames)
# predict classes on test images
y_pred = predict_classes(resmaps=tensor_test.resmaps,
min_area=min_area,
threshold=threshold)
# confusion matrix
tnr, fp, fn, tpr = confusion_matrix(y_true, y_pred,
normalize="true").ravel()
# initialize dictionary to store test results
test_result = {
"min_area": min_area,
"threshold": threshold,
"TPR": tpr,
"TNR": tnr,
"score": (tpr + tnr) / 2,
"method": method,
"dtype": dtype,
}
# ====================== SAVE TEST RESULTS =========================
# create directory to save test results
save_dir = os.path.join(
os.getcwd(),
"results",
input_directory,
architecture,
loss,
model_dir_name,
"test",
subdir,
)
if not os.path.isdir(save_dir):
os.makedirs(save_dir)
# save test result
with open(os.path.join(save_dir, "test_result.json"),
"w") as json_file:
json.dump(test_result, json_file, indent=4, sort_keys=False)
# save classification of image files in a .txt file
classification = {
"filenames": filenames,
"predictions": y_pred,
"truth": y_true,
"accurate_predictions": np.array(y_true) == np.array(y_pred),
}
df_clf = pd.DataFrame.from_dict(classification)
with open(os.path.join(save_dir, "classification.txt"), "w") as f:
f.write(
"min_area = {}, threshold = {}, method = {}, dtype = {}\n\n".
format(min_area, threshold, method, dtype))
f.write(df_clf.to_string(header=True, index=True))
# print classification results to console
with pd.option_context("display.max_rows", None, "display.max_columns",
None):
print(df_clf)
# save segmented resmaps
if save:
save_segmented_images(tensor_test.resmaps, threshold, filenames,
save_dir)
# print test_results to console
print("test results: {}".format(test_result))
def main(args):
# get parsed arguments from user
input_dir = args.input_dir
architecture = args.architecture
color_mode = args.color
loss = args.loss
batch_size = args.batch
# check arguments
check_arguments(architecture, color_mode, loss)
# get autoencoder
autoencoder = AutoEncoder(input_dir, architecture, color_mode, loss,
batch_size)
# load data as generators that yield batches of preprocessed images
preprocessor = Preprocessor(
input_directory=input_dir,
rescale=autoencoder.rescale,
shape=autoencoder.shape,
color_mode=autoencoder.color_mode,
preprocessing_function=autoencoder.preprocessing_function,
)
train_generator = preprocessor.get_train_generator(
batch_size=autoencoder.batch_size, shuffle=True)
validation_generator = preprocessor.get_val_generator(
batch_size=autoencoder.batch_size, shuffle=True)
# find best learning rates for training
autoencoder.find_opt_lr(train_generator, validation_generator)
# train
autoencoder.fit()
# save model
autoencoder.save()
if args.inspect:
# -------------- INSPECTING VALIDATION IMAGES --------------
logger.info("generating inspection plots of validation images...")
# create a directory to save inspection plots
inspection_val_dir = os.path.join(autoencoder.save_dir,
"inspection_val")
if not os.path.isdir(inspection_val_dir):
os.makedirs(inspection_val_dir)
inspection_val_generator = preprocessor.get_val_generator(
batch_size=autoencoder.learner.val_data.samples, shuffle=False)
imgs_val_input = inspection_val_generator.next()[0]
filenames_val = inspection_val_generator.filenames
# get reconstructed images (i.e predictions) on validation dataset
logger.info("reconstructing validation images...")
imgs_val_pred = autoencoder.model.predict(imgs_val_input)
# convert to grayscale if RGB
if color_mode == "rgb":
imgs_val_input = tf.image.rgb_to_grayscale(imgs_val_input).numpy()
imgs_val_pred = tf.image.rgb_to_grayscale(imgs_val_pred).numpy()
# remove last channel since images are grayscale
imgs_val_input = imgs_val_input[:, :, :, 0]
imgs_val_pred = imgs_val_pred[:, :, :, 0]
# instantiate TensorImages object to compute validation resmaps
tensor_val = postprocessing.TensorImages(
imgs_input=imgs_val_input,
imgs_pred=imgs_val_pred,
vmin=autoencoder.vmin,
vmax=autoencoder.vmax,
method=autoencoder.loss,
dtype="float64",
filenames=filenames_val,
)
# generate and save inspection validation plots
tensor_val.generate_inspection_plots(group="validation",
save_dir=inspection_val_dir)
# -------------- INSPECTING TEST IMAGES --------------
logger.info("generating inspection plots of test images...")
# create a directory to save inspection plots
inspection_test_dir = os.path.join(autoencoder.save_dir,
"inspection_test")
if not os.path.isdir(inspection_test_dir):
os.makedirs(inspection_test_dir)
nb_test_images = preprocessor.get_total_number_test_images()
inspection_test_generator = preprocessor.get_test_generator(
batch_size=nb_test_images, shuffle=False)
imgs_test_input = inspection_test_generator.next()[0]
filenames_test = inspection_test_generator.filenames
# get reconstructed images (i.e predictions) on validation dataset
logger.info("reconstructing test images...")
imgs_test_pred = autoencoder.model.predict(imgs_test_input)
# convert to grayscale if RGB
if color_mode == "rgb":
imgs_test_input = tf.image.rgb_to_grayscale(
imgs_test_input).numpy()
imgs_test_pred = tf.image.rgb_to_grayscale(imgs_test_pred).numpy()
# remove last channel since images are grayscale
imgs_test_input = imgs_test_input[:, :, :, 0]
imgs_test_pred = imgs_test_pred[:, :, :, 0]
# instantiate TensorImages object to compute test resmaps
tensor_test = postprocessing.TensorImages(
imgs_input=imgs_test_input,
imgs_pred=imgs_test_pred,
vmin=autoencoder.vmin,
vmax=autoencoder.vmax,
method=autoencoder.loss,
dtype="float64",
filenames=filenames_test,
)
# generate and save inspection test plots
tensor_test.generate_inspection_plots(group="test",
save_dir=inspection_test_dir)
logger.info("done.")
return
def inspect_images(model_path):
# load model for inspection
logger.info("loading model for inspection...")
model, info, _ = utils.load_model_HDF5(model_path)
save_dir = os.path.dirname(model_path)
input_dir = info["data"]["input_directory"]
# architecture = info["model"]["architecture"]
# loss = info["model"]["loss"]
rescale = info["preprocessing"]["rescale"]
shape = info["preprocessing"]["shape"]
color_mode = info["preprocessing"]["color_mode"]
vmin = info["preprocessing"]["vmin"]
vmax = info["preprocessing"]["vmax"]
nb_validation_images = info["data"]["nb_validation_images"]
# instantiate preprocessor object to preprocess validation and test inspection images
preprocessor = Preprocessor(
input_directory=input_dir,
rescale=rescale,
shape=shape,
color_mode=color_mode,
)
# -------------- INSPECTING VALIDATION IMAGES --------------
logger.info("generating inspection plots for validation images...")
inspection_val_generator = preprocessor.get_val_generator(
batch_size=nb_validation_images, shuffle=False)
imgs_val_input = inspection_val_generator.next()[0]
filenames_val = inspection_val_generator.filenames
# get indices of validation inspection images
val_insp_i = [
filenames_val.index(filename)
for filename in config.FILENAMES_VAL_INSPECTION
]
imgs_val_input = imgs_val_input[val_insp_i]
# reconstruct validation inspection images (i.e predict)
imgs_val_pred = model.predict(imgs_val_input)
# instantiate ResmapPlotter object to compute resmaps
postproc_val = postprocessing.ResmapPlotter(
imgs_input=imgs_val_input,
imgs_pred=imgs_val_pred,
filenames=config.FILENAMES_VAL_INSPECTION,
color="grayscale",
vmin=vmin,
vmax=vmax,
)
# generate resmaps and save
fig_res_val = postproc_val.generate_inspection_figure()
fig_res_val.savefig(os.path.join(save_dir, "fig_insp_val.svg"))
# -------------- INSPECTING TEST IMAGES --------------
logger.info("generating inspection plots for test images...")
nb_test_images = preprocessor.get_total_number_test_images()
inspection_test_generator = preprocessor.get_test_generator(
batch_size=nb_test_images, shuffle=False)
# get preprocessed test images
imgs_test_input = inspection_test_generator.next()[0]
filenames_test = inspection_test_generator.filenames
# get indices of test inspection images
test_insp_i = [
filenames_test.index(filename)
for filename in config.FILENAMES_TEST_INSPECTION
]
imgs_test_input = imgs_test_input[test_insp_i]
# reconstruct inspection test images (i.e predict)
imgs_test_pred = model.predict(imgs_test_input)
# instantiate ResmapPlotter object to compute resmaps
postproc_test = postprocessing.ResmapPlotter(
imgs_input=imgs_test_input,
imgs_pred=imgs_test_pred,
filenames=config.FILENAMES_TEST_INSPECTION,
color="grayscale",
vmin=vmin,
vmax=vmax,
)
# generate resmaps and save
fig_res_test = postproc_test.generate_inspection_figure()
fig_res_test.savefig(os.path.join(save_dir, "fig_insp_test.svg"))
# --------------------------------------------------
# fig_score_insp = postproc_test.generate_score_scatter_plot(
# inspection_test_generator, model_path, filenames_test_insp
# )
# fig_score_insp.savefig(os.path.join(save_dir, "fig_score_insp.svg"))
# fig_score_test = postproc_test.generate_score_scatter_plot(
# inspection_test_generator, model_path
# )
# fig_score_test.savefig(os.path.join(save_dir, "fig_score_test.svg"))
return