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cloud_fraction_fcn_viirs.py
cloud_fraction_fcn_viirs.py 38.16 KiB
import glob
import tensorflow as tf
from util.plot_cm import confusion_matrix_values
from util.setup import logdir, modeldir, now, ancillary_path
from util.util import EarlyStop, normalize, denormalize, get_grid_values_all
import os, datetime
import numpy as np
import pickle
import h5py
import xarray as xr
import gc
AUTOTUNE = tf.data.AUTOTUNE
LOG_DEVICE_PLACEMENT = False
PROC_BATCH_SIZE = 4
PROC_BATCH_BUFFER_SIZE = 5000
NumClasses = 5
if NumClasses == 2:
NumLogits = 1
else:
NumLogits = NumClasses
BATCH_SIZE = 128
NUM_EPOCHS = 80
TRACK_MOVING_AVERAGE = False
EARLY_STOP = True
NOISE_TRAINING = False
NOISE_STDDEV = 0.01
DO_AUGMENT = False
DO_SMOOTH = False
SIGMA = 1.0
DO_ZERO_OUT = False
# setup scaling parameters dictionary
mean_std_dct = {}
mean_std_file = ancillary_path+'mean_std_lo_hi_l2.pkl'
f = open(mean_std_file, 'rb')
mean_std_dct_l2 = pickle.load(f)
f.close()
mean_std_file = ancillary_path+'mean_std_lo_hi_l1b.pkl'
f = open(mean_std_file, 'rb')
mean_std_dct_l1b = pickle.load(f)
f.close()
mean_std_dct.update(mean_std_dct_l1b)
mean_std_dct.update(mean_std_dct_l2)
IMG_DEPTH = 1
label_param = 'cloud_probability'
params = ['temp_11_0um_nom', 'refl_0_65um_nom', label_param]
params_i = ['temp_11_0um_nom', 'refl_0_65um_nom', label_param]
data_params_half = ['temp_11_0um_nom']
data_params_full = ['refl_0_65um_nom']
label_idx_i = params_i.index(label_param)
label_idx = params.index(label_param)
print('data_params_half: ', data_params_half)
print('data_params_full: ', data_params_full)
print('label_param: ', label_param)
KERNEL_SIZE = 3 # target size: (128, 128)
X_LEN = Y_LEN = 128
if KERNEL_SIZE == 3:
slc_x = slice(1, int(X_LEN/2) + 3)
slc_y = slice(1, int(Y_LEN/2) + 3)
x_128 = slice(4, X_LEN + 4)
y_128 = slice(4, Y_LEN + 4)
# ----------------------------------------
def build_residual_conv2d_block(conv, num_filters, block_name, activation=tf.nn.relu, padding='SAME',
kernel_initializer='he_uniform', scale=None, kernel_size=3,
do_drop_out=True, drop_rate=0.5, do_batch_norm=True):
with tf.name_scope(block_name):
skip = tf.keras.layers.Conv2D(num_filters, kernel_size=kernel_size, padding=padding, kernel_initializer=kernel_initializer, activation=activation)(conv)
skip = tf.keras.layers.Conv2D(num_filters, kernel_size=kernel_size, padding=padding, activation=None)(skip)
if scale is not None:
skip = tf.keras.layers.Lambda(lambda x: x * scale)(skip)
if do_drop_out:
skip = tf.keras.layers.Dropout(drop_rate)(skip)
if do_batch_norm:
skip = tf.keras.layers.BatchNormalization()(skip)
conv = conv + skip
print(block_name+':', conv.shape)
return conv
def upsample_mean(grd):
bsize, ylen, xlen = grd.shape
up = np.zeros((bsize, ylen*2, xlen*2))
up[:, ::2, ::2] = grd[:, ::2, ::2]
up[:, 1::2, ::2] = grd[:, ::2, ::2]
up[:, ::2, 1::2] = grd[:, ::2, ::2]
up[:, 1::2, 1::2] = grd[:, ::2, ::2]
return up
def get_grid_cell_mean(grd_k):
# grd_k = np.where(np.isnan(grd_k), 0, grd_k)
a = grd_k[:, 0::2, 0::2]
b = grd_k[:, 1::2, 0::2]
c = grd_k[:, 0::2, 1::2]
d = grd_k[:, 1::2, 1::2]
mean = np.nanmean([a, b, c, d], axis=0)
return mean
def get_min_max_std(grd_k):
# grd_k = np.where(np.isnan(grd_k), 0, grd_k)
a = grd_k[:, 0::2, 0::2]
b = grd_k[:, 1::2, 0::2]
c = grd_k[:, 0::2, 1::2]
d = grd_k[:, 1::2, 1::2]
lo = np.nanmin([a, b, c, d], axis=0)
hi = np.nanmax([a, b, c, d], axis=0)
std = np.nanstd([a, b, c, d], axis=0)
avg = np.nanmean([a, b, c, d], axis=0)
return lo, hi, std, avg
def get_label_data(grd_k):
grd_k = np.where(np.isnan(grd_k), 0, grd_k)
grd_k = np.where(grd_k < 0.50, 0, 1)
a = grd_k[:, 0::2, 0::2]
b = grd_k[:, 1::2, 0::2]
c = grd_k[:, 0::2, 1::2]
d = grd_k[:, 1::2, 1::2]
s = a + b + c + d
cat_0 = (s == 0)
cat_1 = np.logical_and(s > 0, s < 4)
cat_2 = (s == 4)
s[cat_0] = 0
s[cat_1] = 1
s[cat_2] = 2
return s
def get_label_data_5cat(grd_k):
grd_k = np.where(np.isnan(grd_k), 0, grd_k)
grd_k = np.where(grd_k < 0.5, 0, 1)
a = grd_k[:, 0::2, 0::2]
b = grd_k[:, 1::2, 0::2]
c = grd_k[:, 0::2, 1::2]
d = grd_k[:, 1::2, 1::2]
s = a + b + c + d
cat_0 = (s == 0)
cat_1 = (s == 1)
cat_2 = (s == 2)
cat_3 = (s == 3)
cat_4 = (s == 4)
s[cat_0] = 0
s[cat_1] = 1
s[cat_2] = 2
s[cat_3] = 3
s[cat_4] = 4
return s
class SRCNN:
def __init__(self):
self.train_data = None
self.train_label = None
self.test_data = None
self.test_label = None
self.test_data_denorm = None
self.train_dataset = None
self.inner_train_dataset = None
self.test_dataset = None
self.eval_dataset = None
self.X_img = None
self.X_prof = None
self.X_u = None
self.X_v = None
self.X_sfc = None
self.inputs = []
self.y = None
self.handle = None
self.inner_handle = None
self.in_mem_batch = None
self.h5f_l1b_trn = None
self.h5f_l1b_tst = None
self.h5f_l2_trn = None
self.h5f_l2_tst = None
self.logits = None
self.predict_data = None
self.predict_dataset = None
self.mean_list = None
self.std_list = None
self.training_op = None
self.correct = None
self.accuracy = None
self.loss = None
self.pred_class = None
self.variable_averages = None
self.global_step = None
self.writer_train = None
self.writer_valid = None
self.writer_train_valid_loss = None
self.OUT_OF_RANGE = False
self.model = None
self.optimizer = None
self.ema = None
self.train_loss = None
self.train_accuracy = None
self.test_loss = None
self.test_accuracy = None
self.test_auc = None
self.test_recall = None
self.test_precision = None
self.test_confusion_matrix = None
self.test_true_pos = None
self.test_true_neg = None
self.test_false_pos = None
self.test_false_neg = None
self.test_labels = []
self.test_preds = []
self.test_probs = None
self.test_input = []
self.learningRateSchedule = None
self.num_data_samples = None
self.initial_learning_rate = None
self.data_dct = None
self.train_data_files = None
self.train_label_files = None
self.test_data_files = None
self.test_label_files = None
# self.n_chans = len(data_params_half) + len(data_params_full) + 1
self.n_chans = 5
self.X_img = tf.keras.Input(shape=(None, None, self.n_chans))
self.inputs.append(self.X_img)
tf.debugging.set_log_device_placement(LOG_DEVICE_PLACEMENT)
def get_in_mem_data_batch(self, idxs, is_training):
if is_training:
data_files = self.train_data_files
label_files = self.train_label_files
else:
data_files = self.test_data_files
label_files = self.test_label_files
data_s = []
label_s = []
for k in idxs:
f = data_files[k]
nda = np.load(f)
data_s.append(nda)
f = label_files[k]
nda = np.load(f)
label_s.append(nda)
input_data = np.concatenate(data_s)
input_label = np.concatenate(label_s)
data_norm = []
for param in data_params_half:
# If next 2 uncommented, take out get_grid_cell_mean
idx = params.index(param)
tmp = input_data[:, idx, :, :]
# idx = params_i.index(param)
# tmp = input_label[:, idx, :, :]
# tmp = get_grid_cell_mean(tmp)
tmp = tmp[:, slc_y, slc_x]
tmp = normalize(tmp, param, mean_std_dct)
data_norm.append(tmp)
for param in data_params_full:
idx = params_i.index(param)
tmp = input_label[:, idx, :, :]
lo, hi, std, avg = get_min_max_std(tmp)
lo = normalize(lo, param, mean_std_dct)
hi = normalize(hi, param, mean_std_dct)
avg = normalize(avg, param, mean_std_dct)
data_norm.append(lo[:, slc_y, slc_x])
data_norm.append(hi[:, slc_y, slc_x])
data_norm.append(avg[:, slc_y, slc_x])
# ---------------------------------------------------
# If next uncommented, take out get_grid_cell_mean
# tmp = input_data[:, label_idx, :, :]
tmp = input_label[:, label_idx_i, :, :]
tmp = get_grid_cell_mean(tmp)
tmp = tmp[:, slc_y, slc_x]
data_norm.append(tmp)
# ---------
data = np.stack(data_norm, axis=3)
data = data.astype(np.float32)
# -----------------------------------------------------
# -----------------------------------------------------
label = input_label[:, label_idx_i, :, :]
label = label[:, y_128, x_128]
if NumClasses == 5:
label = get_label_data_5cat(label)
else:
label = get_label_data(label)
label = np.where(np.isnan(label), 0, label)
label = np.expand_dims(label, axis=3)
data = data.astype(np.float32)
label = label.astype(np.float32)
if is_training and DO_AUGMENT:
data_ud = np.flip(data, axis=1)
label_ud = np.flip(label, axis=1)
data_lr = np.flip(data, axis=2)
label_lr = np.flip(label, axis=2)
data = np.concatenate([data, data_ud, data_lr])
label = np.concatenate([label, label_ud, label_lr])
return data, label
def get_in_mem_data_batch_train(self, idxs):
return self.get_in_mem_data_batch(idxs, True)
def get_in_mem_data_batch_test(self, idxs):
return self.get_in_mem_data_batch(idxs, False)
@tf.function(input_signature=[tf.TensorSpec(None, tf.int32)])
def data_function(self, indexes):
out = tf.numpy_function(self.get_in_mem_data_batch_train, [indexes], [tf.float32, tf.float32])
return out
@tf.function(input_signature=[tf.TensorSpec(None, tf.int32)])
def data_function_test(self, indexes):
out = tf.numpy_function(self.get_in_mem_data_batch_test, [indexes], [tf.float32, tf.float32])
return out
def get_train_dataset(self, indexes):
indexes = list(indexes)
dataset = tf.data.Dataset.from_tensor_slices(indexes)
dataset = dataset.batch(PROC_BATCH_SIZE)
dataset = dataset.map(self.data_function, num_parallel_calls=AUTOTUNE)
dataset = dataset.cache()
if DO_AUGMENT:
dataset = dataset.shuffle(PROC_BATCH_BUFFER_SIZE)
dataset = dataset.prefetch(buffer_size=AUTOTUNE)
self.train_dataset = dataset
def get_test_dataset(self, indexes):
indexes = list(indexes)
dataset = tf.data.Dataset.from_tensor_slices(indexes)
dataset = dataset.batch(PROC_BATCH_SIZE)
dataset = dataset.map(self.data_function_test, num_parallel_calls=AUTOTUNE)
dataset = dataset.cache()
self.test_dataset = dataset
def setup_pipeline(self, train_data_files, train_label_files, test_data_files, test_label_files, num_train_samples):
self.train_data_files = train_data_files
self.train_label_files = train_label_files
self.test_data_files = test_data_files
self.test_label_files = test_label_files
trn_idxs = np.arange(len(train_data_files))
np.random.shuffle(trn_idxs)
tst_idxs = np.arange(len(test_data_files))
self.get_train_dataset(trn_idxs)
self.get_test_dataset(tst_idxs)
self.num_data_samples = num_train_samples # approximately
print('datetime: ', now)
print('training and test data: ')
print('---------------------------')
print('num train samples: ', self.num_data_samples)
print('BATCH SIZE: ', BATCH_SIZE)
print('num test samples: ', tst_idxs.shape[0])
print('setup_pipeline: Done')
def setup_test_pipeline(self, test_data_files, test_label_files):
self.test_data_files = test_data_files
self.test_label_files = test_label_files
tst_idxs = np.arange(len(test_data_files))
self.get_test_dataset(tst_idxs)
print('setup_test_pipeline: Done')
def build_srcnn(self, do_drop_out=False, do_batch_norm=False, drop_rate=0.5, factor=2):
print('build_cnn')
padding = "SAME"
# activation = tf.nn.relu
# activation = tf.nn.elu
activation = tf.nn.relu
momentum = 0.99
num_filters = 64
input_2d = self.inputs[0]
print('input: ', input_2d.shape)
conv = conv_b = tf.keras.layers.Conv2D(num_filters, kernel_size=KERNEL_SIZE, kernel_initializer='he_uniform', activation=activation, padding='VALID')(input_2d)
print(conv.shape)
# if NOISE_TRAINING:
# conv = conv_b = tf.keras.layers.GaussianNoise(stddev=NOISE_STDDEV)(conv)
scale = 0.2
conv_b = build_residual_conv2d_block(conv_b, num_filters, 'Residual_Block_1', kernel_size=KERNEL_SIZE, scale=scale)
conv_b = build_residual_conv2d_block(conv_b, num_filters, 'Residual_Block_2', kernel_size=KERNEL_SIZE, scale=scale)
conv_b = build_residual_conv2d_block(conv_b, num_filters, 'Residual_Block_3', kernel_size=KERNEL_SIZE, scale=scale)
conv_b = build_residual_conv2d_block(conv_b, num_filters, 'Residual_Block_4', kernel_size=KERNEL_SIZE, scale=scale)
conv_b = build_residual_conv2d_block(conv_b, num_filters, 'Residual_Block_5', kernel_size=KERNEL_SIZE, scale=scale)
conv_b = build_residual_conv2d_block(conv_b, num_filters, 'Residual_Block_6', kernel_size=KERNEL_SIZE, scale=scale)
conv_b = tf.keras.layers.Conv2D(num_filters, kernel_size=3, strides=1, activation=activation, kernel_initializer='he_uniform', padding=padding)(conv_b)
# conv = conv + conv_b
conv = conv_b
print(conv.shape)
if NumClasses == 2:
final_activation = tf.nn.sigmoid # For binary
else:
final_activation = tf.nn.softmax # For multi-class
# This is effectively a Dense layer
self.logits = tf.keras.layers.Conv2D(NumLogits, kernel_size=1, strides=1, padding=padding, activation=final_activation)(conv)
print(self.logits.shape)
def build_training(self):
if NumClasses == 2:
self.loss = tf.keras.losses.BinaryCrossentropy(from_logits=False) # for two-class only
else:
self.loss = tf.keras.losses.SparseCategoricalCrossentropy(from_logits=False) # For multi-class
# self.loss = tf.keras.losses.MeanAbsoluteError() # Regression
# decayed_learning_rate = learning_rate * decay_rate ^ (global_step / decay_steps)
initial_learning_rate = 0.002
decay_rate = 0.95
steps_per_epoch = int(self.num_data_samples/BATCH_SIZE) # one epoch
decay_steps = int(steps_per_epoch) * 4
print('initial rate, decay rate, steps/epoch, decay steps: ', initial_learning_rate, decay_rate, steps_per_epoch, decay_steps)
self.learningRateSchedule = tf.keras.optimizers.schedules.ExponentialDecay(initial_learning_rate, decay_steps, decay_rate)
optimizer = tf.keras.optimizers.Adam(learning_rate=self.learningRateSchedule)
if TRACK_MOVING_AVERAGE:
# Not sure that this works properly (from tfa)
# optimizer = tfa.optimizers.MovingAverage(optimizer)
self.ema = tf.train.ExponentialMovingAverage(decay=0.9999)
self.optimizer = optimizer
self.initial_learning_rate = initial_learning_rate
def build_evaluation(self):
self.train_loss = tf.keras.metrics.Mean(name='train_loss')
self.test_loss = tf.keras.metrics.Mean(name='test_loss')
if NumClasses == 2:
self.train_accuracy = tf.keras.metrics.BinaryAccuracy(name='train_accuracy')
self.test_accuracy = tf.keras.metrics.BinaryAccuracy(name='test_accuracy')
self.test_auc = tf.keras.metrics.AUC(name='test_auc')
self.test_recall = tf.keras.metrics.Recall(name='test_recall')
self.test_precision = tf.keras.metrics.Precision(name='test_precision')
self.test_true_neg = tf.keras.metrics.TrueNegatives(name='test_true_neg')
self.test_true_pos = tf.keras.metrics.TruePositives(name='test_true_pos')
self.test_false_neg = tf.keras.metrics.FalseNegatives(name='test_false_neg')
self.test_false_pos = tf.keras.metrics.FalsePositives(name='test_false_pos')
else:
self.train_accuracy = tf.keras.metrics.SparseCategoricalAccuracy(name='train_accuracy')
self.test_accuracy = tf.keras.metrics.SparseCategoricalAccuracy(name='test_accuracy')
@tf.function(input_signature=[tf.TensorSpec(None, tf.float32), tf.TensorSpec(None, tf.float32)])
def train_step(self, inputs, labels):
labels = tf.squeeze(labels, axis=[3])
with tf.GradientTape() as tape:
pred = self.model([inputs], training=True)
loss = self.loss(labels, pred)
total_loss = loss
if len(self.model.losses) > 0:
reg_loss = tf.math.add_n(self.model.losses)
total_loss = loss + reg_loss
gradients = tape.gradient(total_loss, self.model.trainable_variables)
self.optimizer.apply_gradients(zip(gradients, self.model.trainable_variables))
if TRACK_MOVING_AVERAGE:
self.ema.apply(self.model.trainable_variables)
self.train_loss(loss)
self.train_accuracy(labels, pred)
return loss
@tf.function(input_signature=[tf.TensorSpec(None, tf.float32), tf.TensorSpec(None, tf.float32)])
def test_step(self, inputs, labels):
labels = tf.squeeze(labels, axis=[3])
pred = self.model([inputs], training=False)
t_loss = self.loss(labels, pred)
self.test_loss(t_loss)
self.test_accuracy(labels, pred)
# @tf.function(input_signature=[tf.TensorSpec(None, tf.float32), tf.TensorSpec(None, tf.float32)])
# decorator commented out because pred.numpy(): pred not evaluated yet.
def predict(self, inputs, labels):
pred = self.model([inputs], training=False)
# t_loss = self.loss(tf.squeeze(labels, axis=[3]), pred)
t_loss = self.loss(labels, pred)
self.test_labels.append(labels)
self.test_preds.append(pred.numpy())
self.test_input.append(inputs)
self.test_loss(t_loss)
self.test_accuracy(labels, pred)
def reset_test_metrics(self):
self.test_loss.reset_states()
self.test_accuracy.reset_states()
def get_metrics(self):
recall = self.test_recall.result()
precsn = self.test_precision.result()
f1 = 2 * (precsn * recall) / (precsn + recall)
tn = self.test_true_neg.result()
tp = self.test_true_pos.result()
fn = self.test_false_neg.result()
fp = self.test_false_pos.result()
mcc = ((tp * tn) - (fp * fn)) / np.sqrt((tp + fp) * (tp + fn) * (tn + fp) * (tn + fn))
return f1, mcc
def do_training(self, ckpt_dir=None):
if ckpt_dir is None:
if not os.path.exists(modeldir):
os.mkdir(modeldir)
ckpt = tf.train.Checkpoint(step=tf.Variable(1), model=self.model)
ckpt_manager = tf.train.CheckpointManager(ckpt, modeldir, max_to_keep=3)
else:
ckpt = tf.train.Checkpoint(step=tf.Variable(1), model=self.model)
ckpt_manager = tf.train.CheckpointManager(ckpt, ckpt_dir, max_to_keep=3)
ckpt.restore(ckpt_manager.latest_checkpoint)
self.writer_train = tf.summary.create_file_writer(os.path.join(logdir, 'plot_train'))
self.writer_valid = tf.summary.create_file_writer(os.path.join(logdir, 'plot_valid'))
self.writer_train_valid_loss = tf.summary.create_file_writer(os.path.join(logdir, 'plot_train_valid_loss'))
step = 0
total_time = 0
best_test_loss = np.finfo(dtype=np.float).max
if EARLY_STOP:
es = EarlyStop()
for epoch in range(NUM_EPOCHS):
self.train_loss.reset_states()
self.train_accuracy.reset_states()
t0 = datetime.datetime.now().timestamp()
proc_batch_cnt = 0
n_samples = 0
for data, label in self.train_dataset:
trn_ds = tf.data.Dataset.from_tensor_slices((data, label))
trn_ds = trn_ds.batch(BATCH_SIZE)
for mini_batch in trn_ds:
if self.learningRateSchedule is not None:
loss = self.train_step(mini_batch[0], mini_batch[1])
if (step % 100) == 0:
with self.writer_train.as_default():
tf.summary.scalar('loss_trn', loss.numpy(), step=step)
tf.summary.scalar('learning_rate', self.optimizer._decayed_lr('float32').numpy(), step=step)
tf.summary.scalar('num_train_steps', step, step=step)
tf.summary.scalar('num_epochs', epoch, step=step)
self.reset_test_metrics()
for data_tst, label_tst in self.test_dataset:
tst_ds = tf.data.Dataset.from_tensor_slices((data_tst, label_tst))
tst_ds = tst_ds.batch(BATCH_SIZE)
for mini_batch_test in tst_ds:
self.test_step(mini_batch_test[0], mini_batch_test[1])
with self.writer_valid.as_default():
tf.summary.scalar('loss_val', self.test_loss.result(), step=step)
tf.summary.scalar('acc_val', self.test_accuracy.result(), step=step)
with self.writer_train_valid_loss.as_default():
tf.summary.scalar('loss_trn', loss.numpy(), step=step)
tf.summary.scalar('loss_val', self.test_loss.result(), step=step)
print('****** test loss, acc, lr: ', self.test_loss.result().numpy(), self.test_accuracy.result().numpy(),
self.optimizer._decayed_lr('float32').numpy())
step += 1
print('train loss: ', loss.numpy())
proc_batch_cnt += 1
n_samples += data.shape[0]
print('proc_batch_cnt: ', proc_batch_cnt, n_samples)
t1 = datetime.datetime.now().timestamp()
print('End of Epoch: ', epoch+1, 'elapsed time: ', (t1-t0))
total_time += (t1-t0)
self.reset_test_metrics()
for data, label in self.test_dataset:
ds = tf.data.Dataset.from_tensor_slices((data, label))
ds = ds.batch(BATCH_SIZE)
for mini_batch in ds:
self.test_step(mini_batch[0], mini_batch[1])
print('loss, acc: ', self.test_loss.result().numpy(), self.test_accuracy.result().numpy())
print('------------------------------------------------------')
tst_loss = self.test_loss.result().numpy()
if tst_loss < best_test_loss:
best_test_loss = tst_loss
ckpt_manager.save()
if EARLY_STOP and es.check_stop(tst_loss):
break
print('total time: ', total_time)
self.writer_train.close()
self.writer_valid.close()
self.writer_train_valid_loss.close()
def build_model(self):
self.build_srcnn()
self.model = tf.keras.Model(self.inputs, self.logits)
def restore(self, ckpt_dir):
ckpt = tf.train.Checkpoint(step=tf.Variable(1), model=self.model)
ckpt_manager = tf.train.CheckpointManager(ckpt, ckpt_dir, max_to_keep=3)
ckpt.restore(ckpt_manager.latest_checkpoint)
self.reset_test_metrics()
for data, label in self.test_dataset:
ds = tf.data.Dataset.from_tensor_slices((data, label))
ds = ds.batch(BATCH_SIZE)
for mini_batch_test in ds:
self.predict(mini_batch_test[0], mini_batch_test[1])
print('loss, acc: ', self.test_loss.result().numpy(), self.test_accuracy.result().numpy())
labels = np.concatenate(self.test_labels)
preds = np.concatenate(self.test_preds)
inputs = np.concatenate(self.test_input)
print(labels.shape, preds.shape)
return labels, preds, inputs
def do_evaluate(self, inputs, ckpt_dir):
ckpt = tf.train.Checkpoint(step=tf.Variable(1), model=self.model)
ckpt_manager = tf.train.CheckpointManager(ckpt, ckpt_dir, max_to_keep=3)
ckpt.restore(ckpt_manager.latest_checkpoint)
self.reset_test_metrics()
pred = self.model([inputs], training=False)
self.test_probs = pred
pred = pred.numpy()
return pred
def run(self, directory, ckpt_dir=None, num_data_samples=50000):
train_data_files = glob.glob(directory+'train*mres*.npy')
valid_data_files = glob.glob(directory+'valid*mres*.npy')
train_label_files = glob.glob(directory+'train*ires*.npy')
valid_label_files = glob.glob(directory+'valid*ires*.npy')
self.setup_pipeline(train_data_files, train_label_files, valid_data_files, valid_label_files, num_data_samples)
self.build_model()
self.build_training()
self.build_evaluation()
self.do_training(ckpt_dir=ckpt_dir)
def run_restore(self, directory, ckpt_dir):
self.num_data_samples = 1000
valid_data_files = glob.glob(directory + 'valid*mres*.npy')
valid_label_files = glob.glob(directory + 'valid*ires*.npy')
self.setup_test_pipeline(valid_data_files, valid_label_files)
self.build_model()
self.build_training()
self.build_evaluation()
return self.restore(ckpt_dir)
def run_evaluate(self, data, ckpt_dir):
# data = tf.convert_to_tensor(data, dtype=tf.float32)
self.num_data_samples = 80000
self.build_model()
self.build_training()
self.build_evaluation()
return self.do_evaluate(data, ckpt_dir)
def run_restore_static(directory, ckpt_dir, out_file=None):
nn = SRCNN()
labels, preds, inputs = nn.run_restore(directory, ckpt_dir)
if out_file is not None:
np.save(out_file,
[np.squeeze(labels), preds.argmax(axis=3),
denormalize(inputs[:, 1:65, 1:65, 0], 'temp_11_0um_nom', mean_std_dct),
denormalize(inputs[:, 1:65, 1:65, 1], 'refl_0_65um_nom', mean_std_dct),
denormalize(inputs[:, 1:65, 1:65, 2], 'refl_0_65um_nom', mean_std_dct),
denormalize(inputs[:, 1:65, 1:65, 3], 'refl_0_65um_nom', mean_std_dct),
inputs[:, 1:65, 1:65, 4]])
def run_evaluate_static(in_file, out_file, ckpt_dir):
gc.collect()
h5f = h5py.File(in_file, 'r')
bt = get_grid_values_all(h5f, 'orig/temp_11_0um')
y_len, x_len = bt.shape[0], bt.shape[1]
lons = get_grid_values_all(h5f, 'orig/longitude')
lats = get_grid_values_all(h5f, 'orig/latitude')
bt = np.where(np.isnan(bt), 0, bt)
bt = normalize(bt, 'temp_11_0um_nom', mean_std_dct)
refl = get_grid_values_all(h5f, 'super/refl_0_65um')
refl = np.where(np.isnan(refl), 0, refl)
refl = np.expand_dims(refl, axis=0)
refl_lo, refl_hi, refl_std, refl_avg = get_min_max_std(refl)
refl_lo = normalize(refl_lo, 'refl_0_65um_nom', mean_std_dct)
refl_hi = normalize(refl_hi, 'refl_0_65um_nom', mean_std_dct)
refl_avg = normalize(refl_avg, 'refl_0_65um_nom', mean_std_dct)
refl_lo = np.squeeze(refl_lo)
refl_hi = np.squeeze(refl_hi)
refl_avg = np.squeeze(refl_avg)
cp = get_grid_values_all(h5f, 'orig/'+label_param)
cp = np.where(np.isnan(cp), 0, cp)
data = np.stack([bt, refl_lo, refl_hi, refl_avg, cp], axis=2)
data = np.expand_dims(data, axis=0)
h5f.close()
nn = SRCNN()
probs = nn.run_evaluate(data, ckpt_dir)
cld_frac = probs.argmax(axis=3)
cld_frac = cld_frac.astype(np.int8)
cld_frac_out = np.zeros((y_len, x_len), dtype=np.int8)
border = int((KERNEL_SIZE - 1)/2)
cld_frac_out[border:y_len - border, border:x_len - border] = cld_frac[0, :, :]
bt = denormalize(bt, 'temp_11_0um_nom', mean_std_dct)
refl_avg = denormalize(refl_avg, 'refl_0_65um_nom', mean_std_dct)
var_names = ['cloud_fraction', 'temp_11_0um', 'refl_0_65um']
dims = ['num_params', 'y', 'x']
da = xr.DataArray(np.stack([cld_frac_out, bt, refl_avg], axis=0), dims=dims)
da.assign_coords({
'num_params': var_names,
'lat': (['y', 'x'], lats),
'lon': (['y', 'x'], lons)
})
if out_file is not None:
np.save(out_file, (cld_frac_out, bt, refl_avg, cp, lons, lats))
else:
return [cld_frac_out, bt, refl_avg, cp, lons, lats]
def analyze_3cat(file):
tup = np.load(file, allow_pickle=True)
lbls = tup[0]
pred = tup[1]
lbls = lbls.flatten()
pred = pred.flatten()
print(np.sum(lbls == 0), np.sum(lbls == 1), np.sum(lbls == 2))
msk_0_1 = lbls != 2
msk_1_2 = lbls != 0
msk_0_2 = lbls != 1
lbls_0_1 = lbls[msk_0_1]
pred_0_1 = pred[msk_0_1]
pred_0_1 = np.where(pred_0_1 == 2, 1, pred_0_1)
# ----
lbls_1_2 = lbls[msk_1_2]
lbls_1_2 = np.where(lbls_1_2 == 1, 0, lbls_1_2)
lbls_1_2 = np.where(lbls_1_2 == 2, 1, lbls_1_2)
pred_1_2 = pred[msk_1_2]
pred_1_2 = np.where(pred_1_2 == 0, -9, pred_1_2)
pred_1_2 = np.where(pred_1_2 == 1, 0, pred_1_2)
pred_1_2 = np.where(pred_1_2 == 2, 1, pred_1_2)
pred_1_2 = np.where(pred_1_2 == -9, 1, pred_1_2)
# ----
lbls_0_2 = lbls[msk_0_2]
lbls_0_2 = np.where(lbls_0_2 == 2, 1, lbls_0_2)
pred_0_2 = pred[msk_0_2]
pred_0_2 = np.where(pred_0_2 == 2, 1, pred_0_2)
cm_0_1 = confusion_matrix_values(lbls_0_1, pred_0_1)
cm_1_2 = confusion_matrix_values(lbls_1_2, pred_1_2)
cm_0_2 = confusion_matrix_values(lbls_0_2, pred_0_2)
true_0_1 = (lbls_0_1 == 0) & (pred_0_1 == 0)
false_0_1 = (lbls_0_1 == 1) & (pred_0_1 == 0)
true_no_0_1 = (lbls_0_1 == 1) & (pred_0_1 == 1)
false_no_0_1 = (lbls_0_1 == 0) & (pred_0_1 == 1)
true_0_2 = (lbls_0_2 == 0) & (pred_0_2 == 0)
false_0_2 = (lbls_0_2 == 1) & (pred_0_2 == 0)
true_no_0_2 = (lbls_0_2 == 1) & (pred_0_2 == 1)
false_no_0_2 = (lbls_0_2 == 0) & (pred_0_2 == 1)
true_1_2 = (lbls_1_2 == 0) & (pred_1_2 == 0)
false_1_2 = (lbls_1_2 == 1) & (pred_1_2 == 0)
true_no_1_2 = (lbls_1_2 == 1) & (pred_1_2 == 1)
false_no_1_2 = (lbls_1_2 == 0) & (pred_1_2 == 1)
tp_0 = np.sum(true_0_1).astype(np.float64)
tp_1 = np.sum(true_1_2).astype(np.float64)
tp_2 = np.sum(true_0_2).astype(np.float64)
tn_0 = np.sum(true_no_0_1).astype(np.float64)
tn_1 = np.sum(true_no_1_2).astype(np.float64)
tn_2 = np.sum(true_no_0_2).astype(np.float64)
fp_0 = np.sum(false_0_1).astype(np.float64)
fp_1 = np.sum(false_1_2).astype(np.float64)
fp_2 = np.sum(false_0_2).astype(np.float64)
fn_0 = np.sum(false_no_0_1).astype(np.float64)
fn_1 = np.sum(false_no_1_2).astype(np.float64)
fn_2 = np.sum(false_no_0_2).astype(np.float64)
recall_0 = tp_0 / (tp_0 + fn_0)
recall_1 = tp_1 / (tp_1 + fn_1)
recall_2 = tp_2 / (tp_2 + fn_2)
precision_0 = tp_0 / (tp_0 + fp_0)
precision_1 = tp_1 / (tp_1 + fp_1)
precision_2 = tp_2 / (tp_2 + fp_2)
mcc_0 = ((tp_0 * tn_0) - (fp_0 * fn_0)) / np.sqrt((tp_0 + fp_0) * (tp_0 + fn_0) * (tn_0 + fp_0) * (tn_0 + fn_0))
mcc_1 = ((tp_1 * tn_1) - (fp_1 * fn_1)) / np.sqrt((tp_1 + fp_1) * (tp_1 + fn_1) * (tn_1 + fp_1) * (tn_1 + fn_1))
mcc_2 = ((tp_2 * tn_2) - (fp_2 * fn_2)) / np.sqrt((tp_2 + fp_2) * (tp_2 + fn_2) * (tn_2 + fp_2) * (tn_2 + fn_2))
acc_0 = np.sum(lbls_0_1 == pred_0_1)/pred_0_1.size
acc_1 = np.sum(lbls_1_2 == pred_1_2)/pred_1_2.size
acc_2 = np.sum(lbls_0_2 == pred_0_2)/pred_0_2.size
print(acc_0, recall_0, precision_0, mcc_0)
print(acc_1, recall_1, precision_1, mcc_1)
print(acc_2, recall_2, precision_2, mcc_2)
return cm_0_1, cm_1_2, cm_0_2, [acc_0, acc_1, acc_2], [recall_0, recall_1, recall_2],\
[precision_0, precision_1, precision_2], [mcc_0, mcc_1, mcc_2]
def analyze_5cat(file):
tup = np.load(file, allow_pickle=True)
lbls = tup[0]
pred = tup[1]
lbls = lbls.flatten()
pred = pred.flatten()
np.histogram(lbls, bins=5)
np.histogram(pred, bins=5)
new_lbls = np.zeros(lbls.size, dtype=np.int32)
new_pred = np.zeros(pred.size, dtype=np.int32)
new_lbls[lbls == 0] = 0
new_lbls[lbls == 1] = 1
new_lbls[lbls == 2] = 1
new_lbls[lbls == 3] = 1
new_lbls[lbls == 4] = 2
new_pred[pred == 0] = 0
new_pred[pred == 1] = 1
new_pred[pred == 2] = 1
new_pred[pred == 3] = 1
new_pred[pred == 4] = 2
np.histogram(new_lbls, bins=3)
np.histogram(new_pred, bins=3)
lbls = new_lbls
pred = new_pred
print(np.sum(lbls == 0), np.sum(lbls == 1), np.sum(lbls == 2))
msk_0_1 = lbls != 2
msk_1_2 = lbls != 0
msk_0_2 = lbls != 1
lbls_0_1 = lbls[msk_0_1]
pred_0_1 = pred[msk_0_1]
pred_0_1 = np.where(pred_0_1 == 2, 1, pred_0_1)
# ----------------------------------------------
lbls_1_2 = lbls[msk_1_2]
lbls_1_2 = np.where(lbls_1_2 == 1, 0, lbls_1_2)
lbls_1_2 = np.where(lbls_1_2 == 2, 1, lbls_1_2)
pred_1_2 = pred[msk_1_2]
pred_1_2 = np.where(pred_1_2 == 0, -9, pred_1_2)
pred_1_2 = np.where(pred_1_2 == 1, 0, pred_1_2)
pred_1_2 = np.where(pred_1_2 == 2, 1, pred_1_2)
pred_1_2 = np.where(pred_1_2 == -9, 1, pred_1_2)
# -----------------------------------------------
lbls_0_2 = lbls[msk_0_2]
lbls_0_2 = np.where(lbls_0_2 == 2, 1, lbls_0_2)
pred_0_2 = pred[msk_0_2]
pred_0_2 = np.where(pred_0_2 == 2, 1, pred_0_2)
cm_0_1 = confusion_matrix_values(lbls_0_1, pred_0_1)
cm_1_2 = confusion_matrix_values(lbls_1_2, pred_1_2)
cm_0_2 = confusion_matrix_values(lbls_0_2, pred_0_2)
true_0_1 = (lbls_0_1 == 0) & (pred_0_1 == 0)
false_0_1 = (lbls_0_1 == 1) & (pred_0_1 == 0)
true_no_0_1 = (lbls_0_1 == 1) & (pred_0_1 == 1)
false_no_0_1 = (lbls_0_1 == 0) & (pred_0_1 == 1)
true_0_2 = (lbls_0_2 == 0) & (pred_0_2 == 0)
false_0_2 = (lbls_0_2 == 1) & (pred_0_2 == 0)
true_no_0_2 = (lbls_0_2 == 1) & (pred_0_2 == 1)
false_no_0_2 = (lbls_0_2 == 0) & (pred_0_2 == 1)
true_1_2 = (lbls_1_2 == 0) & (pred_1_2 == 0)
false_1_2 = (lbls_1_2 == 1) & (pred_1_2 == 0)
true_no_1_2 = (lbls_1_2 == 1) & (pred_1_2 == 1)
false_no_1_2 = (lbls_1_2 == 0) & (pred_1_2 == 1)
tp_0 = np.sum(true_0_1).astype(np.float64)
tp_1 = np.sum(true_1_2).astype(np.float64)
tp_2 = np.sum(true_0_2).astype(np.float64)
tn_0 = np.sum(true_no_0_1).astype(np.float64)
tn_1 = np.sum(true_no_1_2).astype(np.float64)
tn_2 = np.sum(true_no_0_2).astype(np.float64)
fp_0 = np.sum(false_0_1).astype(np.float64)
fp_1 = np.sum(false_1_2).astype(np.float64)
fp_2 = np.sum(false_0_2).astype(np.float64)
fn_0 = np.sum(false_no_0_1).astype(np.float64)
fn_1 = np.sum(false_no_1_2).astype(np.float64)
fn_2 = np.sum(false_no_0_2).astype(np.float64)
recall_0 = tp_0 / (tp_0 + fn_0)
recall_1 = tp_1 / (tp_1 + fn_1)
recall_2 = tp_2 / (tp_2 + fn_2)
precision_0 = tp_0 / (tp_0 + fp_0)
precision_1 = tp_1 / (tp_1 + fp_1)
precision_2 = tp_2 / (tp_2 + fp_2)
mcc_0 = ((tp_0 * tn_0) - (fp_0 * fn_0)) / np.sqrt((tp_0 + fp_0) * (tp_0 + fn_0) * (tn_0 + fp_0) * (tn_0 + fn_0))
mcc_1 = ((tp_1 * tn_1) - (fp_1 * fn_1)) / np.sqrt((tp_1 + fp_1) * (tp_1 + fn_1) * (tn_1 + fp_1) * (tn_1 + fn_1))
mcc_2 = ((tp_2 * tn_2) - (fp_2 * fn_2)) / np.sqrt((tp_2 + fp_2) * (tp_2 + fn_2) * (tn_2 + fp_2) * (tn_2 + fn_2))
acc_0 = np.sum(lbls_0_1 == pred_0_1)/pred_0_1.size
acc_1 = np.sum(lbls_1_2 == pred_1_2)/pred_1_2.size
acc_2 = np.sum(lbls_0_2 == pred_0_2)/pred_0_2.size
print(acc_0, recall_0, precision_0, mcc_0)
print(acc_1, recall_1, precision_1, mcc_1)
print(acc_2, recall_2, precision_2, mcc_2)
return cm_0_1, cm_1_2, cm_0_2, [acc_0, acc_1, acc_2], [recall_0, recall_1, recall_2],\
[precision_0, precision_1, precision_2], [mcc_0, mcc_1, mcc_2], lbls, pred
# from util.plot_cm import *
# from sklearn.metrics import confusion_matrix
# import numpy as np
# tup = np.load('/Users/tomrink/cld_frac_viirs.npy', allow_pickle=True)
# lbls = tup[0]
# pred = tup[1]
# bt = tup[2]
# refl_lo = tup[3]
# refl_hi = tup[4]
# refl_avg = tup[5]
# cld_prob = tup[6]
# from util.plot import plot_image
# cm = confusion_matrix(lbls.flatten(), pred.flatten())
# plot_confusion_matrix(cm, ['CLR', '1/4', '1/2', '3/4', 'CLD'], normalize=True, axis=0)
# lbls = lbls.flatten()
# pred = pred.flatten()
# cld_prob = cld_prob.flatten()
# cat_0 = lbls == 0
# cat_1 = lbls == 1
# cat_2 = lbls == 2
# cat_3 = lbls == 3
# cat_4 = lbls == 4
# plt.hist(cld_prob[cat_0], log=True, histtype='step')
# plt.hist(cld_prob[cat_1], log=True, histtype='step')
# plt.hist(cld_prob[cat_2], log=True, histtype='step')
# plt.hist(cld_prob[cat_3], log=True, histtype='step')
# plt.hist(cld_prob[cat_4], log=True, histtype='step')
# from deeplearning.cloud_fraction_fcn_viirs import run_evaluate_static
# run_evaluate_static('/Users/tomrink/clavrx_VNP02IMG.A2019306.1912.001.2019307003236.uwssec.nc',
# '/Users/tomrink/cld_frac_A2019306.1912', '/Users/tomrink/tf_model_cld_frac_viirs/run-20230421193944/')
# import numpy as np
# tup = np.load('/Users/tomrink/cld_frac_A2019306.1912.npy', allow_pickle=True)
# cfrac = tup[0]
# bt = tup[1]
# refl = tup[2]
# cp = tup[3]
# from util.plot import plot_image
# from deeplearning.cloud_fraction_fcn_viirs import analyze_5cat
# cm_0_1, cm_1_2, cm_0_2, acc, recall, prec, mcc, lbls, pred = analyze_5cat('/Users/tomrink/cld_frac_viirs.npy')
# from util.bar_plot import do_plot
# do_plot(['ACC', 'RECALL', 'PREC', 'MCC'], [[acc[0], recall[0], prec[0], mcc[0]],
# [acc[1], recall[1], prec[1], mcc[1]],
# [acc[2], recall[2], prec[2], mcc[2]]],
# ['CLR v MIX', 'MIX v CLD', 'CLR v CLD'], ['green', 'blue', 'black'],
# title='CLD FRAC', xlabel='Metric', barWidth=0.15, ylim=[0.4, 1.0])
if __name__ == "__main__":
nn = SRCNN()
nn.run('matchup_filename')