diff --git a/app.py b/app.py
index 38f18f608958061f79ca16a9354fa69585f0dcce..252f539abe9246637d98d3a3dbd2aed768944a98 100644
--- a/app.py
+++ b/app.py
@@ -1,11 +1,63 @@
-import os
import streamlit as st
import zipfile
-import torch
from utils import *
+import numpy as np
import matplotlib.pyplot as plt
+import matplotlib.animation as animation
+import streamlit.components.v1 as components
from matplotlib import colors
+st.set_page_config(layout="wide")
+
+def create_animation(images, pred_dates):
+ print('Creating composition of images...')
+ fps = 2
+ fig_an, ax_an = plt.subplots()
+ plt.title("")
+ a = images[0]
+ im = ax_an.imshow(a, interpolation='none', aspect='auto', vmin=0, vmax=1)
+
+ title = ax_an.text(0.5, 0.85, "", bbox={'facecolor': 'w', 'alpha': 0.5, 'pad': 5},
+ transform=ax_an.transAxes, ha="center")
+
+ def animate_func(idx):
+ title.set_text("date: " + pred_dates[idx])
+ im.set_array(images[idx])
+ return [im]
+
+ anima = animation.FuncAnimation(fig_an, animate_func, frames=len(images), interval=1000 / fps, blit=True,
+ repeat=False)
+ print('Done!')
+ return anima
+
+
+def load_daily_preds_as_animations(pred_full_paths, pred_dates):
+ daily_preds = []
+ for path in pred_full_paths:
+ img, _ = read(path)
+ img = np.squeeze(img)
+ img = [classes_color_map[p] for p in img]
+ daily_preds.append(img)
+ anima = create_animation(daily_preds, pred_dates)
+ return anima
+
+
+def load_src_images_as_animations(img_paths, pred_dates):
+ imgs = []
+ for path in img_paths:
+ img, _ = read(path)
+
+ # https://custom-scripts.sentinel-hub.com/custom-scripts/sentinel-2/composites/
+ # IREA image:
+ # False colors (8,4,3): 2,blue-B3,green-B4,5,6,7,red-B8,11,12
+ # Simple RGB (4, 3, 2): blue-B2,green-B3,red-B4,5,6,7,8,11,12
+ rgb = img[[2, 1, 0], :, :]
+ rgb = np.moveaxis(rgb, 0, -1)
+ imgs.append(rgb/np.amax(rgb))
+ anima = create_animation(imgs, pred_dates)
+ return anima
+
+
if not hasattr(st, 'paths'):
st.paths = None
if not hasattr(st, 'daily_model'):
@@ -43,7 +95,7 @@ if not hasattr(st, 'daily_model'):
st.title('In-season and dynamic crop mapping using 3D convolution neural networks and sentinel-2 time series')
-st.markdown(""" Demo App for the model presented in the paper:
+st.markdown(""" Demo App for the model presented in the [paper](https://www.sciencedirect.com/science/article/pii/S0924271622003203):
```
@article{gallo2022in_season,
title = {In-season and dynamic crop mapping using 3D convolution neural networks and sentinel-2 time series},
@@ -57,6 +109,7 @@ st.markdown(""" Demo App for the model presented in the paper:
author = {Ignazio Gallo and Luigi Ranghetti and Nicola Landro and Riccardo {La Grassa} and Mirco Boschetti},
}
```
+***The demo doesn't work properly, we are working to fix the bugs!*
""")
file_uploaded = st.file_uploader(
@@ -65,6 +118,7 @@ file_uploaded = st.file_uploader(
accept_multiple_files=False,
)
sample_path = None
+tileids = None
if file_uploaded is not None:
with zipfile.ZipFile(file_uploaded, "r") as z:
z.extractall("uploaded_samples")
@@ -72,10 +126,20 @@ if file_uploaded is not None:
st.markdown('or use a demo sample')
if st.button('sample 1'):
sample_path = 'demo_data/lombardia'
+ tileids = ['24']
+if st.button('sample 2'):
+ sample_path = 'demo_data/lombardia'
+ tileids = ['712']
+if st.button('sample 3'):
+ sample_path = 'demo_data/lombardia'
+ tileids = ['814']
+if st.button('sample 4'):
+ sample_path = 'demo_data/lombardia'
+ tileids = ['1509']
paths = None
if sample_path is not None:
- st.markdown(f'elaborating {sample_path}...')
+ # st.markdown(f'elaborating {sample_path} ...')
validationdataset = SentinelDailyAnnualDatasetNoLabel(
sample_path,
@@ -83,11 +147,11 @@ if sample_path is not None:
opt.classes_path,
opt.sample_duration,
opt.win_size,
- tileids=None)
+ tileids=tileids)
validationdataloader = torch.utils.data.DataLoader(
validationdataset, batch_size=opt.batch_size, shuffle=False, num_workers=opt.workers)
- st.markdown(f'predict in progress...')
+ st.markdown('Model prediction in progress ...')
out_dir = os.path.join(opt.result_path, "seg_maps")
if not os.path.exists(out_dir):
@@ -154,7 +218,7 @@ if sample_path is not None:
# save GT image in opt.root_path
full_pth_date = os.path.join(
- full_pth_patch, dates[ch][batch] + f'-ch{ch}-b{batch}-daily-pred.tif')
+ full_pth_patch, dates[ch] + '-daily-pred.tif')
profile.update({
'nodata': None,
'dtype': 'uint8',
@@ -164,15 +228,21 @@ if sample_path is not None:
st.markdown('End prediction')
- folder = "demo_data/results/seg_maps/example-lombardia/2"
- st.paths = os.listdir(folder)
+ # folder_out = "demo_data/results/seg_maps/example-lombardia/2"
+ folder_out = os.path.join("demo_data/results/seg_maps/"+opt.years[0]+"-lombardia/", tileids[0])
+ st.paths = os.listdir(folder_out)
+ st.paths.sort()
if st.paths is not None:
- folder = "demo_data/results/seg_maps/example-lombardia/2"
- file_picker = st.selectbox("Select day predict (annual is patch-pred-nn.tif)",
- st.paths, index=st.paths.index('patch-pred-nn.tif'))
+ # folder_out = os.path.join("demo_data/results/seg_maps/example-lombardia/", tileids[0])
+ folder_src = os.path.join("demo_data/lombardia/", opt.years[0], tileids[0])
+ st.markdown("""
+ ### Predictions
+ """)
+ # file_picker = st.selectbox("Select day predict (annual is patch-pred-nn.tif)",
+ # st.paths, index=st.paths.index('patch-pred-nn.tif'))
- file_path = os.path.join(folder, file_picker)
+ file_path = os.path.join(folder_out, 'patch-pred-nn.tif')
# print(file_path)
target, profile = read(file_path)
target = np.squeeze(target)
@@ -186,18 +256,33 @@ if st.paths is not None:
# print(colors.to_hex(c))
markdown_legend += f'{l}
'
- col1, col2 = st.columns(2)
+ col1, col2 = st.columns([2,1])
with col1:
+ st.markdown("**Long-term (annual) prediction**")
st.pyplot(fig)
with col2:
+ st.markdown("**Legend**")
st.markdown(markdown_legend, unsafe_allow_html=True)
+ st.markdown("**Short-term (daily) prediction**")
+ img_full_paths = [os.path.join(folder_out, path) for path in st.paths if 'daily-pred' in path]
+ pred_dates = [path[:8] for path in st.paths if 'daily-pred' in path]
+ anim = load_daily_preds_as_animations(img_full_paths, pred_dates)
+ components.html(anim.to_jshtml(), height=600)
+
+ st.markdown("**Input time series**")
+ list_dir = os.listdir(folder_src)
+ list_dir.sort()
+ img_full_paths = [os.path.join(folder_src, f) for f in list_dir if f.endswith(".tif")]
+ pred_dates = [f[:8] for f in list_dir if f.endswith(".tif")]
+ anim_src = load_src_images_as_animations(img_full_paths, pred_dates)
+ components.html(anim_src.to_jshtml(), height=600)
+
st.markdown("""
## Lombardia Dataset
You can download other patches from the original dataset created and published on
[Kaggle](https://www.kaggle.com/datasets/ignazio/sentinel2-crop-mapping) and used in our paper.
-
+
## How to build an input file for the Demo
- Using a daily FPN and giving a zip that contains 30 tiff with 7 channels, correctly named you can reach prediction of
- crop mapping og the area...
+ Working in progress: to be defined ...
""")
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diff --git a/utils.py b/utils.py
index a49c93a6f65332d453f7c2848aed8263e1507889..12314c3d8e1f09bee5934d19cb69544738e30278 100644
--- a/utils.py
+++ b/utils.py
@@ -57,7 +57,7 @@ def get_all_dates(path, num_max_dates):
files = os.listdir(path)
dates = list()
for f in files:
- f = f.split("_")[0]
+ f = f.split(".")[0]
if len(f) == 8: # 20160101
dates.append(f)
@@ -185,10 +185,10 @@ class SentinelDailyAnnualDatasetNoLabel(torch.utils.data.Dataset):
dirs.extend(dirs_path)
else:
# tileids e.g. "tileids/train_fold0.tileids" path of line separated tileids specifying
- with open(os.path.join(root_dir, tileids), 'r') as f:
- files = [el.replace("\n", "") for el in f.readlines()]
+ # with open(os.path.join(root_dir, tileids), 'r') as f:
+ # files = [el.replace("\n", "") for el in f.readlines()]
for d in self.data_dirs:
- dirs_path = [os.path.join(root_dir, d, f) for f in files]
+ dirs_path = [os.path.join(root_dir, d, f) for f in tileids]
dirs.extend(dirs_path)
for path in dirs:
@@ -210,6 +210,11 @@ class SentinelDailyAnnualDatasetNoLabel(torch.utils.data.Dataset):
patch_id, path = get_patch_id(self.samples, idx_img)
dates = get_all_dates(path, self.max_seq_length)
+ # print("idx_img:", idx_img)
+ # print("self.samples:", self.samples)
+ # print("path:", path)
+ # print("self.max_seq_length:", self.max_seq_length)
+ # print(dates)
x_annual = list()
@@ -717,7 +722,7 @@ opt.resnet_shortcut = 'B'
opt.result_path = 'demo_data/results'
input_data_folder = 'demo_data/lombardia' #@param {type:"string"}
opt.root_path = [input_data_folder]
-opt.years = ['example']
+opt.years = ['2019']
opt.classes_path = 'demo_data/classes-newmapping.txt'
opt.resume_path = 'demo_data'
opt.pretrain_path = ''
@@ -746,6 +751,7 @@ classes_color_map = np.array([[255/255.0, 255/255.0, 255/255.0],
[139/255, 35/255, 35/255],
[0, 0, 0], # Black - 17 - No Arable land
])
-color_labels = [classes_color_map[1], classes_color_map[2], classes_color_map[4], classes_color_map[7],
- classes_color_map[9], classes_color_map[12], classes_color_map[17]]
-labels_map = ['Unknow cropland', 'Other cereals', 'Woods and other tree crops', 'Forage', 'Corn', 'Rice', 'No arable land']
\ No newline at end of file
+color_labels = [classes_color_map[0], classes_color_map[1], classes_color_map[2], classes_color_map[4],
+ classes_color_map[7], classes_color_map[9], classes_color_map[12], classes_color_map[17]]
+labels_map = ['Unknown', 'Unknown cropland', 'Other cereals', 'Woods and other tree crops', 'Forage', 'Corn', 'Rice',
+ 'No arable land']