forked from weecology/EvergladesTools
-
Notifications
You must be signed in to change notification settings - Fork 0
/
manifest.py
197 lines (154 loc) · 5.81 KB
/
manifest.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
#Zooniverse upload module
import glob
import os
import pandas as pd
from panoptes_client import Panoptes, Project, SubjectSet, Subject
import rasterio
from rasterio.warp import calculate_default_transform, reproject, Resampling
from PIL import Image
import numpy as np
from deepforest import deepforest
from deepforest import utilities
import tile_raster
import utils
def utm_project(path):
#Everglades UTM Zone
dst_crs = 'EPSG:32617'
with rasterio.open(path) as src:
transform, width, height = calculate_default_transform(
src.crs, dst_crs, src.width, src.height, *src.bounds)
kwargs = src.meta.copy()
kwargs.update({
'crs': dst_crs,
'transform': transform,
'width': width,
'height': height
})
dest_name = "{}_projected.tif".format(os.path.splitext(path)[0])
with rasterio.open(dest_name, 'w', **kwargs) as dst:
for i in range(1, src.count + 1):
reproject(
source=rasterio.band(src, i),
destination=rasterio.band(dst, i),
src_transform=src.transform,
src_crs=src.crs,
dst_transform=transform,
dst_crs=dst_crs,
resampling=Resampling.nearest)
return dest_name
def is_white(path):
d = rasterio.open(path)
numpy_image = d.read()
left, bottom, right, top = d.bounds
assert numpy_image.shape[0] == 3
#Check if image is all white
img_reshaped = numpy_image.reshape(-1, 3)
white = np.sum(img_reshaped == [255,255,255])/img_reshaped.size
if white > 0.55:
return True
else:
return False
def find_files(path):
"""Search and filter images"""
images = {}
image_paths = glob.glob(os.path.join(path, "*.tif"))
counter = 1
#extract site name
site_name = os.path.basename(path)
for i in image_paths:
#Load and get metadata
d = rasterio.open(i)
numpy_image = d.read()
left, bottom, right, top = d.bounds
#Write as a png
basename = os.path.splitext(i)[0]
png_name = "{}.png".format(basename)
img = Image.open(i)
img.save(png_name)
#Create dict
#crs = d.crs.to_epsg()
crs = None
images[png_name] = {"subject_reference":counter, "bounds":[left,bottom,right,top],"crs":crs,"site":site_name,"resolution":d.res,"filename":png_name}
counter +=1
return images
#Create manifests
def create_subject_set(everglades_watch, name="demo"):
subject_set = SubjectSet()
subject_set.links.project = everglades_watch
subject_set.display_name = name
subject_set.save()
return subject_set
def upload(subject_set, images, everglades_watch):
"""Assign images to projecti"""
new_subjects = []
print("Uploading {} images".format(len(images)))
for filename, metadata in images.items():
subject = Subject()
subject.links.project = everglades_watch
subject.add_location(filename)
subject.metadata.update(metadata)
#Trigger upload
subject.save()
new_subjects.append(subject)
subject_set.add(new_subjects)
def screen_blanks(images, model):
#Load detection model
model = deepforest.deepforest(weights=model)
#model.classes_file = utilities.create_classes("/orange/ewhite/everglades/Zooniverse/parsed_images/test.csv")
#model.read_classes()
screened_images = {}
for filename, metadata in images.items():
boxes = model.predict_image(filename, return_plot=False)
#small score filter
boxes = boxes[boxes.score > 0.4]
if not boxes.empty:
#if any([x in boxes.label.unique() for x in ["Great Blue Heron","Snowy Egret","Wood Stork","Roseate Spoonbill"]]):
screened_images[filename] = metadata
else:
print("Remove {}, screened empty".format(filename))
return screened_images
def main(path, everglades_watch, model=None, save_dir="/orange/ewhite/everglades/Zooniverse/"):
"""Args:
path: a .tif to run
"""
#Create new directory in save_dir
basename = os.path.splitext(os.path.basename(path))[0]
event = os.path.basename(os.path.dirname(os.path.dirname(path))).replace(" ","")
basename = "{}_{}".format(event,basename)
dirname = "{}/{}".format(save_dir,basename)
try:
os.mkdir(dirname)
except:
pass
#raise ValueError("dirname: {} exists)".format(dirname))
#Crop tif
#Project from longlat to utm
#check if exists
#projected_raster_path = "{}_projected.tif".format(os.path.splitext(path)[0])
#if not os.path.exists(projected_raster_path):
#projected_raster_path = utm_project(path)
saved_file = tile_raster.run(path=path, save_dir=dirname)
print("Created cropped files at {}".format(saved_file))
#Generate metadata
images = find_files(saved_file)
#Screen for blanks
if model:
screened_images = screen_blanks(images, model)
print("{} images ready for upload".format(len(screened_images)))
else:
screened_images = images
#Create a new subject set
subject_set = create_subject_set(name="{}".format(basename), everglades_watch=everglades_watch)
#Upload
upload(subject_set, screened_images, everglades_watch)
return saved_file
if __name__ == "__main__":
#auth
everglades_watch = utils.connect()
model = "/orange/ewhite/everglades/Zooniverse/predictions/20210224_121421.h5"
#Currently debugging with just one site
paths = glob.glob("/orange/ewhite/everglades/WadingBirds2020/Raw/Cypress City_03_25_2020/Mapping Photos/*.JPG")
paths = [x for x in paths if "projected" not in x]
for path in paths:
print(path)
saved_file = main(path, everglades_watch, model)