-
Notifications
You must be signed in to change notification settings - Fork 54
/
seq.py
390 lines (309 loc) · 13 KB
/
seq.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
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
import logging
import os
import re
import subprocess
from glob import glob, iglob
import numpy as nump
import tqdm
from PIL import Image
from tqdm.auto import tqdm
try:
from pathlib import Path
except ImportError:
from pathlib2 import Path # python 2 backport
from flirpy.io.fff import Fff
from flirpy.util.exiftool import Exiftool
logger = logging.getLogger(__name__)
class Seq:
def __init__(self, input_file, height=None, width=None, raw=False):
"""
Load a FLIR SEQ file. Currently this must be a SEQ
file containing FFF files. The resulting object can
be indexed as a normal array and will return the
"""
with open(input_file, "rb") as seq_file:
self.seq_blob = seq_file.read()
self._fff_it = self._get_fff_iterator(self.seq_blob)
self.pos = []
prev_pos = 0
self.raw = raw
# Iterate through sequence to get frame offsets
for match in self._fff_it:
index = match.start()
chunksize = index - prev_pos
self.pos.append((index, chunksize))
prev_pos = index
# Fix up the first chunk size
if len(self.pos) > 1:
self.pos[0] = (0, self.pos[1][1])
elif len(self.pos) == 1:
self.pos[0] = (0, len(self.seq_blob))
self.width = width
self.height = height
def _get_fff_iterator(self, seq_blob):
"""
Internal function which returns an iterator containing the
indices of the files in the SEQ. Probably this should be
converted to something a bit more intelligent which
actually identifies the size of the records in the file.
"""
magic_pattern_fff = "\x46\x46\x46\x00".encode()
valid = re.compile(magic_pattern_fff)
return valid.finditer(seq_blob)
def __len__(self):
"""
Returns the length of the sequence
"""
return len(self.pos)
def __getitem__(self, index):
"""
Retuns a FFF image in the sequence
"""
offset, chunksize = self.pos[index]
chunk = self.seq_blob[offset : offset + chunksize]
if self.raw:
return chunk
else:
return Fff(chunk)
class Splitter:
def __init__(
self,
output_folder="./",
exiftool_path=None,
start_index=0,
step=1,
split_folders=True,
preview_format="jpg",
width=None,
height=None,
):
self.exiftool = Exiftool(exiftool_path)
self.start_index = start_index
self.step = step
self.frame_count = self.start_index
self.export_tiff = True
self.export_meta = True
self.export_preview = True
self.export_radiometric = True
self.overwrite = True
self.split_folders = split_folders
self.split_filetypes = True
self.width = width
self.height = height
if preview_format in ["jpg", "jpeg", "png", "tiff"]:
self.preview_format = preview_format
else:
raise ValueError("Preview format not recognised")
self.output_folder = os.path.expanduser(output_folder)
Path(self.output_folder).mkdir(exist_ok=True)
def set_start_index(self, index):
self.start_index = int(index)
def process(self, file_list):
if isinstance(file_list, str):
file_list = [file_list]
file_list = [os.path.expanduser(f) for f in file_list]
logger.info("Splitting {} files".format(len(file_list)))
self.frame_count = self.start_index
folders = []
for seq in tqdm(file_list):
if self.split_folders:
subfolder, _ = os.path.splitext(os.path.basename(seq))
folder = os.path.join(self.output_folder, subfolder)
folders.append(folder)
else:
folder = self.output_folder
Path(folder).mkdir(exist_ok=True)
logger.info("Splitting {} into {}".format(seq, folder))
self._process_seq(seq, folder)
# Batch export meta data
if self.export_meta:
logger.info("Extracting metadata")
if self.split_filetypes:
filemask = os.path.join(folder, "raw", "frame_*.fff")
copy_filemask = os.path.normpath("./raw/%f.fff")
radiometric_folder = os.path.normpath("./radiometric")
preview_folder = os.path.normpath("./preview")
else:
filemask = os.path.join(folder, "frame_*.fff")
copy_filemask = os.path.normpath("%f.fff")
radiometric_folder = os.path.normpath("./")
preview_folder = os.path.normpath("./")
self.exiftool.write_meta(filemask)
# Copy geotags
if self.export_tiff:
logger.info("Copying tags to radiometric")
self.exiftool.copy_meta(
folder,
filemask=copy_filemask,
output_folder=radiometric_folder,
ext="tiff",
)
if self.export_preview:
logger.info("Copying tags to preview")
self.exiftool.copy_meta(
folder,
filemask=copy_filemask,
output_folder=preview_folder,
ext=self.preview_format,
)
return folders
def _write_tiff(self, filename, data):
logger.debug("Writing {}", filename)
Image.fromarray(data.astype("uint16")).save(filename)
def _write_preview(self, filename, data):
drange = data.max() - data.min()
preview_data = 255.0 * ((data - data.min()) / drange)
logger.debug("Writing {}", filename)
Image.fromarray(preview_data.astype("uint8")).save(filename)
def _make_split_folders(self, output_folder):
Path(os.path.join(output_folder, "raw")).mkdir(exist_ok=True)
Path(os.path.join(output_folder, "radiometric")).mkdir(exist_ok=True)
Path(os.path.join(output_folder, "preview")).mkdir(exist_ok=True)
def _check_overwrite(self, path):
exists = os.path.exists(path)
return (not exists) or (exists and self.overwrite)
def _get_seq(self, input_file):
return Seq(input_file, self.height, self.width)
def _process_seq(self, input_file, output_subfolder):
logger.debug("Processing {}".format(input_file))
for count, frame in enumerate(tqdm(self._get_seq(input_file))):
if frame.meta is None:
self.frame_count += 1
continue
if self.split_filetypes:
self._make_split_folders(output_subfolder)
filename_fff = os.path.join(
output_subfolder,
"raw",
"frame_{0:06d}.fff".format(self.frame_count),
)
filename_tiff = os.path.join(
output_subfolder,
"radiometric",
"frame_{0:06d}.tiff".format(self.frame_count),
)
filename_preview = os.path.join(
output_subfolder,
"preview",
"frame_{:06d}.{}".format(self.frame_count, self.preview_format),
)
filename_meta = os.path.join(
output_subfolder,
"raw",
"frame_{0:06d}.txt".format(self.frame_count),
)
else:
filename_fff = os.path.join(
output_subfolder, "frame_{0:06d}.fff".format(self.frame_count)
)
filename_tiff = os.path.join(
output_subfolder, "frame_{0:06d}.tiff".format(self.frame_count)
)
filename_preview = os.path.join(
output_subfolder,
"frame_{:06d}.{}".format(self.frame_count, self.preview_format),
)
filename_meta = os.path.join(
output_subfolder, "frame_{0:06d}.txt".format(self.frame_count)
)
if self.frame_count % self.step == 0:
if self.export_meta and self._check_overwrite(filename_fff):
frame.write(filename_fff)
# Export raw files and/or radiometric convert them
if self.export_tiff and self._check_overwrite(filename_tiff):
if self.export_radiometric:
# Use Exiftool to extract metadata
if self.width is not None and self.height is not None:
# Export the first metadata
if count == 0:
self.exiftool.write_meta(filename_fff)
meta = self.exiftool.meta_from_file(filename_meta)
else:
meta = None
image = frame.get_radiometric_image(meta=meta)
image += 273.15 # Convert to Kelvin
image /= 0.04 # Standard FLIR scale factor
else:
image = frame.get_image()
self._write_tiff(filename_tiff, image)
# Export preview frame (crushed to 8-bit)
if self.export_preview and self._check_overwrite(filename_preview):
self._write_preview(filename_preview, image)
self.frame_count += 1
return
def _write_frame(self, frame, filename):
logger.debug("Writing {}", filename)
frame.write(filename)
class ExifToolSplitter(Splitter):
def _get_seq(self, input_file):
return Seq(input_file, self.height, self.width, raw=True)
def _write_frame(self, frame, filename):
# Write file
with open(filename, "wb") as f:
f.write(frame)
self.exiftool.write_meta(filename)
def _process_seq(self, input_file, output_subfolder):
logger.debug("Processing {}".format(input_file))
for count, frame in enumerate(tqdm(self._get_seq(input_file))):
if self.split_filetypes:
self._make_split_folders(output_subfolder)
filename_fff = os.path.join(
output_subfolder,
"raw",
"frame_{0:06d}.fff".format(self.frame_count),
)
filename_tiff = os.path.join(
output_subfolder,
"radiometric",
"frame_{0:06d}.tiff".format(self.frame_count),
)
filename_preview = os.path.join(
output_subfolder,
"preview",
"frame_{:06d}.{}".format(self.frame_count, self.preview_format),
)
filename_meta = os.path.join(
output_subfolder,
"raw",
"frame_{0:06d}.txt".format(self.frame_count),
)
else:
filename_fff = os.path.join(
output_subfolder, "frame_{0:06d}.fff".format(self.frame_count)
)
filename_tiff = os.path.join(
output_subfolder, "frame_{0:06d}.tiff".format(self.frame_count)
)
filename_preview = os.path.join(
output_subfolder,
"frame_{:06d}.{}".format(self.frame_count, self.preview_format),
)
filename_meta = os.path.join(
output_subfolder, "frame_{0:06d}.txt".format(self.frame_count)
)
self._write_frame(frame, filename_fff)
if self.frame_count % self.step == 0:
self._write_frame(frame, filename_fff)
meta = self.exiftool.meta_from_file(filename_meta)
self.width = int(meta["Raw Thermal Image Width"])
self.height = int(meta["Raw Thermal Image Height"])
frame = Fff(
filename_fff,
width=self.width,
height=self.height,
use_exiftool=True,
)
# Export raw files and/or radiometric convert them
if self.export_tiff and self._check_overwrite(filename_tiff):
if self.export_radiometric:
image = frame.get_radiometric_image(meta=meta)
image += 273.15 # Convert to Kelvin
image /= 0.04 # Standard FLIR scale factor
else:
image = frame.get_image()
self._write_tiff(filename_tiff, image)
# Export preview frame (crushed to 8-bit)
if self.export_preview and self._check_overwrite(filename_preview):
self._write_preview(filename_preview, image)
self.frame_count += 1
return