analysis program for chewing behavior of Zhang's Lab.
直接调整lime.sh中的各项参数，后运行该脚本，bash lime.sh即可。
对于小鼠体重，也可用同样地方法修改limeWeight.sh并运行。
使用方法与相关可调参数如下。运行后会首先弹出第一帧，拖拽可画水平线作为截取的区域，高度默认为2px。先选取左侧(0)，再选取右侧(1)；完成后键入回车。程序运行完后(ca. 6min.), 会输出综合的chew count与chew duration值。
数据文件(*_PW.txt, *.mov)默认放于data文件夹(或者自行修改--input参数)中。最终数据输出于chart文件夹中(或者自行修改--output参数)；另外，chew count与chew duration值仅输出在终端，请注意保存。
体重信息的录入，请使用limeWight.py文件。
NOTE: 如果重复运算同一个session，可能会出现sqlite3.IntegrityError: UNIQUE constraint failed: summary.SessionID的报错，下次再改吧[苦笑脸]。解决方法: 在sqlite3里手工把那个条目删除再运行。
Lime
analysis program for chewing behavior of Zhang's Lab.
Usage: lime.py [options] SENSORFILE [VIDEOFILE]
Options:
-c GAP --climbEpisode=GAP # climbing episode gap length, unit as second [default: 0]
--debug # debug mode
-d DATE --date=DATE # session date [default: YYYYMMDD]
-e GAP --episode=GAP # episode gap length, unit as second [default: 4]
-f FOOD --food=FOOD # food weight data, unit as gram [default: 2.000_1.000]
-i INDIR --input=INDIR # data directory [default: data]
-l LENGTH --length=LENGTH # session length, unit as minute [default: 60]
-m MICESEQ --miceSequence=MICESEQ # mice sequence, from left to right [default: C1M1/C1M2/C1M3/C1M4]
-n NCAGE --cageNum=NCAGE # total mice number in this session [default: 2]
-o OUTDIR --output=OUTDIR # chart directory [default: chart]
-p --poseAnalysis # need pose analysis only? [default: false]
-r RANGE --timeRange=RANGE # checking range, unit as second [default: 60_3600]
-t TIME --startTime=TIME # start time point [default: HHMM]
-u SETUP --setup=SETUP # setup prefix, one of "TtC_NN","TtC_NH", "TtC_HH", "TtV_NN","TtV_NH", "TtV_HH" [default: TtV_NN]
-v OFFSET --videoOffset=OFFSET # video offset, aligning with sensor time, counts as second [default: 0.0]
-w WIDTH --width=WIDTH # target area width, unit as px [default: 20]
""".format(version=__version__)
LimeWeight {version}
Usage: LimeWeight.py -c CAGENUM -d DATE [options] (WEIGHTSEQ ...)
Options:
--debug # debug mode
-c CAGENUM # cage number
-n NMICE # total mice sum [default: 8]
-i INPUTDIR # input data directory [default: data]
-f DATABASE # database file [default: chewing.db]
typical command:
- 2 mice set:
python3 lime.py -d 20171213 -t 1430 -u TtC_NH -m C1M1/C2M1 -v 17 -f 3.653_3.142 20171213001_PW.txt 20171213001.mov - 4 mice set:
python3 lime.py -d 20171213 -t 1430 -u TtC_NH -n 4 -m C1M1/C2M1/C1M2/C2M2 -v 17 -f 3.653_3.142 20171213001_PW.txt 20171213001.mov
( drag to draw two lines for target area, the left line first; then press ENTER for further procedures )
LimeOne
+-data
| +- chewing.db
| +- 20171123001_PW.txt
| +- 20171123001.mov
| +- ...
+-LimeOne
| +- ...
+-chart
| +- 20171123001_PW_4_0
| | +- ...
| +- 20171123001_PW_4_1
| | +- ...
+-lime.py
+-README.txt
+-requirements.txt
-
docopt
-
matplotlib
-
numpy
-
scipy [optional]
-
pandas
-
opencv-python
-
Cython [optional]
-
halo [optional]
-
tqdm
-
SQLite3