Known issues and FAQ
Opened this issue · 34 comments
Unfortunately, I cannot update this LiCSBAS repository for a reason.
All known issues are solved in LiCSBAS2 and it will keep updated. I recommend using LiCSBAS2 if you encounter an issue.
ValueError: A colormap named "SCM.roma0" is already registered
#176 (comment)
#195 (comment)
#198
Downgrade matplotlib, e.g., to 3.4.2.
Step16 (LiCSBAS16_filt_ts.py) gets stuck.
#62
#86
Try p16_n_para="1".
Line 111 in dfdb8fa
Other parallel processing in other steps may also be stuck. In that case, try setting p*_n_para="1" for the stuck step or setting for for all steps:
Line 24 in 5ca6550
It seems that WSL tends to have such a stuck issue. I suggest using VirtualBox.
Problem solved. It worked!
Thank you again
ModuleNotFoundError: No module named '_gdal'
If you have any requests or questions about LiCSAR products (not LiCSBAS), please send an email to 'Contact us' shown at the bottom of https://comet.nerc.ac.uk/COMET-LiCS-portal/.
#323 (comment)
Merge frames: #24
In step13:
File "LiCSBAS/bin/LiCSBAS13_sb_inv.py", line 785, in main
refy1s, refx1s = refy1s[0], refx1s[0] ## Only first index
IndexError: index 0 is out of bounds for axis 0 with size 0
In step12:
File "LiCSBAS/bin/LiCSBAS12_loop_closure.py", line 356, in main
refy1 = refyx[0][0] # start from 0, not 1
IndexError: index 0 is out of bounds for axis 0 with size 0
The cause of the error is
- The number of interferograms is too small
- Too many unwrapping errors are included
Try
- change p11_unw_thre, p11_coh_thre, and/or p12_loop_thre
- crop the area by step05
- improve unwrapping quality and/or increase unwrapped data if you created them manually
thank you sir for your response, can you give me some explanation of the variable p11_unw_thre, p11_coh_thre, and/or p12_loop_thre?
LiCSBAS04op_mask_unw.py ver1.3.5 20210105 Y. Morishita
LiCSBAS04op_mask_unw.py -i GEOCml1 -o GEOCml1mask -c 0.1
LiCSBAS/bin/LiCSBAS04op_mask_unw.py:176: FutureWarning: In the future np.bool will be defined as the corresponding NumPy scalar.
bool_mask = np.zeros((length, width), dtype=np.bool)
Traceback (most recent call last):
File "LiCSBAS/bin/LiCSBAS04op_mask_unw.py", line 326, in
sys.exit(main())
^^^^^^
File "LiCSBAS/bin/LiCSBAS04op_mask_unw.py", line 176, in main
bool_mask = np.zeros((length, width), dtype=np.bool)
^^^^^^^
File "miniconda3/envs/licsbas/lib/python3.11/site-packages/numpy/init.py", line 324, in getattr
raise AttributeError(former_attrs[attr])
AttributeError: module 'numpy' has no attribute 'bool'.
np.bool was a deprecated alias for the builtin bool. To avoid this error in existing code, use bool by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.bool_ here.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations. Did you mean: 'bool_'?
Discussion about parameter tuning for a specific case or interpretation of a specific result is out of the scope of the issues in this repository. Please carefully read the LiCSBAS paper, understand the logic, try changing the parameters, and check the result yourself.
LiCSBAS_plot_ts.py and LiCSBAS_cum2vel.py
...
Reading TS_GEOCml1clip/cum_filt.h5
Traceback (most recent call last):
File "LiCSBAS/bin/LiCSBAS_plot_ts.py", line 363, in
refx1, refx2, refy1, refy2 = [int(s) for s in re.split('[:/]', refarea)]
File "re.py", line 231, in split
return _compile(pattern, flags).split(string, maxsplit)
TypeError: cannot use a string pattern on a bytes-like object
Modify
refarea = cumh5['refarea'][()] to refarea = cumh5['refarea'][()].decode('utf-8')
Traceback (most recent call last):
File "LiCSBAS/bin/LiCSBAS11_check_unw.py", line 348, in
sys.exit(main())
File "LiCSBAS/bin/LiCSBAS11_check_unw.py", line 281, in main
os.symlink(os.path.relpath(rasorg, ifg_rasdir), os.path.join(ifg_rasdir, rasname))
PermissionError: [Errno 1] Operation not permitted: '...unw.png' -> '/media/...unw.png'
- Please check the format of the disk
- Recommend not using mounted disk
Searching latest epoch for mli...
Traceback (most recent call last):
File "LiCSBAS2/bin/LiCSBAS01_get_geotiff.py", line 500, in
sys.exit(main())
^^^^^^
File "LiCSBAS2/bin/LiCSBAS01_get_geotiff.py", line 213, in main
response = requests.get(url)
^^^^^^^^^^^^^^^^^
File "miniconda3/envs/licsbas/lib/python3.12/site-packages/requests/api.py", line 73, in get
return request("get", url, params=params, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "miniconda3/envs/licsbas/lib/python3.12/site-packages/requests/api.py", line 59, in request
return session.request(method=method, url=url, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "miniconda3/envs/licsbas/lib/python3.12/site-packages/requests/sessions.py", line 589, in request
resp = self.send(prep, **send_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "miniconda3/envs/licsbas/lib/python3.12/site-packages/requests/sessions.py", line 725, in send
history = [resp for resp in gen]
^^^^^^^^^^^^^^^^^^^^^^
File "miniconda3/envs/licsbas/lib/python3.12/site-packages/requests/sessions.py", line 191, in resolve_redirects
raise TooManyRedirects(
requests.exceptions.TooManyRedirects: Exceeded 30 redirects.
or
Download geotiff of unw and cc
Traceback (most recent call last):
File "LiCSBAS2/bin/LiCSBAS01_get_geotiff.py", line 500, in <module>
sys.exit(main())
^^^^^^
File "LiCSBAS2/bin/LiCSBAS01_get_geotiff.py", line 340, in main
print('{} IFGs available from {} to {}'.format(n_ifg, imdates[0], imdates[-1]), flush=True)
~~~~~~~^^^
IndexError: list index out of range
The bug was fixed in LiCSBAS2 (yumorishita/LiCSBAS2#55). Please use LiCSBAS2 or apply the fix in your local LiCSBAS script.
What are vel(1) and vel(2) in LiCSBAS_plot_ts.py?
They correspond to cum*.h5 files indicated by -i and --i2 options. By default vel(1) and vel(2) are velocities of filtered and unfiltered time series, respectively.
Cannot download files or the downloading speed is slow in LiCSBAS01_get_geotiff.py.
It could be because of LiCSAR server maintenance and there is nothing to do from the LiCSBAS side. Please contact COMET.
https://comet.nerc.ac.uk/comet-lics-portal/
comet@leeds.ac.uk
https://x.com/COMET_database
Dear Professor, can LICSBAS process cc and unw data processed by envi
Yes, as long as you prepare the files with the correct format for LiCSBAS.
https://github.com/yumorishita/LiCSBAS/wiki/file_structure#input-for-step-1-1-or-steps-0-3-to-0-5-output-of-step-0-2
If you are using the COMET version LiCSBAS, I cannot support it. Please report any issues to its repository.
Dear professor,how can i change the ref_area to get velocity after i complete all steps?
Unfortunately, I cannot update this LiCSBAS repository for a reason. All known issues are solved in LiCSBAS2 and it will keep updated. I recommend using LiCSBAS2 if you encounter an issue.
Dear Professor,
How to update LiCSBAS to LiCSBAS2?
How to update LiCSBAS to LiCSBAS2?
Remove LiCSABS and install LiCSBAS2.
Dear Professor,
Thank you for your answer.
I am not able to find the instructions for installing LiCSBAS2.
Can you please provide ?
Same as LiCSBAS.
Dear Professor,
I only found one installation process. ( mentoned in the link: https://github.com/yumorishita/LiCSBAS/wiki/1_Installation)
And if the instruction is same, what is the difference between licsbas and licsbas2 installation?
Please help me to install licsbas2.
Replace git clone https://github.com/yumorishita/LiCSBAS.git with git clone https://github.com/yumorishita/LiCSBAS2.git.
Dear Professor,
I found an error that saying this:
Traceback (most recent call last):
File "/home/darmasanjaya/LiCSBAS2/bin/LiCSBAS03op_GACOS.py", line 549, in
sys.exit(main())
File "/home/darmasanjaya/LiCSBAS2/bin/LiCSBAS03op_GACOS.py", line 368, in main
plot_lib.plot_gacos_info(gacinfofile, pngfile)
File "/home/darmasanjaya/LiCSBAS2/LiCSBAS_lib/LiCSBAS_plot_lib.py", line 152, in plot_gacos_info
xylim1 = np.max(np.concatenate((std_bf, std_af)))+1
File "<array_function internals>", line 180, in amax
File "/home/darmasanjaya/miniconda3/envs/adillahana/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 2791, in amax
return _wrapreduction(a, np.maximum, 'max', axis, None, out,
File "/home/darmasanjaya/miniconda3/envs/adillahana/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 86, in _wrapreduction
return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
ValueError: zero-size array to reduction operation maximum which has no identity
How could i solve it? Thank you Prof
Hii Prof.. I have an issue when running the batch script that stop in this step for a long time. I've made sure that connection and storage is okay. Before this, it can run successfull but when i do run again it stuck there. How could i solve this? Thank you Prof.
Elapsed time: 00h 00m 23s
LiCSBAS02_ml_prep.py Successfully finished!!
Output directory: GEOCml1
LiCSBAS03op_GACOS.py ver1.5.5 20201119 Y. Morishita
LiCSBAS03op_GACOS.py -i GEOCml1 -o GEOCml1GACOS --fillhole
Convert ztd/sltd.geo.tif files to sltd.geo files...
8 parallel processing...
Finished 0/ 9th sltd...
Use 20181007.sltd.geo.tif
Use 20181031.sltd.geo.tif
Use 20181019.sltd.geo.tif
Use 20181112.sltd.geo.tif
Use 20181206.sltd.geo.tif
Use 20181218.sltd.geo.tif
Use 20181230.sltd.geo.tif
Use 20181124.sltd.geo.tif
Use 20190111.sltd.geo.tif
Correct unw data...
8 parallel processing...
Finished 0/ 21th unw...
Finished 10/ 21th unw...
Finished 20/ 21th unw...
Module versions I have confirmed:
#441 (comment)
Python3.10
# Name Version Build Channel
astropy 5.1 py310ha9d4c09_0
beautifulsoup4 4.11.1 py310h06a4308_0
gdal 3.4.1 py310h8f0303e_0
h5py 3.7.0 py310he06866b_0
matplotlib 3.7.0 py310h06a4308_0
numpy 1.23.5 py310hd5efca6_0
psutil 5.9.0 py310h5eee18b_0
python 3.10.9 h7a1cb2a_0
requests 2.28.1 py310h06a4308_0
shapely 1.8.4 py310h81ba7c5_0
statsmodels 0.13.5 py310ha9d4c09_0
Python3.11
# Name Version Build Channel
astropy 5.1 py311hbed6279_0
beautifulsoup4 4.12.2 py311h06a4308_0
gdal 3.6.2 py311h4618797_1
h5py 3.7.0 py311h021c08c_0
matplotlib 3.7.1 py311h06a4308_1
numpy 1.24.3 py311hc206e33_0
psutil 5.9.0 py311h5eee18b_0
python 3.11.3 h7a1cb2a_0
requests 2.29.0 py311h06a4308_0
shapely 2.0.1 py311h24a2a10_0
statsmodels 0.13.5 py311h5eee18b_1