cosmo-ethz / seek Goto Github PK
View Code? Open in Web Editor NEWA flexible and easy-to-extend data processing pipeline for single dish radio telescopes
License: GNU General Public License v3.0
A flexible and easy-to-extend data processing pipeline for single dish radio telescopes
License: GNU General Public License v3.0
(Should have posted this for HIDE instead of SEEK)
Running HIDE I encountered this error:
$ hide --strategy-start=2017-01-01-00:00:00 --strategy-end=2017-01-05-00:00:00 --verbose=True hide.config.bleien7m
Traceback (most recent call last):
File "/u/zazz00r5/.local/bin/hide", line 12, in
load_entry_point('hide==0.1.0', 'console_scripts', 'hide')()
File "/u/zazz00r5/anaconda3/envs/py27/lib/python2.7/site-packages/ivy/cli/main.py", line 28, in run
_main(*sys.argv[1:])
File "/u/zazz00r5/anaconda3/envs/py27/lib/python2.7/site-packages/ivy/cli/main.py", line 37, in _main
mgr.launch()
File "/u/zazz00r5/anaconda3/envs/py27/lib/python2.7/site-packages/ivy/workflow_manager.py", line 107, in launch
executor.run(ctx().params.plugins)
File "/u/zazz00r5/anaconda3/envs/py27/lib/python2.7/site-packages/ivy/backend.py", line 48, in run
return map(LoopWrapper(loop), mapPlugin.getWorkload())
File "/u/zazz00r5/anaconda3/envs/py27/lib/python2.7/site-packages/ivy/backend.py", line 129, in call
plugin()
File "/u/zazz00r5/.local/lib/python2.7/site-packages/hide-0.1.0-py2.7.egg/hide/plugins/load_beam_profile.py", line 55, in call
beam_profiles, beam_norms = mod.load_beam_profile(beam_spec, frequencies, self.ctx.params)
File "/u/zazz00r5/.local/lib/python2.7/site-packages/hide-0.1.0-py2.7.egg/hide/beam/airy.py", line 43, in load_beam_profile
gain_sun = np.genfromtxt(path, skip_header=True)
File "/u/zazz00r5/anaconda3/envs/py27/lib/python2.7/site-packages/numpy/lib/npyio.py", line 1707, in genfromtxt
next(fhd)
File "/u/zazz00r5/anaconda3/envs/py27/lib/python2.7/encodings/ascii.py", line 27, in decode
return codecs.ascii_decode(input, self.errors)[0]
UnicodeDecodeError: 'ascii' codec can't decode byte 0xb0 in position 22: ordinal not in range(128)
Tried the solutions suggested here and here without luck. Any suggestions?
Dear developers;
I found out that there is an inconsistency between your package and newer version of numpy, so I've correct it as below way:
sum_threshold.py: line 189:
dilated_mask = binary_mask_dilation(np.logical_xor(dilated_mask, mask), **di_kwargs)
Hi community!
Anyone who has installed seek recently? Can you specify the environment, packages version etc?
And which guide you followed?
Thanks!
Hi,
I am trying to install HIDE & SEEK in my laptop. It seems the HIDE installation went well and I can run it to get the example plot.
Then I install SEEK according to the instruction and it seem to go well, but when I try to run it I am getting this following error:
/////////////////////////////////////////////////////////////////////
abhik@cosmos: seek --file-prefix=./bgs_example_data --map-name=BGS_maps.hdf --verbose=True seek.config.process_survey_fft
Total number of days found: 1
Total number of calibration days found: 0
Current files: ./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_000000.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_001403.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_002906.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_004402.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_005905.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_011401.h5
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./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_224403.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_225905.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_231402.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_232904.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_234401.h5
Traceback (most recent call last):
File "/home/abhik/.local/bin/seek", line 11, in
load_entry_point('seek', 'console_scripts', 'seek')()
File "/usr/local/lib/python2.7/dist-packages/ivy/cli/main.py", line 28, in run
_main(*sys.argv[1:])
File "/usr/local/lib/python2.7/dist-packages/ivy/cli/main.py", line 37, in _main
mgr.launch()
File "/usr/local/lib/python2.7/dist-packages/ivy/workflow_manager.py", line 107, in launch
executor.run(ctx().params.plugins)
File "/usr/local/lib/python2.7/dist-packages/ivy/backend.py", line 48, in run
return map(LoopWrapper(loop), mapPlugin.getWorkload())
File "/usr/local/lib/python2.7/dist-packages/ivy/backend.py", line 129, in call
plugin()
File "/usr/local/lib/python2.7/dist-packages/ivy/plugin/parallel_plugin_collection.py", line 81, in call
ctxList = backendImpl.run(self.pluginList, mapPlugin)
File "/usr/local/lib/python2.7/dist-packages/ivy/backend.py", line 48, in run
return map(LoopWrapper(loop), mapPlugin.getWorkload())
File "/usr/local/lib/python2.7/dist-packages/ivy/backend.py", line 129, in call
plugin()
File "/home/abhik/IM/seek/seek/plugins/remove_RFI.py", line 35, in call
rfi_mask_vx, rfi_mask_vy = mod.rm_rfi(self.ctx)
File "/home/abhik/IM/seek/seek/mitigation/sum_threshold.py", line 252, in rm_rfi
di_kwargs=di_kwargs)
File "/home/abhik/IM/seek/seek/mitigation/sum_threshold.py", line 183, in get_rfi_mask
st_mask = _run_sumthreshold(data, st_mask, eta, M, chi_i, sm_kwargs, plotting)
File "/home/abhik/IM/seek/seek/mitigation/sum_threshold.py", line 100, in _run_sumthreshold
smoothed_data = filter.gaussian_filter(data, init_mask, **sm_kwargs)
File "/home/abhik/IM/seek/seek/utils/filter.py", line 42, in gaussian_filter
Vp[N/2:-N/2,M/2:-M/2] = V[:]
TypeError: slice indices must be integers or None or have an index method
//////////////////////////////////////////
I am not quite sure what may be going wrong. Any suggestion would be helpful. Thanks.
Cheers,
Abhik
$ conda create -n seek_py27 python=2.7
$ conda activate seek_py27
(seek_py27)$ git clone https://github.com/cosmo-ethz/seek.git
(seek_py27)$ cd seek
(seek_py27)$ pip install -r requirements.txt
(seek_py27)$ python setup.py install --user
(seek_py27)$ wget -r -nH -np --cut-dirs=2 https://people.phys.ethz.ch/~ipa/cosmo/bgs_example_data/
(seek_py27)$ mkdir -p bgs_example_data/seek_cache
Traceback (most recent call last):
File "/home/liangbo/.local/bin/seek", line 11, in
load_entry_point('seek==0.1.0', 'console_scripts', 'seek')()
File "/home/liangbo/anaconda3/envs/seek_py27/lib/python2.7/site-packages/ivy/cli/main.py", line 28, in run
_main(*sys.argv[1:])
File "/home/liangbo/anaconda3/envs/seek_py27/lib/python2.7/site-packages/ivy/cli/main.py", line 37, in _main
mgr.launch()
File "/home/liangbo/anaconda3/envs/seek_py27/lib/python2.7/site-packages/ivy/workflow_manager.py", line 107, in launch
executor.run(ctx().params.plugins)
File "/home/liangbo/anaconda3/envs/seek_py27/lib/python2.7/site-packages/ivy/backend.py", line 48, in run
return map(LoopWrapper(loop), mapPlugin.getWorkload())
File "/home/liangbo/anaconda3/envs/seek_py27/lib/python2.7/site-packages/ivy/backend.py", line 129, in call
plugin()
File "/home/liangbo/.local/lib/python2.7/site-packages/seek-0.1.0-py2.7.egg/seek/plugins/calibration.py", line 34, in call
self.ctx.gain_file = load_file(self.ctx.params.gain_file_default)
File "/home/liangbo/.local/lib/python2.7/site-packages/seek-0.1.0-py2.7.egg/seek/utils/init.py", line 44, in load_file
return np.genfromtxt(path, **kwargs)
File "/home/liangbo/anaconda3/envs/seek_py27/lib/python2.7/site-packages/numpy/lib/npyio.py", line 1744, in genfromtxt
fhd = iter(np.lib._datasource.open(fname, 'rt', encoding=encoding))
File "/home/liangbo/anaconda3/envs/seek_py27/lib/python2.7/site-packages/numpy/lib/_datasource.py", line 266, in open
return ds.open(path, mode, encoding=encoding, newline=newline)
File "/home/liangbo/anaconda3/envs/seek_py27/lib/python2.7/site-packages/numpy/lib/_datasource.py", line 624, in open
raise IOError("%s not found." % path)
IOError: /home/liangbo/.local/lib/python2.7/site-packages/seek-0.1.0-py2.7.egg/seek/data/gain_template_7m_FFT_phase_switch_ADU_K.dat not found.
How do I display the graph as shown here after processing them and getting the rfi mask?
Hello,
I am trying to make rfi_mask for my data, that contains signals and different RFI using the following code:
import numpy as np from seek.mitigation import sum_threshold
rfi_mask= sum_threshold.get_rfi_mask(tod=np.ma.array(data), chi_1=20, sm_kwargs=sum_threshold.get_sm_kwargs(40, 20, 15, 7.5), di_kwargs=sum_threshold.get_di_kwrags(3, 7))
but I am getting the following error:
ValueError: x and y can be no greater than 2-D, but have shapes (32,) and (32, 128, 2)
Shape of my data is data.shape (100, 32, 128, 2)
Any suggestions on what might be wrong? Thank you in advance!
I installed seek according to documentation
But I am not sure what to do in order to make seek works in terminal
when I type seek in terminal, it isn't recognized.
///////////////////////////////////////////
$seek
No command 'seek' found, did you mean:
Command 'reek' from package 'ruby-reek' (universe)
Command 'spek' from package 'spek' (universe)
Command 'see' from package 'mime-support' (main)
seek: command not found
After using the example given in the HIDE documentation to generate data along with RFI, I want to calibrate the data using SEEK. If the command for producing the data with HIDE is:
$ hide --strategy-start=2016-03-21-00:00:00 --strategy-end=2016-03-21-23:59:00 --verbose=True hide.config.bleien7m
... is it as simple as replacing 'hide' with 'seek' to do the calibration? As in:
$ seek --strategy-start=2016-03-21-00:00:00 --strategy-end=2016-03-21-23:59:00 --verbose=True hide.config.bleien7m
Can't execute SEEK command from notebook neither terminal, getting this:
Traceback (most recent call last):
File "/Users/dimitrioslazarou/.local/bin/seek", line 11, in <module>
load_entry_point('seek==0.1.0', 'console_scripts', 'seek')()
File "/Users/dimitrioslazarou/anaconda3/envs/tf1/lib/python3.6/site-packages/pkg_resources/__init__.py", line 489, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "/Users/dimitrioslazarou/anaconda3/envs/tf1/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2852, in load_entry_point
return ep.load()
File "/Users/dimitrioslazarou/anaconda3/envs/tf1/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2443, in load
return self.resolve()
File "/Users/dimitrioslazarou/anaconda3/envs/tf1/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2449, in resolve
module = __import__(self.module_name, fromlist=['__name__'], level=0)
File "/Users/dimitrioslazarou/anaconda3/envs/tf1/lib/python3.6/site-packages/ivy/__init__.py", line 7, in <module>
import copy_reg
ModuleNotFoundError: No module named 'copy_reg'
I uninstalled and installed SEEK again from the repo, same issue
OS: Ubuntu 16.04 Running Miniconda 2
The data folder inside seek.seek is not copied to the installation directory after running setup.py install
. We have to manually copy the folder there for the tool to work. It would be great if you could fix that bug.
In my case I had to copy it to /home/kaushiksk/miniconda2/lib/python2.7/site-packages/seek-0.1.0-py2.7.egg/seek
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