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A flexible and easy-to-extend data processing pipeline for single dish radio telescopes

License: GNU General Public License v3.0

Makefile 0.64% Python 99.36%

seek's People

Stargazers

Watchers

Forkers

vafaei-ar yabebalfantaye dufanxin sinianyutian astrojhgu crcosmo lao19881213 philbull casteryh josephwkania zxcorr katrinachang wangy-nao gjerse amadeuswi mvsantosdev andrewdao11

seek's Issues

UnicodeDecodeError: 'ascii' codec can't decode...

(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?

Boolean operation error

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(dilated_mask - mask, **di_kwargs)

    dilated_mask = binary_mask_dilation(np.logical_xor(dilated_mask, mask), **di_kwargs)

Anyone who has installed seek recently?

Hi community!

Anyone who has installed seek recently? Can you specify the environment, packages version etc?

And which guide you followed?

Thanks!

seek installation in ubuntu 14.04

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
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_012904.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_014400.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_015903.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_021405.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_022902.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_024404.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_025901.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_031403.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_032906.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_034402.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_035905.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_041401.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_042904.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_044406.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_045903.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_051405.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_052902.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_054404.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_055901.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_061404.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_062900.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_064403.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_065906.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_071403.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_072906.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_074402.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_075903.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_081406.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_082902.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_084405.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_085902.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_091405.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_092902.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_094405.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_095907.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_101404.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_102901.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_104403.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_105906.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_111403.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_112906.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_114402.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_115905.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_121402.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_122905.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_124402.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_125904.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_131401.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_132903.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_134400.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_135903.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_141400.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_142903.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_144406.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_145902.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_151405.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_152902.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_154405.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_155901.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_161405.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_162901.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_164404.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_165901.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_171404.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_172906.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_174403.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_175906.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_181403.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_182905.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_184402.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_185905.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_191401.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_192904.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_194401.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_195904.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_201406.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_202903.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_204406.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_205902.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_211405.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_212902.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_214404.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_215901.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_221404.h5
./bgs_example_data/2016/03/21/HIMap_RSG7M_A1_24_MP_PXX_Z0_C0-M9703A_DPUA_20160321_222906.h5
./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

gain_template_7m_FFT_phase_switch_ADU_K.dat not found

When I attempted to use the 'seek' tool, I executed the following command (I tried to use this tool through a conda environment):

$ 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

and there were no error messages during the execution of the above code.

Then, I try to use it:

(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

(seek_py27)$ seek --file-prefix='./bgs_example_data' --post-processing-prefix='bgs_example_data/seek_cache' --chi-1=20 --overwrite=True seek.config.process_survey_fft

and I got error messages:

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.

Is there angone can help me? Thank you very much for providing me with advice.

How to generate the image shown in the RFI Mitigation page in the docs ?

How do I display the graph as shown here after processing them and getting the rfi mask?

Generating rfi_mask for different data

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!

No command 'seek' found, did you mean:

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

Using SEEK for calibrating HIDE data

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 due to a missing module

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

data folder not copied to installation directory

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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