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BenthicSubstrateMapping / PyHum

Python code to read, display, export and analyse Humminbird sidescan sonar data
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Error In Post Install Tests #65

Closed geojed closed 5 years ago

geojed commented 5 years ago

HI so I just installed everything on a brand new Anaconda (4.6.11) installation on Debian (4.19) with the git version of PyHum (but got the same error with the pip version). All packages seem to install fine but when I run the post install test it fails with this error. I dug through the code a little bit and it seems like maybe some null values are getting added to the array, but couldn't pin it down. Any ideas?

=================================================== Input file is /home/dale/pyhum_test/test.DAT Sonar file path is /home/dale/pyhum_test Max. transducer power is 1000.0 W pH is 7.0 Temperature is 10.0 Traceback (most recent call last): File "", line 1, in File "/home/dale/anaconda2/envs/pyhum/lib/python2.7/site-packages/PyHum/test.py", line 138, in dotest PyHum.correct(humfile, sonpath, maxW, doplot, dofilt, correct_withwater, ph, temp, salinity, dconcfile) File "/home/dale/anaconda2/envs/pyhum/lib/python2.7/site-packages/PyHum/_pyhum_correct.py", line 314, in correct Zt, R, A = remove_water(star_fp, bed, shape_star, dep_m, pix_m, 1, maxW) File "/home/dale/anaconda2/envs/pyhum/lib/python2.7/site-packages/PyHum/_pyhum_correct.py", line 705, in remove_water a[:,k] = d[k]/yvec ValueError: could not broadcast input array from shape (1479,1) into shape (1479)

dbuscombe-usgs commented 5 years ago

Either a, d or yvec need to be squeezed to remove the singleton dimension. The numpy function is squeeze

geojed commented 5 years ago

Got it, so is it a problem with the the testing script or the function itself. Because its the output I got from running :

python -c"import PyHum;PyHum.dotest()"

Immediately after instalation.

Is this a change that should be made to the min branch of the code? Because I reproduced the error in a VM so I don't think it's isolated to my machine.

dbuscombe-usgs commented 5 years ago

Yes, the code needs to be changed. Be warned: it will not be the only change you will need to. As I have tried to make clear in my responses to others and on my github profile, PyHum is legacy code and is no longer supported. I will no longer make any changes to it.

geojed commented 5 years ago

Got it. Thank you for all your work on this project. I'll spend some time trying to parse through fixing this problem this weekend