Trouble comparing NOAA webpage and echoSMs

[swill-24]

Hello,

I ran the example code to compare results from the NOAA KRM webpage and echoSMs. I can see comparisons for some of the fish (i.e. Sardine, Bocaccio), but for other fish (i.e. WhiteCatfish_185, StripedBass_205), I get the following error. Do you know why this might be? Thanks!

CODE SECTION:

%%

Try the KRM model and compare to the NOAA online KRM calculator results

mod = KRMModel()

fishes = ['Sardine', 'StripedBass_205']

for fname in fishes:
fish = KRMdata().model(fname)
fish.plot()

# Create the dict that echoSMs models use and add required parameters
p = {'medium_c': 1490, 'medium_rho': 1030, 'organism': fish, 'theta': 90,
     'f': np.arange(12, 121, 1)*1e3,
     'high_ka_medium': 'water', 'low_ka_medium': 'water'}
# Note 'water' is used for the high_ka_medium and low_ka_medium parameters to
# match the TS in the available from KRMdata() class (which came from the
# online NOAA KRM calculator). To see the results when 'body' is used, uncomment these two
# lines:
# p['high_ka_medium'] = 'body'
# p['low_ka_medium'] = 'body'

krm_ts = mod.calculate_ts(p, progress=True)

# Get the TS from the NOAA KRM webpage (cached locally)
noaa_ts = KRMdata.ts(fname)
plot_compare_freq(p['f'], krm_ts,
                  'KRM echoSMs', p['f'], noaa_ts[' TS (dB).1'], 'KRM NOAA', fname)

ERROR:
TypeError Traceback (most recent call last)
Cell In[16], line 27
23
24 # Get the TS from the NOAA KRM webpage (cached locally)
25 noaa_ts = KRMdata.ts(fname)
26 plot_compare_freq(p['f'], krm_ts,
---> 27 'KRM echoSMs', p['f'], noaa_ts[' TS (dB).1'], 'KRM NOAA', fname)

TypeError: 'NoneType' object is not subscriptable

[gavinmacaulay]

The error happens because echoSMs only contains the TS results for the Sardine, Cod, Bocaccio, and SkipjackTuna_46.54cm NOAA shapes, so when your example code tries to get TS values for other shapes (e.g., StripedBass_205), the call to KRMdata.ts(fname) returns None instead of TS values and the plot_compare_freq() function then fails.

To fix this, I have added the missing NOAA KRM ts results to echoSMs and created a new echoSMs version (v0.26.0). I also changed the example_code.py script to run the comparison on all NOAA shapes, but your code above should now work with the new version.

If you need it, hints on how to upgrade echoSMs are available here https://ices-tools-dev.github.io/echoSMs/usage/#versions