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firasmidani / amiga

Analysis of Microbial Growth Assays
https://firasmidani.github.io/amiga/
GNU General Public License v3.0
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ValueError: could not broadcast input array from shape (0,) into shape (0,2) #7

Closed Edison2021 closed 2 years ago

Edison2021 commented 2 years ago

Hi Firas

Got an error below

Traceback (most recent call last): File "/home/manager/src/amiga-master/amiga.py", line 392, in AMiGA() File "/home/manager/src/amiga-master/amiga.py", line 90, in init getattr(self, args.command)() File "/home/manager/src/amiga-master/amiga.py", line 210, in fit Command(args).fit() File "/home/manager/src/amiga-master/libs/commands.py", line 114, in fit runGrowthFitting(data,mappings,self.directory,args,verbose=args.verbose) File "/home/manager/src/amiga-master/libs/analyze.py", line 168, in runGrowthFitting sub_plate.model(nthin=args.time_step_size,store=store,verbose=verbose) File "/home/manager/src/amiga-master/libs/growth.py", line 705, in model curve = gm.run(name=sample_id) File "/home/manager/src/amiga-master/libs/model.py", line 249, in run curve = GrowthCurve(x=time,y=actual_input,y0=self.y0,y1=self.y1,y2=self.y2, File "/home/manager/src/amiga-master/libs/curve.py", line 132, in init self.describe() File "/home/manager/src/amiga-master/libs/curve.py", line 192, in describe dx = detectDiauxie(self.x,self.y0,self.y1,self.y2,self.cov0,self.cov1, File "/home/manager/src/amiga-master/libs/diauxie.py", line 88, in detectDiauxie ret[:,4:6] = [[y1[l-1],y1[r-1]] for l,r in bounds] # growth rate at both bounds ValueError: could not broadcast input array from shape (0,) into shape (0,2)

What kind of problems caused the error?

Thanks Edison

firasmidani commented 2 years ago

Hmm, error suggests that there is a problem with the function that detects diauxic shifts. My best guess is that your data set has a particular growth curve with a weird behavior that the function has not seen before and does not know how to handle. But it's hard to tell without replicating the error myself.

Can you try to re-run your command with the --verbose argument? This will help you determine which well in which file or plate causes the problem. If you share that particular growth curve with me here, I can try to replicate the error. You can also share the whole file with me too instead.

firasmidani commented 2 years ago

Thanks for sharing your data. I was able to replicate the error and it was a fairly simple fix. Please re-install AMiGA and run again. If you cloned the repository, you can simply git pull, otherwise, just simply replace the old amiga folder with the new one. Let me know if that fixes the problem.

Edison2021 commented 2 years ago

Thanks for your prompt response. It is working now,