Data conversion error with numpy

Question

i am in the process of making mu code nicer and i saw that numpy has some very nifty functions already built-in. However the following code throws an error that i cannot explain:

data = numpy.genfromtxt('table.oout',unpack=True,names=True,dtype=None)

real_ov_data=np.float32(data['real_overlap'])
ana_ov_data= np.float32(data['Analyt_overlap'])
length_data =np.float32(data['Residues'])

plot(length_data,real_ov_data,label="overlapped Peaks, exponential function",marker="x", markeredgecolor="blue", markersize=3.0, linestyle=" ",color="blue")
plot(length_data,ana_ov_data,label="expected overlapped Peaks",marker="o", markeredgecolor="green", markersize=3.0, linestyle=" ",color="green")

throws the error

Traceback (most recent call last):
  File "length_vs_overlap.py", line 52, in <module>
    real_ov_data=np.float32(data['real_overlap'])
ValueError: invalid literal for float(): real_overlap
>Exit code: 1

when i am trying to read the following file:

  'Residues'  'Analyt_overlap'  'anz_analyt_overlap'  'real_overlap' 
  21          1.2502        29            0.0000  
  13          1.0306        25            0.0000  
  56          5.8513        84            2.8741  
  190         68.0940       329           28.4706 
  54          5.4271        83            2.4999

What am i doing wrong? My piece of code should be simple enough?

It might help to see what gets printed out when you iterate through data, perhaps this numpy.genfromtxt('table.oout',unpack=True,names=True,dtype=None) isn't doing exactly what you think. — Rob Wagner
– Rob Wagner, Commented Jun 28, 2012 at 15:30
This works for me, the data loads just fine. An aside, you shouldn't have two namespaces for numpy. You have both numpy. and np.. I'd remove one of those import statements and unify it. — Hooked
– Hooked, Commented Jun 28, 2012 at 15:33
The fact that the data loads on the minimal example posted suggests that you are doing something fishy in the 50 lines of code before the error. Can you post a complete example where this fails, including all needed import statements? — Hooked
– Hooked, Commented Jun 28, 2012 at 15:35
ok, but the code is too long to be pasted here. i will just upload both code and data to pastebin. — tarrasch
– tarrasch, Commented Jun 28, 2012 at 16:11

ecatmur · Accepted Answer · 2012-06-28 16:12:08Z

1

You've either repeated the header line, or you're specifying the names as a list.

That's causing each column to be read as a string type starting with the column title.

answered Jun 28, 2012 at 16:12

ecatmur

158k28 gold badges311 silver badges387 bronze badges

Sign up to request clarification or add additional context in comments.

Collectives™ on Stack Overflow

Data conversion error with numpy

1 Answer 1

Comments

Your Answer

Hot Network Questions

Collectives™ on Stack Overflow

1 Answer 1

Comments

Your Answer

Sign up or log in

Post as a guest

Related