Access data from a reshaped numpy array

Question

I am using the following code to write an array of statistic values into a text file (row wise):

data_in = np.loadtxt('input_file.asc')

with open('output_file.txt', 'a+') as outfile:
    values = data_in[:,1]
    min_data = np.min(values)
    max_data = np.max(values)
    avg_data = np.mean(values)
    stats = np.array([min_data, max_data, avg_data])
    np.savetxt(outfile, stats.reshape(1,stats.shape[0]), delimiter=' ', newline='\n')

I want to use this code to read multiple data_in files and append the statistics into a new row of 'output_file.txt'. I'm using the reshape function as suggested in a previous post here, so every batch of statistics is stored in a new row.

My problem is when I want to access the data stored in 'output_file.txt' for later plotting. If I use:

stats_out = np.loadtxt('output_file.txt') 
min_values = stats_out[:,0]
max_values = stats_out[:,1] 
avg_values = stats_out[:,2]

I get the Error message: IndexError: too many indices

Is this error caused because I'm using the reshape function?

An example of output_file.txt after running the script several times is:

0.077 -0.330 0.303
0.107 -0.506 0.350
0.092 -0.548 0.405
0.138 -2.358 0.445
0.100 -0.461 0.337

An example of input_file.asc:

-1492.292540 -87.984545   95.515548       NaN    NaN  8.18
-1491.349103 -87.982864   93.908249       NaN    NaN 10.55
-1490.405666 -87.979607   92.304869       NaN    NaN 10.73
-1489.462227 -87.974784   90.707865       NaN  7.740 10.60
-1488.518791 -87.968404   89.119650       NaN    NaN 10.18
-1487.575353 -87.960482   87.542539       NaN    NaN 10.10
-1486.631915 -87.951037   85.978759       NaN    NaN 10.11

Please post the full traceback. At the moment I'm not able to reproduce the problem. — miindlek
– miindlek, Commented Jul 28, 2014 at 9:29
Not too sure how traceback works, sorry. I've added an example of my input_file.asc to the question — Pau
– Pau, Commented Jul 28, 2014 at 10:29
Traceback is the full output of your programm code after the error arises. — miindlek
– miindlek, Commented Jul 28, 2014 at 10:58
After running the script I'm still not able to reproduce the problem. — miindlek
– miindlek, Commented Jul 28, 2014 at 11:03
min_values = stats_out[:,0] IndexError: too many indices I'm running Python2.7.8 |Anaconda 2.0.1 — Pau
– Pau, Commented Jul 28, 2014 at 11:40

miindlek · Accepted Answer · 2014-07-28 12:13:10Z

1

The problem is that your output file has only one line. So with stats_out = np.loadtxt('output_file.txt') you will only get a onedimensional array. If you then call stats_out[:,0] you will get an IndexError.

To solve this problem, you should check the number of dimensions of your data, for example:

stats_out = np.loadtxt('output_file.txt')
if stats_out.ndim > 1:
    min_values = stats_out[:,0]
    max_values = stats_out[:,1] 
    avg_values = stats_out[:,2]
else:
    min_values = stats_out[0]
    max_values = stats_out[1] 
    avg_values = stats_out[2]

answered Jul 28, 2014 at 12:13

miindlek

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