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POValue Error :Storing data from binary file into numpy 3d arrays
 

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  1. POValue Error :Storing data from binary file into numpy 3d arrays
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    <p>I am trying to read float numbers from a Binary file using Struct module and then storing them in numpy 3D arrays.When I run it as an independent script, it works fine.But when I call it as a class's function from another script(after import) it gives value error Here is my code.</p> <pre><code>import struct from numpy import * class DCD_read: def read_cord(self,total_atoms,dcd_data): cord_data=dcd_data[276:len(dcd_data)] ## binary data string byte=0 count=0 total_frames=info_dict['nset'] coord=numpy.zeros((total_frames,total_atoms,3)) ## 3d array for frames in range(0,total_frames): for atoms in range(0,total_atoms): x = list(struct.unpack('&lt;f',cord_data[60+byte:64+byte])) ###reading float byte+=4 y = list(struct.unpack('&lt;f',cord_data[60+byte:64+byte])) byte+=4 z = list(struct.unpack('&lt;f',cord_data[60+byte:64+byte])) byte+=4 ls=x ls.extend(y) ls.extend(z) coord[frames][atoms]=ls return coord </code></pre> <p>Error:</p> <pre><code>Traceback (most recent call last): File "C:\Users\Hira\Documents\PROJECT\md.py", line 24, in &lt;module&gt; coord=dcd.read_cord(total_atoms,dcd_data) File "C:\Users\Hira\Documents\PROJECT\DCD_read.py", line 51, in read_cord coord=numpy.zeros((total_frames,total_atoms,3)) File "C:\Python27\numpy\core\numeric.py", line 148, in ones a = empty(shape, dtype, order) ValueError: negative dimensions are not allowed </code></pre> <p>md.py is the main (calling script) while DCD_read.py is module. Here is code for md.py (main script)</p> <pre><code>from DCD_read import * import numpy dcd_file=open('frame3.dcd',"rb") dcd_data=dcd_file.read() dcd=read_dcd() total_atoms=6141 coord=dcd.read_cord(total_atoms,dcd_data) </code></pre> <p>Please can any one help???? I hope I explained it completely and clearly.Thanx</p>
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    1. PTQuestion
    1. USSaullo G. P. Castro
    1. USZBatool
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    1. VO
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      1. POValue Error :Storing data from binary file into numpy 3d arrays
      1. This table or related slice is empty.
      1. VTUpMod
    2. VO
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      1. POValue Error :Storing data from binary file into numpy 3d arrays
      1. This table or related slice is empty.
      1. VTUpMod
    3. VO
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      1. POValue Error :Storing data from binary file into numpy 3d arrays
      1. This table or related slice is empty.
      1. VTUpMod
    1. COWhere is `info_dict` defined? Check the value of `info_dict['nset']` (which you assign to `total_frames`).
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      1. POValue Error :Storing data from binary file into numpy 3d arrays
      1. USWarren Weckesser
    2. COinfo_dict is a global dictionary which is initialized and assigned in another function of the same class. info_dict['nset'] value can be in hundreds or thousands
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      1. POValue Error :Storing data from binary file into numpy 3d arrays
      1. USZBatool
    3. CO@ZBatool I would suggest you to put `info_dict` as an attribute of your class and avoid the global variable to see if the strange behavior will still happens...
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      1. POValue Error :Storing data from binary file into numpy 3d arrays
      1. USSaullo G. P. Castro
 

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