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POProjecting Coordinates in Numpy array
 

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  1. POProjecting Coordinates in Numpy array
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    <p>So I have come across a rather large bottle neck in my software. I have a set of co-ordinates in <code>cords</code> where each row corresponds to <code>X,Y,Z</code> co-ordinates. Each co-ordinate in <code>cords</code> has a defined area in <code>atom_proj</code>. The <code>atoms</code> variable corresponds to the <code>cords</code> variable and provides the key to the <code>atom_proj</code>.</p> <p>I project the co-ordinates onto the <code>grid</code> array then rotate and repeat until the number of rotations is satisfied. I only project the X and Z co-ordinates ignoring the Y.</p> <p>I have simplified version of my code below. The code runs relatively quick for small co-ordinate sets and number of rotations. But can take a long time if both co-ordinate set and rotation list is large. The number of co-ordinates can vary from a few hundred to tens of thousands. I project the area on the <code>grid</code> over a number or rotations to produce a heat map. An example of the heat map for a co-ordinate set is also shown below.</p> <p><strong>Question:</strong></p> <p>(i) - How can I decrease the projection time of the co-ordinates onto the matrix</p> <p>(ii) - Is there a more pythonic way of applying the co-ordinate area to the <code>grid</code> rather than array splicing?</p> <pre><code>import numpy as np cords = np.array([[5,4,5],[5,4,3],[6,4,6]]) atoms = np.array([['C'],['H'],['C']]) atom_proj = {'H':np.array([[0,0,0,0,0],[0,0,1,0,0],[0,1,1,1,0],[0,0,1,0,0],[0,0,0,0,0]]),'C':np.array([[0,0,0,0,0,0,0],[0,0,0,0,0,0,0],[0,0,1,1,1,0,0],[0,0,1,1,1,0,0],[0,0,1,1,1,0,0],[0,0,0,0,0,0,0],[0,0,0,0,0,0,0]])} grid = np.zeros((10,10)) for rot in xrange(1,10): # This for loop would contain a list of list of rotations to apply which are calculated before hand. # apply rotation for values in zip(cords, atoms): atom_shape = np.shape(atom_proj[values[1][0]]) rad = (atom_shape[0]-1)/2 grid[values[0][2]-rad:values[0][2]+rad+1,values[0][0]-rad:values[0][0]+rad+1] += atom_proj[values[1][0]] print grid </code></pre> <p>Heat map: <img src="https://i.stack.imgur.com/B1W0z.png" alt="enter image description here"></p>
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    1. COWhat changes between `rot` iterations? I htink you are currently repeating the same operation 10 times and rewriting the same variables.
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      1. USJaime
    2. COThe rot variable would contain the rotations to apply. For example rot would iterate through [[0,0],[0,5],[0,10]...]. Where the first value is the x axis rotation and the second value is the z-axis rotation. In the code I provided it is just a place holder for where the rotations would be applied.
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    3. COAt first glance, it looks like this could be expressed as a convolution, but I'm having trouble entirely wrapping my head around what you're doing... Excellent question, regardless!
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      1. USJoe Kington
 

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