Create Sequences by Group ID using numpy array

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I have written a function to get a sequence for LSTM/GRU sequence model based on group ID. I am not getting expected output.

Python Function:

def windowGeneratorByID(data, target, id_col_index, lookback, offset, batch_size=16):
  min_index=0
  max_index = data.shape[0]-offset
  i = min_index + lookback
  while 1:
    if i + batch_size >= max_index:
      i = min_index + lookback
    rows = np.arange(i, min(i + batch_size, max_index))
    i += len(rows)
    samples = np.zeros((len(rows), lookback, data.shape[-1]))
    targets = np.zeros((len(rows), target.shape[-1]))

    for j, row in enumerate(rows):
      indices = range(rows[j] - lookback, rows[j])
      if data[rows[j] + offset][id_col_index] in set(data[indices][:, id_col_index]):
        if len(set(data[indices][:, id_col_index])) == 1:
            samples[j] = data[indices]
            targets[j] = target[rows[j] + offset]

    yield  np.delete(samples,id_col_index,axis=2) , targets

Input:

df=np.array([[1,1,0.1,11],[1,2,0.2,12], [1,3,0.3,13], [1,4,0.4,14], [2,5,0.5,15], [2,6,0.6,16], [2,7,0.7,17],[3,8,0.8,18],[3,9,0.9,19],[3,10,0.7,20]])

Output Code:

lookback=2
batch_size=2
offset = 0
windows = windowGeneratorByID(data=df, target=df[:,2:4],id_col_index=0 , offset=offset, lookback=lookback,batch_size=batch_size)

#The number of total batches are equal to the number of (training examples - lookback-offset)/batch_size 
no_batches=int((df.shape[0]-lookback-offset)/batch_size)

# #print the batches
for i in range(no_batches):
  #get the next batch from the windowGenerator
  input,output=next(windows)
  print("{}th batch: \ninput is:\n{}\n and \ntarget is:\n{}\n".format(i+1, input, output))

Expected Output:

1th batch: 
input is:
[[[ 1.   0.1 11. ]
  [ 2.   0.2 12. ]]

 [[ 2.   0.2 12. ]
  [ 3.   0.3 13. ]]]
 and 
target is:
[[ 0.3 13. ]
 [ 0.4 14. ]]

2nd batch: 
input is:
[[[ 5.   0.5 15. ]
  [ 6.   0.6 16. ]]

 [[[ 8.   0.8 18. ]
  [ 9.   0.9 19. ]]
 and 
target is:
[[ 0.7 17. ]
 [ 0.7 20. ]]
pandas python-3.x numpy arrays python
1 Answers

Here are two methods that will get you what you are trying to solve. One is a generator method like yours to get 1 batch at a time, and the second is a vectorized NumPy method that operates on the complete data at once to get all the batches (This method can be used on chunks of df instead of complete).

Generator method

  1. A chunk, with offset and lookback, is basically a single set of rows X to y. So if I want lookback 2, offset 1. Then I need 4 rows from df. The first 2 will go to X and the last one will go to y. Similarly, if I need lookback 1 offset 0, then I need just 2 rows. First goes to X and last goes to y.
  2. With this understanding, I can calculate the max number of chunks I can get from each group with rolling windows and store it in c
  3. Once I have this, I simply need to create a function that lets me rolling iterate over the rows of df, selecting the number of chunks and then skipping a few since those few will have elements from different groups. So, if I have [0,1,2,3,4,5,6] and I have c = [2,1,1] and skip (aka lookback+offset) = 1. Then I have to take 2, skip 1, take 1, skip 1, take 1, skip 1. So, [0,1,3,5], is what I would iterate. And I would take the size of chunk starting from each of these indexes.
  4. Next it's super simple. Just get a generator setup that pulls these chunks and for a batch size = n, pulls n chunks and stacks them before returning.
df=np.array([[1,1,0.1,11],
             [1,2,0.2,12], 
             [1,3,0.3,13], 
             [1,4,0.4,14], 
             [2,5,0.5,15], 
             [2,6,0.6,16], 
             [2,7,0.7,17],
             [3,8,0.8,18],
             [3,9,0.9,19],
             [3,10,0.7,20]])

def take(xs, runs, skip_size):
    'https://stackoverflow.com/questions/65163947/iterate-over-a-list-based-on-list-with-set-of-iteration-steps'
    ixs = iter(xs)
    for run_size in runs:
        for _ in range(run_size ):
            yield next(ixs)
        for _ in range(skip_size):
            next(ixs)
            
def get_batch(df, target, lookback, offset, batch_size):
    _ , c = np.unique(df[:,0], return_counts=True)
    rows = (lookback+offset+1)
    w = c-rows+1
    itr = take(range(len(df)), w, lookback+offset)
    while 1:
        X, Y = [],[]
        for _ in range(batch_size):
            k = next(itr, 'out of batches!')
            x = df[k:lookback+k, 1:]
            y = df[rows+k-1:rows+k, target]
            X.append(x)
            Y.append(y)
        try: yield np.stack(X), np.stack(Y)
        except: break
            
            
lookback = 2
offset = 0
batch_size = 2
target = slice(2,4) #set the target as a slice instead of a separate df view

windows = get_batch(df, target, lookback, offset, batch_size)

no_batches = int(np.sum(np.unique(df[:,0], return_counts=True)[1] - lookback - offset)/batch_size)

for i in range(no_batches):
    input,output=next(windows)
    print("{}th batch: \ninput is:\n{}\n and \ntarget is:\n{}\n".format(i+1, input, output))

#Lookback = 2, offset = 0, batch_size = 2 

1th batch: 
input is:
[[[ 1.   0.1 11. ]
  [ 2.   0.2 12. ]]

 [[ 2.   0.2 12. ]
  [ 3.   0.3 13. ]]]
 and 
target is:
[[[ 0.3 13. ]]

 [[ 0.4 14. ]]]

2th batch: 
input is:
[[[ 5.   0.5 15. ]
  [ 6.   0.6 16. ]]

 [[ 8.   0.8 18. ]
  [ 9.   0.9 19. ]]]
 and 
target is:
[[[ 0.7 17. ]]

Another example -

lookback = 1
offset = 1
batch_size = 1
target = slice(2,4) #set the target as a slice instead of a separate df view

windows = get_batch(df, target, lookback, offset, batch_size)

no_batches = int(np.sum(np.unique(df[:,0], return_counts=True)[1] - lookback - offset)/batch_size)

for i in range(no_batches):
    input,output=next(windows)
    print("{}th batch: \ninput is:\n{}\n and \ntarget is:\n{}\n".format(i+1, input, output))
    

#Lookback = 1, offset = 1, batch_size = 1

1th batch: 
input is:
[[[ 1.   0.1 11. ]]]
 and 
target is:
[[[ 0.3 13. ]]]

2th batch: 
input is:
[[[ 2.   0.2 12. ]]]
 and 
target is:
[[[ 0.4 14. ]]]

3th batch: 
input is:
[[[ 5.   0.5 15. ]]]
 and 
target is:
[[[ 0.7 17. ]]]

4th batch: 
input is:
[[[ 8.   0.8 18. ]]]
 and 
target is:
[[[ 0.7 20. ]]]

Vectorized NumPy method

If however, you are ok to use a vectorized NumPy compute over all of the data at once, instead of the generator method, I have written the following as well. If df is massive, then you can simply pass chunks of df to this function and get a set of batches for that chunk.

  1. Break array into unequal length groups based on id_column
  2. Get rolling windows over axis=0 using stride tricks
  3. Stack all the windows into a block
  4. Calculate the number of batches possible
  5. Keep only the number of blocks that can successfully be stacked into equal-sized batches
  6. Split block by num batches and get X
  7. Split block by num batches and get y
  8. Return all the X, y as batches in a single array
df=np.array([[1,1,0.1,11],
             [1,2,0.2,12], 
             [1,3,0.3,13], 
             [1,4,0.4,14], 
             [2,5,0.5,15], 
             [2,6,0.6,16], 
             [2,7,0.7,17],
             [3,8,0.8,18],
             [3,9,0.9,19],
             [3,10,0.7,20]])

lookback=1
batch_size=2
offset = 1

def window_split_2d(g, window):
    shp = (g.shape[0] - window + 1, window, g.shape[-1])
    strd = (g.strides[0], g.strides[0], g.strides[1])
    return np.lib.stride_tricks.as_strided(g, shape=shp, strides=strd)

def get_batches_vectorized(df, target, id_col_index, lookback, offset, batch_size):

    #Break array into unequal length groups based on id_column
    groups = np.split(df, np.where(np.diff(df[:,id_col_index]))[0]+1)
    
    #Get rolling windows over axis=0 using stride tricks
    chunks = [window_split_2d(i,lookback+offset+1) for i in groups]
    
    #Stack all the windows into a block
    block = np.vstack(chunks)
    
    #Calculate number of batches possible
    n_batches = block.shape[0]//batch_size
    
    #Keep only the number of blocks that can successfully be stacked into equal sized batches
    keep = block.shape[0]-(block.shape[0]%batch_size)
    block = block[:keep]
    
    #Split block by num batches and get X
    X = np.split(block[:,:lookback,1:], n_batches)

    #Split block by num batches and get y
    y = np.split(block[:,-1,target], n_batches)
    return X, y
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