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pythonscipysparse-matrix

Scipy error - ValueError: row index exceeds matrix dimensions

I used the code below to build train and test matrices so as to use them in my NN model.

from scipy.sparse import csr_matrix
import pandas as pd
from sklearn.model_selection import train_test_split

df = pd.read_csv('data.csv', names=['x', 'y', 'z'])


x = df.x.unique().shape[0]
y = df.y.unique().shape[0]

train_data, test_data = train_test_split(df, test_size=0.2)
train_data = pd.DataFrame(train_data)
test_data = pd.DataFrame(test_data)

#Build train matrix
train_x = []
train_y = []
train_z = []

for line in train_data.itertuples():
    u = line[1] - 1
    i = line[2] - 1
    train_x.append(u)
    train_y.append(i)
    train_z.append(line[3])
train_matrix = csr_matrix((train_z, (train_x, train_y)), shape=(x, y))

#Build test matrix
test_x = []
test_y = []
test_z = []
for line in test_data.itertuples():
    test_x.append(line[1] - 1)
    test_y.append(line[2] - 1)
    test_z.append(line[3])
test_matrix = csr_matrix((test_z, (test_x, test_y)), shape=(x, y))

When I work with small datasets, it works perfectly. However, when I use it to handle a little bit larger datasets (600 MB), it doesn't work. It rather shows me this error:

 File "C:\Users\Mus\Anaconda3\lib\site-packages\scipy\sparse\compressed.py", line 51, in __init__
    other = self.__class__(coo_matrix(arg1, shape=shape))
  File "C:\Users\Mus\Anaconda3\lib\site-packages\scipy\sparse\coo.py", line 192, in __init__
    self._check()
  File "C:\Users\Mus\Anaconda3\lib\site-packages\scipy\sparse\coo.py", line 272, in _check
    raise ValueError('row index exceeds matrix dimensions')
ValueError: row index exceeds matrix dimensions

When I tried the code below it showed me another error in the same line:

train_data, test_data = train_test_split(csr_matrix(df[z].values, (df[x].values, df[y].values)), test_size=0.2)

File "C:\Users\Mus\Anaconda3\lib\site-packages\pandas\core\frame.py", line 2688, in __getitem__
    return self._getitem_column(key)
  File "C:\Users\Mus\Anaconda3\lib\site-packages\pandas\core\frame.py", line 2695, in _getitem_column
    return self._get_item_cache(key)
  File "C:\Users\Mus\Anaconda3\lib\site-packages\pandas\core\generic.py", line 2489, in _get_item_cache
    values = self._data.get(item)
  File "C:\Users\Mus\Anaconda3\lib\site-packages\pandas\core\internals.py", line 4115, in get
    loc = self.items.get_loc(item)
  File "C:\Users\Mus\Anaconda3\lib\site-packages\pandas\core\indexes\base.py", line 3080, in get_loc
    return self._engine.get_loc(self._maybe_cast_indexer(key))
  File "pandas\_libs\index.pyx", line 140, in pandas._libs.index.IndexEngine.get_loc
  File "pandas\_libs\index.pyx", line 162, in pandas._libs.index.IndexEngine.get_loc
  File "pandas\_libs\hashtable_class_helper.pxi", line 1492, in pandas._libs.hashtable.PyObjectHashTable.get_item
  File "pandas\_libs\hashtable_class_helper.pxi", line 1500, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 5

I appreciate your help

Solution

  • This code proposed by @CJR replaces all the code of building the train and test matrices

    train_matrix, test_matrix = train_test_split(csr_matrix((df['z'].values, (df['x'].values, df['y'].values))), test_size=0.2)