NumPy reading file with filtering lines on the fly

Question

I have a large array of numbers written in a CSV file and need to load only a slice of that array. Conceptually I want to call np.genfromtxt() and then row-slice the resulting array, but

1. the file is so large that may not to fit in RAM
2. the number of relevant rows might be small, so there is no need to parse every line.

MATLAB has the function textscan() that can take a file descriptor and read only a chunk of the file. Is there anything like that in NumPy?

For now, I defined the following function that reads only the lines that satisfy the given condition:

def genfromtxt_cond(fname, cond=(lambda str: True)):
  res = []
  with open(fname) as file:
    for line in file:
      if cond(line):
        res.append([float(s) for s in line.split()])

  return np.array(res, dtype=np.float64)

There are several problems with this solution:

• not general: supports only the float type, while genfromtxt detects the types, which may vary from column to column; also missing values, converters, skipping, etc.;
• not efficient: when the condition is difficult, every line may be parsed twice, also the used data structure and reading bufferization may be suboptimal;
• requires writing code.

Is there a standard function that implements filtering, or some counterpart of MATLAB’s textscan?

Answer 1

I can think of two approaches that provide some of the functionality you are asking for:

1. To read a file either in chunks / or in strides of n-lines / etc.:
   You can pass a generator to numpy.genfromtxt as well as to numpy.loadtxt. This way you can load a large dataset from a textfile memory-efficiently while retaining all the convenient parsing features of the two functions.

2. To read data only from lines that match a criterion that can be expressed as a regex:
   You can use numpy.fromregex and use a regular expression to precisely define which tokens from a given line in the input file should be loaded. Lines not matching the pattern will be ignored.

To illustrate the two approaches, I'm going to use an example from my research context.
I often need to load files with the following structure:

6
 generated by VMD
  CM         5.420501        3.880814        6.988216
  HM1        5.645992        2.839786        7.044024
  HM2        5.707437        4.336298        7.926170
  HM3        4.279596        4.059821        7.029471
  OD1        3.587806        6.069084        8.018103
  OD2        4.504519        4.977242        9.709150
6
 generated by VMD
  CM         5.421396        3.878586        6.989128
  HM1        5.639769        2.841884        7.045364
  HM2        5.707584        4.343513        7.928119
  HM3        4.277448        4.057222        7.022429
  OD1        3.588119        6.069086        8.017814

These files can be huge (GBs) and I'm only interested in the numerical data. All data blocks have the same size -- 6 in this example -- and they are always separated by two lines. So the stride of the blocks is 8.

Using the first approach:

First I'm going to define a generator that filters out the undesired lines:

def filter_lines(f, stride):
    for i, line in enumerate(f):
        if i%stride and (i-1)%stride:
            yield line

Then I open the file, create a filter_lines-generator (here I need to know the stride), and pass that generator to genfromtxt:

with open(fname) as f:
    data = np.genfromtxt(filter_lines(f, 8),
                         dtype='f',
                         usecols=(1, 2, 3))

This works like a breeze. Note that I'm able to use usecols to get rid of the first column of the data. In the same way, you could use all the other features of genfromtxt -- detecting the types, varying types from column to column, missing values, converters, etc.

In this example data.shape was (204000, 3) while the original file consisted of 272000 lines.

Here the generator is used to filter homogenously strided lines but one can likewise imagine it filtering out inhomogenous blocks of lines based on (simple) criteria.

Using the second approach:

Here's the regexp I'm going to use:

regexp = r'\s+\w+' + r'\s+([-.0-9]+)' * 3 + r'\s*\n'

Groups -- i.e. inside () -- define the tokens to be extracted from a given line. Next, fromregex does the job and ignores lines not matching the pattern:

data = np.fromregex(fname, regexp, dtype='f')

The result is exactly the same as in the first approach.

Answer 2

If you pass a list of types (the format condition), use a try block and use yield to use genfromtxt as a generator, we should be able to replicate textscan().

def genfromtext(fname, formatTypes):
    with open(fname, 'r') as file:
        for line in file:
            try:
                line = line.split(',')  # Do you care about line anymore?
                r = []
                for type, cell in zip(formatTypes, line):
                    r.append(type(cell))
            except:
                pass  # Fail silently on this line since we hit an error
            yield r

Edit: I forgot the except block. It runs okay now and you can use genfromtext as a generator like so (using a random CSV log I have sitting around):

>>> a = genfromtext('log.txt', [str, str, str, int])
>>> a.next()
['10.10.9.45', ' 2013/01/17 16:29:26', '00:00:36', 0]
>>> a.next()
['10.10.9.45', ' 2013/01/17 16:22:20', '00:08:14', 0]
>>> a.next()
['10.10.9.45', ' 2013/01/17 16:31:05', '00:00:11', 3]

I should probably note that I'm using zip to zip together the comma split line and the formatSpec which will tuplify the two lists (stopping when one of the lists runs out of items) so we can iterate over them together, avoiding a loop dependent on len(line) or something like that.

Answer 3

Trying to demonstrate comment to OP.

def fread(name, cond):
    with open(name) as file:
        for line in file:
            if cond(line):
                yield line.split()

def a_genfromtxt_cond(fname, cond=(lambda str: True)):
    """Seems to work without need to convert to float."""
    return np.array(list(fread(fname, cond)), dtype=np.float64)

def b_genfromtxt_cond(fname, cond=(lambda str: True)):
    r = [[int(float(i)) for i in l] for l in fread(fname, cond)]
    return np.array(r, dtype=np.integer)


a = a_genfromtxt_cond("tar.data")
print a
aa = b_genfromtxt_cond("tar.data")
print aa

Output

[[ 1.   2.3  4.5]
 [ 4.7  9.2  6.7]
 [ 4.7  1.8  4.3]]
[[1 2 4]
 [4 9 6]
 [4 1 4]]