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Basic use

Ultra-short cheat sheet:

from datamatrix import DataMatrix, io
# Read a DataMatrix from file
dm = io.readtxt('data.csv')
# Create a new DataMatrix
dm = DataMatrix(length=5)
# The first two rows
print(dm[:2])
# Create a new column and initialize it with the Fibonacci series
dm.fibonacci = 0, 1, 1, 2, 3
# You can also specify column names as if they are dict keys
dm['fibonacci'] = 0, 1, 1, 2, 3
# Remove 0 and 3 with a simple selection
dm = (dm.fibonacci > 0) & (dm.fibonacci < 3)
# Get a list of indices that match certain criteria
print(dm[(dm.fibonacci > 0) & (dm.fibonacci < 3)])
# Select 1, 1, and 2 by matching any of the values in a set
dm = dm.fibonacci == {1, 2}
# Select all odd numbers with a lambda expression
dm = dm.fibonacci == (lambda x: x % 2)
# Change all 1s to -1
dm.fibonacci[dm.fibonacci == 1] = -1
# The first two cells from the fibonacci column
print(dm.fibonacci[:2])
# Column mean
print('Mean: %s' % dm.fibonacci.mean)
# Multiply all fibonacci cells by 2
dm.fibonacci_times_two = dm.fibonacci * 2
# Loop through all rows
for row in dm:
    print(row.fibonacci) # get the fibonacci cell from the row
# Loop through all columns
for colname, col in dm.columns:
    for cell in col: # Loop through all cells in the column
        print(cell) # do something with the cell
# Or just see which columns exist
print(dm.column_names)

Important note: Because of a limitation (or feature, if you will) of the Python language, the behavior of and, or, and chained (x < y < z) comparisons cannot be modified. These therefore do not work with DataMatrix objects as you would expect them to:

# INCORRECT: The following does *not* work as expected
dm = dm.fibonacci > 0 and dm.fibonacci < 3
# INCORRECT: The following does *not* work as expected
dm = 0 < dm.fibonacci < 3
# CORRECT: Use the '&' operator
dm = (dm.fibonacci > 0) & (dm.fibonacci < 3)

Slightly longer cheat sheet:

Basic operations

Creating a DataMatrix

Create a new DataMatrix object, and add a column (named col). By default, the column is of the MixedColumn type, which can store numeric and string data.

import sys
from datamatrix import DataMatrix, __version__
dm = DataMatrix(length=2)
dm.col = ':-)'
print(
    'Examples generated with DataMatrix v{} on Python {}\n'.format(
        __version__,
        sys.version
    )
)
print(dm)

Output:

Examples generated with DataMatrix v0.15.0 on Python 3.10.5 | packaged by conda-forge | (main, Jun 14 2022, 07:04:59) [GCC 10.3.0]

+---+-----+
| # | col |
+---+-----+
| 0 | :-) |
| 1 | :-) |
+---+-----+

You can change the length of the DataMatrix later on. If you reduce the length, data will be lost. If you increase the length, empty cells will be added.

dm.length = 3

Concatenating two DataMatrix objects

You can concatenate two DataMatrix objects using the << operator. Matching columns will be combined. (Note that row 2 is empty. This is because we have increased the length of dm in the previous step, causing an empty row to be added.)

dm2 = DataMatrix(length=2)
dm2.col = ';-)'
dm2.col2 = 10, 20
dm3 = dm << dm2
print(dm3)

Output:

+---+-----+------+
| # | col | col2 |
+---+-----+------+
| 0 | :-) |      |
| 1 | :-) |      |
| 2 |     |      |
| 3 | ;-) |  10  |
| 4 | ;-) |  20  |
+---+-----+------+

Creating columns

You can change all cells in column to a single value. This creates a new column if it doesn't exist yet.

dm.col = 'Another value'
print(dm)

Output:

+---+---------------+
| # |      col      |
+---+---------------+
| 0 | Another value |
| 1 | Another value |
| 2 | Another value |
+---+---------------+

You can change all cells in a column based on a sequence. This creates a new column if it doesn't exist yet. This sequence must have the same length as the column (3 in this case).

dm.col = 1, 2, 3
print(dm)

Output:

+---+-----+
| # | col |
+---+-----+
| 0 |  1  |
| 1 |  2  |
| 2 |  3  |
+---+-----+

If you do not know the name of a column, for example because it is defined by a variable, you can also refer to columns as though they are items of a dict. However, this is not recommended, because it makes it less clear whether you are referring to column or a row.

dm['col'] = 'X'
print(dm)

Output:

+---+-----+
| # | col |
+---+-----+
| 0 |  X  |
| 1 |  X  |
| 2 |  X  |
+---+-----+

Renaming columns

dm.rename('col', 'col2')
print(dm)

Output:

+---+------+
| # | col2 |
+---+------+
| 0 |  X   |
| 1 |  X   |
| 2 |  X   |
+---+------+

Deleting columns

You can delete a column using the del keyword:

dm.col = 'x'
del dm.col2
print(dm)

Output:

+---+-----+
| # | col |
+---+-----+
| 0 |  x  |
| 1 |  x  |
| 2 |  x  |
+---+-----+

Slicing and assigning to column cells

Assign to one cell

dm.col[1] = ':-)'
print(dm)

Output:

+---+-----+
| # | col |
+---+-----+
| 0 |  x  |
| 1 | :-) |
| 2 |  x  |
+---+-----+

Assign to multiple cells

This changes row 0 and 2. It is not a slice!

dm.col[0,2] = ':P'
print(dm)

Output:

+---+-----+
| # | col |
+---+-----+
| 0 |  :P |
| 1 | :-) |
| 2 |  :P |
+---+-----+

Assign to a slice of cells

dm.col[1:] = ':D'
print(dm)

Output:

+---+-----+
| # | col |
+---+-----+
| 0 |  :P |
| 1 |  :D |
| 2 |  :D |
+---+-----+

Assign to cells that match a selection criterion

dm.col[1:] = ':D'
dm.is_happy = 'no'
dm.is_happy[dm.col == ':D'] = 'yes'
print(dm)

Output:

+---+-----+----------+
| # | col | is_happy |
+---+-----+----------+
| 0 |  :P |    no    |
| 1 |  :D |   yes    |
| 2 |  :D |   yes    |
+---+-----+----------+

Column properties

Basic numeric properties, such as the mean, can be accessed directly. Only numeric values are taken into account.

dm.col = 1, 2, 'not a number'
# Numeric descriptives
print('mean: %s' % dm.col.mean)
print('median: %s' % dm.col.median)
print('standard deviation: %s' % dm.col.std)
print('sum: %s' % dm.col.sum)
print('min: %s' % dm.col.min)
print('max: %s' % dm.col.max)
# Other properties
print('unique values: %s' % dm.col.unique)
print('number of unique values: %s' % dm.col.count)
print('column name: %s' % dm.col.name)

Output:

mean: 1.5
median: 1.5
standard deviation: 0.7071067811865476
sum: 3.0
min: 1.0
max: 2.0
unique values: [1, 2, 'not a number']
number of unique values: 3
column name: col

Iterating over rows, columns, and cells

By iterating directly over a DataMatrix object, you get successive Row objects. From a Row object, you can directly access cells.

dm.col = 'a', 'b', 'c'
for row in dm:
    print(row)
    print(row.col)

Output:

+----------+-------+
|   Name   | Value |
+----------+-------+
|   col    |   a   |
| is_happy |   no  |
+----------+-------+
a
+----------+-------+
|   Name   | Value |
+----------+-------+
|   col    |   b   |
| is_happy |  yes  |
+----------+-------+
b
+----------+-------+
|   Name   | Value |
+----------+-------+
|   col    |   c   |
| is_happy |  yes  |
+----------+-------+
c

By iterating over DataMatrix.columns, you get successive (column_name, column) tuples.

for colname, col in dm.columns:
    print('%s = %s' % (colname, col))

Output:

col = col['a', 'b', 'c']
is_happy = col['no', 'yes', 'yes']

By iterating over a column, you get successive cells:

for cell in dm.col:
    print(cell)

Output:

a
b
c

By iterating over a Row object, you get (column_name, cell) tuples:

row = dm[0] # Get the first row
for colname, cell in row:
    print('%s = %s' % (colname, cell))

Output:

col = a
is_happy = no

The column_names property gives a sorted list of all column names (without the corresponding column objects):

print(dm.column_names)

Output:

['col', 'is_happy']

Selecting data

Comparing a column to a value

You can select by directly comparing columns to values. This returns a new DataMatrix object with only the selected rows.

dm = DataMatrix(length=10)
dm.col = range(10)
dm_subset = dm.col > 5
print(dm_subset)

Output:

+---+-----+
| # | col |
+---+-----+
| 6 |  6  |
| 7 |  7  |
| 8 |  8  |
| 9 |  9  |
+---+-----+

Selecting by multiple criteria with | (or), & (and), and ^ (xor)

You can select by multiple criteria using the | (or), & (and), and ^ (xor) operators (but not the actual words 'and' and 'or'). Note the parentheses, which are necessary because |, &, and ^ have priority over other operators.

dm_subset = (dm.col < 1) | (dm.col > 8)
print(dm_subset)

Output:

+---+-----+
| # | col |
+---+-----+
| 0 |  0  |
| 9 |  9  |
+---+-----+

dm_subset = (dm.col > 1) & (dm.col < 8)
print(dm_subset)

Output:

+---+-----+
| # | col |
+---+-----+
| 2 |  2  |
| 3 |  3  |
| 4 |  4  |
| 5 |  5  |
| 6 |  6  |
| 7 |  7  |
+---+-----+

Selecting by multiple criteria by comparing to a set {}

If you want to check whether column values are identical to, or different from, a set of test values, you can compare the column to a set object. (This is considerably faster than comparing the column values to each of the test values separately, and then merging the result using & or |.)

dm_subset = dm.col == {1, 3, 5, 7}
print(dm_subset)

Output:

+---+-----+
| # | col |
+---+-----+
| 1 |  1  |
| 3 |  3  |
| 5 |  5  |
| 7 |  7  |
+---+-----+

Selecting with a function or lambda expression

You can also use a function or lambda expression to select column values. The function must take a single argument and its return value determines whether the column value is selected. This is analogous to the classic filter() function.

dm_subset = dm.col == (lambda x: x % 2)
print(dm_subset)

Output:

+---+-----+
| # | col |
+---+-----+
| 1 |  1  |
| 3 |  3  |
| 5 |  5  |
| 7 |  7  |
| 9 |  9  |
+---+-----+

Selecting values that match another column (or sequence)

You can also select by comparing a column to a sequence, in which case a row-by-row comparison is done. This requires that the sequence has the same length as the column, is not a set object (because set objects are treated as described above).

dm = DataMatrix(length=4)
dm.col = 'a', 'b', 'c', 'd'
dm_subset = dm.col == ['a', 'b', 'x', 'y']
print(dm_subset)

Output:

+---+-----+
| # | col |
+---+-----+
| 0 |  a  |
| 1 |  b  |
+---+-----+

When a column contains values of different types, you can also select values by type: (Note: On Python 2, all str values are automatically decoded to unicode, so you'd need to compare the column to unicode to extract str values.)

dm = DataMatrix(length=4)
dm.col = 'a', 1, 'c', 2
dm_subset = dm.col == int
print(dm_subset)

Output:

+---+-----+
| # | col |
+---+-----+
| 1 |  1  |
| 3 |  2  |
+---+-----+

Getting indices for rows that match selection criteria ('where')

You can get the indices for rows that match certain selection criteria by slicing a DataMatrix with a subset of itself. This is similar to the numpy.where() function.

dm = DataMatrix(length=4)
dm.col = 1, 2, 3, 4
print(dm[(dm.col > 1) & (dm.col < 4)])

Output:

[1, 2]

Element-wise column operations

Multiplication, addition, etc.

You can apply basic mathematical operations on all cells in a column simultaneously. Cells with non-numeric values are ignored, except by the + operator, which then results in concatenation.

dm = DataMatrix(length=3)
dm.col = 0, 'a', 20
dm.col2 = dm.col*.5
dm.col3 = dm.col+10
dm.col4 = dm.col-10
dm.col5 = dm.col/50
print(dm)

Output:

+---+-----+------+------+------+------+
| # | col | col2 | col3 | col4 | col5 |
+---+-----+------+------+------+------+
| 0 |  0  | 0.0  |  10  | -10  | 0.0  |
| 1 |  a  |  a   | a10  |  a   |  a   |
| 2 |  20 | 10.0 |  30  |  10  | 0.4  |
+---+-----+------+------+------+------+

Applying a function or lambda expression

The @ operator is only available in Python 3.5 and later.

You can apply a function or lambda expression to all cells in a column simultaneously with the @ operator.

dm = DataMatrix(length=3)
dm.col = 0, 1, 2
dm.col2 = dm.col @ (lambda x: x*2)
print(dm)

Output:

+---+-----+------+
| # | col | col2 |
+---+-----+------+
| 0 |  0  |  0   |
| 1 |  1  |  2   |
| 2 |  2  |  4   |
+---+-----+------+

Column types

When you create a DataMatrix, you can indicate a default column type. If you do not specify a default column type, a MixedColumn is used by default.

from datamatrix import DataMatrix, IntColumn
dm = DataMatrix(length=2, default_col_type=IntColumn)
dm.i = 1, 2 # This is an IntColumn

You can also explicitly indicate the column type when creating a new column:

from datamatrix import FloatColumn
dm.f = FloatColumn

MixedColumn (default)

A MixedColumn contains text (unicode in Python 2, str in Python 3), int, float, or None.

Important notes:

  • utf-8 encoding is assumed for byte strings
  • String with numeric values, including NAN and INF, are automatically converted to the most appropriate type
  • The string 'None' is not converted to the type None
  • Trying to assign a non-supported type results in a TypeError
from datamatrix import DataMatrix, NAN, INF
dm = DataMatrix(length=12)
dm.datatype = (
    'int',
    'int (converted)',
    'float',
    'float (converted)',
    'None',
    'str',
    'float',
    'float (converted)',
    'float',
    'float (converted)',
    'float',
    'float (converted)',
)
dm.value = (
    1,
    '1',
    1.2,
    '1.2',
    None,
    'None',
    NAN,
    'nan',
    INF,
    'inf',
    -INF,
    '-inf'
)
print(dm)

Output:

+----+-------------------+-------+
| #  |      datatype     | value |
+----+-------------------+-------+
| 0  |        int        |   1   |
| 1  |  int (converted)  |   1   |
| 2  |       float       |  1.2  |
| 3  | float (converted) |  1.2  |
| 4  |        None       |  None |
| 5  |        str        |  None |
| 6  |       float       |  nan  |
| 7  | float (converted) |  nan  |
| 8  |       float       |  INF  |
| 9  | float (converted) |  INF  |
| 10 |       float       |  -inf |
| 11 | float (converted) |  -inf |
+----+-------------------+-------+

IntColumn (requires numpy)

The IntColumn contains only int values. As of 0.14, the easiest way to create a IntColumn column is to assign int to a new column name.

Important notes:

  • Trying to assign a value that cannot be converted to an int results in a TypeError
  • Float values will be rounded down (i.e. the decimals will be lost)
  • NAN or INF values are not supported because these are float
from datamatrix import DataMatrix
dm = DataMatrix(length=2)
dm.i = int
dm.i = 1, 2
print(dm)

Output:

+---+---+
| # | i |
+---+---+
| 0 | 1 |
| 1 | 2 |
+---+---+

If you insert non-int values, they are automatically converted to int if possible. Decimals are discarded (i.e. values are floored, not rounded):

dm.i = '3', 4.7
print(dm)

Output:

+---+---+
| # | i |
+---+---+
| 0 | 3 |
| 1 | 4 |
+---+---+

If you insert values that cannot converted to int, a TypeError is raised:

try:
    dm.i = 'x'
except TypeError as e:
    print(repr(e))

Output:

TypeError('IntColumn expects integers, not x')

FloatColumn (requires numpy)

The FloatColumn contains float, nan, and inf values. As of 0.14, the easiest way to create a FloatColumn column is to assign float to a new column name.

Important notes:

  • Values that are accepted by a MixedColumn but cannot be converted to a numeric value become NAN. Examples are non-numeric strings or None.
  • Trying to assign a non-supported type results in a TypeError
import numpy as np
from datamatrix import DataMatrix, FloatColumn
dm = DataMatrix(length=3)
dm.f = float
dm.f = 1, np.nan, np.inf
print(dm)

Output:

+---+-----+
| # |  f  |
+---+-----+
| 0 | 1.0 |
| 1 | nan |
| 2 | INF |
+---+-----+

If you insert other values, they are automatically converted if possible.

dm.f = '3.3', 'inf', 'nan'
print(dm)

Output:

+---+-----+
| # |  f  |
+---+-----+
| 0 | 3.3 |
| 1 | INF |
| 2 | nan |
+---+-----+

If you insert values that cannot be converted to float, they become nan.

dm.f = 'x'
print(dm)

Output:

/home/sebastiaan/anaconda3/envs/pydata/lib/python3.10/site-packages/datamatrix/py3compat.py:105: UserWarning: Invalid type for 
FloatColumn: x
  warnings.warn(safe_str(msg), *args)
â ™ Generating...+---+-----+
| # |  f  |
+---+-----+
| 0 | nan |
| 1 | nan |
| 2 | nan |
+---+-----+
Note: Careful when working with nan data!

You have to take special care when working with nan data. In general, nan is not equal to anything else, not even to itself: nan != nan. You can see this behavior when selecting data from a FloatColumn with nan values in it.

from datamatrix import DataMatrix, FloatColumn
dm = DataMatrix(length=3)
dm.f = FloatColumn
dm.f = 0, np.nan, 1
dm = dm.f == [0, np.nan, 1]
print(dm)

Output:

+---+-----+
| # |  f  |
+---+-----+
| 0 | 0.0 |
| 2 | 1.0 |
+---+-----+

However, for convenience, you can select all nan values by comparing a FloatColumn to a single nan value:

from datamatrix import DataMatrix, FloatColumn
dm = DataMatrix(length=3)
dm.f = FloatColumn
dm.f = 0, np.nan, 1
print('NaN values')
print(dm.f == np.nan)
print('Non-NaN values')
print(dm.f != np.nan)

Output:

NaN values
+---+-----+
| # |  f  |
+---+-----+
| 1 | nan |
+---+-----+
Non-NaN values
+---+-----+
| # |  f  |
+---+-----+
| 0 | 0.0 |
| 2 | 1.0 |
+---+-----+

SeriesColumn: Working with continuous data (requires numpy)

The SeriesColumn is 2 dimensional; that is, each cell is by itself an array of values. Therefore, the SeriesColumn can be used to work with sets of continuous data, such as EEG or eye-position traces.

For more information about series, see:

import numpy as np
from matplotlib import pyplot as plt
from datamatrix import SeriesColumn

length = 10 # Number of traces
depth = 50 # Size of each trace

x = np.linspace(0, 2*np.pi, depth)
sinewave = np.sin(x)
noise = np.random.random(depth)*2-1

dm = DataMatrix(length=length)
dm.series = SeriesColumn(depth=depth)
dm.series[0] = noise
dm.series[1:].setallrows(sinewave)
dm.series[1:] *= np.linspace(-1, 1, 9)

plt.xlim(x.min(), x.max())
plt.plot(x, dm.series.plottable, color='green', linestyle=':')
y1 = dm.series.mean-dm.series.std
y2 = dm.series.mean+dm.series.std
plt.fill_between(x, y1, y2, alpha=.2, color='blue')
plt.plot(x, dm.series.mean, color='blue')
plt.show()

Output:

/home/sebastiaan/anaconda3/envs/pydata/lib/python3.10/site-packages/numpy/lib/nanfunctions.py:1879: RuntimeWarning: Degrees of 
freedom <= 0 for slice.
  var = nanvar(a, axis=axis, dtype=dtype, out=out, ddof=ddof,
â ´ Generating...

You can also create a SeriesColumn by assigning a 2D numpy array to a new column, where one of the dimensions matches the length of the DataMatrix. The other dimension is then assumed to be the depth of the SeriesColumn:

dm = DataMatrix(length=3)
dm.random_noise = np.random.random((3, 10))

Reading and writing files

You can read and write files with functions from the datamatrix.io module. The main supported file types are csv and xlsx.

from datamatrix import io

dm = DataMatrix(length=3)
dm.col = 1, 2, 3
# Write to disk
io.writetxt(dm, 'my_datamatrix.csv')
io.writexlsx(dm, 'my_datamatrix.xlsx')
# And read it back from disk!
dm = io.readtxt('my_datamatrix.csv')
dm = io.readxlsx('my_datamatrix.xlsx')
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