Most efficient way to store scientific notation in Python and MySQL - python

So I'm trying to store a LOT of numbers, and I want to optimize storage space.
A lot of the numbers generated have pretty high precision floating points, so:
0.000000213213 or 323224.23125523 - long, high memory floats.
I want to figure out the best way, either in Python with MySQL(MariaDB) - to store the number with smallest data size.
So 2.132e-7 or 3.232e5, just to basically store it as with as little footprint as possible, with a decimal range that I can specify - but removing the information after n decimals.
I assume storing as a DOUBLE is the way to go, but can I truncate the precision and save on space too?
I'm thinking some number formating / truncating in Python followed by just normal storage as a DOUBLE would work - but would that actually save any space as opposed to just immediately storing the double with N decimals attached.
Thanks!

All python floats have the same precision and take the same amount of storage. If you want to reduce overall storage numpy arrays should do the trick.

if, on the other hand, you are trying to minimize the representation of numbers for say transmission via json or xml, you could use f-strings.
>>> from math import pi
>>> pi
3.141592653589793
>>> f'{pi:3.2}.'
'3.1.'
>>> bigpi = pi*10e+100
>>> bigpi
3.141592653589793e+101
>>> f'{bigpi:3.2}'
'3.1e+101'

Related

How to avoid floating point arithmetics issues?

Python (and almost anything else) has known limitations while working with floating point numbers (nice overview provided here).
While problem is described well in the documentation it avoids providing any approach to fixing it. And with this question I am seeking to find a more or less robust way to avoid situations like the following:
print(math.floor(0.09/0.015)) # >> 6
print(math.floor(0.009/0.0015)) # >> 5
print(99.99-99.973) # >> 0.016999999999825377
print(.99-.973) # >> 0.017000000000000015
var = 0.009
step = 0.0015
print(var < math.floor(var/step)*step+step) # False
print(var < (math.floor(var/step)+1)*step) # True
And unlike suggested in this question, their solution does not help to fix a problem like next peace of code failing randomly:
total_bins = math.ceil((data_max - data_min) / width) # round to upper
new_max = data_min + total_bins * width
assert new_max >= data_max
# fails. because for example 1.9459999999999997 < 1.946
If you deal in discrete quantities, use int.
Sometimes people use float in places where they definitely shouldn't. If you're counting something (like number of cars in the world) as opposed to measuring something (like how much gasoline is used per day), floating-point is probably the wrong choice. Currency is another example where floating point numbers are often abused: if you're storing your bank account balance in a database, it's really not 123.45 dollars, it's 12345 cents. (But also see below about Decimal.)
Most of the rest of the time, use float.
Floating-point numbers are general-purpose. They're extremely accurate; they just can't represent certain fractions, like finite decimal numbers can't represent the number 1/3. Floats are generally suited for any kind of analog quantity where the measurement has error bars: length, mass, frequency, energy -- if there's uncertainty on the order of 2^(-52) or greater, there's probably no good reason not to use float.
If you need human-readable numbers, use float but format it.
"This number looks weird" is a bad reason not to use float. But that doesn't mean you have to display the number to arbitrary precision. If a number with only three significant figures comes out to 19.99909997918947, format it to one decimal place and be done with it.
>>> print('{:0.1f}'.format(e**pi - pi))
20.0
If you need precise decimal representation, use Decimal.
Sraw's answer refers to the decimal module, which is part of the standard library. I already mentioned currency as a discrete quantity, but you may need to do calculations on amounts of currency in which not all numbers are discrete, for example calculating interest. If you're writing code for an accounting system, there will be rules that say when rounding is applied and to what accuracy various calculations are done, and those specifications will be written in terms of decimal places. In this situation and others where the decimal representation is inherent to the problem specification, you'll want to use a decimal type.
>>> from decimal import Decimal
>>> rate = Decimal('0.0345')
>>> principal = Decimal('3412.65')
>>> interest = rate*principal
>>> interest
Decimal('117.736425')
>>> interest.quantize(Decimal('0.01'))
Decimal('117.74')
But most importantly, use data types and operations that make sense in context.
Several of your examples use math.floor, which takes a float and chops off the fractional part. In any situation where you should use math.floor, floating-point error doesn't matter. (If you want to round to the nearest integer, use round instead.) Yes, there are ways to use floating-point operations that have wrong results from a mathematical standpoint. But real-world quantities usually fall into one of these categories:
Exact, and therefore should not be put in a float;
Imprecise to a degree far exceeding the likely accumulation of floating-point error.
As a programmer, it's part of your job to know the quantities you're dealing with and choose appropriate data types. So there's no "fix" for floating point numbers, because there's no "problem" really -- just people using the wrong type for the wrong thing.
Let's talk about decimal. Actually, this library converts number into a string-like object, and then do any arithmetical operation based on chars.
So in this case, it can handle significantly huge number with almost perfect precision.
But, as it calculate number based on chars, it cost much more.
Further, if you want to use decimal, to ensure precision, you need consistently use it. If you mix decimal with normal types such as float, it may cause unexpected problems.
Finally, when you construct a Decimal object, it is better to pass a string but not a number.
>>> print(Decimal(99.99) - Decimal(99.973))
0.01699999999999590727384202182
>>> print(Decimal("99.99") - Decimal("99.973"))
0.017
It depends what your end goal is - there is no way to "perfectly" store floating point numbers. Only "good enough".
If you are working with money for example (dollars and cents) it is common practice to not store dollars - and only cents. (dollar = 100 cents) - this is how paypal stores your account balance on their servers.
There is also the python Decimal class for fixed point arithmetic.

Python rounding and inserting into array does not round [duplicate]

So I have a list of tuples of two floats each. Each tuple represents a range. I am going through another list of floats which represent values to be fit into the ranges. All of these floats are < 1 but positive, so precision matter. One of my tests to determine if a value fits into a range is failing when it should pass. If I print the value and the range that is causing problems I can tell this much:
curValue = 0.00145000000671
range = (0.0014500000067055225, 0.0020968749796738849)
The conditional that is failing is:
if curValue > range[0] and ... blah :
# do some stuff
From the values given by curValue and range, the test should clearly pass (don't worry about what is in the conditional). Now, if I print explicitly what the value of range[0] is I get:
range[0] = 0.00145000000671
Which would explain why the test is failing. So my question then, is why is the float changing when it is accessed. It has decimal values available up to a certain precision when part of a tuple, and a different precision when accessed. Why would this be? What can I do to ensure my data maintains a consistent amount of precision across my calculations?
The float doesn't change. The built-in numberic types are all immutable. The cause for what you're observing is that:
print range[0] uses str on the float, which (up until very recent versions of Python) printed less digits of a float.
Printing a tuple (be it with repr or str) uses repr on the individual items, which gives a much more accurate representation (again, this isn't true anymore in recent releases which use a better algorithm for both).
As for why the condition doesn't work out the way you expect, it's propably the usual culprit, the limited precision of floats. Try print repr(curVal), repr(range[0]) to see if what Python decided was the closest representation of your float literal possible.
In modern day PC's floats aren't that precise. So even if you enter pi as a constant to 100 decimals, it's only getting a few of them accurate. The same is happening to you. This is because in 32-bit floats you only get 24 bits of mantissa, which limits your precision (and in unexpected ways because it's in base2).
Please note, 0.00145000000671 isn't the exact value as stored by Python. Python only diplays a few decimals of the complete stored float if you use print. If you want to see exactly how python stores the float use repr.
If you want better precision use the decimal module.
It isn't changing per se. Python is doing its best to store the data as a float, but that number is too precise for float, so Python modifies it before it is even accessed (in the very process of storing it). Funny how something so small is such a big pain.
You need to use a arbitrary fixed point module like Simple Python Fixed Point or the decimal module.
Not sure it would work in this case, because I don't know if Python's limiting in the output or in the storage itself, but you could try doing:
if curValue - range[0] > 0 and...

Python default behavior of str(x)

I am depending on some code that uses the Decimal class because it needs precision to a certain number of decimal places. Some of the functions allow inputs to be floats because of the way that it interfaces with other parts of the codebase. To convert them to decimal objects, it uses things like
mydec = decimal.Decimal(str(x))
where x is the float taken as input. My question is, does anyone know what the standard is for the 'str' method as applied to floats?
For example, take the number 2.1234512. It is stored internally as 2.12345119999999999 because of how floats are represented.
>>> x = 2.12345119999999999
>>> x
2.1234511999999999
>>> str(x)
'2.1234512'
Ok, str(x) in this case is doing something like '%.6f' % x. This is a problem with the way my code converts to decimals. Take the following:
>>> d = decimal.Decimal('2.12345119999999999')
>>> ds = decimal.Decimal(str(2.12345119999999999))
>>> d - ds
Decimal('-1E-17')
So if I have the float, 2.12345119999999999, and I want to pass it to Decimal, converting it to a string using str() gets me the wrong answer. I need to know what are the rules for str(x) that determine what the formatting will be, because I need to determine whether this code needs to be re-written to avoid this error (note that it might be OK, because, for example, the code might round to the 10th decimal place once we have a decimal object)
There must be some set of rules in python's docs that hopefully someone here can point me to. Thanks!
In the Python source, look in "Include/floatobject.h". The precision for the string conversion is set a few lines from the top after an comment with some explanation of the choice:
/* The str() precision PyFloat_STR_PRECISION is chosen so that in most cases,
the rounding noise created by various operations is suppressed, while
giving plenty of precision for practical use. */
#define PyFloat_STR_PRECISION 12
You have the option of rebuilding, if you need something different. Any changes will change formatting of floats and complex numbers. See ./Objects/complexobject.c and ./Objects/floatobject.c. Also, you can compare the difference between how repr and str convert doubles in these two files.
There's a couple of issues worth discussing here, but the summary is: you cannot extract information that is not stored on your system already.
If you've taken a decimal number and stored it as a floating point, you'll have lost information, since most decimal (base 10) numbers with a finite number of digits cannot be stored using a finite number of digits in base 2 (binary).
As was mentioned, str(a_float) will really call a_float.__str__(). As the documentation states, the purpose of that method is to
return a string containing a nicely printable representation of an object
There's no particular definition for the float case. My opinion is that, for your purposes, you should consider __str__'s behavior to be undefined, since there's no official documentation on it - the current implementation can change anytime.
If you don't have the original strings, there's no way to extract the missing digits of the decimal representation from the float objects. All you can do is round predictably, using string formatting (which you mention):
Decimal( "{0:.5f}".format(a_float) )
You can also remove 0s on the right with resulting_string.rstrip("0").
Again, this method does not recover the information that has been lost.

Exponential of very small number in python

I am trying to calculate the exponential of -1200 in python (it's an example, I don't need -1200 in particular but a collection of numbers that are around -1200).
>>> math.exp(-1200)
0.0
It is giving me an underflow; How may I go around this problem?
Thanks for any help :)
In the standard library, you can look at the decimal module:
>>> import decimal
>>> decimal.Decimal(-1200)
Decimal('-1200')
>>> decimal.Decimal(-1200).exp()
Decimal('7.024601888177132554529322758E-522')
If you need more functions than decimal supports, you could look at the library mpmath, which I use and like a lot:
>>> import mpmath
>>> mpmath.exp(-1200)
mpf('7.0246018881771323e-522')
>>> mpmath.mp.dps = 200
>>> mpmath.exp(-1200)
mpf('7.0246018881771325545293227583680003334372949620241053728126200964731446389957280922886658181655138626308272350874157946618434229308939128146439669946631241632494494046687627223476088395986988628688095132e-522')
but if possible, you should see if you can recast your equations to work entirely in the log space.
Try calculating in logarithmic domain as long as possible. I.e. avoid calculating the exact value but keep working with exponents.
exp(-1200) IS a very very small number (just as exp(1200) is a very very big one), so maybe the exact value is not really what you are interested in. If you only need to compare these numbers then logarithmic space should be enough.

Convert Double to Single without loss of precision in MATLAB

I don't think this is possible, hence I decided to ask here to see as googling around hasn't returned any results that hint that I can do so.
Especially after reading this:
Can doubles be used to represent a 64 bit number without loss of precision
Though my numbers can be held in 32bit as the example below shows.
But is there any way in MATLAB to convert a double precision value to single without loosing information?
e.g. in MATLAB
> a = 103364148
a =
103364148
> single(a)
ans =
103364144
Or maybe there is another way in another language, e.g. Python?
I'm working with GPUMat where I can only use GPUSingle, so I'm trying to find a way to work with stuff that is double to MATLAB in single to the GPU.
Thanks,
A single can hold integer numbers up to 2^24 (16,777,216) without loss of precision - some bits are required for the sign and the exponent .
In other words, no, there is no way that you can make a number larger than 2^24 fit into a single without error (note that it can hold some larger numbers, as long as they can be written as the product of a number smaller 2^24 and some power of 2).
However, are you sure you need that kind of precision for your calculations? As long as all your integers are less than 2^24, you should be fine.
When you're doing these kinds of experiments, you should turn on
format long
so you can see more decimal values. For example,
>> pi
ans =
3.1416
>> format long
>> ans
ans =
3.141592653589793
If your only concern are integers, you could use int32 instead

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