Polymaths,

What do you think of General_Data_Protection_Regulation? I'm interested to know if your companies are behind it or minimally complying, more interested to know if you think individuals ought to have the rights expressed in that law and if there is really a moral obligation on site owners to comply. Or, if it should be scrapped or changed.

The right of erasure specifically contradicts PM policy which is defended with the same argument that Wikipedia uses, the "Memory hole" argument. If one user decides to revoke the site owners permission to use their nodes, that creates a hole in the link of the chain, and every user is negatively affected. That is a pretty utilitarian view point. It smells slightly self serving to me to hear that argument from sites whose success directly rides on user generated content.

It really only benefits future users, because if you were there, you don't need a tattoo of the conversation to remember it later. I don't see that a site owner, especially if it's not the hoster ie back in time machines, gets a perpetual license after you leave. Recipe sites -- let's say you participate for years honing the craft and eventually decide to write a cookbook, you don't ever have the right to revoke your recipes down off the boards and make the world pay for your stuff? But your dishes have probably benefited from all that recipe sharing, so it seems you would owe something too.

I can't help but think of the social contract put forth in Crito. You have a good idea of what you are getting into when you participate online, seems reasonable that the site architects who built your playground would be able to dictate the terms, but I don't see how they have the right to continue to do so once you leave.

I googled: Social contract, copyright law, landlord tenant, looked up about 10 web sites that were closing down or blocking EU Customer, but I can't make up my mind. There seems to be a lot of data players operating in the shadows without consent that should be addressed, but I can't see how it affects my life at all. I see an ad about something I almost bought on Amazon, big deal.

Well surely we do not live in a perfect world, but does the GDPR move the decimal point either direction? Or just adding more compliance factories to the world? And who are the people who wrote the bill that made me get all this TOS spam. I tried to find the authors' names and I could not. Maybe this is a stepping stone to better "digital rights"?

I have for a time entertained the idea, that if God is the creator, he would have left his signature in the DNA of human species. If I was the creator, I would have encoded the entire Hebrew Bible in DNA, so to let no one doubt that DNA was created by God and that the Bible is the word of God.

I finally took up the challenge and wrote a perl script to check if the first five verses of Bible are encoded in DNA. Naturally there is an infinite number of ways to encode information in DNA, but I assumed that God would have used something quite obvious in order for us to be able to find information encoded in DNA. I’m assuming that if the Bible is encoded in DNA, the encoding used would be the same as for protein synthesis, namely that triplets of DNA base pairs would encode for one character. There are 64 possible codons so there is plenty of redundancy when they are used for encoding 22 hebrew alphabets (plus sofit forms for five characters).

Like so:

AAA -> Y
AAC -> XXX
AAG -> B
AAT -> XXX
ACA -> A
ACC -> M
ACG -> XXX
ACT -> XXX
AGA -> R
AGC -> R
AGG -> W
AGT -> W
ATA -> H
ATC -> XXX
ATG -> A
ATT -> H
CAA -> XXX
CAC -> XXX
CAG -> I
CAT -> XXX
CCA -> XXX
CCC -> XXX
CCG -> XXX
CCT -> V
CGA -> XXX
CGC -> XXX
CGG -> O
CGT -> XXX
CTA -> XXX
CTC -> E
CTG -> V
CTT -> H
GAA -> H
GAC -> I
GAG -> XXX
GAT -> T
GCA -> XXX
GCC -> B
GCG -> XXX
GCT -> H
GGA -> V
GGC -> H
GGG -> Y
GGT -> A
GTA -> Y
GTC -> V
GTG -> A
GTT -> I
TAA -> E
TAC -> XXX
TAG -> XXX
TAT -> O
TCA -> A
TCC -> Y
TCG -> XXX
TCT -> XXX
TGA -> R
TGC -> H
TGG -> A
TGT -> XXX
TTA -> XXX
TTC -> L
TTG -> B
TTT -> A
[download]

My dirty little perl script reads a FASTA file one character at a time and when a triplet is read, it check to see if that codon is already defined. If it is not, the first character of the target sequence is added to a hash containing all the codons. The algorithm then moves to the next triplet in DNA and check to see if that triplet is defined and so on. When a triplet is already defined and the character stored does not equal the target sequence, the script records the maximum length of the sequence found and goes back to the beginning of DNA and moves forward one base pair to continue the search.

I’m not a computer science expert and I’m sure that my script is dirty and messy, but it does work. It takes 33h to search one target sequence against the 3 billion base pairs of human DNA. The FASTA files are in chunks of roughly 150 million base pairs, so several files need to be checked by hand, but this is not much of a problem. My computer crashes when I try to load more than 10million base pairs at a time, so the script reads each FASTA file in chunks of 5 million base pairs at a time.

I could not get hebrew characters to work properly, so I simply translitterated the first five chapters of Genesis to ASCII characters. This is a dirty way of going about it, but it works.

Aleph A
Bet B
Gimmel G
Dalet D
Hey H
Vav V
Zayin Z
Chet C
Tet T
Yod Y
Kaf K G
Lamed L
Mem M O
Nun N J
Samekh S
Ayin X
Pey P
Tsadi U W
Kuf Q
Resh R
Shin E
Tav I
Gen 1:1-5
BRAEYI BRA ALHYO AI HEMYO VAT HARW VHARW HYIH IHV VBHV VCEG XL PNY IHV
+O VRVC ALHYO MRCPI AL PNY HMYO VYAMR ALHYO YHY AVR VYHY AVR VYRA ALHY
+O AI HAVR KY TVB VYBDL ALHYO BYJ HAVR VBYJ HCEG VYQRA ALHYO LAVR YVO 
+VLCEG QRA LYLH VYHY XRB BYHY BQR YVO ACD
[download]

For control sequences I used Lorem ipsum, War and Peace and a random string. For the control sequences I checked the first one million base pairs only.

The results so far:

Lorem ipsum 42 characters found (250 million searched)

War and peace 35 characters found (one million searched)

Random string 35 characters found (one million searched)
[download]

Having checked the hebrew Bible against so far 500 million base pairs, the maximum sequence found was 45 characters. This is more than the control sequences, but only because much more base pairs were compared. To be sure that the sequence was encoded in DNA by God, I would expect to find a sequence of hundreds of characters, preferably all the first five verses of Genesis. I’m not a mathematician, so I have not calculated what the maximum sequence length would be if left to chance alone. But the control sequences do give some estimate.

I’m of course assuming that God used the hebrew Bible, because some say hebrew is the holy language, but I’ve also checked the King James English for the first verses of Matthew and John. If God is omnipotent, surely he could have encoded the Bible in DNA in any language. In the future I’ll check if New Testament passeges are encoded in Greek, but thus far I’m working with the assumption that the most awesome thing for God to do would have been to encode the biginning of Genesis. Will post results when I find anything.

Let me know what you think of my efforts, I know this is nuts.

My code can be downloaded at kristitty.net/blog/finding-bible-verses-in-dna/

Edit: Just noticed that PDL 2.019 has been released, this was written against 2.018. There shouldn't be many (if any) changes, but I'll update this comment accordingly once I've checked it over.

Edit2: longlong range fixed.

As there was significant interest in the porting of numpy to PDL documentation, I've been continuing to document my explorations with PDL.

The following document is my own personal PDL 'QuickRef', which I've created as both a reference to myself and as a summary of PDL

I've tidied it up and now I'm posting it here for others, should they find it useful. Hopefully, it's both useful to new users of PDL (exploring along with perldl shell) and as a reference for experienced users.

Hopefully I've put this in the correct place, but mods feel free to move it if this is the wrong section.

I will continue to update the 100 PDL Exercises offline and will post an updated version incorporating all feedback soon.

PDL QuickRef

Arguably, this is just a rehashing of the existing documentation available via the modules in the PDL::* namespace. However, I found it useful when learning PDL to have everything in a single place.

PDL Creation

Creation of Vectors

The pdl function creates piddles from implicit and explicit scalars and variables. It accepts an optional first argument, $type, which specifies the internal data type of the piddle.

PDL Datatypes

All piddles store matrices of data in the same data type. PDL supports the following datatypes:

pdl Examples

Piddle Helper Creation Functions

In the following functions, where arguments are marked as ..., accept arguments in the following form:

• $type - an optional data type (see above)
• $x,$y,$z,... - A list of n dimensions for the resulting piddle, OR
• $M - Another piddle, from which the dimensions will be re-used

The following functions create piddles with dimensions taken from another piddle, $M and distribute values between two endpoints ($min and $max) inclusively:

Co-ordinate Piddles

Finally the ndcoords utility function creates a piddle of co-ordinates for the supplied arguments. It may be called in two ways:

• $coords = ndcoords($M); - Take dimensions from another piddle
• $coords = ndcoords(@dims); - Take dimensions from a Perl list

Piddle Conversion

A piddle can be converted into a different type using the datatype names as a method upon the piddle. This returns the converted piddle as a new piddle. The inplace method does not work with these conversion methods.

Obtaining Piddle Information

PDL provides a number of functions to obtain information about piddles:

Indexing, Slicing and Views

Points To Note

PDL internally stores matrices in column major format. This affects the indexing of piddle elements.

For example, take the following matrix $M:

    [
     [0 1 2]
     [3 4 5]
     [6 7 8]
    ]
[download]

In standard mathematical notation, the element at M_i,j will be i elements down and j elements across, with the elements 0 and 3 at M_1,1 and M_2,1 respectively.

With PDL indexing, indexes start at zero, and the first two dimensions are 'swapped'. Therefore, the elements 0 and 3 are at PDL indices (0,0) and (0,1) respectively.

Views are References

PDL attempts to do as little work as possible in that it will try to avoid memory copying of piddle values when it can. The most common operations where this is the case is when taking piddle slices or views across a piddle matrix. The piddles returned by these functions are views upon the original data, rather than copies, so modifications to them will affect the original matrix.

Slicing

A common operation is to view only a subset of a piddle. This is called slicing.

As slicing is such a common operation, there is a module to implement a shorter syntax for the slice method. This module is PDL::NiceSlice. This document only uses this syntax.

A rectangular slice of a piddle is returned via using the default method on a piddle. This takes up to n arguments, where n is the number of dimensions in the piddle.

Each argument must be one of the following forms:

The following examples operate on the matrix $M:

    [
     [0 1 2]
     [3 4 5]
     [6 7 8]
    ]
[download]

Dicing

Occasionally it is required to extract non-contiguous regions along a dimension. This is called dicing. The dice method accepts an array of indices for each dimension, which do not have to be contiguous.

The following examples operate on the matrix $M:

    [
     [0 1 2]
     [3 4 5]
     [6 7 8]
    ]
[download]

Which and Where Clauses

The other common operation to perform over a piddle is to apply a boolean operation over the entire piddle elementwise. This is achieved in PDL with the where method.

The where method accepts a single argument of a boolean operation. The element is referred to within this argument with the same variable name as the piddle. The values in the returned piddle are references to the values in the initial piddle.

In a similar mannor to which clauses outlined above, there is the where method. The difference between these two methods is that which returns the values, while where returns the indices.

This is best explained with examples over a matrix $M:

Note that there is also the which_both function. This function returns an array of two piddles. The first is a list of indices for which the boolean operation was true, the second for which the result was false.

Again, as where clauses as so common PDL::NiceSlice has syntatic support for it through the default method. This is acheived through an argument modifier, which is appended to the single argument.

The modifiers are seperated from the original argument via a ; character, and the following modifiers are supported:

Using this syntax, the following where commands are identical:

    $M->where($M > 3);
    $M->($M > 3;?);
[download]

View Modification

PDL contains many functions to modify the view of a piddle. These are outlined below:

Matrix Multiplication

PDL supports four main matrix multiplication methods between two piddles of compatible dimensions. These are:

As the x operator is overloaded to be the dot product, it can also be used to multiply vectors, matrices and scalars.

Arithmetic Operations

PDL supports a number of arithmetic operations, both elementwise, over an entire matrix and along the first dimension. Double precision variants are prefixed with d.

Comparison Operations:

PDL supports a number of different elementwise comparison functions between matrices of the same shape.

Binary Operations

PDL also allows binary operations to occur over piddles. PDL will convert any real number datatype piddles (float, double) to an integer before performing the operation.

Trigonometric Functions

These PDL functions operate in units of radians elementwise over a piddle.

Statistical Functions

PDL contains many methods to obtain statistics from piddles. Double precision variants are prefixed with d.

The 'various statistics' described above are returned as a Perl array of the following items:

• mean
• population RMS deviation from the mean
• median
• minimum
• maximum
• average absolute deviation
• RMS deviation from the mean

Zero Detection, Sorting, Unique Element Extraction

Rounding and Clipping of Values

PDL contains multiple methods to round and clip values. These all opererate elementwise over a piddle.

Set Operations

PDL contains methods to treat piddles as sets of values. Mathematically, a set cannot contain the same value twice, but if this happens to be the case with the piddles, PDL takes care of this for you.

Kernel Convolusion

PDL supports kernel convolution across multiple dimensions:

Miscellaneous Mathematical Methods

Here is all the other stuff which doesn't fit anywhere else:

I'm curious to know if Perl Monks believe that Perl is still worth learning as a primary programming language. I've used it in the past for some bioinformatics programming and really like the language. I'm interested in a change of career and wonder if it is worth the time investment really learning Perl in depth with the aim of becoming a Perl developer some time in the future. I know that there are a lot of 'trendier' programming languages out there like Python, PHP and Ruby. My logic behind learning Perl is that there are fewer people learning it compared to other languages. I assume that the market is awash with programmers using these other languages and that there might be a niche for perl programmer. Does anyone here work as a professional Perl programmer, either as an employee or a freelancer? Is there a future in Perl programming, or is a lot of the work migrating Perl to another platform? Are any start ups still using Perl frameworks like Catalyst?

I've been trying to slowly learn PDL over the last few months. While I'm aware of some available documentation (the PDL::* perldoc, The PDL Book, etc.) I've found the beginner documentation to be lacking. Therefore, I thought it would be a good idea to start 'porting' some numpy documentation to PDL for new users such as myself.

I've started with 100 numpy exercises, and this is the work in progress port to Perl/PDL.

As I'm still learning PDL, some solutions may be less than optimal, while others do not currently have solutions as they are outside my of level of competency. Therefore, I'm posting this WIP to PM to ask for comments and contributions.

As with most of Perl, there is more than one way to do it for most of these. I've decided to keep the $var->function() syntax as much as possible to easily be able to chain operations.

Thanks in advance!

100 PDL Exercises

1. Load the PDL library:

use PDL;

2. Print the PDL version:

use PDL::Version;
print $PDL::Version::VERSION;
[download]

3. Create a null vector of size 10:

my $z = zeros(10);
print $z;
[download]

4. How to find the memory size of any matrix?

use PDL::Core ':Internal'
my $z = zeros(10);
my $size = howbig($z->get_datatype) * $z->nelem;
print $size;
[download]

5. How to get the documentation of the numpy add function from the command line?

# To get top level PDL help
perldoc PDL
[download]

6. Create a null vector of size 10 and set the fifth value to 1:

my $z = zeros(10);
$z->slice(4) .= 1;
print $z;
[download]

or with PDL::NiceSlice loaded:

my $z = zeros(10);
$z(4) .= 1;
print $z;
[download]

Note: It will be assumed that PDL::NiceSlice will be loaded from now on.

7. Create a vector with values ranging from 10 to 49:

my $z = 10 + sequence(40);
print $z;
[download]

8. Reverse a vector (first element becomes last)

my $z = sequence(10);
$z = $z(-1:0);
print $z;
[download]

9. Create a 3x3 matrix with values from 0 to 8:

my $z = sequence(3,3);
print $z;
[download]

10. Find indices of non-zero elements in the vector [1,2,0,0,4,0]:

my $vec = pdl [1,2,0,0,4,0];
my $nz = $vec->which;
print $nz;
[download]

11. Create a 3x3 identity matrix:

my $z = identity(3);
print $z;
[download]

12. Create a 3x3x3 matrix of random values:

my $z = random(3,3,3);
print $z;
[download]

13. Create a 10x10 matrix of random values and find the minimum and maximum values:

my $z = random(10,10);
print $z->min, $z->max;
[download]

14. Create a random vector of size 30 and find the mean value:

my $z = random(30);
print $z->avg;
[download]

15. Create a 2D matrix with 1 on the border and 0 inside:

my $z = ones(10,10);
$z(1:8,1:8) .= 0;
print $z;
[download]

16. How to add a border (filled with 0's) around an existing matrix?

my $a = random(8,8);
my $x = zeros(2 + $a->dim(0), 2 + $a->dim(1));
$x(1:8,1:8) .= $a;
print $x;
[download]

17. What is the result of the following expression?

n/a

18. Create a 5x5 matrix with values 1,2,3,4 just below the diagonal:

my $z = identity(5) * (1 + sequence(5));
$z->where($z > 4) .= 0;
$z = $z->transpose->rotate(1)->transpose;
print $z;
[download]

19. Create a 8x8 matrix and fill it with a checkerboard pattern:

my $z = zeros(8,8);
$z("0::2","0::2") .= 1
$z("1::2","1::2") .= 1
print $z;
[download]

20. Consider a (6,7,8) shape matrix, what is the index (x,y,z) of the 100th element?

my $z = random(6,7,8);
my $hundreth = $z->clump($z->ndims)->(100);
# TODO: find index of $hundreth in $z
[download]

21. Create a checkerboard 8x8 matrix using the tile function:

n/a

22. Normalize a 5x5 random matrix:

my $z = random(5,5);
$z = (($z - $z->min) / ($z->max - $z->min));
print $z;
[download]

23. Create a custom dtype that describes a color as four unsigned bytes (RGBA):

n/a

24. Multiply a 5x3 matrix by a 3x2 matrix (real matrix product):

my $x = ones(3,5);
my $y = ones(2,3);
print $x x $y;
[download]

25. Given a 1D matrix, negate all elements which are between 3 and 8, in place.

my $z = sequence(10);
$z->where($z <= 8 & $z>= 3) *= -1;
print $z;
[download]

26. What is the output of the following script?

n/a

27. Consider an integer vector Z, which of these expressions are legal?

my $z = sequence(long, 10);
$z ** $z;
2 << $z >> 2;
$z <- $z;
1j * $z;
$z / 1 / 1;
$z < $z > $z;
[download]

28. What are the result of the following expressions?

print pdl(0) / pdl(0);
print pdl(0) // pdl(0);
print float int pdl(NaN);
[download]

29. How to round away from zero a float matrix?

$z = 20 * random(10) - 10;
$z->where($z < 0) .= - $z->where($z < 0)->abs->ceil;
$z->where($z > 0) .= $z->where($z > 0)->ceil;
print $z;
[download]

30. How to find common values between two matrix?

my $z1 = long 256 * random(10);
my $z2 = long 256 * random(10);
print intersect $z1, $z2;
[download]

31. How to ignore all numpy warnings (not recommended)?

n/a for PDL

32. Is the following expressions true?

n/a

33. How to get the dates of yesterday, today and tomorrow?

# No built in PDL time/date functions
my $yesterday = time() - (60 * 60 * 24);
my $today = time();
my $tomorrow = time() + (60 * 60 * 24);
[download]

34. How to get all the dates corresponding to the month of July 2016?

n/a

35. How to compute ((A+B)*(-A/2)) in place?

my $a = ones(3);
my $b = 2 * ones(3);
my $c = 3 * ones(3);
print ($a + $b) * (- $a/2)
[download]

36. Extract the integer part of a random matrix using 5 different methods:

my $z = 10 * random(10);
print $z->ceil;
print $z->floor;
print byte $z;
print long $z;
print longlong $z;
[download]

37. Create a 5x5 matrix with row values ranging from 0 to 4:

my $z = xvals zeros(5,5);
print $z;
[download]

38. Consider a generator function that generates 10 integers and use it to build an matrix:

n/a

39. Create a vector of size 10 with values ranging from 0 to 1, both excluded:

my $z = (sequence(12) / 11)->slice("1:10");
print $z;
[download]

40. Create a random vector of size 10 and sort it:

my $z = random(10)->qsort;
print $z;
[download]

41. How to sum a small matrix faster than np.sum?

n/a

42. Consider two random matrices A and B, check if they are equal:

my $a = random(10);
my $b = random(10);
print $a == $b;
[download]

43. Make an array immutable (read-only):

n/a

44. Consider a random 10x2 matrix representing cartesian coordinates, convert them to polar coordinates:

use PDL::Complex;
my $z = random(2,10);
my $p = Cr2p($z);
print $p;
[download]

45. Create random vector of size 10 and replace the maximum value by 0:

my $z = random(10);
$z->where($z == $z->max) .= 0;
print $z;
[download]

46. Create a structured array with x and y coordinates covering the [0,1]x[0,1] area.

n/a

47. Given two arrays, X and Y, construct the Cauchy matrix C (Cij =1/(xi - yj)):

TODO

48. Print the minimum and maximum representable value for each data type:

# This cannot be done directly, but you can extract the underlying
# C type used for each PDL type:

print byte->realctype;
print short->realctype;
print ushort->realctype;
print long->realctype;
print longlong->realctype;
print indx->realctype;
print float->realctype;
print double->realctype;
[download]

49. How to print all the values of an array?

# Set maximum print limit to one million elements
$PDL::toolongtoprint = 1_000_000;
$z = zeros(1000,1000);
print $z;
[download]

50. Find the nearest value from a given value in an array:

TODO

51. Create a structured array representing a position (x,y) and a color (r,g,b):

n/a

52. Consider a random vector with shape (100,2) representing coordinates, find point by point distances:

my $z = random(10,2);
my ($x,$y) = ($z(:,0), $z(:,1));
my $d = (($x - $x->transpose)->ipow(2)) +
        (($y - $y->transpose)->ipow(2));
print $d;
[download]

53. How to convert a float (32 bits) array into an integer (32 bits) in place?

my $z = float 1000 * random(10);
$z = long $z;
[download]

54. Consider the following file:

1,2,3,4,5
6,,,7,8
,,9,10,11
[download]

How to read it?

my $z = rcols "data.csv", { COLSEP => ',' }, [];
$z = $z->transpose;     # optional (PDL is column major)
print $z;
[download]

55. What is the equivalent of enumerate for numpy arrays?

n/a

56. Generate a generic 2D Gaussian-like array:

my $z = grandom(10,10);     # correct?
print $z;
[download]

57. How to randomly place p elements in a 2D array?

my $p = 3;
my $z = zeros(10,10);
my $i = indx $z->nelem * random($p)
$z->clump($z->ndims)->($i) .= 1;
print $z;
[download]

58. Subtract the mean of each row of a matrix:

my $z = random(5, 10);
$z = $z - $z->avgover->transpose;
print $z;
[download]

59. How to I sort an array by the nth column?

TODO

60. How to tell if a given 2D array has null columns?

TODO

61. Find the nearest value from a given value in an array:

TODO

62. Considering two arrays with shape (1,3) and (3,1), how to compute their sum using an iterator?

n/a

63. Create an array class that has a name attribute:

n/a

64. Consider a given vector, how to add 1 to each element indexed by a second vector (be careful with repeated indices)?

TODO

65. How to accumulate elements of a vector (X) to an array (F) based on an index list (I)?

TODO

66. Considering a (w,h,3) image of (dtype=ubyte), compute the number of unique colors:

my ($w, $h) = (16, 16);
my $i = byte 256 * random($w, $h, 3);
my $uniqcol = $i->uniq->nelem;
print $uniqcol;
[download]

67. Considering a four dimensions array, how to get sum over the last two axis at once?

TODO

68. Considering a one-dimensional vector D, how to compute means of subsets of D using a vector S of same size describing subset indices?

TODO

69. How to get the diagonal of a dot product?

my $z1 = random(10, 10);
my $z2 = random(10, 10);
print $z1->inner($z2);
[download]

70. Consider the vector [1, 2, 3, 4, 5], how to build a new vector with 3 consecutive zeros interleaved between each value ?

my $z = pdl [1,2,3,4,5];
my $nz = 3;
my $x = zeros($z->dim(0) * $nz);
$x("0::$nz") .= $z;
print $x;
[download]

71. Consider an array of dimension (5,5,3), how to multiply it by an array with dimensions (5,5)?

my $z1 = ones(5,5,3);
my $z2 = 2 * ones(5,5);
print $z1 * $z2;
[download]

72. How to swap two rows of an array?

my $z = sequence(5,5);
$z(0:1,) .= $z(1:0,)->sever;
print $z;
[download]

73. Consider a set of 10 triplets describing 10 triangles (with shared vertices), find the set of unique line segments composing all the triangles:

TODO

74. Given an array C that is a bincount, how to produce an array A such that np.bincount(A) == C?

TODO

75. How to compute averages using a sliding window over an array?

TODO

76. Consider a one-dimensional array Z, build a two-dimensional array whose first row is (Z[0],Z[1],Z[2]) and each subsequent row is shifted by 1 (last row should be (Z[-3],Z[-2],Z[-1])

TODO

77. How to negate a boolean, or to change the sign of a float inplace?

my $z = long 2 * random(10);
$z = not $z;
print $z;
$z = -5 + sequence(10);
$z = -1 * $z;
print $z;
[download]

78. Consider 2 sets of points P0,P1 describing lines (2d) and a point p, how to compute distance from p to each line i (P0[i],P1[i])?

TODO

79. Consider 2 sets of points P0,P1 describing lines (2d) and a set of points P, how to compute distance from each point j (P[j]) to each line i (P0[i],P1[i])?

TODO

80. Consider an arbitrary array, write a function that extract a subpart with a fixed shape and centered on a given element (pad with a fill value when necessary):

TODO

81. Consider an array Z = [1,2,3,4,5,6,7,8,9,10,11,12,13,14], how to generate an array R = [[1,2,3,4], [2,3,4,5], [3,4,5,6], ..., [11,12,13,14]]:

$z = 10 * random(15);
$len = 4;
my @r = ();
push @r,  $z($_:$_ + $len-1) for (0 .. $z->nelem - $len)
$r = pdl @r;
print $r;
[download]

82. Compute a matrix rank:

my $z = 10 * random(10,10);
my ($u, $s, $v) = $z->svd;
my $rank = $s->where($s > 1e-10);
print $rank;
[download]

83. How to find the most frequent value in an array?

TODO

84. Extract all the contiguous 3x3 blocks from a random 10x10 matrix:

my $z = long 5 * random(10,10);
my $dim = 3;
my (@out, $out);
for my $i ( 0 .. $z->dim(0) - $dim - 1) {
    for my $j ( 0 .. $z->dim(1) - $dim - 1) {
        push @out, $z($i:$i+$dim,$j:$j+$dim);
    }
}
$out = pdl @out;
print $out;
[download]

85. Create a 2D array subclass such that Z[i,j] == Z[j,i]:

TODO

86. Consider a set of p matrices wich shape (n,n) and a set of p vectors with shape (n,1). How to compute the sum of of the p matrix products at once? (result has shape (n,1))

TODO

87. Consider a 16x16 array, how to get the block-sum (block size is 4x4)?

TODO

88. How to implement the Game of Life using PDL arrays?

TODO

89. How to get the n largest values of an array:

my $z = 10 * random(20);
my $n = 3;
print $z->qsort->(-$n:);
[download]

90. Given an arbitrary number of vectors, build the cartesian product (every combinations of every item)

TODO

91. How to create a record array from a regular array?

n/a?

92. Consider a large vector Z, compute Z to the power of 3 using 3 different methods:

my $z = random(5e7);
$z ** 3;
$z->ipow(3);
$z->power(3,0);
[download]

93. Consider two arrays A and B of shape (8,3) and (2,2). How to find rows of A that contain elements of each row of B regardless of the order of the elements in B?

TODO

94. Considering a 10x3 matrix, extract rows with unequal values (e.g. [2,2,3]):

TODO

95. Convert a vector of ints into a matrix binary representation:

my $z = pdl [0,1,2,3,15,16,32,64,128];
my $bits = ($z->transpose & (2 ** xvals(9)));
$bits->where($bits > 0) .= 1;
print $bits;
[download]

96. Given a two dimensional array, how to extract unique rows?

my $z = long 2 * random(3,6);
print $z->uniqvec;
[download]

97. Considering 2 vectors A & B, write the einsum equivalent of inner, outer, sum, and mul function:

TODO

98. Considering a path described by two vectors (X,Y), how to sample it using equidistant samples:

TODO

99. Given an integer n and a 2D array X, select from X the rows which can be interpreted as draws from a multinomial distribution with n degrees, i.e., the rows which only contain integers and which sum to n:

TODO

100. Compute bootstrapped 95% confidence intervals for the mean of a 1D array X (i.e., resample the elements of an array with replacement N times, compute the mean of each sample, and then compute percentiles over the means):

TODO

edit: link to PDL for those who do not know what it is

First of all, forgive me if this isn't quite the right place. I am a new user and am not entirely sure about the rubric for this area of the site, though I'm pretty sure this is the right place.

About a decade ago, when I was in my late teens and early twenties, I was very proficient in and eager to use Perl. Though it was a little idiosyncratic, it was certainly much less tedious to get things done in than C, which I had used earlier. Gradually I drifted away towards Python and now I use it for most things. I've since forgotten virtually everything I knew about Perl. I know that Python will still be obviously superior for, for example, most aspects of scientific computing (possibly excepting bioinformatics?) and machine learning, but where does Perl really shine these days? That goes equally for the more conventional Perl 5 as well as the newer Perl 6. Also, what are hot items on CPAN these days?

Recently, I was in need to compare two versions of the same perl module containing many subs. I was interested to see the difference between the contents of subs with the same name. This happened because I forked the same code in two different machines and made changes in the modules in both machines.

For this purpose I wrote the following basic script which I place here for public use but also for comments from the monastic community.

The simple script makes use of two excellent modules, namely PPI and Text::WordDiff. PPI parses perl code and is capable of extracting subs and their contents. Text::WordDiff outlines (and color-codes) the differences between two blocks of text (the contents of identically-named subs in two files).

Unix's diff is a fine tool in general, but code has a few idiosyngracies which make diffing sometimes impractical. For example when same-content subs have different order in their respective files.

That said, I wanted a quick tool to check my two versions of the perl module, find enhancements in either file I made and produce a final version.

Here is the script:

#!/usr/bin/env perl

use strict;
use warnings;

use PPI;
use Text::WordDiff;

if( scalar(@ARGV) != 2 ){ print usage($0) . "\n"; exit(0); }

my ($infile1, $infile2) = @ARGV;

my $doc = PPI::Document->new($infile1);
if( ! defined($doc) ){ print STDERR "$0 : call to ".'PPI::Document->ne
+w()'." has failed for input file '$infile2'.\n"; exit(1); }
my (%subs1, %subs2, $asub);
for $asub ( @{ $doc->find('PPI::Statement::Sub') || [] } ) {
    # loop over all subs in file
    unless ( $asub->forward ) {
        # store sub's contents in hash keyed on sub's name
        $subs1{ $asub->name } = $asub->content;
    }
}

$doc = PPI::Document->new($infile2);
if( ! defined($doc) ){ print STDERR "$0 : call to ".'PPI::Document->ne
+w()'." has failed for input file '$infile2'.\n"; exit(1); }
for $asub ( @{ $doc->find('PPI::Statement::Sub') || [] } ) {
    # loop over all subs in file
    unless ( $asub->forward ) {
        # store sub's contents in hash keyed on sub's name
        $subs2{ $asub->name } = $asub->content;
    }
}
my ($k, $v1, $v2, $res, $anitem);
my @dont_exist = ();
my %allkeys = map { $_ => 1 } (keys %subs1, keys %subs2);
foreach $k (sort keys %allkeys){
    if( ! defined($v1=$subs1{$k}) ){
        push(@dont_exist, "$k : Does not exist in '$infile1'\n");
        next
    } elsif( ! defined($v2=$subs2{$k}) ){
        push(@dont_exist, "$k : Does not exist in '$infile2'\n");
        next
    }

    # sub (same name) exists in both files, diff sub's contents in fil
+es:
    $res = Text::WordDiff::word_diff(
        \$v1,
        \$v2,
    );
    # print diff results
    print
      "----- begin '$k' -----\n"
    . $res
    . "\n----- end '$k' ------\n"
    ;
}
# and also print the subs which exist in one file but not the other fi
+le
print join("", @dont_exist);

exit(0);

sub    usage {
    return "Usage : ".$_[0]." file1 file2\nColor output guide:\n\tRED 
+: file1\n\tGREEN: file2\n"
}
[download]

bliako

I don't know how well known this is (it's probably quite old new for you) but recently I had the problem of wanting to run a Perl-script on a non-rooted Android-tablet and came across the fabulous Termux-project.

Installing this app gives you a terminal-environment and with a simple

pkg install perl

you get a working 5.26.1 perl. Now add

pkg install make
pgk install clang
[download]

and voila you have a fully functional cpan-client that allows you to install even xs-modules.

Really nice...

In order to deal with Japanese orders, I recently had to convert my whole system to UTF-8. A day or 2's job I thought. 2.5 weeks later, I'm finally there. There is a lot of stuff on Perlmonks and the internet in general about this but it is hard to understand and even harder to implement. Most of the advice I read was along the lines of RTFM or did not give the whole story. It's pretty clear this is a common problem, too. I wanted to give something back to the community as perlmonks has helped me a lot, so I thought I would share some insights that I hope will be practical and useful.

There is a lot out there telling you to used decode/encode and giving lectures on internal representation of UTF8 in Perl and wotnot. In the end I've only had to use decode in one place where data is coming in from elsewhere. If you get all the other stuff right, I believe you shouldn't need any or many instances of decode/encode.

Our system involves a local website using MySQL, a live website, static webpages, generated webpages, various text files and CGI website forms. All of this needs work to make it work. Here are the things that I needed to do:

Checklist of changes to make

* Firstly, every script file is converted to UTF-8 format. Easy.

* Every script to have this at the top: use utf8; This tells perl that the script itself is in UTF format. So a £ in the script will be interpreted as a UTF-8 £. It's no good just putting this in the calling script as it only seems to extend for the scope of the script underneath; not any other scripts that are imported with require...

* Ideally each database table must be turned to UTF-8 format. This turns out to be difficult and time-consuming because any tables with foreign keys won't convert unless you first delete the foreign keys. For those that won't easily convert, you can convert only the fields that might hold UTF-8 encoded characters to UTF-8 format. Also BLOB fields are a problem unless the whole table is UTF-8. I had to convert problem BLOB fields to TEXT fields and then convert them to UTF-8 format (a 2 step process, doing both in 1 step fails).

* Rose::DB (or whatever database method you are using) needs to be told that incoming data from the Database is in UTF-8. For Rose:DB, add this to the connector in DB.pm and then regenerate connect_options => {mysql_enable_utf8 => 1}

* binmode(STDOUT, ":utf8"); # Put this at the top of a script - tells it to output UTF to stdout. Not sure if this is just needed only once in the opening script or in any requires, too?

* Webpages must have this in the head section: <meta http-equiv="content-type" content="text/html; charset=UTF-8">

* use CGI qw(-utf8); to treat incoming CGI parameters as UTF-8. Getting this working was subtle - test carefully.

* When outputting a CGI webpage, the first thing to do is to output the http header and this needs to be told about UTF8 too: Personally I found that print header(-type=>'text/html', -cookie=>'', -charset=>'utf-8'); gave problems with cookies so ended up outputting it direct: print "Content-type: text/html; charset=utf-8\n$cookie\n\n";

* use open ':encoding(utf8)'; # tells it to deal with all files in a UTF8 way. In fact, I was more careful with this and did not use it in general. Instead, I have specifically opened each file that needed it with open($fh, '<:encoding(UTF-8)', $filename);. Because some files that I have to deal with have not been given to me in UTF-8 format. Careful - this can fail if the $filename variable is not also in UTF8!

Identifying Errors

In doing this, you will make mistakes and see weird characters appearing in unexpected places. I developed my own personal understanding of how to deal with them. These are my own notes for practical situations so please bear with me, if the explanations are not exactly correct - it was about fixing stuff not being a perl rocket scientist.

• You see £ displayed as '£'
• If £ sign is coming from dbase and is stored correctly in dbase and webpage is correctly displaying UTF-8 characters from elsewhere (e.g. write japanese text into the perl script and print it), then the UTF-8 is not being retrieved from the database as UTF-8 (presumably being assumed to be Latin1).
• The £ is within a UTF-8 encoded PERL script but use utf8; is not set at the top of the script.
• The £ is displayed correctly in a form initially but when the form is saved/updated, the £ then displays as '£'. Use the -utf8 CGI pragma to treat incoming parameters as UTF-8: use CGI ('-utf8');

• £ is displayed on a webpage as �
• This happens when the http header Content Type is not UTF8 and the meta tag is similarly <meta http-equiv="Content-Type" content="text/html" />

• £ or other characters are being displayed as a diamond with ? inside it
• StackOverflow:...usually the sign of an invalid (non-UTF-8) character showing up in an output (like a page) that has been declared to be UTF-8. Can be fixed by putting the following at the top of script: binmode(STDOUT, ":utf8");

• Error message: Wide character in print
• Means a print statement (to STDOUT or a file) that is outputting Latin1 includes a UTF-8 character... To fix, add '>:encoding (UTF-8) to the open statement or #binmode(STDOUT, ":utf8");

Using placeholders are a must in SQL!

#prepare
my $sth = $dbh->prepare('SELECT * FROM people WHERE lastname = ? AND f
+irstname = ?');

#execute with list of bindvars
$sth->execute( $lastname, $firstname );
[download]

But it's a bit cumbersome to adjust the bind values if the order changes.

It's even more work if you have to use an array of values like inside an IN ( ?, ?, ?) operation.

I started to hack something to auto-generate placeholders, for a string passed inside a code-block:

• $scalars from the closure are replaced with a placeholder ?
• @arrays are replaced with a list of comma separated placeholders ?,?,?
• underscored _var_names are ignored ( placeholders can't be everywhere)

Parsing the output of B::Deparse is even more fragile than I thought, the next version will walk the OP-Tree directly. (For instance parsing multiline SQL doesn't work yet.)

I'm not yet sure how to combine this in the best way with DBI.

This is a one days job in the sense of "release often".

Comments?

update

Hmmm ... I can probably avoid the hassle of parsing the OP-tree by tying the variables ...

use strict;
use warnings;

use B::Deparse;
use PadWalker qw/closed_over peek_sub set_closed_over/;
use Data::Dump qw/pp/;

# ========= Tests

use Test::More;

# lexicals for placeholders
my $a = 'A';
my @list = qw/L I S T/;
my $x = 'X';

# no placeholders for underscore vars
my @_table = "any_table";

my $sql = sub { "SELECT * FROM @_table WHERE a = $a AND b IN (@list) A
+ND c = $x" };

my @stm = holderplace($sql);

is_deeply( \@stm,
           [
             "SELECT * FROM any_table WHERE a = ? AND b IN (?, ?, ?, ?
+) AND c = ?",
            [\"A", ["L", "I", "S", "T"], \"X"]
           ],
           "statement with placeholders plus bind variables"
         );


# change bind variables
$a = 'AA';
@list = qw/LL II SS TT/;
$x = 'XX';

is_deeply( \@stm,
           [
             "SELECT * FROM any_table WHERE a = ? AND b IN (?, ?, ?, ?
+) AND c = ?",
            [\"AA", ["LL", "II", "SS", "TT"], \"XX"]
           ],
           "statement with placeholders plus changed variables"
         );



done_testing();


# ========== Code

sub holderplace {
   my ($lambda)=@_;

   my $h_vars = closed_over($lambda);

   my %new_vars;
   my @value_refs;


   for my $key ( keys %$h_vars) {

      my $sigil = substr $key,0,1;

      # exclude variables starting with _
      next if $key =~ m/^\Q${sigil}\E_/;


      if ( '$' eq $sigil ) {
         $new_vars{$key} = \'?';
      } elsif ( '@' eq $sigil ) {
         $new_vars{$key} = [ join ", ", ("?") x @{$h_vars->{$key} } ];
      } else {
         next;                          # Error?
      }
   }


   # Create Statement with placeholders
   set_closed_over( $lambda, \%new_vars );
   my $newstr = $lambda->();

   # Variable refs in order of placeholders
   my @var_refs =
     map { $h_vars->{$_} }
       grep { $new_vars{$_} }
         @{ get_vars($lambda) };

   return ("$newstr", \@var_refs );
}




sub get_vars {
   # scans output of B::Deparse to get interpolated vars in order
   my ($lambda)=@_;

   # deparse sub body
   my $source = B::Deparse->new('-q')->coderef2text($lambda);
   # returns something like:
   # {
   #  use warnings;
   #  use strict;
   #  'SELECT * FROM ' . join($", @_table) . ' WHERE x = ' . $a . ' AN
+D b IN (' . join($", @list) . ') ' . $x;
   # }

   # truncate {block} and use statements
   $source =~ s/^{\s*(use.*?;\s*)*//s;
   $source =~ s/;\s*}$//s;
   #warn $source;

   my %quotes = qw"[ ] ( ) < > { } / /";
   $quotes{'#'}='#';

   # single quotes like q(...)
   my $re_q = join "|", map { "q\\$_.*?\\$quotes{$_}" } keys %quotes;

   #warn pp
     my @parts = split /\s* (?: '(?:\\'|[^'])*?' | $re_q )\s*/msx, $so
+urce;

   for my $part (@parts) {
      next unless $part =~ /^\..*\.?$/;

      if ( $part =~ /^\. join\(.*? (\@\w+)\)( \.)?$/) {
         $part = $1;                    # array
      }
      elsif ( $part =~ /^\. (\$\w+)( \.)?$/) {
         $part = $1;                    # scalar
      }
   }

   return \@parts;
}
[download]

I post this under meditation because this is not really a question by me, even if some question mark is in the text.

Art needs restauration and restauration needs keen eyes and gentle hands. We have here at the monastery precious and invaluable masterpieces ruining as the time passes.

The most incredible things I ever seen in Perl is 3-D Stereogram, Self replicating source. by the genial monk Toodles but unfortunately it just run on perl 5.8 (or as someone said in 5.10).

Is some monk able to spot why this happens?

Is someone able to make this masterpiece run as expected on modern perl versions? Infact it doesnt fail on 5.26 but doesnt produce the stereogram effect: only sparse lines.

L*

Thank you to all who helped me get this started. Even though my name is on it that just means that I borrowed most of it from others. You will see your suggested way of doing things throughout this post.

I will describe how I created the postgresql database. Any and all comments are welcome.

I did not use these tables but I am strongly considering them.

CREATE TABLE seven_stud_spread_stakes(bring_in int, fourth_street int 
+check(fourth_street >= bring_in), fifth_street int check(fifth_street
+ >= bring_in), sixth_street int check(sixth_street >= bring_in), seve
+nth_street int check(seventh_street >= bring_in));

CREATE TABLE colorado_limit_stakes(small_blind int, big_blind int chec
+k(big_blind >= small_blind), preflop int check(preflop <= 100), flop 
+int check(flop <= 100), turn int check(turn <= 100), river int check(
+river >= big_blind));

CREATE TABLE spread_limit_stakes(small_blind int, big_blind int check(
+big_blind >= small_blind), preflop int check(preflop >= small_blind),
+ flop int check(flop >= small_blind), turn int check(turn >= small_bl
+ind), river int check(river >= small_blind));

CREATE TABLE seven_stud_stakes(bring_in int, fourth_street int check(f
+ourth_street >= bring_in), fifth_street int check(fifth_street >= fou
+rth_street), sixth_street int check(sixth_street >= fifth_street), se
+venth_street int check(seventh_street >= sixth_street));

CREATE TABLE stakes(small_blind int, big_blind int check(big_blind >= 
+small_blind), preflop int check(preflop >= big_blind), flop int check
+(flop >= preflop), turn int check(turn >= flop), river int check(rive
+r >= turn));
INSERT INTO stakes VALUES(1, 3, 3, 3, 6, 9);
[download]

I am using the following tables. Note that I am using v_limits since limit is a reserved word in postgresql.

CREATE TABLE v_limits(v_limit TEXT PRIMARY KEY);
CREATE TABLE states(abbreviation TEXT PRIMARY KEY, state TEXT);
CREATE TABLE cities(city TEXT PRIMARY KEY);
CREATE TABLE games(game TEXT PRIMARY KEY);
CREATE TABLE hi_lows(hi_lo TEXT PRIMARY KEY);
CREATE TABLE kills(kill TEXT PRIMAY KEY);
CREATE TABLE stakes(stake TEXT PRIMARY KEY);
CREATE TABLE venues(venue TEXT PRIMAY KEY);

CREATE TABLE visits(id INT PRIMARY KEY, arrival_date DATE, departure_d
+ate DATE, arrival_time TIME, departure_time TIME, venue TEXT REFERENC
+ES venues(venue), city TEXT REFERENCES cities(city), state TEXT REFER
+ENCES states(abbreviation), game TEXT REFERENCES games(game), stake T
+EXT REFERENCES stakes(stake), kill TEXT REFERENCES kills(kill), hi_lo
+ TEXT REFERENCES hi_lows(hi_lo), v_limit REFERENCES v_limits(v_limit)
+, buy_in MONEY, cash_out MONEY);
[download]

This is the visit_configuration.yaml file I am using.

arrival_date:   20180214
departure_date: 20180215
arrival_time:   1000
departure_time: 1800
venue:          "Binion's"
city:           "Las Vegas"
state:          "NV"
game:           "hold'em"
stake:          "4-8"
kill:           "no-kill"
hi_lo:          "hi"
limit:          "fixed"
buy_in:         200
cash_out:       400
[download]

Next I will post the perl file I am using.

› ver
Microsoft Windows [Version 10.0.16299.125]

› chcp 65001
Aktive Codepage: 65001.

› type αω.bat
@echo hiαω

› node -p "require('child_process').execSync('αω.bat').toString()"
hiαω


› perl6 -e "run 'αω.bat'"
hiαω

› php -r "system('αω.bat');"
hiαω

› python -c "import subprocess; subprocess.call('αω.bat')"
hiαω

› ruby -e "system 'αω.bat'"
hiαω

› perl -Mutf8 -e "system 'αω.bat'"
Der Befehl "a?.bat" ist entweder falsch geschrieben oder
konnte nicht gefunden werden.

› perl -Mutf8 -MWin32::Unicode::Process=systemW -e "systemW('αω.bat')"
Der Befehl "a?.bat" ist entweder falsch geschrieben oder
konnte nicht gefunden werden.

Now tell me why this is a stupid idea, but keep in mind that

• if all the other languages can hack it, then so can we, no matter how shitty and insufficient you think the initial patch is
• the better is the enemy of the good and a "better" solution did not turn up for decades
• if I simply file a perlbug it just gets marked by p5p as a duplicate of a discussion whose proposed "better" solution did not turn up for decades

Periodically, I'll go through my posts via the normal mechanism and sort by lowest-highest-this-that-other, and sometimes, like today, I have found one that I'd like to reply to.

Now, this post has a (relatively) high XP count, and the responses have 15-25% higher than that.

I want to reply to a poster on such thread legitimately (orig post count was ~45, replies were 60+), but I don't want it realized that I'm doing it in order to get exposure on the overall hierarchical post.

How do Monks handle these situations? Shatter humility or what?

-stevieb

ps. I have been accused of raising posts for XP+ before, but those who raised that are irrelevant to me.

In the string 123456789, you can prepend + or - before any digit to form an expression. You should

• list all the possible expressions that evaluate to 100
• show the number that is a result of the maximal number of expressions
• show the lowest positive number that can't be expressed
• show the ten highest numbers that can be expressed

Here's my solution:

I tried to avoid eval to evaluate the expressions, at the same time, I didn't want to implement the traditional full math expression parser as there were only two operations of the same precedence in use.

$sum += $_ for $expression =~ /([-+]?[0-9]+)/g;
[download]

Feel free to comment on perlishness, effectiveness, golfness, or beauty of the solution, or propose your own.

Note: Those interested in Perl 6 can read the solution just below mine.

($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,
[download]