Matlab structure to MySql database - mysql

I have a structure in Matlab. The structure contain 2.1 million rows with a mixture of Double, Integers and Char. The structure is called TaqQ;
TaqQ.time 2100000x1 uint32,
TaqQ.bid 2100000x1 double,
TaqQ.ex 2100000x4 char,
How can i in a fast, way transfere that structure to MySql?
Maybe by save the structure to an csv file and then import it to mysql. I tried that:
csvwrite('test.csv',[TaqQ.time TaqQ.bid TaqQ.ex]) %this is very slow
csvwrite('test.csv',[TaqQ.time' ; TaqQ.bid'; TaqQ.ex']) % fast but don't know how to deal with it in MySql!?
I also tried using fastinsert, but i was way to slow.
I also tried:
connHandle = conn.Handle;
stmt = connHandle.createStatement;
for i= 1:2100000
stmt.addBatch('INSERT INTO Quotes (time,bid,ex) VALUES (TaqQ.time(i),
TaqQ.bid(i), TaqQ.ex(i))')
end
stmt.executeBatch;
stmt.close;
`
But i was also way to slow
can somebody help me??

This will take a lot of RAM, but it will do things in memory, minimize the number of function calls, and will write everything at once, so it should be fast:
% Test struct
TaqQ = struct( ...
'time', [1;2;3;4;5], ...
'bid', [110.1;120.1;130.1;140.1;150.1], ...
'ex', ['ABCD';'EFGH';'IJKL';'MNOP';'QRST'] ...
);
% Writing the file
NL = 10; % ASCII new line
DQ = double('"'); % ASCII double quote
f = fopen('test.csv', 'wb');
fwrite(f, [ ...
reshape(sprintf('% 10u,', TaqQ.time), 11, []); ... % 10 digits
reshape(sprintf('% 10.3f,', TaqQ.bid), 11, []); ... % 10 digits + point + sign
char(DQ*(ones(1,size(TaqQ.ex,1)))); ... % open quotes
TaqQ.ex.'; ... % already char
char(DQ*(ones(1,size(TaqQ.ex,1)))); ... % end quotes
char(NL*(ones(1,size(TaqQ.ex,1)))) ... % newlines
]);
fclose(f);
Actually I'm curious if it's fast, I could not test on huge data. Please let me know.
If you want to squeeze out all the spaces, then this is a (slower) variant:
% Preparing content
NL = 10; % ASCII new line
DQ = double('"'); % ASCII double quote
bytes = [ ...
reshape(sprintf('% 10u,', TaqQ.time), 11, []); ... % 10 digits
reshape(sprintf('% 10.3f,', TaqQ.bid), 11, []); ... % 10 digits + point + sign
char(DQ*(ones(1,size(TaqQ.ex,1)))); ... % open quotes
TaqQ.ex.'; ... % already char
char(DQ*(ones(1,size(TaqQ.ex,1)))); ... % end quotes
char(NL*(ones(1,size(TaqQ.ex,1)))) ... % newlines
];
% Writing content without spaces
f = fopen('test.csv', 'wb');
fwrite(f,bytes(bytes~=' '));
fclose(f);

Related

Why octave error with function huffmandeco about large index types?

I've got a little MatLab script, which I try to understand. It doesn't do very much. It only reads a text from a file and encode and decode it with the Huffman-functions.
But it throws an error while decoding:
"error: out of memory or dimension too large for Octave's index type
error: called from huffmandeco>dict2tree at line 95 column 19"
I don't know why, because I debugged it and don't see a large index type.
I added the part which calculates p from the input text.
%text is a random input text file in ASCII
%calculate the relative frequency of every Symbol
for i=0:127
nlet=length(find(text==i));
p(i+1)=nlet/length(text);
end
symb = 0:127;
dict = huffmandict(symb,p); % Create dictionary
compdata = huffmanenco(fdata,dict); % Encode the data
dsig = huffmandeco(compdata,dict); % Decode the Huffman code
I can oly use octave instead of MatLab. I don't know, if there is an unexpected error. I use the Octave Version 6.2.0 on Win10. I tried the version for large data, it didn't change anything.
Maybe anyone knows the error in this context?
EDIT:
I debugged the code again. In the function huffmandeco I found the following function:
function tree = dict2tree (dict)
L = length (dict);
lengths = zeros (1, L);
## the depth of the tree is limited by the maximum word length.
for i = 1:L
lengths(i) = length (dict{i});
endfor
m = max (lengths);
tree = zeros (1, 2^(m+1)-1)-1;
for i = 1:L
pointer = 1;
word = dict{i};
for bit = word
pointer = 2 * pointer + bit;
endfor
tree(pointer) = i;
endfor
endfunction
The maximum length m in this case is 82. So the function calculates:
tree = zeros (1, 2^(82+1)-1)-1.
So it's obvious why the error called a too large index type.
But there must be a solution or another error, because the code is tested before.
I haven't weeded through the code enough to know why yet, but huffmandict is not ignoring zero-probability symbols the way it claims to. Nor have I been able to find a bug report on Savannah, but again I haven't searched thoroughly.
A workaround is to limit the symbol list and their probabilities to only the symbols that actually occur. Using containers.Map would be ideal, but in Octave you can do that with a couple of the outputs from unique:
% Create a symbol table of the unique characters in the input string
% and the indices into the table for each character in the string.
[symbols, ~, inds] = unique(textstr);
inds = inds.'; % just make it easier to read
For the string
textstr = 'Random String Input.';
the result is:
>> symbols
symbols = .IRSadgimnoprtu
>> inds
inds =
Columns 1 through 19:
4 6 11 7 12 10 1 5 15 14 9 11 8 1 3 11 13 16 15
Column 20:
2
So the first symbol in the input string is symbols(4), the second is symbols(6), and so on.
From there, you just use symbols and inds to create the dictionary and encode/decode the signal. Here's a quick demo script:
textstr = 'Random String Input.';
fprintf("Starting string: %s\n", textstr);
% Create a symbol table of the unique characters in the input string
% and the indices into the table for each character in the string.
[symbols, ~, inds] = unique(textstr);
inds = inds.'; % just make it easier to read
% Calculate the frequency of each symbol in table
% max(inds) == numel(symbols)
p = histc(inds, 1:max(inds))/numel(inds);
dict = huffmandict(symbols, p);
compdata = huffmanenco(inds, dict);
dsig = huffmandeco(compdata, dict);
fprintf("Decoded string: %s\n", symbols(dsig));
And the output:
Starting string: Random String Input.
Decoded string: Random String Input.
To encode strings other than the original input string, you would have to map the characters to symbol indices (ensuring that all symbols in the string are actually present in the symbol table, obviously):
>> [~, s_idx] = ismember('trogdor', symbols)
s_idx =
15 14 12 8 7 12 14
>> compdata = huffmanenco(s_idx, dict);
>> dsig = huffmandeco(compdata, dict);
>> fprintf("Decoded string: %s\n", symbols(dsig));
Decoded string: trogdor

How does the 'k' modifier in FINDC() work in SAS?

I'm reading through the book, "SAS Functions by Example - Second Edition" and having trouble trying to understand a certain function due to the example and output they get.
Function: FINDC
Purpose: To locate a character that appears or does not appear within a string. With optional arguments, you can define the starting point for the search, set the direction of the search, ignore case or trailing blanks, or look for characters except the ones listed.
Syntax: FINDC(character-value, find-characters <,'modifiers'> <,start>)
Two of the modifiers are i and k:
i ignore case
k count only characters that are not in the list of find-characters
So now one of the examples has this:
Note: STRING1 = "Apples and Books"
FINDC(STRING1,"aple",'ki')
For the Output, they said it returns 1 because the position of "A" in Apple. However this is what confuses me, because I thought the k modifier says to find characters that are not in the find-characters list. So why is it searching for a when the letter "A", case-ignored, is in the find-characters list. To me, I feel like this example should output 6 for the "s" in Apples.
Is anyone able to help explain the k modifier to me any better, and why the output for this answer is 1 instead of 6?
Edit 1
Reading the SAS documentation online, I found this example which seems to contradict the book I'm reading:
Example 3: Searching for Characters and Using the K Modifier
This example searches a character string and returns the characters that do
not appear in the character list.
data _null_;
string = 'Hi, ho!';
charlist = 'hi';
j = 0;
do until (j = 0);
j = findc(string, charlist, "k", j+1);
if j = 0 then put +3 "That's all";
else do;
c = substr(string, j, 1);
put +3 j= c=;
end;
end;
run;
SAS writes the following output to the log:
j=1 c=H
j=3 c=,
j=4 c=
j=6 c=o
j=7 c=!
That's all
So, is the book wrong?
The book is wrong.
511 data _null_;
512 STRING1 = "Apples and Books" ;
513 x=FINDC(STRING1,"aple",'ki');
514 put x=;
515 if x then do;
516 ch=char(string1,x);
517 put ch=;
518 end;
519 run;
x=6
ch=s

Summing binary numbers representing fractions in Sagemath

I'm just starting to learn how to code in Sagemath, I know it's similar to python but I don't have much experience with that either.
I'm trying to add two binary numbers representing fractions. That is, something like
a = '110'
b = '011'
bin(int(a,2) + int(b,2))
But using values representing fractions, such as '1.1'.
Thanks in advance!
If you want to do this in vanilla Python, parsing the binary fractions by hand isn't too bad (the first part being from this answer);
def binstr_to_float(s):
t = s.split('.')
return int(t[0], 2) + int(t[1], 2) / 2.**len(t[1])
def float_to_binstr(f):
i = 0
while int(f) != f:
f *= 2
i += 1
as_str = str(bin(int(f)))
if i == 0:
return as_str[2:]
return as_str[2:-i] + '.' + as_str[-i:]
float_to_binstr(parse_bin('11.1') + parse_bin('0.111')) # is '100.011'
In python you can use the Binary fractions package. With this package you can convert binary-fraction strings into floats and vice-versa. Then, you can perform operations on them.
Example:
>>> from binary_fractions import Binary
>>> sum = Binary("1.1") + Binary("10.01")
>>> str(sum)
'0b11.11'
>>> float(sum)
3.75
>>>
It has many more helper functions to manipulate binary strings such as: shift, add, fill, to_exponential, invert...
PS: Shameless plug, I'm the author of this package.

counting non-empty lines and sum of lengths of those lines in python

Am trying to create a function that takes a filename and it returns a 2-tuple with the number of the non-empty lines in that program, and the sum of the lengths of all those lines. Here is my current program:
def code_metric(file):
with open(file, 'r') as f:
lines = len(list(filter(lambda x: x.strip(), f)))
num_chars = sum(map(lambda l: len(re.sub('\s', '', l)), f))
return(lines, num_chars)
The result I get is get if I do:
if __name__=="__main__":
print(code_metric('cmtest.py'))
is
(3, 0)
when it should be:
(3,85)
Also is there a better way of finding the sum of the length of lines using using the functionals map, filter, and reduce? I did it for the first part but couldn't figure out the second half. AM kinda new to python so any help would be great.
Here is the test file called cmtest.py:
import prompt,math
x = prompt.for_int('Enter x')
print(x,'!=',math.factorial(x),sep='')
First line has 18 characters (including white space)
Second line has 29 characters
Third line has 38 characters
[(1, 18), (1, 29), (1, 38)]
The line count is 85 characters including white spaces. I apologize, I mis-read the problem. The length total for each line should include the whitespaces as well.
A fairly simple approach is to build a generator to strip trailing whitespace, then enumerate over that (with a start value of 1) filtering out blank lines, and summing the length of each line in turn, eg:
def code_metric(filename):
line_count = char_count = 0
with open(filename) as fin:
stripped = (line.rstrip() for line in fin)
for line_count, line in enumerate(filter(None, stripped), 1):
char_count += len(line)
return line_count, char_count
print(code_metric('cmtest.py'))
# (3, 85)
In order to count lines, maybe this code is cleaner:
with open(file) as f:
lines = len(file.readlines())
For the second part of your program, if you intend to count only non-empty characters, then you forgot to remove '\t' and '\n'. If that's the case
with open(file) as f:
num_chars = len(re.sub('\s', '', f.read()))
Some people have advised you to do both things in one loop. That is fine, but if you keep them separated you can make them into different functions and have more reusability of them that way. Unless you are handling huge files (or executing this coded millions of times), it shouldn't matter in terms of performance.

Split a string ignoring quoted sections

Given a string like this:
a,"string, with",various,"values, and some",quoted
What is a good algorithm to split this based on commas while ignoring the commas inside the quoted sections?
The output should be an array:
[ "a", "string, with", "various", "values, and some", "quoted" ]
Looks like you've got some good answers here.
For those of you looking to handle your own CSV file parsing, heed the advice from the experts and Don't roll your own CSV parser.
Your first thought is, "I need to handle commas inside of quotes."
Your next thought will be, "Oh, crap, I need to handle quotes inside of quotes. Escaped quotes. Double quotes. Single quotes..."
It's a road to madness. Don't write your own. Find a library with an extensive unit test coverage that hits all the hard parts and has gone through hell for you. For .NET, use the free FileHelpers library.
Python:
import csv
reader = csv.reader(open("some.csv"))
for row in reader:
print row
If my language of choice didn't offer a way to do this without thinking then I would initially consider two options as the easy way out:
Pre-parse and replace the commas within the string with another control character then split them, followed by a post-parse on the array to replace the control character used previously with the commas.
Alternatively split them on the commas then post-parse the resulting array into another array checking for leading quotes on each array entry and concatenating the entries until I reached a terminating quote.
These are hacks however, and if this is a pure 'mental' exercise then I suspect they will prove unhelpful. If this is a real world problem then it would help to know the language so that we could offer some specific advice.
Of course using a CSV parser is better but just for the fun of it you could:
Loop on the string letter by letter.
If current_letter == quote :
toggle inside_quote variable.
Else if (current_letter ==comma and not inside_quote) :
push current_word into array and clear current_word.
Else
append the current_letter to current_word
When the loop is done push the current_word into array
The author here dropped in a blob of C# code that handles the scenario you're having a problem with:
CSV File Imports in .Net
Shouldn't be too difficult to translate.
What if an odd number of quotes appear
in the original string?
This looks uncannily like CSV parsing, which has some peculiarities to handling quoted fields. The field is only escaped if the field is delimited with double quotations, so:
field1, "field2, field3", field4, "field5, field6" field7
becomes
field1
field2, field3
field4
"field5
field6" field7
Notice if it doesn't both start and end with a quotation, then it's not a quoted field and the double quotes are simply treated as double quotes.
Insedently my code that someone linked to doesn't actually handle this correctly, if I recall correctly.
Here's a simple python implementation based on Pat's pseudocode:
def splitIgnoringSingleQuote(string, split_char, remove_quotes=False):
string_split = []
current_word = ""
inside_quote = False
for letter in string:
if letter == "'":
if not remove_quotes:
current_word += letter
if inside_quote:
inside_quote = False
else:
inside_quote = True
elif letter == split_char and not inside_quote:
string_split.append(current_word)
current_word = ""
else:
current_word += letter
string_split.append(current_word)
return string_split
I use this to parse strings, not sure if it helps here; but with some minor modifications perhaps?
function getstringbetween($string, $start, $end){
$string = " ".$string;
$ini = strpos($string,$start);
if ($ini == 0) return "";
$ini += strlen($start);
$len = strpos($string,$end,$ini) - $ini;
return substr($string,$ini,$len);
}
$fullstring = "this is my [tag]dog[/tag]";
$parsed = getstringbetween($fullstring, "[tag]", "[/tag]");
echo $parsed; // (result = dog)
/mp
This is a standard CSV-style parse. A lot of people try to do this with regular expressions. You can get to about 90% with regexes, but you really need a real CSV parser to do it properly. I found a fast, excellent C# CSV parser on CodeProject a few months ago that I highly recommend!
Here's one in pseudocode (a.k.a. Python) in one pass :-P
def parsecsv(instr):
i = 0
j = 0
outstrs = []
# i is fixed until a match occurs, then it advances
# up to j. j inches forward each time through:
while i < len(instr):
if j < len(instr) and instr[j] == '"':
# skip the opening quote...
j += 1
# then iterate until we find a closing quote.
while instr[j] != '"':
j += 1
if j == len(instr):
raise Exception("Unmatched double quote at end of input.")
if j == len(instr) or instr[j] == ',':
s = instr[i:j] # get the substring we've found
s = s.strip() # remove extra whitespace
# remove surrounding quotes if they're there
if len(s) > 2 and s[0] == '"' and s[-1] == '"':
s = s[1:-1]
# add it to the result
outstrs.append(s)
# skip over the comma, move i up (to where
# j will be at the end of the iteration)
i = j+1
j = j+1
return outstrs
def testcase(instr, expected):
outstr = parsecsv(instr)
print outstr
assert expected == outstr
# Doesn't handle things like '1, 2, "a, b, c" d, 2' or
# escaped quotes, but those can be added pretty easily.
testcase('a, b, "1, 2, 3", c', ['a', 'b', '1, 2, 3', 'c'])
testcase('a,b,"1, 2, 3" , c', ['a', 'b', '1, 2, 3', 'c'])
# odd number of quotes gives a "unmatched quote" exception
#testcase('a,b,"1, 2, 3" , "c', ['a', 'b', '1, 2, 3', 'c'])
Here's a simple algorithm:
Determine if the string begins with a '"' character
Split the string into an array delimited by the '"' character.
Mark the quoted commas with a placeholder #COMMA#
If the input starts with a '"', mark those items in the array where the index % 2 == 0
Otherwise mark those items in the array where the index % 2 == 1
Concatenate the items in the array to form a modified input string.
Split the string into an array delimited by the ',' character.
Replace all instances in the array of #COMMA# placeholders with the ',' character.
The array is your output.
Heres the python implementation:
(fixed to handle '"a,b",c,"d,e,f,h","i,j,k"')
def parse_input(input):
quote_mod = int(not input.startswith('"'))
input = input.split('"')
for item in input:
if item == '':
input.remove(item)
for i in range(len(input)):
if i % 2 == quoted_mod:
input[i] = input[i].replace(",", "#COMMA#")
input = "".join(input).split(",")
for item in input:
if item == '':
input.remove(item)
for i in range(len(input)):
input[i] = input[i].replace("#COMMA#", ",")
return input
# parse_input('a,"string, with",various,"values, and some",quoted')
# -> ['a,string', ' with,various,values', ' and some,quoted']
# parse_input('"a,b",c,"d,e,f,h","i,j,k"')
# -> ['a,b', 'c', 'd,e,f,h', 'i,j,k']
I just couldn't resist to see if I could make it work in a Python one-liner:
arr = [i.replace("|", ",") for i in re.sub('"([^"]*)\,([^"]*)"',"\g<1>|\g<2>", str_to_test).split(",")]
Returns ['a', 'string, with', 'various', 'values, and some', 'quoted']
It works by first replacing the ',' inside quotes to another separator (|),
splitting the string on ',' and replacing the | separator again.
Since you said language agnostic, I wrote my algorithm in the language that's closest to pseudocode as posible:
def find_character_indices(s, ch):
return [i for i, ltr in enumerate(s) if ltr == ch]
def split_text_preserving_quotes(content, include_quotes=False):
quote_indices = find_character_indices(content, '"')
output = content[:quote_indices[0]].split()
for i in range(1, len(quote_indices)):
if i % 2 == 1: # end of quoted sequence
start = quote_indices[i - 1]
end = quote_indices[i] + 1
output.extend([content[start:end]])
else:
start = quote_indices[i - 1] + 1
end = quote_indices[i]
split_section = content[start:end].split()
output.extend(split_section)
output += content[quote_indices[-1] + 1:].split()
return output