# Announcement

MDArray version 0.5.4 has Just been released. MDArray is a multi

dimensional array implemented

for JRuby inspired by NumPy (www.numpy.org) and Masahiro Tanakas Narray

(

narray.rubyforge.org).

MDArray stands on the shoulders of Java-NetCDF and Parallel Colt. At

this

point MDArray has

libraries for mathematical, trigonometric and descriptive statistics

methods.

NetCDF-Java Library is a Java interface to NetCDF files, as well as to

many

other types of

scientific data formats. It is developed and distributed by Unidata

(http://www.unidata.ucar.edu).

Parallel Colt (

http://grepcode.com/snapshot/repo1.maven.org/maven2/net.sourceforge.parallelcolt/

parallelcolt/0.10.0/) is a multithreaded version of Colt (

redirect...).

Colt provides a set of Open Source Libraries for High Performance

Scientific and Technical

Computing in Java. Scientific and technical computing is characterized

by

demanding problem

sizes and a need for high performance at reasonably small memory

footprint.

For more information and (some) documentation please go to:

# Whats new:

## NetCDF-3 File Support

From Wikipedia, the free encyclopedia:

"NetCDF (Network Common Data Form) is a set of software libraries and

self-describing,

machine-independent data formats that support the creation, access, and

sharing of array-oriented

scientific data. The project homepage is hosted by the Unidata program

at

the University

Corporation for Atmospheric Research (UCAR). They are also the chief

source

of netCDF software,

standards development, updates, etc. The format is an open standard.

NetCDF

Classic and 64-bit

Offset Format are an international standard of the Open Geospatial

Consortium.

The project is actively supported by UCAR. Version 4.0 (released in

2008)

allows the use of the

HDF5 data file format. Version 4.1 (2010) adds support for C and Fortran

client access to

specified subsets of remote data via OPeNDAP.

The format was originally based on the conceptual model of the Common

Data

Format developed by

NASA, but has since diverged and is not compatible with it."

This version of MDArray implements NetCDF-3 file support only. NetCDF-4

is

not yet supported. At

the end of this announcement we show the MDArray implementation of the

NetCDF-3 file writing

from the tutorial at:

http://www.unidata.ucar.edu/software/netcdf-java/tutorial/NetcdfWriting.html

# MDArray and SciRuby:

MDArray subscribes fully to the SciRuby Manifesto (http://sciruby.com/).

Ruby has for some time had no equivalent to the beautifully constructed

NumPy, SciPy, and

matplotlib libraries for Python.

We believe that the time for a Ruby science and visualization package

has

come. Sometimes

when a solution of sugar and water becomes super-saturated, from it

precipitates a pure,

delicious, and diabetes-inducing crystal of sweetness, induced by no

more

than the tap of a

finger. So is occurring now, we believe, with numeric and visualization

libraries for Ruby.

# MDArray main properties are:

- Homogeneous multidimensional array, a table of elements (usually

numbers), all of the

same type, indexed by a tuple of positive integers; - Easy calculation for large numerical multi dimensional arrays;
- Basic types are: boolean, byte, short, int, long, float, double,

string,

structure; - Based on JRuby, which allows importing Java libraries;
- Operator: +,-,*,/,%,**, >, >=, etc.;
- Functions: abs, ceil, floor, truncate, is_zero, square, cube, fourth;
- Binary Operators: &, |, ^, ~ (binary_ones_complement), <<, >>;
- Ruby Math functions: acos, acosh, asin, asinh, atan, atan2, atanh,

cbrt,

cos, erf, exp,

gamma, hypot, ldexp, log, log10, log2, sin, sinh, sqrt, tan, tanh,

neg; - Boolean operations on boolean arrays: and, or, not;
- Fast descriptive statistics from Parallel Colt (complete list found

bellow); - Easy manipulation of arrays: reshape, reduce dimension, permute,

section, slice, etc.; - Support for reading and writing NetCDF-3 files;
- Reading of two dimensional arrays from CSV files (mainly for

debugging

and simple testing

purposes); - StatList: a list that can grow/shrink and that can compute Parallel

Colt

descriptive

statistics; - Experimental lazy evaluation (still slower than eager evaluation).

# Descriptive statistics methods imported from Parallel Colt:

- auto_correlation, correlation, covariance, durbin_watson,

frequencies,

geometric_mean, - harmonic_mean, kurtosis, lag1, max, mean, mean_deviation, median,

min,

moment, moment3, - moment4, pooled_mean, pooled_variance, product, quantile,

quantile_inverse, - rank_interpolated, rms, sample_covariance, sample_kurtosis,

sample_kurtosis_standard_error, - sample_skew, sample_skew_standard_error, sample_standard_deviation,

sample_variance, - sample_weighted_variance, skew, split, standard_deviation,

standard_error, sum, - sum_of_inversions, sum_of_logarithms, sum_of_powers,

sum_of_power_deviations, - sum_of_squares, sum_of_squared_deviations, trimmed_mean, variance,

weighted_mean, - weighted_rms, weighted_sums, winsorized_mean.

# Double and Float methods from Parallel Colt:

- acos, asin, atan, atan2, ceil, cos, exp, floor, greater,

IEEEremainder,

inv, less, lg, - log, log2, rint, sin, sqrt, tan.

# Double, Float, Long and Int methods from Parallel Colt:

- abs, compare, div, divNeg, equals, isEqual (is_equal), isGreater

(is_greater), - isles (is_less), max, min, minus, mod, mult, multNeg (mult_neg),

multSquare (mult_square), - neg, plus (add), plusAbs (plus_abs), pow (power), sign, square.

# Long and Int methods from Parallel Colt

- and, dec, factorial, inc, not, or, shiftLeft (shift_left),

shiftRightSigned

(shift_right_signed), shiftRightUnsigned (shift_right_unsigned),

xor.

# MDArray installation and download:

- Install Jruby
- jruby S gem install mdarray

# MDArray Homepages:

# Contributors:

Contributors are welcome.

# MDArray History:

- 07/08/2013: Version 0.5.4 - Support for reading and writing NetCDF-3

files - 24/06/2013: Version 0.5.3 Over 90% Performance improvements for

methods imported

from Parallel Colt and over 40% performance improvements for all

other methods

(implemented in Ruby); - 16/05/2013: Version 0.5.0 - All loops transferred to Java with over

50%

performance

improvements. Descriptive statistics from Parallel Colt; - 19/04/2013: Version 0.4.3 - Fixes a simple, but fatal bug in 0.4.2.

No

new features; - 17/04/2013: Version 0.4.2 - Adds simple statistics and boolean

operators; - 05/04/2013: Version 0.4.0 Initial release.

# NetCDF-3 Writing with MDArray API

require ‘mdarray’

class NetCDF

attr_reader :dir, :filename, :max_strlen

#---------------------------------------------------------------------------------------

#---------------------------------------------------------------------------------------

def initialize

@dir = “~/tmp”

@filename1 = “testWriter”

@filename2 = “testWriteRecord2”

@max_strlen = 80

end

#---------------------------------------------------------------------------------------

# Define the NetCDF-3 file

#---------------------------------------------------------------------------------------

def define_file

```
# We pass the directory, filename, filetype and optionaly the
```

outside_scope.

#

# I’m implementing in cygwin, so the need for method cygpath that

converts the

# directory name to a Windows name. In another environment, just

pass

the directory

# name.

#

# Inside a block we have another scope, so the block cannot access

any

variables, etc.

# from the ouside scope. If we pass the outside scope, in this case

we

are passing self,

# we can access variables in the outside scope by using

@outside_scope..

NetCDF.define(cygpath(@dir), @filename1, “netcdf3”, self) do

```
# add dimensions
dimension "lat", 64
dimension "lon", 128
# add variables and attributes
# add Variable double temperature(lat, lon)
variable "temperature", "double", [@dim_lat, @dim_lon]
variable_att @var_temperature, "units", "K"
variable_att @var_temperature, "scale", [1, 2, 3]
# add a string-value variable: char svar(80)
# note that this is created as a scalar variable although in
```

NetCDF-3

there is no

# string type and the string has to be represented as a char type.

variable “svar”, “string”, [], {:max_strlen =>

@outside_scope.max_strlen}

```
# add a 2D string-valued variable: char names(names, 80)
dimension "names", 3
variable "names", "string", [@dim_names], {:max_strlen =>
```

@outside_scope.max_strlen}

```
# add a scalar variable
variable "scalar", "double", []
# add global attributes
global_att "yo", "face"
global_att "versionD", 1.2, "double"
global_att "versionF", 1.2, "float"
global_att "versionI", 1, "int"
global_att "versionS", 2, "short"
global_att "versionB", 3, "byte"
end
```

end

#---------------------------------------------------------------------------------------

# write data on the above define file

#---------------------------------------------------------------------------------------

def write_file

```
NetCDF.write(cygpath(@dir), @filename1, self) do
temperature = find_variable("temperature")
shape = temperature.shape
data = MDArray.fromfunction("double", shape) do |i, j|
i * 1_000_000 + j * 1_000
end
write(temperature, data)
svar = find_variable("svar")
write_string(svar, "Two pairs of ladies stockings!")
names = find_variable("names")
# careful here with the shape of a string variable. A string
```

variable has one

# more dimension than it should as there is no string type in

NetCDF-3. As such,

# if we look as names’ shape it has 2 dimensions, be we need to

create a one

# dimension string array.

data = MDArray.string([3], [“No pairs of ladies stockings!”,

“One pair of ladies stockings!”,

“Two pairs of ladies stockings!”])

write_string(names, data)

```
# write scalar data
scalar = find_variable("scalar")
write(scalar, 222.333 )
end
```

end

#---------------------------------------------------------------------------------------

# Define a file for writing one record at a time

#---------------------------------------------------------------------------------------

def define_one_at_time

```
NetCDF.define(cygpath(@dir), @filename2, "netcdf3", self) do
dimension "lat", 3
dimension "lon", 4
# zero sized dimension is an unlimited dimension
dimension "time", 0
variable "lat", "float", [@dim_lat]
variable_att @var_lat, "units", "degree_north"
variable "lon", "float", [@dim_lon]
variable_att @var_lon, "units", "degree_east"
variable "rh", "int", [@dim_time, @dim_lat, @dim_lon]
variable_att @var_rh, "long_name", "relative humidity"
variable_att @var_rh, "units", "percent"
variable "T", "double", [@dim_time, @dim_lat, @dim_lon]
variable_att @var_t, "long_name", "surface temperature"
variable_att @var_t, "units", "degC"
variable "time", "int", [@dim_time]
variable_att @var_time, "units", "hours since 1990-01-01"
end
```

end

#---------------------------------------------------------------------------------------

# Define a file for writing one record at a time

#---------------------------------------------------------------------------------------

def write_one_at_time

```
NetCDF.write(cygpath(@dir), @filename2, self) do
lat = find_variable("lat")
lon = find_variable("lon")
# write non recored data to the variables
write(lat, MDArray.float([3], [41, 40, 39]))
write(lon, MDArray.float([4], [-109, -107, -105, -103]))
# get record variables from file
rh = find_variable("rh")
time = find_variable("time")
t = find_variable("T")
# there is no method find_dimension for NetcdfFileWriter, so we
```

need

to get the

# dimension from a variable.

rh_shape = rh.shape

dim_lat = rh_shape[1]

dim_lon = rh_shape[2]

```
(0...10).each do |time_idx|
# fill rh_data array
rh_data = MDArray.fromfunction("int", [dim_lat, dim_lon]) do
```

|lat,

lon|

time_idx * lat * lon

end

# reshape rh_data so that it has the same shape as rh variable

# Method reshape! reshapes the array in-place without data

copying.

rh_data.reshape!([1, dim_lat, dim_lon])

```
# fill temp_data array
temp_data = MDArray.fromfunction("double", [dim_lat, dim_lon])
```

do

|lat, lon|

time_idx * lat * lon / 3.14159

end

# reshape temp_data array so that it has the same shape as temp

variable.

temp_data.reshape!([1, dim_lat, dim_lon])

```
# write the variables
write(time, MDArray.int([1], [time_idx * 12]), [time_idx])
write(rh, rh_data, [time_idx, 0, 0])
write(t, temp_data, [time_idx, 0, 0])
end # End time_idx loop
end
```

end

end

netcdf = NetCDF.new

netcdf.define_file

netcdf.write_file

netcdf.define_one_at_time

netcdf.write_one_at_time