Climate Data Analysis Tools

(CDAT): A Beginner’s Guide

Version 3.3

PCMDI Computational Support

Program for Climate Model Diagnosis and

Intercomparison (PCMDI)
Lawrence Livermore National Laboratory
Livermore, CA 94550
United States of America
http://cdat.sf.net

11/1/02
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 Table of Contents

CHAPTER 1 CDAT 1
Introduction 1
Downloading CDAT 2
Installing CDAT 3
System Requirements 3
How to use this guide 3

CHAPTER 2 Getting Started 5

Try the Visual CDAT browser first 5
Description of the VCDAT Interface 7
A brief introduction to Python scripting 16
Variables and arithmetic expressions 18
Conditional statements 19
File Input and Output 20
Lists and Tuples 21
Loops 22
Dictionaries 23
Functions 24
Modules 25
How to get the tutorials and data 25
What do the tutorials cover? 26
getting_started_tutorial.py 26
times_tutorial.py 27
statistics_tutorial.py 27
vcs_tutorial.py 27
xmgrace_tutorial.py 28
Documentation and Help 28
Online Documentation 28
Printable documentation 30
Getting Support 31
CHAPTER 3 What’s in CDAT 33
File/Data Handling 33
File I/O 33
Reading, creating, and altering variables 36
Handling Time 43
Axes and Domains 45
Data Selection. 46
Regridding Data 47
Working with masks 49
Databases 49
Averaging and Statistics 50
Area averaging 50
Generating weights 53
Time averaging 53
Useful statistical functions 58
Data Visualization 60
Visualization and Control System (VCS) 60
Displaying data 62
Interface to Grace (genutil.xmgrace) 71
Other useful packages 71
Interface to Spherepack 72
Interface to Regridpack 72
Empirical Orthogonal Functions 72
Interface to the L-moments library 72
Interface to the ngmath library 72
Using existing Fortran code 73
Migrating from GrADS (grads) 74
ort 74
trends 74
pyclimate 74

CHAPTER 4 Contributions to CDAT 75

How to add your packages 75
Index 77
CHAPTER 1 CDAT

1.1 Introduction
Climate Data Analysis Tools (CDAT) is a software
infrastructure that uses an object-oriented scripting language to link
together separate software subsystems and packages, thus forming an
integrated environment for solving model diagnosis problems. The
power of the system comes from Python and its ability to seamlessly
interconnect software. Python provides a general purpose and full-
featured scripting language with a variety of user interfaces including
command-line interaction, stand-alone scripts (applications) and
graphical user interfaces (GUI). The CDAT subsystems, implemented
as modules, provide access to and management of gridded data
(Climate Data Management System or CDMS); large-array
numerical operations (Numerical Python); and visualization
(Visualization and Control System or VCS).

One of the most difficult challenges facing climate researchers today

is the cataloging and analysis of massive amounts of multi-
dimensional global atmospheric and oceanic model data. To reduce

Getting Started With CDAT 1

CDAT

the labor intensive and time-consuming process of data management,

retrieval, and analysis, PCMDI and other DOE sites have come
together to develop intelligent filing system and data management
software for the linking of storage devices located throughout the
United States and the international climate research community. This
effort known as the Earth System Grid (ESG) and headed by PCMDI,
NCAR, and ANL will allow users anywhere to remotely access this
distributed multi-petabyte archive and perform analysis. PCMDI's
CDAT utilizes ESG and is an innovative system that supports
exploration and visualization of climate scientific datasets. As an
"open system", the software sub-systems (i.e., modules) are
independent and freely available to the global climate community.
CDAT is easily extended to include new modules and as a result of its
flexibility, PCMDI has integrated other popular software
components, such as: the popular Live Access Server (LAS) and the
Open Data Access Protocol (OPeNDAP) - formerly known by the
name Distributed Oceanographic Data System (DODS). Together
with ANL's Globus middleware software, CDAT's focus is to allow
climate researchers the ability to access and analyze multi-
dimensional distributed climate datasets.

1.2 Downloading CDAT

CDAT can be downloaded from the CDAT Home Page at
http://cdat.sf.net as a gzipped tar file (cdat.tar.gz). Links to the latest
source can be found there. If you are using CDAT for the first time, it
is recommended that you also download the tutorials and tutorial data
from the CDAT home page at http://cdat.sf.net. The tutorial files are
in cdat_tutorial.tar.gz and the data files used in the tutorials are in
cdat_tutorial_data.tar.gz.

2 Getting Started with CDAT

Installing CDAT

1.3 Installing CDAT

The downloadable tar file contains a README.TXT file which
lists the requirements and instructions to install CDAT. The
instructions are not listed here so that this document is not outdated
when new versions of CDAT are released.

1.4 System Requirements

CDAT has been successfully installed on a variety of platforms.
The specific platforms it has been tested on include Sun/Solaris (5.8),
IBM AIX, DEC OSF 1 (5.x), Irix (6.5), HP-UX 11.0 (We know 10
will not work), MacOSX "Darwin" and various versions of Linux
(Kernel 2.2 or greater). The source distribution of CDAT includes
packages required by CDAT and the installation script handles the
task of installing them in the appropriate areas.

1.5 How to use this guide

This guide is intended to provide users who are new to CDAT a
single document where they can get an overall view of CDAT and to
provide pointers to more detailed information. There are numerous
packages that comprise CDAT. To document all their features here
would make this document unreasonably large and daunting to the
new user. Instead, the approach adopted here is to give a brief
overview of how tasks are accomplished in CDAT and point the
reader to other documents or methods of getting additional
documentation should they require more details. In that sense this is
also a "Documentation of Available Documentation".

Chapter 2 contains instructions on getting started with using CDAT.

The Graphical User Interface, VCDAT (which stands for Visual

Getting Started With CDAT 3

CDAT

Climate Data Analysis Tools), is introduced in this chapter. It is a

powerful tool to browse through data, perform data analysis, find
documentation, and to learn the scripting and other capabilities of
CDAT. However, CDAT does not require that you use the graphical
interface and it is easily executed from the Python command line. A
brief introduction to Python is included in this section. The tutorials
have example scripts and a set of example datasets. These tutorial
scripts are easy to run and provide a range of real life applications
that a climate scientist can see in action. The various methods of
getting the necessary documentation and help in using CDAT,
ranging from printable files to online documentation, FAQs, and
discussion groups are listed in this chapter.

Having gone through the tutorial, the next step is to become aware of
CDAT’s features. Chapter 3 entitled "What’s in CDAT?" addresses
this. To illustrate the features of CDAT, we have tried to address some
of the tasks that a climate scientist may wish to accomplish.
Therefore, the organization of tasks is broken up along the lines of
File I/O, creating databases and accessing data from them, data
extraction, altering variables and metadata, regridding data, spatial
and temporal averaging, statistics, and visualization. In addition to
these, other sample scripts which describe such tasks as making use
of exiting Fortran or C code, and interfacing to specialized packages
such as spherepack and EOFs, provide the reader with a flavor for
what is already possible to do with CDAT and also how easy it is to
leverage off previous efforts. The final chapter in this guide explains
how you can contribute to CDAT.

4 Getting Started with CDAT

CHAPTER 2 Getting Started

CDAT uses the Python language as a glue to link together the various tools. Python has
one of the fastest growing user bases among programming languages today and is extensively
documented online and in publications. It must be stressed that it is not essential to have any
knowledge of Python before being able to use CDAT tools. The Graphical User Interface
(VCDAT) can be used with no knowledge of Python and is the first topic introduced in this
chapter. This is highly recommended for beginners. For the more adventurous beginner who
wishes to learn the use of scripting capabilities, a brief background of the Python language
and syntax is provided in the next section.

CDAT comes with a suite of tutorials in the form of online video

tutorials and scripts to help you learn how to use it. These tutorials
are described in brief to enable the user to find the appropriate
tutorials and to give a flavor of the power of CDAT. Finally, the
various documentation and help avenues available to the user are
described in this chapter.

2.1 Try the Visual CDAT browser first

The beginning user is encouraged to try the VCDAT browser
first. This is accomplished by simply typing the command "vcdat" at
your shell prompt, i.e:
% vcdat

Online video tutorials are available through the CDAT home page at
http://cdat.sf.net. These short streaming video tutorials are a
convenient way to see VCDAT in action. VCDAT was designed to be
used from left-to-right and top-to-bottom and has on-line help

Getting Started With CDAT 5

Getting Started

balloons to assist the user in navigating through the interface. That is,
if the user becomes unsure of what to do at any give time, then by
moving the mouse over the region of question and letting it rest will
result in a help balloon popup with information to assist the user.
VCDAT allows the user to enter command line instructions and logs
most button click instructions in a script file for later reference.
Although it is not required to learn CDAT scripting in order to use
VCDAT, the interface can be used as a CDAT script-learning tool by
translating every button press and keystroke into a script file. All
scripts include comment lines to assist the user. The script file can be
modified, saved, and executed by the user. Thus, helping the user
learn how to read and write CDAT scripts. This facility also allows
the non-interactive repetition of common tasks.

To demonstrate quickly, the use of VCDAT try the following example

sequence of button clicks:

Example 1: To quickly browse and plot data:

1. Select the directory where the data is stored
2. Select the desired file that is located in the directory
3. Select a variable from the file
4. Click the "Plot" button.

Example 2: To select data ranges and plot type:

1. Select the directory where the data is stored
2. Select the desired file that is located in the directory
3. Select a variable from the file
4. Select variable ranges (i.e., experiment by adjusting the horizontal
slider bars located just below the "Plot" button)
5. Select graphics method (e.g., select "Isofill" in the choice button
located to the right of the "Plot" button)
6. Click the "Plot" button.

6 Getting Started with CDAT

Try the Visual CDAT browser first

Example 3: To average over a dimension:

1. Select the directory where the data is stored
2. Select the desired file that is located in the directory
3. Select a variable from the file
4. Select "avg" if applicable (e.g., to the right of the horizontal slider
bars, which are located below the "Plot" button, are choice buttons
displaying "def". Select "avg" in place of "def".)
5. Click the "Plot" button.

Example 4: To define a variable in memory:

1. Select the directory where the data is stored
2. Select the desired file that is located in the directory
3. Select a variable from the file
4. If desired, select dimension sub ranges
5. Select the "Define" button
6. Select the defined variable located in the "Defined Variables" win-
dow located just below the "Dimension" panel
7. Click the "Plot" button.

2.1.1 Description of the VCDAT Interface

There are six sections of the VCDAT interface (figure 1) that
are listed here from top-to-bottom: Main Menu (i.e., File, Options,
Tools, PCMDI Tools, Help); Select Variable (Directory, File, and
Variable); Graphics (i.e., Plot, Boxfill, VCS Canvas 1, Options,
Define); Dimensions (Z-time, Y-latitude, X-longitude); Defined
Variables (Operational Icons, Defined Variable List, Function Icons);
and Variable Information.

Getting Started With CDAT 7

Getting Started

Figure 1. The VCDAT Interface

Main Menu

Select
Variable
Graphics

Dimensions

Defined
Variables

Function
Icons

Operational
Icons

Variable
Information

8 Getting Started with CDAT

Try the Visual CDAT browser first

2.1.1.1 Main Menu (i.e., File, Options, Tools, PCMDI Tools,

Help)
There are five static pull down options in VCDAT's main menu.
In addition, the user can add their own customized pull down menus
to VCDAT's main menu.
• File: Under the "File" option, the user can choose to: open data
files located on their local disk, select searches for specific data
types (e.g., netCDF, XML, etc.), send plots directly to local
printers, save the state of the system for total recall, read Python or
VCS script files into the system, and exit out of VCDAT.
• Options: The "Options" option sets information referring to a
selected or defined variable, or sets the state of the graphical user
interface. For example, the "Select Predefined Region" selects a
region of the globe (e.g., "Africa", "Asia", etc.). Thus, every
selected or defined variable will automatically be set to the
predefined region. Note: This works only if the x-axis equals
longitude and the y-axis equals latitude.
Dimension aliases for longitude, latitude, time, and level can also
be set under the "Options" pull down menu. For example, the user
can set "X", "lon" and "X_Long" as aliases for longitude. So when
VCDAT sees these dimension names it will interpret them as
longitude axes.
If the user modifies the VCDAT GUI and wants to save the
settings for the next session, then select "Save GUI State…"
located under this option.
• Tools (IDLE): The "Tools" option displays additional GUIs that
allow the user to: create new script files for edit, edit old script
files, issue keystroke commands, add new user menu options to
the "Main Menu" (note, the new menu option will be placed
between the PCMDITools and Help menu options), and view
recorded script commands.
When invoked, the "Command Line Window…" option is really
executing the Python Integrated DeveLopment Environment

Getting Started With CDAT 9

Getting Started

(IDLE) developed by Guido van Rossum, who is also the

developer of Python. The Python Shell Window gives the user
access into Python's interactive mode. This Python Shell Window
has been slightly modified to allow the user to register keystroke
script commands and GUI button commands simultaneously and
seamlessly in VCDAT.
When the "Python Shell Window" (i.e., called "VCDAT's
Command Line Window" in VCDAT) appears, the user should
read the information describing hooks into VCS. For additional
online information about the "Python Shell Window", select the
"F1" button while running it.
The script editors are also part of IDLE. IDLE can also be invoked
outside of VCDAT. That is, at the prompt type, "idle". For more
information on IDLE, visit: http://www.python.org/idle.
To add more menus to "Main Menu", the user must select the "Add
User New Menu…" menu item. See help balloons to assist with
the addition of new menus. Once the new menu has been added,
the user must select "Save GUI State…" located under "Main
Menu" -> "Options" to retain the new menu for later VCDAT
sessions.
• PCMDITools: The "PCMDITools" option contains the start of
time tools and statistical functions deemed necessary (by the
PCMDI climate researchers) to do common fundamental analysis.
For the "Time Tools", the data must have a time dimension in
order to work. Under "Options", see "Dimension Aliases for"
specifying additional time axis names.
For in-depth information on these tools and their functionalities,
see the CDAT Utilities Reference Guide.
• Help: The "Help" option allows the user to turn the help balloons
off or on, display CDAT related web sites by means of the user's
client web browser, and displays information about VCDAT to the
user (for example, version number and place of execution).

10 Getting Started with CDAT

Try the Visual CDAT browser first

2.1.1.2 Select Variable

The main purpose of this section is to select a variable for
analysis and/or display. There are five main components here: the
"Directory"; the "Database", this component take the place of the
"Directory" when it is invoked; the "File"; the "Datasets", this
component takes the place of the "File" when the "Database" is
invoked, and the Variable.
• Directory: The "Directory" component of "Select Variable"
contains: a home directory icon, which if selected will take the
user directly to their $HOME directory; a file selection browser
icon that will display a file selection GUI for selecting the
directory and a file; an input window for specifying the directory
by means of a keypad; a bookmark icon for saving favorite
working directories; and a cycle icon for cycling through the list of
favorite working directories.
Note: the "Directory" input window will turn salmon pink when
the user enters text. The textual information requesting a new
directory will not be excepted until the <Return> key is depressed.
• Database: The "Database" component is displayed only when the
user has changed the choice button from "Directory" to
"Database". If the user has not installed "esg" on their system and
the environment variable "CDMSROOT" has not been set, then
the "Database" option will not appear. If the "Database" option is
selected, then a popup will appear allowing the user to log onto a
remote database. After connecting to a remote database the "File"
component will change to display "Datasets".
• File: The "File" component displays all the files located in the
directory. To view only a specific file type, select under "Main
Menu" -> "File" -> "Open File Types" the desired file
specifications. If an OPeNDAP enabled version of CDAT has been
installed, then, a URL of a dataset on an OPeNDAP server may be
entered.

Getting Started With CDAT 11

Getting Started

• Datasets: The "Datasets" components displays all the datasets

located in the database. This is only visible if the "Database"
component is visible.
• Variable: The "Variable" component displays the variables, axes,
and bounds in a file or dataset. To alter the viewing of "Variable"
(i.e., don't display or display axes, bounds and weights), toggle
"Main Menu" -> "Options" -> "View axes in Variable List" and
"Main Menu" -> "Options" -> "View bounds and weights in
Variable List".

2.1.1.3 Graphics (i.e., Plot, Boxfill, VCS Canvas 1, Options,

Define)
There are only four components to "Graphics", but because of
screen real estate and design considerations, the "Define" button was
added to this row. Therefore, "Graphics" consist of five components:
the "Plot" button, the "Graphics Method" (e.g., "Boxfill", "Isofill",
etc.) choice button, the "VCS Canvas" choice button, the graphics
"Options" menu, and the "Define" button.
• Plot: After the "Variable" has been selected, the user can select the
"Plot" button to display the variable. The user can also select the
"Plot" button to display a "Define Variable", which is described
later in this document.
• Graphics Method: By default, the "Boxfill" graphics method will
be displayed. To choose a different graphics method, the user must
depress and hold the choice menu button. Then move the pointer
over the desired graphics method (e.g., "Isofill"). At this point, the
user can reselect the "Plot" button to redisplay the variable.
• VCS Canvas: VCDAT allows up to four VCS Canvases. More can
be added if necessary. The user can select which canvas to display
the variable information. Note, if the user wishes to display the
information on the "Background Canvas", then rendering is done
in memory and no canvas drawing is visible to the user, but the

12 Getting Started with CDAT

Try the Visual CDAT browser first

user can still send the unseen plot to the printer or to a graphics
output file. See "Main Menu" -> "Save Plot As" and "Main Menu"
-> "Print Plot On" for sections on file output and printer selections.
Also, view the VCS document for details on the
PCMDI_GRAPHICS directory and the HARD_COPY file.
• Options: The "Options" menu displays additional GUIs for
controlling the outcome of the plot. These plot options are:
"Continents Types", "Page Orientation", "Overlay", "Isoline
Labels", "Annotation", "Set VCS Canvas Geometry", "Set Min
Max Values", "Set Graphics Method Attributes", Number of Plots
on VCS Canvas", "Set Plot Map Projection", "Editors",
"Animate", "Clear VCS Canvas", and "Close VCS Canvas".
• Define: After the "Variable" has been selected, the user can select
the "Define" button to transfer the variable from a file or remote
database to memory. The selected variable will be visible in the
"Defined Variables" below.
The "Define" button is also used to save a defined variable under a
new name and can be used to overwrite an existing defined
variable. That is, in the "Defined Variable List" window, select a
defined variable, and then select the "Define" button. A pop up
will appear with simple instructions for both actions.

2.1.1.4 Dimensions Panel

The "Dimension Panel" is blank if no variable or defined
variable is selected. It is located just under the "Graphics" section. It
can currently display up to six dimensions. But more display
dimensions can be easily added if necessary. The displayed
dimensions are separated by lines and contain four components: the
"Dimension Menu"; the "Dimension Selection"; the "Dimension
Sliders"; and the "Dimension Functions".
• Dimension Menu: The "Dimension Menu" allows the user to
change the view of the "Dimension Selection" from axes defined

Getting Started With CDAT 13

Getting Started

values to index values. For example, from longitude or latitude

coordinate values to index values. In the case of the time
dimension, the user can change the time coordinate values, i.e.,
"units since base time" (See “Handling Time” on page 43.) to
either raw time values or index values.
The user can get the weights of an axis' by selecting the "Get Axis
Weight Values" menu item. The weights variable will be stored in
memory and displayed in the "Defined Variable" window below.
By selecting the "Replace Axis Values", the user can replace the
axis node values with a defined variable, provided that the axes
and the defined variable are the same size. The new axis must be
visible in the "Defined Variables" window.
To reorder the dimensions, depress and hold the "Re-Order
Dimensions". Then select the desired dimension to trade places.
The "Dimensions Panel" will restructure itself accordingly.
• Dimension Selection: The "Dimension Selection" allows the user
to select a single node value, a subset of node values, and a
selection of every nth node value. When selecting the arrow button
to the right will display the list axes node values. The highlighted
value indicates the selected node(s). The input text window
representation the dimension as "first: last by stride".
The user can enter the node value(s) in the input text window.
When entering values, the input window becomes salmon pink. To
except the changes, the user must depress the <Return> key. To
select every nth node value, the user must enter the stride number
after the "by" and then depress the <Return> key.
To select a single node, the user can either enter the value in the
input text window or select the arrow button to the right and then
select the desired node value. To select a sub-range, the user can
either enter the values in the input text window or select the arrow
button to the right and then select the second desired node value.
• Dimension Slider: The slider bars are yet another way to select
the first and last values of a sub-range or single node point. The
top slider changes the first selected node value and the bottom

14 Getting Started with CDAT

Try the Visual CDAT browser first

slider changes the last selected node value. The values below the
second slider bar represent the first selected node value and the
last selected node value.
• Dimension Functions: Each dimension can have a function
operate on it exclusively. Select the choice menu button for a
detailed description of each function operation. The last two
functions "awt" and "gtm" are slightly different. "awt" allows the
user to replace the weights before operating the weighted average
function. The new weights must be located in the "Defined
Variables" window before using this function. The geometrical
mean "gtm" is generated by the following function: gtm(x) =
exp(mean ( log(x)))).

2.1.1.5 Defined Variables

The "Defined Variables" section operates on variables that are
stored in memory. Variables can be defined in memory by selecting
the "Define" button located in the "Graphics" section. Variables can
also be defined by operations located in the "Main Menu" section.
For example: selecting from "Main Menu" -> "PCMDITools" ->
"Statistics" -> "Mean" on a variable would produce
"_Statistics_mean_variablename ()" in the "Defined Variables List".
Other possible ways to produce a defined variable are: by the use of
"Function Icons" and command line operations via VCDAT's
"Command Line Window". For example: typing "import MV; a =
MV.array((1,2,3))" in the VCDAT "Command Line Window" would
produce "a (3)" in the "Defined Variables List".

Note that everything associated with defined variables has the same
background color as the "Define" button located in the "Graphics"
section.
• Operational Icons: The first column of icons (from top to bottom)
allows the user to: edit the variable's attributes, save the variable to

Getting Started With CDAT 15

Getting Started

a netCDF file, display variable information, move selected defined

variables to the trashcan, move all variables to the trashcan, view
logged information about the size of variables in memory, and
permanently remove or restore defined variables.
• Defined Variables List: The "Defined Variables List" is located to
the right of the "Operational Icons" and contains, in alphabetical,
the list of all variables stored in memory. As the user selects
variables in the list, a record of the order of selection is kept.
Among other things, this selection list is important when it
becomes necessary to plot or do calculations by means of the
"Function Icons".
• Function Icons: The "Function Icons" are located to the right of
the "Defined Variables List". There are two modes for calculating
defined variables. If the user moves the pointer over the top left
icon, a detailed description of how the calculation works in both
modes is given.

2.1.1.6 Variable Information

The "Variable Information" section immediately displays
variable or defined variable information to the user. To quickly
browser through many variables and examine their content, resize the
variable information panel by selecting the small button located to the
upper right of the "Variable Information" text. While keeping the
button depressed, move the panel to the desired location.

2.2 A brief introduction to Python scripting

Python is documented down to the last detail at the Python
language website http://python.org and the SourceForge website
http://python.sourceforge.net. There are now many books
discussing the use of Python and how to use it with other open source

16 Getting Started with CDAT

A brief introduction to Python scripting

software. We can recommend the free tutorial available at

www.python.org in the documentation section. The book "Learning
Python" from O’Reilly Press is another excellent resource. This
section provides a very brief introduction to some basic concepts
aimed at "getting started". The interested reader can refer to any of
the other sources referred to above for details.

We begin with the traditional "Hello World" program. To start the

python interpreter type:
% python

Python 2.2.1c2 (#1, Apr 11 2002, 12:36:10)

[GCC egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)]
on linux2
Type "help", "copyright", "credits" or "license" for
more information.
>>> print "Hello World"
Hello World

Programs can be placed in files with a .py extension. The

helloworld.py program would contain the following lines:
# helloworld.py
print "Hello World"

The program can then be executed by providing the name of the

program file to the interpreter as follows:
% python helloworld.py
Hello World
%

Getting Started With CDAT 17

Getting Started

2.2.1 Variables and arithmetic expressions

A simple program can best illustrate the use of arithmetic

expressions.
# simple_program.py
pi = 3.1415
degrees = 0
while degs <= 90:
rads = degs * pi / 180.0
print degs, " degrees = ", rads, " radians"
degs = degs + 10.

The output of this program is the following table:

0 degrees = 0.0 radians
10.0 degrees = 0.174527777778 radians
20.0 degrees = 0.349055555556 radians
30.0 degrees = 0.523583333333 radians
40.0 degrees = 0.698111111111 radians
50.0 degrees = 0.872638888889 radians
60.0 degrees = 1.04716666667 radians
70.0 degrees = 1.22169444444 radians
80.0 degrees = 1.39622222222 radians
90.0 degrees = 1.57075 radians

Python is a dynamically typed language (i.e you do not need to

declare the variable types apriori) and the names can represent
different types depending on the arithmetic operations performed. In
the above example, "degs" was initially set to the integer 0, and is
seen in the first line printed. Subsequently a real number (10.) is
added at each stage of the loop and this changed the type of "degs" as
it can be seen that "degs" values printed are real. Note that the above
example is contrived to illustrate this point and there is no real reason
to add a real value 10.0 in the loop.

The output of the program looks less than ideally formatted. To make
it look better, we can make use of format strings. For example:

18 Getting Started with CDAT

A brief introduction to Python scripting

>>> print "%3d degrees = %0.4f radians" %(degs, rads)

would produce output that looks like this:

0 degrees = 0.0000 radians
10 degrees = 0.1745 radians
20 degrees = 0.3491 radians
30 degrees = 0.5236 radians
40 degrees = 0.6981 radians
50 degrees = 0.8726 radians
60 degrees = 1.0472 radians
70 degrees = 1.2217 radians
80 degrees = 1.3962 radians
90 degrees = 1.5708 radians

The format strings %d, %s denote integers and strings respectively,

and %g and %f denote floats.

2.2.2 Conditional statements

The if and else statements provide an easy way to perform tests.

For instance:
>>> if x != y:
>>> print ’x is not equal to y’
>>> else:
>>> print ’x and y are equal’

The indentation is required to isolate the if and else clauses, but

the else clause is optional. Do nothing clauses can be created by using
the pass statement.
>>> if x != y:
>>> pass
>>> else:
>>> print ’x and y are equal!’

Multiple test cases can be implemented using the elif clause.

>>> if x == ’n’:

Getting Started With CDAT 19

Getting Started

>>> print ’Answered no’

>>> elif x == ’y’:
>>> print ’Answered yes’
>>> else:
>>> print ’invalid answer’

Boolean expressions can be formed by using or, and, and not

keywords.
>>> if x > y and z > x:
>>> print ’z is the max value’
>>> if not (x==z or y==z or x==y):
>>> print ’There are no equal values’

2.2.3 File Input and Output

To open a text file and read its contents you would

>>> f = open("myfile.txt")
# The above line returns a file object
>>> line = f.readline()
# The readline() method is invoked on file
# and one line is read from the file.
# The following section keeps printing and reading
# subsequent lines of data while there are new lines to
# be read
>>> while line:
>>> print line
>>> line = f.readline()
# The while loop is exited when there are no more lines
# to be read. To close the open file:
>>> f.close()

To write output to a file,

>>> fout = open("out.txt", ‘w’)
# The ‘w’ indicates file should be opened for writing
# and is created if it does not already exist.

20 Getting Started with CDAT

A brief introduction to Python scripting

>>> fout.write("hello\n")
# or equivalently
>>> print >>fout, "hello"

2.2.4 Lists and Tuples

Lists and tuples are sequences of arbitrary objects. Lists can be
created by:
>>> mylist = ["a", 1.0, "c", 4]

Note that you can mix items of any type in a list. You can also have
lists nested inside lists.
>>> my_other_list = ["a", "b", [1,2,3], "d"]

The lists are indexed by integers starting with zero. To see the first
item in mylist, you would:
>>> firstitem = mylist[0]
# returns the item "a"
# To set an item:
>>> mylist[2] = "x"
# Changes the item in the index position 2.
>>> print mylist
["a", 1.0, "x", 4]

To append new members to the list, the append() method is used as

follows:
>>> mylist.append("nextitem")
>>> print mylist
["a", 1.0, "x", 4, "nextitem"]

Similarly, individual items can be removed from the list using the
remove() method:
>>> mylist.remove(1.0)
>>> print mylist
["a", "x", 4, "nextitem"]

Getting Started With CDAT 21

Getting Started

You can also insert items into specific positions:

>>> mylist.insert(1, "inserted_item")
>>> print mylist
["a", "inserted_item", "x", 4, "nextitem"]

Lists can be concatenated by using the "+" operator:

>>> newlist = mylist + [9, 10, 11]
>>> print newlist
["a", "inserted_item", "x", 4, "nextitem", 9, 10, 11]

Tuples are very similar to lists and are constructed by using

parentheses instead of brackets or just a comma-separated list.
>>> mytuple = (1, 2, -3)
>>> myvector = (magnitude, direction)
# is the same as
>>> myvector = magnitude, direction

Tuples support the same operations as are supported by lists except

the appending or modification of elements after they are created. That
is, you cannot modify elements or append elements to a tuple.

2.2.5 Loops

We saw the simple loop using the while statement in the previous
examples. Other looping constructs such as the for statement are
available to the user. It is important to note that statements within the
loop are indented. An example of its usage is:
>>> for i in range(3):
>>> print "10 raised to ", i, " is ", 10**i
# will produce the result
10 raised to 0 is 1
10 raised to 1 is 10
10 raised to 2 is 100

22 Getting Started with CDAT

A brief introduction to Python scripting

Note that a=range(3) is equivalent to a=[0,1,2]. Similarly the range(1,

6) is equivalent to [1,2,3,4,5] and range(10, 8, -1) is equivalent to [10,
9]. To generalize, range(i, j, k) produces a list of integers from i to j-1
using a stride k. If i is omitted, it is taken to be zero and k defaults to
1 if omitted. A more efficient (in terms of memory and runtime) is the
xrange() function used exactly like range().

One can also loop through lists using the for statement so:
>>> mylist = [‘a’, ‘b’, 3]
>>> for item in mylist:
>>> print item
# produces the output
a
b
3

2.2.6 Dictionaries

A dictionary allows you to associate values index by keys.

Dictionaries can be created using values in curly braces like this:
>>> a = {
"name" : "CCM3",
"center" : "NCAR,"
"model_of" : "Atmosphere"
}

To access members of the dictionary, we use the key-indexing facility

>>> model_name = a["model"]
>>> modelling_center = a["center"]

The keys associated with a dictionary can be obtained as a list by:

>>> b = a.keys()

Getting Started With CDAT 23

Getting Started

and you can check the dictionary membership by using the has_key()
method:
>>> if a.has_key("model_of"):
>>> print a["model_of"]
>>> else:
>>> print "Unknown model of"

2.2.7 Functions

A function can be created using the def statement as shown below.

def myadd(a, b):
c = a*10 + b
return c

Note once again that the statements inside the function are indented
after the “def” statement. To invoke the function we do the following:
>>> addvalue = myadd(2, 5)

It is possible to return multiple values using comma separated names

in the return statement inside the function.
def myaddsub(a, b):
c = a*10 + b
d = a*10 - b
return c, d

In this case the function is invoked as follows:

>>> addvalue, subvalue = myaddsub(2, 5)

The function definition can also be done in a way such that default
values for input parameters can be set.
def myaddsub(a, b, base=10):
c = a*base + b

24 Getting Started with CDAT

How to get the tutorials and data

d = a*base - b
return c, d

Then, when you need base to take a different value than the default
10, you can
>>> addvalue, subvalue = myaddsub(2, 5, base=2)

2.2.8 Modules
To keep your programs manageable as they grow in size, you
may want to break them up into several files. Python allows you to
put multiple function definitions into a file and use them as a module
that can be imported into other scripts and programs. These files must
have a .py extension. For example
# file my_function.py
def minmax(a,b):
if a <= b:
min, max = a, b
else:
min, max = b, a
return min, max

To use the above module in other programs, you would use the
import statement.
>>> import my_function
>>> x,y = my_function.minmax(25, 6.3)

2.3 How to get the tutorials and data

The tutorials are designed to introduce you to the most common
operations for climate data analysis. They are available as a Python
script from our download area under "Tutorials". If you want to try
executing these examples, follow these steps:

Getting Started With CDAT 25

Getting Started

1. From the Tutorials section of the download facility under the

CDAT home page at http://cdat.sf.net, download the data files
tarball (cdat_tutorial_data.tar.gz) and unpack it.
2. Download the tutorial files tarball (cdat_tutorials.tar.gz) and
unpack it. In each tutorial you may need to edit the line(s) near the
top that sets the location of the data files to match the location
where the data will be on your system.
3. At some point during the tutorials you may wish to also read
“Reading, creating, and altering variables” on page 36 for a dis-
cussion of the difference between several array-like abstractions
that our software uses: numerical arrays, masked arrays, transient
variables, and file variables.

2.4 What do the tutorials cover?

There are five tutorial files provided with data required to run
them. The tutorials are CDAT scripts that give the user a flavor of
how scripts work and to give an idea of how to accomplish specific
tasks. A brief description of the tutorials follows:

2.4.1 getting_started_tutorial.py
This tutorial is the first one to study. The tutorial consists of
three examples:

2.4.1.1 Example 0: The basics

This example runs through some basic operations such as opening,

closing, writing to files, and reading data by location or at specified
time intervals. The tutorial is presented with a series of questions and
answers in the style of a FAQ.

26 Getting Started with CDAT

What do the tutorials cover?

2.4.1.2 Example 1: Dealing with data from other sources

This example shows (in excruciating detail) how to read in Fortran

formatted data, use it within CDAT, and writing to a netCDF file.
Some simple averaging operations are carried out on the data. This
example also shows how to change/insert metadata for the variable.

2.4.1.3 Example 2. Using Masks.

This example shows how to generate data masks, applying masks and
averaging using area weights.

2.4.2 times_tutorial.py
This tutorial demonstrates the uses of the time averaging
functions. Basic examples cover topics such as computing the
December-February seasonal means, computing the climatology,
anomalies (departures) from climatology, construction of seasons not
already defined, customization, and use of powerful criteria to
specify minimum temporal coverage and data distribution.

2.4.3 statistics_tutorial.py
This tutorial covers some of the basic statistical functions such
as rms, correlation, mean absolute difference and their usage with
climate data.

2.4.4 vcs_tutorial.py
This tutorial guides you through some basic plotting functions
and features to visualize the data and produce presentation quality
output. This is by no means an exhaustive demonstration of features -
just a very basic set of capabilities are addressed. Specific examples
cover animations, creating and altering graphics methods, creating
and altering display templates, producing output files for printing and
displaying and changing colormaps etc.

Getting Started With CDAT 27

Getting Started

2.4.5 xmgrace_tutorial.py
In this tutorial, the interface to the XmGrace utility is
demonstrated by showing simple plot generation and customization.
XmGrace is a plotting tool developed independent of CDAT and has
a wide user base. To download and install XmGrace, see the Grace
home page at http://plasma-gate.weizmann.ac.il/Grace

2.5 Documentation and Help

The CDAT home page http://cdat.sf.net is your source for

documentation- both online and printable and support.
Documentation is available to help users at various levels of expertise
starting with the beginning user’s guide (this document) to the
advanced user who needs a quick reference to commands or details of
usage in the programming API reference guides. CDAT makes heavy
use of Numerical Python, a fast array facility for Python. The
Numerical Python website at http://numpy.sourceforge.net
contains extensive documentation.

2.5.1 Online Documentation

2.5.1.1 Using VCDAT

The VCDAT graphical user interface has a "help" button that
provides access to all the documentation that a user may require at the
click of a button. The interface also has helpful information in pop-up
balloons that instruct the user when the cursor is moved over the
buttons.

2.5.1.2 Using "docstrings"

Python also has a powerful feature: most objects in Python,
including the modules, classes, and functions, have documentation
strings ("docstrings") attached to them. The special attribute name

28 Getting Started with CDAT

Documentation and Help

"__doc__" (which has two underscores on each end) is used to access

this string supplied by the module author. If you have an object x, try
the command
>>> print x.__doc__

2.5.1.3 Using pydoc to generate documentation

You can also use the pydoc utility. This is a standard facility for
extracting documentation from Python installations.

You can generate Python documentation in HTML or text for

interactive use.

2.5.1.4 Interactive use

In the Python interpreter, do "from pydoc import help" to provide

online help. Calling help(thing) on a Python object documents the
object. Also, typing help() will put the user in a help environment
indicated by the prompt changing to
help>

2.5.1.5 From the shell

At the shell command line outside of Python: Run "pydoc <name>"

to show documentation on something. <name> may be the name of a
function, module, package, or a dotted reference to a class or function
within a module or module in a package. If the argument contains a
path segment delimiter (e.g. slash on Unix, backslash on Windows) it
is treated as the path to a Python source file. Run "pydoc -k
<keyword>" to search for a keyword in the synopsis lines of all
available modules.

2.5.1.6 Starting a browser / server

pydoc -g starts an HTTP server and also pops up a little window for
controlling it.

Getting Started With CDAT 29

Getting Started

2.5.1.7 Writing out HTML

Run "pydoc -w <name>" to write out the HTML documentation for a

module to a file named "<name>.html".

2.5.1.8 Using happydoc

A utility named "happydoc" is able to generate documentation
for modules written in Python.

2.5.2 Printable documentation

2.5.2.1 Quick Start Guides

The documents cdms_quick_start.pdf and vcs_quick_start.pdf
provide a quick look at useful commands in the core CDAT modules;
cdms and vcs respectively on a single page that is useful even to the
experienced user.

2.5.2.2 Programming reference guides

The core CDAT modules cdms and vcs are extensively
documented in separate documents that can be downloaded from
http://cdat.sf.net. The most up-to-date versions of the following
guides can be found there.
• cdat.pdf: This document
• cdms.pdf: Climate Data Management System
• vcs.pdf: Visualization and Control System: Python Command Line
and Application Programming Interface
• cdat_utilities.pdf: CDAT Utilities Reference Guide
• numpy.pdf: Numerical Python
• vcs_quick_ref.pdfA one page reference to VCS commands.

30 Getting Started with CDAT

Documentation and Help

2.5.3 Getting Support

The CDAT Home Page is http://cdat.sf.net. CDAT is hosted
at SourceForge, a free service provided by VA Linux, Inc. to the
Open Source Community. SourceForge enables us to provide the
following services for users:
• A release facility, where users can download binary and source
releases and see release notes.
• A bug-tracking facility, where users can submit bugs and track
their status, and receive mail when they are fixed.
• A facility to request feature enhancements.
• A mailing list for discussion ([email protected]).

You can use these facilities without registering at SourceForge, but

registration, which is quick, easy, and free, will enable you to
participate in the fullest possible way. In particular, it is very helpful
to us if you are registered when you submit a bug report.

Getting Started With CDAT 31

Getting Started

32 Getting Started with CDAT

CHAPTER 3 What’s in CDAT

A complete description of all of CDAT’s capabilities is beyond the scope of this

document. In this chapter common operations on climate data are chosed for description.

3.1 File/Data Handling

3.1.1 File I/O

3.1.1.1 Reading/writing data from/to self-describing formats

A variable (defined in more detail in “Reading, creating, and
altering variables” on page 36) can be obtained from a file or
collection of files, or can be generated as the result of a computation.
Files can be in any of the self-describing formats netCDF, HDF,
GrADS/GRIB (GRIB with a GrADS control file) or xml files
generated by CDMS.

For instance, to read the variable u from file sample.nc:

>>> import cdms
>>> f = cdms.open(’sample.nc’)
>>> u = f(’u’)

Getting Started With CDAT 33

What’s in CDAT

Data can be read by index or by world coordinate values. The

following reads the n-th timepoint of u:
>>> u0 = f(’u’,time=slice(n,n+1))

and this reads u at time 366.0:

>>> u1 = f(’u’,time=366.)

If an OPeNDAP (formerly known as DODS) enabled version of

CDAT was installed, datasets on remote OPeNDAP servers can be
accessed:
f = cdms.open(‘http://cdc.noaa.gov/cgi-bin/nph-nc/
Datasets/ncep/air.1990.nc’)

A variable can be written to a file with the write function:

>>> g = cdms.open(’sample2.nc’,’w’)
>>> g.write(u)
<Variable: u, file: sample2.nc, shape: (1, 16, 32)>
>>> g.close()

More details on reading and writing data can be found in Climate

Data Management System (cdms.pdf).

3.1.1.2 Reading/Writing Fortran formatted data. (Scientific.IO)

The Scientific Python package maintained by Konrad Hinsen
contains numerous subpackages useful in scientific applications. The
"IO" subpackage is useful for reading and writing data using Fortran
format statements. The example shown below demonstrates how easy
it is to read Fortran formatted data.
>>> f = open(ascii_filename, 'r')
# Import the module that does the work.
>>> from Scientific.IO import FortranFormat
# Declare the fortran formats used to create the data.
>>> ff1 = FortranFormat.FortranFormat('2i6')
>>> ff2 = FortranFormat.FortranFormat('12i6')
>>> data_line = f.readline()

34 Getting Started with CDAT

File/Data Handling

>>> mon, yr = FortranFormat.FortranLine(data_line, ff1)

# Now define an array to read the data into.
>>> import Numeric
>>> T_array = Numeric.zeros((14,))
# In the next line you are assigning the values.
>>> T_array[start_index: end_index] = \
FortranFormat.FortranLine(f.readline(), ff2)
# Note: You must have previously defined T_array.
#See tutorial examples for more details.

3.1.1.3 Reading data from ASCII text files. (asciidata)

The asciidata module is useful in reading (and writing) data
that is in ASCII format with the ability to specify tab or comma or
space delimited fields. This is particularly useful to deal with
importing (or exporting) spreadsheet data. For example,
>>> import asciidata
>> time, pressure =
asciidata.comma_delimited(’myfile.txt’)

The IO subpackage of Scientific also contains other useful facilities

of this type.

3.1.1.4 Reading/Writing unformatted data (binaryio)

To handle binary or unformatted data, the module binaryio
offers a convenient interface. The following example illustrates the
use of this module. Note that binary files are platform and compiler
dependent.
# To write binary data.
>>> import binaryio
>>> iunit = binaryio.bincreate(’filename’)
>>> binaryio.binwrite(iunit, \
my_array_with_upto_4_dimensions)
>>> binaryio.binclose(iunit)
# To read binary data
>>> iunit = binaryio.binopen(’filename’)
>>> y = binaryio.binread(iunit, n, ...)

Getting Started With CDAT 35

What’s in CDAT

>>> binaryio.binclose(iunit)

3.1.2 Reading, creating, and altering variables

Climate data comes in many different file formats, organized in
many different ways. The cdms package gives you a uniform
interface so that you can write processing algorithms and graphics
that will work with a wide variety of different data formats.

In CDMS, the basic unit of data is the variable. A variable is

essentially a multidimensional array, augmented with a domain and
with metadata. The domain describes the spatial location and
temporal information associated with the array. For example, a
variable on an orthogonal grid may have a domain consisting of (but
not limited to) time, level, latitude, and longitude axes. The metadata
associated with a variable consists of a collection of attribute-value
pairs. The set of attributes of a variable is not predefined, although
some attributes, such as the units and the missing data value, are
commonly used.

A variable may be stored in a single physical file or in a collection of

files, called a dataset. The files themselves may be in any of several
self-describing formats, such as netCDF, HDF, and GraDS/GRIB.
CDMS provides a uniform interface to data, so that the same
processing algorithm or graphics routine will work with any of the
supported data formats.

For computing tasks, variables can be used much like arrays. The
common arithmetic functions are defined for variables, as well as I/O
and slicing operations. One advantage of using CDMS variables for
computation is that the associated domain and metadata information
is carried along with the computation. The benefit of this approach is
that, for example, if we average over time, and then plot the result,
the plotting routines can still be aware that the other dimensions
represent latitude and longitude and draw the continental outlines, do

36 Getting Started with CDAT

File/Data Handling

projections correctly, etc. If the result were merely the averaged data,
that interpretation of it would have been lost. This frequently results
in much simpler scripts than otherwise would be the case.

However, CDAT is also designed for extensibility. The capability to

add external C or Fortran modules is extremely important for
advanced applications. For example, many external modules use the
"array" type defined by the Numerical Python (NumPy) module. To
accomodate the need for interoperability, CDAT provides a hierarchy
of representations for data arrays:
• Numeric Array: a multidimensional array, all elements have the
same datatype (real, integer etc.). This type is supported by the
Numerical Python (NumPy) module.
• Masked Array (MA): A Numeric array with an optional missing
data mask. Operations on these compute the mask of the result.
• Masked Variable (MV): A masked array having a domain and
metadata. Computations carry along the domain and metadata
information where possible. A masked variable in memory is
referred to as transient variable and a masked variable in a dataset
is called a file variable

A schematic of the array hierarchy is shown in Fig. 1.

Getting Started With CDAT 37

What’s in CDAT

FIGURE 1. Relationships between array abstractions.

NumPy Array
Numeric

NumPy Array Mask

MA

NumPy Array Mask MV

Domain
Information

+ + + Metadata

While the above figure represents the general schematic of the

different array constructs, the user should be aware that the individual
constructs also include functions (for e.g. arithmetic functions) that
operate on these arrays. Some of these functions are intended to
convert arrays of one type to the other. These allow the user to
convert the array to the necessary level to suit the algorithm. The
conversion from one level of array abstraction to the other is dealt
with in the following sections.

38 Getting Started with CDAT

File/Data Handling

3.1.2.1 Constructing Numeric arrays

As explained in the Numerical Python manual, a Numeric array can

be constructed in many ways. The basic usage is to apply the array
"constructor" Numeric.array:
>>> import Numeric
>>> x = Numeric.array (s)

where s can be a Python list, tuple, or another Numeric array.

For many applications, space allocation for newly defined variables

needs to be controlled so as not to run out of memory. CDAT allows
for some control over this. For example, ff you do not require a
separate copy of the data, copy=0 can be added.
>>> x = Numeric.array(s, copy=0)

If you want to control the type of the data, you can supply a typecode,
usually in the form of one of the abstract constants supplied in
Numeric for this purpose. For example,
>>> y = Numeric.array([1,2,3], Numeric.Float)

would create y as an array containing the floating-point numbers 1.,

2., and 3. By the way, a very frequent beginner error is to say
something like:
>>> y = Numeric.array(1,2,3) # Error !

which is an error that will result in a very strange message:

>>> import Numeric
>>> y = Numeric.array(1,2,3)
Traceback (most recent call last):
File "<pyshell#1>", line 1, in ?
y = Numeric.array(1,2,3)
TypeError: typecode argument must be a string.
>>>

Getting Started With CDAT 39

What’s in CDAT

What has happened is that the second argument to Numeric.array was

the number 2, and Numeric is expecting one of its typecode letters
such as ’d’ in that position.

3.1.2.2 Numeric to MA

Given a Numeric array x, if we wish to construct a masked array, it

will be one of these cases:
1. We want to treat x as a masked array xm, but none of its values are cur-
rently missing, and wish to share x’s data space, so that a modification to
xm is also a modification to x. Solution:
>>> import MA
>>> xm = MA.masked_array (x)
2. We want to treat x as a masked array xm with no values considered miss-
ing and without sharing x’s space. Solution:
>>> xm = MA.array (x)
3. We want to treat x as a masked array xm with a certain value v treated as
a missing value. Solution:
>>> xm = MA.masked_value (x, v).
See the MA manual for other arguments, such as controlling the
precision with which a value in x must be equal to v in order to be
considered missing.
4. We want to treat x as a masked array xm but with those values consid-
ered missing that correspond to non-zero values in an array m of zeros
and ones. Solution:
>>> xm = MA.array(x, mask=m).
Again, see the manual for more options on this.
5. The array x is of a numeric type and we want to mask all those values
greater than a certain value v. Solution:
>>> xm = MA.masked_greater (x, v).
Similarly, there are functions masked_greater_equal, masked_less,
masked_less_equal, masked_equal and masked_where.

40 Getting Started with CDAT

File/Data Handling

3.1.2.3 Numeric or MA to Transient Variable (MV)

The array constructor cdms.MV.array is similar to the MA.array

constructor but allows additional arguments specifying the metadata.
For full usage, see Climate Data Management Systam (cdms.pdf).
The options discussed in the previous section will produce transient
variables as long as you use the functions in cdms.MV instead of
those in MA.

The most frequent additional argument to MV.array is to specify a list

of axes using the axes=alist argument. Often these axes have been
extracted from another variable using getAxis or getAxisList, or
created from data.

For example, if you were going to operate on variable v using some

process that returns a Numeric array, and in the process remove its
time dimension, you might do something like this:
>>> import cdms, MV
>>> f = cdms.open('../data_directory/clt.nc')
>>> v = f('clt')
>>> alist = v.getAxisList(omit='time')
>>> u = v(time=(’1979-1-1’, ’1979-1-1’), squeeze=1)
>>> x = MV.array(u, axes=alist)

Now, x is again a transient variable and it has the geographic

information reattached so that plots will show the continents. Note
that it is usually not necessary to do this. Any ordinary arithmetic,
and any use of the functions in MV, will return transient variables
with appropriate axes.

As mentioned above, transient variables can have associated

attributes which are accessed and set using the Python dot notation:
>>> u.units=’m/s’
>>> print u.units
m/s

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What’s in CDAT

Attribute values can be strings, scalars, or 1-D Numeric arrays. More

details on variables and the available functions and methods can be
found in Climate Data Management System (cdms.pdf).

3.1.2.4 MA or Transient Variable to Numeric

Many packages that support Numerical Python arrays have
been developed. You can find links to some of them on the CDAT
website. These packages work with Numerical Python arrays. For
these and other applications (such as modules that are written in
Fortran that expect data as Numeric arrays), it is necessary to convert
existing arrays that are Transient Variables or Masked Arrays to
Numeric arrays. This is easily accomplished using the filled method.
For example:
>>> import cdms, MV
>>> f = cdms.open('../data_directory/clt.nc')
>>> v = f('clt')
# If we want the Numeric array to have 1.e+20
# where the value is missing.
>>> v_array = MV.filled(v, 1.e+20)

Figure 2 summarizes the functions we have just seen.

42 Getting Started with CDAT

File/Data Handling

FIGURE 2. Array functions.

Transient
Variable
(MV)
MV.array MV.array
MV Functions

Masked
Array
(MA)
MA.array MA Functions

MA.filled MV.filled
Numeric
Array

Numeric Functions

3.1.3 Handling Time

The cdtime module implements the cdms time types, methods,
and calendars. These are made available with the command
>>> import cdtime

Two time types are available: relative time and component time.
Relative time is time relative to a fixed base time. It consists of:
• a units string, of the form "units since basetime", and
• a floating-point value

For example, the time "28.0 days since 1996-1-1" has value=28.0,
and units="days since 1996-1-1" Component time consists of the

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What’s in CDAT

integer fields year, month, day, hour, minute, and the floating-point
field second. A sample component time is 1996-2-28 12:10:30.0

The cdtime module contains functions for converting between these

forms, based on the common calendars used in climate simulation.

Basic arithmetic and comparison operators are also available. Some

examples are shown below.
# Example: Creating component and relative times.
>>> import cdtime
>>> c = cdtime.comptime(1996,2,28)
>>> r = cdtime.reltime(28,"days since 1996-1-1")
# Example: Adding and subtracting times.
>>> print r.add(1,Days)
29.00 days since 1996-1-1
>>> print c.add(36,Hour)
1996-2-29 12:0:0.0
>>> print r.sub(10,Days)
18.00 days since 1996-1-1
>>> print c.sub(30,Days)
1996-1-29 0:0:0.0
# Example: Comparing times.
>>> r = cdtime.reltime(28,"days since 1996-1-1")
>>> c = cdtime.comptime(1996,2,28)
>>> print r.cmp(c)
-1
>>> print c.cmp(r)
1
>>> print r.cmp(r)
0
# Example: Extracting year/month/day information
>>> print c.year
1996
>>> print c.month
2
# Example: Converting between time types.
>>> r.tocomp()
1996-1-29 0:0:0.0
>>> print c.torel("days since 1996-1-1")

44 Getting Started with CDAT

File/Data Handling

58.00 days since 1996-1-1

>>> print r.torel("days since 1995")
393.00 days since 1995
>>> print r.torel("days since 1995").value
393.0

More details of the cdtime module can be found in Climate Data

Management System (cdms.pdf).

3.1.4 Axes and Domains

The spatial and temporal information associated with a variable
is represented by the variable domain, an ordered tuple of axes and/or
grids. In the above example, the domain of the variable u is the tuple
(time, latitude, longitude). This indicates the order of the dimensions,
with the slowest-varying dimension listed first (time). Each element
of the tuple is an axis. An axis is like a 1-D variable, in that it can be
sliced, and has attributes. A number of functions are available to
access axis information. For example, to see the list of time values
associated with u:
>>> t = u.getTime()
>>> print t[:]
[ 0., 366., 731.,]
# Similar methods of extracting the latitude, longitude
# and level axes or the lat-lon Grid are available
>>> myGrid = u.getGrid()
>>> lat_axis = u.getLatitude()
# Individual axes can also be accessed by their index
>>> first_axis = u.getAxis(0)

Similarly, creating axes and domains are easily accomplished using

the constructor functions. Some of the basic constructors and
methods are illustrated in the tutorials. More details of dealing with
axes and domains can be found in Climate Data Management System
(cdms.pdf).

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What’s in CDAT

3.1.5 Data Selection.

As seen previously, the cdms module is used to open files and
extract data. Currently, cdms only handles data on regular
(rectangular) grids. In the near future cdms will be able to handle data
on irregular grids with all the same functionality. The cdms module
also allows for easy selection of subsets of the data stored in files or
in memory. The use of keywords to describe specific axes,
"Selectors" to describe specific portions of interest, and control over
the precision of extracted areas are some of the features that make
this a powerful package. A few simple examples are shown here.
>>> import cdms
>>> f = cdms.open(’file_name’)
# To extract data for specified times
>>> ta_1996_only =f('ta',time=('1996-1-1','1996-12-1'))
# To extract data for specified latitude and
# longitude areas
>>> x =f('t', latitude=(-5.,5.), longitude=(210., 270.))
# To extract data at a single level (or any other
dimension)
>>> x = f(‘t’, level=(250.,250.))
# The above will extract data at the prescribed level
# if that level is present in the data. It will also
# result in the level dimension being retained as a
# singleton dimension. To eliminate singleton dimensions
# set the ‘squeeze’ option.
>>> x = f(‘t’, level=(250.,250.), squeeze=1)
#
# Using cdutil to specify regions precisely.
>>> import cdutil
>>> NINO3 = cdutil.region.domain( \
latitude=(-5.,5.), longitude=(210., 270.))
>>> nino3_area_exact = f('t', NINO3)
# In the above case, the precise region is returned with
# the weights and grid cell bounds set to match the
# request.

Some commonly used domains have been pre-defined for

convenience. They are:

46 Getting Started with CDAT

File/Data Handling

NH | NorthernHemisphere

SH | SouthernHemisphere

Tropics : latitude extends from -23.4 to 23.4

NPZ | AZ | ArcticZone : latitude extends from 66.6N to 90.0N

SPZ | AAZ | AntarcticZone : latitude extends from 90.0S to 66.6S

Example:
>>> from cdutil import region
>>> t_northern_hemisphere_only = f(’t’, region.NH)

The tutorial examples illustrate these features in more detail. For

details of the available commands and their usage refer to Climate
Data Management System (cdms.pdf).

3.1.6 Regridding Data

CDMS has functions to interpolate gridded data:
• from one horizontal (lat/lon) grid to another
• from one set of pressure levels to another
• from one vertical (lat/level) cross-section to another vertical cross-
section.

The simplest method to regrid a variable from one horizontal, lat/lon

grid to another is to use the regrid function defined for variables.
This function takes the target grid as an argument, and returns the
variable regridded to the target grid:
>>> import cdms
>>> f = cdms.open(’../data_directory/ccc/perturb.xml’)
# Read the data and check the shape of the data
>>> rlsf = f(’rls’)
>>> rlsf.shape

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What’s in CDAT

(4, 48, 96)

# Now choose a file that contains data in the
# desired output (target) grid.
>>> g = cdms.open(’../data_directory/mri/perturb.xml’)
# Get the file variable. The data is not actually read
# in when we use square bracket pairs like so:
>>> rlsg = g[’rls’]
# Get the target grid
>>> outgrid = rlsg.getGrid()
# Apply the regrid method to get the desired result.
>>> rlsnew = rlsf.regrid(outgrid)
>>> rlsnew.shape
(4, 46, 72)
>>> outgrid.shape
(46, 72)
A somewhat more efficient method is to create a regridder
function. This has the advantage that the mapping is created only
once and can be used for multiple arrays.The steps in this process
are:
• Given an input grid and output grid, generate a regridder function.
• Call the regridder function on an array, resulting in an array
defined on the output grid. The regridder function can be called
with any array or variable defined on the input grid.

The following example illustrates this process.

>>> import cdms
>>> from regrid import Regridder
>>> f = cdms.open(’../data_directory/ccc/perturb.xml’)
>>> rlsf = f[’rls’]
>>> ingrid = rlsf.getGrid()
>>> g = cdms.open(’../data_directory/mri/perturb.xml’)
>>> outgrid = g[’rls’].getGrid()
>>> regridfunc = Regridder(ingrid, outgrid)
>>> rlsnew = regridfunc(rlsf)
>>> f.close()
>>> g.close()

48 Getting Started with CDAT

File/Data Handling

For more details on regridding functions and methods please refer to

Climate Data Management System (cdms.pdf).

3.1.7 Working with masks

Masks were introduced earlier in “Reading, creating, and
altering variables” on page 36. They are a convenient way to deal
with data that either has missing values or where one would have to
deal with masking out regions. The masks can be handled seperately
from the data to keep the computational expense down and one can
also use the logical and/or operators to perform complex tasks easily.
A small example is shown below. More details of how to use masks
are in the Numeric manual and examples of masks and masking
operations in action can be found in the geting started tutorials listed
in Chapter 2.
# Let us open a data file that contains surface type
# (land fraction) data and extract data
>>> import cdms, MV
>>> f_surface = cdms.open('sftlf_ta.nc')
>>> surf = f_surface('sftlf')
# Designate land where "surf" has values
# not equal to 100
>>> land_only = MV.masked_not_equal(surf, 100.)
>>> land_mask = MV.getmask(land_only)
# Now extract a variable from another file
>>> f = cdms.open('ta_1994-1998.nc')
>>> ta = f('ta')
# Apply this mask to retain only land values.
>>> ta_land = cdms.createVariable(ta, mask=land_mask,
copy=0, id='ta_land')

3.1.8 Databases

A Database is a collection of datasets and other CDMS objects. It

consists of a hierarchical collection of objects, with the database
being at the root, or top of the hierarchy. A database is used to:

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What’s in CDAT

• search for metadata

• access data
• provide authentication and access control for data and metadata

Details of creating, altering, and searching through databases are

beyond the scope of this beginners document. The interested reader
should refer to Climate Data Management System (cdms.pdf).

3.2 Averaging and Statistics

3.2.1 Area averaging

Area averaging is one of the most common data reduction
procedures used in climate data analysis. The cdutil package has a
powerful area averaging function. The averager() function provides a
convenient way of averaging your data giving you control over the
order of operations (i.e which dimensions are averaged over first) and
also the weighting for the different axes. You can pass your own array
of weights for each dimension or use the default (grid) weights or
specify equal weighting.

Examples:
>>> import cdms, cdutil
>>> f = cdms.open(’data_file_name’)
>>> result = cdutil.averager(f(’var_name’), axis=’1’)
# extracts the variable ’var_name’ from f
# and averages over the dimension whose position is 1.
# Since no other options are specified,
# defaults kick in i.e weights=’generate’ (same as
# weights=’weighted’) and returned=0
# Some ways of using the averager are shown below.
#
# A quick zonal mean calculation would be:
>>> V_zonal_ave = cdutil.averager(V, axis=’x’)
# In the above case, default weights option of

50 Getting Started with CDAT

Averaging and Statistics

# ’generate’ (or ’weighted’) is implemented

#
# If you want to average first over the x (longitude)
# dimension with area weighting and then over
# y (latitude) with equal weighting, then you would:
>>> Vavg = cdutil.averager(V, axis=’xy’, \
weight=[’generate’,’equal’])
# Similarly for equally weighted time averaging:
>>> cdutil.averager(V, axis=’t’, weight=’equal’)
#
>>> cdutil.averager(V, axis=’x’, weight=mywts)
# where mywts is an array of shape (len(xaxis))
# or shape(V)
#
>>> cdutil.averager(V, axis=’(lon)y’, weight=[myxwts,
myywts])
# where myxwts is of shape len(xaxis) and
# myywts is of shape len(yaxis)
#
>>> cdutil.averager(V, axis=’xy’, weight=V_wts)
# where V_wts is a Masked Variable of shape V
# or
>>> cdutil.averager(V, axis=’x’, weight=’equal’,
action=’sum’)
# will return the equally weighted sum
# over the x dimension or
>>> ywt = cdutil.area_weights(y)
>>> fractional_area= cdutil.averager(ywt, axis=’xy’,\
weight=[’equal’,’equal’],\
action=’sum’)
# is a good way to compute the area fraction that the
# data y that is non-missing

Note: When averaging data with missing values, extra care needs to
be taken. It is recommended that you use the default
weight='generate' option. This uses cdutil.area_weights(V) to get
the correct weights to pass to the averager.

>>> cdutil.averager(V, axis=’xy’, weight=’generate’)

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What’s in CDAT

# The above is equivalent to:

>>> V_wts = cdutil.area_weights(V)
>>> result = cdutil.averager(V, axis=’xy’, weight=V_wts)
#
>>> result = cdutil.averager(V, axis=’xy’,
weight=cdutil.area_weights(V))

However, the area_weights function requires that the axis bounds are
stored or can be calculated. In the case that such weights are not
stored with the axis specifications (or the user desires to specify
weights from another source), the use of combinewts option can
produce the same results. In short, the following two are equivalent:
>>> xavg_1 = averager(X, axis = 'xy', weights =
area_weights(X))
>>> xavg_2 = averager(X, axis = 'xy', weights =
['weighted', 'weighted', 'weighted'],
combinewts=1)

Where X is a function of latitude, longitude and a third dimension

such as time or level. In general, where the 'weighted' keyword
appears above, it can be substituted with arrays of weights .

The following example will help you see the averager() function in
context

>>> import cdms, cdutil

>>> f = cdms.open(’file_name’)
# Using cdutil.domain to specify the NINO3 region
>>> NINO3 = cdutil.domain(latitude=(-5.,5.),\
longitude=(210.,270.)))
# Extract the variable over the specified domain
>>> nino3_area_exact = f(’t’, NINO3)
# Average first over the longitude axis
# (denoted by ’x’) and then the latitude axis
# (denoted by ’y’)
>>> nino3_avg = cdutil.averager(nino3_area_exact,
axis=’xy’)

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Averaging and Statistics

Axis options can also be specified by name such as axis = ’(depth)’ or

by index such as axis = ’20’ (note the numbers are enclosed in
quotes). By default, the appropriate area weights are generated from
the grid information and the result of the averaging is the area
weighted value. More control over the weights used is available. It is
possible to specify the weights used to average over the longitude and
latitude axes seperately.
>>> nino3avg2 = cdutil.averager(nino3_area_exact,
axis=’yx’,weights=[’generate’,’equal’])

In the above example, we averaged over the latitude axis first (using
generated weights) and then over the longitude axis (using equal
weights). The weights can be "equal" or "generate"(generates the
weights for the grid information contained in the variable) or any
array of numbers the user wishes to apply.

3.2.2 Generating weights

For most averaging applications, the weights used are critical
especially when there are missing data. The cdutil package provides
a way of generating the weights using grid information that is tied to
the variable. The averager function uses this to generate the weights
when the default averaging weights option kicks in. This function is
easily called for some variable ’x’ in memory:
>>> gen_weights = cdutil.area_weights(x)

The resultant gen_weights is in the same shape as the variable x and

has the appropriate area weights set to missing values where data was
missing in x.

3.2.3 Time averaging

Averaging over time is a special problem in climate data
analysis. The cdutil package pays special attention to this issue to

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What’s in CDAT

make the extraction of time averages and climatologies simple. Apart

from functions that enable easy computation of annual, seasonal and
monthly averages and climatologies, one can also define seasons
other than those already available and specify criteria for data
availability and temporal distribution to suit individual needs.

Note: It is essential that the data have an appropriate axis designated

as the "time" axis. In addition to this, the results depend on the time
axis having correctly set "bounds". If "bounds" are not stored with
the data in files, default "bounds" are generated by the data
extraction steps in cdms. However, they are not always correct. The
user must take care to verify that the bounds are set correctly.

The predefined time averaging periods are:

• JAN, FEB, MAR, ...., DEC (months)
• DJF, MAM, JJA, SON (seasons)
• YEAR (annual means)
• ANNUALCYCLE (monthly means for each month of the year)
• SEASONNALCYCLE (means for the 4 predefined seasons)

Some simple examples of time averaging operations are shown here.

>>> import cdutil
# To compute the DJF (december-January-February)
# climatology of a variable x
>>> djfclim = cdutil.DJF.climatology(x)
# The individual DJF seasons are extracted using
>>> djfs = cdutil.DJF(x)
# To extract DJF seasonal anomalies (from climatology)
>>> djf_anom = cdutil.DJF.departures(x)
# The monthly anomalies for x are computed by:
>>> x_anom = cdutil.ANNUALCYCLE.departures(x)

3.2.3.1 Creating Custom Seasons

You can even create your own "custom seasons" beyond the
pre-defined seasons listed above. For example:

54 Getting Started with CDAT

Averaging and Statistics

>>> JJAS = cdutil.times.Seasons(’JJAS’)

3.2.3.2 Specifying time periods for climatologies

So far we have seen the way to compute the means,
climatologies, and anomalies for the entire length of the time-series.
The typical application may require specified time intervals over
which climatologies are computed and used in calculating departures.
For example, to compute the DJF climatology for the time period
1979-1988 we would do the following:
>>> import cdtime
>>> start_time = cdtime.comptime(1979)
>>> print 'start_time = ', start_time
>>> end_time = cdtime.comptime(1989)
>>> print 'end_time = ', end_time

Note that we created the time point 'end_time' at the begining of 89 so

we can select all the time between 'start_time' and 'end_time' but not
including 'end_time' by specifying the option 'co' - shorthand for
'c'losed at start_time and 'o'pen at end_time. For more details on
different options available, refer to Climate Data Management
System (cdms.pdf).
>>> djfclim = cdutil.DJF.climatology(x(time= \
(start_time, end_time, 'co')))

Now that we have our climatology over the desired period we can to
compute anomalies over the full period relative to that climatology.
>>> djfdep2 = cdutil.DJF.departures(s, ref=djfclim)

3.2.3.3 Specifying Data Coverage Criteria

The real power of these functions is in the ability to specify
minimum data coverage and to also be able to specify the distribution
(both in the temporal sense) which are required for the averages to be
computed. The default behaviour of the functions that compute

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What’s in CDAT

seasonal averages, climatologies etc. is to require that a minimum of

50% of the data be present. Now let's say you like to extract DJF but
without restricting it to 50% of the data being present. You would do:
>>> djfs = cdutil.DJF(avg, criteriaarg=[0., None])

The above statement comutes the DJF average with "criteriaarg"

(passed as a list) which has 2 arguments.
• The first argument represents the minimum fraction of time that is
required to compute the seasonal mean. So you can pass a
fractional value between 0.0 and 1.0 (including both extremes) or
even a representation such as 3.0/4.0 (in case you need at least 3
out of 4 months of data in the case of the average JJAS we defined
previously).
• The second argument in the criteriaarg is "None". This implies no
"centroid function" is used. In other cases this argument represents
the maximum value of the "centroid function".A value between 0
and 1 represents the spread of values across the mean time. The
centroid value of 0.0 represents a full even distribution of data
across the time interval. For example, if you are considering the
DJF average, then if data is available for Dec, Jan and Feb months
then the centroid is 0.0. On the other hand, the following criteria
will "mask"(i.e ignore) a DJF season if there is only a december
month with data (and therefore has a centroid value of 1.0).
Therefore any seasons resulting in centroid values above 0.5 will
result in missing values!
>>> djfs = cdutil.DJF(avg, criteriaarg = [0., .5])

In the case of computing an annual mean, having data only in Jan and
Dec months leads to a centroid value of 0 for the regular centroid, and
the resulting annual mean for the year is biased toward the winter. In
this situation, you should use a cyclical centroid where the circular
nature of the year is recognised and the centroid is calculated
accordingly. Here are some examples of typical usage:

56 Getting Started with CDAT

Averaging and Statistics

1) Default behaviour is criteriaarg=[0.5, None]

>>> annavg_1 = cdutil.YEAR(s_glavg)

2) Criteria to say compute annual average for any number of months.

>>> annavg_2 = cdutil.YEAR(s_glavg, criteriaarg =
[0.,None])

3) Criteria for computing annual average based on the minimum

number of months (8 out of 12).
>>> annavg_3 = cdutil.YEAR(s_glavg, \
criteriaarg = [8./12., None])

4) Same criteria as in 3, but we account for the fact that a year is

cyclical i.e Dec and Jan are adjacent months. So the centroid is
computed over a circle where Dec and Jan are contiguous.
>>> annavg_4 = cdutil.YEAR(s_glavg, \
criteriaarg = [8./12., 0.1, 'cyclical'])

So far we have the annual means calculated using various criteria.

Now if we wish to compute the climatological annual mean, we can
average the individual annual means. However, we can apply more
criteria to the calculation of that annual mean climatology. Here we
simply require 60% of the years to be present, and a criteria on the
temporal distribution (i.e the centroid = 0.7) to make sure all of the
annual means are not clustered at the end of the record.
>>> annavg_clim = cdutil.YEAR.average(annavg_4,\
criteriaarg =[.6,.7])

The tutorial file times_tutorial.py has detailed examples of time

averaging in action. Further documentation is available in the CDAT
Utilities Reference Manual cdat_utilities.pdf.

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What’s in CDAT

3.2.4 Useful statistical functions

Commonly used statistical functions such as corrrelation,
covariance, autocorrelation, autocovariance, laggedcorrelation,
laggedcovariance, rms, variance, standard deviation, mean absolute
difference, geometric mean, and linearregression have been
implemented to allow easy computation of statistics. The statistics
functions are implemented as part of the genutil package. These
functions are implemented so as to not require the full variable
information in MV. That is, these functions accept Numeric arrays.
However, they also accept MV’s so that the user can specify axes
over which statistics are computed (to allow for spatial or temporal
statistics etc.). The tutorial file statistics_tutorial.py shows some of
the statistics functions in action.

Example 1

Let us try an example where we want to look at a variable ’tas’ from

the NCEP reanalysis and compute some spatial statistics between
data slices for time periods from 1960-1970 and 1980-1990.
>>> import cdms
>>> from genutil import statistics
>>> f = cdms.open('tas.rnl_ncep.nc')
>>> ncep1 = f('tas',time=(’1960-1-1’, ’1970-1-1’, 'co'))
>>> ncep2 = f('tas',time=(’1980-1-1’, ’1990-1-1’, 'co'))
# We have the two time periods extracted.
# Now let us compute the correlation.
>>> cor = statistics.correlation(ncep1, ncep2,\
axis=’xy’)
# We could compute the spatial correlation weighted by
# area. To accomplish this we can use the ’generate’
# option for weights.
>>> wcor = statistics.correlation(ncep1, ncep2,\
weights=’generate’, axis='xy')

Example 2

58 Getting Started with CDAT

Averaging and Statistics

To compute the mean absolute difference between ncep1 and ncep2

defined in Example 1.
>>> absd = statistics.meanabsdiff(ncep1, \
ncep2,axis='xy')

Example 3

To compute the temporal rms difference between the two time

periods
>>> rms = statistics.rms(ncep1, ncep2, axis='t')

Example 4

In this example, we examine the default behaviour of the

linearregression function.
>>> Values = statistics.linearregression(y)

The returned "Values" is actually a tuple consisting of the slope and

itercept. They can also be accessed as follows:
>>> slope, intercept = statistics.linearregression(y)

If error estimates are also required, then:

>>> Values, Errors = linearregression(y, error=1)

where "Values" and "Errors" are tuples containing answer for slope
AND intercept. You can break them as follows. slope, intercept =
Value and slope_error, intercept_error = Errors. i.e.
>>> (slope, intercept), (slope_error, intercept_error) =
\ linearregression(y, error=1)

WARNING: The following will not work.

>>> slope, intercept, slo_error, int_error =
linearregression(y, error=1)

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To get the standard error non adjusted result for slope only, do the
following:
>>> slope, slope_error = linearregression(y, error=1,
nointercept=1)

In the line below all the returned values are tuples.

>>> Values,Errors,Pt1,Pt2,Pf1,Pf2 = \
linearregression(y, error=2,probability=1)

That means in the above statement is returning tuples ordered so:

(slope, intercept), (slo_error, int_error), (pt1_slo, pt1_int), (pt2_slo,
pt2_int), (pf1_slo, pf1_int), (pf2_slo, pf2_int).

If we want results returned for the intercept only, do the following:

>>> intercept,intercept_error,pt1,pt2,pf1,pf2=\
linearregression(y,error=2,probability=1,noslope=1)

3.3 Data Visualization

Data visualization is a very important aspect of analysing
climate data. Visualization as a part of analysis and creating
presentation quality graphics are accomplished in CDAT by using the
point and click GUI in VCDAT, from the CDAT command line, or in
a program. The primary tool inside CDAT to visualize the data is the
Visualization and Control System (VCS). Additionally, because of
the ease of controlling other applications using Python as a link
language, an interface to Grace (an open source application) is also
available to users.

3.3.1 Visualization and Control System (VCS)

VCS is expressly designed to meet the needs of climate
scientists. Because of the breadth of its capabilities, VCS can be a

60 Getting Started with CDAT

Data Visualization

useful tool for other scientific applications as well. VCS allows wide-
ranging changes to be made to the data display, provides for
presentation hardcopy output, and includes a means for recovery of a
previous display.

In the VCS model, the data display is defined by a trio of named

object sets, designated the" primary objects" (or "primary elements").
These include:
• the data, which define what is to be displayed and is ingested via
other CDAT software components;
• the graphics method, which specifies the display technique; and
• the picture template, which determines the appearance of each
segment of the display.

Tables for manipulating these primary objects are stored in VCS for
later recall and possible use. In addition, detailed specification of the
primary objects' attributes is provided by eight "secondary objects"
(or "secondary elements"):
1. colormap: specification of combinations of 256 available colors
2. fillarea: style, style index, and color index
3. format: specifications for converting numbers to display strings
4. line: line type, width and color index
5. list: a sequence of pairs of numerical and character values
6. marker: marker type, size, and color index
7. texttable: text font type, character spacing, expansion and color index
8. textorientation: character height, angle, path, and horizontal/vertical
alignment

By combining primary and secondary objects in various ways (either

at the command line or in a program), the VCS user can
comprehensively diagnose and inter-compare climate model
simulations. VCS provides capabilities to:

Getting Started With CDAT 61

What’s in CDAT

• Create and modify existing template attributes and graphics

methods
• Save the state-of-the-system as a script to be run interactively or in
a program
• Save a display as a Computer Graphics Metafile (CGM), GIF,
Postscript, Sun Raster, or Encapsulated Postscript file
• Create and modify colormaps
• zoom into a specified portion of a display
• Change the orientation (portrait vs. landscape) or size (partial vs.
full-screen) of a display
• Animate a single data variable or more than one data variable
simultaneously
• Display different map projections

3.3.2 Displaying data

VCS can handle the CDMS data objects (such as Transient
Variables seen earlier in addition to Numeric arrays, MA arrays,
python lists and tuples). Plotting data is simply accomplished by
importing the vcs module and issuing the plot command. For
example
>>> import cdms, vcs
>>> f =cdms.open(’example.nc’)
>>> my_data = f(’clt’)
>>> v = vcs.init()
>>> v.plot(my_data)

The plot will display the data "my_data" using default settings.
However, the user can control every aspect of the plot’s appearance
individually. The first of those is the "Graphics Method" described in
the next section.

3.3.2.1 Graphics Methods

A graphics method simply defines how data is to be displayed
on the screen. Currently, there are eleven different graphics methods

62 Getting Started with CDAT

Data Visualization

with more on the way. Each graphics method has its own unique set
of attributes (or members) and functions. They also have a set of core
attributes that are common in all graphics methods. The descriptions
of the current set of graphics methods are as follows:
• boxfill - The boxfill graphics method draws color grid cells to
represent the data on the VCS Canvas.
• isofill - The isofill graphics method fills the area between selected
isolevels (levels of constant value) of a two-dimensional array
with a user-specified color.
• isoline - The isoline graphics method draws lines of constant value
at specified levels in order to graphically represent a two-
dimensional array. It also labels the values of these isolines on the
VCS Canvas.
• outfill - The outfill graphics method fills a set of integer values in
any data array. Its primary purpose is to display continents by
filling their area as defined by a surface type array that indicates
land, ocean, and sea-ice points.
• outline - The Outline graphics method outlines a set of integer
values in any data array. Its primary purpose is to display
continental outlines as defined by a surface type array that
indicates land, ocean, and sea-ice points.
• scatter - The scatter graphics method displays a scatter plot of two
4-dimensional data arrays, e.g. A(x,y,z,t) and B(x,y,z,t).
• vector - The Vector graphics method displays a vector plot of a 2D
vector field. Vectors are located at the coordinate locations and
point in the direction of the data vector field. Vector magnitudes
are the product of data vector field lengths and a scaling factor.
• xvsy - The XvsY graphics method displays a line plot from two
1D data arrays, that is X(t) and Y(t), where ’t’ represents the 1D
coordinate values.
• xyvsy - The Xyvsy graphics method displays a line plot from a 1D
data array, i.e. a plot of X(y) where ’y’ represents the 1D
coordinate values.

Getting Started With CDAT 63

What’s in CDAT

• yxvsx - The Yxvsx graphics method displays a line plot from a 1D

data array, i.e. a plot of Y(x) where ’x’ represents the 1D
coordinate values.

Say for example you would like to plot the data object "my_object"
using the "isofill" graphics method (instead of the default "boxfill"
method), you would type:
>>> v.isofill(my_data)

The user can control any aspect of the isofill method to get the precise
appearance on the plot. To alter the isofill methods for use in your
plot it will be necessary to "create" an isofill object. The create
functions allow the user to create VCS objects which can be modified
directly to produce the desired results. Since the VCS "default"
objects allow for modifications, it is best to either create a new VCS
object or get an existing one. When a VCS object is created, it is
stored in an internal table for later use and/or recall.
>>> my_new_isofill = v.createisofill(’newisofillname’)

To show the list of existing isofill graphics methods type:

>>> v.show(’isofill’)

If there is an existing isofill method you have created and would like
to use it (or alter it), then type:
>>> my_old_isofill =
v.getisofill(’existing_isofillobjectname’)

or use this "existing_isofillname" as a base to create the new one:

>>> new_isofill2 = v.createisofill(’newisofillname’,\
’existing_isofillobjectname’)

The list of attributes can be viewed with the following command:

>>> my_old_isofill.list()

64 Getting Started with CDAT

Data Visualization

You can explicitly set each of the attributes. For example, to change
the levels to be used in plotting:
>>> my_old_isofill.levels = [2., 3., 4., 6]

The graphics method can also be used as an optional argument to the

plot command so that VCS now allows you to issue the command:
>>> v.plot(my_data, my_old_isofill)
# You can also pass the name of the graphics
# method object or the object itself as shown below
>>> v.plot(my_data, "isofill", "isofill_name")

To enable the user to check whether an object is of a certain graphics

method (or any VCS object), there are a whole set of query functions
made available. Therefore you can check if my_old_isofill is an
isofill object and get a yes/no (1|0) answer by saying:
>>> my_old_isofill.isisofill()

For help with queries type (at the shell prompt):

% pydoc vcs.queries

For more information you can type:

>>> vcs.help(’plot’)

or
>>> print v.plot.__doc__

Extensive documentation can be found in Visualization and Control

System: Command Line and Application Programming Interface
(vcs.pdf).

Getting Started With CDAT 65

What’s in CDAT

3.3.2.2 Graphics Primitives

Graphics primitives are useful in enhancing plots and in creating

additional ways of displaying data beyond the existing graphics
methods. These primitive objects are created and altered using the
same syntax as in the case of graphics methods. The following
primitive objects are available:
• fillareaobject - The fillarea objects allows the user to edit fillarea
attributes, including fillarea interior style, style index, and color
index. The fill area attributes are used to display regions defined
by closed polygons, which can be filled with a uniform color, a
pattern, or a hatch style. Attributes specify the style, color,
position, and dimensions of the fill area.
• lineobject – The line object allows the editing of line type, width,
and color index. The line attributes specify the type, width, and
color of the line to be drawn for a graphical display.
• markerobject – The marker object allows the editing of the marker
type, width, and color index. The marker attribute specifies
graphical symbols, symbol sizes, and colors used in appropriate
graphics methods.
• textobject - Graphical displays often contain textual inscriptions,
which provide further information. The text-table object attributes
allow the generation of character strings on the VCS Canvas by
defining the character font, precision, expansion, spacing, and
color. The text-orientation object attributes allow the appearance
of text character strings to be changed by defining the character
height, up-angle, path, and horizon tal and vertical alignment. The
text-combined object is a combination of both text-table and text-
orientation objects.

3.3.2.3 Templates
A picture template determines the location of each picture
segment, the space to be allocated to it, and related properties

66 Getting Started with CDAT

Data Visualization

relevant to its display. The description of the picture template is as

follows:
• template - Picture Template attributes describe where and how
segments of a picture will be displayed. The segments are
graphical representations of: textual identification of the data
formatted values of single-valued dimensions and mean,
maximum, and minimum data values axes, tick marks, labels,
boxes, lines, and a legend that is graphics-method specific to the
data. Picture templates describe where to display all segments
including the data.

Templates also can be created and altered just like the graphics
methods seen in the previous section. The syntax is retained the same
for all objects in VCS so as to avoid confusion. The general
philosophy behind templates is - "You should be able to specify the
behaviour of every picture segment - text, data, line, etc. precisely
according to your needs."

By setting the "priority" attribute of each picture segment you can

control the order in which segments are drawn and whether they are
drawn at all. The higher the priority number (integer value), the later
it is drawn during plot creation ensuring that it is on top. Setting
priority = 0 means you do not want it drawn!

The following segments of a template can be controlled and the

values that can be set are.
• data : The location where the data is plotted (x1, x2, y1, y2) and
its priority can be specified.
• title : The location(x, y), priority and the text objects (font type,
size, angle, justification, etc. etc.) (More on text objects later).
The title plotted is the title of your data read in. If you are plotting
the variable "tdata", tdata.title is shown in the location specified
for title. You can alter the title by doing:
>>> tdata.title = 'My new title!!’

Getting Started With CDAT 67

What’s in CDAT

• units : The data units. For example: "Degrees C" You can set the
x,y location, priority and text object (more later on text objects).
• dataname : The name of the variable.
• source : The data source description.
• function : If computed data, the user can give the algebraic
equation.
• file : The location of the file.
• crdate : The date of creation of plot. You can control x,y location,
priority, and text object.
• crtime : The time of creation of plot. You can control x,y location,
priority, and text object.
• mean, max, min : The values are computed automatically from
the data you are plotting and you can set the x,y location, text
object, priority and display format.
• legend : You can set the legend bar location and dimensions (x1,
x2, y1, y2), the line type object, text object and of course priority.
• comment1, comment2, comment3, comment4 : Four text
comments can be drawn. For each of these you can set priority,
location(x, y), and text object.You would have to set the comment
on the data. Say you are plotting "tdata" using the x.plot(tdata)
command, then you need to have done:
>>> tdata.comment1 = 'Your specified comment1"
• line1, line2, line3, line4 : Four lines can be drawn. For each of
these lines you can set priority, start location (x1, y1), end location
(x2, y2) and line object.
• box1, box2, box3, box4 : Four boxes can be drawn. Same as line
except the x1, x2, y1, y2 settings refer to corners of the box.
• xname, yname, zname, tname : These are the possible axes of
x,y,z and t. Note in the case you are trying the plot is a latitude x
longitude plot. If it was a timexlongitude plot then you would be
setting the xname and tname values. You can set the x,y location
for the name, the priority and text object.

68 Getting Started with CDAT

Data Visualization

• xunits, yunits, zunits, tunits : These are the respective axis units
for whichyou can set the x,y location, text object, and priority .
• xvalue, yvalue, zvalue, tvalue :
• xlabel1, xlabel2 : The x axis labels (bottom and top of your plot)
can be independently set. You can specify the y location (x is
determined by the data), priority and the text object.
• ylabel1, ylabel2 : Same as above except for the left and right side
of your plot. Here you can only specify the x location of the label.
• xtic1, xtic2 : The major tic marks on the bottom and top. You can
control the priority, y1 and y2 (in effect specifying the length!),
and line object (Things like line style, thickness, arrow, etc. etc.
More on the line object later).
• xmintic1, xmintic2: The minitic specifications. Exactly the same
as above otherwise.
• ytic1, ytic2 : The major tic marks on the left and right. You can
control the priority, x1 and x2 (in effect specifying the length!),
and line object.
• ymintic1, ymintic2: The minitic specifications. Exactly the same
as above otherwise.

In addition to the attributes that can be specified, a few useful

functions that operate on templates are also available.
• scale : This is useful in scaling the entire template (and all the
objects within) by a specified factor.
• move : This is useful in moving the template (and all the objects
within) to a specified location

3.3.2.4 Animation
VCS allows the user to animate the contents of the VCS
Canvas. This function pops up the animation GUI which lets the user
control all aspects of the animation.
>>> v.plot(array,’default’,’isofill’,’quick’)
>>> v.animate.gui()

Getting Started With CDAT 69

What’s in CDAT

Alternately, animation can be controlled from the command line

using the following methods:
>>> v.animate.create()
>>> v.animate.run()
>>> v.animate.zoom(3)
>>> v.animate.horizontal(50)
>>> v.animate.vertical(-50)
>>> v.animate.pause(4)
>>> v.animate.frame(2)
>>> v.animate.stop()

3.3.2.5 Output
Before attempting to print your plots, make sure that gplot is
built and installed on your system. The VCS graphics can be output
to files of various formats or directly to printers with postscript
capability. The available graphics file formats that one can print to are
postscript, encapsulated postscript (EPS), GIF, CGM, and raster. To
print directly to a printer and optionally specifying a portrait
orientation:
>>> v.printer(’printer_name’, ’p’)

To create gif, postscript, cgm, raster, encapsulated postscript and

portable document format (pdf) files, the commands are :
>>> v.gif(’example.gif’,’r’,’p’)
>>> v.postscript(’example.ps’, ’r’, ’p’)
>>> v.cgm(’example.cgm’, ’p’)
>>> v.raster(’example.ras’, ’p’)
>>> v.eps(’example.eps’, ’r’, ’p’)
>>> v.pdf(‘example.pdf’)

3.3.2.6 Using VCS Scripts

Script commands define the actions that are necessary to
preserve an interactive session as a script and to mimic that session in

70 Getting Started with CDAT

Other useful packages

a non-interactive replay of the script. Many attributes are needed to

create a graphical representation of a variable, e.g. attributes to
identify the variable and to label the plotting axes. By use of VCS and
Python scripts, most of these attributes can be manipulated to create
the desired visual effect, and the resulting attributes can be saved for
later use. VCS and Python scripts also allow the user to save a
sequence of interactive operations for replay, and to recover from a
system failure. To re-save the initial.attributes file, use the function
saveinitialfile(). To save VCS objects as Python scripts or VCS
scripts, use the function scriptobject(). To save the state of the
system, use the function scriptstate(). To run a VCS script file, use the
function scriptrun()

3.3.3 Interface to Grace (genutil.xmgrace)

Nothing emphases the fact that CDAT is a collection of tools
that can be extended by the user better than the xmgrace module.
This module provides an interface to the popular Grace plotting
utility (which you must have installed separately. Downloads and
information are available from http://plasma-gate.weizmann.ac.il/
Grace ). The xmgrace tutorial which is introduced in
“xmgrace_tutorial.py” on page 28 teaches you how to use it.

3.4 Other useful packages

The following packages are contributions from users. The
module descriptions are shown in the CDAT Utilities Reference
Guide cdat_utilities.pdf. They are provided "as-is" and may not be
supported unless the package is considered useful by a large user
community.

Getting Started With CDAT 71

What’s in CDAT

3.4.1 Interface to Spherepack

This package contains a Python interface to the subroutine
library Spherepack. To see list of functions type
% pydoc -w sphere

3.4.2 Interface to Regridpack

This package contains a Python interface to the subroutine
library regridpack. For further details type:
% pydoc -w adamsregrid

3.4.3 Empirical Orthogonal Functions

Available in the eof package. Calculates Empirical Orthogonal
Functions of either one variable or two variables jointly. For more
documentation type:
% pydoc -w eof.

3.4.4 Interface to the L-moments library

An interface to an L-moments library by J. R. M. Hosking. To
see list of functions type:
% pydoc -w lmoments

3.4.5 Interface to the ngmath library

The ngmath library is a collection of interpolators and
approximatorsfor one-dimensional, two-dimensional and three-
dimensional data. The packages, which were obtained from NCAR,
are:
• natgrid - a two-dimensional random data interpolation package
based on Dave Watson's nngridr. NOT built by default in CDAT
due to compile problems on some platforms. Works on linux.

72 Getting Started with CDAT

Other useful packages

• dsgrid - a three-dimensional random data interpolator based on a

simple inverse distance weighting algorithm.
• fitgrid - an interpolation package for one-dimensional and two-
dimensional gridded data based on Alan Cline's Fitpack. Fitpack
uses splines under tension to interpolate in one and two
dimensions. NOT IN CDAT.
• csagrid - an approximation package for one-dimensional, two-
dimensional and three-dimensional random data based on David
Fulker's Splpack. csagrid uses cubic splines to calculate its
approximation function.

3.4.6 Using existing Fortran code

3.4.6.1 Pyfort
Pyfort is a tool for connecting Fortran (Fortran90) routines to
Python (www.python.org). Pyfort translates an input file that
describes the Fortran functions and subroutines you wish to access
from Python into a C language source file defining a Python module.
Fortran was changed significantly by the introduction of the Fortran
90 standard. We will use the phrase "modern Fortran" to indicate
versions of Fortran from Fortran 90 onwards. Pyfort’s input uses a
syntax that is a subset of the modern Fortran syntax for declaring
routines and their arguments. The current release does not yet support
modern Fortran’s "explicit-interface" routines. However, the tool was
designed with this in mind for a future release. Pyfort can in most
cases also build and install the extension you create.

The Pyfort project page at SourceForge contains documentation and

releases. It is: http://sourceforge.net/projects/pyfortran

3.4.6.2 F2PY (previously known as fpig)

Writing Python C/API wrappers for Fortran routines can be a
very tedious task, especially if a Fortran routine takes more than 20
arguments but only few of them are relevant for the problems that

Getting Started With CDAT 73

What’s in CDAT

they solve. Pearu Petersen has developed a tool that generates the C/
API modules containing wrapper functions of Fortran routines. This
tool is called F2PY - Fortran to Python Interface Generator. It is
completely written in Python language and can be called from the
command line as f2py. F2PY is released under the terms of GNU
LGPL. The F2PY package and documentation can be downloaded
from http://cens.ioc.ee/projects/f2py2e/

3.4.7 Migrating from GrADS (grads)

The grads module supplies an interface to CDMS that will be
familiar to users of GrADS. See the CDAT website for
documentation.

3.4.8 ort
Read data from an Oort file.

3.4.9 trends
Computes variance estimate taking auto-correlation into
account.

3.4.10 pyclimate
This package - also python based, is written and maintained at
the Universidad del País Vasco in Bilbao, Spain. It provides useful
statistical functions for climate applications.

74 Getting Started with CDAT

CHAPTER 4 Contributions to CDAT

CDAT is a collaboration. You can be part of the collaboration. You don’t need permis-
sion or PCMDI’s approval. You don’t need PCMDI’s programmers to add your algorithms.
Here are descriptions of how to contribute packages the packages contributed to the "contrib"
section of the CDAT source.

4.1 How to add your packages

One of CDAT’s strengths is that it is an open system. You can
add your own software written in C, Python, or Fortran. The easiest
way to learn to do this is to copy our examples. Get the CDAT source
distribution and look for subdirectory ’contrib’ in the top-level direc-
tory. The README file in contrib explains what to do.

There are tools that may be useful to you.

• The SWIG utility (Simplified Wrapper and Interface Generator,
http://www.swig.org) can wrap C and C++ routines.
• Pyfort (http://pyfortran.sourceforge.net) connects Fortran rou-
tines to Python.

Depending on your needs, you may wish to use a layer of Python

along with the automatically created interface, in order to make a
nicer interface or to use the Fortran or C simply as computational
engines. An example of this is the EOF package described below: it

Getting Started With CDAT 75

Contributions to CDAT

uses a Fortran linear algebra routine to enhance performance, but the

"science" is in Python.

If you follow the protocols in ’contrib’ then your package can be

added to the PCMDI distribution as well. Just send it to us and be
sure to include a README that explains:
• How to use the package
• Contact information about the author.

You may also be able to generate useful documentation by executing

the routines happydoc or pydoc. happydoc works only on Python
code; pydoc works on the installed modules. Both routines print help
packages if executed with the argument, ’--help’, and both are
already installed in your cdat ’bin’ directory.

If you have the source distribution, use the README files in the sub-
directories of the contrib directory for full documentation. Alter-
nately, type
% pydoc -w <name_of_package>

to create a web page showing the package’s interface.

76 Getting Started with CDAT

 Index

A
adding your packages 75
Animate 62
Animation 69
Area averaging 50
arrays 38
ASCII text files 35
asciidata 35
autocorrelation 58
autocovariance 58
axis 45

B
base time 43
binaryio 35
boxfill 63
bug-tracking facility 31

C
CDAT Home Page 2, 31
CDAT Website 31
cdms 36
cdtime 43, 44
cdutil 50, 53
centroid function 56
CGM 62
colormap 61, 62
component time 43
contrib 76
corrrelation 58
covariance 58
criteriaarg 56
custom seasons 54

D
data, conversion to Numeric 42
databases 49
docstrings 28
documentation 28
documentation, run-time 76
DODS 2
domain 36, 45

E
Empirical Orthogonal Functions 72
Encapsulated Postscript 62
eof (package) 72

F
F2PY 73
File I/O. 33
file variable 37
fill area 61
fillareaobject 66
format 61
Fortran formatted data 34
fpig 73

G
Generating weights 53
genutil 58
geometric mean 58
GIF 62
Grace 60, 71
GrADS 74
grads (module) 74
GrADS/GRIB 33
graphics method 61
Graphics Methods 62
Graphics Primitives 66

H
happydoc 30, 76
HDF 33

I
isofill 63
isoline 63
L
laggedcorrelation 58
laggedcovariance 58
Learning Python 17
line 61
linearregression 58
lineobject 66
list 61
L-moments 72

M
MA 38
mailing list 31
marker 61
markerobject 66
Masked Array 37
masked arrays 38
Masked Variable 37
masks 49
mean absolute difference 58
metadata 36
missing values 38
MV 38

N
netCDF 33
Numeric 38
Numeric array 37, 39
Numerical Python 28, 39

O
OPeNDAP 2, 34
orientation 62
ort (package) 74
outfill 63
outline 63

P
picture template 61
Postscript 62
primary objects 61
projections 62
pyclimate 74
pydoc 29, 76
Pyfort 73
Python 5
Python scripts 71

R
Raster 62
regrid 47
regridder function 48
Regridding 47
Regridpack 72
regridpack (package) 72
relative time 43
rms 58

S
scatter 63
Scientific Python 34
Script 70
secondary objects 61
Selectors 46
self-describing formats 33
singleton dimensions 46
sphere (package) 72
Spherepack 72
squeeze 46
standard deviation 58
statistical functions 58
statistics_tutorial.py 58
SWIG 75
System Requirements 3

T
Templates 66
text 61
text orientation 61
textobject 66
Time averaging 53
times_tutorial.py 57
transient variable 37
trends (package) 74
U
unformatted data 35

V
variable 36
variables 38
variance 58
VCDAT 5, 28
VCS 60
VCS scripts 71
VCS, scripting 70
vector 63
Visualization 60
Visualization Control System 60

X
xmgrace (package) 71
xml 33
xvsy 63

Z
zoom 62