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Quirks with parfor vs. for

A few months ago, I discussed several tips regarding Matlab’s parfor command, which is used by the Parallel Computing Toolbox (PCT) for parallelizing loops. Today I wish to extend that post with some unexplained oddities when using parfor, compared to a standard for loop.

Data serialization quirks

Dimitri Shvorob may not appear at first glance to be a prolific contributor on Matlab Central, but from the little he has posted over the years I regard him to be a Matlab power-user. So when Dimitri reports something, I take it seriously. Such was the case several months ago, when he contacted me regarding very odd behavior that he saw in his code: the for loop worked well, but the parfor version returned different (incorrect) results. Eventually, Dimitry traced the problem to something originally reported by Dan Austin on his Fluffy Nuke It blog.

The core issue is that if we have a class object that is used within a for loop, Matlab can access the object directly in memory. But with a parfor loop, the object needs to be serialized in order to be sent over to the parallel workers, and deserialized within each worker. If this serialization/deserialization process involves internal class methods, the workers might see a different version of the class object than the one seen in the serial for loop. This could happen, for example, if the serialization/deserialization method croaks on an error, or depends on some dynamic (or random) conditions to create data.

In other words, when we use data objects in a parfor loop, the data object is not necessarily sent “as-is”: additional processing may be involved under the hood that modify the data in a way that may be invisible to the user (or the loop code), resulting in different processing results of the parallel (parfor) vs. serial (for) loops.

For additional aspects of Matlab serialization/deserialization, see my article from 2 years ago (and its interesting feedback comments).

Data precision quirks

The following section was contributed by guest blogger Lior Perlmuter-Shoshany, head algorithmician at a private equity fund.

In my work, I had to work with matrixes in the order of 109 cells. To reduce the memory footprint (and hopefully also improve performance), I decided to work with data of type single instead of Matlab’s default double. Furthermore, in order to speed up the calculation I use parfor rather than for in the main calculation. In the end of the run I am running a mini for-loop to see the best results.

What I discovered to my surprise is that the results from the parfor and for loop variants is not the same!
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Categories: Guest bloggers, Medium risk of breaking in future versions, Memory, Stock Matlab function, Undocumented feature
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Checking status of warning messages in MEX

Once again I would like to welcome guest blogger Pavel Holoborodko, the developer of the Advanpix Multiprecision Computing Toolbox. Pavel has already posted here as a guest blogger about undocumented Matlab MEX functions. Today he will discuss another little-known aspect of advanced MEX programming with Matlab, a repost of an article that was originally posted on his own blog. Happy holidays everybody!

Matlab allows flexible adjustment of visibility of warning messages. Some, or even all, messages can be disabled from showing on the screen by warning command.

The little known fact is that status of some warnings may be used to change the execution path in algorithms. For example, if warning 'Matlab:nearlySingularMatrix' is disabled, then the linear system solver (mldivide operator) might skip estimation of reciprocal condition number which is used exactly for the purpose of detection of nearly singular matrices. If the trick is used, it allows 20%-50% boost in solver performance, since rcond estimation is a time consuming process.

Therefore it is important to be able to retrieve status of warnings in Matlab. Especially in MEX libraries targeted for improved performance. Unfortunately Matlab provides no simple way to check status of warning message from MEX module.

Today’s article outlines two workarounds for the issue:

  1. Using mexCallMATLABWithTrap (documented)
  2. Using utGetWarningStatus (undocumented)

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Categories: Guest bloggers, Medium risk of breaking in future versions, Undocumented function
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Password & spinner controls in Matlab GUI

I often include configuration panels in my programs, to enable the user to configure various program aspects, such as which emails should automatically be sent by the program to alert when certain conditions occur. Last week I presented such a configuration panel, which is mainly composed of standard documented Matlab controls (sub-panels, uitables and uicontrols). As promised, today’s post will discuss two undocumented controls that are often useful in similar configuration panels (not necessarily for emails): password fields and spinners.

Matlab GUI configuration panel including password and spinner controls (click to zoom-in)
Matlab GUI configuration panel including password and spinner controls (click to zoom-in)

Password fields are basically editboxes that hide the typed text with some generic echo character (such as * or a bullet); spinners are editboxes that only enable typing certain preconfigured values (e.g., numbers in a certain range). Both controls are part of the standard Java Swing package, on which the current (non-web-based) Matlab GUIs relies. In both cases, we can use the javacomponent function to place the built-in Swing component in our Matlab GUI.
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Categories: GUI, High risk of breaking in future versions, Java, Semi-documented function
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Sending email/text messages from Matlab

In this day and age, applications are expected to communicate with users by sending email/text messages to alert them about applicative events (“IBM stock purchased @$99.99” or “House is on fire!”). Matlab has included the sendmail function to handle this for many years. Unfortunately, sendmail requires some tweaking to be useful on all but the most basic/insecure mail servers. Today’s post will hopefully fill the missing gaps.

None of the information I’ll present today is really new – it was all there already if you just knew what to search for online. But hopefully today’s post will concentrate all these loose ends in a single place, so it may have some value:

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Categories: GUI, Java, Medium risk of breaking in future versions, Semi-documented feature, Stock Matlab function
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Afterthoughts on implicit expansion

Matlab release R2016b introduced implicit arithmetic expansion, which is a great and long-awaited natural expansion of Matlab’s arithmetic syntax (if you are still unaware of this or what it means, now would be a good time to read about it). This is a well-documented new feature. The reason for today’s post is that this new feature contains an undocumented aspect that should very well have been documented and even highlighted.

The undocumented aspect that I’m referring to is the fact that code that until R2016a produced an error, in R2016b produces a valid result:

% R2016a
>> [1:5] + [1:3]'
Error using  + 
Matrix dimensions must agree.
 
% R2016b
>> [1:5] + [1:3]'
ans =
     2     3     4     5     6
     3     4     5     6     7
     4     5     6     7     8

This incompatibility is indeed documented, but not where it matters most (read on).

I first discovered this feature by chance when trying to track down a very strange phenomenon with client code that produced different numeric results on R2015b and earlier, compared to R2016a Pre-release. After some debugging the problem was traced to a code snippet in the client’s code that looked something like this (simplified):

% Ensure compatible input data
try
    dataA + dataB;  % this will (?) error if dataA, dataB are incompatible
catch
    dataB = dataB';
end

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Categories: Low risk of breaking in future versions, Stock Matlab function, Undocumented feature
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Speeding up Matlab-JDBC SQL queries

Many of my consulting projects involve interfacing a Matlab program to an SQL database. In such cases, using MathWorks’ Database Toolbox is a viable solution. Users who don’t have the toolbox can also easily connect directly to the database using either the standard ODBC bridge (which is horrible for performance and stability), or a direct JDBC connection (which is also what the Database Toolbox uses under the hood). I explained this Matlab-JDBC interface in detail in chapter 2 of my Matlab-Java programming book. A bare-bones implementation of an SQL SELECT query follows (data update queries are a bit different and will not be discussed here):

% Load the appropriate JDBC driver class into Matlab's memory
% (but not directly, to bypass JIT pre-processing - we must do it in run-time!)
driver = eval('com.mysql.jdbc.Driver');  % or com.microsoft.sqlserver.jdbc.SQLServerDriver or whatever
 
% Connect to DB
dbPort = '3306'; % mySQL=3306; SQLServer=1433; Oracle=...
connectionStr = ['jdbc:mysql://' dbURL ':' dbPort '/' schemaName];  % or ['jdbc:sqlserver://' dbURL ':' dbPort ';database=' schemaName ';'] or whatever
dbConnObj = java.sql.DriverManager.getConnection(connectionStr, username, password);
 
% Send an SQL query statement to the DB and get the ResultSet
stmt = dbConnObj.createStatement(java.sql.ResultSet.TYPE_SCROLL_INSENSITIVE, java.sql.ResultSet.CONCUR_READ_ONLY);
try stmt.setFetchSize(1000); catch, end  % the default fetch size is ridiculously small in many DBs
rs = stmt.executeQuery(sqlQueryStr);
 
% Get the column names and data-types from the ResultSet's meta-data
MetaData = rs.getMetaData;
numCols = MetaData.getColumnCount;
data = cell(0,numCols);  % initialize
for colIdx = numCols : -1 : 1
    ColumnNames{colIdx} = char(MetaData.getColumnLabel(colIdx));
    ColumnType{colIdx}  = char(MetaData.getColumnClassName(colIdx));  % http://docs.oracle.com/javase/7/docs/api/java/sql/Types.html
end
ColumnType = regexprep(ColumnType,'.*\.','');
 
% Get the data from the ResultSet into a Matlab cell array
rowIdx = 1;
while rs.next  % loop over all ResultSet rows (records)
    for colIdx = 1 : numCols  % loop over all columns in the row
        switch ColumnType{colIdx}
            case {'Float','Double'}
                data{rowIdx,colIdx} = rs.getDouble(colIdx);
            case {'Long','Integer','Short','BigDecimal'}
                data{rowIdx,colIdx} = double(rs.getDouble(colIdx));
            case 'Boolean'
                data{rowIdx,colIdx} = logical(rs.getBoolean(colIdx));
            otherwise %case {'String','Date','Time','Timestamp'}
                data{rowIdx,colIdx} = char(rs.getString(colIdx));
        end
    end
    rowIdx = rowIdx + 1;
end
 
% Close the connection and clear resources
try rs.close();   catch, end
try stmt.close(); catch, end
try dbConnObj.closeAllStatements(); catch, end
try dbConnObj.close(); catch, end  % comment this to keep the dbConnObj open and reuse it for subsequent queries

Naturally, in a real-world implementation you also need to handle database timeouts and various other errors, handle data-manipulation queries (not just SELECTs), etc.

Anyway, this works well in general, but when you try to fetch a ResultSet that has many thousands of records you start to feel the pain – The SQL statement may execute much faster on the DB server (the time it takes for the stmt.executeQuery call), yet the subsequent double-loop processing to fetch the data from the Java ResultSet object into a Matlab cell array takes much longer.

In one of my recent projects, performance was of paramount importance, and the DB query speed from the code above was simply not good enough. Continue reading

Categories: Java, Low risk of breaking in future versions, Toolbox, Undocumented feature
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Working with non-standard DPI displays

With high-density displays becoming increasingly popular, some users set their display’s DPI to a higher-than-standard (i.e., >100%) value, in order to compensate for the increased pixel density to achieve readable interfaces. This OS setting tells the running applications that there are fewer visible screen pixels, and these are spread over a larger number of physical pixels. This works well for most cases (at least on recent OSes, it was a bit buggy in non-recet ones). Unfortunately, in some cases we might actually want to know the screen size in physical, rather than logical, pixels. Apparently, Matlab root’s ScreenSize property only reports the logical (scaled) pixel size, not the physical (unscaled) one:

>> get(0,'ScreenSize')   % with 100% DPI (unscaled standard)
ans =
        1       1      1366       768
 
>> get(0,'ScreenSize')   % with 125% DPI (scaled)
ans =
        1       1      1092.8     614.4

The same phenomenon also affects other related properties, for example MonitorPositions.

Raimund Schlüßler, a reader on this blog, was kind enough to point me to this problem and its workaround, which I thought worthy to share here: To get the physical screen-size, use the following builtin Java command:

>> jScreenSize = java.awt.Toolkit.getDefaultToolkit.getScreenSize
jScreenSize =
java.awt.Dimension[width=1366,height=768]
 
>> width = jScreenSize.getWidth
width =
        1366
 
>> height = jScreenSize.getHeight
height =
        768

Also see the related recent article on an issue with the DPI-aware feature starting with R2015b.

Upcoming travels – London/Belfast, Zürich & Geneva

I will shortly be traveling to consult some clients in Belfast (via London), Zürich and Geneva. If you are in the area and wish to meet me to discuss how I could bring value to your work, then please email me (altmany at gmail):

  • Belfast: Nov 28 – Dec 1 (flying via London)
  • Zürich: Dec 11-12
  • Geneva: Dec 13-15
Categories: Desktop, Figure window, GUI, Java, Low risk of breaking in future versions, Undocumented feature
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uigetfile/uiputfile customizations

Matlab includes a few built-in file and folder selection dialog windows, namely uigetfile, uiputfile and uigetdir. Unfortunately, these functions are not easily extendable for user-defined functionalities. Over the years, several of my consulting clients have asked me to provide them with versions of these dialog functions that are customized in certain ways. In today’s post I discuss a few of these customizations: a file selector dialog with a preview panel, and automatic folder update as-you-type in the file-name edit box.

It is often useful to have an integrated preview panel to display the contents of a file in a file-selection dialog. Clicking the various files in the tree-view would display a user-defined preview in the panel below, based on the file’s contents. An integrated panel avoids the need to manage multiple figure windows, one for the selector dialog and another for the preview. It also reduces the screen real-estate used by the dialog (also see the related resizing customization below).

I call the end-result uigetfile_with_preview; you can download it from the Matlab File Exchange:

filename = uigetfile_with_preview(filterSpec, prompt, folder, callbackFunction, multiSelectFlag)

uigetfile_with_preview

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Categories: GUI, High risk of breaking in future versions, Java, Undocumented feature
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Icon images & text in Matlab uicontrols

One of my consulting clients recently asked me if I knew any builtin Matlab GUI control that could display a list of colormap names alongside their respective image icons, in a listbox or popup menu (drop-down/combo-box):

Matlab listbox with icon images   Matlab popup menu (dropdown/combobox) with icon images

Matlab listbox (left) & popup menu (right) with icon images

My initial thought was that this should surely be possible, since Colormap is a documented figure property, that should therefore be listed inside the inspector window, and should therefore have an associated builtin Java control for the dropdown (just like other inspector controls, which are part of the com.mathworks.mlwidgets package, or possibly as a standalone control in the com.mathworks.mwswing package). To my surprise it turns out that for some unknown reason MathWorks neglected to add the Colormap property (and associated Java controls) to the inspector. This property is fully documented and all, just like Color and other standard figure properties, but unlike them Colormap can only be modified programmatically, not via the inspector window. Matlab does provide the related colormapeditor function and associated dialog window, but I would have expected a simple drop-down of the standard builtin colormaps to be available in the inspector. Anyway, this turned out to be a dead-end.

It turns out that we can relatively easily implement the requested listbox/combo-box using a bit of HTML magic, as I explained last week. The basic idea is for each of the listbox/combobox items to be an HTML string that contains both an <img> tag for the icon and the item label text. For example, such a string might contain something like this (parula is Matlab’s default colormap in HG2, starting in R2014b):

<html><img src="http://www.mathworks.com/help/matlab/ref/colormap_parula.png"/>parula</html>

parula colormap image

parula colormap image

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Categories: GUI, Medium risk of breaking in future versions, UI controls, Undocumented feature
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Aligning uicontrol contents

Matlab automatically aligns the text contents of uicontrols: button labels are centered, listbox contents are left-aligned, and table cells align depending on their contents (left-aligned for strings, centered for logical values, and right-aligned for numbers). Unfortunately, the control’s HorizontalAlignment property is generally ignored by uicontrols. So how can we force Matlab buttons (for example) to have right-aligned labels, or for listbox/table cells to be centered? Undocumented Matlab has the answer, yet again…

It turns out that there are at least two distinct ways to set uicontrol alignment, using HTML and using Java. Today I will only discuss the HTML variant.

The HTML method relies on the fact that Matlab uicontrols accept and process HTML strings. This was true ever since Matlab GUI started relying on Java Swing components (which inherently accept HTML labels) over a decade ago. This is expected to remain true even in Matlab’s upcoming web-based GUI system, since Matlab would need to consciously disable HTML in its web components, and I see no reason for MathWorks to do so. In short, HTML parsing of GUI control strings is here to stay for the foreseeable future.

% note: no need to close HTML tags, e.g. 
uicontrol('Style','list', 'Position',[10,10,70,70], 'String', ...
          {'<html><font color="red">Hello</font></html>', 'world', ...
           '<html><font style="font-family:impact;color:green"><i>What a', ...
           '<html><font color="blue" face="Comic Sans MS">nice day!'});
</font></html></i></font></html>

Listbox with HTML items

Listbox with HTML items

While HTML formatting is generally frowned-upon compared to the alternatives, it provides a very quick and easy way to format text labels in various different manners, including using a combination of font faces, sizes, colors and other aspects (bold, italic, super/sub-script, underline etc.) within a single text label. This is naturally impossible to do with Matlab’s standard properties, but is super-easy with HTML placed in the label’s String property.

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Categories: GUI, Low risk of breaking in future versions, UI controls, Undocumented feature
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