## Submissions requested for the next Carnival of Mathematics

July 21st, 2014

It’s been quite some time since I hosted a Carnival of Mathematics with the last one being #90 back in September 2012. I am very pleased to announce that I’ll be hosting #113 next month and am currently accepting articles.  If you’ve written a mathematical blog post recently and would like to give it more exposure, send in a submission.

## Software Carpentry: Draft of Windows Scripting Tutorial using PowerShell

July 17th, 2014

Update: September 2014 – The notes in this blog post have been uploaded to github: https://github.com/mikecroucher/Windows_Scientific_Computing. The blog post will be kept as-is for posterity reasons. For the most up to date version of the notes, see the github version.

Some time in 2013, I helped out at a Software Carpentry event at The University of Bath.  As with most software carpentry boot camps, one of the topics covered was shell scripting and the scripting language of choice was bash.  As I wandered around the room, I asked the delegates which operating system they use for the majority of their research and the most popular answer, by far, was Windows.

This led me to wonder if we should teach using a native Windows solution rather than relying on bash?

A few years ago, this would be an insane proposition since the Windows command shell is very weak compared to bash.  PowerShell, on the other hand, is modern, powerful and installed on all modern Windows operating systems by default.

My problem was that I didn’t know PowerShell very well.  So, I took the notes for the 2013 Bath shell scripting session – https://github.com/swcarpentry/boot-camps/tree/2013-07-bath/shell – and gave myself the exercise of converting them to PowerShell.

I got close to completing this exercise last summer but various things took higher priority and so the project languished.  Rather than sit on the notes any longer, I’ve decided to just publish what I have so far in case they are useful to anyone.

You are free to use them with the following caveats

• This is not necessarily the right way to teach PowerShell. It is an experiment in converting some classroom-tested Linux based notes to PowerShell.
• If you use them, attribution would be nice. I am Mike Croucher, my site is www.walkingrandomly.com Details on how to contact me at https://www.walkingrandomly.com/?page_id=2055
• I have not yet tested these notes in a classroom situation
• These notes aren’t finished yet
• These notes have been developed and tested on Windows 7.  Behaviour may be different using different versions of Windows.
• These notes are given as they were left sometime in mid 2013. Some things may be out of date.
• I was learning PowerShell as I developed these notes. As such, I fully expect them to be full of mistakes.  Corrections and improvements would be welcomed.

If anyone is interested in developing these notes into something that’s classroom-ready, contact me.

## The old Windows Command Shell

The traditional Windows command shell is a program called cmd.exe which can trace its roots all the way back to the old, pre-Windows DOS prompt.

You can launch this command shell as follows

• Hold down both the Windows button and the letter R to open the Run prompt
• Type cmd and press Enter or click OK

• You should see a window similar to the one below

The Windows command shell hasn’t changed significantly for over twenty years and is relatively feature poor compared to more modern shells. For this reason, it is recommended that you use Windows PowerShell instead. Mention of cmd.exe is only included here since, despite its deficiencies, it is still widely in use

## PowerShell

To launch PowerShell:

• Hold down both the Windows button and the letter R to open the Run prompt
• Type powershell and press Enter or click OK

• You should see a window similar to the one below

Note that although the header of the above window mentions v1.0, it could be a screenshot from either version 1.0 or version 2.0. This is a well-known bug. If you are using Windows 7 you will have version 2 at the minimum.

## PowerShell versions

At the time of writing, PowerShell is at version 3. Ideally, you should at least have version 2.0 installed. To check version:

$psversiontable.psversion Major Minor Build Revision ----- ----- ----- -------- 3 0 -1 -1  If this variable does not exist, you are probably using version 1.0 and should upgrade. ## Comments # This is a comment in Powershell. It is not executed  ## Directories Users of Bash will feel right at home at first since PowerShell appears to have the same set of commands pwd #Path to current folder ls #List directory ls *.txt #Wild Card ls *_hai* ls -R #Recursive folder listing ls . #List current folder ls .. #List Parent folder cd .. #Change current folder to parent. (Move up a folder) cd ~ #Change current folder to your user directory. mkdir myfolder #Create a folder mkdir ~/myfolder mv myfolder new_myfolder #rename myfolder to new_myfolder rm -r new_myfolder #Delete new_myfolder if its empty  # Files cat file # View file more file # Page through file cat file | select -first 3 # first N lines cat file | select -last 2 # Last N lines cp file1 file2 # Copy cp *.txt directory rm file.txt # Delete - no recycle bin. rm -r directory # Recurse  ## Different command types in PowerShell: Aliases, Functions and Cmdlets Many of the PowerShell ‘commands’ we’ve used so far are actually aliases to Powershell Cmdlets which have a Verb-Noun naming convention. We can discover what each command is an alias of using the get-alias cmdlet. PS > get-alias ls CommandType Name Definition ----------- ---- ---------- Alias ls Get-ChildItem  This shows that ls is an alias for the Cmdlet Get-ChildItem A list of aliases for common Bash commands: • cat (Get-Content) • cd (Set-Location) • ls (Get-ChildItem) • pwd (Get-Location) One reason why aliases were created is to make PowerShell a more familiar environment for users of other shells such as the old Windows cmd.exe or Linux’s Bash environment and also to save on typing. You can get a list of all aliases using get-alias on its own. PS > get-alias  Finally, here’s how you get all of the aliases for the Get-ChildItem cmdlet. get-alias | where-object {$_.Definition -match "Get-Childitem"}


For more details on Powershell aliases, see Microsoft’s documentation at http://technet.microsoft.com/en-us/library/ee692685.aspx

### What type of command is mkdir?

The mkdir command looks like it might be an alias as well since it doesn’t have the verb-noun naming convention of Cmdlets. Let’s try to see which Cmdlet it might be an alias of:

PS > get-alias mkdir

Get-Alias : This command cannot find a matching alias because alias with name 'mkdir' do not exist.
At line:1 char:6
+ alias <<<<  mkdir
+ CategoryInfo          : ObjectNotFound: (mkdir:String) [Get-Alias], ItemNotFoundException
+ FullyQualifiedErrorId : ItemNotFoundException,Microsoft.PowerShell.Commands.GetAliasCommand


It turns out that mkdir isn’t an alias at all but is actually yet another PowerShell command type, a function. We can see this by using the get-command Cmdlet

PS > get-command mkdir
CommandType     Name                                                Definition
-----------     ----                                                ----------
Function        mkdir                                               ...
Application     mkdir.exe                                           C:\Program Files (x86)\Git\bin\mkdir.exe


Now we can clearly see that mkdir is a PowerShell function. The mkdir.exe is an Application which you’ll only see if you installed git for windows as I have.

## Cmdlets

A Cmdlet (pronounced ‘command-let’) is a .NET class but you don’t need to worry abut what this means until you get into advanced PowerShell usage. Just think of Cmdlets as the base type of PowerShell command. They are always named according to the convention verb-noun; for example Set-Location and Get-ChildItem.

#### Listing all Cmdlets

The following lists all Cmdlets

Get-Command


You can pipe this list to a pager

Get-Command | more


## Getting help

You can get help on any PowerShell command using the -? switch. For example

ls -?


When you do this, you’ll get help for the Get-ChildItem Cmdlet which would be confusing if you didn’t know that ls is actually an alias for Get-ChildItem

## History

Up arrow browses previous commands.

By default, PowerShell version 2 remembers the last 64 commands whereas PowerShell version 3 remembers 4096. This number is controlled by the $MaximumHistoryCount variable PS >$MaximumHistoryCount           #Display the current value
PS > $MaximumHistoryCount=150 #Change it to 150 PS > history #Display recent history using the alias version of the command PS > get-history #Display recent history using the Cmdlet direct  Although it remembers more, PowerShell only shows the last 32 commands by default. To see a different number, use the count switch PS > get-history -count 50  To run the Nth command in the history use Invoke-History PS > invoke-history 7  ## Word count (and more) using Measure-Object Linux has a command called wc that counts the number of lines and words in a file. Powershell has no such command but we can do something similar with the Measure-Object Cmdlet. Say we want to count the number of lines, words and characters in the file foo.txt. The first step is to get the content of the file get-content foo.txt # gets the content of foo.txt  Next, we pipe the result of the get-content Cmdlet to Measure-Object, requesting lines, words and characters get-content foo.txt | measure-object -line -character -word  The measure-object Cmdlet can also count files ls *.txt | measure-object #Counts number of .txt files in the current folder  When you execute the above command, a table of results will be returned: Count : 3 Average : Sum : Maximum : Minimum : Property :  This is because the measure-object Cmdlet, like all PowerShell Cmdlets, actually returns an object and the above table is the textual representation of that object. The fields in this table hint that measure-object can do a lot more than simply count things. For example, here we find some statistics concerning the file lengths found by the ls *.txt command ls *.txt | measure-object -property length -minimum -maximum -sum -average  You may wonder exactly what type of object has been returned from measure-object and we can discover this by running the gettype() method of the returned object (ls *.txt | measure-object).gettype()  Request just the name as follows (ls *.txt | measure-object).gettype().Name GenericMeasureInfo  To find out what properties an object has, pass it to the get-member Cmdlet #Return all member types ls *.txt | get-member #Return only Properties ls *.txt | get-member -membertype property  Sometimes, you’ll want to simply return the numerical value of an object’s property and you do this using the select-object Cmdlet. Here we ask for just the Count property of the GenericMeasureInfo object returned by measure-object. #Counts the number of *.txt files and returns just the numerical result ls *.txt | measure-object | select-object -expand Count  ## Searching within files The Unix world has grep, PowerShell has Select String. Try running the following on haiku.txt Select-String the haiku.txt #Case insensitive by default, unlike grep Select-String the haiku.txt -CaseSensitive #Behaves more like grep Select-String day haiku.txt -CaseSensitive Select-String is haiku.txt -CaseSensitive Select-String 'it is' haiku.txt -Casesensitive  There is no direct equivalent to grep’s -w switch. grep -w is haiku.txt #exact match  However, you can get the same behaviour using the word boundary anchors, \b Select-String \bis\b haiku.txt -casesensitive  Grep has a -v switch that shows all lines that do not match a pattern. Select-String makes use of the -notmatch switch. BASH: grep -v "is" haiku.txxt PS: select-string -notmatch "is" haiku.txt -CaseSensitive  Grep has an -r switch which stands for ‘recursive’. The following will search through all files and subfolders of your current directory, looking for files that contain is grep -r is *  Select-String has no direct equivalent to this. However, you can do the same thing by using get-childitem to get the list of files, piping the output to select-string get-childitem * -recurse | select-string is  One difference between grep and Select-String is that the latter includes the filename and line number of each match. grep the haiku.txt Is not the true Tao, until and the presence of absence: Select-String the haiku.txt -CaseSensitive haiku.txt:2:Is not the true Tao, until haiku.txt:6:and the presence of absence:  To get the grep-like output, use the following Select-String the haiku.txt -CaseSensitive | ForEach-Object {$_.Line}

Is not the true Tao, until
and the presence of absence:


To understand how this works, you first have to know that Select-String returns an array of MatchInfo objects when there is more than one match. To demonstrate this:

$mymatches = Select-String the haiku.txt -CaseSensitive #Put all matches in the variable 'mymatches'$mymatches -is [Array]          #query if 'match' is an array

True


So, mymatches is an array. We can see how many elements it has using the array’s Count property

$mymatches.Count 2  The type of elements in PowerShell arrays don’t necessarily have to be the same. In this case, however, they are. $mymatches[0].gettype()
$mymatches[1].gettype()  both of these give the output IsPublic IsSerial Name BaseType -------- -------- ---- -------- True False MatchInfo System.Object  If all you wanted was the name of the first object type, you’d do $mymatches[0].gettype().name

MatchInfo


Alternatively, we could have asked for each element’s type using the For-Each-Object Cmdlet to loop over every object in the array.

$mymatches | Foreach-Object {$_.gettype().Name}


Where $_ is a special variable that effectively means ‘current object’ or ‘The object currently being considered by Foreach-Object’ if you want to be more verbose. So, we know that we have an array of 2 MatchInfo objects in our variable mymatches. What does this mean? What properties do MatchInfo objects have? We can find out by piping one of them to the Get-Member Cmdlet. $mymatches[0] | Get-Member

TypeName: Microsoft.PowerShell.Commands.MatchInfo

Name         MemberType Definition
----         ---------- ----------
Equals       Method     bool Equals(System.Object obj)
GetHashCode  Method     int GetHashCode()
GetType      Method     type GetType()
RelativePath Method     string RelativePath(string directory)
ToString     Method     string ToString(), string ToString(string directory)
Context      Property   Microsoft.PowerShell.Commands.MatchInfoContext Context {get;se
Filename     Property   System.String Filename {get;}
IgnoreCase   Property   System.Boolean IgnoreCase {get;set;}
Line         Property   System.String Line {get;set;}
LineNumber   Property   System.Int32 LineNumber {get;set;}
Matches      Property   System.Text.RegularExpressions.Match[] Matches {get;set;}
Path         Property   System.String Path {get;set;}
Pattern      Property   System.String Pattern {get;set;}


Now we can see that each MatchInfo object has a Line property and it’s reasonable to guess that this contains a Line containing a match. Taking a look:

$mymatches[0].Line Is not the true Tao, until  Bringing together everything we’ve seen so far, we pull out the Line property of each element in the array as follows $mymatches | Foreach-Object {$_.Line}  Alternatively, we can ditch the$mymatches variable and pipe in the output of Select-String directly

Select-String the haiku.txt -CaseSensitive | ForEach-Object {$_.Line} Is not the true Tao, until and the presence of absence:  ## Regular expressions select-string 's*is' haiku.txt # * Zero or more of preceding token select-string 's+is' haiku.txt # + On or more of preceding token select-string '.nd' haiku.txt # . Any token followed by 'nd' select-string 'es' haiku.txt # matches 'es' select-string 'es[ht]' haiku.txt # Exactly one of the characters listed select-string 'es[^ht]' haiku.txt # Matches everything except h and t select-string 'ex[ select-string '\bis\b' haiku.txt # \b word boundaries  ## Input and output redirection > redirects output (AKA standard output). This works in both Bash and Powershell scripts. For example, in Bash we might do #BASH grep -r not * > found_nots.txt  Drawing on what we’ve learned so far, you might write the PowerShell version of this command as #PS get-childitem *.txt -recurse | select-string not > found_nots.txt  However, if you do this, you will find that the script will run forever with the hard-disk chugging like crazy. If you’ve run the above command, CTRL and C will stop it. This is because Powershell is including the output file, found_nots.txt, in its input which leads to an infinite loop. To prevent this, we must explicitly exclude the output file from the get-childitem search get-childitem *.txt -Exclude 'found_nots.txt' -recurse | select-string not > found_nots.txt cat found_nots.txt ls *.txt > txt_files.txt cat txt_files.txt  In Linux, < redirects input (AKA standard input). This does not work in PowerShell: cat < haiku.txt At line:1 char:5 + cat < haiku.txt + ~ The '<' operator is reserved for future use. + CategoryInfo : ParserError: (:) [], ParentContainsErrorRecordException + FullyQualifiedErrorId : RedirectionNotSupported  The above is a forced use of < since one could simply do cat haiku.txt  Recall that cat is an alias for get-content. The use of get-content is an idiom that gets around the lack an < operator. For example, instead of foo < input.txt  One does get-content input.txt | foo  Error messages are output on standard error ls idontexist.txt > output.txt cat output.txt #output.txt is empty ls idontexist.txt 2> output.txt # 2 is standard error ls haiku.txt 1> output.txt # 1 is standard output ls haiku.txt,test_file.txt 2>&1 > output.txt # Combine the two streams.  ## Searching for files # Find all UNIX: find . PS: get-childitem . -Recurse PS: get-childitem . -Recurse | foreach-object {$_.FullName}    #To give identical output as find


To save on typing, you can use the alias gci instead of get-childitem

# Directories only
UNIX: find . -type d
PS2: gci . -recurse | where { $_.PSIsContainer } PS3: gci -recurse -Directory  If you have PowerShell 2, you can only use the long winded version. It’s simpler in PowerShell 3. Similarly for searching for files only. # Files only UNIX: find . -type f PS2: get-childitem -recurse | where { !$_.PSIsContainer }
PS3: gci -recurse -File


With the Unix find command, you can specify the maximum and minimum search depths. There is no direct equivalent in PowerShell although you could write a function that will do this. Such a function can be found at http://windows-powershell-scripts.blogspot.co.uk/2009/08/unix-linux-find-equivalent-in.html although I have not tested this!

# Maximum depth of tree
UNIX: find . -maxdepth 2
PS : No direct equivalent
# Minimum depth of tree
UNIX: find . -mindepth 3
PS : No direct equivalent


You can also filter by name. Confusingly, PowerShell offers two ways of doing this. More details on the differences between these can be found at http://tfl09.blogspot.co.uk/2012/02/get-childitem-and-theinclude-and-filter.html

One key difference between find and get-childitem is that the latter is case-insenstive whereas find is case sensitive.

# Find by name
UNIX: find . -name '*.txt'
PS: gci -recurse -include *.txt
PS: gci -recurse -filter *.txt

#Find empty files
UNIX: find . -empty
PS: gci -recurse | where ($_.Length -eq 0) | Select FullName #Create empty file UNIX: touch emptyfile.txt PS: new-item emptyfile.txt -type file  ## Command Substituion In bash, you can execute a command using backticks and the result is substituted in place. i.e. #bash foo bar  The backticks are used as escape characters in PowerShell so you do the following instead #PS foo$(bar)


In both cases, the command bar is executed and result is substituted into the call to foo.

## Power of the pipe

| is a pipe. Use the pipe to connect the output of one command to the input of another:

Count text files

ls -filter *.txt | measure


ls outputs a list of files, measure inputs a list of files.

echo "Number of .txt files:"; ls -filter *.txt | measure | select -expand count


; equivalent to running two commands on separate lines.

Question: what does this do?

ls -name | select-string s | measure


Answer: counts the number of files with s in their name.

history | select-string 'echo'


Power of well-defined modular components with well-defined interfaces,

• Bolt together to create powerful computational and data processing workflows.
• Good design principle applicable to programming – Python modules, C libraries, Java classes – modularity and reuse.
• “little pieces loosely joined” – history + select-string = function to search for a command.

## Variables

get-variable                            # See all variables
$MYFILE="data.txt" # Need quotes around strings echo$MYFILE
echo "My file name is $MYFILE"$num = 1                                #Numbers don't need quotes
$num =$num+1                           #Simple Arithmetic
$TEXT_FILES=get-childitem Save output of get-childitem echo$TEXT_FILES


Variables only persist for the duration of the current PowerShell Session

## Environment variables

Windows environment variables don’t show up when you execute get-variable; to list them all you do

#PS
get-childitem env:                  #Show all Windows Environment variables
echo $env:PATH #Show the contents of PATH$env:Path = $env:Path + ";C:\YourApp\bin\" #temporarily add a folder to PATH  This modification to PATH will only last as long as the current session. It is possible to permanently modify the system PATH but this should only be done with extreme care and is not covered here. ## PowerShell Profile The PowerShell profile is a script that is executed whenever you launch a new session. Every user has their own profile. The location of your PowerShell profile is defined by the variable$profile

$profile  Open it with notepad$profile


Add something to it such as

echo "Welcome to PowerShell.  This is a message from your profile"


Restart PowerShell and you should see the message. You can use this profile to customise your PowerShell sessions. For example, if you have installed NotePad++, you might find adding the following function to your PowerShell Profile to be useful.

# Launch notepad++ using the npp command
function npp($file) { if ($file -eq $null) { & "C:\Program Files (x86)\Notepad++\notepad++.exe"; } else { & "C:\Program Files (x86)\Notepad++\notepad++.exe"$file;
}
}


With this function in your profile, you can open Notepad++ with the command npp or npp(filename.txt)

## Conditionals

$num = 1 if($num -eq 1)
{
write-host 'num equals 1'
}

$word="hello" if($word -eq "hello")
{
write-host 'The same'
}


By default, string tests are case insensitive

$word="hello" if($word -eq "HELLO")
{
write-host 'The same'
}


To force them to be case sensitive, add a c to the operator:

$word="hello" if($word -ceq "HELLO")
{
write-host 'The Same. This won't be printed'
}


You can similarly be explicitly case insensitive by adding an i. Although this is the the same behaviour as the undecorated operators and so might seem unnecessary, it shows your intent to the reader.

    $word="hello" if($word -ieq "HELLO")
{
write-host 'The same'
}

##### Comparison Operators
-eq Equal to
-lt Less than
-gt Greater than
-ge Greater than or equal to
-le Less than or equal to
-ne Not equal to

##### Logical operators
-not    Not
!       Not
-or     Or
-and    And


## Loops

PowerShell has several looping constructs. Here, I only consider two.

### for

Allows you to run a block of code a set number of times.

for ($i=1;$i -le 5; $i=$i+1)
{
Write-Host $i }  ### foreach Do something with every element of a collection foreach($item in $(ls *.txt)) {echo$item.Name}


TODO

## Shell scripts

• Save retyping.
• PowerShell scripts have the extension .ps1
• PowerShell scripts must be created with plain text editors such as Notepad or Notepad++. NEVER use Microsoft Word!

Here is a very simple script

notepad protein_filter.ps1                  #Open the file

#A simple protein filter
$DATE = get-date echo "Processing date:$DATE"

foreach($item in get-childitem *.pdb) { echo$item.Name
}

echo "Processing complete"


To run this just type the filename:

protein_filter.ps1


If you get an error message, it may be because your execution policy is set not to run scripts locally. Change this with the command

Set-ExecutionPolicy RemoteSigned            #Allow local scripts to run.  Needs to be run with admin privileges
protein_filter.ps1                          #Run the script


Primary Care Trust Prescribing Data – April 2011 onwards

$file="prim-care-trus-pres-data-apr-jun-2011-dat.csv"$path="$pwd\$file"   #Path needs to be fully qualified. This puts it in the current folder
$url = "http://www.ic.nhs.uk/catalogue/PUB02342/$file"
$client = new-object System.Net.WebClient$client.DownloadFile( $url,$path )


## Permissions

Windows file permissions are rather more complicated than those of Linux but most users won’t need to worry about them in day to day use.

## The call operator

It is sometimes convenient to construct strings that contain the full path to a PowerShell script we want to execute. For example:

$fullpath = "$pwd\myscript.ps1"


To actually run the script pointed to by this variable, you need to use the call operator &

& $fullpath #Runs myscript.ps1  You also need to do this if you try to call any script where the path contains spaces "C:\Program Files\myscript.ps1" #Will just display the string literal & "C:\Program Files\myscript.ps1" #Runs the script  ## Background Jobs Consider the script counter.ps1 param($step=1)
#counter.ps1: A simple, long running job to demonstrate background jobs

$i=1 while ($i -lt 200000 )
{
echo $i$i=$i+$step
}


This counts up to 200000 in user-defined steps.

./counter.ps1   > 1step.txt                 #Counts in steps of 1
./counter.ps1 -step 2 > 2step.txt           #Counts in steps of 2


The script takes quite a while to complete and you cannot do anything else in your PowerShell session while it is working. Using the start-job Cmdlet, we can run counter.ps1 in the background

start-job -scriptblock { C:\Users\walkingrandomly\Dropbox\SSI_Windows\dir_full_of_files\some_directory\counter.ps1 >  C:\Users\walkingrandomly\Dropbox\SSI_Windows\dir_full_of_files\some_directory\outcount1.txt }


Note that you have to use the full path to both the counter.ps1 script and the output file. You can see the status of the job with get-job

get-job

Id              Name            State      HasMoreData     Location             Command
--              ----            -----      -----------     --------             -------
1              Job1             Running    True            localhost             C:\Users\walkingrando...


get-job

Id              Name            State      HasMoreData     Location             Command
--              ----            -----      -----------     --------             -------
1               Job1            Completed  False           localhost             C:\Users\walkingrando...

ls outcount*                    #Ensure that output file has been created
remove-job 1                    #remove remnants of job 1 from the queue
get-job                         #Check that queue is empty


You can run as many simultaneous jobs as you like but it is best not to run too many or your computer will grind to a halt.

Here’s an example that runs 5 counter.ps1 jobs concurrently

#parallel_counters.ps1
#Runs 5 instances of counter.ps1 in parallel

$scriptname = "counter.ps1"$outputfileBase = "outfile"
$outputfileExt = ".txt"$scriptPath = "$pwd\$scriptname"

for ($i=1;$i -le 5; $i++) {$outputfilePath = "$pwd\$outputfileBase" + $i +$outputfileExt
$command = "$scriptPath -step $i >$outputfilePath"
$myScriptBlock = [scriptblock]::Create($command)
start-job -scriptblock $myScriptBlock }  Run this as a demonstration parallel_counters.ps1 get-job #Keep running until all have completed ls outfile* more outfile5.txt more outfile2.txt$myjob=get-job 2                    #Get info on job Id 2 and store in variable $myjob$myjob.Command                      #Look at the command that comprised job 2
remove-job *                        #Remove all job remnants from the queue
get-job                             #Should be empty


TODO: Dealing with output, recieve-job

## Secure Shell

There is no equivalent to the Linux commands ssh and sftp in PowerShell. The following free programs are recommended

## Packaging

There are no direct PowerShell equivalents to zip, unzip, tar etc. There are write-zip, write-tar and write-gzip cmdlets in the third party, free PowerShell Community Extensions but I have not investigated them yet.

## Transcripts

Start-transcript Initializes a transcript file which records all subsequent input/Output. Use the following syntax:

Start-Transcript [[-path] FilePath] [-force] [-noClobber] [-append]


Stop-transcript Stops recording and finalizes the transcript.

start-transcript -path ./diary.txt
ls
echo "Hello dear diary"
stop-transcript
cat diary.txt

• Record commands typed, commands with lots of outputs, trial-and-error when building software.
• Send exact copy of command and error message to support.
• Turn into blog or tutorial.

## Shell power

(Bentley, Knuth, McIlroy 1986) Programming pearls: a literate program Communications of the ACM, 29(6), pp471-483, June 1986. DOI: [10.1145/5948.315654].

Dr. Drang, More shell, less egg, December 4th, 2011.

Common words problem: read a text file, identify the N most frequently-occurring words, print out a sorted list of the words with their frequencies.

10 plus pages of Pascal … or … 1 line of shell

#BASH version
$nano words.sh tr -cs A-Za-z '\n' | tr A-Z a-z | sort | uniq -c | sort -rn | sed${1}q
$chmod +x words.sh$ nano words.sh < README.md
$nano words.sh < README.md 10  The PowerShell version is more complicated but still very short compared to the 10 pages of Pascal #count_words.ps1 Param([string]$filename,[int]$num)$text=get-content $filename$split = foreach($line in$text) {$line.tolower() -split "\W"}$split | where-object{-not [string]::IsNullorEmpty($_)} | group -noelement | sort Count -Descending | select -first$num



“A wise engineering solution would produce, or better, exploit-reusable parts.” – Doug McIlroy

## A random walk through Mathematica 10

July 10th, 2014

Introduction

Mathematica 10 was released yesterday amid the usual marketing storm we’ve come to expect for a new product release from Wolfram Research. Some of the highlights of this marketing information include

Without a doubt, there is a lot of great new functionality in this release and I’ve been fortunate enough to have access to some pre-releases for a while now.  There is no chance that I can compete with the in-depth treatments given by Wolfram Research of the 700+ new functions in Mathematica 10 so I won’t try.  Instead, I’ll hop around some of the new features, settling on those that take my fancy.

Multiple Undo

I’ve been a Mathematica user since version 4 of the product which was released way back in 1999.  For the intervening 15 years, one aspect of Mathematica that always frustrated me was the fact that the undo feature could only undo the most recent action. I, along with many other users, repeatedly asked for multiple undo to be implemented but were bitterly disappointed for release after release.

Few things have united Mathematica users more than the need for multiple undo:

Finally, with version 10, our hopes and dreams have been answered and multiple undo is finally here. To be perfectly honest, THIS is the biggest reason to upgrade to version 10. Everything else is just tasty gravy.

Key new areas of functionality

Most of the things considered in this article are whimsical and only scratch the surface of what’s new in Mathematica 10.  I support Mathematica (and several other products) at the University of Manchester in the UK and so I tend to be interested in things that my users are interested in. Here’s a brief list of new functionality areas that I’ll be shouting about

• Machine Learning I know several people who are seriously into machine learning but few of them are Mathematica users.  I’d love to know what they make of the things on offer here.
• New image processing functions The Image Processing Toolbox is one of the most popular MATLAB toolboxes on my site. I wonder if this will help turn MATLAB-heads. I also know people in a visualisation group who may be interested in the new 3D functions on offer.
• Nonlinear control theoryVarious people in our electrical engineering department are looking at alternatives to MATLAB for control theory. Maple/Maplesim and Scilab/Xcos are the key contenders. SystemModeler is too expensive for us to consider but the amount of control functionality built into Mathematica is useful.

Entities – a new data type for things that Mathematica knows stuff about

One of the new functions I’m excited about is GeoGraphics that pulls down map data from Wolfram’s servers and displays them in the notebook.  Obviously, I did not read the manual and so my first attempt at getting a map of the United Kingdom was

GeoGraphics["United Kingdom"]

What I got was a map of my home town, Sheffield, surrounded by a red cell border indicating an error message

The error message is “United Kingdom is not a Graphics primitive or directive.”  The practical upshot of this is that GeoGraphics is not built to take strings as arguments.  Fair enough, but why the map of Sheffield?  Well, if you call GeoGraphics[] on its own, the default action is to return a map centred on the GeoLocation found by considering your current IP address and it seems that it also does this if you send something bizarre to GeoGraphics.  In all honesty, I’d have preferred no map and a simple error message.

In order to get what I want, I have to pass an Entity that represents the UK to the GeoGraphics function.  Entities are a new data type in Mathematica 10 and, as far as I can tell, they formally represent ‘things’ that Mathematica knows about. There are several ways to create entities but here I use the new Interpreter function

From the above, you can see that Entities have a special new StandardForm but their InputForm looks straightforward enough. One thing to bear in mind here is that all of the above functions require a live internet connection in order to work.  For example, on thinking that I had gotten the hang of the Entity syntax, I switched off my internet connection and did

mycity = Entity["City", "Manchester"]

During evaluation of In[92]:= URLFetch::invhttp: Couldn't resolve host name. >>

During evaluation of In[92]:= WolframAlpha::conopen: Using WolframAlpha requires internet connectivity. Please check your network connection. You may need to configure your firewall program or set a proxy in the Internet Connectivity tab of the Preferences dialog. >>

Out[92]= Entity["City", "Manchester"]

So, you need an internet connection even to create entities at this most fundamental level.  Perhaps it’s for validation?  Turning the internet connection back on and re-running the above command removes the error message but the thing that’s returned isn’t in the new StandardForm:

If I attempt to display a map using the mycity variable, I get the map of Sheffield that I currently associate with something having gone wrong (If I’d tried this out at work,in Manchester, on the other hand, I would think it had worked perfectly!).  So, there is something very wrong with the entity I am using here – It doesn’t look right and it doesn’t work right – clearly that connection to WolframAlpha during its creation was not to do with validation (or if it was, it hasn’t helped).  I turn back to the Interpreter function:

In[102]:= mycity2 = Interpreter["City"]["Manchester"] // InputForm

Out[102]//InputForm:= Entity["City", {"Manchester", "Manchester", "UnitedKingdom"}]

So, clearly my guess at how a City entity should look was completely incorrect.  For now, I think I’m going to avoid creating Entities directly and rely on the various helper functions such as Interpreter.

What are the limitations of knowledge based computation in Mathematica?

All of the computable data resides in the Wolfram Knowledgebase which is a new name for the data store used by Wolfram Alpha, Mathematica and many other Wolfram products. In his recent blog post, Stephen Wolfram says that they’ll soon release the Wolfram Discovery Platform  which will allow large scale access to the Knowledgebase and indicated that ‘basic versions of Mathematica 10 are just set up for small-scale data access.’  I have no idea what this means and what limitations are in place and can’t find anything in the documentation.

Until I understand what limitations there might be, I find myself unwilling to use these data-centric functions for anything important.

IntervalSlider – a new control for Manipulate

I’ll never forget the first time I saw a Mathematica Manipulate – it was at the 2006 International Mathematica Symposium in Avignon when version 6 was still in beta. A Wolfram employee created a fully functional, interactive graphical user interface with just a few lines of code in about 2 minutes –I’d never seen anything like it and was seriously excited about the possibilities it represented.

8 years and 4 Mathematica versions later and we can see just how amazing this interactive functionality turned out to be. It forms the basis of the Wolfram Demonstrations project which currently has 9677 interactive demonstrations covering dozens of fields in engineering, mathematics and science.

Not long after Mathematica introduced Manipulate, the sage team introduced a similar function called interact. The interact function had something that Manipulate did not – an interval slider (see the interaction called ‘Numerical integrals with various rules’ at http://wiki.sagemath.org/interact/calculus for an example of it in use). This control allows the user to specify intervals on a single slider and is very useful in certain circumstances.

As of version 10, Mathematica has a similar control called an IntervalSlider.  Here’s some example code of it in use

Manipulate[
pl1 = Plot[Sin[x], {x, -Pi, Pi}];
pl2 = Plot[Sin[x], {x, range[[1]], range[[2]]}, Filling -> Axis,
PlotRange -> {-Pi, Pi}];
inset = Inset["The Integral is approx " <> ToString[
NumberForm[
Integrate[Sin[x], {x, range[[1]], range[[2]]}]
, {3, 3}, ExponentFunction -> (Null &)]], {2, -0.5}];
Show[{pl1, pl2}, Epilog -> inset], {{range, {-1.57, 1.57}}, -3.14,
3.14, ControlType -> IntervalSlider, Appearance -> "Labeled"}]

and here’s the result:

Associations – A new kind of brackets

Mathematica 10 brings a new fundamental data type to the language, associations. As far as I can tell, these are analogous to dictionaries in Python or Julia since they consist of key,value pairs.  Since Mathematica has already used every bracket type there is, Wolfram Research have had to invent a new one for associations.

Let’s create an association called scores that links 3 people to their test results

In[1]:= scores = <|"Mike" -> 50.2, "Chris" -> 100.00, "Johnathan" -> 62.3|>

Out[1]= <|"Mike" -> 50.2, "Chris" -> 100., "Johnathan" -> 62.3|>

We can see that the Head of the scores object is Association

In[2]:= Head[scores]

Out[2]= Association

We can pull out a value by supplying a key. For example, let’s see what value is associated with “Mike”

In[3]:= scores["Mike"]

Out[3]= 50.2

All of the usual functions you expect to see for dictionary-type objects are there:-

In[4]:= Keys[scores]

Out[4]= {"Mike", "Chris", "Johnathan"}

In[5]:= Values[scores]

Out[5]= {50.2, 100., 62.3}

In[6]:= (*Show that the key "Bob" does not exist in scores*)
KeyExistsQ[scores, "Bob"]

Out[6]= False

If you ask for a key that does not exist this happens:

In[7]:= scores["Bob"]

Out[7]= Missing["KeyAbsent", "Bob"]

There’s a new function called Counts that takes a list and returns an association which counts the unique elements in the list:

In[8]:= Counts[{q, w, e, r, t, y, u, q, w, e}]

Out[8]= <|q -> 2, w -> 2, e -> 2, r -> 1, t -> 1, y -> 1, u -> 1|>

Let’s use this to find something out something interesting, such as the most used words in the classic text, Moby Dick

In[1]:= (*Import Moby Dick from Project gutenberg*)

MobyDick =
Import["http://www.gutenberg.org/cache/epub/2701/pg2701.txt"];
(*Split into words*)
words = StringSplit[MobyDick];
(*Convert all words to lowercase*)

words = Map[ToLowerCase[#] &, words];
(*Create an association of words and corresponding word count*)

wordcounts = Counts[words];
(*Sort the association by key value*)

wordcounts = Sort[wordcounts, Greater];
(*Show the top 10*)
wordcounts[[1 ;; 10]]

Out[6]= <|"the" -> 14413, "of" -> 6668, "and" -> 6309, "a" -> 4658,
"to" -> 4595, "in" -> 4116, "that" -> 2759, "his" -> 2485,
"it" -> 1776, "with" -> 1750|>

All told, associations are a useful addition to the Mathematica language and I’m happy to see them included.  Many existing functions have been updated to handle Associations making them a fundamental part of the language.

s/Mathematica/Wolfram Language/g

I’ve been programming in Mathematica for well over a decade but the language is no longer called ‘Mathematica’, it’s now called ‘The Wolfram Language.’  I’ll not lie to you, this grates a little but I guess I’ll just have to get used to it.  Flicking through the documentation, it seems that a global search and replace has happened and almost every occurrence of ‘Mathematica’ has been changed to ‘The Wolfram Language’

This is part of a huge marketing exercise for Wolfram Research and I guess that part of the reason for doing it is to shift the emphasis away from mathematics to general purpose programming.  I wonder if this marketing push will increase the popularity of The Wolfram Language as measured by the TIOBE index? Neither ‘Mathematica’ or ‘The Wolfram Language’ is listed in the top 100 and last time I saw more detailed results had it at number 128.

Fractal exploration

One of Mathematica’s competitors, Maple, had a new release recently which saw the inclusion of a set of fractal exploration functions. Although I found this a fun and interesting addition to the product, I did think it rather an odd thing to do.  After all, if any software vendor is stuck for functionality to implement, there is a whole host of things to do that rank higher in most user’s list of priorities than a function that plots a standard fractal.

It seems, however, that both Maplesoft and Wolfram Research have seen a market for such functionality.  Mathematica 10 comes with a set of functions for exploring the Mandelbrot and Julia sets. The Mandelbrot set alone accounts for at least 5 of Mathematica 10’s 700 new functions:- MandelbrotSetBoettcherMandelbrotSetDistanceMandelbrotSetIterationCount, MandelbrotSetMemberQ and MandelbrotSetPlot.

MandelbrotSetPlot[]

Barcodes

I found this more fun than is reasonable!  Mathematica can generate and recognize bar codes and QR codes in various formats.  For example

BarcodeImage["www.walkingrandomly.com", "QR"]



Scanning the result using my mobile phone brings me right back home :)

Unit Testing

A decent unit testing framework is essential to anyone who’s planning to do serious software development. Python has had one for years, MATLAB got one in 2013a and now Mathematica has one.  This is good news!  I’ve not had chance to look at it in any detail, however. For now, I’ll simply nod in approval and send you to the documentation. Opinions welcomed.

Disappointments in Mathematica 10

There’s a lot to like in Mathematica 10 but there’s also several aspects that disappointed me

Version 9 of Mathematica included integration with R which excited quite a few people I work with. Sadly, it seems that there has been no work on RLink at all between version 9 and 10.  Issues include:

• The version of R bundled with RLink is stuck at 2.14.0 which is almost 3 years old. On Mac and Linux, it is not possible to use your own installation of R so we really are stuck with 2.14. On Windows, it is possible to use your own installation of R but CHECK THAT version 3 issue has been fixed http://mathematica.stackexchange.com/questions/27064/rlink-and-r-v3-0-1
• It is only possible to install extra R packages on Windows. Mac and Linux users are stuck with just base R.

This lack of work on RLink really is a shame since the original release was a very nice piece of work.

If the combination of R and notebook environment is something that interests you, I think that the current best solution is to use the R magics from within the IPython notebook.

No update to CUDA/OpenCL functions

Mathematica introduced OpenCL and CUDA functionality back in version 8 but very little appears to have been done in this area since. In contrast, MATLAB has improved on its CUDA functionality (it has never supported OpenCL) every release since its introduction in 2010b and is now superb!

Accelerating computations using GPUs is a big deal at the University of Manchester (my employer) which has a GPU-club made up of around 250 researchers. Sadly, I’ll have nothing to report at the next meeting as far as Mathematica is concerned.

FinancialData is broken (and this worries me more than you might expect)

I wrote some code a while ago that used the FinancialData function and it suddenly stopped working because of some issue with the underlying data source. In short, this happens:

In[12]:= FinancialData["^FTAS", "Members"]

Out[12]= Missing["NotAvailable"]

This wouldn’t be so bad if it were not for the fact that an example given in Mathematica’s own documentation fails in exactly the same way! The documentation in both version 9 and 10 give this example:

In[1]:= FinancialData["^DJI", "Members"]

Out[1]= {"AA", "AXP", "BA", "BAC", "CAT", "CSCO", "CVX", "DD", "DIS", \
"GE", "HD", "HPQ", "IBM", "INTC", "JNJ", "JPM", "KFT", "KO", "MCD", \
"MMM", "MRK", "MSFT", "PFE", "PG", "T", "TRV", "UTX", "VZ", "WMT", \
"XOM"}

but what you actually get is

In[1]:= FinancialData["^DJI", "Members"]

Out[1]= Missing["NotAvailable"]`

For me, the implications of this bug are far more reaching than a few broken examples.  Wolfram Research are making a big deal of the fact that Mathematica gives you access to computable data sets, data sets that you can just use in your code and not worry about the details.

Well, I did just as they suggest, and it broke!

Summary

I’ve had a lot of fun playing with Mathematica 10 but that’s all I’ve really done so far – play – something that’s probably obvious from my choice of topics in this article. Even through play, however, I can tell you that this is a very solid new release with some exciting new functionality. Old-time Mathematica users will want to upgrade for multiple-undo alone and people new to the system have an awful lot of toys to play with.

Looking to the future of the system, I feel excited and concerned in equal measure. There is so much new functionality on offer that it’s almost overwhelming and I love the fact that its all integrated into the core system. I’ve always been grateful of the fact that Mathematica hasn’t gone down the route of hiving functionality off into add-on products like MATLAB does with its numerous toolboxes.

My concerns center around the data and Stephen Wolfram’s comment ‘basic versions of Mathematica 10 are just set up for small-scale data access.’  What does this mean? What are the limitations and will this lead to serious users having to purchase add-ons that would effectively be data-toolboxes?

Final

Have you used Mathematica 10 yet? If so, what do you think of it? Any problems? What’s your favorite function?