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Changed the title, because it was misleading. There was no question about "best practices on scripting".
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Best practices for Doubts on scripting: processingerror messages when trying to run and how to process lots of files

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Best practices for scripting: processing lots of files

I have created my first mathematica 'program' as I think of it, to do some image processing. After reading in an image, it does a lot of stuff (including smoothing, fourier transform, functional representation, searching for critical points, outputing various files).

Now, I have hundreds of images that I want to process: obviously a job for a script. But I am somehow not understanding the whole mess of CommandLine, ScriptCommandline, or even how to properly edit script files (am I supposed to do it in the notebook? Because I'm using a lot of mathematica symbols, so I'm not sure how I could edit otherwise) or how to get scripts to run! It seems part of the problem is that scripting has changed in Mathematica 9 and a lot of previous Q&A entries focus on solutions for prior versions.

I have tried to get a basic script working on my system and I get really odd errors. E.g.,

#!/Applications/Mathematica.app/Contents/MacOS/MathematicaScript - script (*generate "num" samples of a mixed distribution*) num = ToExpression[$ScriptCommandLine[[2]]]; Print /@ RandomVariate[ MixtureDistribution[{1, 2}, {NormalDistribution[1, 0.2], NormalDistribution[3, 0.1]}], num, WorkingPrecision -> 50] 

I get:

$ ./test.m 10

./test.m: line 1: F814W_knotD_ACSHRC_2.91772_J8L001031_50_.fits: command not found

./test.m: line 3: F814W_knotD_ACSHRC_2.91772_J8L001031_50_.fits: command not found

./test.m: line 4: *#!/Applications/Mathematica.app/Contents/MacOS/MathematicaScript: No such file or directory

./test.m: line 5: F814W_knotD_ACSHRC_2.91772_J8L001031_50_.fits: command not found

./test.m: line 6: syntax error near unexpected token `*generate'

./test.m: line 6: `((generate "num" samples of a mixed distribution))'

(those fits files are in the same directory, and I have NO IDEA why it is talking about them)

Apologies for the newbie questions... hopefully this will be the last one for a while!!