Adapting Code Introduction to OOP Code what code

Adapting Code • Introduction to OOP • Code, what code? What & where • Why adapt code anyway? • How? Astro-WISE Tutorial, Leiden 18 -20 August 2008

Introduction to OOP (1) • OOP is programming with classes • Programming in the problem domain – Describe a problem in one sentence, then the nouns are the classes/objects: • Let’s reduce a bias of ccd 50 of the WFI instrument – Classes are blue-prints describing real world “things” – Can also map to abstract “things” Astro-WISE Tutorial, Leiden 18 -20 August 2008

Introduction to OOP (2) • Advantages of using OOP: – Reuse of code – Readability of code – Bug tracking • Important concepts: – Inheritance – Polymorphism Astro-WISE Tutorial, Leiden 18 -20 August 2008

Structure of a class, members class Cat: age = 3. 0 weight = 5. 2 attribute def miaw(self): print ‘Miaw!’ method object def kill_other_cat(self, other): . . awe> cat = Cat() awe> cat. age 3. 0 awe> cat. age = 5. 0 awe> cat. age 5. 0 Astro-WISE Tutorial, Leiden 18 -20 August 2008

Inheritance class Mammal: weight = -1 def breathe(self): . . class Cat(Mammal): inheritance def miaw(self): print ‘Miaw!’ def kill_other_cat(self, other): . . Astro-WISE Tutorial, Leiden 18 -20 August 2008 cat = Cat() cat. breate()

Polymorphism class Mammal: def swim(self): . . polymorphism class Cat(Mammal): def swim(self): # head up, move paws class Dolphin(Mammal): def swim(self): # head down, move fins class Toddler(Mammal): def yell(self, txt): print txt. upper() + ‘!!’ def swim(self): self. yell(‘I can’t swim’) Astro-WISE Tutorial, Leiden 18 -20 August 2008

Getting a checkout • CVS checkout = local copy of the code – Two versions: AWBASE and “most recent’’ • Must use “pserver” to log in anonymously – User anoncvs, password <ask representative, on request> >cvs –d cvs. astro-wise. org: /cvsroot co awe >cvs -d : pserver: anoncvs@cvs. astrowise. org: /cvsroot login ># base version >cvs -d : pserver: anoncvs@cvs. astro-wise. org: /cvsroot checkout -r AWBASE awe Astro-WISE Tutorial, Leiden 18 -20 August 2008

Using your own checkout • Set environment AWEPIPE to point to the checkout directory (“awe”) > setenv AWEPIPE /data/users/helmich/awe (add to. cshrc) Astro-WISE Tutorial, Leiden 18 -20 August 2008

Why adapt code? • Hopefully not often necessary • Make scripts to speed up process, and as a memory tool • Create objects with your own methods Astro-WISE Tutorial, Leiden 18 -20 August 2008

Directory structure • Top level: awe • common, astro, lofar, ai – Isolate specific code Astro-WISE Tutorial, Leiden 18 -20 August 2008

Directory structure: common config database log math net services toolbox util | Startup and environment/configuration files | Persistency mechanism and implementations of its interface | Logging and messaging | Mathematical Python routines such as statistics & least squares | General network-related python modules | Common (web-) services | Scripts for e. g. maintenance of the database, installation, etc. | Routines for compression, checksumming, datetime manipulation. Astro-WISE Tutorial, Leiden 18 -20 August 2008

Directory structure: astro config database experimental external | Startup and environment/configuration files | Astronomy specific database modules | Experimental modules | Python wrappers for tools such as LDAC, Sextractor and Swarp filerecipes | Data reduction recipes for use without database instrument | Instrument specific modules main | Modules for the pipeline processing of images plot | Various plotting modules recipes | Data reduction recipes (to create classes in "main") services | (Web-) services for astronomy test | Unittests toolbox | Scripts for ingestion, installation, various maintenance util | Utility modules usable throughout the code Astro-WISE Tutorial, Leiden 18 -20 August 2008

Making a script (1/2) • Based around dpu instance • Based around a task • As a sort of task • Write the script in a file with. py extension • Run with this command: > awe script. py Astro-WISE Tutorial, Leiden 18 -20 August 2008

Making a script (2/2) • Classes/models need to be imported • Dotted (directory) structure: – from astro. recipes. Reduce import Reduce. Task Astro-WISE Tutorial, Leiden 18 -20 August 2008

Script based around dpu from astro. recipes. mods. dpu import Processor from astro. main. Raw. Frame import Raw. Bias. Frame dpu = Processor('dpu. hpc. rug. astro-wise. org') ccd 50 = [r. filename for r in Raw. Bias. Frame. select(date='2000 -04 -28', instrument='WFI', chip='ccd 50')] ccd 51 = [r. filename for r in Raw. Bias. Frame. select(date='2000 -04 -28', instrument='WFI', chip='ccd 51')] dpu. run('Bias', instrument='WFI', raw_filenames=ccd 50) dpu. run('Bias', instrument='WFI', raw_filenames=ccd 51) Astro-WISE Tutorial, Leiden 18 -20 August 2008

Script based around Task • In particular to store configuration from astro. recipes. Gal. Phot import Gal. Phot. Task from astro. util. Pars import Pars p=Pars(Gal. Phot. Task) p. Gal. Phot. Model. process_params. r 1 = 10. 0 p. Gal. Phot. Model. process_params. dangmax=0. 2 # etc. task = Gal. Phot. Task(instrument='WFI', slid=423431, sids=[16246], pars=p. get(), commit=0) task. execute() Astro-WISE Tutorial, Leiden 18 -20 August 2008

Simple eclipse script • Eclipse is used for image arithmetic import eclipse import glob filenames = glob('*. red. fits') images = [eclipse. image(filename) for filename in filenames] cube = eclipse. cube(images) median = cube. median() median. save('eclipse_med. fits') Astro-WISE Tutorial, Leiden 18 -20 August 2008

Adapting classes • Process. Target classes are located in astro. main – Lets look at Bias. Frame: class Bias. Frame(Base. Frame): . . def make_image(self). . cube = eclipse. cube([raw. image for raw in self. raw_bias_frames]) # current method does an average with sigma rejection self. image = cube. median() # use a median instead Astro-WISE Tutorial, Leiden 18 -20 August 2008