Add aa.cls & fix typos
Merge pull request #1 from jdswinbank/aa.cls

Add aa.cls & fix typos
Proper citation, removed (almost) all blue section descriptors
Update Computational Perf with bulletpoints
Collated Ionospheric description, justified text, major/minor iteration plot
Merge remote-tracking branch 'origin/master'

Conflicts:
	aartfaac_RT_calib_v1.tex
	aartfaac_RT_calib_v1.tex~
Further flesh out computational performance section
Reorganization of directory structure; added Figs folder containing data and plot
files for generating the plots in the paper.
Merge branch 'master' of github.com:hsuyeep/AARTFAAC_track_cal
Changes to text after reorganization of plots, see below
	modified:   Makefile
		Included cleaning up via make -i clean

	modified:   aartfaac_RT_calib_v1.tex
		- Rewrote the abstract, include more results.
		- Removed part about timescales of transients at edge of field of view,
		  which required calculation of smearing effects on field edge sources
          due to a zenith phase center.
		- Removed Discussion section completely
		- Removed references to subsection on depth of deconvolution.
		- Included references to Folkert's performance table.
		- Added plot showing model efficacy in lieu of visibility amplitude error
		  plot. The phase error plot remains.
		- Removed TODO on error of estimated params against number of iterations
		- Edited RFI section text removed TODO on statistics of flagged times.
		- Edited section on Solar flares.
		- Removed mention of plot in the creeping bias subsection.
		- Slightly edited the conclusions.
		- NOTE: THE Previous commit after organizing figures had a snafu due to
		  locally moving the Figs/ folder to Figs.old, and populating a new Figs/
		  folder with data and plots. I should have used git rm to do so!
Computational perf update
Commit prior to incorporation of Swinbank's comments, figure updates
Computational Perf: Add daytime timings
Commit incorporating most of John's, Alexander's and Ralph's comments. Prior
to shakedown with Stefan.
Various updates on comp perf
Major commit with several new additions.
	new file:   Figs/Data/combined_SB002_2_convcalsol.bin.gains
		- Data corresponding to dawn time gains.
	new file:   Figs/SB000_ch30-35_5sec_3hr_9_convcalsol_bin_iter_major.png
	new file:   Figs/SB000_ch30-35_5sec_3hr_9_convcalsol_bin_iter_minor.png
		- Split major and minor iteration plots for better placement
	new file:   Figs/Src/func_single_iter.m
	   - Generates calvis and model ratio for phase analysis
	new file:   Figs/combined_SB002_2_convcalsol_bin_gains.png
		- Added dawn time gains
	new file:   Figs/selfcal_phase_behaviour.png
		- Generated using func_singleiter.m
	new file:   Figs/uncal_cal_deconv_night.png
		- Added all-sky images, per Alexander's recommendation.
	modified:   aartfaac_RT_calib_v1.tex
		- Switched sections 2 and 3.
		- Added Brief overview of main results
		- Added algorithmic summary
		- Removed section on bias of flux estimator
		- Split performance section into observational and computational parts.
		- Moved difference imaging section into observational performance.
Merge branch 'master' of github.com:hsuyeep/AARTFAAC_track_cal

Conflicts:
	aartfaac_RT_calib_v1.tex
add daytime results
Commit with all (except 1) TODOs removed.
	  - Changed abstract
	  - Rewrote conclusions
	  - Rewrote section on pipeline architecture and performance
	  - Edited section on all-sky calibration
	  - Moved block on selfcal constraints around.
	  - Added variance of phase and gain estimates on displayed observation.
	  - Modified sec. on time/freq binning, added bandwidth smearing vals.
	  - Added difference imaging equation.
	  - Modified RFI, creeping bias, active Sun sections.
Major commit with Wijnholds' comments
	new file:   Figs/CasAsrcposoff.eps
		- Updated time label
	new file:   Figs/Data/cmpcalsol_27-Jan-2014 21:03:52.txt
		- New error metric in cmpcalsol.m
	new file:   Figs/SB000_LBA_OUTER_2222-2258_1ch_1_convcalsol_bin_sigmas.eps
		- pltsigmas output
	new file:   Figs/SB000_ch30-35_5sec_3hr_9_convcalsol_bin_iter_major.eps
		- pltiter output
	new file:   Figs/SB000_ch30-35_5sec_3hr_9_convcalsol_bin_iter_minor.eps
		- pltiter output
	new file:   Figs/SB002_LBA_OUTER_SPREAD_1ch_6_convcal_7_el_fftimg_bin_save_mat_tseries.eps
		- pltlightcurve output
	new file:   Figs/SB002_LBA_OUTER_SPREAD_1ch_8_convcalsol_bin_gains.eps
		- pltgains output
	new file:   Figs/SB002_LBA_OUTER_SPREAD_1ch_8_convcalsol_bin_sigmas.eps
		- pltsigmas output
	modified:   Figs/Src/pltcmpcalsol.m
		- Generated a new datafile containing MAD values, writing to eps.
	modified:   Figs/Src/pltconv.m
		- Writing to eps.
	modified:   Figs/Src/pltfreqwsfdiff.m
		- Fixed timestamp, fixed disappearing ylabel, writing to eps.
	modified:   Figs/Src/pltgains.m
		- Fixed timestamp, writing to eps.
	modified:   Figs/Src/pltiter.m
		- Fixed timestamp, writing to eps.
	modified:   Figs/Src/pltlightcurve.m
		- Fixed timestamp, writing to eps.
	modified:   Figs/Src/pltmodelefficacy.m
		- Bold ylabel, writing to eps.
	modified:   Figs/Src/pltsigmas.m
		- Fixed UTC label, writing to eps
	modified:   Figs/Src/tracking_cal_schematic.odp
		- Removed confusing median window on incoming timeslices
	new file:   Figs/cmpcalsol.eps
		- Now using Mean Absolute Deviation due to systematic offsets in gainsol. phase
		  which raise the MSE error very high.
	modified:   Figs/cmpcalsol.png
		- Redundant: Use eps
	new file:   Figs/combined_SB002_2_convcalsol_bin_gains.eps
		- Regenerated from data file.
	new file:   Figs/combined_SB002_2_convcalsol_bin_sigmas.eps
		- From regenerated file, after hdd crash. Fixed UTC label
	new file:   Figs/major_minor_cycle_conv.eps
		- Fixed timing error, UTC label
	modified:   Figs/major_minor_cycle_conv.png
		- Redundant: Use eps
	new file:   Figs/model_efficacy.eps
		- eps file shows ylabel in bold
	modified:   Figs/model_efficacy.png
		- Redundant: Use eps
	modified:   Figs/pipeline-design.png
		- Cropped wasted whitespace
	new file:   Figs/tracking_cal_schematic_new.png
		- Removed confusing median window on incoming timeslices

	modified:   Makefile
	new file:   aa_instructions.pdf
		- Added for checking table/figure/citation rules

	modified:   aartfaac_RT_calib_v1.tex
		- using epstppdf package for figures in eps
		- Added missing references, fixed \citep and \citet usage.
		- Fixed size of array as 300m from 350m earlier.
		- Fixed tables to reflect A&A style, including captions and lack of column separaters
		- Fixed segment on 2D imaging and not needing W-projection etc.
		- More sensible paragraph breaks, per Wijnholds' suggestions.
		- DDE handling (sec. 3.1): removed implicit assumption on not being able to handle more than one direction.
		- ACM = Array covariance matrix.
		- Calibration flow diagram is now single column, at 70% zoom
		- Eq. 3,4 and in between: consistent bold usage (using \bm).
		- Se. 4.1.3: Clarified masking of shortest baselines in new sigmas estimator.
		- Removed para just above Sec. 4.1.4 due to algorithmic summary block.
		- Tracking cal. bullet description cleanup.
		- Added reference to Fig. 4, now it does not appear before Fig. 5.
		- Fixed legend of same color on Fig. 5
		- Fixed referencing of test obseravations, checked their calls for consistency
		- Regenerated Fig. 8 using a difference error criteria.
		- Fixed spectral bin order of magnitude difference (just above Sec. 5.5)
		- Fixed duration of integration in difference imaging.
		- Enlarged pipeline design schematic.
		- Made changes to conclusion.
	modified:   aartfaac_RT_calib_v1.tex~

	modified:   ref.bib
		- Added several new citations, still to check consistency of references