deletions | additions       diff --git a/Makefile b/Makefile  index 86e0ae8..bbda12f 100644  --- a/Makefile  +++ b/Makefile 
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${BIBTEX} mwe  ${LATEX} mwe.tex  .PHONY #.PHONY  : %.tex %.tex #%.tex  : #  ${PDFLATEX} $@ #  ${BIBTEX} $(basename @) #  ${PDFLATEX} $@ #  ${BIBTEX} $(basename @) #  ${PDFLATEX} $@ ch_h2colarge:   diff --git a/ch_h2colarge.tex b/ch_h2colarge.tex  index 39bf32a..1b25cde 100644  --- a/ch_h2colarge.tex  +++ b/ch_h2colarge.tex 
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\chapter{\formaldehyde observations of BGPS sources not previously observed with Arecibo}  \label{ch:h2colarge}  \section{Preface}   Given our success with the simple 4-hour GBT observation of $\sim20$ sources, 
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% on the outer galaxy in detail.  \subimport{/Users/adam/work/h2co/outergal/paper/}{h2co_outergal}  \subimport{/Users/adam/work/thesis/}{h2co_maps}  \subimport{/Users/adam/work/thesis/}{h2co_lowdens} \subimport{/Users/adam/work/h2co/maps/paper/}{h2co_maps}  \subimport{/Users/adam/work/h2co/lowdens/paper/}{h2co_lowdens}  \input{solobib}  \end{document}  diff --git a/ch_software.tex b/ch_software.tex  index 12e67c3..a050bf1 100644  --- a/ch_software.tex  +++ b/ch_software.tex 
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\chapter{Software developed during this thesis}  \label{ch:software}  \section{Preface}  Software development is severely often  underappreciated in astronomy. It is not particularly difficult for expert developers to make production-level codes  useable by a large community, but that level of support is rarely provided to  astronomers. %  For the majority of major telescope facilities, data reduction is %  left entirely to the user, which leads to major delays in science and prevents %  re-use of archival data. The JCMT and STSCI have been exceptions to this rule %  - they have supported significant groups of software developers with the goal %  of producing useable archive data products. Similarly, the NRAO has recently %  taken on a greater level of software support for ALMA and EVLA products, %  producing fully pipeline-reduced data for observers. Unfortunately, the NOAO %  has instead cut funding to their software developers, leaving IRAF as an %  under-supported hulk of a code that everyone still uses. In this section, I summarize the codes I've written primarily for performing  reduction of data not supported by any standard reduction software. The text 
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IRAF is still the only software capable of efficiently fitting and performing  geometric transforms of images, which is necessary for both world coordinate  corrections and two-dimensional spectroscopy. These limitations will, hopefully,  be alleviated with new packages being build built  for astropy. The standard TripleSpec pipeline is the SPEXTOOL data pipeline written by Michael  Cushing. This pipeline is useful for deep spectra of single objects, but not  diff --git a/h2co_lowdens.tex b/h2co_lowdens.tex  index 88ff56b..c8801fd 100644  --- a/h2co_lowdens.tex  +++ b/h2co_lowdens.tex 
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are 73 K at 6 cm and 11 K at 2 cm for the south component, and 194 K at 6 cm  and 28 K at 2 cm for the north component.  \FigureTwo{figures_chH2CO/G43.17+0.01_H2CO_overplot_gbt9x.png}  {figures_chH2CO/G43.16-0.03_H2CO_overplot_gbt9x.png} \FigureTwo{figures/G43.17+0.01_H2CO_overplot_gbt9x.png}  {figures/G43.16-0.03_H2CO_overplot_gbt9x.png}  {Spectra of the \formaldehyde \oneone (black), \twotwo (red), and \thirteenco  1-0 (green) lines towards G43.17+0.01 (left) and G43.16-0.03 (right).  The \formaldehyde spectra are shown continuum-subtracted, and the \thirteenco 
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cloud. However, it is much smaller, with $M\approx8.3\ee{3}\pm3.2\ee{3} \msun$  compared to California's $\sim10^5$.  \Figure{figures_chH2CO/W49_RGB_40kms_aplpy.png} \Figure{figures/W49_RGB_40kms_aplpy.png}  {The G43 40 \kms cloud. The background image shows Herschel SPIRE 70 \um (red),  Spitzer MIPS 24 \um (green), and Spitzer IRAC 8 \um (blue) in the background with  the \thirteenco integrated image from $v=36 \kms$ to $v=43 \kms$ at contour levels of 
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where $S_\nu$ is the spectrum (with continuum included) and $\bar{C_\nu}$ is  the measured continuum.  \FigureTwo{figures_chH2CO/G43.16-0.03_40kms_h2codensfit.png}  {figures_chH2CO/G43.17+0.01_40kms_h2codensfit.png} \FigureTwo{figures/G43.16-0.03_40kms_h2codensfit.png}  {figures/G43.17+0.01_40kms_h2codensfit.png}  {Optical depth spectra of the \oneone and \twotwo lines towards the two W49  lines of sight, G43.16 (left) and G43.17 (right). The fitted parameters, along with the statistical 1-$\sigma$  errors, are shown in the legend. The optical depth ratio falls in a regime 
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% functions of column density that have recently become popular  % \citep[e.g][]{Kainulainen2009}.  %\input{solobib} \input{solobib}  \end{document}  diff --git a/h2co_maps.tex b/h2co_maps.tex  index 4e45162..6f0e6bb 100644  --- a/h2co_maps.tex  +++ b/h2co_maps.tex 
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% radius = 40 arcsec = 0.35 pc  % density = 120 * 2e33 / (4/3*np.pi*(0.35*3.08e18)**3) / ( 2.8 * 1.67e-24 ) = 1.3e4  \Figure{figures_chH2CO/S233IR_multipanel} \Figure{figures/S233IR_multipanel}  {The S233IR / IRAS 05358+3543 region and its neighbor G173.58+2.45.  \textit{Top left:} The \formaldehyde density map covering densities  $10^2 \percc 
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% tried subtracting "envelope" from "core" and still got absorption  \subsection{W51}  The W51 survey was completed in September 2011. The data reduction process  presented unique challenges: at C-band, the entire region surveyed contains 
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This was done by interpolating across the line-containing region with a  polynomial fit (Figure \ref{fig:h2comask}).   \Figure{figures_chH2CO/a2705.20120915.b0s1g0.00000_offspectra.png} \Figure{figures/a2705.20120915.b0s1g0.00000_offspectra.png}  {An example of the \formaldehyde line masking procedure for building an Off  spectrum. The line-containing regions for each polarization are shown in cyan  and purple, with the interpolated replacement in red and green. 
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speed is very high).  \FigureTwo{figures_chH2CO/W51_H2CO_2parfit_v1_densityvelocity.png}  {figures_chH2CO/W51_H2CO_2parfit_v2_densityvelocity.png} \FigureTwo{figures/W51_H2CO_2parfit_v1_densityvelocity.png}  {figures/W51_H2CO_2parfit_v2_densityvelocity.png}  {Density and velocity fits to the W51 Arecibo and GBT \formaldehyde   data cubes. The yellow regions in the top panel correspond to \oneone  detections and \twotwo nondetections, indicating upper limits $n<10^{3.8}$ 
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\oneone/\twotwo optical depth ratio in this object is $\sim10-20$, indicating that  the volume density must be low.  \FigureTwo{figures_chH2CO/MCMC_DensColplot_67_64.png}{figures_chH2CO/spec67_64_bestfit_MCMC.png} \FigureTwo{figures/MCMC_DensColplot_67_64.png}{figures/spec67_64_bestfit_MCMC.png}  {Plots demonstrating upper limit fits. The left plot shows the allowed  parameter space from MCMC sampling of the data given the RADEX model. The  right plot shows the `best-fit' model to the optical depth spectra, which is 
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infalling clump. The spectra, along with multicomponent fits, are shown in  Figure \ref{fig:w51hiispectra}.  \FigureTwo{figures_chH2CO/W51_bestfit_spec53_49_IRS2.png}{figures_chH2CO/W51_bestfit_spec53_49_W51e2.png} \FigureTwo{figures/W51_bestfit_spec53_49_IRS2.png}{figures/W51_bestfit_spec53_49_W51e2.png}  {Plots of the optical depth spectra centered on W51 IRS2 (left) and W51 e2, an  ultracompact HII region (right). IRS2 shows high-density gas with a slight  hint of infall, but otherwise a somewhat vanilla spectrum. W51e2 has a large, 
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\emph{must} be moving towards the \uchii region.}  {fig:w51hiispectra}{1}  %\input{solobib} \input{solobib}  \end{document}  diff --git a/preface.tex b/preface.tex  index 4cd2d80..8d0c27d 100644  --- a/preface.tex  +++ b/preface.tex 
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\usepackage{lscape}  \usepackage{grffile}  \usepackage{standalone}  \standalonetrue %\standalonetrue  \usepackage{import}  \usepackage[utf8]{inputenc}  \usepackage{longtable} 
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% % \renewcommand{\thefootnote}{\fnsymbol{footnote}}  % % \setcounter{footnote}{0}  \input macros.tex \input{macros}  % file containing author's macro definitions \begin{document}  % \input{introduction}  diff --git a/thesis.bib b/thesis.bib  index 4ff0562..141cfe5 100644  --- a/thesis.bib  +++ b/thesis.bib 
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 @INPROCEEDINGS{Goodman2013a,  author = {{Goodman}, A.~A. and {Alves}, J.~F. and {Beaumont}, C. and {Benjamin}, R.~A. and  {Borkin}, M.~A. and {Burkert}, A. and {Dame}, T.~M. and {Kauffmann}, J. and  {Robitaille}, T.},  title = "{The Bones of the Milky Way}",  booktitle = {American Astronomical Society Meeting Abstracts},  year = 2013,  series = {American Astronomical Society Meeting Abstracts},  volume = 221,  month = jan,  pages = {234.01},  adsurl = {http://adsabs.harvard.edu/abs/2013AAS...22123401G},  adsnote = {Provided by the SAO/NASA Astrophysics Data System}  }  @article{EllsworthBowers2013,  Author = {{Ellsworth-Bowers}, Timothy~P. and {Glenn}, Jason and  {Rosolowsky}, Erik and {Mairs}, Steven and {II}, Neal~J.~Evans and  diff --git a/thesis.tex b/thesis.tex  index f521209..654b2ba 100644  --- a/thesis.tex  +++ b/thesis.tex 
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\usepackage{lscape}  \usepackage{grffile}  \usepackage{standalone}  \standalonefalse %\standalonefalse  \usepackage{import}  \usepackage[utf8]{inputenc}  \usepackage{longtable}