todo

--- 
create a function like 
extract_label_ids 

where basically we have to talk all the points again and then basically figure out the order in which they should actually appear 
--maybe we need to rewrite bibgboy? 

basically the current arrays are all indexed with the pointID? 
and that's how it appears in prelim analysis too? 
but i'm unsure how we can get the right point's information, but then when we try to attach the arrays the shit breaks. that's really interesting. 

i wonder if setting teh point is now breaking something -- i'm gonna have to see if attaching the arrays before that all happens will make a difference



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To run the FSI code for dye retention time 
- all results
- mesh:
	 rca_m5_asi2
	 	all_results.vtu
		mesh-complete.mesh.vtu
		inflow.vtp


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THINGS TO CHANGE IN MANUSCRIPT 

REFERENCE CHANGES
add some more references:
- the kim et al paper that includes coronary BC 
- papers w/ other methods, closed-looop LPN, 

WRITING CHANGES: 
- figure out figure organization
- include more motivation about which aneurysm shape parameters were chosen 
- developing a framework that allows significant testing, optimizes utilization of patient data 
- this framework allows for experimentation with material property effects as well 
- talk about FSI in the paper (both why we haven't done it yet, and also that it's a nice future step)
- using rigid simulations bc anatomical changes are central to hemodynamics, and potentially localized changes matter less


methodology changes: 
- figure out secondary flows/how to quantify jet fluctuation 


(DONE)


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FORMATTING REQUIREMENTS FROM Biomechanics and Modeling in Mechanobiology

Title page: 
	author names
	title
	affiliations + addresses
	email address + telephone number of ocrresponding author
	ORCIDs

Abstract 
	150 - 250 words

Keywords
	4 - 6 keywords

Text
	LaTeX?? 
	submission should include original source including all style files and figures and a PDF version of the compiled output

	but word files are also accepted


Acknowledgments
	placed in a separate section on the titl,e page 
	names of funding organizations should be written in full


Scientific Style
	italic for single letters that denote mathematical constants, variables, unknown quantities

	roman/upright for numerals, operators, punctuation, commonly defined functions or abbreviations

	bold for vectors, tensors, matrices


REFERENCES
	Cite references by name and year in parentheses ([last name] year; [last name] year; ...)

	List of refeerences should only include works that are cited in the text and that have been published or accepted for publication

	Alphabetize by last name of the first author of each work -> later authors -> chronologically

tables
	Numebr tbales using Arabic numerals, cite in numerical order 

	supply a table caption explaining hte componentso f the table 


Figures
	MSOffice files are also acceptable? 
	
	name figures files Fig[number].eps
	
	use sans serif fonts to number figures using 8-12 point font with consistent type size

	figures should have a concise caption describing accurately what the figure depicts. include the captions in the text file of the manuscript, not in the figure file. 

	figure captiosn with the term Fig. in bold type, followed by figure number, also in bold type. 
		no punctuation after the number, no puncutation at the end of the caption 

	size figures to fit column width

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literally fml lol i need to re run simulations 

1) upload meshes and stuff again 
2) prepare svpre file again 
3) run preprocessing
4) test out gcode 
5) run simulation 
6) compress restart files -> restart, geombc
7) run FSI simulation
8) look at FSI simulation results





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so i need to 
- cite justins paper about using FSI 
- cite the paper about RT vs dye advection vs particle tracing 
- interpret the dye advection results 
- add secondary flow results, make that figure