Day 30 (Aug 16 - Last Work Day)

The majority of the work today has been doing last minute run through's of our presentations. Everyone's sounds very put together and knowledgable. We are all still working on fluency and where to fix our "scripts".

Dr. Messinger really liked Madi and my presentation when we went over it with him in the morning. We just had to fix a couple of slides that had been messed up when the slide show was converted from Google Slide show to Microsoft Slide show.

We went to Global Village for the last time and have been enjoying our last day together as High School Interns.

Tomorrow's the big day. All of us are nervous and excited.

Day 29 (Aug 15 - Varsity Swimming Starts Today)

Madi was able to work more on the power point over the weekend while I was in Canada. She has a way better idea of how to do presentations than I do.

I finally typed up a suitable script for it and now we just have to practice... a lot. My flashcards for last Friday could not hold enough information and were a pain to look back upon to read.

Now I know that I also have to edit my script. I forgot to put in a section on Classification processes. But Madi and I were able to present in 15 minutes and maintained everyone's attention.


I have to leave early today to swim. yay. Good news: I won't have to run in scorching hot weather. Bad news: I haven't been running all summer, only swimming. As per usual, I will be the snail in the group. (This is why I like academics-based activities, like this internship, better.)

Day 28 (Aug 12 - Better Day)

Making flash cards (should have done this before the peer review...)

Editing slide show to fit my needs (there was way too much writing)

Happier by 11:00. Swimming after internship is a great physical stress reliever, but I tend to mentally wander and don't pace correctly and lose track of number of laps. (not good during sets) Then I am physically and mentally incapable to doing much of anything productive once I get home. (This includes packing stuff for the next day... I've been pretty good by 1/2 way through the internship. Then I forgot to bring the double batch of salsa that I made for today's cookout. Damnit!!!)

My mom brought the salsa... Good news: everyone loved it. Better news: I got to make another batch this evening.

 Presentation try 2 was better than try 1. It still needs a lot of work though. Our slides were better presented, but I definitely saw our fellow interns' eyes glaze over by 15 minutes. Dr. Easton was coming down to the auditorium to check out the presentations but we had already finished. He got my email and told me to talk to my advisers if I was interested in continuing work with the center in the future.

Now I have two questions in my heading running on never ending repeat:

What do I want to do for the rest of my life? (job)

Where do I want to go to college to get to that point? (RIT? elsewhere?)

At least Madi and I don't have any videos in our slide. But it's still difficult for me to explain the Spectral Profile graph and the Hyperspectral Cube. not to mention I forgot to properly label the Spectral Profile. Oops. Atleast our presentation is 20 min. instead of 30.

Day 27 (Aug 11 - Presenting is Not my Cup of Tea. It's extremely bitter coffee)

Blunt version: Presentations are scary.

I understand the idea that sharing knowledge furthers the search and discovery for other people. But I never liked the spotlight. Spotlight = Limelight for me. 30 min. presentation. Madi and I need to cut that in half by using an actual script. I had one bad year of presentations already. I don't need that for next Wednesday.

I stuck in way too much writing into the slide show. We confused our friends with what the goal of our research group was about.

We need to practice a lot tomorrow and finish our edits.

Day 26 (Aug 10 - Doc. Restoration)

Most of the day was continuing to revise the power point presentation. So far so good with it. Madi and I should just practice now and look for how the flow feels... and then some.

Wednesday talk was by Dr. Roger L. Easton. Madi and I met him earlier this week through Dr. Messinger. I would say he is a bit difficult to describe. He is very knowledgeable and experienced, outgoing and very pleasant to be around. I think that's its because of people like Mr. Cullen's, Mr. Pow, Dr. Messinger, Dr. Easton and all of the other people who work in the center that I am considering Imaging Science for college. They contribute a lot to society and have fun with what they do. (Most of the time that is. I know through the summer work that that imaging processing can get tedious and repetitive very quickly. But knowing that there is still so much more work to do out in the world with this knowledge is motivation enough and interesting to know about. (Repetitive and improper grammar. Sorry readers.) I look forward to talking with him more tomorrow about his travels. We had to cut him off short when he started to get into his trip in Georgia (not sure on the spelling, it's an ex-Soviet country North of Armenia).

Tomorrow's plans:

• work in the morning and practice presenting/ visit with Dr. Easton
• lunch: practice informal presentation of slide show amongst fellow interns
• Work on revisions after practice presentation
• Meet with the Doc. early afternoon to run-through presentation
• Break time @ end of day and sometime before lunch?

Day 25 (Aug 9 - Planetary Model)

Everyone is working on their final presentations. I still find it difficult to work on it. It's almost done now, Madi and I need to get in our results pages, fine tune the other slides, and practice presenting.

Day 24 (Aug 8th - Back to Slaughter Hall/ Bye Bye 21st Century Music/ Presentation Slides started)

Morning:

• updating blog
• We have a Document Restoration professor coming in for a Wednesday talk this week.
• Morning meeting with Doc. M: going over specifics of slide show: exactly what each general program is:
• Classification
• Principal Components Analysis (PCA)
• Signature Detection
• Spatial Processing
• Starting the slide show presentation. Work on the Gough Map is temporarily suspended. If there is extra time, then we will continue with last minute processing. Approximate number of slides established, labeled, and bulleted where possible.
• I'm realizing that perhaps presenting to a knowledgeable audience would be way easier with Madi and my level of knowledge than with a more general public audience. I had this idea in my head for the longest time that presenting to a general audience would be less terrifying than presenting in front of a knowledgeable audience because I could b.s. my way through something I don't know. Oh that young, ignorant, immature of brain of mine from way back when. (Ok, maybe five years ago -ish. Just a personal reflection here.)
• Madi was between working and talking/ laughing with Cici. (My point of view)

 Afternoon:

• Alice, Maria and I stop by the Physicians Assistant section of Louis Slaughter Hall (more like an adjacent building that can be accessed through Slaughter Hall). I was there during College and Careers for a P.A. panel. Maria brought up how she was interested in maybe going for a P.A. program when I shared a (somewhat) brief synopsis of each of the panels I had attended. I couldn't give her a very good description of the RIT P.A. program, so I thought maybe I could help her track down one of the presenters during C&C and have her give Maria a brief rundown of how to get into RIT's P.A. program. The department is more specific than either of us realized... A lot of shadowing appears to be in order before applying.
• I continued working on putting more stuff into the slide show. Goal: a rough draft slide show done by Wednesday. Putting some images in now.
• Maybe work on 2-day College and Careers EXTRA blogs later? (Gotta figure out a better way to transfer phone pictures to a PC...)

Listening to the 60s, 70s, and 80s music for most of the day. What can I say, I like my parents' music. I get a bit tired of 21st century country singers, love songs, and boy bands sometimes.

Day 23 (Aug 5 - Hit the Trails Running)

RU Symposium today:

• Breakfast at the Louis Slaughter building (home base for the simposium). Met up with Emily, Maria, Zihao, Niels and Alice. Eventually met up with Madi and her friend, Hannah, as well as Aaron from the Fast Forward program (and outdoor grill friday).
• Emily, Maria, Zihao, Niels and Alice went to a 9:15 talk
• Cici and I got caught at the the beginning of a rain shower while walking back to CIS from the Slaughter Hall. (We interns now have the inside joke that it stands for Louise Slaughter, not a butchery for pigs and cows. Mmmmm, bacon and burgers.
• Cici, Madi and I plan to see John's talk about "Music Source Identification and the Linear Mixing Model" at 12:00
• Cici and I made it on time, Madi and her friend were late and were kinda locked out of the presentation : }. Whoops.
• Excellent lunch presentation by Doctor Susan Spencer, Ph.D, President & CEO, ROCSPOT. I am still suspicious when I think of business and business people. (I have probably seen too much Marvel and other shows/ movies with corrupt businessmen. BOO TRUMP!!! Where has the term "noblesse oblige" gone off to? Come back!!!) To hear and see what she has accomplished and is still working towards really moved me to reconsider RIT as a college to apply to.
•  Afterward, Niels, Maria and I got stuck with some other people in the Art Gallery (where lunch was being held) by a rain downpour. I had an umbrella with me but it could only hold one person, maybe two.
• I managed to get Madi and my additional 30 slides to Doc. Messenger before we both had to leave at 2:30. I ended up meeting him in the reading room right before I left for RIT College and Careers.

Summary: not much work was done today due to the Symposium. I managed to take a second look at my MF and ACE results from the other day and put some of the better ones in the slide show to send to the Doc. I also managed to run MF and ACE on another image with little success, I think I did something wrong again. MADI HELP!!!!!!

Day 22 (Aug 4 - Fast Forward Presents...)

I started my day by correctly predicting to be two minutes late to our morning meeting in order to grab a couple of teas for Madi and I at Starbucks. Our morning meeting pretty much went over the Fast Forward presentations that will be given this afternoon and then the Undergrad Research Symposium tomorrow. I hope John is doing okay with his data and presentation... Dr. Messenger is almost done with the presentation (I know I said this yesterday). Madi and I need to stick in some good blur and divides and ACE/ MF's into our Google presentation to send to the Doc.

Madi plans to bring a friend for tomorrow's symposium. I only plan on going to see one of them at noon and people were kinda supposed to sign up for this event. So I planned with her for her friend to take my name-tag to go see the different talks after I see John's. (I still plan to take the complementary breakfast and lunch.)

I took a second look at all of the processed rules from the MF (Spectral Match Filter) and ACE tools from yesterday. I cleared up the two main splotch areas (more squiggly S's) and still couldn't get the blotted out castle label. Now I really need to get this stuff into Madi and my slide show to send to the Doc.

(look at black ink splotch in the middle of the image and the slight shadowy area below the castle in the upper left) 

(I got something, I don't know what it is though. This is our results most of the time with images of the sea.)

Day 21 (Aug 3 Testing, Testing)

Our day started with a trip to the library. Dr. Adwoa Boateng gave all of us a presentation of the RIT online library website for scholarly research materials. The computers at the RIT library didn't like Madi nor my logins/ passwords so we had to watch and could not follow along with her. She was very passionate about her work and very kind about helping many of us to first find some good scholarly article databases: PubMed, SciFinder, JAMA, ACM, IEEE Explore. (I don't know what any of these acronyms stand for.) OOh, and Turnitin.com and Retraction Watch (the soap opera channel for famous people caught plagiarizing and other unethical publishing practices). We all thanked her immensely for the help

Madi and I did not get much done yesterday. We ran a few programs on some of our images and had Di load another one of his fabulous codes onto our temporary user logins. (I still need to check that out.) Dr. Messenger is planning to send the powerpoint presentation sometime at the end of this week or beginning of next week and needs one blur and divide (or subtract) and an ACE or MF. ( Adoptive Coherence/Cosine Estimator and Spectral Match Filter. I know I know. I'm throwing these acronyms around and not explaining them. Both of these last two acronyms helps to find the center of data clusters (spectral coordinates of pixels). It helps with pixel/ color classification and identification stuff).

I had a huge headache after participating in a color imaging science experiment and then listening to the weekly Wednesday talk. The experiment brought me back to my photography class (again) and how a good picture is taken and what it would look like. (Thank you Mrs. Burger. Everyone who has had you at Brighton misses you a lot.) It took me 1/2 and hour to complete in a dark room setting. Niels went later and was 15 minutes late since he couldn't find the building : P. Ah well. I did volunteer to to take him there.

The weekly talk was about one of the professor's studies in Africa. He was looking at the dynamics of the Lake Kivu System in terms of biodiversity, terrain, and environment effects.

• Apparently there is about $20 billion worth of Methane trapped in the bottom layers of water in the lake that locals can benefit from. The lake is stable due to horizontal water circulation instead of vertical water circulation (water molecules continue to move as they normally would, just in a different direction). The water temperature gets warmer as one moves deeper into Lake Kivu, probably due to nearby, underground running magma. Due to this and immense pressure, methane and CO2 are dissolved in the water in the deeper levels of the lake. With different temperature levels and different pressure levels, different amounts of CO2, methane, and other minerals and gasses are dissolved in different water depths and maintain different layers due to different densities. (Run on. Sorry.)
• The biodiversity is low in this lake probably due to methane release into the water when the lower levels of the water are churned/ mixed up. This action would destabilize the water in the lake and the different materials dissolved in the different levels would float up to the upper 50 meters of the lake, killing much of the water-life (Cichlid fish species and algae). Some of the different species of Cichlid fish would have managed to survive such events and continue to reproduce. Thus there are only about 15 species of this fish in Lake Kivu while Lake Kivu's run-off and children lakes hold over double the number of Cichlid species.
• Other parts of Africa had similar concerns about the trapped methane in lakes. Lake Nyos in Cameroon endured a land slide that deposited a lot of sediment into the bottom of the lake. Nyos is way more shallow than Kivo, so much of the methane trapped beneath the water was released due to the resulting vertical circulation and into the river valley close to Nyos. Over 1500 people died from methane inhalation plus wildlife.
• Another concern is if volcano lava from nearby volcanoes could ignite methane-saturated lakes if lava were to flow into the lake (it happened before in 2006 or so). The observed lake from around 2006 was alright when large amounts of the nearby volcano lava flowed straight into it because the lava only traveled about 100 meters deep (the lake in question was I think over 300 meters or something.) So the people living in the city and other areas on along the coast were safe (other than the 75 people who died when the liquidy lava field rushed into the city at 70 mph). It is possible however that magma can leak into the lake from the lower levels though.
• The professor and his team took some sediment-core samples and found that Lake Kivu has the most diverse and abruptly striated sediment layers.
• The locals have already begun methane extraction from the lake and had to revise their plans slightly as to limit the amount of vertical circulation. (Vertical circulation=lake instability=methane released from solution=mass death).

All of us interns started to watch "The Dark Knight Rises" at the end of the day.

Day 20 (Aug 2 - RIT +1)

I brought Jaqueline to RIT today. I met her through my Photography 2 class back in my sophomore year. She graduated from Brighton a year ago and last I had heard, she had not yet chosen a major. I though imaging science might be interesting to her since she loved math (although MCC calculus was really difficult this year) and she loves photography, both of which are a part of the area. She still doesn't have her driver's license so I drove both of us. (Hey, I'm pretty decent at stick shift. At least I don't stall the car every day anymore.)

Both Jaqueline and I ended up knowing Madi's +1, Molly. I was a counselor in training (CIT) with her two summers ago at Creative Themes kids summer camp in East Rochester. Jaqueline attended the camp for a good six or so summers and had met Molly there as a fellow camper. (I was the only CIT in our 4 week session that had not attended the camp in over eight years. I went there for a couple of summers then my mom found other cool camps for me to attend after my primary school years, such as the WE@RIT program during the summer of my 7th-->8th grade. (Women's Engineering @ RIT.) It was a lot of fun:

• building and shooting off rockets during lunch
• building workable stop-lights by sautering stuff to the a mini-motherboard (thing)
• trying out the HARRIS skateboard assembly line
• building and running solar-powered cars [I remember accidentally mounting the solar panel backwards on the car. So, instead of the car moving towards a light source, it moved away from it : P.]
• checking out different inventions being worked on that summer by grad and undergrad students [Hydrogen powered car engine]

(Sorry, rambled)

Morning outline review felt brutal. There were at least twice as many eyes looking at each one. Not to mention Yiqun and Mat from my school came at Zihao's invitation. They were a part of last year's CIS H.S. internship and are two of the smartest engineers in my school (from my point of view). They both are brilliant builders and testers on the Brighton Science Olympiad team. Summary: nerve-wracking hour.

Madi and I then took our friends to see Mr. Messenger to give them a run-down of exactly what we do and why we do it. (Thank you Doc!!!) He also showed all of us some pictures his trip to Oxford and other places in England during his conference over there a month ago. (Bad grammar. My bad.) He had pictures of Stonehenge, Brexit protesters, and Hogwarts (the parts of Oxford used to shoot Harry Potter) while searching for a picture of Oxford-David's $200,000 spectral imaging machine. (Sorry to make our friends sit for another hour of presentation.)

To summarize the day: no work was done. We gave Molly and Jaqueline a taste of ENVI's classifications and the rest of the day was mostly fun stuff. I felt really bad during lunch because Salsarita's didn't have food to fit Jaqueline' s lactose intolerance and nut allergy diet. I had completely forgotton that Jaqueline had developed lactose intolerance her senior year. No one really knows why. She had brought food just in case.

When we got back to the imaging science center, we all played Volleyball, Frisbee, then some Contact. Twice I ended up tracking down the COL (color imaging science) center. I don't remember why the building's acronym is this. and Jaqueline and I ended up trekking accross campus 6 times. (Hey Coach Christina, I got my walking cardio in for the day and am ready to swim.)

So the day was mostly fun stuff and not much serious work : )...

Day 19 (Aug 1 - CC's In, Madi's Out)

Morning Meeting:

• Time sheets
• Outlines tomorrow (meet in the reading room first, slasaritas for lunch, freshman promotional video)
• Wednsday library research (1 hour)
• Friday RU Research Symposium
• Aug 17th: make sure visitors get a parking pass, starts at 9, ends before 12
• Estimate last week of hours
• CC reviews her trip

Mr. Messenger:

• Tomorrow: give RIT +1's a synopsis of what we're doing
• Create chips for the+1's to try

To Do:

• Create more sea chips =
•  compile chips for +1's =
• continue running programs =
• maybe ask Di to review how to use his Matlab code

After lunch, CiCi and I headed down to 1255 at John's invitation to play some fun improv games. These included a short-term memory game, a party game where the host had to guess what his/ her guests were, an interview game where the interviewee had to guess what the job was he/ she was applying for, a game like "Whoosh". I got out pretty early into the memory game and it took me a while with the the host game. I knew that John was impersonating a boyfriend or something, one person was a lizard-man, and the last person I thought was a human magnet or glue-girl. Turned out she was Velcro.

CiCi did way better with the memory game. We both ended up leaving a little early because she was meeting a friend for lunch at 1:30. (She only snacked around noon.)

Worked on compiling all saved images into power points in the afternoon. Did not finish this.

Day 18 (July 29th - We're Pretty Much 1/2 Way There)

Morning Meetings:

• Eastman House Summary
• Good: Very knowledgeable guides, good lunch, great bus (there was way more room than we needed)
• What should be done for next time: More time to explore other exhibits in the house, have the guide from the archive show us more of his work and not just explain it.
• I was really happy to go to the Eastman House for a second time. I went there once before with my Photography 2 class and had the chance to look at the exhibits showing at that time as well as the rest of the museum areas. We did not have a chance to go see the archives however.
• The archive area that we interns were given a tour of was pretty interesting. There is a lot of tech and chemistry involved to repair damaged artworks. I kept thinking of Oxford's really expensive camera that they had bought to image their library's ancient documents and how it could possibly help with the Eastman House's picture and artwork restoration. Oxford's camera is extremely expensive though, so I don't think that buying one and using it would be very practical.

Work:

• slow and steady. I have been running mostly Classifications, PCA and SAM on my image chips for the past few days. I will eventually re-run everything of mine through ACE, and MF to pull more stuff out. I really should also get some practice in with using Di's mask code and Anna's Blur and Divide spatial method. I will get to those eventually.
• Madi left early for a family trip (like, right after lunch). I think I can manage without her, maybe... (Come back soon!!!!)
•  None of us interns can believe that we are half-way through our internship; our time together to laugh, play and work. I started to feel that sensation of "The End" today. Everyone comes up to work in the Reading Room by now for at least a few hours a day.

*************Emily: Rio Olympics this year: The Russians, Zika and Katy Perry. Good Lord! (This is just a summary of what she said and how she feels. Feel free to tell me to take this bullet out or edit it, Emily).************************

Lunch:

• Cookout day. I met Aaron (RIT honors incoming freshman) and James (Byron Bergen Junior in the fall). They both work with coding. Aaron has been working with Biotechnology on DNA strands. He has already completed around twenty. James is really interested in Computer game management and design, although Byron Bergen does not have a strong technology program. I wish them both all of the best.
• We interns played some volleyball and Frisbee. I ended up joining some of the grad students in their Frisbee game/ toss. The intern Frisbee was way too light for me to throw and I can't throw Frisbees well under trees.

*********** I think almost everyone has stopped working by 3:00 and is now taking a break by playing different, old platform games. YES!!!! In their defense, everyone has been staring at some shape or form of code for the past week. We needed a break from work. *******************8

Day 17 (July 28 The Eastman House)

Everyone came in around 9:15 this morning instead of the usual 8:45. All of us high school interns, one RU student, Mr. Pow and Mr. Callens went to the Eastman house for a tour of one of their exhibits and a tour of their picture restoration area (in the guarded archives). Memories of my previous visit there with my Photography 2 class continued to flood back during the tour. Once we got to the archives though, I was out of familiar waters. Our tour guides were absolutely marvelous.
 

Afternoon work:

• Madi fixed my bad Kmeans habit
• I finished running image 7 through all of the programs
• I started running image 8
• Most of the sea looks the same by now. There were few interesting blotches in the last few image chips.

Day 16 (July 27 Don't forget the Outlines!)

Morning Intern Meeting:

• We don't know who will be presenting today
• Field trip tomorrow
• Outline and Cookout on Friday
• For Outline: Keep it Simple

• RIT +1 (Tuesday) 
• Ithaca Teganic Park water level at all time low
• Code Academy
• Movie Night

Morning Meeting with Mr. Messenger:

• See "Outline for July 29 (web readable)"

Lunch Talk:

• Perform Lab: Why Eyes Do Eyes look where they do? (I wrote 3 pages of notes.)  
• What in the image drew a person's attnention?
• Giving tasks matter! (different question phrasing leads to different results/focus areas)
• Humans are subject to motor delays
• Ball catching simulation game with Motion Capture (virtual reality headset)
• Testing eye Fixation, Saccade and Pursuit

Work:

• Typed up outline
• continued working on image 6 (not much was found)

• worked through image 7

• Anna kindly reviewed the Blur and Divide process with Madi and me before lunch. Madi helped me again with it after lunch and now I know that I should not try processing more than one band image at a time.
• Brain officially overloaded for the 5th workday in a row.

Outline for July 29 (web readable)

Enhancement of Hyperspectral Imagery of Historical Documents

Presentation Outline

Abstract/ Project Introduction and Description (1)

• Historical Documents
• Spectral Imaging
• Spatial/ Spectral Image Processing
• Spectral (color
• Spatial (Brightness and location)

Hyperspectral Imaging (1)

• (define, what does it mean-Collecting hundreds of colors)
• Pictures of Oxford Set-up
• Example of spectra of images

Processing (2)

• Overview
• ENVI
• Classification
• PCA Signature Matching (SAM, ACE, MF)
• Spatial Processing

Classification (1)

• (K-means, Mahalanobis Distance, etc.)
• Example (picture of each)

PCA (1)

• (exploration and visualization)
• Example

Di’s masks in PCA (picture and explanation) (1)

Signature Matching (1)

• SAM [ACE, MF]
• Reference spectrum to compare
• Examples (pictures)

Spatial (1)

• Blur and Divide
• Examples (pictures)

Gough Map (1)

• History
• What’s in it
• What we’re looking for
• Data

Pictures (3)

• Big picture (high resolution)
• Big picture (HSI [“data” picture file]))
• Zoom ins

Results (Pictures, Spectral Graphs, etc.) and summary (7-10)

Day 15 (July 26 Let's Try Blur and Divide)

Morning Intern Meeting:

• Same events as yesterday
• Updates on everyone's progress:
• Mr. Pow: getting ready for incoming freshman with Bob and preparing the CIS annual report
• Nathan, Alice and Maria: finished going over interns' recorded data from eye tracker experiment
• Emily: something about RZ Pisces and BC Pisces, calibration changes and R,I and G Bands, for now whe's back to reading about Jet Stream identification
• Nick: turning black and white images to color, working on the Model format of the game (game functions not controlled by player)
• Madi and I: Learned more Spectral programs, just learned some Blur and Divide for spatial programming, still working on the Gough Map, maybe will get working on the Codex
• Zihao: asked to borrow material samples from a library, took around 200 samples through low spectrum
• Outlines of our final slide show due this Friday on blog (it will be subject to change later.)

 Lunch:
       Debate over Pokemon movies and who ate the Boston Cream doughnut. (Thanks again Bob for the donuts!)

Work:
        Continue to process chip files from the Gough Map while having occasional conversations. I could not get the Blur and Divide programs to work so I'll have to ask Ana for help later. I ran SAM and PCA on image 4 and Classifications, SAM and PCA on image 5. Image 5 did not have any interesting hidden features. It did give me a headache though.

Day 14 (July 25 The Sky Finally Opens)

Almost everyone got caught in the 8:10 - 9:00 AM morning downpour.

Morning intern meeting announcements:

• This Week's events
• Wednesday Lunch Talk
• Thursday Field trip to Eastman house (leave by 9:30)
• Friday Cook Out (please no rain or blazing heat)
• Next Week:
• Aug. 2 RIT +1
• Aug. 3 Library Talk
• Aug. 5 REU Presentations (open to the public)

Morning adviser meeting:

•  Spectral Matched Filter (MF) - finds center of data by applying a perpendicular vector to the vector connecting a pixel's coordinates to it origin. (higher number = pixel spectrums are more similar to target pixel)
• Adaptive Coherence/Cosine Estimator (ACE) - combo of MF and a cone (attached to the perpendicular vector)
• SAM - (lower number = pixel spectrums are more similar)

Madi, Di, Mr. Messenger and I visited Anna's lab in the lower level of the CIS building. She uses Spatial ENVI programs to enhance and better contrast old (Blur and Define), faded texts unlike Di, who uses Spectral ENVI programs and a MATLab computer code to get a similar result. Spatial processing is different from Spectral processing in that one involves creating contrast based on a pixel's color spectrum while the other involves creating contrast based on a pixel's brightness. (Greater contrast sharpens the image details to be less blurry).

Madi and I have been receiving a lot of crash courses in learning the ENVI programs and what those programs do. Most of the mathematical details were not explained to us or have flown over Madi and my heads (due to their high level of difficulty) along with some detailed concepts so I'm not confident in giving a good description of how everything works.

Day 13 (July 22, Lights, Music, Chicken)

Our morning intern meeting topics:

• Weather for the cookout (hot, maybe rain?)
• Library Lecture/presentation about RIT online databases on August 3rd
• End Presentation tips and works:
• peer review of run through
• think about the title now
• be sure to acknowledge the sponsors and corporations who are funding your research groups
• invites won't be sent until next week (invite guests, family, friends and counselors?)
• Finding Undergrads for Imaging Science

 Mr. Messenger reviewed how to make spectral profiles of pixel colors and explained the Radiometry process and equation used to Madi and I. My Y-value numbers ended up being not quite right because I made my chips from file copy named "raw" of the Gough Map section while I should have been using the file called "data". I had no idea how the two files were different until he explained it to us. The the "raw" file had the overall observable light intensity while the "data" file is a documented "part" of the overall observable light intensity. I had been using the "raw" file for my chips which turns out to be alright for the ENVI programs, but not for spectral profiling.


These two graphs contain different spectrum data samples, but the y-axes are different.

"raw" pixel spectrum (above)

"data" pixel spectrum (above)

Mr. Messenger also helped Emily figure out a problem with the images she is processing of the night sky. What I heard of that conversation was that there was a piece of thread on the the telescope lens when the pictures were taken, but it only appears in some of the images. He introduced Emily to a pixel-sample process to try (I don't remember any specifics). I like the idea that the same process ideas can be used on both the macro and micro images.

Cecilia (aka CiCi), Emily, Madi and I headed over to the Interfaith Center with REU student  John to help him collect data for his music research algorithm. We H.S. interns took turns playing the piano (in the Interfaith Center) and the violin (CC and I brought ours) while John collected sound recordings and data on his computer to process later. This included playing the violin and piano at the same tempo both together and individually, and recording a duet between Madi (piano) and CC (violin) playing the Swallowtail Jig. (I happened to find it among the music papers stored in my violin case. It was fun to listen to!) It turned out that I was the only person who knew how to tune the violin strings by ear (without the help of fine tuners). Emily had a way better sense of when the individual strings were in tune though. Each of us H.S. interns were given a chicken drum-stick during the lunch cook-out in return. They took a while to cook, but they were delicious! (Thank you again John!!!)

Mr. Messinger had time today to read over the Gough Map article that Di gave Madi and I last week and revised his thinking of how to go at cleaning up the Gough Map. By the rate of our work, I think all of us can get through most of the Gough Map while Madi and I are around.

Day 12 (July 21 We All Laugh)

Our day started off with the question "What happened at your school this year?" The most common topics that were brought up were: pulled fire alarms, senior pranks, school lunches and complaints about high school teachers. Madi and my morning meeting with Mr. Messinger involved growing interest in the seemingly unchangeable ocean area in the Gough Map section that I had been working on the last two days. I had found small bits of text that had faded into what looked like brown splotches. Both yesterday and today I can not recall all of my findings, but the images I saved have helped me recall some of them.I tried showing Di later this morning and he was interested as well.

Most of the work day for Madi and I was reworking and posting the chips we had already created. I have been submitting my images into the shared google power point and Madi has been working on running other programs on the chips she processed the last two days. She had already submitted the chips she had worked on thus far. I tagged Di into Madi and my joint presentation so if he sees anything or wants to look at our work, it should be there.

Mr. Messenger had to leave a couple of hours early today, but Madi and I are hard workers while he is gone. All of the interns had lunch at the Student Union. (We all experienced waves of contagious, uncontrollable laughter for both hilarious and stupid reasons.) then Madi and I worked our way across campus to find the place to register another parking permit for my dad's car. (The one that I should be driving by now. It's one thing to drive remote control vehicles. It's another to actually be in the vehicle while driving.)

My Created Chips for This Week

Day 11 (July 20 MRI Interns Talk Banned Color Pigment Materials)

This morning started out with the intern morning meeting introducing the lunch speaker Mr. Kanan's, our field trip to the Eastman House next Thursday (the original plan of going to an observatory was canceled), and we discussed who would bring what Lunch Friday. The morning meeting with Mr. Messinger will stop in periodically to see what we have found. He's not as busy today.

Morning Work: Listening to CC and Zihao talk of how and where to get color pigment samples (Paris Green, etc.) I finished running SAM on MapEast image 2. Worked and finished all programs on MapEast image 3 (sea) (Located below images 1 and 2)

Lunch and Lecture: Mr. Christopher Kanan's labwork (Machine Learning and Visual Recognition)

Afternoon work: walk-around, running RGB on different program runs of image 3 to make out scribbles/writing. Created chips 4-8. Presented work to Mr. Messenger.

Day 10 (July 19th, The Drone and the Tree/ Work continued )

Our morning began as usual: Morning meeting with all fellow interns (Aug. 2nd is the Bring a Friend day), and morning meeting with Mr. Messinger (keep working with the new section of the map).

Madi had already started working on creating chips of the land area of the new section of the Gough Map, so I started running programs on chips of the sea. I think it's the English Channel. But I'm not the greatest with European Geography so it's the portion of the sea that is southeast of England. I think I cleaned up a depth line (a boundary line that may have served to show how deep the sea would be). But nothing else showed up otherwise. I only managed to get to two 800x800 pixel chips through all of the programs that I know thus far.

I took a break to be a test subject for the Visual Perception Lab just before lunch. I almost spilled the beans afterwards. The interns had a little bit of trouble with hooking me up to the Eye Tracker. I can't talk about what I saw so that the experiment materials can be reused (Phewy).

I ended the day with an Entrepreneurship talk that turned into a "Presenting to Non-Science Audiences" presentation. I had to leave in the middle of it though. The points in this presentation this should help with all of our presentations at the end of this internship.

Original

PAC in RGB with Enhancement

Day 9 (July 18th, Abstract peer review day)

I started the day by getting to the internship three minutes late and forgetting that all of the interns and the internship advisors would be in Bob's workroom to review our abstracts thus far. (Thanks Emily for texting me your location. I know you read everyone's blog at least twice a day so you'll get this message, eventually.) Everyone picked apart everyone's abstracts for a total of about 35 minutes. The one outstanding abstract was written by Nieles (note to self: check spelling later) if I can remember correctly. His area of the astronomical imaging internship group involves creating a fun astronomical education game that is played somewhat like Agar.io or Slither.io except with cooler features (images and graphics of the cosmos are added to a collection/ gallery and are earned as rewards, educational information integration in the gaming features and gameplay, etc). I hope I understood his explanation alright. (Note to self 2: check Nieles's abstract again sometime.) I sooooooo want to try out this game once he gets the basic mechanics finished. I definitely would not be able to do what Nieles or Emily are doing if I got in with the Astronomical Imaging advisors. I like working with data and images as well as learning about the stars and their properties. But, I definitely need visuals to work with and pure representative data and coding are not my areas of expertise. I actually have nearly no coding experience at all.


Back to the topic at hand:
 Other than a couple of minor grammar problems, CC and Zihao's abstract was flawless. Madi and mine was alright ... it definitely needs to get cut down and re-worded. I thought we signed up for an Imaging Science Internship, not an English Writing Course focused on the field of Science. (I'm joking of course. It's too serious and quiet in the workrooms with everyone using earphones to listen to music individually. LIGHTEN UP PEOPLE!!!!!!!! Geez!!!)


Madi made Oreo balls and they were delicious! I only had cake balls and weird cheesecake balls before. Madi's recipe trumps them all!


Ok, Ok. I'll try to stay on topic for the remainder of this post. Sorry, there's something about the concept of Monday that I don't like.


                  I had to leave early today for a couple of medical appointments around town, so I was only able to "work" for a couple of hours today. Mr. Messinger introduced another ENVI program to Madi and I today, Anomaly Detection. It functions by finding a mean and standard deviation of the pixel properties (colors and brightness) in an image and then comparing each individual pixel to the determined mean. So, the program pretty much works Z-scores for the entire image. (I remember Z-scores very faintly from the end of the Algebra 2/ Common Core class this past year. I don't really want to relive my days in that class. Moving on -->)  It comes up as RX Anomaly Detection in the ENVI --> Spectral -->Tools. RX stands for Reed and Xioli. Mr. Messinger also showed Madi and I how to create our own chips and how to Profile the data pixel colors (figure out their reactivity to different wavelengths of photons). I think I have my facts straight at this point.
                 Di uploaded another segment of the Gough Map onto my temporary user computer account so I'll "play around" with it tomorrow. Madi definitely has a head-start on the work. And Mr. Messinger confirmed my fear: I should not have tried to reboot the computer in the reading room on Friday. I had no idea that those things were THAT sensitive. Someone else from the internship tried to reboot the Shut-Down reading room computer at the end of the table last week. (It's a different one from the one I glitched, and you know who you are.) and it was also showing raw code. So .... I'll go have a talk with the tech-support crew tomorrow if the computers were not fixed and give them an apology for my ignorance of computer technicalities.

Day 8 (Abstract for 7/18)

Madeline Loui and Allyse Toporek

Enhancement of Hyperspectral Imagery of Historical Documents

       Several Weeks ago, Dr. Messinger attended a conference at Oxford Univeristy to present new computer processing methods to enhance the faded and illegible writings on images collected of historical documents. The work he presented was of images the university sent to him of the Gough Map of England. This document is around 600 years old and has undergone much work (updates) since its first creation. However, some of the ink has faded with time or other environmental factors and what remains of the ancient writing and pictures are grey, organic, unrecognizable structures or nothing at all.

      We have worked to learn those computer processes and programs in the ENVI software and custom processing code created by Di Bai, a PhD student in CIS. We are using them on smaller sections of the overall Gough Map in order to identify the original, hidden texts and figures. These include, but are not limited to, Classification processes, Principal Components Analysis (PCA), and Spectral Angle Mapper (SAM). Our finished works will be sent along with those of Dr. Messinger and those of Di Bai to Oxford for analysis and, hopefully, description. A broader goal is to assess the different methods and their capabilities.

Day 8 (power point vs. libre office)

Our morning began with talk of the "Bring a Friend Day" for later on in the internship. This would give us a chance to show our research and results to them and stimulate their interest in science.

The majority of Madi and my work time was taken up putting the remainder of my images onto our power point presentation for Mr. Messinger to look through and incorporate into the power point compilation to be sent to David and Nick at Oxford. (My images from days 5-7, PCA w/masks and SAM results) We all have a little idea of what they want to analyze, so fingers crossed. Madi and my PCA and SAM results have given the better results. We also figured out how to put a picture of the overall Gough Map onto the slide show to indicate where each of our chips were. (Whoever invented screenshot is a lifesaver, at times.) We compiled a total of 100 slides (way more than for my APUSH Debate this year ; P)

(Madi and I are still enemies of the copycat LibreOffice on the computers we use. We still prefer good old Microsoft Powerpoint.)

The Neapolitan ice cream was a hit during lunch. It had kind of melted while in the cooler outside though. There's a little left over that will be left in 2nd floor break room for anyone who wants it. Someone else should be in charge of bringing the ice cream next week. The lunch today was fun again, although a bit windy with some rain and thunder for the first half-hour.

Chip 10 (Vanilla colored)

Chip 10 (Cookies 'n Cream color )

Day 7 (Rerunning SAM)

We all started our morning meeting with donuts (Thanks Bob!) and going over what to put in our first abstracts for our final presentations (due tomorrow). By what everyone has been saying, a lot of people in the same research groups will have the same abstracts since their work are pretty much the same, except for Emily and Niels in Astrological Imaging. Niels has been working on coding and program creation for the group. Emily, meanwhile, will probably be doing data reduction and photometry. This would be after she has finished reading all of the manuals and textbooks necessary to fully understand her work (which is still ongoing since we all first started our work).

The entire morning was made up of re-running all of our images from yesterday (Madi chips 1-5 and me chips 6-10) through SAM (see Day 6) and coming out with full processed images. It took me the first ten minutes or so to figure out how I was still getting the band of black on the top of the image (which I still don't understand) but gave up and began running a more manual-like version of SAM on ENVI called SAM Target Finder with BandMax. That worked but I still felt like I am falling behind Madi in processing speed. I then realized that she was running less pixel sample trials than I was.

Original (infamous) Chip 10

(The red wall is Hadrian's Wall. To the left is Scotland and to the right is England)

SAM Chip 10 red pixel sample (with enhancement) from yesterday

SAM Chip 10 red pixel (with enhancement) from today

(These images look better on the ENVI viewing pages)

We all gathered around 11:45 to head to Global Village for lunch for a nice break. (We missed the lunch-rush by about 15 minutes.) It was nice to feel a breeze and the sun since all of us are somewhat cooped-up in our work areas (but by no means bored).


The afternoon was mostly finishing up the SAM reruns and typing up a draft of our abstract. All of us interns have been putting in a lot of time with our research groups and we have been discussing a little of what each of us have been putting in our blogs (since we can all see each others from the website cis.rit.edu/2016INTERNS , now an operational shortcut). Since Madi finished her portion of the power point early and her work, she went looking through previous interns' pages. She noticed that during previous years' internships, there was a "Bring Your Friend Day" and a "Biking Day". I'm really wondering if we will be able to do these this year since I like this idea.

Day 6 (SAM and Madi Describes "The Secret History")

We interns started our day planning who would bring what for our weekly Friday picnic. I volunteered to bring the ice cream this time. I couldn't remember if the ice cream name was pronounced as tripolitan or neapolitan. I figured it out later.

Mr. Messinger taught Madi and I the process and ideas behind SAM the program. It stands for Spectral Angle Mapper and it functions to search for pixel similarity to a reference point. All of Madi and my work for today was running the SAM program on the data chips given us on day one. For some reason though, the top 1/4 of all of our processed chips were cut off from the SAM processing and appeared as a black strip at the top of the viewing page. Mr. Messinger could not figure out exactly what Madi or I did to have a part of the image cut out. For most of the afternoon, Madi and I put together a power point of our best saved image results.

(After SAM and correct orientation)

Madi attempted to give a detailed summary about the book "The Secret History" before lunch. This took about an hour with interruptions and questions which included confusion about who died in the book and which characters played what parts in the plot. After this we had lunch and attended a talk about Eye Movement and Illusion of Continuity by Jeff B. Pelz. He talked about "optical illusion" (which is realy neural illusion), The Foveal Compromise, coping systems (Dual Retina and Eye Movement System), and the uses of an eye tracker camera in his area of work. This gave us interns an inside look of what the Visual Perception lab work was. The interns working in the lab could not disclose information to us about our work because the other H.S. interns will be test subjects for their experiment.

Day 5 MatLab and Coding Implementation

Di introduced his code on MatLab to Madi and me.

His code is designed to block pixels on an image. In the context of our work, the prominent red and green inks on the Gough Map would be blocked out of the image clips that Madi and I work on. Blocking the red and green inks would allow the PCA program to run a better data analysis on the more subtle and less prominent areas of ink.

Di's code then converts the final image into a file that the ENVI program can read and the PCA program and enhancement tools can be run on the processed image.

The orientation of the image was originally given to Madi and me rotated. After running PCA and Di's code, the images are flipped and rotated again. If you track the areas that look shadowed or smudged on the original image onto the enhanced images, some cursive-like writing can be made out. The bottom two images are my best enhanced images today.


(According Mr. Messinger, images of our results are alright to be added to the blogs. The raw codes are not.)

Original Image

After Di's Code/ After running the PCA program

After PCA Enhancement (black and white) 

After PCA in RGB
(blue ink writing was originally barely visible)

In other news:

• The fire alarm went off unexpectedly around 11:00 and resulted in a visit from the Henrietta Police Dept. and some of the security guards on campus. (Thanks for coming!) This brought up my question of: Where should the interns gather outside in an emergency like this?
• A presentation was given between 4:00 (16:00)and 5:00 (17:00). Madi and I could not attend sadley.

Day 4 (Yay, first Monday)

Mr. Messinger introduced the Principle Componants Analysis (PCA) program to Madi and I during our morning meeting. The PCA programs are designed to identify a cooridnate system to best fit given data. In the case of using ENVI for color identification, each color in a document are a coordinate and PCA changes the coordinate system (the coordinates of the graph) to best fit the color data distribution.

So the majority of our work today was running Di initially gave us through PCA. We were able to clear up a lot more of the images and found more hidden text with PCA and image enhancement tools. We also checked some of each other's work and took a long walk at the end of the day to clear the headaches we got while staring at the computer screens for hours on end.

Day 3 (July 8th)

Madi and I are quickly assimilating to a kind of routine by now. The group has the 15 minute opening meeting, then Madi and I have a morning meeting with Di and Mr. Messinger about our progress with the Gouge Map, other interesting parts of the map they have found thus far through their research with Oxford, and what ENVI programs and tools Madi and I would be working/practicing and all of the details behind the programs. The rest of the day would be used running the ENVI programs we know on different image files that contained sections (chips) of the Gouge Map. Di would check up on us about every hour and a half to check our progress (or whenever Madi or I called him because I thought I froze the computer : | ) and we end the day with a 4:00 meeting to go over the day's work.

There was another Ph.D. defense at 2:00, however neither Madi nor I felt up to going to it after being fascinated and somewhat lost by Lady's presentation on her work (see Day 2). Even though it would have probably been interesting to check this one out, we couldn't find the room until Mr. Messinger told us we were on the wrong floor and we just felt the need to get back to the chips we were working on. I reasoned that we had an hour and a half lunch period for the Friday cookout and volleyball in the muggy weather and a stroll around the building was the only afternoon break that we should afford. It was a pretty good day for the planned event and it was interesting to chat with some of the attending college students.
In my opinion, my work on the chips was not as fruitful as Madi's thus far. But this is just my perspective and it has only been the third day of work for both of us. (Love the steep learning curve [double thumbs up].) She did clean up an image to find hidden writing at the end of the day which was extremely exciting for the both of us. It looked like original town names that were smudge out by an excessive amount of map-use and then someone rewrote the names with the red ink used to label all of the other towns and cities on the map. Another "stick man"-like blob also appeared. It kind of resembled the one that Di had discovered on another portion of the map before Mr. Messinger's meeting in Oxford.

To Madi and I, the resulting image with the discovery looked like a mistake. Madi had the program identify six different colors but an overall image with the six "false" colors, used to mark the areas with similar color shades, wouldn't process through ENVI. Only black and white images of each color detection would show individually. Her results also did not in any way resemble the work results I had from the same chip. I should not have been so quick to regard the result as a mistake. Mr. Messinger's explanation of the significant finds really surprised Madi and I. He continued to talk with Di about further work on the chip and area of the discovery which both excited and overwhelmed us interns. Every time we have a meeting, Mr. Messinger readjusts what Madi and I should look for on the Gouge Map during program processing and how it can be done. There is a "program processing" phase and an "analysis of the results" phase. Madi and I have been working on the "program processing" learning. For next week, I am eager to continue refining the ability to effectively analyze the results of the program processing.

Day 2

Today started out with planning for the cookout lunch that the supervisors scheduled for this Friday (tomorrow). After a quick, 15-minute morning group meeting, Madi and I split up so that one of us could grab our locker keys and the other could notify Mr. Messinger that the other was on the way. Madi forgot where Bob's office was so I ended up grabbing the keys for us and was a couple of minutes late.



During our morning meeting with Mr. Messinger, he told us of ENVI's origins and gave a quick overview of what Madi and I learned yesterday using ENVI's classification programs. Interestingly, ENVI was first designed by a duo in Colorado for geological use. ENVI was later implemented in the field of astrology in the 90's. It was around then that, Mr. Messinger came across the program (if I remember the story correctly). The program was eventually sold and the creators now live comfortably.


ENVI was originally designed to be used by Ph.D. knowledge-level professors, but later versions were written with ease of access in mind for a wider variety of users. Di had Madi and I try the new version available on the computers we were using (I think he said the version was something like 8.5) and they worked alright. The screen appears way more like Photoshop and, in my opinion, displays many functions more openly than the "classic" version. But Madi and I switched back to the ENVI -classic (I think it was a version 5) for we were originally given our first instructions based on this older version and none of us could figure out where some of the basic functions were located on the newer version. (For example, we could not locate "True Color" to change the original images from black and white to color.)

At 10 A.M., Madi and I went to see a Ph.D. defense by a woman named Lady. (My apologies for misspelling your name Ma'am and I am so sorry for walking into your presentation late.) Her presentation was about an application that would improve Remote Sensors. We could not understand the vast majority of the mathematics she was presenting due to our inexperience with college-level mathematics, so I can not justly summarize what Ms. Lady presented. (I am also not certain if any of the specific information she presented is considered to be ready for publication.) However, we both listened attentively and I tried to take notes on a few parts that I had somewhat understood. I still do not completely comprehend about half of what I wrote (5 single sided composition notebook pages written total) however thanks to Mr. Messinger's explanations over the past two days, I did understand Ms. Lady's idea of targeting pixels with like-color on maps and trying to eliminate a great deal of background pixels, false positives, and no matches. Mr. Messinger later explained that our research will eventually be moving towards that stage.


For the remainder of the day, Madi and I practiced using different Classification programs on the same image chip (picture-section) of the Gouge Map. I adopted Madi's idea of taking screenshots of our trials and documenting them as we worked on them to help us later when we will have to give final presentations. We both struggled with the labeling and organizing of our files and I know that some of my trials are lost as undecipherable files. (They were mostly trial command inputs so it was alright, I think.) We pushed through and did our best.
Mr. Messinger took a look at my files at the end of the day and pointed out what Madi and I should be looking for when comparing the different color-gradient image copies that we produced. A lot of the images I had were the same as Madi's. Whenever I look at the processed images, I see them resembling really flashy-colored wallpaper. Mr. Messinger's points just made me more interested in jumping back on ENVI and trying again. (I am still nervous when I am under observation though : I)


(OOH last little note: Picnic/Cook-out tomorrow! 11:45-1:00 last time I heard. All are welcome!!!!!! I bought what I volunteered to bring and a little more since I heard some of my other interns say they were not sure if they would remember what they would bring.)

Day 1

Joe Pow and Bob Cullen started this first day with a tour of the Chester A. Carlson Imaging Center. All of the interns and I were then led to a red barn on campus to do some fun teamwork-building activities for the rest of the morning. All of the activities were very thought provoking and fun to figure out. The temperature quickly rose from comfortable to just-bearable faster than I thought, but it did not take away from the team-building, in my opinion.


After lunch (provided by Mr. Pow and Mr. Cullen, thank you for this!) Madi Loui and I were introduced to our advisor for Document Restoration, David Messinger. He and his grad student Di re-introduced Madi and I to their current project works: the Gough Map (of England) and the Archimedes Palimpsest. Mr. Messinger told us of his trip to Oxford and the overwhelming positive response he received to the results of his research on the Gouge Map. (What he was saying brought back many pleasant memories of sophomore year world history classes; in which we analyzed the significance of different historical documents that survived through the unforgiving dimensions of time and space.) Di then introduced Madi and I to the general works of the wonder-program that all of us would be using: ENVI. After getting over the fear my possible failure to use its programs, Madi and I quickly absorbed Di's instructions on how to use ENVI. The computer program appears to me like a cousin of Photoshop but requires more manual control of its tools, and more patience and practice to efficiently using it.


I love the idea that Madi and I will be able to help Mr. Messinger and Di with their research in this area of imaging science. I can't wait to practice more tomorrow!