Thursday – 10/07/2010

not what i intended to do today, but here it is: my near final LAI map of my study transect..not an easy task! (due to field collection, and then serious sun/canopy topography cosine noise, fortunately was able to model it out and derive this…

Wednesday – 10/06/2010

NSF proposal writing and IDL coding for LAI2000 image extraction.

Tuesday – 10/05/2010

• Bibliography for NSF proposal
• Starting to write NSF proposal
• Continuing work on LAI2000 image extraction program
• Get high elevation data logger running
• Put interior forest microclimate sensors back together with newly calibrated PAR sensors.
• Finish two reviews due today and tomorrow

Monday – 10/04/2010

• Job applications
• NSF research proposal
• Set up lower elevation climate tower
• Working on IDL program to extract image data based on forest height and LAI-2000 bands used (2 bands = 28 degrees).

Saturday – 10/02/2010

• Job application work
• Coding non-linear parameter solver, works good so far on its own data:
• 

400-1050 nm reflectance directional. Two lines, input and modeled are shown (hard to tell there are 2).

 

Changes in leaf angle cause major errors in the LAI estimation. This would need to be held constant if used ultimately. I will try to code an EVI at multiple spatial scales extractor, this should deal with the issues effecting the NDVI relationship…hopefully.

 

relationship for LAI of 8..good, with slight difference in low nm area. Input LAI of 8, output of 6.5. could be improved, but saturation is known to occur at high LAIs (leaf area index) for all vegetation indices so also would be happening within our hyperspectral dataset.

Friday – 10/01/2010

• Job applications, post-doctoral fellowships, letters of recommendation, yikes!
• Making some progress on the LAI mapping. The preliminary relationship with NDVI was not so hot, so will write a script to get average of multiple pixels per location (the actual cone of the LAI-2000 is 28 degrees from 1 m height – something like 5-6 pixels at the canopy height).
• Also tinkering with an idea to couple prosail with a shade endmember to derive non-linear paramterization through least squares unmixing of prosail parameters, including LAI, from shade.

Here I used the pixel purity feature in ENVI to identify endmember shade fractions (green) versus an example of full sun canopy direction reflectance. The red curve would be modeled from PROSAIL while the green (shade) would remain as is (the average of multiple pure shade pixels). The issue with this approach is the reduction in the signal/noise ratio with increasing shade levels until parameterization becomes meaningless…

Thursday – 09/30/2010

Finishing resume for first job application.

Send letter to recommenders.

Working on method to derive LAI from hyperspectral. First idea is to extract shade using a linear unmixing method. This could be coupled with PROSAIL to derive a least squares estimation of LAI with inclusion of shade spectra (as identified from deep forest gaps).

Tuesday – 09/28/2010

Completed field LAI measurements using the new LAI-2000’s made available through Sue and Paul from IPIF. A total of 65 good points georeferenced to within 10 cm XYZ. Now I am using an offset IDL program to extract hyperspectral and LiDAR information for each pixel LAI location which I will input into a statistics program (JMP) to compare methods for LAI calculation, including simple vegetation indices and more advanced radiative transfer approaches. One of the main issues I am dealing with is how to minimize the shade resulting from canopy topography. Even ‘normalized’ indices, which use ratios to remove much of this effect, do not do a perfect job. First, I will look into how different spectral bands relate to canopy shade positions and see if it is possible to regress shade out of the spectra prior to running indices.

 

LAI variation 1-8 with all fixed parameters.

Dealing with a few floating underflow errors in prosail when sun or observer angle are greater than 85 degrees

Monday – 09/27/2010

• Finished IDL version of PROSAIL code: below see an example of holding all physiological parameters constant while varying LAI:

Next step is to link this to a non-linear curve fitting code in order to model LAI out of our hyperspectral imagery.

Sunday – 09/26/2010

• Making progress on translation of PROSAIL 5B into IDL.
• Found method to solve for multiple parameters using least squares approach, will use this to best fit PROSAIL to CAO hyperspectral data, deriving LAI data for my study area. See:

http://www.physics.wisc.edu/~craigm/idl/

 

Of particular interest is his code:

MPFIT - Robust non-linear least squares curve fitting.

• New and recalibrated PAR sensors arrived on Saturday. Need to install these on the microclimate stations.

Friday – 09/24/2010

• Verifying new AutoMCU Landsat imagery coming in our FTP site after processing at Asnerlab. Had issues with Ascii file transfer resolved by using binary encoding format.
• Near completion of translation from Matlab to IDL of the PROSAIL canopy reflectance model, integrating a within canopy and atmospheric radiative transfer model. Once I have verified the coding is correct and obtains same results as from Matlab I will work on using it to develop LAI maps of my study area through hyperspectral/waveform LiDAR fusion.
• This will require addressing canopy self-shading issues which influence reflectance and thus LAI estimates.
• Have a new LAI-2000 unit to replace broken unit and will finish LAI measurements on Monday and Tuesday.
• Just received the new and recalibrated PAR sensors from Apogee to reinstall on microclimate stations and place back in the canopy on Wednesday.

Example screenshot of PROSAIL module in IDL format.

Wednesday – 09/22/2010

• Working with LiCOR to fix LAI-2000 from corrosion dust.
• Organizing job search
• Data entry
• Went to high elevation climate tower to bring back data logger to change desiccant. Also re-routed anchor rope and checked the levelness and stability of the PAR sensor.

Tuesday – 09/21/2010

coding offset calculations, then after converting differential stake lat long to utm coordinates will calculate utm zone 5 locations for all lai measurements collected so far (~40).

code snippet from preliminary version pre-testing

Laupahoehoe magnetic declination:

http://www.ngdc.noaa.gov/geomagmodels/struts/calcIGRFWMM

Monday – 09/20/2010

• Entering LAI data into spreadsheet.
• Prepping for field work LAI collection later in day (raining now)
• Organizing job post-doctoral applications
• Recalibrated PAR sensors are being shipped, one was replaced by Apogee due to sensor drift.
• Bring entire high elevation top of canopy climate datalogger down to house for drying and data download. Setup both of them running at same time tomorrow morning.

Today summary:

1. wake up, enter data, pack field gear

2. Set up LAI-2000 top of canopy unit, get all programmed and running correctly, wait for rain to stop and weather to be perfect.

3. Finally in the forest, all tripods set up and ready to collect data, then the unit stops working. I take it apart and realize nobody has ever changed the batteries (since 2008) and they have exploded in the interior..

4. Packed up all gear, drove to store bought new batteries, went home, cleaned unit, crossed fingers that it would turn on, and itd did. now its sitting in the dry box looking pretty and ready for field work trial #8 tomorrow…

Friday & Saturday – 09/18-19/2010

• Have a home ftp server up and running for large image sharing with Carnegie. Setup was difficult due to the dynamic ip of our router (dyndns is a good solution to get a static server address), its firewall, virtual server port forwarding, windows firewall with inbound/outbound port access rules, sophos antivirus, defender, passive port ranges, etc… two days later i feel sort of an pseudo-expert in ftp setup! a new skill :)
• Organizing job and post-doctoral applications, need to have this done in the next few days to meet deadlines for letters of recommendation, etc…
• Entering LAI data (1/2 way there)
• Field work for LAI collection in the lower valley of the giants forest today in the late afternoon when diffuse light fraction is high enough…direct sunlight will reduce calculated LAI readings by up to 50% due to reflection off leaf surfaces.

Thursday – 09/16/2010

• Working on a personal ftp site to download processed AutoMCU Landsat imagery from Carnegie.
• Purchased new radios so we can communicate when collecting LAI measurements on variable climate days.

 

• 35 mile range! of course in the forest, I hope it will make it .35 miles which would be adequate.
• Organizing post-doctoral fellowship and job applications.

Monday – Wednesday: 09/13-15/2010

Working on the LAI measurements. First step was to find an open location at the high elevation area, much easier than the low elevation much taller forest. For this we used a Suunto Inclinometer mounted on a tripod.

The low elevation required some more creativity to find an sufficiently open location, we’ll start collecting data with this system on Friday when we have finished the high elevation parcels.

 

Here is the remote open area LAI 2000 setup and collecting measurements every 15 seconds. I take basically the same system into the forest interior to collect LAI values, georeferenced using our Trupulse system.

Monday – 09/13/2010

Heading to field for LAI-2000 measurements. Today’s goal is to complete measurements on T1,2,3 and 4. We have 4 hours of 15 second remote LAI-2000 measurements possible in given the RAM capacity.

Required gear:

2 LAI-2000 units + wands;

1 TruPulse 360 for georeferencing + non-magnetic mounting bracket;

1. Tape for measuring height of Trupulse above differentially corrected stake;

3 tripods (one extra large) for mounting LAI-2000s and Trupulse;

2 reflectors for TruPulse;

1 Suunto Inclinometer for locating suitable location for remote top of canopy LAI-2000.

 

Day synopsis: well, went to the field in the morning and it was too sunny to collect LAI measurements, then went back in the afternoon and it was too rainy! Man, this equipment is way too picky for a tropical forest… Tomorrow I’m up and out of here at 5 am to take advantage of the increased diffuse radiation from 6-9, hopefully collect abundant LAI points!

Sunday – 091210

Finished calibration of low and high elevation PAR sensors.

Calculated calibration coefficients for interior forest PAR sensors.

Glad to know that following re-calibration of sensors they have an average difference versus the LiCOR calibrated sensor of only 24 PPF with a max of 54 over the 3 hours of 1 minute data, covering 800-2400 PPF. Sweet!

Friday – 09102010

Working to recalibrate top of canopy PAR sensors to tower mounted LiCOR sensor.

The high elevation is complicated. There is obvious diurnal and seasonal offsets to the sensor position (i.e., leans to the East and North, I think). I will model this out using julian day and fractional day.

The low elevation sensor is a much simpler situation requiring only a fractional change to the multiplier, maintaining the linear relationship between the two sensors. This one must be in a leveled position.

Saturday – 09/11/2010

Completed the LAI-2000 protocol and test data looks good. Will start collecting forest data on Monday through Friday. The Apogee PAR sensors were calibrated versus the LiCOR and then sent back to Apogee for recalibration (250$..argg). Now starting to work on calibration of the top of canopy PAR sensors, dealing with an obvious leveling issue with the high elevation sensor which can be modeled out.

 

See LAI-2000 Protocol below:

 

Broadbent, E. 09112010 LAI-2000 Protocol, Remote X/Y Units

Collection of LAI values using two LAI-2000 units in remote X/Y mode

Basic:

1) Have 2 LAI-2000 units and two wands,

2) Make sure lens are clean and that protective covers are in place,

3) Make sure units power up and batteries seems adequate.

4) Avoid direct sunlight when collecting data. Collect on overcast days or close to sunrise or sunset. Direct sunlight can cause major errors in LAI (up to 50%).

Validate stored settings in control unit:

5) Power up both units (‘on’) and press ‘setup’,

6) FCT-01 & FCT-02: Start with factory calibrations on both units,

7) Above Canopy Unit X (PCH-0922): 4023, 1254, 1000, 1012, 1493

8) Below Canopy Unit Y (PCH-0916): 4040, 1256, 1000, 1011, 1393

9) FCT-04: Set resolution to high on both units,

10) FCT-05: Make sure date and time is exact same on both units (press enter to leave the same, xxx indicates invalid entry),

11) FCT-06: Check that distances are set to default values. 1.008, 1.087, 1.270, 1.662, 2.670. Different values would be calculated if foliage density was being obtained. These are mid-ring angles.

12) FCT-07: Check Ring angle values. Should be: 7, 23, 38, 53, 68.

13) FCT-08: Turn all channels to ‘off’ (unless LiCOR PAR sensors are connected).

14) Press ‘file’,

15) Select ‘Clear RAM’ (if all data has been downloaded!) on both units.

16) Verify using ‘memory status’ that no files are in RAM / Press ‘Break’ to exit to main screen,

17) FCT-13: Verify that wand log key is set to FCT-14.

18) FCT-16: set ‘bad readings’ to Beep and Ignore,

19) Turn off units using FCT-09.

Unit inter-calibration procedure:

20) Bring to open location close to field site.

21) Use sensor X control unit.

22) Attach sensor X (above canopy; PCH-0922) to X port.

23) Attach sensor Y (below canopy; PCH-0916) to Y port.

24) FCT-11: Set to ‘2 sensor’ mode to compare values / ave = 0,

25) Press ‘break’ and use up/down and left/right keys to select X1 & Y1 for compare.

26) Level and place side by side with exact same view.

27) FCT-55: Check that log buttons are functioning properly on both units.

28) FCT-03: Access ‘Comp X’

29) Move out of view of units.

30) Press ‘enter’ to calculate new X calibration values.

31) Verify that both units are measuring the same for all rings using up/down and left/right keys,

32) Press ‘edit’ in FCT-03 under X values to see new values. Record these in notebook.

33) FCT-01: to see X calibration defaults. Change these to use new calculations.

34) Change Y sensor to Y control unit.

35) Select ‘break’ and verify that corresponding rings read the same when sensors are side by side.

Set up above X unit:

36) FCT-11: Select ‘Rmt Below Y’

37) Select ‘avg’ to 0 (i.e., unknown).

38) FCT-12: Set up prompts (most likely not necessary).

Set up above X unit:

39) Set up A (reference unit) in large gap, open road or TOC position,

40) FCT-11: Select ‘Rmt Above X’.

41) Select ‘log interval’ of 15 seconds.

42) Enter ‘start’ and ‘stop’ times.

43) Verify there is enough memory available by checking ‘Room for’ # of files.

a. T/F = time to fill one file.

b. Num Files = How many files will be created.

c. Room for = How many files will fit in available RAM memory.

d. File 1 time: when the first file is started to be made.

44) FCT-14: Start logging (when start time is reached).

45) Enter descriptive location information (plot and person):

46) Verify taking LAI measurements as it will beep every 15 seconds.

Data collection:

47) Set up at point, level on tripod, georeference locations (Azi (mag; degrees), inc (degrees), SD (m). Make clear if location is from or to LAI-2000 from GPS stake.

48) FCT-14: For Plot: input traverse #, stake #, point #, height (L or H). i.e., T1S1P1H

49) Collect 5 points, one every 5 seconds, per location.

50) For each location collect a set of points at 1 m (H-HIGH) or 0.2 m (L-LOW).

51) Each location requires FCT-14 command again to collect new information. Press enter to log data point or button on wand (pressing log on keyboard starts a new log file).

Data collection (using the FV-2200 software):

1) Plug in unit X (A; above) to computer via USB RS-232 adaptor.

2) Verify that:

a. FCT-31: Baud=4800; Data bits=8; Parity=None; XON/XOFF = NO

b. FCT-33: Format: Standard; Print Obs: Yes

3) Turn on FV-2200 software and select acquire.

4) When prompted select: FCT-32 enter page: Start:1, End: 1000.

5) Open in new view named “LAI Elevation Traverse (s) Raw Date”, and save to .txt file in folder named as above in LAI-2000 data folder,

6) Repeat for unit Y (below), clearing print view between imports using ‘select all’ and ‘delete’, and opening in pre-existing view named as above, also saving as .txt file as above,

7) Strip all ? data points (using ‘strip’ button) from all files,

8) Select all B files and then select import, select A file, use interpolate A,

9) Recompute using band filters (leaving only 1 and 2), use A interpolation, and horizontal canopy model, and skip records with transmittance > 1,

10) Verify that each file looks acceptable, remove strange data points if found, and recompute if necessary,

11) Deselect all files and save as LAI-2000 format file with name as “LAI Elevation Traverse (s) Computed Date”,

12) Copy calculated final LAI values for each location and transfer to Excel with georeferencing coordinates, date, misc information, etc...

Notes misc:

Ø Sin(@)*height = 0.5*horizontal view necessary at that height.

Ø The distance from the sensor to the nearest leaf over it should be at least four times the leaf width.

o 1 ring = 0-13 degrees

o 2 rings = 16-28 degrees

o 3 rings = 32-43 degrees

o 4 rings = 47-58 degrees

Ø Use 2 rings minimum for each unit.

Ø LAI is dimensionless but can be thought of as {m2 leaf area (one sided) / m2 ground area}

Ø Press up arrow to enter letters

Ø See page 4-8 of the manual to get an estimate equation of the ground area covered by the sensor at different ring angles. A=f(pi)H^2

Ø Compute foliage density? Using 5-3, changing the dist factor for the first two rings. The dist factor would be obtained from the lidar data.

Ø If the unit locks up open the back case (4 screws) and unplug for 10 seconds. If this fails you can do a hard reset which will delete all data stored located on the processor board (approximately under the setup key).

Ø FV-2200 software is freely available for download for LiCOR ftp site, search their website to identify path location.

 

TOC Sensor calibration.

1) All dates converted to Julian style day and fraction day.

Trends in high elev sensor versus JD and FD (fractional day).

 

Calculate the new multipliers linear relationship with JD and FD.

New high elevation PAR values after fractional day noise removed.

Next step is to pull out any seasonal (NS offset) differences. Then finalize the calibration and apply to all high elevation PAR data.

 

Original data relationship looked like this (1 to 1):

 

Following diurnal correction no significant seasonal correction is found, therefore only the diurnal correction will be used. This correction is:

 

LiCOR calibrated PAR = (1.3974048 - 0.8695949 * :Fraction_Day) * Raw High PAR

Wednesday – 09/10/10

PAR calibration ongoing. Setup measures every 30 seconds in high resolution, the Apogee sensors are single ended measurements while the LiCOR is differential. Measurements are within range, but updating the multipliers will definitely be necessary.

 

Pre correction mid elevation tower PAR sensor data. Post-correction the values are perfect.

Tuesday – 09/09/10

Replaced HOBO Robot 4 with new one.

temp/rh calibration good

insanity for par calibration. the 4 apogee sensors were too far off. we’ve developed a calibration method versus a new LiCOR par sensor which is set up and will be run tomorrow, then sending the apogee units back to check for any hardware malfunctions.

we’ve also developed a method to calibrate all the top of canopy data as well as interior forest par sensors to new LiCOR par sensors recently calibrated. phew…a mind-boggle to work through!

preliminary calibration work in the morning prior to discovering that something was seriously not right…..

Wednesday – 09/08/10

• Developing and testing LAI-2000 procedure.
• Prepping for field work tomorrow setting up the interior forest climate sensors at a new low elevation plot.
• Replace HOBO 4 with new unit (broken).

Tuesday – 090710

• Organizing files, replacing broken sensors, picked up 2 LAI-2000 units which I need to learn tomorrow.

Friday – 09/03/10

• Brought down interior forest sensors.
• Downloaded data from tower climate stations.
• QC checked data downloads.
• Configured LAI protocol using an LAI-2000 (dual) and the start to hyperspectral LiDAR fusion approach.

Thursday – 09/02/10

• Figure out LAI methods for conversion of waveform, to LAD via hyperspectral LAI measurements as determined versus field LAI measurements (LAI-2000).
• Make methods for correction of LAI data once it is collected.
• Look into the pre-processing the hyperspectral received, does it still require conversion to surface reflectance via atmospheric correction (or already performed?)?
• Review article for the Journal of Applied Ecology,
• Organize HIPPNET tower data just downloaded
• Organize gear to collect interior forest microclimate stations and download climate data from low and high elevation climate towers. Need extra desiccant/batteries/laptop, etc…

Wednesday – 09/01/10

• Working to understand full waveform deconvolution. In particular the Richardson-Lucy iterative approach.
• Coding a method to read in/ write out very large datasets (images > 8 GB), based on the ASSOC IDL command.
• Picking up and installing new RAM (8 GB upgrade, from 6 to 12 GB).
• Organizing and delivering to IPIF the LiCOR 6400 on loan through Tuesday.
• Getting field gear organized for geo-location and removal of micro-climate stations. Then data download and QC analyses.

Monday – 08/30/10

• Preparing committee member research status update.
• Pick up and install additional 8 GB RAM! After crashing the computer several times last night, this is a welcome addition.
• New publication out today in Biotropica titled ‘Distinct Leaf-Trait Syndromes of Evergreen and Deciduous Trees in a Seasonally Dry Tropical Forest’ located in Western Mexico in which we investigate biotic and abiotic selective pressures on leaf traits, including herbivory, phylogenetic signal, and phenologic status.

Sunday – 08/29/10

• Refining direct and diffuse PAR models.
• Learning to write IDL code using multi-threading (using multiple processors simultaneously) techniques for improved computation speed.

Saturday – 08/28/10

First direct path forest structure rays are returned from direct par model. Needs much refinement but nice to have the first chunk functioning. Below see for 45 deg. elevation and 37 azimuth with a max distance of 100 horizontal meters.

Example path through a randomly generated forest. next step is to deal with azimuth and elevation issues beyond 180 degrees, etc…

 

Considering now various approaches to deal with light extinction, including a inverted Beer-Lambert exponential extinction equation where “y = e-k*LAI”

Friday – 08/27/10

• Working on diffuse PAR model. Who knew how simple it was to calculate Euclidean distances within a variable size array, meaning the diffuse model can be adjusted on the fly (using only the code below), and therefore much better parameterized to actual microclimate conditions. Joy!

 

x_2 = (findgen(nx) - xcen) ^ 2     ;X distances (squared)
y_2 = (findgen(ny) - ycen) ^ 2     ;Y distances (squared)  
im = fltarr( nx, ny, /NOZERO)     ;Make uninitialized output array

for i = 0L, ny-1 do begin                      ;Row loop
       im[0,i] = sqrt(x_2 + y_2[i])      ;Euclidian distance
endfor

thanks to NASA GSFC for base code! Here’s a small example from the procedure…

Here is output in cell fractions for a 5x5 array.

2.82843      2.23607      2.00000      2.23607      2.82843
2.23607      1.41421      1.00000      1.41421      2.23607
2.00000      1.00000     0.000000      1.00000      2.00000
2.23607      1.41421      1.00000      1.41421      2.23607
2.82843      2.23607      2.00000      2.23607      2.82843

 

Now how to make this work except within a variable size cylinder?

 

excellent, here it is for 4 cells above our z base in meters, corrected for different x and z dimensions (0.56 and 0.15 m).

1.69375      1.38852      1.27059      1.38852      1.69375
1.38852     0.993579     0.820731     0.993579      1.38852
1.27059     0.820731     0.600000     0.820731      1.27059
1.38852     0.993579     0.820731     0.993579      1.38852
1.69375      1.38852      1.27059      1.38852      1.69375

 

On to the direct PAR model for a change of pace. Here is the preliminary brainstorm, a load of basic trig.

Thursday – 08/26/10

Continuing advances in the brutal world of LiDAR modeling. Memory is such a big problem!

 

Wednesday – 08/25/10

• Ongoing programming work. Now working to read into memory the waveform LiDAR image in small enough chunks to fit into RAM…However, I did upgrade to 12 GB ram after realizing that 6 was completely inadequate. Making progress and hopefully today will begin to code the actual direct and diffuse PAR models based on the waveform structure data.

Random screenshot of the IDL programming environment.

Tuesday – 08/24/10

• Refine the data read in code. Need to code it able to both run iteratively through the entire image for the full on model, with adjustable temporal resolution and output parameters, and also to return specific location data.
• Start the microclimate model.
• Start to consider the approach for linking the leaf area density profiles and branch vs... leaf offsets with the hyperspectral and waveform data.

Example screen shot of one binned waveform, resolution 0.15 m vertical, 0.56 horizontal.

 

• Also prep for field work tomorrow, unless I’m on a programming roll, then will stay here…

Monday – 08/23/10

• Working on IDL code to read in a 3D  image subset based on specified UTM coordinates. Necessary as the waveform LiDAR image is 6 GB in size. Not as easy as it seems…  (1:45 pm; currently have a working script to read in a portion of an image, now improving it to read in correct area for microclimate modeling work)
• Prepping gear for field work starting tomorrow through Thursday collecting LiCOR curves.

Sunday – 08/22/2010

• Revising solar positioning software, (finished)
• Working on IDL code to convert from UTM to Lat long coordinates. This is necessary to link my waveform LiDAR voxels ('”volumetric pixels”) 3D locations, which are in UTM coordinates, to my solar positioning model which uses Latitude Longitude Altitude. (finished)

 

Yes! Just finished and tested to sub-meter conversion accuracy versus online sources. View of part of the code below…

Friday & Saturday – 08/20-21/10

• Finished R stats and figure generation for Peru and Bolivia datasets for Angelica’s presentation at IUFRO S. Korea.
• Completed preliminary version of solar positioning software. The code uses JPL ephemeris data for maximum accuracy, reads rectangular universal coordinates of earth and sun locations and converts them to celestial equatorial  (right ascension and declination) compensating for light-time displacement and gravitational effects of other planetary bodies, then converts from celestial to topocentric using lat, long and altitude for location adjusting from true to apparent location caused by refraction, then adjusts from Gregorian to Julian date and compensates for precision issues with double floating point precision data in IDL, maintaining < second temporal accuracy via normalizing all Julian dates to the epoch 01.01.2009 at 00:00:00 Universal Time.
• Accuracy/Precision of the code has been tested extensively versus the JPL Horizons online ephemeris generator and has < 0.2 degrees of Elevation and Azimuth from 1950-2050, more than adequate!

* Image from http://www.bsu.edu.

Wed-Thur: 08/18-19/10

Mired in the depths of IDL astronomy programming trying to create a high precision solar path model, an important module within my microclimate / physiology model.

Tuesday – 08/17/10

• Finished new LiCOR programs,
• Installed new internal hard drive (1.5 TB) for upcoming modeling work,
• Started coding sun tracking IDL module,

Mon – 08/16/10

• Finish entering foliar data (done),
• Calculate leaf areas and input (done),
• Check LiCOR data quality for each sample (9; done) – have 5 valid sets from traverse 1, leaving one day of understory LiCOR work there,
• Update LiCOR programs,
• Clean and organize low & high tower climate data,
• Clean and organize first interior climate dataset,

 

Work with Angelica to develop R stat codes for Bolivia dataset.

 

Calculating scanned leaf areas using magnetic lasso tool in Photoshop at 600 dpi…

Sat & Sun – 08/14-15/10

• Finished entering leaf/trunk offset data,
• Entering foliar data and organizing,

Friday – 08/12/2010

Finally came up with a working method to rain proof the LiCOR head while taking measurements, thanks to some great new clamps found at Home Depot.

Next steps are:

1. to get the interior forest station running. (Done)
2. finish entering leaf vs. wood data. (in progress)
3. Finish calculating leaf areas for collected leaves, (later i guess)
4. update LiCOR programs. (tomorrow i guess)

Sensors up and running:

One of 4. this one is setup to show the lowest strata micro-climate.

Final weatherproof setup, charged desiccant and ready for the next 10 days of data collection.