Analyzing Hemispherical Photographs Using SLIM software

Transcription

1 Analyzing Hemispherical Photographs Using SLIM software Phil Comeau (April 19, 2010) [Based on notes originally compiled by Dan MacIsaac November 2002]. Program Version: SLIM V2.2M: June 2009 Notes on SLIM **** For proper orientation, images should be taken with bottom of camera facing south (top to the north). If it wasn t done this way, you can rotate the image 180degrees in SLIM. With the proper configuration, the images have east to the left, west to the right, north at the top and south at the bottom. E N W Correct image (As you see it after taking the picture)- taken with camera facing south S S Incorrect image - taken with camera facing north W E N To correct this, need to rotate (not flip) the image 180 degrees. Can rotate the image in SLIM, by clicking on a yellow cardinal direction line that is on the picture while in the first Photo Wizard screen, and rotating the grid around 180. The photo keeps its original orientation, but just has the grid overlay showing the proper directions. Other software can also be used to rotate images 180 degrees (eg. Windows picture and fax viewer) (and is probably easier to use). To properly set up SLIM for your digital camera you also need a registration image taken in the open or with clearly contrasting (bright) objects all around the point where the photo is taken. You need to be able to clearly see the edges of the image for proper registration. This registration process provides information to SLIM on where the image is within the frame, pixel sizes, and other details. 1

2 Sequence of Steps 1. Create a New File (File) 2. Edit Plot Properties (Plot) a) World Location: enter in Lat (North) and Long (West) If not entered, the program uses the last settings used. b) Set Time Zone: (Use Mountain) c) Set Azimuth = 0 This determines how the plot is offset from north (azimuth of y axis). Because SLIM treats each photo separately, this doesn t need to be set here (has no effect on SLIM). It can be set in LITE. d) Click on Constant Horizon for Plot (use default of 8.63) This is more important in mountainous terrain. The default is based on the observation that very little light comes from this region close to the horizon. 3. Set Lens and Camera Characteristics (File/Lens and Camera Characteristics) The lens and camera characteristics file contains information common to all photos to be processed as part of a batch. This includes lens characteristics, image characteristics, thresholding information, and sky resolution. When running a batch file, all this information will remain constant. Once the batch file is processed, users can not go back and alter the data for the photos without deleting them and reading them in again. To create a lens and camera characteristics file, create or open a GFR document and select "Lens and Camera Characteristics..." from the File menu. A dialog will come up, displaying the current default characteristics information used by the application. Note that no information can be directly edited from this dialog. In order to change information, you must go to one of the sub-dialogs as follows. Set Lens Information 2

3 This brings up the Lens Calibration dialog. From here, information regarding the camera lens used to take the photographs can be entered. If you have the correct parameter values for the polynomial calibration equation for your camera these than be entered in File/Lens and Camera Characteristics. If not - use the default (these are the values published for a Nikon 8mm fisheye lens for a film SLR camera) it does not appear to make very much difference. 4. Set Sky Conditions (Atmosphere) Several options a. Insert default ppfd (from Sechelt B.C. in 1998, near Vancouver) b. Load sky transmission file (*.stv) (average sky transmissivity values for each hour determined from weather observations; clear=0.8, light overcast=0.6, moderate overcast=0.3, heavy overcast=0.05) c. Load ppfd file (*.pfd) (average total ppfd values (and, optional direct ppfd and diffuse ppfd) for each hour from a sensor in the open). d. Load monthly values (*.sky) (number of clear, light overcast, moderate overcast and heavy overcast days for each month of the year). e. You can modify conditions for the month or for a particular day use either the menu or click on a month or day f. You can create a new pfd file based on modified data (Save PPFD) or a new monthly (sky) file (Save Monthly values) 3

4 5. For Each Stake Location, Run Photo Wizard (Plot/Run Photo Wizard) Ensure it contributes to plot crown. a) Circle Selection Type: Automatic Selection (see below) b) Select New Photo, then select Color Threshold (see below) c) Photo Attribute Settings Sky Resolution Use Standard Below Canopy Reading Resolution (BCR) - gives 480 segments This is based on paper by Spitters, estimating diffuse fraction Phil tried with finer resolution - didn t see much gain in going with more than 480 segments, but longer computer time to process. Do not exclude any altitude or azimuth ranges Set this as default. Image Selection Type: Automatic (Make Default) (works only for digital) With regular film camera images, cannot use automatic image edge selection. Select Color Threshold: Blue is generally the best (and sufficient). Click on 5 canopy (right button) and 5 sky (left button) pixels on the image. Be sure to do some clicks on lightest foliage (eg aspen boles and leaves). Once you have the threshold, move the slider bar to go between them. Manual thresholding is a subjective process. d) Press Next - will have two images. Compare the threshold image vs the original. Ensure the threshold image is OK. Make sure there is finer detail (esp fine branches near zenith and gaps near horizon). *** There is a glitch in the program - if you play with the windows size, sometimes you have to restart to photo wizard to be able to see all screens during processing. e) Set Gap Specifications Check Calculate Gaps - minimum gap size is 1.00 degrees Don t worry about output files f) Press Next - will have three images Attach the image to a specific stake. BCR (Below Canopy Readings) View Properties: do not click High Contrast Click Show Grid 4

5 d) PPFD Calculations (Window/ Open Long-Term PPFD Calculations) This displays information for each stake (sample location) in the dataset. Scope (This only affects Leaf Area Index and gap fraction output, does not affect light calculation; ie light calculation uses the full 180 degree view in the image) Use 60 degrees (this is angle off zenith used in cone). So a scope of 60, includes a 120 degree cone. Could also use a scope of 45. When you change the scope value, the Gap Fraction changes automatically. It is the Gap fraction in the cone specified by Scope. As Scope values increase, gap fraction declines (as you are including foliage closer to the horizon in gap fraction estimates - where there are fewer openings). Leaf Area Index: This screen has nothing to do with the light readings. Will use one of the following three ways to calculate LAI (all are output, you don t have to select one in particular. a) Poisson - Phil recommends using this, if you don t have a good estimate of clumping. It assumes random leaf distribution (leaves are just distributed randomly - does not take into account tree architecture). - this value is generated automatically, and is affected by Scope setting (set by user) b) Binomial - can use this if you have a good estimate of clumping (determined by research) - may be best if there is a very clumpy (gappy) canopy (leaves plus branches) (leaves are just distributed based on tree architecture - i.e. leaves on fine branches, fine branches on coarse branches, branches on trunk). - this negative binomial value is generated automatically, and is affected by Scope setting and Clumping (set by user). I think Phil said you could use a scope of 60 degrees and clumping of c) Linear Avg. - Phil says don t use - this is generated automatically, and is affected by Scope setting and Leaf Angle (set by user). Times: Time period over which PPFD is calculated. PPFD Calculation Options - use default (Use Standard Overhead Conditions Model (SOC)), with H Factor. The SOC assumes that Gap Fraction by Partition is shown ** When you make a change to long-term PPFD calculation screen options, need to press recalculate (can tell, as all PPFD values are set to zero). But, in batch export mode, values are recalculated based on options last saved. The values are cumulative PPFD (micromoles per square metre over the time interval selected). All data on this screen (except for Segment Gap Fraction) is output to the Long Term 5

6 PPFD File in batch output (File/Export Atmospheric Readings). Output Using File/Export Atmospheric Readings - this is how we get results. Can export all values at once, when you want only one PPFD value per stake (i.e. not split into fractions). Times: make same as leaf on or leaf off (e.g., May 15-Sept 30). Make sure proper year is selected when entering the dates for leaf off (eg. Oct May ). Interval - Calculation Interval - Phil suggests 1 hour (Sun path in 1 hour intervals). Can also use 15 mins Output Interval - 1 day or 1 week Use All Contributing Stakes. Long-Term PPFD file is the major one of interest. To export the output click on -File -Export Atmospheric Readings -Only select Produce Long Term PPFD file (unless you want the others for some reason) -Indicate output file name -Use all contributing stakes -select Export Now The output file is in excel tab delimited format. It gives diffuse direct and total PPFD (last three columns). Recalculate (overwrite) to get it to give it in decimals. (import it into excel as a tab delimited file). There are many other options but these notes provide you with a quick overview of how to get started. Output Files Can choose to output any of the following: Phil suggests the Long-Term PPFD only, for my needs. Sky Brightness distribution of the beam component over all 480 cells during the calculation interval (the diffuse component is distributed evenly among all cells). Above Canopy Readings Below Canopy Readings is the total, beam, and diffuse PPFD at various times. The user specifies a start date, stop date, time interval and stakes that contribute to the file. same as above. Canopy Chart shows the occlusion factors of each cell of each cell where 0.0 is full occlusion and 1.0 is no occlusion. 6

7 Sunfleck Table Long Term PPFD provides a frequency table describing the number of seconds during the defined period when total PPFD is within certain ranges. contains output of gap fraction and long-term PPFD as specified by the user in the long term PPFD dialog. Definitions Gap Fraction (GFR) indicates the area of overhead view (in percent) which constitute canopy gaps. Stake Scope Time Clumping is the location where the hemispherical photo and the according values are assigned in the plot. angular view (degrees from zenith) which is used for LAI calculation. Beginning and end times for all PPFD calculations. allows the user to set the aggregation parameter for use with the negative binomial method of LAI calculation. Calculations If the calculation interval is less than the output interval, all calculated values are accumulated until the next output interval occurs. For example, a time period from 8:00 8:30, with a 15 minute interval, would have values equal to those valued calculated during the middle of the interval and multiplied by the number of seconds in the interval. Thus, the sun position and the PPFD would be at 8:07:30 and 8:22:30 - if contributes to plot crown is not toggled, neither the stake nor any of its sky readings are used during the crown generation process. 7

8 Notes about the SLIM Program - Generic Settings Under File\Options Options: Warnings: Application Defaults - settings used in all program runs Document - can save customized settings, attached to a specific file Most warnings relate to data from LAI Can keep all on. Input Options: All options on this page are for LAI-2000, except for very bottom one (check use active photograph readings ) Options: Select the output format. Some of the Files Created By SLIM *.gfr - saved data and other settings *.map - saved stake data, location (x-eastings,y-northing, z-elevation), canopy top and bottom Under Plot/Attach DAT File - this is to add LAI 2000 files. Long-term ppfd output (File\Export Atmospheric Readings) LAI-2000 plant canopy analyzer files can also be processed by SLIM. These *.dat files can be read in using the Plot\Attach Dat File. If you want to make use of the spatial location of points (stakes) in a plot, and set up SLIM results for spatial integration using the LITE model then you will want to give each stake a spatial location in the plot (and you will need to create separate files for each plot, unless they are adjacent and mapped contiguously). 8

9 Creating and executing a batch file in the SLIM program Phil Comeau April 5, 2008 SLIM now has the capability to execute a batch file containing a list of DAT s or photos. These pictures will automatically be processed and added to the specified stakes within the users' plot. This tutorial will guide you through the creation of a batch file and successful execution within the SLIM application. Step 1: Create a lens and camera characteristics file The lens and camera characteristics file contains information common to all photos to be processed as part of a batch. This includes lens characteristics, image characteristics, thresholding information, and sky resolution. When running a batch file, all this information will remain constant. Once the batch file is processed, users can not go back and alter the data for the photos without deleting them and reading them in again. To create a lens and camera characteristics file, create or open a GFR document and select "Lens and Camera Characteristics..." from the File menu. A dialog will come up, displaying the current default characteristics information used by the application. Note that no information can be directly edited from this dialog. In order to change information, you must go to one of the sub-dialogs as follows. 9

10 6. Set Lens Information This brings up the Lens Calibration dialog. From here, information regarding the camera lens used to take the photographs can be entered. 7. Set SBC Circle Information In order to set SBC circle information, the user must use a sample photograph on which they will specify the location of the image circle edges (as is done in the current Photo Wizard) for the camera and lens being used. For this purpose it is best use a photograph taken with an open sky or white background on all sides as a registration image. First select Change Circle Selection Type and select one of the two manual options (three points or circle diameter). 10

11 With 3 points selected the user users the mouse to point to the edge of the image circle at each of 3 locations. When the pointer is in the correct location double click with the left mouse button to select this point and a green marker will be indicated at this location. Then do this for the second and third points distributed around the edges of the image. First point selected (image below). 11

12 Second point selected: After selection of the third point: After locating the third point, the full circle and the overlying sky segment grid will be shown on your image. The location of circle edges can be adjusted by pointing to one of the green markers, holding down the left mouse button, and moving the mouse. 12

13 The image information of this sample photograph, along with information about the circle, will be used in the characteristics file. It is possible to specify a sample photo without specifying a circle, however any batch file using that characteristics file will not run. 13

14 8. Set Threshold Information This brings up the Select Color Threshold dialog. From here, you need to select either the Automatic - Nobis and Hunziker or the Automatic - Ridler clustering method for batch processing. After selecting either of these thresholding methods click OK (nb. For manual thresholding runs you can click on Make Default to set any of the desired thresholding methods as the default). 14

15 9. Set Sky Resolution Information This brings up the Set Sky Resolution dialog which allows users to change information related to the resolution of the sky. This relates to how many "sky segments" there will be, as well as which sky segments to ignore. For most uses, the Standard BCR works well. This window also allows setting of ranges of azimuth and altitude which can be ignored. If the boxes beside these items are blank, SLIM will be using the full 360 degrees of azimuth and the full 90 degrees of altitude that are visible in the image. 15

16 Once all the information has been entered and is to your liking, you can press the "Save Characteristics" button to save the characteristics to a.lns file for use with batch processing. You can use this methodology to create and save several.lns files, each with different characteristics. For example, you may have three.lns files that are all the same with the exception of having a different thresholding method. You can use Load Characteristics to open and load a previously save lens characteristics file. Note that lens files for earlier (pre November 2007) versions of SLIM (files with a LNS extension) can be loaded using the "Load Characteristics" button, however this will only affect the lens information (the values on the left side of the dialog). Step 2: Create a batch input file A batch input file is a simple text file with a list of photographs to process along with some information about the stake or location to associate each photo with as well as a height. The format of the file is such that one line at the top is reserved for headings. This line will always be ignored by the batch processor. After this line is the data with information for each photo on a separate line in comma-separated format. The first piece of information is the name of the photograph itself, along with a full path if the photos are going to be a different directory than the batch input file. Next is the stake name. This is the name of the stake in the plot which this photograph will be added to. If no name is given, the program will create a new stake using the name of the photograph. The next two pieces of information are the x and y coordinates of the photograph. This information is really only necessary when creating a new stake, as existing stakes already have x/y coordinates associated with them. If you try to associate a photo with an existing stake and provide conflicting x/y coordinates, the batch processor will complain and will not add the photo. The final piece of information is the height, with the default being zero centimetres. Note that different photos attached to the same stake can have different heights. 16

17 An example of a batch input file might look like this: Photo name, stake name, x coord, y coord, height PHOTO1.BMP, STAKEA,,, 10 PHOTO2.BMP,, 10, 20, 15 d:\sample\testfiles\photo3.jpg, STAKEB,,, 0 PHOTO4.JPG, STAKEC,,, 0 In this example: Photo PHOTO1.BMP will be attached to stake STAKEA at a height of 10m. Photo PHOTO2.BMP will be attached to stake PHOTO2 at location x=10, y=20 at a height of 15m. Photo PHOTO3.JPG (which is in a different location than the other photos) will be attached to stake STAKEB at a height of 0m. Photo PHOTO4.JPG will be attached to stake STAKEC at a height of 0m. This file should be saved with a CSV (comma-separated values) extension. Step 3: Running the batch file in SLIM In the SLIM program, create a new plot or open an existing one. Go to the File menu and select "Process a batch file". The program will prompt for the lens and camera characteristics file created in step 1 and then the batch input file created in step 2. Once this is done, the program will automatically process the photos line by line. Any errors encountered during the processing of the batch file will be displayed to the user in the message window. These errors include such things as: A bad photo file name, or a file which cannot be opened. An x or y coordinate outside the acceptable range (i.e., less than zero). A negative height. A photo with dimensions which do not match that recorded in the characteristics file. An x or y coordinate which does not correspond with the coordinates of a named stake. Once the batch processing is complete, the user will have a record of which photos were successfully added to the plot. This information, displayed in the message window, can be saved using the Save Batch File Message Information tool from the File menu. You can run multiple batch files, each with different configurations, by using different characteristics files. 17