Nikon D200 IR Calibration

Below are camera calibration values for the CAST Nikon D200 IR camera with Nikkor 28 mm lens. For projects requiring highest accuracy it is recommended that you perform your own calibration, otherwise these values can be used.

PhotoModeler v2012 Calibration Values (August 2013, F-stop of f/8, overall RMS 0.218 pixels):
– Focal Length: 29.630373 mm
– Xp: 11.836279 mm
– Yp: 8.051145 mm
– Fw: 23.999451 mm
– Fh: 16.066116 mm
– K1: 1.435e-004
– K2: -1.481e-007
– P1: 5.659e-006
– P2: -1.311e-005

Calibration Values for PhotoScan (converted from PhotoModeler values using Agisoft Lens):
– fx: 4.7804273068544844e+003
– fy: 4.7803319847309840e+003
– cx: 1.9096258642704192e+003
– cy: 1.2989255852147951e+003
– skew: -8.0217439143733470e-004
– k1: -1.2545715047710407e-001
– k2: 1.5266014429827224e-001
– k3: -7.6547741407995973e-002
– p1: 3.5948192692070413e-004
– p2: -1.5418228415832919e-004

Nikon D200 IR Light Transmission

Because of the light transmission properties of the filter installed in the CAST Nikon D200 IR DSLR camera, it is possible to isolate infrared and red light into separate channels. These channels can then be used to generate an NDVI image using the well known formula:

NDVI = (NIR – Red) / (NIR + Red)

We’re calling this pseudo-NDVI for a couple reasons; 1) the IR filter installed only captures a portion of the visible red (probably less than half), so this bit of information is relatively weak, and 2) our method of isolating the “reflected red” (Band1 – Band3) is overly simplistic. However, we have tried more complicated methods (e.g. principal components, also averaging bands 2 and 3) but results did not improve. Without more work, the results of this process should not be compared to calibrated NDVI images.

1. Load (individually) bands 1 and 3. Band 1 represents Red+IR, Band 3 is IR only.

Nikon D200 IR Bands 1 and 3

2. Run the Raster Calculator tool to produce a “reflected red” raster using the following raster math:
Band1 – Band3

Nikon D200IR “Reflected Red”

3. Run the Raster Calculator tool to produce NDVI raster using:
(Float(“Band3”) – Float(“ReflectedRed”)) / (Float(“Band3”) + Float(“Reflected Red”))

Nikon D200IR Quasi NDVI

Note: If you don’t use the Float functions in step 3 you end up with integers (-1,0,1), which are useless.

Nikon D70 and Nikkor lenses

Along with the generic advise given in the Acquire Images for Close-Range Photogrammetry and Custom White Balance for Nikon D200 IR posts, here are some important settings to consider when using the standard or IR modified Nikon D200 cameras:

– Rotate Tall: Set “Rotate Tall” to Off if the images are to be used for photogrammetry or GIS applications

– Image Quality: Use either the “NEF (RAW)” or “NEF (RAW)+JPEG” image quality setting. Capturing RAW images will preserve all image information and give you much more control over editing later

– Image Size: Set to “Large 3872×2592/10.0M”

– Optimize Image: Use these “Custom” settings and adjust as needed:

–Image Sharpening = None
–Tone Compensation = Normal (0)
–Color Mode = III
–Saturation = Normal (0)
–Hue Adjustment = 0
–Make sure you select “Done” after making adjustments to theses settings or they will be lost.

– Color Space: Should be set to “sRGB”

– JPEG Compression: For highest quality set to “Optimal Quality”

– RAW Compression: If memory card space is not an issue, set to “NEF (RAW)” for no compression. Otherwise turning on compression will cut the size of RAW images from 16MB to 9MB

– Intvl Timer Shooting: This setting can be used to take a predetermined number of images with a certain amount of time between each shot. To use this setting, three setting must be set:

1. Start: Two options exist including “Now” (starts taking images right away) or “Start Time” (allows you to set a time (e.g. 13:00, aka 1pm). If using Start Time, make sure the cameras time setting is correct
2. Interval: Sets the amount of time between each interval using hours, minutes, and/or seconds (one second minimum)
3. Select Intvl*Shots: This setting ask you to set 1. the total number of intervals and 2. number of images at each interval. If mounting the camera to the octocopter for example, one could set the Interval to 10 seconds, the total number of intervals to 50, and the number of images at each interval to two. This would result in 100 total images, with two at each of the 50 positions (interval)

Nikon D200IR Custom White Balance Results

Because some red light is transmitted by the IR filter, any of the standard white balance settings will produce reddish images. A custom white balance using the “White Balance Preset” option can be used for better images. It’s important to note that the white balance setting is only applied to JPEG images saved on the memory card – RAW images are saved to the memory card exactly as they are recorded by the image sensor, without any processing. However, even when capturing RAW images, the image preview on the camera’s LCD will use the white balance setting, and will therefore be easier to evaluate exposure in the field.

To use the White Balance Preset option, follow these instructions to capture an appropriate custom WB image:

1. Hold down the “WB” button and rotate the rear wheel to select the “PRE” setting, release WB
2. Hold down the “WB” button until “PRE” begins to flash
3. Use the shutter release button to capture a photograph of healthy green grass in similar lighting as your intended subject (e.g. direct sun)
4. The camera should indicate “Good” or “No Gd” – if “No Gd” try again
5. If the camera indicates Good, take a test image to visually check your white balance

This document is under development…Please check back soon!

This document is under development…Please check back soon!

___  VIVID 9i Scanner (Large orange hard case)

___  Turntable – optional (Medium black hard case)

___   Manfrotto tripod

___ Laptop with Polyworks installed (with REQUIRED Plugins Add-on).  If you are going to be off the network, then you must borrow a license from the Polyworks license server to be able to use the software.  Note:  The laptop must be 32 bit with Windows XP with a PCMCIA card slot and serial connection.  The Panasonic Toughbook is most commonly used with VIVID 9i and has the required configuration.

___  Black lens box

___  Small black case with cables and accessories

___  Additional lighting – optional (not shown above)  Note:  In addition to capturing surface information and detail of an object, the VIVID 9i also captures color (RGD) data.  If the color properties of an object are important to your project, then we advise to use additional lighting to ensure more accurate color capture.  CAST has a three light setup that uses white flicker-free flourescents that is available for checkout.  If color is important – use good lighting (it can make all the difference).

[wptabs style=”wpui-alma” mode=”vertical”] [wptabtitle] CALIBRATION [/wptabtitle]

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1.  White Balance Calibration: Before you begin scanning, you need to perform the white balance calibration on the scanner.  Make sure the lighting conditions in your environment are set to what they will be during the scanning process. 

A.  Next, remove the white balance lens from the lens box and screw it onto the top front of the scanner. 

B.  Press the Menu button the back of the scanner and select White Balance and press Enter. Under the White Balance menu, choose Calibration and press Enter.  Do not touch or pass in front of the scanner while it is performing the calibration. 

C.  When the calibration is complete, remove the white balance lens and put it back in the lens box.  You are now ready to begin your scanning project.

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[wptabtitle] TITLE OF SLIDE [/wptabtitle] [wptabcontent]
2.  Open Polyworks IMAlign (v 10.1 in this example) and select the Plugins menu – Minolta – VIVID 9i – Step Scan.  The One Scan option is used if you are not using the turntable.  If you do not see the Plugins menu, you will need to install the Plugins Add On from the Polyworks installation directory.

3.  When the VIVID 9i window opens, you should see a live view from the scanner camera.  Select the Options button on the right.  Under Scan Parameters, select Standard Mode.  Extended mode offers a greater scan range however it limits noise filtering operations.  Standard mode should work for most projects.   The number of scans are the number of passes the scanner makes per scan position.  From the manual:  “It averages the data from each pass to produce a single scan file therefore more scans theoretically will give you the most accurate data.   We recommend 3 or 4 scans, however if time constraints are an issue then this number may be lowered.

4.   Under Convert Parameter, check the VVD File Format and a Reduction Rate of 1/1 (No data reduction).   Under filter, select H.Q. & N.F. (High quality and noise filter).  This is the highest filter setting and is most effective for minimizing scanner noise.  Also, make sure Fill Holes is Off and under Remove, it is generally advised to select 20deg & B.  (20 degrees and Boundary).  This last parameter removes data around the perimeter of a scan that tends to be less reliable.  In previous experiences, it was noted the data around the scan edge often curves up creating an artificial lip in the data.  Researchers found that increasing the Remove parameter to the highest setting, removed the “scan edge lip.”  All of the settings above are just suggestions and may need to be altered to suit individual project needs.

5.  Under Stage Parameter – Model, select Parker 6105 (Fast); this selects the correct turn table model.  Finally select the desired Rotation Step.  A Rotation step of 60 is suggested which will result in collecting 6 scans per object rotation.

6.  Hit Apply and then OK.

7.  Back in the VIVID 9i Window, select the Stage Apply button to apply the stage parameters.  Next, we will calibrate the turntable by using the black and white calibration charts found in the turntable case. 

8.    The smaller chart is used with the tele lense and the larger chart is used with both the mid and wide angle lenses. Place the appropriate calibration chart on the system turntable facing the scanner.  The smaller chart has two pegs that fit associated holes on the turntable.  The larger chart also has two smaller pegs that rest in a recessed ring on the turntable.  In either case, it is important for the center of the chart to rest in the center of the turntable and for each chart to be completely upright.  The black line that runs down the center of each chart is used to identify the center axis of the turntable which is then used to coarsely align or register the scans from a single scan rotation.  In this example, the tele lense and small chart will be used.

9.  You should now see the scanner chart in the live view window.  It is recommended to fill the view with the scan chart as best as possible.  You may need to adjust the scanner position and rotation to achieve the correct view.  NOTE:  You will not be able to move the scanner after you perform the turntable calibration.  If you do move the scanner after this step, then the turntable will need to be re-calibrated.

10.  Next, hit the Chart Scan button.  The scanner will then scan the chart and indicate whether or not the calibration was successful.   It is not necessary to store the chart scan.

11.  You are now ready to begin scanning.  Place the desired object on the center of the turntable.  It is advised to perform a single scan to test system perameters before completing a scan rotation.  First, select the AF (Auto Focus button).  This auto focuses the scanner camera and determines the object’s distance from the scanner, displaying the value in the Distance box.   The Distance value can be altered to acquire object data at a specified distance.  Next, press the Scan button.  Once completed the scan should appear in the Store window on the right.  Check the scan for any anomalies such as holes, poor color, etc.  If you wish to keep the scan, you MUST click the Store button.  If you do not click the Store button, the scan will be overwritten.  If you are happy with the scan results, then you are ready to proceed with a scan rotation.

12.  To perform a scan rotation, first select the Auto Scan and Auto Store options.  Next, press the Scan button.  The scanner will perform 6 scans rotating 60 degrees between each scan and will automatically store the results in the IMAlign project.  Once the scans are complete, click in the IMAlign project window to view the results.

13.  The six scans are displayed in the Tree view (table of contents) on the left with the name “scan” followed by a suffix indicating the scan angle (0, 60, 120, etc…) and represent one complete scan rotation.   These scans have been roughly aligned to one another based on the central axis of the system’s turntable.  We recommend to clean and align scans as you go as it takes little additional time and it ensures that all of the required data has been captured (and all holes/voids have been filled in).

14.  Using the middle mouse button, select and delete any data that are not associated with your scan object.  Next, make sure all of your scans are unlocked and run a Best Fit alignment.  The Best Fit operation is an iterative alignment that produces a more accurate alignment between the scans. 

15.  Now that the scan rotation has been cleaned and better aligned, prepare for the next scan rotation by first locking all of the scans of the first rotation (select all in the Tree View, right click and select Edit – Lock or use Ctrl+Shft+L) and then by grouping the scans together (select all in the Tree View, right click and select Group).  Now observe the data that you have collected, note holes or voids in the digital object, and identify what areas need to be scanned next.  If you are scanning a large object, perhaps you will need to perform another scan rotation to acquire more of the object or if it’s a smaller object, perhaps a few single scans are needed in order capture the bottom and top views of the object.   Reposition the object on the turntable to prep for the next scan sequence. 

16.  Next, return to the scan window and complete another scan/scan rotation.  In this example, we will complete another scan rotation in order to show how align two rotations to one another.

17.  Because the object has been repositioned, it is always good to Auto Focus (press the AF button) before each scan/scan rotation.  Complete the second scan or scan rotation.

18.  In the IMAlign window, you may have to hide the first scan rotation (simply middle click on the group name or right click the name and select View – Hide or use Strl+Shft+D) to more easily view the new data.  Go ahead and delete any extraneous data from the scene and group the scans from the second rotation (select all, right click and select Group).

19.  To align the second rotation to the first rotation, first unhide the first rotation (middle click the group name or right click and select View – Restore or use Ctrl+Shft+R).  Next select the split view alignment button and independly rotate each view so that they are roughly the same perspective of the scan object .  

20.  Now select the N Point Pairs button (Align Menu – N Point Pairs) and identify at least three pick points between the two views.  Right click when complete and you should now see the second rotation roughly aligned to the first.  Run a best fit alignment to optimize the alignment and then lock the second scan group.  This is a very basic description of alignment in IMAlign, for more detail please refer to the Registering (aligning) Scan in Polyworks IMAlign workflow.

21.

• Complete as many scans/scan rotations that are necessary in order to get a complete digital model of your object.  Small holes can be holefilled with additional post processing in IMEdit.

22.  Refer to the Registering (aligning) Scan in Polyworks IMAlign workflow for further details on scan alignment and the Creating a Polygonal Mesh using IMMerge workflow for more information on creating a polygonal mesh file in Polyworks.

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[wptabs style=”wpui-alma” mode=”vertical”] [wptabtitle] TRIPOD & MOUNT [/wptabtitle]

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1.  Setup the scanner tripod.  The tripod doesn’t have to be completely level but you want it to be stable so some degree of leveling is required.

2.   Prep the scanner mount by pulling the black lever out, pushing up the gold pin, and then releasing the lever.  This widens the slot where the scanner mount rests. 

When done correctly, the lever will continue to stick out.

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[wptabtitle] CONNECT SCANNER [/wptabtitle] [wptabcontent]

3.  Place the scanner on the tripod until it locks into place (you will hear a ‘click’ sound when the mount has locked).  Once the scanner has been mounted, ensure that your setup is stable.

4.  Remove the power cable and gray  SCSI cable with the PCMCIA card adapter from the small black case.  Plug the scanner power cable in and connect the SCSI cable.  DO NOT TURN THE SCANNER ON.

5.  Remove the card insert from the PCMCIA slot on the laptop and plug the PCMCIA card into the laptop.

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[wptabtitle] SETUP TURNTABLE [/wptabtitle] [wptabcontent]

6.  Remove the turntable, black power box, and all cables from the black case.  Set the two, black and white calibration charts to the side for now.  Place the turntable approximately 1 meter (or slightly less) from the scanner with the corded end facing towards the front i.e. towards the scanner. The suggested scan range for the tele and mid lenses is .6 to 1 meter.  When you begin scanning, the distance parameter will be displayed in the scan window.  We generally suggest to keep the distance in the range of 700-800 mm to avoid data loss that can occur when an object is either too close or too far from the scanner.

7.  Plug the gray cable from turntable into the black power box; also plug the power cable into the black power box. Next, take the blue serial cable and plug the green end (with 4 prongs) into the COM1 port on the black box.  NOTE:  Theprongs on the green end are directional and will face down.

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[wptabtitle] CONNECT LAPTOP [/wptabtitle] [wptabcontent]

8.  Next, take the other end of the serial cable and plug it into the serial connection on the laptop.  To work with a laptop, you will probably have to remove the black case around the plug end using a small screwdriver.

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[wptabtitle] POWER UP SCANNER [/wptabtitle] [wptabcontent]

9.  Once everything has been plugged in and you have the desired lens in place (see the Changing Lenses section in the final slides of this post if you need to change the scanner lens). Next power on the scanner. It will take a minute to load, when it is complete, it will display the following message on screen “Please open laser barrier and press any key.”

10.  Next, pull the large round cap off of the front of the scanner (bottom) and remove the lens cap (top), and then press any button on the back of the scanner to continue.

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[wptabtitle] OPEN POLYWORKS [/wptabtitle] [wptabcontent]

11.  Next power on the laptop and log on.  Note:  It is important to power the scanner first and then the laptop so the connection is established.

12.  Once everything has been turned on, open Polyworks on the laptop.  Once the Polyworks Workspace Manager opens, open the IMAlign Module.  Next, go to Scanners menu, and select Minolta – VIVID 9i.  In the window that comes up,  you should see a live camera view from the scanner (connection successful – hooray.)  You are now ready to continue to the Konica-Minota Vivid 9i – Scan Settings post.

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[wptabtitle] VIVID 9i LENSES [/wptabtitle] [wptabcontent]

Changing the Lenses on the VIVID 9i

The VIVID 9i comes with a set of three interchangeable lenses: tele, middle, and wide.  The scanner’s camera array is fixed 640X480 pixels.  Each lens offers a different field of view with the tele being the smallest.  The FOV for each lens is provided below.

The tele lens offers the best resolution and is ideal for scanning objects smaller than a baseball or larger objects with a higher resolution.  The mid lens works well for objects that are basketball size and was the lens predominantly used for scanning pottery vessels in the Virtual Hampson Museum project.  CAST researchers generally do not recommend use of the wide angle lens.

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[wptabtitle] CHANGING LENSES I [/wptabtitle] [wptabcontent]

A.  To change the lens on the VIVID 9i, first make sure the scanner is turned off.

B.  Next remove the lens that you wish to use from the lens box and its plastic bag.

C.  Next remove the lens protector and unscrew the lens that is currently on the scanner.  IMMEDIATELY place the lens cap (located on the lens box) on the back of the lens.

NOTE: Every lens should always have 2 lens caps (one of the front and back of the lens) when the lens is not in use or is being stored.

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[wptabtitle] CHANGING LENSES II [/wptabtitle] [wptabcontent]

D.  Remove the back lens cap from the desired lens and screw the new lens into the scanner by first lining up the red dots found on both the lens and the scanner.

E. Replace the black lens protector on the scanner.  Replace both lens caps on the newly removed lens, place in a plastic bag, and store in the lens box.

F.  You are ready to begin scanning.  Power on the scanner and continue with Step 9 on the ‘Power up Scanner’ Slide  above.

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[wptabtitle] CONTINUE TO… [/wptabtitle] [wptabcontent]

Continue to Konica-Minota Vivid 9i – Scan Settings.

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