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

[wptabs mode=”vertical”] [wptabtitle] Rebuild Geometry[/wptabtitle]
[wptabcontent]After the model is georeferenced, rebuild geometry at the desired resolution. Photoscan produces very high poly-count models, so we like to build two models, a high resolution one for archiving and measurements and a lower resolution one for import into ArcGIS for visualization and general reference. Keeping the polycount low (circa 100,000 faces) in the ArcGIS database helps conserve space and speeds up loading time on complicated scenes with multiple models. To make sure the lower poly-count model looks good, we build the textures using the high poly-count model and apply them to the lower poly-count model.

So… Select ‘Workflow’ and ‘Build Geometry’ from the main menu as before. Then select ‘Workflow’ and ‘Build Texture’.

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[wptabtitle]Decimate the model[/wptabtitle]

[wptabcontent]Under ‘Tools’ in the main menu you can select ‘Decimate’ and set the desired poly-count for the model. The decimated model will likely have a smoother appearance when rendered based on vertex color, but will appear similar to the higher poly-count model once the texture is applied.

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[wptabtitle]Export the model[/wptabtitle]
[wptabcontent] Export the models and save them as collada files (.dae) for import into ArcGIS. You may select a different format for archiving, depending on your project’s system. Choose ‘File’ and ‘Export Model’ from the main menu.

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[wptabtitle] Continue to…[/wptabtitle]

Continue to Photoscan to ArcGIS

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Many archaeological projects now use photogrammetric modeling to record stratigraphic units and other features during the course of excavation. In another post we discussed bringing photogrammetric or laserscanning derived models into a GIS in situations where you don’t have precise georeferencing information for the model. In this post we will demonstrate how to use bring a photogrammetric model for which georeferenced coordinates are available, using Agisoft’s Photoscan Pro and ArcGIS.

[wptabs mode=”vertical”] [wptabtitle] Load Photos[/wptabtitle] [wptabcontent]Begin by adding the photos used to create the model to an empty project in Photoscan.

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[wptabtitle] Align Photos[/wptabtitle] [wptabcontent]Following the Photoscan Workflow, next align the images. From the menu at the top choose ‘Workflow’>’Align Images’. A popup box will appear where you can input the alignment parameters. We recommend selecting ‘High’ for the accuracy and ‘Generic’ for the pair pre-selection for most convergent photogrammetry projects.

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[wptabtitle] A choice[/wptabtitle] [wptabcontent]At this point there are two approaches to adding the georeferenced points to the project. You can place the points directly on each image and then perform the bundle adjustment, or you can build geometry and then place the points on the 3d model, which will automatically place points on each image, after which you can adjust their positions. We normally follow the second approach, especially for projects where there are a large number of photos.
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[wptabtitle]Build Geometry[/wptabtitle]
[wptabcontent]Under ‘Workflow’ in the main menu, select ‘Build Geometry’. At this point we don’t need to build an uber-high resolution model, because this version of the model is just going to be used to place the markers for the georeferenced points. A higher resolution model can be built later in the process if desired. Therefore either ‘Low’ or ‘Medium’ are good choices for the model resolution, and all other parameters may be left as the defaults. Here we have selected ‘Medium’ as the resolution.

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[wptabtitle]Get the georeferenced points[/wptabtitle]
[wptabcontent]When the photos for this model were taken, targets were places around the feature (highly technical coca-cola bottle caps!) and surveyed using a total station. These surveyed targets are used to georeference the entire model. In this project all surveyed and georeferenced points are stored in an ArcGIS geodatabase. The points for this model are selected using a definition query and exported from ArcGIS.

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[wptabtitle]Add the georeferenced points[/wptabtitle]
[wptabcontent]On the left you have two tabbed menus, ‘Workspace’ and ‘Ground Control’. Switch to the the ‘Ground Control’ menu. Using the ‘Place Markers’ tool from the top menu, place a point on each surveyed target. Enter the corresponding coordinates from the surveyed points through the ‘Ground Control’ menu. Be careful to check that the northing, easting and height fields map correctly when importing points into Photoscan, as they may be in a different order than in ArcGIS.

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[wptabtitle]Local coordinates and projections[/wptabtitle]
[wptabcontent] In practice we have found that many 3d modelling programs don’t like it if the model is too far from the world’s origin. This means that while Photoscan provides the tools for you to store your model in a real world coordinate system, and this works nicely for producing models as DEMs, you will need to use a local coordinate system if you want to produce models as .obj, .dae, .x3d or other modeling formats and work with them in editing programs like Rapidform or Meshlab. If your surveyed coordinates involve large numbers e.g. UTM coordinates, we suggest creating a local grid by splicing the coordinates so they only have 3-4 pre decimal digits. [/wptabcontent]

[wptabtitle]Bundle Adjust – Another Choice[/wptabtitle]
[wptabcontent]After all the points have been placed select all of them (checks on). If you believe the accuracy of the model is at least three time greater than the accuracy of the ground control survey you may select ‘update’ and the model will be block shifted to the ground control coordinates. If you believe the accuracy of the ground control survey is near to or greater than the accuracy of the model, you should include these points in your bundle adjustment to increase the overall accuracy of the model. To do this select ‘optimize’ from the ‘Ground Control’ menu after you have added the points. After the process runs, you can check the errors on each point. They should be less than 20 pixels. If the errors are high, you can attempt to improve the solution by turning off the surveyed points with the highest error, removing poorly referenced photos from the project, or adjusting the location of the surveyed points in individual images. After adjustments are made select ‘update’ and then ‘optimize’ again to reprocess the model.

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[wptabtitle] Continue to…[/wptabtitle]

Continue to PhotoScan – Building Geometry & Texture for Photogrammetry

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Mesh vertex spacing circa 1cm.

[wptabtitle] Cloud Compare[/wptabtitle] [wptabcontent]

The open source software Cloud Compare, developed by Daniel Girardeau-Montaut, can be used to perform this kind of assessment. The assessment method described here is based on the application of a series of perceptual metrics to 3D models. In this example we compare two 3D models of the same object, one derived from a C10 scanner and one from from a photogrammetric model developed using Agisoft Photoscan.[/wptabcontent]

[wptabtitle] Selecting Test Features[/wptabtitle] [wptabcontent]

Shallow but broad cuttings decorating stones are common features of interest in archaeology. The features here are on the centimetric scale across (in the xy-plane) and on the millimetric scale in depth (z-plane). In this example we assess the resolution at which a characteristic spiral and circles pattern, in this case from the ‘calendar stone’ at Knowth, Ireland is legible, as recorded by a C10 scanner at a nominal 0.5cm point spacing, and by a photogrammetric model built using Agisoft’s photoscan from 16 images.

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[wptabtitle] Perceptual and Saliency Metrics[/wptabtitle] [wptabcontent]

Models from scanning data of photogrammetry can be both large and complex. Even as models grow in size and complexity, people studying them continue to mentally, subconsciously simplify the model by identifying and extracting the important features.

There are a number of measurements of saliency, or visual attractiveness, of a region of a mesh. These metrics generally incorporate both geometric factors and models of low-level human visual attention.

Local roughness mapped on a subsection of the calendar stone at Knowth.

Roughness is a good example of a relatively simple metric which is an important indicator for mesh saliency. Rough areas are often areas with detail, and areas of concentrated high roughness values are often important areas of the mesh in terms of the recognizability of the essential characteristic features. In the image above you can see roughness values mapped onto the decorative carving, with higher roughness values following the edges of carved areas.

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[wptabtitle] Distribution of Roughness Values[/wptabtitle] [wptabcontent]The presence of roughness isn’t enough. The spatial distribution, or the spatial autocorrelation of the values, is also very important. Randomly distributed small areas with high roughness values usually indicate noise in the mesh. Concentrated, or spatially autocorrelated, areas of high and low roughness in a mesh can indicate a clean model with areas of greater detail.

High roughness values combined with low spatial autocorrelation of these values indicates noise in the model.

[wptabtitle] Picking Relevant Kernel Sizes[/wptabtitle] [wptabcontent]

To use the local roughness values and their distribution to understand the scale at which features are recognizable, we run the metric over our mesh at different, relevant, kernel sizes. In this example, the data in the C10 was recorded at a nominal resolution of 5mm. We run the metric with the kernel at 7mm, 5mm, and 3mm.

Local roughness value calculated at kernel size: 7mm.

Local roughness value calculated at kernel size: 5mm.

Local roughness value calculated at kernel size: 3mm.

Visually we can see that the distribution of roughness values becomes more random as we move past the effective resolution of the C10 data: 5mm. At 7mm the feature of interest -the characteristic spiral- is clearly visible. At 5mm it is still recognizable, but a little noisy. At 3mm, the picture is dominated by instrument noise.
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[wptabs style=”wpui-alma” mode=”vertical”] [wptabtitle] GETTING STARTED [/wptabtitle]

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Transparency Unit – The EPSON 10000 XL scanner should have the transparency unit attached. If it is not attached, the user needs to turn off the power of the scanner, remove the regular cover, and attach the transparency unit. The transparency guide is not needed for scanning film.

Epson 10000XL Flatbed Scanner

1 – Put on white gloves when handling film to avoid fingerprints rubbing onto film.

2 – Take film out of canister and find the glossy side, which will need to be face down for scanning.

3 – Unroll film to find flight direction markings, which are usually at the beginning of the roll.  If there are none, then use your own judgment on flight direction so film data is correctly oriented.

4 – Put film on roller that allows film to feed through scanner with the glossy side down and with the data correctly oriented; switch spindles if necessary.  This can be changed if the user later discovers that the film is incorrectly oriented.

5 – Push bars of rollers together to a distance with the film right between them and then tighten the knobs of the rollers.

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[wptabtitle] PLACING FILM [/wptabtitle] [wptabcontent]

6 – Open Adobe Photoshop program and click on file, import, and select the Silverfast program.

7 – Roll the handle on the roller to feed film onto scanner.  Film should be scanned at the top of the scanner.  Rollers can be adjusted as necessary and scanner can be moved so the film is rolled across the top.

8 – When scanning portions of film that are not on the edge of the roll, attach the end of the film to the opening on the spindle of opposite roller.

9 – Once film is attached to spindle, use this roller to unroll and feed film through the scanner.

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[wptabtitle] GENERAL SETTINGS [/wptabtitle] [wptabcontent]

10 – After Silverfast opens, click on Pre-Scan button at lower left corner for visualization of imagery.  This provides an initial preview. Settings need to be changed as listed in the following step.

11 – Select the general tab and set the following settings:

1 – Scan mode-normal

2 – Original– reflective

3 – Pos/neg– positive

4 – Frame-set– save

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[wptabtitle] SCAN QUALITY [/wptabtitle] [wptabcontent]

12 – Select the frame tab to control quality of scanning procedures and set
the following settings:

1 – Scan type – 16-8 bit grayscale

2 – Filter – GANE, to maximize dust and grain removal settings

3 – Setting – save

4 – Image type – standard

5 – Name – untitled, user can add a title when saving image

6 – Original– this setting displays the width and height of area being  scanned and can be changed by typing in values or clicking and dragging on box in preview window.

7 – Scale – 100

8 – Q-factor – 2.5, maximizes quality of scan

9 – Screen – 480 lpi

10 – Scanning resolution is below screen and q-factor, but unlabeled, set to 1200 dpi

11 – Click pre-scan again for new preview of imagery.  Re-size window to include only the area of film that contains data.

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[wptabtitle] SCANNING [/wptabtitle] [wptabcontent]

13 – If desired, check additional options by clicking on options button at right corner to open extra options menu.  These options do not need to be changed from default settings.

14 – If desired, check additional options located on top row of SilverFast menu, such as histogram and gradation curve adjustment – alter as the user sees fit.  The auto-adjust tool is also located on this row and can improve scanned imagery if needed.

15 – Click on Scan button at bottom of tab to begin scanning imagery.

16 – Saving : Scanned imagery is loaded into Adobe Photoshop. The user needs to name the file and save it to a folder of your choice as a .tiff file.

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[wptabtitle] FINISHING SCANS / GENERAL TIPS [/wptabtitle] [wptabcontent]

17 – Continue rolling film as needed to scan imagery and repeat scanning process.

18 – When finished scanning, use the roller on the original spindle to roll the film back.

TIPS

For clear scans : When scanning aerial photography, the user needs to either place sheets of paper behind the film or put the cover back over the transparency unit glass portion.  It is also possible that this process could improve scanning results of other series as well.

Distortion : Each roll of film tightens as the user rolls the film through the scanner and attaches it to the roller on the opposite side.  Occasionally, this results in the film becoming very tight and resists laying down flat on the scanner bed.  When this happens, the portions of the scanned image on the edge of the scanner bed become distorted.  Unrolling some of the film on the receiving roller relieves some of the tightness, but does not totally eliminate distortion from the image.  The best way to eliminate the distortion is to select not to scan the area that is distorted during the pre-scan.

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

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A current version of EPSON Scan Utility software can be freely downloaded from the Epson website and used to scan a variety of media, including transparent film and photographic prints.

Epson 10000XL Flatbed Scanner

To get started, make sure the scanner is connected to the computer and turn both the scanner and computer on. Log in to the computer and start the EPSON Scan software.

1. Mode – In the EPSON Scan dialog (Figure 1), change the “Mode” to “Professional Mode.”

2. Media – If scanning transparent film media, choose “Film” in the “Document Type” drop-down menu. If scanning paper, prints, or other reflective type media choose “Reflective.”

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[wptabtitle] SETTINGS [/wptabtitle] [wptabcontent]

3. The “Document Source” should always be set to “Document Table.”

4. In the “Image Type” drop-down menu, choose the appropriate setting for the media you’re scanning.
-When scanning transparent film media we recommend using a 16-bit Grayscale (for B&W film) or 24-bit     Color (for color natural or false color film).

Figure 1: Settings for scanning with EPSON Scan software

5. Choose a resolution that is appropriate for the media you’re scanning.

–   When scanning transparent film media we recommend using a minimum resolution of 1200 dpi
–   For high quality film, we recommend using 2400 or 3200 dpi in order to capture all of the available     detail contained within the film
–   When scanning print or paper media, a scanning resolution of 300-350 dpi should capture all of the     available detail contained within the print.

6. Un-check the “Thumbnail” check box.  All other settings in the EPSON Scan dialog will depend on the media you’re scanning, or on your personal preference.

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[wptabtitle] SCANNING [/wptabtitle] [wptabcontent]

Figure 2: Transparent Film on Scan Bed

7. Placement – Carefully place the media face down in the upper left corner of the scan bed (Figure 2). We recommend using clean gloves when handling transparent film or print media.

8. Click the “Preview” button at the bottom of the dialog and the scanner will begin scanning.

Figure 3: EPSON Scan software Preview

9. Once the preview scan is complete, the “Preview” dialog should appear (Figure 3). Use the Marquee tools to select the area of the media you would like to include in your scan. Be sure not to crop an image you plan on using for photogrammetry, and to include any visible fiducial marks.

10. Begin Scan – In the “EPSON Scan” dialog window, click “Scan” to start the scanning process.

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[wptabtitle] SAVING YOUR FILE [/wptabtitle] [wptabcontent]

11. In the “File Save Settings” dialog, choose a location, format, and name for output file.

NOTE: For best practice (and especially projects considering archival), we recommend scanning to the TIFF (.tif) file format.

12. Time – Depending on the size of your media and the resolution you chose, the scanning process could take up to 1-2 hours.

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[wptabs style=”wpui-alma” mode=”vertical”] [wptabtitle] A BASIC INTRODUCTION [/wptabtitle]

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Why is pre-processing necessary?

For most close-range photogrammetry projects digital images will need to be captured in a RAW format, preserving the maximum pixel information which is important for archival purposes. Therefore it will likely be necessary to do some pre-processing in order to convert RAW images into a file format accepted by the photogrammetry software being used for the project.

If a color chart or gray card was using during image capture, it may also be useful to perform a white balance on the image set. There are a number of tools/software packages available for this purpose, but below we will describe a potential workflow using Adobe products for batch processing.

Overall steps of this workflow:

–  Batch convert RAW to DNG (Adobe DNG Converter)
–  Batch white balance (Camera Raw)
–  Batch image adjustments (Camera Raw)
–  Batch save to JPEG (or TIFF) format (Camera Raw)

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[wptabtitle] BATCH CONVERT RAW DATA [/wptabtitle] [wptabcontent]

Batch RAW to DNG with Adobe Digital Negative (DNG) Converter Software

As an open extension of the TIFF/EP standard with support for EXIF, IPTC and XMP metadata, the Adobe DNG format is rapidly becoming accepted as a standards for storing raw image data (primarily from digital photography).

For more information about file formats for archival, see the Archaeological Data Service (ADS) Guides to Good Practice.

Steps to Batch Convert:

1. Download and install Adobe DNG Converter. As of the date this workflow was published, version 7.2 of Adobe DNG Converter is a free tool available for download on the Adobe website.

Adobe DNG Converter is a free tool available for download on the Adobe website.

2. This tool converts an entire folder (aka batch) of images at one time. Use the tool interface to select the appropriate input folder containing the RAW images.

3. If needed, use the interface to design a naming scheme to be used for the new file names.

4. Set preferences for compatibility (e.g. Camera Raw 5.4 and later) and JPEG Preview (e.g. medium size). As an option, you can embed the original RAW file inside the new DNG files. This will, or course, increase the file size of the new DNG file.

5. Click “Convert” to start the process. Wait for this to finish.

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[wptabtitle] BATCH WHITE BALANCE – 1 [/wptabtitle] [wptabcontent]

Batch white balance, image processing, and exporting with Adobe – Part 1: Adobe Bridge

It is considered best practice to (correctly) use a quality color chart or gray card when capturing digital images for any CRP project.  Performing a white balance for each image set (or each lighting condition) can dramatically enhance the appearance of a final product (i.e. ortho-mosaic). This particular workflow uses Adobe Bridge and the Adobe Camera Raw tool, but a similar process can be done in other (free) software as well.

Adobe Bridge – Open in Camera Raw

1. Open Adobe Bridge and navigate to the folder containing the digital images (DNG files).

2. Select the appropriate images (including images with color chart/gray card).

3. Use the “File” menu to select “Open in Camera Raw”

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[wptabtitle] BATCH WHITE BALANCE – 2 [/wptabtitle] [wptabcontent]

Batch white balance, image processing, and exporting with Adobe – Part 2 : Camera Raw tool

4. Camera Raw will open and all of the selected images will appear on the left side of the window. Select the image with the color chart/gray card you would like to use for white balancing and other adjustments. Do all adjustments to this one image. We will apply the same changes to all images in the following slide ‘Batch Image Adjustment’.

Adobe Camera Raw – Image Processing Settings

5. By default, Camera Raw may attempt to apply a number of image processing settings that you should remove. This can be done using the interface on the right hand side of the screen. Check that all settings (with the exception of Temperature and Tint, which are set by the white balance tool in the next step) are set to zero. Be sure to check under each of the tabs.

6. Select the “Color Sampler Tool”  found in tool bar at the top of the window and:

A. If using a color chart, add a color sample inside the black and white squares. After adding these you should see the RGB pixel values for each sample.

B. If using a gray card, add a color sample inside the gray portion of the card.

7. Select the “White Balance Tool” from the tool bar at the top of the window and click on the gray portion of the chart (or card) to apply a white balance. At the same time, notice how the RGB values of the color sample(s) change. The RGB values should not differ by more than five or six (e.g. the white sample could be R: 50, G: 50, B: 51). If they differ by too much there could be a problem with the white balance. Try clicking a slightly different spot in the gray portion of the chart.

8. If other adjustments need to be made (i.e. exposure, brightness, contrast) make them now.

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[wptabtitle] BATCH IMAGE ADJUSTMENTS [/wptabtitle] [wptabcontent]

Applying adjustments to all

Once the white balance and adjustments have been made to this one image, we can apply the same to all the other images open in Camera Raw.

To do this, click “Select All” in the top left corner of the window – then click “Synchronize.” Wait for this to finish.

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[wptabtitle] BATCH SAVE TO JPEG OR TIFF [/wptabtitle] [wptabcontent]

Saving

Once the Synchronization is complete, click the “Save Images” in the bottom left corner of the window (make sure all images are still selected). The “Save Options” dialog allows you to choose a folder for the images to be saved to, a naming scheme, a file extension and format, and a quality/compression. Choose the settings you prefer and click “Save.”

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

Continue to PhotoScan – Basic Processing for Photogrammetry

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