Running Flat Field Analysis

Flatfield Interactive - file selection:

Very large files (height x width x colors over 40 MB) sometimes caused memory overflow problems on older 32-bit systems.  Files over 40 or 80 MB can be automatically reduced 1/2x linearly (using 1/4 the memory) in Settings, by making the appropriate setting in LARGE FILES (Flatfield, Blemish...).

After the input file has been read, the Flatfield-Interactive window, showing the most recently displayed results, is displayed.

Results are displayed using the previous settings (saved in imatest-v2.ini), in this case the pixel contour plot with unnormalized contours superposed on the image.

Flatfield controls

• Read Image file reads an image, then performs calculations and displays results.
• Display dropdown menu selects the results to display. Selections are shown in the Table, below.
• Primary display settings (below Display) lets you select the most important settings for the selected display, for example how to normalize the results, whether to display a pseudocolor plot, etc. Additional settings are available by pressing More Settings, immediately to the right.
• The Uniformity button at the bottom of the screen opens the Flatfield Uniformity Settings dialog box, shown below. This contains advanced settings not shown in the Primary display settings dropdown menu.
• The Blemish button opens the Blemish Detect settings dialog box.
• 

  Zoom/Rotate 3D/Data Cursor
  selects the action when you click on the image. Zoom zooms in on the image. It zooms out when you shift-click or double-click. Rotate 3D is used to rotate 3D images (2D images are zoomed). Data Cursor opens a tiny window called a Datatip that displays values of the image or curve. Right-click on the Datatip to remove it or access additional options.

• Acquire from device checkbox may be removed because Settings, Device manager is better for setting up direct acquisition.
• Reload reloads the image. Most valuable for Image Acquisition, which allows images to be read directly from devices like USB cameras or manufacturer's evaluation boards.
• Save screen Saves and optionally displays the Flatfield window.
• Save data Saves results in CSV and/or XML files. Opens the Save dialog box.
• Help opens this web page. (Others are available in the Help dropdown window on the top toolbar.)
• Exit exits the Flatfield window.

Flatfield-Interactive settings window

The settings window opens when you answer Yes (not Express mode) when reading an image or when you press the Uniformity button at the bottom of the Flatfield Interactive screen. It is similar to the Flatfield settings window, but some display selections are missing because they're made in the Flatfield-Interactive Display dropdown menu.

• Title Defaults to the file name. You can change it if you wish.
• Expert/Simplified modes Simplified mode grays out advanced selections that may not be needed by beginners.
• Standard settings selects commonly-used settings: good choices for beginners.

Plot area

Most of the settings in this area apply to displays that are selected in the Flatfield-Interactive window. For this reason, Some display selections used in Flatfield are missing (or disabled). (And a few should probably be disabled.) Some of the settings listed below are duplicated in the Primary display settings dropdown menu of the Flatfield-Interactive window.

• Contour plot display options Eight display options are available. 3D plots are available. Normalized refers to the Pixel contour display only.

• Color shading (Plot 1): Select Red/Blue, Red/Green, Green/Blue, or any of several variants of ΔE and ΔC (76 (i.e., plain), 94, and 2000).
  • Display type: Exaggerated color, Pseudocolor, and 3D options.
  • Pixels (gamma-encoded), Intensity (linear— using gamma), and f-stop difference.
• (Dropdown menu below Uniformity profiles) Choose between several different normalizations or R, G, B, and Y, R/G and B/G, or Delta-L*, a*, b*, and C*.
• (Dropdown menu below V&H Spectrogram plot) Select frequency & spatial plot smoothing. 
• Highpass filter (HPF) dropdown:  Turn on box HPF for EMVA 1288 calculations. Used for histograms.
• (Dropdown menu to right of Grid plot) Select parameters to display: mean & sigma, Delta-C & Delta-E, etc. 
• (Dropdown menu to right of Grid contour map) Select a single parameter to display (value and contour). Settings listed below.
• Special calculation:  None, CPIQ, or ISO 17957.
• Grid size  for Grid plot and contour map. From single region to 32×18. 10×10 is typical. 

Fine detail display Choose between exaggerated local noise with or without contour lines, pseudocolor contours, spot detection (which includes nonlinear processing), or several 3D plots.

Settings area

• Gamma  Gamma is the average slope of the log pixel level vs. log exposure curve, taken from a specified maximum value through dark gray values. It only affects the f-stop contour plot and ISO 18844 flare measurements; it has no effect on the other measurements. The default value (0.5) is typical for digital cameras. Gamma is measured by Color/Tone Interactive or Auto using any one of several widely-available grayscale step charts, or by legacy modules Stepchart or Colorcheck. Some issues in calculating gamma are discussed next to f-stop contour plot. 
• Corner and side regions (default 32x32 pixels) allows you to select the areas at the corners and sides of the images to be analyzed. These affect the numeric readouts below the plots (example: Corners: worst = ...). Choices include 10x10 pixels, 32x32 pixels, 1% (min. 10x10), 2% (min. 10x10), 5%, and 10%.
• Crop pixels near borders (L, R, T, B) (Settings area). Available only if Don't ask to crop. (Use Crop ... borders settings in LF input dialog box.) is selected in Settings. If checked, the image is cropped by the number of pixels indicated near the left, right, top, and bottom borders.
• Color space  affects Color shading ΔE and ΔC measurements in Color Shading, Grid, and Grid Contour plots.

The following options are not available in Imatest Studio. They are discussed in detail in Using Flatfield Part 2.

• Channel  You can choose between Red, Blue, Green, and Y (luminance) channel
• Hot and dead pixels  By checking the appropriate boxes you can display hot pixels (red ¤) and/or dead pixels (blue •). Hot pixels are stuck at or near the sensor's maximum value (255 in 8-bit files) and dead pixels are stuck at or near 0. You can choose between hot/dhead pixel detection in any channel, all channels or the selected channel.

Because signal processing— especially JPEG compression— can cause defect pixel levels to shift, you can use the sliders to set the detection threshold between 6-255 for hot pixels and 0-249 pixels for dead pixels. (The extreme values are for measurements made on white or black fields.) Clicking on < or > at the ends of the sliders adjusts the threshold by 1. The default values are 252 and 4, respectively. JPEG files must be saved at the highest quality level for this feature to work; isolated hot and dead pixels tend to be smudged at lower quality levels. Details are described in  Using Uniformity Part 2.

Dropdown menus

There are four dropdown menus, located just below the top of the Flatfield Interactive window: File, Settings, INI File Settings, Help.

File contains several file-related functions

• Read image file
• Print
• Save image to file
• Save temporal noise image. Only applies when temporal noise is calculated — when signal averaging is applied and Calculate image^2 while averaging is checked
• Save pseudo-raw/remosaiced image — Save the image as an undemosiaced (Bayer raw image). 
• Save screen  — displays screen and optionally saves it (most of the time we don't save the screen)
• Open image file folder
• Open recent save folder
• Preview JSON results
• View all EXIF data 
• Image statistics/viewer
• Close

Settings

• Small, Normal, Large, X-Large fonts
• Reset screen — resets screen to original size and position (above the Main Window)
• Image from file
• Device manager — Opens the Device manager for selecting an image acquisition device, adjusting the settings, and previewing the image.
• Image from device >  Lets you select a device for acquiring an image. Not recommended. Device manager is more reliable.
• Signal averaging >  Lets you average up to 128 directly-acquired images for reducing noise and for separating temporal and spatial noise in EMVA-1288-based nonFlatfield calculations and for calculating noise images.
• Calculate image^2 while averaging. Required for separating spatial and temporal noise 

Input settings

The following settings are available in all Imatest versions:

• • Title  Defaults to the file name. You can change it if you wish.
  • Display Uniformity contour plots (Plot area; on by default).
    Turns the main light falloff contour plots off or on. Normally on (checked), but may be turned off by Imatest Master users interested in other results, such as hot/dead pixels and color shading. Four display options are available. Normalized refers to the first (level) plot only.
    Examples on Using Flat Field, Part 1.

• Speedup  When checked, several results (those that require significant calculation time) are not calculated (and hence not saved in the CSV output file) if the corresponding plot is not selected. This can save significant time in production environments. If you need to use Speedup, you should run Flat Field with and without Speedup checked and examine the CSV output file to see if it contains the results you require.
• Gamma  The default value of gamma, 0.5, is typical for digital cameras. Gamma affects only the second figure (the light falloff measured in f-stops); it has no effect on the first figure. Gamma can be measured by Stepchart using any one of several widely-available step charts. (Reflection charts are easiest to use but transmission charts can also be used to measure dynamic range.) Some issues in calculating gamma are discussed below the second figure.
  
• Corner and side regions  (default 32x32 pixels) allows you to select the areas at the corners and sides of the images to be analyzed. Choices include 10x10 pixels, 32x32 pixels, 1% (min. 10x10), 2% (min. 10x10), 5%, and 10%. These regions can be used as the reference for the Color shading ΔE and ΔC calculations.
• Crop pixels near borders (L, R, T, B)  (Settings area). If checked, the image is cropped by the number of pixels indicated near the left, right, top, and bottom borders. Several cropping (ROI selection) options are available in Settings. These incluce
  

  Don't ask to crop. (Use settings in LF input dialog box.)

  Select crop by dragging cursor. Ask to repeat crop for same sized image.

  Select crop by dragging cursor. Do not ask to repeat crop.

  Although the first option (Don't ask to crop...) was the default prior to Imatest 2.3.12, the second option (Select crop by dragging cursor. Ask to repeat crop for same sized image), which is similar to the ROI selection in SFR, may be preferred.

Uniformity settings window (for Imatest Master).

The following options are available in Imatest Master and IT:

• Color shading (nonuniformity)  Display the color nonuniformity, i.e., the quotient of or difference between two of the three (R, G, B) channels or one of the L*a*b* color difference metrics (ΔE = sqrt(ΔL*² + Δa*² + Δb*² ), ΔC = sqrt(Δa*² + Δb*² ), ΔE₉₄, ΔC₉₄, ΔE₀₀, ΔC₀₀ ), referred to the center of the image (either the central region, with size specified in the Corner and side regions box or the central 25% by area). Color shading often results from the angle at which light strikes the sensor. It tends to be worst in sensors with tiny pixels. Several options are available. [Note: the center of the image is used for the reference for calculating ΔC and ΔE in the Color shading plots, but for the grid plot, which implements the CPIQ Phase 2 specification, the mean of the entire image is used as the reference for calculating  ΔC and ΔE.]
  
  • Color shading  Select not displayed (turns off plot), Red/Blue, Red/Green, Green/Blue, or ΔE or ΔC (various flavors & reference regions). Red/Blue (the extremes of the spectrum) is the most popular choice for displaying shading. for (plot units).  To the right of the Color shading box. Select Pixels (gamma-encoded), Intensity (linear), or f-stop difference. Grayed out if ΔE or ΔC metrics are selected.
    

    Pixels	Displays the ratio of the the pixel values for the selected channels. If Normalized is checked, the plot is normalized to 1.0 (maximum).
    Intensity (linear)	Removes the gamma encoding of the image file using the value of Gamma entered and displays the ratio of the intensities for the selected channels. If Normalized is checked, the plot is normalized to 1.0 (maximum).
    F-stop	Displays the f-stop difference between the selected channels. If Normalized is checked, the plot is normalized to 0 (maximum).

  • Display   Select the display type. Four choices.
    Examples are shown below
    

    Exaggerated color	2D. Increases the color saturation to increase the visibility of color nonuniformities.
    Pseudocolor	2D
    3D  Pseudocolor, shaded, auto-scaled.	Shading emphasizes contour shapes.
    3D  Pseudocolor, auto-scaled.

  • Normalized  (Checkbox)  If checked (the default), the shading plot is normalized to a maximum of 1 for quotient displays (Red/Green, etc.) Affects only the plot, not the numeric values beneath the plot. The unnormalized maximum and minimum and other values are displayed beneath the plot.
  • Extra smoothing  This increases the smoothing of the contour and shading plots. Checked by default and strongly recommended. When unchecked the contour and color shading plots are much bumpier, more susceptible to noise, and slower. This checkbox may be removed in a future version.
• Color uniformity profiles   Shows pixel levels along diagonal, vertical, and horizontal lines. The specific display is selected in the dropdown menu on the right. Described below.
• Grid plot  Display a grid of results. You can select the grid (m x n) and two parameters to be displayed at each grid location.
  • Grid size:  single region, 3x3 through 10x10, 20x15, 24x16, 32x18, 15x15,16x16, 20x20, 25x25, 27x27 (not in this exact order).
  • Grid calculation:
    • Mean (pixel level) and sigma, 
    • Color differences Delta-C and Delta-E, Delta-C 94 and Delta-E 94, Delta-C 00 and Delta-E 00,all calculated relative to the mean for the entire image. Note: The CPIQ color variability metric (D) is the maximum Delta-C in the grid plot. It is shown below the plot when Delta-C and Delta-E are selected.
    • Mean (pxl) & Delta Color Temp K,
    • R/G and B/G pixel ratios,
    • CIELAB a* and b*,
    • Mean (pixel level) and SNR (s/n), Mean (pixel level) and SNR (dB).
  • Minimum threshold (0-1) (default = 0). A minimum threshold for pixels to be included in grid plot analysis. Useful for automatically excluding dark areas in images like the one on the right.

We can add more grid plot measurements on request.

• Histogram plot  Useful in diagnosing stuck (hot and dead) pixels. Described below.
• Fine detail plot  Display a detailed image of noise and sensor nonuniformity (examples below). Slow variations in image density— vignetting (low spatial frequencies) — are removed so that only short to medium range variations— sensor noise, dust spots, etc.— remain. The calculation can be slow and uses lotsof memory because Matlab calculations are performed in double precision mathematics, which requires 24 bytes per color pixel (8 bytes per channel). 

  Exaggerated local noise (standard)

  Local noise with added contours

  Pseudocolor contours with colorbar

  Spot detection w / threshold (pseudocolor)

  (Several additional 3D displays)

  Several display options are available. The first displays noise exaggerated by a factor of 10. The second superposes contour plots (from a smoothed version of the image) on the noisy image. The third produces a pseudocolor image of local nonuniformities (also smoothed) with a color bar (legend) on the right. The fourth emphasizes dark spots, usually caused by dust. A histogram can also be added beneath the fine detail plot.

• Channel  You can choose between Red, Blue, Green, or Y (luminance) channels. Color space  Used for converting from RGB color space where L*a*b* color difference metrics are displayed.
• Hot and dead pixels  By checking the appropriate boxes you can display hot or light pixels (red x) and/or dead or dark pixels (blue •).
  The definition depends on whether Absolute pixel threshold or Relative % threshold is selected:
  
  

  Display hot or dead pixels (o): Absolute pixel threshold

  Hot pixels are stuck at the sensor's maximum value (255 in 8-bit files) and dead pixels are stuck at 0. Because signal processing— especially JPEG compression— often causes these values to shift, you can use the sliders to set the detection threshold between 6-255 for hot pixels and 0-249 pixels for dead pixels. (The extreme values are for measurements made on white or black fields.) Clicking on < or > at the ends of the sliders adjusts the threshold by 1. The default values are 252 and 4, respectively.

  Display light or dark pixels (o): Relative % threshold

  Light pixels are more than the relative % threshold above the mean of the 8 neighbors; Dark pixels are more than the relative % threshold below the mean of the 8 neighbors.

  Clusters (in Imatest 4.0+) are defined as groups of two or more adjacent pixels.

  JPEG files should be saved at the highest quality level for this feature to work well; isolated hot and dead pixels tend to be smudged at lower quality levels. Details of hot and dead pixels are presented below. You can choose whether to count a pixel as hot or dead (light or dark) if the criteria are met by any color channel (the default), all channels, or the selected channel.

When you press Save data the dialog box shown on the right is opened. It allows you to select which results to save (CSV and/or JSON files) where to save it. The default is subdirectory Results in the data file directory. You can change to another directory the results.  CSV and JSON data are saved in files whose names consist of a root file name with a suffix for plot type and channel (R, G, B, or Y) and extension.

Example: IMG_9875_ISO1600_RGB_f-stop_ctrG.png. The root file name defaults to the image file name, but can be changed using the Results root file name box. Be sure to press enter. After you click on Yes or No, the Main Window reappears.

At the end of the run, a dialog box for saving results appears. It allows you to select figures to save and choose where to save them. The default is subdirectory Results of the image folder. You can change to another existing directory by unchecking the Subfolder Results of image folder check box. The selections are saved between runs.

You can examine the output figures before you check or uncheck the boxes. Figures, CSV, XML, and JSON results are saved in files whose names consist of a root file name with a suffix for plot type and channel (R, G, B, or Y) and extension. Example: IMG_9875_ISO1600_RGB_f-stop_ctrG.png. The root file name defaults to the image file name, but can be changed using the Results root file name box. Be sure to press enter. For batch runs, checking Close figures after save is recommended for preventing a buildup of figures (which slows down most systems). After you click on Yes or No, the Main Window reappears.

Figures can be saved as either PNG files (a standard losslessly-compressed image file format) or as Matlab FIG files, which can be opened with Open Fig file in the Utility menu. Fig files can be manipulated (zoomed and rotated), but they tend to require much more storage than PNG files, and are therefore not recommended.

The CSV and XML files contain EXIF data, which is image file metadata that contains important camera, lens, and exposure settings. By default, Imatest uses a small program, jhead.exe, which works only with JPEG files, to read EXIF data. To read detailed EXIF data from all image file formats, we recommend downloading, installing, and selecting Phil Harvey's ExifTool, as described here.