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Subsections
Image Viewer
The Image Viewer is used to view and analyze diffraction images located on
the file server at SSRL. The image files are subject to the Unix
security restrictions: The user must have a read permission to the
image file in order to load and view the image.
The viewer comprises three frames. The left
frames displays a JPEG of the selected diffraction image. The file
path of the displayed image file is shown above the JPEG image. Next
to the image there is a control panel for adjusting the image display
parameters, such as zooming and panning.
The right frame displays either the selected image header or, when
images analysis is requested, the analysis results.
The bottom frame is a file browser that allows the user to
select an image file and explore directories. The starting search
directory will be the one set in the Preferences tab.
Image files must be in the MC file system and be readable by the
user. There are three ways to select an image to be
displayed:
- Type in an image name (full file path) in the text box below the
image display box in the left frame. The file path typically begins
with /data/username or /home/username, for example:
/data/joeuser/images/remo_1_001.img.
- The second way to select an image is to use the file browser in
the bottom frame as explained below.
- The third way is to click on the Prev or the Next
buttons, located on the right side
of the display image. These buttons only work if an image has already
been loaded. The Prev button loads an image with the immediately
lower index than the current image. For example, if the
current image is remo_3_015.img, clicking the Prev
button will load remo_3_014.img. Similarly, the Next
button loads the image with the next higher index than the current
image. In the previous example, clicking on the Next button
instead, will load remo_3_016.img. If the current image is the
first or last image in the dataset, clicking the Prev or Next button respectively yields no effect.
Displaying the last image collected
If the user has selected a beamline where an experiment is being
carried out, the Last Image button will be active. By clicking
this button the user can display the latest image written to the directory
by the beamline control software.
Using the file browser for image selection
The first line in the file browser displays the current
directory. Clicking on [Refresh] will reload the directory
contents (this is useful, for example, if new images are being
continuously written to the directory).
Clicking on [Up] will change the directory to the
parent of the current one. The following lines are links to
subdirectories or image files. File permissions,
file/directory name, size in bytes, last modification date and
time are displayed for each file. Clicking on a subdirectory name
will list the contents of that subdirectory. Clicking the link for an
image file will display the image.
Note that the user can only browse files and directories that
have a read permission for their Unix login id.
Moving the mouse over the diffraction image will display
the resolution in the box below the image.
Figure 3:
Displaying the resolution at the mouse position in the Image Viewer.
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Adjusting Image Display
The user can zoom, pan, adjust brightness and set display size of
the image by using the image control panel located to the right
of the displayed image.
There are three ways to pan the image. One is by clicking on the
image. The image will be moved so that the mouse click position will
be come the center of the display.
The second way to pan the image is by using the thumbnail located
at the top of the image control panel. When the zoom level is greater
than 1 (the image is zoomed in), the thumbnail displays a red
rectangle representing the area of the image being displayed. The more
the image is zoomed in, the smaller the rectangle. The user can click
anywhere in the thumbnail to move the rectangle.
The third way to pan the image is by clicking one of the pan
buttons, which are located below the thumbnail and above the zoom
buttons.
The user can zoom the image in and out by using the zoom buttons or by
entering a zoom level in the zoom text box. When the image is zoomed
out to the maximum, the zoom is level is 1.0; it can not go lower than
this. The higher the zoom level the more zoomed in the image. The left
arrow button is for zooming out and the right is for zooming in.
Brightness of the image is controlled by the Brightness buttons
and text box below the zoom buttons. The left arrow button makes the
image darker and the right button makes it lighter. The brightness
range is usually between 100 - 2000. The lower the number the darker
the image. Brightness of 200-500 is typically good for most images.
By default the image size is 400 by 400 pixels. The user can
change the image display size by selecting a different size from the
drop down menu located under the brightness buttons.
The image header is retrieved via the image
server. The header displays useful information about
the image.
Table 1:
Header fields for a Q4 image
| Header Name |
Description |
Example |
| OVERLOAD_CUTOFF |
The maximum intensity |
65535 |
| |
value for each pixel |
|
| HEADER_BYTES |
Length of the header |
512 |
| DIM |
Image dimensions |
2 |
| BYTE_ORDER |
Machine byte order |
little_endian |
| |
(little or big endian) |
|
| TYPE |
Type of stored value for each pixel |
unsigned_short |
| SIZE1 |
Width of the image in pixel |
2304 |
| SIZE2 |
Height of the image in pixel |
2304 |
| PIXEL_SIZE |
Size of the pixel in cm |
0.0816 |
| BIN |
Detector binned mode |
none |
| DETECTOR_SN |
Detector serial number |
403 |
| TIME |
Exposure time |
30.041451 |
| DISTANCE |
Detector to sample distance |
175.000000 |
| PHI |
Phi |
89.000000 |
| OSC_START |
Starting Phi/Omega |
89.000000 |
| OSC_RANGE |
Oscillation range |
1.500000 |
| WAVELENGTH |
Wavelength in Angstrom |
0.979413 |
| BEAM_CENTER_X |
Beam center X in mm |
94.000000 |
| BEAM_CENTER_Y |
Beam center Y in mm |
94.000000 |
| PIXEL SIZE |
Size of the pixel in mm |
0.0816 |
| EXPOSURE TIME |
Exposure time in seconds |
30.0415 |
| TWO THETA |
Two-theta angle of the detector |
0 |
| |
(not supported at SSRL) |
|
| DETECTOR |
Detector name |
ADSC QUANTUM4 |
Analyzing the image
When the user clicks on Analyze Image, Web-Ice will run
LABELIT (SPOTFINDER module) to analyze the image. The results of the
analysis will be displayed under Spot Statistics in the right hand side frame of the
Image Viewer page. Alternatively, the user can choose to perform
image analysis automatically for each image selected by setting this
option in the Preferences Tab. When the image has been
analyzed, the user can use the Show spot overlay check box to
toggle between displaying the highlighted spots, ice rings and
resolution limits or the original image.
The output image displays the following features:
- Good spots (potential Bragg spots): green border
- Dubious spots (overloaded, weak, ice diffraction, etc.) :
yellow border.
- Spot maximum pixel: White dot (more than white dot in a spot
indicates multiple maxima).
- Initial estimate of the resolution limit: Green circle.
- Ice rings: Orange circles.
The results displayed by Web-Ice include:
- Number of good Bragg candidates
- Average spot model eccentricity: The closer to 0, the more
circular the spots are. Very high values (around 0.8 or higher) may
indicate high mosaicity.
- Number of ice rings.
- Resolution estimate
- Maximum cell edge estimated from the distance between candidate
Bragg spots.
- Saturation (percentage of the overloaded value) for the
strongest peaks. If it exceeds 50%, there may be too many
overloaded spots.
- Number of spots with overloaded pixels
- A score for the image calculated as follows:
- A score is assigned depending on the resolution (ranging from 14 for
resolution higher than 1.5 Å to 1 for lower than 8 Å.
- The score is then adjusted by -5 to +4 points depending on
the diffraction strength, spot shape and number of ice rings.
- finally the score is normalized reset so that the minimum
score is 0 (for no diffraction).
Both the log and the overlaid image file generate by SPOTFINDER are saved in
the directory
/data/userid/webice/image. For example, if
joeuser analyzes inf_1_001.img, output
files inf_1_001.log and inf_1_001.spt.img will be
saved in the
/data/joeuser/webice/image directory.
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