Saving Crystal Centering Images and Video

The MacCHESS Crystal Centering Interface can save still images or a video stream. A menu "Save Photos" appears along the top of the window. This menu offers three options:

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• Single Snap
  • This option is for saving one image at the current settings.
  • The image should be saved just as you see it, complete with crosshairs and scale bar, if those are turned on.
  • Clicking on the menu option brings up a file chooser. Select the appropriate directory in which to save your image. The default is specuser's home directory, so be sure to specify something on the data collection disk instead (e.g. /A1a, /F1a, /F2a)
  • Specify a file name. If you end your filename with a standard file type for images (e.g. .jpg, .png, .gif), in upper or lower case, that image file type will be used for your image file. Otherwise, it will be saved in a default format (PNG or JPEG? I can't remember.) The Linux file command can tell you the format of an image file.
  • Click "Save" and its done. A "Success" dialog box should pop up, and you can dismiss it. If you get a failure message instead, there is probably a problem with the choice of directory, or with write privilege to the directory.
    
    Image courtesy of Matt Warkentin of the Thorne lab.

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• Multi Snap
  • This option is for saving a series of still images of your crystal, separated by PHI motor rotations.
  • The images should be saved just as you see them, complete with crosshairs and scale bar, if those are turned on.
  • A dialog box should appear. Enter the appropriate values for the number of images, the PHI increment between images, and the PHI starting value.
  • Next enter a filename prefix and select a directory in which to save the images.
  • Click "Snap!" and you should see the PHI rotations being carried out, followed by a "success" dialog box. Your image files will be saved with names prefix###.jpg, where ### indicates the PHI rotation value for each image.
  • A failure could be due to a problem moving the PHI motor, but is more likely to be a problem in choice of the directory, or in write privilege to that directory.
  • The images are saved in full 1024x768 resolution.
    
    This array of images was scaled down and combined for convenience. Images courtesy of Matt Warkentin of the Thorne lab.

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• Video
  • The video option is for saving a video stream. In order to keep up with the frame rate , video is saved in a raw format which needs processing afterwards.
  • The default frame rate at MacCHESS is set for 7.5 frames per second (fps). The hardware limit of the cameras is 15 fps. (See me if you need this.) The frame rate may be slowed down by fiddling with the camera settings in the "Cam" panel at the lower right corner of the crystal centering interface, so if timing is important, be sure to check the actual frame rate on the "FPS" panel before recording your video.
  • The images should be saved just as you see them, complete with crosshairs and scale bar, if those are turned on; except that a time stamp is added to the lower left corner. (Technical note: Not really. In order to keep up the frame rate, the raw video stream is actually saved without the crosshairs, scale bar and time stamp, but sufficient data is saved to the file to recreate these during unpacking.)
  • When you select the "Video" option a dialog box will appear. You should select the number of frames of video to save and the frame interval. E.g. you could save one frame of every 100 if you want a time lapse of a slow process.
  • Select the file prefix and the directory in which you want the file saved. The file will be saved as prefix.uyvy.
  • Click "Snap!" and it will start working. The success dialog box will only appear after all the frames of video have been saved.
  After the raw video file is saved, additional steps are required to end up with a useful video:
  • Run my java application to unpack the individual images from the raw video file with script uyvydecode.csh. (This may not be installed on every MacCHESS computer. It requires Sun Java, which also may not be installed on every MacCHESS computer.) A dialog box should appear. Click on the "Open UYVY Video File" button and select the raw video file with the FileChooser. Click "Open" and it should go to work. It should write a line to the text window for each image file decoded, then write an ERROR message indicating that there are no more files to decode. The individual images will be saved as JPEG files. Once you verify that the JPEG files are OK, you should delete the original .uyvy file. It takes up about 20 times more space than all of the JPEG files put together.
  • Once you have the individual images, you can manipulate them with any image handling software, such as ImageMagick, theGimp or PhotoShop. For example, you might want to select which images to include in a video, or scale the images to a different size, or change background color, or crop a portion of the image. In the file listings below is a sample script for shrinking a set of images using ImageMagick.
  • Assemble the frames into a video using any relevant software you prefer. On Linux this can be done with mencoder. A couple example scripts are linked below.
    
    Crystal of cytochrome bc1 courtesy of Ed Berry.

Source code and scripts

Files for compiling and running the Java application which unpacks individual images from the raw video file
uyvydecode.csh - the script which you would execute to perform the unpacking.
UYVYDecode.java - the main Java source file
CrossHairPluginFeatures.java - Java source file
SnapshotPluginFeatures.java - Java source file
VideoDialog.java - Java source file
VideoFilter.java - Java source file
ZoomPluginFeatures.java - Java source file

Scripts for image manipulation and video creation
shrink.csh - script for scaling a set of images with ImageMagick
mencoder_gif.csh - script for creating an animated GIF file using mencoder
mencoder_mpeg4.csh - script for creating an MPEG4 video using mencoder (Conveniently, MPEG4 will support a frame rate of 7.5 fps)

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