GitHub - iandobbie/OMXeditor-1

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Name		Name	Last commit message	Last commit date
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Priithon		Priithon
.gitignore		.gitignore
OMXeditor.py		OMXeditor.py
README-user.txt		README-user.txt
README.html		README.html
README.txt		README.txt
__init__.py		__init__.py
align.py		align.py
alignProgressWindow.py		alignProgressWindow.py
cmos_stripe_filter.py		cmos_stripe_filter.py
datadoc.py		datadoc.py
dialogs.py		dialogs.py
editor.py		editor.py
histogram.py		histogram.py
mainWindow.py		mainWindow.py
setup.py		setup.py
util.py		util.py
viewControlWindow.py		viewControlWindow.py
viewerWindow.py		viewerWindow.py

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<html>
  <head>
    <style type="text/css">
      div {
        padding-top: 4px;
        padding-bottom: 4px;
        padding-left: 12px;
        width: 800px;
      }
      body {
        width: 1024px;
        margin-left: auto;
        margin-right: auto;
      }
      img {
        padding-top: 20px;
        padding-bottom: 20px;
      }
      h1 {
        padding-top: 30px;
      }
    </style>
    <title>Guide to using the OMX Editor</title>
  </head>
  <body>
    <h1>Overview</h1>
    <div>
      The OMX Editor program is a simple program for interacting with
      MRC data files. Specifically, it provides the following features:
    </div>
    <ul>
      <li>Multi-channel image visualization
      <li>Automatic wavelength alignment
      <li>Image cropping
    </ul>
    <h1>Viewing images</h1>
    <div>
      When you run the Editor for the first time, you will be presented with
      an open-file dialog. Select the MRC file you want to view, and the 
      program will open the file, showing you three different views of it
      as well as a window with a set of parameters and histograms. In the 
      upper left is an XY view; below that is an XZ view and to its right is
      the YZ view. 
    </div>
    <img src="readmeFiles/overview.png"/>
    <div>
      A crosshairs pinpoints a specific pixel, which determines
      which slice each view shows. You can move the crosshairs by dragging it
      with the mouse, or using the numeric keypad. Press 2 and 8 to move it in
      Y, 4 and 6 to move it in X, and 1 and 7 to move it in Z. You can also
      move it through time using 3 and 9. 
    </div>
    <img src="readmeFiles/crosshairs.png"/>
    <div>
      Alternately, you can use the View Controls window to change how you 
      view the file. This window is accessible from the File menu, or by 
      pressing Command-T (Control-T on Windows/Linux). 
    </div>
    <img src="readmeFiles/viewControls.png"/>
    <div>
      From here, you can
      control which 2D views of the image are visible -- by default, you 
      see the XY, XZ, and YZ views, but you can also show kymographs (where
      one of the image axes is time). You can also choose to show a 
      max-intensity projection along an axis. Finally, you can precisely set
      the position of the viewing crosshairs by dragging the sliders for
      each axis.
    </div>
    <h1 style="clear: both">Aligning files</h1>
    <div>
      The Editor includes an automatic adjustment algorithm to fix common
      misalignments between different wavelengths of a file. It uses the 
      Simplex optimization algorithm to try to bring wavelengths into as much
      agreement as possible, by translating, rotating, and scaling the images.
      In order to obtain alignment parameters, the same image needs to be 
      shown in each wavelength; the best way to do this is with a test image
      or bead slide. The more similar the data is in each wavelength, the
      more precise the alignment will be.
    </div>
    <img src="readmeFiles/alignParams.png"\>
    <div>
      Here you can see the controls for how each wavelength is currently 
      transformed. X, Y, and Z translation should be self-explanatory. 
      Rotation is done about the Z axis, and Zoom is a uniform scaling in
      X and Y.
    </div>
    <div>
      Once you have obtained a set of alignment parameters, you can save 
      them to a file using the "Export parameters" button. Likewise, you can
      load a previously-generated parameter set using the "Load parameters"
      button. The files generated in this way can also be used by the 
      OMX Processor program. See later for explanations of the other buttons.
    </div>
    <div>
      Alignment works best if the wavelengths are approximately closely 
      aligned to start with. You can adjust the alignment parameters manually
      by typing values into the boxes (hit Enter when done), or you can 
      manipulate the wavelengths with the mouse. Left-click on the XY, XZ, or
      YZ views and drag to translate; right-click and drag on the XY view to
      rotate. You can change which wavelength(s) move by clicking on the 
      "Control with mouse" checkbox.
    </div>
    <div>
      When aligning, one of the wavelengths will be held fixed, and the others
      will be moved to match that wavelength as closely as possible. To change
      which wavelength does not move, click on the "Use as auto-alignment
      reference" radio button. Once you have everything set to your 
      satisfaction, click on the "Auto-align" button. A window like this 
      will pop up to document the alignment progress:
    </div>
    <img src="readmeFiles/alignProgress.png"/>
    <div>
      The aligner starts with a 2D step, during which it optimizes the X and Y
      translation, rotation, and zoom factors. Once it is unable to further 
      improve these parameters, it performs a 3D optimization using the entire
      dataset to determine the optimal Z translation value. Because the 3D 
      step uses the entire dataset, <b>it is strongly recommended that you not
        use very large files for alignment</b>. You only need enough data to 
      show the beads in focus and a few Z steps on either side. Including 
      too much data will make the 3D step take exponentially longer.
    </div>
    <h1>Cropping images</h1>
    <div>
      You can use the Editor to crop images, to speed up later postprocessing
      steps. The main window includes a set of parameters for cropping in X, Y,
      Z, and time.
    </div>
    <img src="readmeFiles/cropParams.png"/>
    <div>
      Additionally, there is a crop box that can be manipulated with the mouse, 
      much like the crosshairs discussed earlier. The corners of the box start
      out in the corners of the image, so it is almost invisible most of the 
      time. However, if you move the mouse to a corner or edge of the image, 
      then its cursor should change, enabling you to grab and drag the box
      around.
    </div>
    <img src="readmeFiles/croppedImage.png"/>
    <h1>Saving changes</h1>
    <div>
      Cropping and alignment changes are not applied to your file until you 
      save it (by selecting the "Save" or "Save as..." options from the File
      menu). Until you do this, all operations will use the entire dataset.
      Projections made with the View Controls window are never saved. 
    </div>
    <h1>Other features</h1>
    <div>
      The Editor includes a built-in batch-processing mode which allows you to
      apply alignment and/or cropping parameters to a large number of files.
    </div>
    <img src="readmeFiles/batch.png"/>
    <div>
      To use this feature, first load up a file and set up its alignment
      and cropping parameters the way you want them. Then click the "Batch 
      process" button. A dialog will pop up to let you select which of 
      cropping or aligning (or both) you will perform. Then you can select 
      which files you want to modify (hold Shift to select multiple files),
      and where the modified files will be saved. Once you confirm your
      selection, the batch processor will load and modify each file in turn.
    </div>
    <div>
      The OMX Processor program is also capable of cropping and aligning files.
      If you would rather use it, simply export your alignment and cropping
      parameters to a file using the "Export parameters" button, then load
      those parameters into the Processor's "Align and Crop" mode.
    </div>
    <div>
      The "Dice file" button is a simple sub-feature that allows time series
      image files to be split into multiple single files. This is useful for
      SI timeseries data, since Priism's SI reconstruction doesn't handle
      five-dimensional SI data properly. Additionally, from here you can 
      modify the XY and Z pixel sizes if necessary.
    </div>
  </body>
</html>