STEP BY STEP


Step 1: Select spd program


Select Menu->Edit->Preferences
In spd preferences, add spd program. Spd program is available with this release under plugins/spd_1.2.0/bin following by folder named with OS.

Step 2: Choose preprocessor mode online/offline


Preprocessor running mode online or offline can be set as a preference in , or you can switch from one mode to another by pushing the button "Go Online ()" or "Go Offline()" in coolbar, at the top of the main window.

On line mode

This mode is used while getting images in ESRF. Preprocessor connects to Taco/Tango device server and retrieves current experiment, sample name, and folder where files will be acquired. These informations are set in Image files to process group in Processing view.
You don't need to select files to process files online mode.
When you launch Preprocessor, it processes files acquired after it has been launched if new options 'Process files previously scanned' is not checked, otherwise, it process all scanned files while it is running.
Files processed online mode should have the same stem name as the sample (Fable specification).
New files acquired are loaded in Processing table and ouput messages are shown in the first row of the table concerning number of files in the list that should be processed.
If a new sample is created by ESRF/ID11 beamline users (new data get from Taco/Tango), Preprocessor runs with this new sample. Preprocessor should be stopped by users by pushing stop button (red square instead of yellow arrow (only visible when Preprocessor runs)
If user has selected online mode option, next step is Step 4

Off line mode

This mode is used to process files acquired in ESRF.
You need to select directory/files you want to process(select files... button).
When you launch Preprocessor, it processes files selected. When all files have been processed, Preprocessor stops.
You can remove a directory from the list, or one or several files you don't want to process.

Step 3: Select directory/files to process


In Processing view, select several directories or files to process from "select files..." button.
You can check header keys values by adding new columns in table containing new files(see preprocessor help). You may also see which dark, flood and/ or distortion files you need to process if you have these informations stored in the header(key=DarkFileName, FloodFileName, DistortionFileName)

Step 4: Add Spd options in Processing view


see spd options

To do dark subtraction

Select apply Dark. If this option is set, you need to choose a file and/or a dark constant.
If you have selected:
  • get files from header, check if this information is stored in the file (Key=DarkFileName). Warning : if you use preprocessor offline mode on your computer, path file will not be found because it may be /data/opid11/external/maXXX/yourSample/yourSample_dark_XX.edf. During processing, if you want to check filename, add verbose=2 in other options group.
  • file button, please browse... to get a file. The file should have the same size as files to process otherwise an error message occurs in console and preprocessor will not be launched. Check these information on image size with Dim_1, Dim_2 and size keys of the header.
  • no file, please set a dark constant.
For others options available in dark group, please refers to spd help. If you want to add options that are not in the GUI for the dark subtraction, add spd options in other options group

To do flood correction

Select apply Flood. If this option is set, you need to choose a flood file or add other flood options in other options group.
If you have selected:
  • get files from header, check if this information is stored in the file (Key=FloddFileName). Warning : if you use preprocessor offline mode on your computer, path file will not be found because it may be /data/opid11/external/maXXX/yourSample/yourSample_flood_XX.edf. During processing, if you want to check filename, add verbose=2 in other options group.
  • file button, please browse... to get a file. The file should have the same size as files to process otherwise an error message occurs in console and preprocessor will not be launched. Check these information on image size with Dim_1, Dim_2 and size keys of the header.
  • no file, add flood options in other options group.
If you want to add options that are not in the GUI for the flood correction, add spd options in other options group.

To do spatial distortion correction

Select apply Distortion. If this options is set, you need to choose a file to correct spatial distortion (.spline or.spd).
If you have selected:
  • get files from header, check if this information is stored in the file (Key=DistortionFileName). Warning : if you use preprocessor offline mode on your computer, path file will not be found because it may be /data/opid11/external/maXXX/yourSample/spatial.spline. During processing, if you want to check filename, add verbose=2 in other options group.
  • file button, please browse... to get a distortion file.
  • no file, please add other distortion option for spd in other options group.
You can choose to do the spatial distortion correction:
  • after the dark (by default)(do_distortion=1),
  • after the flood(do_distortion=2),
  • or after normalisation(do_distortion=3),
in the list box Do spatial distortion after
If you want to add options add spd options for spatial distortion in other options group.

Corrected image file extension

This is cor_ext spd option. By default spd creates a new file with .cor extension. But you can add your own extension by selecting button other and adding a filename extension in the text field (i.e.:with extension "darked", corrected file will be --> mySample_NNNN.darked).
If you enter punctuation, ! flag appears ; but preprocessor could be launched : This is a non-blocking error message that appears. This is just to avoid strange extension such as mySample_XXX..darked.

Source file extension

This is src_ext option for spd.

Step 5: Launch Preprocessor


Push launch processing button ()
Preprocessor launches spd program. Output messages are viewed in console. Move console to have a larger view of processing messages

Step 6: Stop processing


Push stop processing button ()
This button should be pushed if you want to stop processing.

Step 7: View current image and corrected image via ImageViewer


In toolbar, select open directory button or open files to browse on image files or in Image to process view,
right click on an image and choose pop-up menu imageviewer