Changing / Overwriting Data Files

Once a data file is stored on the microscope control computer with all display settings, comments etc., there shouldn't be much reason to change a data file (after all, as a scientist, you don't want to manipulate your data once it's taken, do you?). SM_GUI can save (overwrite) data files, but we allow only very few parameters to be changed as compared to the original file:

• The info strings in the "Scientist", "Sample", "Comments1" and "Comments2" fields. It just happens frequently that they are left over from a previous sample and are stored wrong at first. They can be edited in the scan parameters window (see Fig. 5.9) and then be written to the file.

• The display parameters: This includes the display minimum and maximum, the gamma value and the display name (which is a combination of the values of the "Signal Type" and "Detector / Display" droplists in SM_GUI. These parameters only determine how the scan is initially displayed when you open the file, and what is read into the khz parameter in read_stxm5.pro by default. They don't change the actual data.

• The pointlist entries (see Sec. 5.14.6).

This applies if you save a file locally as well as when you save it on the server. Note, however, if you save (overwrite) a file on the server which is not from today, it won't be updated in the data archive on the xray1 website (see Chap. 8) unless it's done manually.

If you really have a reason to make other changes to an existing data file, you have two choices:

• In IDL, read the data file (you only need to read the sm_par structure and the image_data_intraw data array). Edit sm_par and / or the data array and write it back:

          IDL> read_stxm5, filename, sm_par, $
               image_data_intraw=data
          IDL> ;; do whatever you want with sm_par and data
          IDL> write_stxm5, filename, sm_par, data, /overwrite
  

• Our data files use the netCDF format. In your favorite programming language with netCDF support, use the appropriate functions to manipulate the file. For instance, in IDL, all these routines start with ncdf_.