epretrack.pro

This is a general-purpose pretracking program. For some description of using this, see our main tutorial at: here (look at Part 2). You can also download stkpretrack.pro which is very similar, click here if that link fails.

General usage:
IDL> epretrack,'files*', ...options...
IDL> pt = stkpretrack(imagestack, ...options...)

epretrack will pretrack as many files as you specify; or, if you already have a single image stack read in, then you can use stkpretrack, which does not write any output files. The options for both are as follows, with the defaults being as shown:

feature & bpass options:

• bplo = 1: The lower number for bpass
• bphi = 5: The higher number for bpass
• dia = 9: The "diameter" for feature
• sep = dia+1: The "sep" for feature -- this is the default feature normally uses
• mass = 0: The "masscut" for feature
• min = 0: The "min" for feature

• Note: defaults for bplo, bphi, and dia work well with the data we often track; for almost everybody else, the defaults are not going to be correct.

• /invert: invert the image before bpass, for example, if you have dark spots on a bright background that you're tracking
• /field: process the even & odd fields separately. This is for interlaced cameras, which take the even & odd rows of the image 1/60th of a second apart. Thus a 30 frame per second interlaced camera is really taking pictures at 60 frames per second.
• /first: only process 1st & 2nd frames from each file (useful for a quick check)
• fskip = 1: regrid the time stamp (useful for time-lapse movies) -- this option is mostly unused

• /gdf: use read_gdf to read images
• /tiff: use read_tiff to read images (built in to IDL)
• /multi: use readtiffstack to read images
  • single = N: read channel N (1, 2, or 3) of multi-channel image. 1=red, 2=green, 3=blue. Technically, loads in a 3D image img and saves img(*,*,N-1). Thanks to Kellianne Kornick for asking for this feature.
• /noran: use read_noran to read images
• /nih: use read_nih to read images

• /quiet: don't print out progress reports
• thresh = 0: apply a threshold before bpass
• /nofix: don't try to fix a bug when using /noran
• prefix = "pt.": change the pretrack file prefix

In this case, the data is written to the file "pretrack.gdf" unless you use the keyword prefix to change the filename, in other words:

IDL> epretrack,imagestack, prefix="filename.gdf", ...options...

Or, you can just use stkpretrack which is a function that returns the pretrack data as a variable, thus bypassing the file-writing part.

This program written by Eric, but based on jpretrack by John. Alternate usage of passing the imagestack suggested and debugged by Kazem Edmond.

Contact us

• John Crocker: jcrocker(at)seas.upenn.edu
• Eric Weeks: weeks(at)physics.emory.edu