Difference: TemimpsXtracedrop (15 vs. 16)

xtracedrop program for characterizing drop shape and quantifying detergent concentrations

Contents

Program Installation

xtracedrop is a python program (xtracedrop.py). It is known to run under python 2.4 (Centos 5) or 2.6 (Windows). It relies on the following python packages

Program Dependencies

• numpy (python package)
• scipy (python package)
  • requires blas and lapack
• python imaging library (PIL) (python package)
• gnuplot is used, both for fitting and for plotting results

download xtracedrop.py.txt, rename it to xtracedrop.py
To make xtracedrop executable, type: chmod +x xtracedrop.py

• you can also type: python xtracedrop.py

download sample drop images to test installation: drop_demo.tgz

Running the xtracedrop

• place drop images to be analyzed into a common directory
• run xtracedrop
• change the filename template to match the files you want to analyze
  • a list of relevant files should appear in the main window
  • 
• if desired, enter the detergent concentrations next to each filename
  • this is useful if you are analyzing a standard curve of known detergent concentrations
  • this information will allow xtracedrop to produce a plot of your results
• change the name of the output file if desired
• adjust the center coordinates of the drops if necessary
  • this value needs only be approximately correct
  • a single center is assumed to apply to all drops
• Hit the "Run" button
• Output will appear in the stdout window only after analysis of all the drops is complete
  • 

View results of xtracedrop

• a summary of the results is shown in the main window
  • namely the ratio of major/minor axes of the fitted ellipse
  • the error of the fit is shown (in pixels) and should typically be ~1
  • 
• the "Plot Results" button will create a plot of concentration (entered by user) vs. a/b ratio (determined by program)
  • this information is also stored in the "results file" and can be imported into another program (e.g. excel)
  • a right-click will bring up the plot and offer to save the image - make sure to specify the directory
  • 
• for information on individual drops, select the number of the relevant file (shown in main window)
  • "Show Img" will bring up a window with the original image
    • 
  • "Show Fit" will bring up a window showing the data fitted to an ellipse
    • this fit is displayed using gnuplot. The gnuplot command file (e.g. DSC_0014-fit.gnuplot) can be used later to recreate the plot
    • 

Files produced by xtracedrop

• • a number of intermediate files are created that could be useful for troubleshooting
  • img-boundary.txt lists the coordinates of all the points found at the boundary of the drop/substrate
  • img-trimmed.txt lists the "trimmed" coordinates though to actually represent the surface of the drop
  • img-edge.txt lists coordinates at the lateral edges of the drop (excluded from the fit)
  • img-fit.gnuplot is a gnuplot command file used to create the plot
    • type gnuplot img-fit.gnuplot to recreate this plot
  • img-plotgnu.gnuplot is a command file for fitting the edge data to an ellipse (alternative fit to the python code)
  • results.dat (or equivalent) has a listing of the final results

• Set ALLOWTOPICVIEW =

-- DavidStokes - 17 Jan 2011