Update log file.
My part of the long write-up is complete. After this merge Mary's contribution and Erik's plots.
Finished draft of long writeup. Also add Erik's report.
Add Erik's analysis code, and modify some of my own code. Will merge my remote working branch after this in order to get the draft of the write-up.
Merge branch 'mike_remote_working'
Add background_analysis.py, a script used to study the pixel count statistics for background studies.
Add a script to make overlay plots of pixel count histograms.
Also a few modifications to background_analysis to take into account the different TIFF naming schemes between Elements and bfconvert
Begin the process of adding Erik's Gaussian Fit and Cluster Code
Include a few more changes to Erik's code. After this, more serious surgery will be required.
Commit of code before I overhaul the output code to deal with multiple clusters.
DBSCAN and kmeans now output their results in a dictionary of lists. Next step is to split the HDF5 output into multiple tables: one per analysis method.
Refactoring complete. Erik's Cluster code now works as a part of the image_analysis.py. His fitting code does not, yet, and has been disabled for now.

All analysis techniques are now setup to find multiple peaks in an image. The HDF5 code has been changed to produce a DataFrame table per analysis technique.
image_analysis.py is now working with output into three different HDF5 tables: one for kmeans, another for DBSCAN, and another for Erik's clustering technique.

All three tables contain the image path, which allows downstream analysis code to correlated entries in these tables with each other as well as the fourth, general info table that is also output.
hdf5_sum.py now works with the new HDF5 output format.
Additionaly modification to hdf5_sum.py to handle corrupted input files.

Also some changes to slimer_ana.py to handle the new file format.
slimer_ana.py is now able to operate on the new data format. Some edge cases remain to be resolved.
Edge cases in slimer_ana.py have been dealt with. It can now process a large hdf5 file, output crunched hdf5 files and make histograms.
Including the rest of the observables into the shawcluster DataFrame.
Put in tweaks to hdf5_sum.py in order to reset index in DataFrames.

Also minor tweaks to image_analysis.py and run_image_analysis
Final commit to this branch......about to sync to master.