histogram_mrc.py is a graphical python program which displays the histogram of voxel intensities contained in an MRC file. It can be useful when deciding what thresholds to use with in the "filter_mrc" and "combine_mrc" programs.
Typical usage:
histogram_mrc file.mrc
or
histogram_mrc -n 100 file.mrc
The "-n num_bins" argument allows you to specify the number of bins in the histogram. (The default number of bins sometimes looks poor, especially when the majority of the voxel intensities are narrowly distributed.)
The "-rescale" argument will shift and multiply all of the voxel intensities so that the minimum and maximum voxel intensities are 0 and 1, respectively.
histogram_mrc.py requires python 2.7 or higher and depends on the matplotlib and mrcfile python modules.
These modules can be installed using
pip install matplotlib
pip install mrcfile
To be safe, you may want to run the following commands beforehand:
virtualenv venv
source venv/bin/activate
(If you do this, then you will have to run "source venv/bin/activate" beforehand every time you want to use this software. The virtualenv tool is explained in detail here )
The histogram_mrc.py program is not currently installable using pip. To use histogram_mrc.py, copy the "histogram_mrc.py" file to somewhere in your path (such as /usr/local/bin/)
sudo cp histogram_mrc.py /usr/local/bin
Alternatively, you can edit your PATH variable manually to include the subdirectory where the "histogram_mrc.py" script is located. Suppose the directory with this README file is named ``visfd/doc'' and it is located in your home directory:
If you use the bash shell, typically you would edit your
~/.profile, ~/.bash_profile or ~/.bashrc files
to contain the following lines:
export PATH="$PATH:$HOME/visfd/bin/histogram_mrc"