DustinMorado

#!/usr/bin/env talua

local tomoauto = require('tomoauto')
local yalgo = require('yalgo')
local io = io

local parser = yalgo:new_parser('Convert pos file from rotx tomogram to slab.')
parser:add_argument({
  name = 'tomogram',
  description = 'Slab style tomogram to change pos file onto.',

DustinMorado

#!/usr/bin/env talua
--[[
  Copyright (c) 2015 Dustin Reed Morado

  Permission is hereby granted, free of charge, to any person obtaining a copy
  of this software and associated documentation files (the "Software"), to deal
  in the Software without restriction, including without limitation the rights
  to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
  copies of the Software, and to permit persons to whom the Software is
  furnished to do so, subject to the following conditions:

DustinMorado

header_fmt =               'iii'                 -- nx, ny, nz
header_fmt = header_fmt .. 'i'                   -- mode
header_fmt = header_fmt .. 'iii'                 -- nxstart, nystart, nzstart
header_fmt = header_fmt .. 'iii'                 -- mx, my, mz
header_fmt = header_fmt .. 'fff'                 -- xlen, ylen, zlen
header_fmt = header_fmt .. 'fff'                 -- alpha, beta, gamma
header_fmt = header_fmt .. 'iii'                 -- mapc, mapr, maps
header_fmt = header_fmt .. 'fff'                 -- amin, amax, amean
header_fmt = header_fmt .. 'i'                   -- ispg
header_fmt = header_fmt .. 'i'                   -- Next

DustinMorado

import argparse
import subprocess
import math
import glob

# Take a number of particles, designed for a single day of data collection
# and using i3paste place them in a large tomogram volume to avoid the limit
# of 1000 tomograms in I3. 

# The size of the tomogram is given by:

DustinMorado

import numpy
import argparse

parser = argparse.ArgumentParser(
  description='Shift particle centers in a TRF file',
  epilog='Written by Dustin R. Morado 28.09.2016')
parser.add_argument('input', help='Input trf file', metavar='IN.trf')
parser.add_argument('output', help='Output trf file', metavar='OUT.trf')

parser.add_argument(

DustinMorado

#!/bin/bash

if [[ ! -d 3DEM ]]
then
    mkdir 3DEM
fi

cd 3DEM

curl -s http://mail.ncmir.ucsd.edu/pipermail/3dem/ |\

DustinMorado

#!/usr/bin/env python
import mrcfile
import numpy
import argparse

parser = argparse.ArgumentParser(description='Print MRC extended header')
parser.add_argument('input_mrc', help='input mrc file')
parser.add_argument('-f', '--field', help='specific key to print')
args = parser.parse_args()