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# Reds

open "../C_reconstruction_cropped.mrc" 
volume voxelsize 1
view orient cofr false
volume median #1 binSize 3
close #1
volume #2 style surface color red
volume #2 projectionmode 3d
volume #2 hide

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# Make the window some standard size
windowsize 1000 1000

# Choose an orientation by going to the default, and then doing rotations.
view cofr false
turn y 90
turn x 180

# And record the movie.
movie record ; turn y 1 360 ; wait ; movie encode

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#!/bin/bash

extension=jpeg

function docrop {
	mogrify -crop $1 $2.$extension
	rm $2-1.$extension
	mv $2-0.$extension $2.$extension
}

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#!/bin/bash

# For my macs.
VIMCOMMAND='mvimdiff -f'
# For unix.
# VIMCOMMAND=vimdiff

cd ~

# RED='\033[0;31m'

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import numpy as np
from tabulate import tabulate
import genfire


print('------------------------------ START ------------------------------')

# List of elements to process.  We handle Sum separately.
Elements = ['C', 'O', 'Mg', 'Al', 'Si', 'S', 'Ca', 'Fe', 'Ni', 'Sum']

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import genfire as gf
import sys, os, shutil
import argparse

# Parse command line arguments.
parser = argparse.ArgumentParser()
parser.add_argument("fileroot", help="There should be an aligned tomo stack named fileroot_aligned.npy in the directory and a the reconstruction will be named fileroot_reconstruction.mrc.")
parser.add_argument("-n", "--numIterations", help="Default number of GENFIRE iterations.  See GENFIRE documentation.  Default=100.", type=int, default=100, action="store")
parser.add_argument("-o", "--oversamplingRatio", help="How many times bigger to make the fourier space.  Bigger is more accurate, but you may run out of memory.  See GENFIRE documentation.  Default=4.", type=int, default=4, action="store")
args = parser.parse_args()

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