%load_ext autoreload
%autoreload 2

import numpy as np
import os

import sys
sys.path.insert(0, '/Users/ageller/VISUALIZATIONS/Firefly')
sys.path.insert(0,'/Users/agurvich/research/repos/firefly/src')
from firefly.data_reader import FIREreader,SimpleFIREreader

Convert FIRE data

In this example notebook we demonstrate how to use the firefly.data_reader.FIREreader sub-class which creates specialized data files for FIRE formatted data. The details of how the FIREreader class is “specialized” see the API documentation and to see the example of this output visit the live demo version.

## create a FIRE reader object
reader = FIREreader(
    ## path to directory containing (optionally multiple) .hdf5 files
    snapdir = "/Users/agurvich/research/snaps/isolated_disks/Control_G4_20/snapdir_050/",
    ## the snapshot number, best to provide separately in order to disambiguate
    snapnum = 50,
    ## particle types one would like to extract from .hdf5 files
    ptypes=[0,4],
    ## what to call them in the UI
    UInames=['Gas','Stars'],
    ## by what factor would we like to reduce the data for performance stability and disk space concerns
    decimation_factors=[10,100],
    ## what fields would we like to extract
    fields=['Density','Velocities','Temperature'],
    ## do we want to take the magnitude of any of these fields?
    magFlags=[False,False,False],
    ## do we want to take the log?
    logFlags=[True,False,True],
    ## which fields do we want to be able to filter on?
    filterFlags=[True,True,True],
    ## which fields do we want to be able to colormap by?
    colormapFlags=[True,True,True],
    ## where should the output .json files be saved to?
    ##  if a relative path is given, like here, saves to $HOME/<JSONdir>
    ##  and creates a soft-link to firefly/static/data
    JSONdir=os.path.abspath(os.path.join(os.getcwd(),'..','static','data','FIREData_50')),
    ## overwrite the existing startup.json file
    write_startup=True)

## fetch data from .hdf5 files
reader.loadData()

## set the color and size of the gas and star particles
##  to be aesthetically pleasing
reader.settings['color']['Gas']=[1,0,0,1]
reader.settings['color']['Stars']=[0,0,1,1]
reader.settings['sizeMult']['Gas']=1
reader.settings['sizeMult']['Stars']=0.5
reader.settings['camera'] = [0,0,-15]

## dump output to .json files
reader.dumpToJSON()

Loading ptype 4
/Users/agurvich/research/snaps/isolated_disks/Control_G4_20/snapdir_050/snapshot_050.hdf5
Loading ptype 0
/Users/agurvich/research/snaps/isolated_disks/Control_G4_20/snapdir_050/snapshot_050.hdf5

''

Using firefly.data_reader.SimpleFIREreader

To simplify this process we have provided firefly.data_reader.SimpleFIREreader which takes a path to a FIRE snapshot and creates a “standard” iteration of Firefly given only a path to the data.

reader = SimpleFIREreader(
    ## path to directory containing (optionally multiple) .hdf5 files
    "/Users/agurvich/research/snaps/isolated_disks/Control_G4_20/snapdir_050/",
    ## overwrite the existing startup.json file
    write_startup=True,
    ## pass absolute path to avoid symlink
    JSONdir=os.path.abspath(os.path.join(os.getcwd(),'..','static','data','FIREData_50')))

Loading ptype 4
/Users/agurvich/research/snaps/isolated_disks/Control_G4_20/snapdir_050/snapshot_050.hdf5
Loading ptype 0
/Users/agurvich/research/snaps/isolated_disks/Control_G4_20/snapdir_050/snapshot_050.hdf5
Outputting: Gas - 106666/1066668 particles - 3 tracked fields
Outputting: Stars - 51411/514118 particles - 3 tracked fields