An interactive tool, using embeded IPython, for exploring and analysing Trees produced by the Calcify Rust crate. Includes plotting and fitting tools.
Clone the repository and from inside run:
(sudo) python(3) setup.py install
This will install the icalcify command line tool and the ICalcify library.
usage: icalcify [-h] [-b] [filename [filename ...]]
ICalcify Explorer: Interactive analysis tool for Calcify Trees.
positional arguments:
filename Filepaths to open as Tree. Must contain file extension.
[.json, .msg]
optional arguments:
-h, --help show this help message and exit
-b, --buffer Buffer reading of Tree files in the Explorer
Run:
> icalcify universe.msg
This will open the an IPython shell with a variable called Explorer of type ICalcify.Explorer.
Python <VERSION>
Type 'copyright', 'credits' or 'license' for more information
IPython <VERSION> -- An enhanced Interactive Python. Type '?' for help.
Welcome to ICalcify. All commands must be valid Python3
IPython version and kernel information above, as usual.
Namespaces included:
ICalcify as ic
ICalcify.fitting as ft
numpy as np
scipy as sc
scipy.optimize as opt
matplotlib.pyplot as plt
plt.show as show
Explorer:
universe: 10 branches
We can save some writing by starting with:
In [1]: Tree = Explorer['universe']
In [2]: Tree
Out[2]:
Name: universe_in_a_box
Desc: A Tree including branches for the simple universe in a box multiparticle simulation.
Details: Universe Range: 1, Number of Particles: 500, Delta T: 0.01, Time steps: 2000, Total Time: 20
Run on: 04/18/2020 17:23
In [3]: print(Tree)
Name: universe_in_a_box
10 branches:
{Name: 'init_state', Type: 'ThreeVec', Length: 500}
{Name: 'init_hist', Type: 'Bin', Length: 500}
{Name: 'mid1_hist', Type: 'Bin', Length: 500}
{Name: 'fin_state', Type: 'ThreeVec', Length: 500}
{Name: 'mid2_state', Type: 'ThreeVec', Length: 500}
{Name: 'mid1_state', Type: 'ThreeVec', Length: 500}
{Name: 'fin_spread', Type: 'Point', Length: 404}
{Name: 'init_spread', Type: 'Point', Length: 383}
{Name: 'mid2_hist', Type: 'Bin', Length: 500}
{Name: 'fin_hist', Type: 'Bin', Length: 500}> icalcify -b universe.msg
Will instead give you:
Python 3.5.3 (default, Sep 27 2018, 17:25:39)
...
Explorer:
universe: *buffered
In [1]: Explorer['universe']
Out[1]:
Name: universe_in_a_box
Desc: A Tree including branches for the simple universe in a box multiparticle simulation.
Details: Universe Range: 1, Number of Particles: 500, Delta T: 0.01, Time steps: 2000, Total Time: 20
Run on: 04/18/2020 17:23
In [2]: Explorer
Out[2]: universe: 10 branchesICalcify.Explorer.load_all() will load all buffered Trees into the Explorer.
If you have a FeedTree of subtype Object it will be read in as a regular tree of ObjectBranches where the data is read in verbatim as python dicts. These branches implement __iter__(self) so they should be easy for the user to convert to whatever type they like.
From here you can run:
In [1]: Tree['fin_hist'].plot(True)(The plot function takes a boolean argument that defaults to False which can call plt.show() if set to True)
which opens a pyplot window such as:
To show multiple plots:
In [1]: Tree['mid2_hist'].plot()
In [2]: Tree['fin_hist'].plot(True)or
In [1]: Tree['mid2_hist'].plot()
In [2]: Tree['fin_hist'].plot()
In [3]: show()will give you:
You can also get a scatter plot of ThreeVec branches with:
In [1]: Tree['mid2_state'].scatter(True)
To show multiple figures without blocking call:
In [1]: plt.ion()
In [2]: Tree['fin_hist'].plot(True)Built in fitting functions include Gaussian, BrietWigner, exponential, and linear.
To do a fit run:
In [1]: Tree['mid2_hist'].fit(ft.Gaussian)
Out[1]:
Parameters:
x0 = 1.340 +- 0.044
x1 = 0.878 +- 0.021
x2 = 0.519 +- 0.030or
In [1]: FitRes = Tree['mid2_hist'].fit(ft.Gaussian)
In [2]: FitRes
Out[2]
Parameters:
x0 = 1.340 +- 0.044
x1 = 0.878 +- 0.021
x2 = 0.519 +- 0.030
In [3]: type(FitRes)
Out[3]: ICalcify.fitting.FittingResultTo plot the result over the original:
In [1]: Tree['mid2_hist'].plot()
In [2]: Tree['mid2_hist'].fit(ft.Gaussian).plot(True)
If you have two FloatBranchs,
In [1]: g = ic.Branch('g','f64',[1.0,2.0,3.0])
...: h = ic.Branch('h','f64',[2.0,4.0,6.0])then you can plot them against each other,
In [2]: type(g.against(h))
Out[2]: ICalcify.branches.PointBranch
In [3]: g.against(h).scatter(True)
If you want to filter/cut a Branch,
In [1]: bib = ic.Branch('Time','Bin',[[i,[i,i]] for i in range(300)])
In [2]: print(bib)
Out[2]: Name: 'Time'
0, range(0.0, 0.0)
1, range(1.0, 1.0)
2, range(2.0, 2.0)
3, range(3.0, 3.0)
4, range(4.0, 4.0)
5, range(5.0, 5.0)
6, range(6.0, 6.0)
7, range(7.0, 7.0)
8, range(8.0, 8.0)
9, range(9.0, 9.0)
...
290, range(290.0, 290.0)
291, range(291.0, 291.0)
292, range(292.0, 292.0)
293, range(293.0, 293.0)
294, range(294.0, 294.0)
295, range(295.0, 295.0)
296, range(296.0, 296.0)
297, range(297.0, 297.0)
298, range(298.0, 298.0)
299, range(299.0, 299.0)
Type: 'Bin', Len: 300
In [3]: print(bib.cut(lambda x: x[1][0] > 100))
Out[3]: Name: 'Time_Cut'
101, range(101.0, 101.0)
102, range(102.0, 102.0)
103, range(103.0, 103.0)
104, range(104.0, 104.0)
105, range(105.0, 105.0)
106, range(106.0, 106.0)
107, range(107.0, 107.0)
108, range(108.0, 108.0)
109, range(109.0, 109.0)
110, range(110.0, 110.0)
...
290, range(290.0, 290.0)
291, range(291.0, 291.0)
292, range(292.0, 292.0)
293, range(293.0, 293.0)
294, range(294.0, 294.0)
295, range(295.0, 295.0)
296, range(296.0, 296.0)
297, range(297.0, 297.0)
298, range(298.0, 298.0)
299, range(299.0, 299.0)
Type: 'Bin', Len: 199