JClassif - documentation

Homepage (JClassif) - Homepage (Galaxie pipeline)

Getting started

The top panel gives you access to the different functions of JClassif:

Import: import data from an ASCII file into Java format
Data: review imported data, save and load data in JClassif format
Diagram: show various spectral classifications in various diagrams, possibility to save/print these diagrams
Cross: show the cross-correlation, success rate, and contamination charts of two classifications.
Export: export derived classifications into an ASCII file
About: informations on the software and included plugins.

Importing data

Supported format

First of all you need to prepare your ASCII file with data to be imported. You don't need to apply your signal-to-noise cut: JClassif will do it for you during the import process.

You must use tabulations ('\t') as column separators
The first line of your ASCII file must start with a '#' and provide the column names separated by tabulations
```
Example: 

#OII_EW	OII_EW_ERR	DN4000
```
All values must be accompanied by an associated error (except for the column of IDs). Please consider to add a column of zeros ("0") if some values don't have an error for you (will be made easier on future revision).
Numerical values must be in international format (the international sign for the decimal separator is the point '.' not the coma ',').
```
Example: -1.2345e67  0.12e-34 ...
```

JClassif is not compatible with various formats, but you may import your data and prepare your ASCII file with topcat or any other table processing software.

Telling JClassif what to import

In the "Import" panel, first select the ASCII file you want to import (1).

Cick on the "add" button for each line you want to import (2).

Edit the parameters of each line (3):

name: the name which will be used in JClassif to identify each line.
value: the column of your ASCII file where JClassif will find this line's value.
error: the column of your ASCII file where JClassif will find this line's error.
sncut: select if you want this line to participate to the global signal-to-noise cut (4) (enter a negative cut if your lines have negative values, like e.g. equivalent widths of emission lines)

New in revision 1.1: You can select the column which contains the IDs of your object (any string without spaces). If you leave this parameter to "unset", your objects's IDs will be the line numbers of the input file.

You can save your parameters for a latter use (5).

Click on "Import data" to start the importation (6).

After the data is imported, you will get the following dialog:

It tells you how many lines have been read in your ASCII files, and how many objects have been imported according to your signal-to-noise cut.

Handling imported data

TOP

You can handle imported data in the "Data" panel.

You can find the number of imported objects (1).

A list gives you the names of each imported lines (2). The derived values such as line ratios or spectral classifications will also appear in this list. You can remove them here if you want JClassif to recompute them.

You can save the imported data for latter use (3).

You may download already imported data samples here.

Showing a classification in a diagram, saving the figure

TOP

First choose a classification scheme (1). It will tell JClassif how to do the classification from the imported data.

Then choose a diagram (2). It will tell JClassif which axis to use, the curves to show, and eventually some text to put on your plot.

Click "Plot" to trace the plot (3).

JClassif gives you the number of objects in each spectral class (4). You can also choose here which class you want to show or to hide in the plot.

You can also tell JClassif to show or to hide the curves and the text associated with this diagram (5).

Finally, you can export your plot to an external file (6).

Cross-corellating two classifications

TOP

Choose the two different classifications you want to cross-correlate, then click "Go" (1).

You will get one table showing the number of objects in each of the spectral classes as a function of each other (2). The columns represent the first classification, the lines the second one.

You get also two more tables showing exacting the same numbers, but as percentages of the total numbers in each spectral class of the first classification (3), or the second classification (4).

Exporting results to an ASCII file

TOP

You can output your data, and in particular derived classifications, to an ASCII file.
This file will first contain a line beginning with "#" followed by the headers of the columns, then the data as one object per line. The columns are separated by tabulations.
You may process the output file with topcat or any other table processing software.

Choose an output file (1).

Your data is shown in two tables: (2): data not exported, (3): data to be exported. You may choose which data to export or not with the two left and right arrow buttons (4).

You can change the order of the output columns with the two up and down arrow buttons (5).

You can save or load your export configuration (6).

Click on "Export data" to start the process (7).

List of basic plugins

TOP

A numer of basic plugins are already included with JClassif in the file named "BasicPlugins.jar". Here is a description for each of them:

Classifications

Name	comment	needed lines in JClassif (spelled like that)	output
K03 (Kauffmann, G. et al. 2003, MNRAS, 346, 1055)
K03(AGN)	does not separate AGNs into Sey2 and LINERs	Halpha, NII, OIII, Hbeta	1.0: SFG 1.5: composite 2.0: AGN
K03(LINER)	separates AGNs into Sey2 and LINERs with Veilleux & Osterbrock (1987, ApJS, 63, 295)	Halpha, NII, OIII, Hbeta	1.0: SFG 1.5: composite 2.0: Sey2 2.1: LINER
L04 (Lamareille, F. et al. 2004, MNRAS, 350, 396)
L04		OIII, Hbeta, OII	1.1: SFG 1.0: cand. SFG 2.1: Sey2 2.0: cand. AGN 2.2: LINER
K06 (Kewley, L. J. et al. 2006, MNRAS, 372, 961)
K06(noOI)	does not use the O3O1 panel	Halpha, NII, SII, OIII, Hbeta	1.0: SFG 1.5: composite 2.0: Sey2 2.1: LINER
K06(OI)	uses the O3O1 panel	Halpha, NII, SII, OIII, Hbeta, OI	1.0: SFG 1.5: composite 2.0: Sey2 2.1: LINER 2.2: ambiguous
S06 (Stasińska, G. et al. 2006, MNRAS, 371, 972)
S06		OII, NeIII, dn4000	1.0: SFG 2.0: AGN
L10 (Lamareille, F. 2010, A&A, 509, 53)
L10(ambiguous)	does not isolate the SF/Sy2 and SF-LIN/comp regions	OIII, Hbeta, OII	1.0: SFG 2.1: Sey2 2.2: LINER
L10(+candidates)	isolates SF/Sy2 and SF-LIN/comp regions	OIII, Hbeta, OII	1.0: SFG 2.1: Sey2 2.2: LINER 2.5: SF/Sey2 1.5: SF-LIN/comp
L10(+candidates2)	also separates SF-LIN/comp into SFG/comp and LIN/comp	OIII, Hbeta, OII	1.0: SFG 2.1: Sey2 2.2: LINER 2.5: SF/Sey2 1.1: SFG/comp 2.3: LIN/comp
M11 (Marocco, J., Hache, E. & Lamareille, F. 2011, A&A)
M11(SF/Sy2)	separates SF/Sy2 region of L10 classification into SFG and Sey2	OIII, Hbeta, OII, NeIII, dn4000	1.0: SFG 2.1: Sey2 2.2: LINER 1.1: SFG/comp 2.3: LIN/comp
M11(SFG/comp)	isolates SFG and composites from SFG/comp and SFG regions of L10 classification	OIII, Hbeta, OII, NeIII, dn4000	1.0: SFG 2.1: Sey2 2.2: LINER 1.5: composite 1.1: SFG/comp 2.3: LIN/comp

Diagrams

Name	comment	X-axis	Y-axis
K03 (Kauffmann, G. et al. 2003, MNRAS, 346, 1055)
K03(O3N2)		log(NII/Halpha)	log(OIII/Hbeta)
L04 (Lamareille, F. et al. 2004, MNRAS, 350, 396)
L04(O3O2)		log(OII/Hbeta)	log(OIII/Hbeta)
K06 (Kewley, L. J. et al. 2006, MNRAS, 372, 961)
K06(O3N2)		log(NII/Halpha)	log(OIII/Hbeta)
K06(O3N2)		log(SII/Halpha)	log(OIII/Hbeta)
K06(O3O1)		log(OI/Halpha)	log(OIII/Hbeta)
S06 (Stasińska, G. et al. 2006, MNRAS, 371, 972)
S06(DEW)		log(max(OII,NeIII))	dn4000
L10 (Lamareille, F. 2010, A&A, 509, 53)
L10(O3O2)		log(OII/Hbeta)	log(OIII/Hbeta)
M11 (Marocco, J., Hache, E. & Lamareille, F. 2011, A&A)
M11(SF/Sy2)	separation lines used in the L10 SF/Sy2 region	log(max(OII,NeIII))	dn4000
M11(SFG/comp)	separation lines used in the L10 SFG/comp region	log(max(OII,NeIII))	dn4000
M11(SFG/comp_2)	separation lines used in the L10 SFG region	log(max(OII,NeIII))	dn4000

Figure exporters

file (pdf): exports the figure as a PDF file in vector format.
file (image): exports the figure as an image (up to now only in PNG format).

Making your own plugin

Not yet documented.