glotaran / glotaran-legacy

The original global and target analysis software - GUI for TIMP built with Java

Glotaran - A tool for Global and Target Analysis

Glotaran is a Glotaran is a free software program developed for global and target analysis of time-resolved spectroscopy and microscopy data.

A publication about Glotaran, with the title "Glotaran: a Java-based graphical user interface for the R-package TIMP" has been published in the Journal of Statistical Software, on July 1st 2012 and can be found here: http://www.jstatsoft.org/v49/i03/

Glotaran is open-source software and therefore free to download and free to use. If you use the software for any scientific publication we do however request that you cite our JSS publication (see below). Also, if you use Glotaran in any way - in research, industry or education - we are always happy to hear how!

Install and use Glotaran

Download and Install Glotaran on your computer.

Get started with the Wiki and watch a Screencast.

Deprecation notice

The 1.0.0 version of Glotaran was released more than 13 years ago, and the creators of Glotaran think it's time for a change. For the past few years they have been working on a successor for Glotaran, re-written from the ground up in Python, called pyglotaran. Please check it out!

Latest releases

Stable

• Latest stable release on glotaran.org is version 1.5.1.

Developer builds

Current version is 1.5.2-SNAPSHOT

License

GPL v2 or later

glotaran-legacy's Issues

Compare analyses: MakeTr button does not work

In compare analysis, when I click 'MakeTr' the tab for Time traces does not appear.
Reported by Janneke R. via e-mail.

export dataset bug

when export dataset from timpdataset to ascii file, there is no EOL after first line.

Result viewer: missing resource bundle

java.util.MissingResourceException: Can't find resource for bundle org.openide.util.NbBundle$PBundle, key SpecResultsTopComponent.jTBShowParametersErrors.text
at java.util.ResourceBundle.getObject(ResourceBundle.java:450)

Create pom.xml for maven building and testing

Glotataran should be buildable with maven, so a pom.xml is needed as well as good project structure like putting srs ins scrc/org/gloteran/... .

While doing this one could think about tests also. Afterall people will rely on it..

Compare analyses: request for scrolling through spectra

In compare analyses it should also be possible to scroll through the compared spectra (rather than just the time traces).
Reported by Janneke R. via e-mail.

Coppy cohspec parameters from fit to new model

Exception when pressing enter in open dataset dialog

On Windows 7 on Develop branch a null pointer exception is raised, when you browse files with keyboard in open dataset dialog and hit "Enter" with directory selected.

This is followed by a one time illegal state exception when right clicking on "Datasets " item afterwards.

Visual modeling: cohspec node appears before adding

When creating a new empty project and then adding the included empty model to the analysis scheme, the cohspec node appears before adding it.

Compare analysis: order of datasets matters

In "compare analyses" Sometimes when you do compare analysis in a certain order it doesn't work (say 1,2,3) whereas in another order (sat 2,3,1) works.
Reported by Janneke R. via e-mail.

R Controller: check for version of TIMP needed

We should check which version is installed in R using:

    packageVersion("TIMP")

And perhaps also do something with the information provided by calling:

    sessionInfo()

Graphics: ColorScale customizer needed

We need to implement some kind of ColorScale picker and customizer, currently it is only possible to choose from 2 predefined color scales in the Options menu.

Dataset editor: dimension panel starts out with 0's

The dimension panel in the Select dialog where you specify the "from" and "to" starts out being initialized to zeros, whereas a min and max value of the current data would be much more intuitive.
Requested by Ivo

Exporting dataset

It would be nice to have the possibility in the Options of specifying a default export location, such as:
1: Project datasets or resources folder
2: Custom location

selecting dataset

After dataset selected from menu, looks like label generator is not updated.

While Starting the Application

Error pasted below
MacOS ./glotaran
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.netbeans.ProxyURLStreamHandlerFactory (file:/Applications/Glotaran.app/Contents/Resources/glotaran/platform/lib/boot.jar) to field java.net.URL.handler
WARNING: Please consider reporting this to the maintainers of org.netbeans.ProxyURLStreamHandlerFactory
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release

Result displayer: also generate R call with fitted starting values

Rather than just generating the R call for TIMP with the initial starting values, also generate a call with the converged values.

Compare analyses: autoselect does not take into account the selected range

When using autoselect traces, the tab for Time traces does appear, however, the range selected is not taken into account: the first wavelength is displayed as the first trace.
Reported by Janneke R. via e-mail.

constraints

Values for the following parameters cannot be constrained:

• IRFPar
• KinPar
• Kmatrix - Starting values K-matrix

Below are global and target analyses using a mix of free, constrained, and fixed parameters. The results show that IRF1 is properly fixed at 4.0, but IRF2 and k2 are fitted to values outside of their constraints for both KinPar and the K-matrix.

Global analysis example of a two-state sequential model:

Target analysis example of the same two-state sequential model:

Kmatrix in XML

If node Kmatrix is deleted not everythign is cliined form XML file, that making impossible to comeback to non kmatrix model.

default location for save and open in property window

add possibilyty to select default location for open and export files

Compare analyses: needs legend

Compare analyses needs a legend to see what is compared.
Reported by Janneke R. via e-mail.

Im unable to run analysis after reinstalling Glotaran 1.5💬

Question

Additional context

🐛

Version information

Glotaran 1.5.1

Describe the bug

Cannot open 'Overview.xml' file which gets created after running the global analysis. Uninstalled and reinstalled Glotaran, now unable to even run the demo project.
Its showing an error file.
In Rserve, its showing the following (attached as screenshot).

please help

Core: updating parameters is broken

Create new Demo project, then drag result file onto model, results in error:

SEVERE [global]
java.lang.NullPointerException
at org.glotaran.tgmfilesupport.TgmDataNode.getUpdatableParams(TgmDataNode.java:242)
at org.glotaran.tgmfilesupport.TgmDataNode.access$000(TgmDataNode.java:30)
at org.glotaran.tgmfilesupport.TgmDataNode$1.paste(TgmDataNode.java:97)

Data displayer: option to plot with respect to manually specified zero

Just like in the results data displayer it would be great if we could plot the data centered around a custom zero value, both in linear and in linlog mode. This could be automatically determined to be the average of the 3-10 absolute maximum values in the data.

Visual modeling: reimplementation needed

The current system of visual modeling is too cumbersome to maintain for much longer, it needs a reimplementation. The 2.0 milestone would be a good target for this.

Add to Options - Plotting the ability to set default font size and types

A user asks:
I am using Glotaran, just wonder how to change the font size? I found the layout of the streak camera images in Glotaran is quite nice, should be good for publications, but the font size for axies is too small,

My reply:
I was planning to add this to the Options - Plotting panel - the ability ot set global font size for all plots
then we just need to modify the code where the plots are set and read from a property, and if it doesn't exist assume a default.

CoreAnalysis wrong modelcall when using model differences with more than 2 datasets

The ArrayLists baseArgs and changedArgs are not cleared when iterating over multiple changecontainers thus carry over in the next iteration causing a faulty model string generated for each dataset after the second.

Modeling: in Double Guassian Width2 and Ratio shows as 0.0 even when value is set

Even when a value is set for the DoubleGaissian parameter the node displays 0.0

Feature request: reading in files from the command line

An options to read in files that Glotaran recognizes from the command line and write an export format to another directory would be a nice option.

glotaran -input streakimage.img -output timpdatafile.ascii

Graphs: distance measure desired for Single Graph

In a single graph window it would be nice to have two movable cursors (crosshairs) to measure distances between two points.

export dataset to tabseparated ascii

There is no "end of the line" after exported wavelenght. Also extencion should be different from ASCII because it is impossible to load it back to glotaran without changing extencion, ASCII - reserved for timp formated files

Cannot open overview result files (created in R 4.1.0 or greater)

In R 4.1.0 the NLS output syntax was changed, which breaks the functionality of the overview file.

Prior to R 4.1.0 NLS would print lines like e.g.:

0.02467975 : 1 0.2 -0.6931472 -2.995732 -4.60517 0.3 -0.1 0.01

And now:

0.02467975 (1.01e+00): par = (1 0.2 -0.6931472 -2.995732 -4.60517 0.3 -0.1 0.01)

This breaks the parsing in Glotaran in AnalysisResultFileViewerTopComponent.java#L295-L326.

A workaround can be to only use Glotaran with R 4.0.5 or earlier, R 4.0.4 has been tested to work.
An older version of R can be downloaded from here.

A fix for this issue would be to fix the parsing of the nlsprogress output in AnalysisResultFileViewerTopComponent.

Stacktrace observed by the user:

java.util.NoSuchElementException
	at java.util.Scanner.throwFor(Scanner.java:862)
	at java.util.Scanner.next(Scanner.java:1371)
	at org.glotaran.core.resultdisplayers.overview.AnalysisResultFileViewerTopComponent.parseNlsProgress(AnalysisResultFileViewerTopComponent.java:310)
	at org.glotaran.core.resultdisplayers.overview.AnalysisResultFileViewerTopComponent.<init>(AnalysisResultFileViewerTopComponent.java:82)
	at org.glotaran.core.resultdisplayers.overview.AnalyisResultFileViewer.getCloneableTopComponent(AnalyisResultFileViewer.java:12)
	at org.glotaran.analysisoverviewfilesupport.AnalysisResultFileOpenSupport.createCloneableTopComponent(AnalysisResultFileOpenSupport.java:18)

The latest R-news describes the change as:

Core: multiple instances of OpenDataset warning

Although it doesn't affect the functionality of Glotaran it does pollute the log file in case people want to report real bugs. Would be great if it could be fixed.

java.lang.IllegalStateException: Warning: multiple instances of shared class org.glotaran.core.main.nodes.actions.OpenDataset created.
[catch] at org.openide.util.SharedClassObject.(SharedClassObject.java:202)
at org.openide.util.actions.SystemAction.(SystemAction.java:87)
at org.openide.util.actions.CallableSystemAction.(CallableSystemAction.java:70)
at org.openide.util.actions.NodeAction.(NodeAction.java:96)
at org.openide.util.actions.CookieAction.(CookieAction.java:77)
at org.glotaran.core.main.nodes.actions.OpenDataset.(OpenDataset.java:40)
at org.glotaran.core.main.nodes.TGDatasetNode.getActions(TGDatasetNode.java:75)
at org.openide.nodes.FilterNode.getActions(FilterNode.java:751)
at org.openide.nodes.NodeOp.findActions(NodeOp.java:162)
at org.openide.explorer.view.TreeView.createPopup(TreeView.java:1056)
at org.openide.explorer.view.TreeView$PopupAdapter.showPopup(TreeView.java:1555)
at org.openide.awt.MouseUtils$PopupMouseAdapter.maybePopup(MouseUtils.java:189)
at org.openide.awt.MouseUtils$PopupMouseAdapter.mousePressed(MouseUtils.java:180)
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:280)
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:279)
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:279)
at java.awt.Component.processMouseEvent(Component.java:6522)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3321)
at java.awt.Component.processEvent(Component.java:6290)
at java.awt.Container.processEvent(Container.java:2234)
at java.awt.Component.dispatchEventImpl(Component.java:4881)
at java.awt.Container.dispatchEventImpl(Container.java:2292)
at java.awt.Component.dispatchEvent(Component.java:4703)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4898)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4530)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4462)
at java.awt.Container.dispatchEventImpl(Container.java:2278)
at java.awt.Window.dispatchEventImpl(Window.java:2739)
at java.awt.Component.dispatchEvent(Component.java:4703)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:746)
at java.awt.EventQueue.access$400(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:697)
at java.awt.EventQueue$3.run(EventQueue.java:691)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:86)
at java.awt.EventQueue$4.run(EventQueue.java:719)
at java.awt.EventQueue$4.run(EventQueue.java:717)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:716)
at org.netbeans.core.TimableEventQueue.dispatchEvent(TimableEventQueue.java:159)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

Simulations

Simulation part should be reenable

Compare datasets bug

array out of bounds errors if datasts has differnt size in waves
in private org.glotaran.core.resultdisplayers.global.spec.calculateToValues()
in line 561
maxToCurves[i] = maxToCurves[i]/maxFromCurves[i];

will give a out of bound error if first dataset has less points in wave dimension

Related to #3

Typos in Glotaran

In the Info screen:

Nuber of -> Number of
bij Average/Resample
Dimention -> Dimension

Multispec dataeditor: fix IntegrateMap, Crosshair and time trace slider

Update traces when IntegrateMap button is pressed
Implement crosshair for the time traces
Disable time trace slider when integrating

[UI] Importing data should be more convenient

From: #1

joernweissenborn commented on Feb 10, 2016
The current way to import datasets is far to cumbersome and feels like win 3.11

Context:

Users often want to have quick look on the data they just acquired. It steals like 10secs of your life importing a file in glotaran which is too much.

Proposal:

Glotaran should remember the last folder when using the the open dataset option
Option screen: Glotaran should offer the option to import arbitrary file endings and let the user choose which scheme to use
Personal file format: the user should have the option to import e.g. a .dat as "time explicit" file and make Glotaran remember the choice for future so it will not ask for every one of the 100 datasets
drag'n'drop: dragging a file (or multiple) from explorer, nautilus, etc into a "Dataset" folder in the tree should add the datasets. If the dataset is not recognized the option screen for data import should opened.

joernweissenborn commented on Feb 10, 2016
Since GlotaranApp will stay a Netbeans App, I think this changes can already be done for Glotaran 1.X and be inhereted by Glotaran2 without problems..

Feature request: Add basic commandline interface

This relates to issue #22

What I would like would be a way to invoke gloteran from commandline like:

gloteran -input myfile.mysupportedformat -parameter myfileana1.yaml -f CSV

The output would be a file containing the DAS in the user specified format, e.g. 'CSV'. This results in this example in a file named 'myfile_das.csv', containing the fitparameters and the resulting DAS.

The parameter are given in a file, which can be in principle of every codec, containing necessary parameters. A example YAML would be:

ps-components:
  - 0.03
  - 0.4
  - 7
irf:
  - type: file
    location: myirf.csv

Ideally, the commandline module would serve as reference implemention of how to use the gloteran core without GUI.

This would greatly help to build e.g. a gloteran server, a webbased gloran-ui, etc. It would also enable to use it in other languages via various java interfaces.

Chirp Corrected Spectra?

glotaran version: 1.5.1
Operating System: Win 10

Description

After fitting a dataset, I want to access chirp corrected kinetics and chirp corrected transient spectra. The kinetics seem to be chirp corrected (as they all begin around a time zero without much delay to each other), but spectra at different times seem to be the original data - are chirp corrected spectra accessible somewhere?