Batch processing mode

In the batch processing mode the program starts as a dialog box with an upper and a lower window. In the upper window the control elements are displayed similarly to the elements in the Plug-Ins bar in the custom processing page. Above the upper

window are three tabs:

Task list - shows the list of operations selected from internal and external plug-ins, which will be applied to the dataset in the sequence shown (top down).

Internal – shows the list of internal plug-ins.

External – shows the list of external plug-ins loaded from the directory specified by File / Preferences… / Directories / Plug-In Directory.

To control the task list use the buttons located to the right of the upper dialog window:

Add adds the selected plug-in from the Internal or External tab to the list of plug-ins in the Task list tab.

Remove deletes a highlighted plug-in from the list on the Task list tab. Move up shifts the selected plug-in up by one line on the list, changing the

sequence of execution of plug-ins on the Task list tab.

Move down shifts the selected plug-in down by one line on the list, changing the sequence of execution of plug-ins on the Task list tab.

In the lower dialog window there is the list of datasets to be processed, and to the right of this window some buttons for customizing the list and controlling the batch processing:

Add adds a dataset to the list. In the opened dialog any image from a dataset can be selected.

Remove removes the highlighted dataset from the list.

ROI indicates the region of interest (.roi) file that will be opened when processing the corresponding dataset. When this file is opened it will apply the grey scale binary thresholds and the vertical boundaries of the dataset volume of interest, or not, as defined in the settings of

File / Preferences / Region of interest.

Results opens the analysis results file for a chosen dataset. This file has the same prefix as the dataset images followed by the double extension

.batman.txt.

Report opens the report (log) file for a chosen dataset. This file has the same prefix as the dataset images followed by the double extension

Properties opens a dialog with information about the dataset, ROI, and the location of the result and report files. Note that the dataset pixel size can be adjusted in the BatMan properties of a loaded dataset.

Import Imports a previously saved dataset list, in the “ctl” format.

Export Exports and saves the currently loaded dataset list, in the “ctl” format.

At the bottom of the BATMAN window, from the left, the following functions are present:

The start button starts batch processing of the list of datasets by the sequence of operations set out in the Task list. Information about the progress of analysis is displayed in the “Status” column in both the upper task window and the lower dataset window.

Selecting this option will result in any previous results of BATMAN calculations in any of the listed datasets, in the default format [prefix]_.batman.txt and

[prefix]_.batman.log, being overwritten by the results of the present analysis.

Selecting this option will cause the computer to be fully shut down at the end of the operation of the task list. This can be useful if you are launching a batch calculation on multiple datasets that will run overnight or over a weekend, for example.

The close button closes the BATMAN window, and stops batch processing if it is in progress.

The Task List has three columns relating to each selected task:

Name the name of the internal or external plug-in;

Description a description of the task performed by the plug-in;

Status the status ofthe plug-in shown in real time during batch operation.

The Dataset list has five columns relating to each selected dataset:

Dataset the path and filename of the dataset which will be opened and analysed;

Region of interest the path and filename of the .roi region of interest file applied to the corresponding dataset during batch analysis;

Status the status of the analysis of the dataset shown in real time.

Results the path and filename of the file where the results of dataset analysis will be written.

Report the path and filename of the file where the report log will be written, listing procedures applied to the dataset.

Preferences in BatMan

Right clicking on the top left corner of BatMan opens a preferences window.

The BatMan preferences are a limited set of the preferences in the main part of CTAn. One additional preference in under the tab “tools”:

Two options are given under the BatMan preferences and Tools concerning the application of preferences previously set in the “main” CTAn. The first option, “apply global read-only CTAn preferences…”, means that, on opening BatMan, the

preferences will be taken from the previous session of the main CTAn. The second option, “apply last used preferences in BatMan…”, will instead on opening BatMan apply preferences as set in the previous BatMan session.