New Features of GeoPIXE

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New Features in GeoPIXE 6.3

New record header information for data from the Maia detector enables per pixel and per detector accounting for dead-time and pile-up losses and the use of the 2 Maia hardware flux counter inputs. New features in GeoPIXE 6.3 use this data to provide: (i) correction for dead-time in images and spectra, (ii) correction for pile-up losses, (iii) use of the hardware counters for accurate pixel-locked integration of flux using pulse streams from V-to-F preamplifiers. A new calibration (DTcal A, B) is included to convert time-over-threshold T to ns for dead-time measurement.
A number of new plugins enable display if (i) raw flux map, (ii) dead-time map, (iii) pile-up loss map, (iv) dwell map, and (v) detector channel activity histogram.
Consistent use of parallel processing options for multi-core acceleration of Maia imaging, spectra import and spectra extraction from regions. Core number is configured in the “geopixe.conf” file, which is normally read from your home .geopixe directory (if not found a copy will copied there from the main geopixe dir).
The Spectrum Select window has been revamped for more flexible selection of spectra based on detector channel, especially for detector arrays. The new “Array…” button opens the Array Detector Channel Selection window, which provides a mimic display of the detector array on which to select desired channels. Selection class options allow selection in groups based on row, column, radial position, odd, even and underlying hardware (chip, quadrant) relevant to the Maia detector array.
A new updater program has been added to GeoPIXE (standalone as “geopixe.update.sav” and spawned from GeoPIXE Image Help menu) to manage updates of software and support files for licensed users from the GeoPIXE FTP site. See the file “Help/GeoPIXE-update.txt” for details.

New Features in GeoPIXE 6.2

While the effects of the varying sensitivity of detectors across a detector array has been used in GeoPIXE for some time to correct model calculated X-ray yields, the relative intensities needed for spectrum fitting have just used the integration through the multi-layered sample and correction for filters and detector efficiency for the ‘central’ detector element only. Now for each spectrum, the detector elements that were active in contributing to the spectrum are used to calculate a weighted average of relative intensities for each detector, including intrinsic efficiency and external filters across the array.
Certain Image parameters displayed in the Image Properties & History window (Windows and File menus) can now be edited. Just double-click on the text fields for Sample, Grain and Comment, the Scan Size or Origin, or the Charge and Conversion factor fields to pop-up an edit window. Most parameters are fixed and reflect parameters used in the Sort or later image processing steps. To change fundamental parameters, such as DA Matrix and element list, Compression or flux PV selection, the data will need to be re-sorted in Sort EVT.
The Association window has been revamped to provide axes and better control over the displayed concentration ranges in X and Y. The 2D histogram Z scale can also be displayed using Sqrt of histogram frequency to compress dynamic range.
Version 6.2 includes a new window for XANES Image Stack construction and exploration, accessed via the Image window Display menu. More on this later …
GeoPIXE preferences are now kept in a config file “geopixe.conf” in the “.geopixe” sub-directory to your home directory (if not found it will search in the GeoPIXE directory). It can be edited to set-up default paths, cluster and parallel processing parameters, window startup and image origin.
Similarly, file path bookmarks, as used in the file requester, are stored in the “.geopixe” sub-directory to your home directory (if not found it will read bookmarks from the GeoPIXE directory). It will save paths back to the .geopixe directory. The token “$HOME” in the bookmark list translates to your home directory (as pointed to by the HOME environment variable).
Support for computer clusters and multiple cores on modern PCs has been added to speed-up Maia data processing. The cluster mode is selected in the new config file “geopixe.conf”. When “cluster type cores” is selected, multiple IDL sessions are used to divide up the processing of raw data. This works for data streams in a series of files, with absolute XY coordinates contained within them and using numeric file extensions on the files. Select the number of cores to use in “cluster nodes n”, and enable cluster mode on the Sort EVT window. Log files are written to the “.geopixe” sub-directory to your home directory.

New Features in GeoPIXE 6.0-6.1

The major reorganization in GeoPIXE 6.0 is the development of Object Oriented Device driver plugins. All device specific code is now gathered together in a single SAV file that is loaded automatically from the “interface” directory as an IDL Object. Each file name has the form “XXX_DEVICE__DEFINE.SAV” for device “XXX” object code. Users can now view and modify their device-dependent IDL code and indeed write new drivers using these as templates. A new guide “Help\Object Oriented Device Driver Modules.doc” is provided to help with this.
Device objects may choose to read and write new device-specific parameters to Image (.DAI) and region files (.REGION). Older, Maia explicit parameters have been removed. Matching read and write methods need to be written in the object definition to do this consistently for each device that needs extra parameters. For this reason, extensions to DAI and REGION files now exist that will make them unreadable to older versions of GeoPIXE 5. User devices will need to handle their own versioning.
The following devices make good templates for writing driver code: (i) MPsys_device – simple PIXE list-mode in a single file, (ii) NSLS_MCA – SXRF raw data stored in pixel MCA spectra files that also scans for variables providing ion chamber count rates and sensitivity, and (iii) Maia_device – uses all methods, including use of Y lookup tables and defining extra widgets and use (and read, write) of local device parameters.
The GeoPIXE directory has been reorganized. Now plugins are located in the “plugins” directory, the Maia config file (used with the Maia device) and the Maia background processes (used with the Maia_Control program for detector monitoring and control) are located in the “maia” directory, the new device objects are in the “interface” directory and image files are located in “images”. Example setup files have been moved to the ‘setup’ directory.
Libraries for low-level processing code have been compiled for both 32 and 64 bit versions of Windows, Linux and Mac OS 10. GeoPIXE should now run on all these platforms, although it is only tested routinely on Windows 32 and Linux 32/64.
An interim version of these libraries was placed on the FTP site without optimization. The new versions are a factor of 2 faster and should be downloaded to replace any interim libraries.

New Features in GeoPIXE 5.5

An extra feature has been added to the Image Table EVT button called “individual”, which allows extracting individual spectra from each detector for the first region in the region list. This complements “array”, which forms a summed spectra of all detectors for each of the regions.
A new checkbox under the element droplist in the main GeoPIXE Image window allows toggling the interpolation of image data when zoomed in. Uncheck the box to suppress bilinear interpolation.
A number of structural extensions have been made to accommodate 3D data-sets for XANES imaging. These include a XANES image stack window and extensions to RGB images, Associations and regions. Image DAI files now contain beam energy and X and Y pixel coordinate vectors. More on this later ...
Two new Region selection types or shapes have been added: “Project X” and “Project Y”. These work like “Traverse”, providing a method to produce linear traverse profiles across images, but are constrained to project only in X or Y. These are useful for pseudo 2D data-sets, such as XE XANES line scans, in which a line is scanned (in X) at each beam energy E and the data-set is built as an image with E as the Y axis. Then “Project Y” provides the XANES spectrum for a selected portion of the scan line. New additions to DAI files store non-uniform X and Y coordinate vectors if available from raw data source.
New TIFF export options have been added to the Image window to export in (i) concentration (ppm), (ii) counts (summed over all detectors), and (iii) ng/cm2 loading per pixel. These options have been added to the Batch Sort window too.
New information is packed into the DA matrix files to allow images to be reported and exported in ng/cm2 units. Older DA files will need to be regenerated to access this feature (e.g. TIFF export).
A “No Q” button has been added to the Spectrum Select window to zero all charge values in the table. If a charge is set for the first spectrum in the table, then a “Fit All” applied to the X-ray Spectrum Fit will apply this charge to all subsequent zero charge spectra. In the case of SXRF, the current conversion factor from IC count to charge will be applied to any valid IC count values in the subsequent spectra to calculate a charge before fitting. Click on “?” next to the charge (Q) field in the fit window to make sure the correct conversion is applied.

New Features in GeoPIXE 5.0-5.4

A number of structural changes have been made to accommodate new Maia 384 detector features, such as real-time spectra and DA image display, as well as underlying changes needed for using parallel processing on computer clusters. The parallel processing features are still under test.
The Import spectrum process looks quite different now. Selection of ion chamber sensitivity for synchrotron data and a button to “scan for Epics PVs” has been added. The flow of operations is more logical.
The Sort EVT window has been updated to incorporate ion chamber PV and sensitivity selection and the conversion factor between IC count and equivalent charge. Now input files, scan details, ion chamber settings and DA settings and energy cal are on separate tab panels.
A new image export has been added to output images in floating point TIFF format for use elsewhere, such as for tomographic reconstruction. It can be accessed on the “File->Export->selected Images as TIFF counts” menu of the main GeoPIXE Image window. The output is one TIFF file per selected element plus a summary HTML file, output to the TIFF subdirectory by default.
A new Multi-image Display window has been added that displays a grid of simple element windows (Image Display menu). These can be zoomed by dragging out a rectangle in the first window.
Maia detector array support has been extended to accommodate the new 384 detector array developed by CSIRO and BNL for the Australian Synchrotron and the NSLS.
Flux handling for synchrotron XRF imaging has been improved. A new “?” button next to “Q” charge in the X-ray Spectrum Fit window provides a place to set ion-chamber count to flux conversion based on charge, or to set charge based on a prior conversion factor. See the Data Analysis Scenarios chapter on SXRF imaging.
Flux is tracked through image, spectra, region and results files. Hence, the format of these files has all changed in version 5. These new files cannot be read by older versions of GeoPIXE (v4).

New Features in GeoPIXE 4.8-4.9

A new File Requester has been developed to provide better file selection, directory navigation, bookmarked paths, content previewing and to give better consistency across platforms.
The Blog_Browser program is available from the Windows menus to browse and probe the details of records in Maia data files.
The saving of HTML files and new DAI output images has been improved to create subdirectories automatically.
Batch processing has been extended to include Maia-96 detector data files.
Support for the CSIRO-BNL Maia-96 advanced fluorescence detector arrays has been extended to support flux measurement in images, and correction of images for flux variation, which has necessitated extension to libraries. This version requires the new “image_dll.dll” file under Windows and “image_lib.so” under Linux.
Support for detector arrays has been extended to “refit” in X-ray Spectrum Fit and adjustments made in Result Properties, which were inherently simple detector array functions before, to now include variation in sensitivity across detector arrays and the selection of an arbitrary subset of detectors in an array.
Extended Maia-96 support for linearization to work with either a single linearization table, or one for each detector, as stored in .linear files. These tables are constructed with plug-ins specific to the Maia-96 detectors.

New Features in GeoPIXE 4.6-4.7

Support for the CSIRO-BNL Maia-384 advanced fluorescence detector arrays has been extended to support gain linearization, pileup rejection, rate throttling and increased number of detector elements up to 384. This has necessitated moving to Combobox widgets for detector selection throughout, which is also necessary to move towards Linux support. The linearization and throttling follow through to extracted spectra as well.
Support for Ortec Maestro spectra format and the Wakasa ACC UniDAQ list-mode data files has been added as well as preliminary support for SLS MCA and HASYLAB FIO image spectra files.
Fixed behaviour of the vertical scale droplist in Spectrum Display for fit overlays and added the ability to normalize spectra within the Cut range. Fixed behaviour of the Shrink, Expand and Widen buttons when in Auto and Norm vertical modes.
Starting with GeoPIXE 4.6, IDL version 7.0 will be used for all code and plugins. GeoPIXE will still be able to load v6 plugins.
The Cal window has a new button “RA” to ‘re-assign’ selected peaks to a new calibration. Use this when all spectra are calibrated relative to each other and you want to re-assign the element identity of the peaks marked for energy calibration. This will change energy calibrations for all spectra to assign the peaks to the new selected energies. RA is a form of global re-calibration adjustment.

New Features in GeoPIXE 4.5

A new Y display scale mode droplist has been added to Spectrum Display to control vertical scale normalization options. This replaces the “Rescale” button. There are now options for automatic scale setting and for re-normalization of multiple spectra to match the vertical range of the first. The Spectrum Display controls have been rearranged to group the X and Y controls together.
The X-ray line identification window has been enhanced. Now all lines for an element are highlighted if one of its lines is selected by clicking on a row. All lines for an element in the line list are selected similarly if an element is selected in the periodic table view.
The X–ray Spectrum Fit “Advanced/Widths” tab now as the ability to fix or adjust the Noise peak width parameter via setting the resolution, based on Mn Ka FWHM. The resolution is still available in Fit Results as before. There is also a check-box to free the Fano factor in fitting peak widths. Use this sparingly as the default works well most of the time and increases fit stability.
A new “Export” menu option has been added to the Associations window. Use it to export to CGM, WMF and EPS, or to display the associations in a new window with detailed axes and axis tick-marks, etc.
Pile-up in GeoPIXE X-ray Spectrum Fit assumes the use of pile-up rejection strategies (electronic rejection or on-demand beam switching). However, finite timing resolution can still lead to a small deficit in the sum-peak amplitudes. A new “Deficit(%)” control has been added to the “Advanced/General” tab of X-ray Spectrum Fit to adjust for this deficit.
Support for list-mode data that does not fill out the specified pixel range completely. The actual bounds is detected and beam flux will be assumed to be spread evenly only within these bounds.

New Features in GeoPIXE 4.4

The scattered beam subtraction options, previously in the Fit Results droplist, have now been moved to the Fluid Inclusion (3 layer) mode of the Result Properties window. Now these corrections are made once, which modifies the data, and stored as a property.
A second detector efficiency curve can now be overlaid in red on the detector efficiency being edited in the Edit Detector window. The ratio of the new detector efficiency to the overlay is also displayed in violet, scaled down to 10.
Spectra in Spectrum Display can be optionally displayed with points and errors bars for data, using a new check-box called “Error bars” next to the Log/Lin button.
The various colour/intensity scales in the main image window (linear, SQRT, Log), introduced in version 4.0, have been extended to the 3 Element RGB Image window. Any scale settings for each element in the main image window are now reflected in the RGB colour scales in the RGB Image window.
A new Import pop-up window is available to import spectra files into Spectrum Display. This replaces the lengthy menus and enables the selection of PIXE versus SXRF laboratories and the selection of various file formats from each.
An extra tab on the Results Properties window for thick targets enables the calculation of target thickness from STIM transmission ion energy loss data. This updates the thickness of the target in the yield model, and upon “Apply” calculates the new yields based on this thickness and applies these to the selected results in Fit Results.

New Features in GeoPIXE 4.0

In the main GeoPIXE Image window, all concentrations between the bottom and top sliders are mapped onto the current colour map, using a linear scale by default. Use the new small droplist between the bottom and top sliders to select between Linear (L), Log (G) and Sqrt (S) scales for the Z axis. The Sqrt and Log scales have the effect of compressing dynamic range, which can be useful for images with strong hot-spots and low-level traces.
The X-ray Spectrum Fit window has been re-vamped to place more subtle parameters and controls on an “Advanced” tab panel. In addition, a number of controls have been added to this panel to control background, tailing and parameters specific to PIXE and SXRF.
“Conc” units can now be specified in “ppm (wt)”, “mmol/l” and “ng/cm2”, the latter being appropriate for a layered sample such as a fluid inclusion.
Full detector array support has been added for yield calculation, image projection and spectrum fitting. Now the take-off angle variation across large arrays can be catered for, as well as arrays with non-planar geometries (e.g. hemi-spherical), round and square pads, and arbitrary tilt relative to the detector-target axis.
Support for the Maia series of detector system has been extended to support full-spectral SXRF (or PIXE) imaging using up to 384 detector elements.

New Features in GeoPIXE 3.9

Ghost features in images, corresponding to second displaced beam at a fixed offset can be corrected using the “Process->Correct->Ghost” menu. The menu offers relative intensities of the ghost feature in 10% and 1% increments. Use these in combination to correct ghost features; the operation is applied to all image s.
GeoPIXE can process the HDF format NSLS scan files now as a new device in Sort EVT and the Spectrum Display Import menu.
Fixed a bug related to Fit Results files (PFR) that contained fits that used multi-layer filters. The file format had an error in it. The fix now permits all old PFR files, which may contain the error, to be read and rectified. All new PFR files have the correct format.
If a region is selected and highlighted based on element Associations, then the exclude operation can now be used to remove pixels from the Association highlighted area.
To remove pixels from the current Associations highlighted area, use the exclude “-“ mode of region select shape. Select exclude, drag out a shape and use the “sigma” button to remove pixels within this region from the current Associations selection. Note for this to work, no include region should be set. To make sure, use the menu “Display->Clear ALL Shapes” and then select the exclude region.

New Features in GeoPIXE 3.8

New features have been added to accommodate the MAIA-32 event-file format produced by the CSIRO Blog server. This device being added to the device list in Sort EVT and to the Import list in Spectrum Display.
For Maia-32 EVT files, Sort EVT includes a file specification entry for a pileup limits file, which specifies the range of valid time-over-threshold for each detector pulse-height. The Import menu of Spectrum Display also has options for sorting spectra with or without pileup removed by this approach. The EVT button on the Image Regions window sorts out spectra with pileup removed, if appropriate for the image data-set.
A new window (Time Amplitude) is available (in the Spectrum Display “Windows” menu) to plot the Time-over-threshold time versus pulse-height amplitude for Maia 32 events. Use the “File” menu to select EVT files to sort. If an image is loaded into Image Display, and a region is selected and the “sigma” button is pressed, then the Time Amplitude window will sort and display the Time-Amplitude points for all events that fall within the selected region.
If a region is selected on an image while Time Amplitude is open, then only the subset of Maia-32 events that fall within the region will be displayed in Time Amplitude. It will sort through as many files as needed to display the requested number of events.

New Features in GeoPIXE 3.7

Entry of energy and A, B data into the Cal window text widgets is now a little smarter, and do not require a to be properly registered.
Images can be corrected for missing scan lines, or portions of scan lines, in both the horizontal and vertical. Look under Image Operations in the Help for tips. Surround the missing line segment with a Box shape, and go to the “Process->Correct->Missing Rows” menu to replace the missing data with the average on either side. Similarly, “missing columns” works for vertical missing data. Use “Double-counted rows” to attenuate double-counted rows by two, and similarly for columns. These operations are applied to all elemental images, and cannot be undone; save the image file first.

New Features in GeoPIXE 3.6

The “Convert->APS MDA to LST” operation, on the Spectrum Display File menu, can now use multiple file select to process a sequence of APS MDA files. These are assumed to use the same assignment for ion chamber PV, sensitivity and live-time correction.
Initial support for Hasylab FOI full-spectral pixel data files has been added.

New Features in GeoPIXE 3.5

Several functions that use regions now will use Association highlighted areas on images, if no valid Region is selected (i.e. Shape tool on Image window is set to “Distance” or no shape has been drawn). These include Correct Current and Kill and Suppress Region.
In the Association window, a spline region can be cleared using a right mouse button click.
A new menu in Spectrum Display (“Display->Get ALL Energy Cals”) can be used to load all energy calibrations for multiple spectra corresponding to elements of an array from a selected spectrum file.
Support has been added for GSE-CARS full-spectral pixel data files at the APS.

New Features in GeoPIXE 3.4

GeoPIXE now includes an improved elastic and inelastic scattering model for SXRF. The intensities of these, and the length of the inelastic and multiple-scattering tail, can be varies in the fit. However, at present there is not control or variation on the electron momentum distribution for inelastic scattering. These will appear later.

New Features in GeoPIXE 3.3

The Image Regions window has a new feature for sorting all detectors of an array into merged spectra for regions. The spectra are mapped onto the energy calibration of the first spectrum before being accumulated into single spectra. The ADC droplist now starts with “array” which means sort all array detector enabled for the image in Sort EVT when the list-mode file was sorted (assumes “Detector Array” type was selected in Sort EVT).
The Detector Setup window has been updated (access from “Edit Detector” menu). Now the solid-angle properly reflects detector tilt angle as well as detector dimensions and distance.
The Filter Setup window now has a new “Special” filter option for Bragg filters. These are log-spiral X-ray lenses tuned to Bragg diffract a certain energy. The centre, width, height (enhancement) and background (scattering) of this transfer function can be specified.
When fitting a series of spectra, using the “Fit All” button on the X-ray Spectrum Fit window, if only the first spectra has a Q value (e.g. entered into the Q box in the fit window) then all spectra will assume the same charge/flux.
Sometimes Spectrum Select was not being updated as spectrum properties were changing. This has been rectified.
Support for Tohoku Labo, NSLS MCA image pixel spectra and Sandia Primecore U48 list-mode formats has been added to GeoPIXE.
Association highlights on images can now be exported as Transparent PNG images using a new File->Export menu.
Results of yield calculations can be exported for examination using the new “Export” button on the PIXE/SXRF Yield Calculation window.

New Features in GeoPIXE 3.2

A simple scheme has been added to enable determination of the conversion from Ion Chamber counts to flux or “charge” for APS generated data using a standard foil. Quantification is then straightforward for unknown samples.
The Image Export options have been enhanced to control the format of Exported output to the printer and various metafile formats. Also, a selected region of an image can be selected for export by dragging a shape on the image and checking the “Crop Image” option.
Export of images to CSV file now has the option to export only a selected region of the image. Use a shape and the new menu item for export of a region.

New Features in GeoPIXE 3.1

The scene has been set for XRF imaging and analysis for synchrotron X-ray microprobe applications with the addition of XRF fundamental parameter databases. To select photons, select “Photons” in the beam particle droplist in the yield calculation window. Beam energies are then in keV.
Detector array handling has been improved, and a new section in the Scenarios chapter has been added.
A new button “Export” has been added to the X-ray Spectrum Fit window to export the Dynamic Analysis matrix to a binary file (extension DMX) for download into a data acquisition system for real-time generation of elemental images.
GeoPIXE has been ported to Linux; the same XDR portable SAV file will run on both Windows and Linux platforms. All binary files are in XDR format and can be used on either platform.
GeoPIXE now assumes IDL version 6.0.

New Features in GeoPIXE 3.0

GeoPIXE now has support for detector arrays. The Sort EVT window can process all detectors of an array simultaneously and project all data onto a common set of elemental images using a Dynamic Analysis matrix. Sort EVT has a droplist to select the array option. Select a DA matrix as usual, and enable all ADCs that are part of the array.
Many device drivers have been moved into external Fortran code to improve the speed of processing list-mode files. Some file formats show significant speed increases with throughput up to 20 Mb/sec (on a 2GHz P4).
A new curvilinear traverse shape “Curve 8” has been added to the GeoPIXE Image Display window. It provides a spline curve to tailor non-linear traverses in order to project changing concentration data along non-linear paths across images.
The “B” button adjacent to the “EVT File:” button in the Sort EVT window brings up the Batch Sort window for editing parameters and controlling batch sorting of entire directory trees of list-mode files. It also enables a tree directory structure to be generated and populated with list-mode and related files.

New Features in GeoPIXE 2.9

GeoPIXE now has Preferences selection (“Preferences” on the “File” menu of the main GeoPIXE Image Display window). These set options for launching various GeoPIXE windows on start-up, and parameters referring to XY stage ranges and stepper resolution. Preferences stored to the file “GeoPIXE.prefs” become the defaults for the next launch of GeoPIXE.

New Features in GeoPIXE 2.8

An accurate pile-up spectrum can now be calculated using image pixel intensity products. Use the “Display->Pileup->from Images” menu in Spectrum Display. PIXE Fit can now use these calculated image pileup spectra to obtain more accurate fits to spectra corresponding to total spectra from PIXE images with wide variation in major element spatial distribution.
Images can now be corrected for pile-up related effects, based on pixel-by-pixel calculation of pile-up components. A new menu in Image Display called “Process->Correct->Image Pile-up” performs this task in concert with the Spectrum Display window. See the expanded manual sections for details.
Export of image plots to structured drawing formats, such as CGM, EPS and WMF has been improved, and now produce plots with concentration legend, labels, and axes in microns (if image size was supplied). The Image Display “File->Export->Save Images as CGM” and “File->Export->Save Images as WMF” menus, as well as the “File->Print” menu, pop-up a requester to tailor the size and weight of characters, line thickness, the placement of optional items, such as a distance bar, and the choice of output format (CGM, WMF, EPS, Printer).
Export of spectra plots to structured drawing formats, such as CGM, EPS and WMF has also been improved. The Spectrum Display “File->Export->CGM Plot” and “File->Export->WMF Plot” menus, as well as the “Print Plot” menu, pop-up a requester to tailor the size and weight of characters, line thickness, etc. and the choice of output format.
The way that user written image processing plug-ins are treated has changed a little. In particular, the format of the returned history record must contain the name of the routine. Please check the code in “template_image_plugin.pro” for details. Image processing plug-ins now appear in the Image Operations list for easy access.
A new menu “Process->“Fold” can be used to remove the toggle bit effect, which produces the effect of a double spectrum. This ‘folds’ a spectrum back on top of itself to half the length in channels adding contributions to channels as it goes.
An accurate pile-up spectrum can now be calculated using image pixel intensity products. Use the “Display->Pileup->from Images” menu in Spectrum Display. PIXE Fit can now use these calculated image pileup spectra to obtain more accurate fits to spectra corresponding to total spectra from PIXE images with wide variation in major element spatial distribution.
Images can now be corrected for pile-up related effects, based on pixel-by-pixel calculation of pile-up components. A new menu in Image Display called “Process->Correct->Image Pile-up” performs this task in concert with the Spectrum Display window. See the expanded manual sections for details.
Image processing operations that were applied to element images in one image file can now be applied selectively to element images in a new image file. This makes digital filtering and smoothing of images in a batch run of many analyses much quicker.
A ten-step colour table has been added to the Image Display “Display->Colours” menu, and the Export->CGM options will now adjust the Z legend tick marks to these colour transitions.
A new output option allows the image shapes to be export as transparent PNG files. See the “File->Export->Current Shape as PNG” menu in Image Display.
Support has been added for reading Fastcom MPAWIN and MPA3 list-mode files and Sandia EVT data-cube files.

New Features in GeoPIXE 2.7

The Edit Filters and Edit Detectors windows now show plots of transmission and intrinsic efficiency, respectively.
Both the HTML save format in Image Display (menu “File->Save All as HTML (PNG)”) and the Chimage format save operation (menu “File->Save as Chimage”) now use a pop-up to select elements. This pop-up also allows selection lists to be saved and restored to enable the use of standard element lists.
The X-ray Identification window (“Display->Identify X-rays” menu, or the “?” button, from Spectrum Display window) now has droplists to select X-ray filters and the detector in “Mark Element” mode. All X-ray line relative intensities are now calculated assuming detector efficiency and absorption through these filters. These lines are shown on the Spectrum Display window as orange markers.
The Sort EVT function now accumulates the total integrated charge for OM DAQ list-mode file during sorting. The charge field is updated AFTER the sort completes, and the charge is written into the image header. A new requester will pop-up to allow editing, or scaling the charge up or down by multiples of 10.
The “File->Save ALL as HTML (PNG)” output menu operation of the Image Display window now pops up a requester for the entry of the desired elements to output. These element selection lists can also be saved and restored from this pop-up panel.
The “Export” buttons on the PIXE Fit and Image Regions windows now bring up pop-up panels to select options for export, including quantities to export and element selection.
Menus under the Image Display “Window” menu can be used to bring up “unlinked” versions of the Image Display or Spectrum Display windows. Normally, all windows are linked together and reflect one dataset under study. By opening unlinked windows, you can load quite independent images or spectra without affecting the current images and spectra, or the current path.
The Layer II Setup window now has a “Plot” button to bring up a plot window to display various calculation results, such as PIXE yields, as a function of depth or energy.
Sort EVT, as well as functions to read IMG spectra files or extract spectra from EVT files in Spectrum Display, all now look for an MP file of the same name. If one is found, relevant details, such as images sizes, energy calibration and integrated charge are retrieved from the MP file.

New Features in GeoPIXE 2.6

GeoPIXE can now process list-mode files generated using the Oxford Microbeams OM DAQ data acquisition systems and software. Select "OM DAQ Data Acquisition for PC" on the input device droplist in the Sort EVT window.
Loading of all spectra, and import of spectra from files or extracted from list-mode files, can now use multiple file selection. Simply use multiple selection in the file requester (using control or shift keys) to select multiple files within a selected directory.
Spectra (single or multiple) can now be appended to the spectra already in memory using the "File->Import->Append-> …" menus. Use the "File->Import->New-> …" menus to clear memory first.
The PIXE Fit window now has a button to fit ALL spectra currently loaded into GeoPIXE. Coupled with the ability to load multiple files, this enables simple batch processing of series of spectra from multi-spectra SPEC files, or loaded from a series of single spectrum files.
The Cal window for energy calibration now has a button to set the calibration for all spectra loaded ("All") or just the currently displayed spectrum ("One"), and a button to set the units to "keV".
The Spectrum Display window now has a user plug-in facility. Now you can write spectrum processing and other user spectrum operations in IDL, such as custom fitting. These are loaded when GeoPIXE runs and appear on the "Process->User Plug-ins" menu.

New Features in GeoPIXE 2.5

A new Image RGB window displays three element images as the Red, Green and Blue components of a 24-bit colour image. The intensity of each element is set in the Image Display windows. The results can be exported as 24-bit PNG or JPEG files.
The Image Display window now has a user plug-in facility. Now you can write image processing and other user image operations in IDL. These are loaded when GeoPIXE runs and appear on the “Process->User Plug-ins” menu. As with other image operations, these add an information line to the image history record. The “Undo” menu (or button on the Image Operations window) can be used to undo this user plug-in operation.
Image processing operations have been added to the Image Display window ("Process" menu) for edge enhancement (Roberts and Sobel filters), erosion and dilation, and rotation and mirroring of images. Many of these are also in the Image Operations window list for quick access.

New Features in GeoPIXE 2.4

A new window Correlation is used to plot correlations of two elements in images. In other words, each pixel in a set of elemental images represents a data point in multi-element space. Correlation displays two-element projections from this space. This can show up discrete phases in a sample, for example, which appear as discreet blobs that may be separated in some two-element views.
A spline tool is available in the Correlation window to select arbitrary areas in two-element space. These selections can be used to highlight all pixels in the element images that represent this area in two-element composition space. These pixel selections, plus the average concentrations within these highlighted areas, are saved in the Image Region s window table. As with normal image region selections, the spectra from any ADCs within these selected areas can be extracted.
If a normal image region is used, to select a spatial area within an image, then the element correlations shown in the Correlation window only show data from within this spatial area of the image. For example, this can be used to learn about specific phases in an image, exclude a dominant phase, or to separate subtle intergrowth compositions.
An Image History window is now available from the “Windows->Image History” menu of the Image Display window. It shows all image processing operations that have been performed on each elemental image. This will show all history for all existing image files as well.
The Image Table window now has a button to update just the currently selected region. To make an adjustment to a region, select it by clicking on the row in Image Table, and then click on the “Update: One” button. This will update the concentrations and store the new region shape and position in the selected table row.
The Image Operations window has been updated. It now includes an “Undo Last” button to undo the last image processing operation performed. This also updates the Image History window accordingly.
Line profiles generated using the “Traverse” region now include an overlaid plot of the detection limit (99% confidence) in each distance step, as a dashed curve.

New Features in GeoPIXE 2.3

Fit Results now has an “Export All” button to export all results and parameter categories to the output ASCII .CSV table.
The “Traverse” image region now has shear control. The side handles, moved using the left mouse button, usually control the width of the traverse region, perpendicular to the projection axis. Now you can shear this projection, so that it’s not perpendicular. Use the right mouse button to select these side handles and slide parallel to the main axis to change the shear.

New Features in GeoPIXE 2.2

Spectrum Display now has two ASCII spectrum file import options. One reads spectra, one from each column, into consecutive spectra. The other reads ASCII spectra files that contain channel energy as the first column (e.g. as produced by the “File->Export->CSV Table” menu) and one or more spectra channel counts as the subsequent columns. These files can be white space, comma or tab delimited, or a combination of these.
More import options have been added for old format GeoPIXE VAX binary spectra files and for ASCII files. The ASCII import option can read files with multiple spectra as columns. There are two menus. One reads files where the first column is channel energy. The second reads all columns as spectra. Both assume that the first row contains column labels, and if energy mode is chosen, it uses the label for the first column as energy units. These functions can handle column separation using white-space (spaces, tabs) or commas, or a combinations of these.
Spectrum Display now has Windows Metafile export options. Go to menu “File->Export->WMF Plot on Black” for output for a dark background, or “File->Export->WMF Plot on White” for output for a light background. These files, like the CGM ones, can be imported into PowerPoint as pictures.
The detector efficiency function has generally followed the function of Cohen (Nucl. Instr. Meth 178 (1980) 481), as corrected by Ryan et al. (C.G. Ryan, D.R. Cousens, S.H. Sie and W.L. Griffin, "Quantitative Analysis of PIXE Spectra in Geoscience Applications", Nucl. Instr. Meth. B49 (1990), 271-276), which uses a multiplicative factor of 0.717. GeoPIXE has used this to be consistent with packages such as PIXAN. A new option in the Detector Setup window makes this factor optional. Use this to be consistent with other packages that do not follow Cohen.
The menus for display of calculated pileup and Si and Ge escape spectra are now active in Spectrum Display, under the Display menu.

New Features in GeoPIXE 2.1

There is a new feature in the Correct Yields window for the correction of artifacts in images caused by the spatial variation of X-ray absorption across the image. Details of the process can be found in (C.G. Ryan, E. van Achterbergh, G. Mark, C.J. Yeats, S.L. Drieberg, B.M. McInnes, T.T. Win, G. Cripps and G.F. Suter, "Quantitative, High Sensitivity, High Resolution, Nuclear Microprobe Imaging of Fluids, Melts and Minerals", Nucl. Instr. Meth. B188 (2002) 18-27.).
The projection onto end-member phases now also produces an image corresponding to the remainder, i.e. the proportion not assigned to the end-member phases.
Support for 4 list-mode formats is provided: Mpsys on Linux and Unix, Sparrow Kmax on Macintosh, and XSYS on VAX/VMS.
Interactive set-up windows for filter and detector definitions are now provided. Go to the Windows menus on the Image Display or Spectrum Display windows.

New Features in GeoPIXE 2.0

There is a new Cuts Setup window for the interactive set-up of energy cuts on spectra. The window also displays background-subtracted peak-areas deduced using cuts. Cuts can be named for use in sorting list-mode data, for example from non-PIXE ADC channels.

New Features in GeoPIXE 1.9

There is a new feature for the correction of concentration due to the spatial variation of PIXE yields caused by changing sample composition across an image. The new Correct Yields window allows for this correction, using a new approximation for combining PIXE yields calculated for end-member components (see C.G. Ryan, "Quantitative Trace Element Imaging using PIXE and the Nuclear Microprobe", International Journal of Imaging Systems and Technology [Special issue on Quantitative Imaging] 11 (2000) 219-230 and C.G. Ryan, E. van Achterbergh, C.J. Yeats, Tin Tin Win and G. Cripps, “Quantitative PIXE trace element imaging of minerals using the new CSIRO-GEMOC Nuclear Microprobe”, Nucl. Instr. Meth. B 189 (2002) 400-407).
The Correct Yields window also provides projection of element images onto images of end-member components.
GeoPIXE can sort list-mode data with up to 16 ADCs.

Features of GeoPIXE II ™

PIXE/SXRF spectrum fitting (unlimited elements and X-ray lines). See C.G. Ryan, D.R. Cousens, S.H. Sie and W.L. Griffin, "Quantitative Analysis of PIXE Spectra in Geoscience Applications", Nucl. Instr. Meth. B49 (1990), 271-276 for details of the fitting algorithm. This has been developed over the past decade, and tried and proven in interlaboratory and blind industry checks over the past 10 years (e.g. Federowich et al., Can. Min. 33(1995) 469-480, show GeoPIXE accuracy of better than 3% in a published blind test).
PIXE/SXRF yield calculation, including secondary fluorescence and able to treat virtually unlimited multilayered targets. A special feature is that the yields of ALL X-ray lines are integrated through the layered structure so that the X-ray relative intensities accurately reflect the full target structure. This gives much better spectrum fits for complex samples.
SNIP background treatment (C.G. Ryan, E. Clayton, W.L. Griffin, S.H. Sie and D.R. Cousens, "SNIP, a Statistics Sensitive Background Treatment for the Quantitative Analysis of PIXE Spectra in Geoscience Applications", Nucl. Instr. Meth. B34 (1988), 396-402). Background shape can accommodate the effects of detector efficiency and filter absorption.
The PIXE/SXRF spectrum fit generates a Dynamic Analysis (DA) transform matrix. This enables the projection of EVT data (list-mode, or event-by-event data) directly onto quantitative elemental images. This process resolves element overlaps, strongly rejecting artifacts from overlapping elements and detector response effects (escape peaks, tails) and subtracts background. Pileups are well treated in many cases which involve a single dominant element or majors in fixed ratios. (A more general approach is under development.) The results are quantitative images in ppm.charge/flux units. Concentration variance images are also accumulated (at half resolution to minimize memory usage), so that error estimates and detection limits can be provided for all extracted concentration values and line profile projections, etc. The DA method is treated elsewhere (C.G. Ryan, D.N. Jamieson, C.L. Churms and J.V. Pilcher, "A New Method for On-Line True Elemental Imaging using PIXE and the Proton Microprobe", Nucl. Instr. Meth. B104 (1995), 157-165; C.G. Ryan, "Quantitative Trace Element Imaging using PIXE and the Nuclear Microprobe", International Journal of Imaging Systems and Technology (Special issue on Quantitative Imaging) 11, (2000) 219-230; C.G. Ryan, "Developments in Dynamic Analysis for Quantitative PIXE True Elemental Imaging", Nucl. Instr. Meth. B181 (2001) 170-179; C.G. Ryan and D.N. Jamieson, Nucl. Instr. Meth. B77 (1993) 203-214).
Direct interrogation of the images to extract concentration data from within arbitrary "regions", or projected along traverses or line projections. These include error estimates and detection limits.
"Regions" supported at present include, box (sizeable, rotatable, movable rectangle), circle, ellipse, 10-point spline curve, 32-point spline curve, line projection rectangle (sizeable, rotatable, movable, and with shear control). All can be positioned and moved, or changed in shape or orientation using "handles". If many image windows are opened, or cloned, to display many elements, then these regions will appear in the same place on all images. Clicking on a button will then extract average concentrations (and errors, MDLs) from within these areas (or projected along a centre line, in the case of line projection mode). These results are tabulated, and can be exported.
Spectra can be extracted from these regions, by sorting the EVT file, by simply pressing a button. The resulting spectra from these regions appear in a spectrum window, overlaid by the "fit" to each. This “fit” is estimated from the DA deduced concentration data and pure-element spectral signatures. This enables an immediate assessment of the quality of the images by looking at the accuracy of the "fit" to the extracted spectra. This can often show up a rare (concentrated in one spot) element that was missed from the initial inspection of the overall PIXE/SXRF spectrum, for example. Such omissions can be corrected, a new DA matrix generated, and the images re-projected. Extraction of spectra from other ADCs is also supported here.
GeoPIXE also supports sorting using energy cuts. Cuts are set-up and named interactively, and can also perform background subtraction during list-mode file processing.
A GUI interface (built on IDL) allowing interactive spectrum fitting, EVT sorting and image projection using Dynamic Analysis (or simple energy windows), and quantitative analysis of arbitrary regions and line projections of the images (all elements simultaneously). The windows are linked and communicate with each other, as outlined below.

Windows include:

IMAGE: Multielement image display (the main GeoPIXE window). Select the element with a droplist. Zoom in steps (in and out), pan using scroll bars (very fast, using fast graphics card features). Image operations (e.g. median filter, boxcar, Gaussian smooth, edge enhancement, ...). Arbitrary region selection (see below). Distance measurement. Colour map selection. Conc range min/max mapped onto colour map. Multiple IMAGE windows can be cloned and positioned at will over the screen. However, these remain linked, so that region selection is visible in all (used to display multiple elements). Menus select sort EVT window, spectrum window, image regions results window, image processing window, yield correction window, mineral end-member mapping window. Any number of these windows can be cloned for the display of multiple elements.
IMAGE OPERATIONS: A range of image operations for smoothing, etc. appear as a list so that these functions can be performed with a single click.
IMAGE HISTORY: A window that lists all image processing operations performed on a selected elemental image.
YIELD CORRECTION: A new method for pixel-by-pixel correction of images for the changing PIXE yields with changing sample composition across an image area can be performed very easily within this popup control panel. (See C.G. Ryan, "Quantitative Trace Element Imaging using PIXE and the Nuclear Microprobe", International Journal of Imaging Systems and Technology [Special issue on Quantitative Imaging] 11 (2000) 219-230).
END-MEMBER PROJECTION: An alternate function of the yield correction window, this projects element images onto a set of end-member composition images.
SORT EVT: Accepts parameters about the imaged area (scan size, pixel ranges, etc.), EVT file, mode (image, line traverse, stepping modes) and controls the sorting of the EVT file. You can sort using DA projection or using simple energy windows (with background subtraction, for PIGE, RBS, etc.). You don't need to specify the list of elements to sort for, as this comes with the DA matrix, straight from the PIXE/SXRF Fit fitting process.
IMAGE REGIONS: Lists the results of integration of images within regions in a table. These can be exported. Clicking on a row of results displays the corresponding region on all images for this data-set on the screen (and displays the corresponding extracted spectrum, if loaded). A droplist selects the display in the table of concentration, error estimates, MDL (99% confidence limits), relative error, and raw results. These can be save/restored to/from files. A button "EVT" on this window starts sorting the EVT file to extract all spectra from within these regions. These are saved to disk, and also popup in the open spectrum window. With these loaded, clicking on a row of results will select the corresponding spectrum in the spectrum window, and overlay it with the “fit” estimated from the concentrations and the pure-element spectral signatures.
SPECTRUM DISPLAY: Displays PIXE/SXRF spectra (also X,Y, line profiles, PIGE, RBS, ...). Can manipulate view, bump up and down, log/linear, and scroll through spectrum (very fast, using fast graphics card features). Set markers for line identification, selecting the fitting range, setting "cuts", energy calibration, etc. A "?" button brings up the X-ray line identification window. Menus select spectrum selection window, digital filters, sort EVT window, and the PIXE Fit window. There is also a growing list of import options.
XRAY IDENTIFICATION: Works in two modes: Line identification mode, uses a marker positioned on the spectrum to identify peaks. As you move this marker, the closest match in the line database is provided in the scrolling identification window, along with a number of lines on each side. The relative intensity threshold adjusts which lines are viewed. In mark element mode, the window transforms into a periodic table. Clicking on an element causes all lines for that element to be marked in the spectrum. You can optionally select K, L and M lines (all, separately or in combinations).
SPECTRUM SELECTION: A window to select which spectra are displayed and overlaid, and whether fit overlays are shown. You can also edit spectrum parameters in this table.
CALIBRATION: A popup window for spectrum energy calibration. Marked peaks can be specified as primary X-ray lines, escape peaks, or pileup, and selected by element names and droplists. An existing calibration can be extracted from another spectrum using a “Get” button.
X-RAY SPECTRUM FIT: Controls the fitting of the PIXE/SXRF spectrum. You select filters, yield calculation (which provides relative line intensities), detector parameter set, energy range (or this comes from spectrum display), optional cuts, background algorithm, and elements to fit. As elements are selected, you immediately see the zeroth-order initial estimate of these on the spectrum. Once the list is complete, press a button to fit the spectrum. The results can be displayed in the FIT RESULTS window. Another button will generate a DA matrix for image projection.
FIT RESULTS: An interactive table of results from spectrum fitting. You can view concentration, error estimates, MDL, as well as fit statistics, PIXE/SXRF yields and relative intensities, detector and filter parameters.
RESULT PROPERTIES: Properties of fitting results, such as filter, detector, or yield selection can be altered, or fluid inclusion geometry modeling performed.
X-RAY YIELD CALCULATION: A button on the X-ray spectrum Fit panel brings up the panel for PIXE/SXRF yield calculation. The calculation includes secondary fluorescence and is based on ECPSSR cross-sections. For SXRF, the calculations use the the recent compilations of sub-shell absorption cross-sections of Ebel ( H. Ebel et al., X-ray Spectrometry 32 (2003) 442.), the Coster-Kronig rates, fluorescence yields and branching ratios of Elam (W.T. Elam et al., Radiation Physics and Chemistry 63 (2002) 121) and an empirical treatment of scatter peaks. The yield calculation can accommodate any arbitrary layered target structure. The GUI panel enables 20 layers to be specified, with thickness in mg/cm2 or microns. Chemical formula can be specified, or entered as oxide components, with weightings in atomic fraction or weight %. There are also parameters to specify target rotation and tilt and detector angle, in and above the plane.
CUTS SETUP: A window that displays energy cuts for set-up or editing.
FILTER SETUP: A window for setting-up or editing filter definition files.
DETECTOR SETUP: A window for setting-up or editing filter definition files.
ASSOCIATION: A window to display element-element correlations between image pixel concentrations, treated as data points in multi-element space. There are tools to highlight regions of the spatial image corresponding to areas in element-element space, to extract spectra from these regions, and to limit the correlation to spatial regions in the image.
IMAGE RGB: A 24-bit colour window that displays three elements as the red, green and blue components of 24-bit colour.
BATCH SORT: Window to perform batch processing of list-mode files. It scans directory trees for list-mode files, builds directory trees with list-modes in each leaf, and provides an interface to edit parameters and monitor batch processing.
EXPORT SET-UP: A window to select options for export of data from GeoPIXE. Different versions of this window are used for export of images, spectra, traverses, fitted results as CGM, WMF, EPS, CSV tables for spreadsheet programs or to the printer.

Return to the main GeoPIXE page.
Go to the main CSIRO-GEMOC Nuclear Microprobe web page.

For further information contact: Dr. Chris Ryan via email: (Chris.Ryan@csiro.au)


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Please direct comments about this web page to Chris Ryan.

Graphics for these pages have been prepared using Amiga rendering and image processing software.