aXis 2000 - Analysis of X-ray Images and Spectra - Summary of changes

Contact Info

Adam P. Hitchcock

Canada Research Chair

in Materials Research
McMaster University
Hamilton, ON
Canada L8S 4M1
V: +1 905 525-9140
F: +1 905 521-2773



This version:   26 July 2015      Last version: 02 July 2015

New or modified routines (since 02 July 2015)

NB this version was compiled in IDL8.3 to enable hdf5 NeXus read-in
      from this point on there will be a pre-8.3 legacy version (Windows only) and the 8.3 version

axis_c - add STXM NeXus read-in (SLS, Bessy-2, Diamond)

axis_config_dir - NEW - save information about author and aXis2000 program

axis_ini - simplify. write axis_win.ini or axis_unix.ini depending on the operating system

axis_ini_save - write different files for Windows and Unix

axis2000 - use OS dependent default ini file names (axis_win.ini or axis_unix.ini); activate auto detection of code path

ax_nexus - NEW - widget to control rad-in of hdf5 NeXus format STXM data files

nexus_com NEW - common block used for read_nexus

read_nexus - NEW -routine to read data in hdf5 NeXus format (SLS, Diamond, Bessy..)

stack_process - correct error associated with XY-calibrate (changing size of stack data)

============= 26-Jul-15 from 02-Jul-2015 ===========

ax_sdf - add View i-ring get_details buttons, re-arrange layout

read_sdf - remove pixel-by-pixel ring current mormalization, improve user feedback

sdf_com - changes to common block

sdf_stack_cur - extracted from read_sdf to allow auto-compile before read_sdf is called

============= 02-Jul-15 from 15-Jan-2015 ===========

axis_c - processing links for reading Mistral TXM hdf5 files

axis_dialog - add buttons for reading Hdf5 TXM files (Alba)

ax_xycal - correct 1-point calibration / truncation system

read_txm_alba - single image and stack reader for Mistral TXM hdf5 files (new)

stack_process - apply correct (x,y) axes / scales to truncated stacks

stack_rotate - (x,y) axes / scales of rotated stack written correctly
                        alert user to stacks with non-square pixels; use avg. value

============= 15-Jan-2015 from 01 Dec 2014 ===========

axb_load - add keyword TITLE

ax_bin - get bin~energy to work correctly

ax_display_ptycho - new routine to display ptychography data from ALS BL 11.0.2

ax_display_ptycho_com - common block for ax_display_ptycho

ax_fix_rollover - add keyword, one, an option to process 1 file

axb_save - add no_aXis keyword to suppress loading result into aXis2000 buffer

ax_select - add no_axis keyword to allow use of ax_select outside of aXis2000

axis_c - fix image~warp, stacks~bin~energy, add ax_display_ptycho

img_warp - get 4-point warp aligning of 2-images to work properly

============= 01 Dec 2014 from 29 Oct 2014 ===========

axis_c - remove use of fpath (it is an IDL routine)

axis_ini_save - update informational text at bottom of axis.ini file; save path and last filename info

axis_ini - save path and last filename info

stack_process - write movie files reliably to defined path; allow spaces in path names;
                               remove all strcompress(/remove_all) calls which prevent strings for folder or filenames to contain blanks

read_sdf - read in ptycho STXM images

============= 29 Oct 2014 from 28 Jul 2014 ===========

axis_dialog - change spacing on X,Y,Z pixels to adapt to larger default Win7 font

ax_img_avg - corrected error - region - no zeros did not work correctly

read_sdf - compute map correctly for non-square pixel images

============= 28 Jul 2014 from 30 Jun 2014 ===========

(NB many files had headers updated to conform to IDL conventions for making a help file from the headers)

ax_ini_save - save last file name as well as path

ax_sdf - put normalization value on widget; start with last file loaded to gui if ax_sdf used last

axis_c - adapt scale bar to add xl, yl; add Axes switch to allow plotting without axes

axis_dialog - change display to remove tics & axis labels for 2d data in Axes = 0 mode - change xz_profile size

axis_ini - save last file name as well as path

parsestring - modify to read comma separated ascii files

plot2d - remove ticks & increase size of main window in Axes= 0 mode; adjust margins so side windows line up

plotbuf - add X-label on same line as scale bar length, when AXES = 0 (do not plot axes)

read_sdf - ensure stand alone operation works; variabilize the ring current normalization value

spc_load - modify to read comma separated ascii files

text_read1 - modify to read comma separated ascii files

zimba_run - start zstack_analyze independent of aXis2000 from stack list (*.sl) or binary stack (*.(dat,ncb))

================================== 30 Jun 2014 from 24 Apr 2014 ================

ax_clear - recover if logo_file cannot be found (e.g. if the CodePath is wrong)

ax_sdf - Browse function works even if start from a file or folder not present

axis_c - add convert to OD with line Io

axis_dialog - add convert to OD with line Io; update version; change stack_analyse to stack_process

read_sdf - corrected error introduced inDec-13 version (sdf_lastfile was defined with the '.hdr' extension)

stack_line_io - NEW - performs convert to OD with line Io

tif_to_ncb - NEW - generate an axis2ooo format stack from a set of tif files (for SSRL TXM tomography)

================================== 24 Apr 2014 from 14 Nov2013 ================

axis2000 - add @sdf_com - so now remembers last SDF file type

axis_c - add @sdf_com; correct command strings;  
               make histograms reals, so can smooth without loosing sparse image data

axis_dialog - get write_tif working; update version

ax_sdf - only display sdf_lastfile if it is a string ; make selector pick last file as default

make_tomo_list - output and write data to file

read_bessy_txm - add call to princeton_header_define

read_sdf - reversed change in what sdf_lastfile is - was main name; had changed to full (path, main * extension)
                      which ended up having the read_sdf widget displaying full version in the name box

stack_process -  rotate stack - correct x, y dimensions; check for existing name BEFORE completing stack write; add convert format~to axis binary from~ tif (to input stacks of tif files from ImageJ)

stack_wb - add OVERWRITE key word, to avoid dulpicated checks for overwriting

text_read1 - unsuccessful attempt to prevent crashes when reading text blocks without numerical characters

win2tif - get actual data and write as FLOAT

================================== 14 Nov 2013 from 01 Sep 2013 ================

axis_c - add stacks~tomography~ (generate stack of all data), add make_tomo_list

axis_dialog - add stacks~tomography~make tomo list

ax_angle_stack - generate full stack of all images

read_sdf -   sdf_lastfile, sdf_path defined in main routine; add keyword no_save ;
                       ignore request to normalize to ring current if beam current not defined or below a threshold

stack_rb - increased field size for indicating the E-range

================================== 01 Sep 2013 from 22-Jul-13 ===================

axis_c - add read_stacks~nsrrc_peem

axis_dialog - merge all write~graphics menu items

axis2000.pdf - updated help file (last one was Aug 2010)

contents.lst - updated list of all files (with a definition for each)

nsrrc_peem_com - (NEW) - common block for reading NSRCC PEEM stack files

read_nsrrc_peem - (NEW) - read in PEEM stack data (*.pem)

read_sdf - make number of stack file the default file name (no leading zeros)

stack_process - establish a correction for 2 identical energies (shift E(i) by 0.25*[E(i-1) -E (i-2)]
                               banner name now stack_process (stack_analyze refers to CJJ's GUI)

================================== 22-Jul-13 from 09-May-13 ==============================

ax_sdf - fix GTK bug (supplied by B. Watts)

axis2000 - adapt to Windows so it will work with IDL version 6.3; use internal routines for CodePath (supplied by B. Watts)

axis2000-batch - add axis standard header

axis_c - update for reading NSRRC SPEM files

axis_dialog - update for reading NSRRC SPEM files

file_overwrite - cleaned up

nsrrc_spem_com - (NEW) - common block for reading NSRCC SPEM files

read_nsrrc_spem - (NEW) - read in SPEM sample curent images & generate stack of 16-channel analyser data

read_nsrrc_spem_gui - (NEW) - widget for supplying parameters for reading NSRCC SPEM files

stack _wb - remove duplicate check for file overwrite

================================== 09-May-13 from 11-Mar-13 ==============================

ax_read_txrm - uses Java code (from Florian Meirer) to read in *.txrm files (Microsoft structured storage)

ax_read_txrm_stack - read in a stack of TXRM images (Xradia)

ax_rgb - remove scale bar (inaccurate)

axis_c - add TXRM image and stack readin

axis_dialog - dd TXRM image and stack readin; re-roder the Read menu to be strictly alphabetic

disp3col - add scale bar to RGB composites (but removed as code generates an inaccurate erorr bar)

stack_process - reduce recommended size of zoomed stacks

================================== 11-Mar-13 from 15-Jan-13 ==============================

gen_e - generate a list of energies from {start, step} file

tif_convert - modified to read in Saga-LS PEEM stacks

================================== 15-Jan-13 from 03-Feb-12 ==============================

ax_curvfit - display the header of the data with log

ax_file_load - implement automatic OD generation

ax_read_xas - add filename to label for 'xas' (NSLS) spectral format read-in

ax_regress_spectra - add header to log to track data

axb_load - get rid of NaN values when read image data

axis_c - clip numeric; add label in *.xas files ; add routines (stacks~rotate, read_Ptychography.Shapiro) ; correct label for calib

axis_dialog - add new routines (rotate stack, clip numerical, read ptychography)

clip - add numerical clipping

h5_read_ptycho - NEW - read Shapiro format pytchography output (HDF5) files (*.pt)

mbuf - position mbuf widget over calling widget

ptycho_select - NEW - widget to select among HDF5 entries (can generalize for any HDF5 file)

ptycho_select_com - common file for ptycho_select

read_h5_ptycho - reach in shapiro format HDF5 pytchography analysis output

read_xas_xrf_stack - allow user to generate '*.ssl' file

read_xrf_stack - correct error (with 'get_num')

spc_load - implement multi-column, read all columns; handle cases where file does not exist better

stack_process - solve problem of avg_image overwriting active buffer; preload filename with name of stack;
                                add stack name to label; default map (2-E); stop overwriting CurBuf when save map image

stack_rotate - NEW - rotates each image of a stack by an arbitrary user-defined angle

xas_xrf_extract - extracts absorption stacks from a 4-d array (*.ssb) & writes them as regular 3D stacks (*.ncb)

================================== 03-Feb-12 from 15-Dec-11 ==============================

ax_regress - add M correlate parameter

axis2000 - start up file modified to work on Macs (but hardwired to APH path)

img_warp - force plotting to be done on MainImg

ln_norm - add switchable normalization to the mean for the H, V lines (to use for pattern noise reduction)

================================== 15-Dec-11 from 24-Nov-11 ============================== - remove duplicate 'hist' label - handle images when all image is zero - rewrote algorithm to improve speed; add an hourglass symbol - correct method to work for all image sizes - rewrote algorithm to work properly; images meshed to finest scale prior to appending - correct method to distort (X,Y) axes in arbitrary ways - correct images~generate mask~manual to work for all image sizes - add energy value to result of 2d-normalization; make horizontal normalize preserve intensity

make_square - adapt to avoid error if there is only 1 x or y value - add hourglass for Oxford (Inca) stack read-in -adjust row / col values to IDL notation (0 to # - 1); add tooltips; add adjustable Path
                                   - preserve aspect ratio in the zoom

================================== 24-Nov-11 from 29-Oct-11 ============================== - add Images~Modify X,Y axes - update default info save (e.g. name of folder) - auto save without asking user unless folder or pre-existing ini file cannot be found

get_num - modify to add TITLE keyword; display '0' - improve reliability for *.sl stack list files in different formats

stack_rb - increased size of field to display stack size - uses fractional zooming for large stacks; selecting YIELD desensitizes OD;
                               read stacks from lists of *.axb as well as *.nc files; fractional zoom as defaults for large stacks

================================== 29-Oct-11 from 31-July-11 ============================== - new routine (derived from to bin single images (*.axb format) - change to default directory; read_bessy_TXM routines added - reads a stack of images from Bessy TXM - reads a single image from Bessy TXM - core routine to read the *spe (and associated *-positions.txt header file) images from Bessy TXM - add button to rotate the whole stack 90 degrees CW, CCW

================================== 31 July -11 from 17-May-11 ==============================

ax_angle_stack - change to read from a set of follders; add 'map' read function

axis_c - add read~spectra~alignment; bin (image, spectra) - add option to SUM; rationalize stacks~tomography;
               get working Read~spectra~NSLS~mapper' spectral files

axis_dialog - add read~spectra~alignment

read_sdf - remove obsolete 'read_bl5' ; converted map routine to use 1,2,3 (people) numbering of images
                   [ instead of 0,1,2,3 (IDL) ] so that the one_image and map image numbering protocols are the same

cryo_to_stxm, init_sd, read_bnl, read_bsp, read_mapper, read_csv, refresh, read_axm,
                 read_stxm, write_stxm, zstack_read_mapper
- changed init_stxm_sd to init_sd; standard header

sav_nsls - remove dead code

stack_process - remove 'wt_spec' (obsolete routine to read BL 7.0 STXM files) (all other stack_analyze versions)

================================== 17-May-11 from 19-Feb-11 ==============================

axis_c - changed default utilities~print to B/W and set up system to remember user selected size, color
               add images~remove lines~auto

ax_make_xyz - reads aXis2000 binary stack (*.dat, *.ncb) and writes data as ascii (x,y,z) tripets
                                  to allow import into other plot programs (SigmaPlot, Origin, etc)

ax_svd - re-activated query to user for global limits on component maps (force non-negativity)

read_xrf_img - improved auto reading of XRF elemental maps written by Oxford Inca softwawre
                          by automatically identifying the row/column limits of rectangular maps

remove_lines - new routine to auto-identify a line strongly deviating from others and automatically replace it
                           with average of 2 adjacent lines (needed due to many drpped lines in present 5321 data)

stack_process - add button to remove bad lines

================================== 19-Feb-11 from 03-Feb-11 ==============================

ax_mesh - OOPS - screwed up this code change & had to redo

read_sdf - corrected I-ring normalization to work with changed format (Nov10) of line in the *.hdr file

================================== 03-Feb-11 from 03-Oct-10 ==============================

axb_load - display only short filename (no path) in axis log

axis_c - remove link to Jacobsen's stack_analyze (& display message it can be run from VM directly)
              NB from Sep 2008 to this version, cannot read or write *.nc files due to conflict with stack_analyze
           - change Utilities~Calculate X-ray parameters (SF) to default to transmission and to compute OD at end

axis_dialog - add stacks~change mesh or size; update versioon

ax_image_append - ensure energy is included in output files

ax_img_del - enlarge small images and reduce large images prior to deletion  
                     (can now delete regions from images larger than the display window size)

ax_mesh - ensure energy is included in output files

ax_rgb_map, ax_rgb_com - add option to force all pixels with values > upper limit to be black

ax_select, ax_select_com - add newe buttos to allow saving of ROI_file or the mask image independently

gen_aa_string - corrected @axis-com to @axis_com

read_sdf - stack read-in - interpolate to square pixels

stack_mesh - new routine to modify mesh (same total image size) or modify image size (same pixel size)
                 NB this is useful if one wants to add or append stacks of same area but slightly different pixelation

stack_process - display Io from files; starts with image intensities rescaled at each image

stack_rb - corrected error introduced in Feb-10 - would not read files written by stack_wb if used integer scale factor

================================== 03-Oct-10 from 24-Jul-10 ==============================

read_XRF_stack - correct read-in of single energy STMX_contol XRF stacks

================================== 24-Jul-10 from 21-Jun-10 ==============================

aa_writeconfig - write configuration of Amino Acid spectra look-up (XSpecSim)

averageval - interpolate spectral data (XSpecSim)

ax_bin - add bin~energy - improve statistics by reducing number of energy points

ax_sdf - correct code errors found by compiling in IDL 7.1

axis_c - incorporate XSpecSim files into aXis2000; extend capabilities to read XRF data (hdf5, re-organized dialog)

axis_dialog - add read_ascii_img - 2d text image; add XRF-map readin for APS and CLS XRF systems; bin~energy

axis_log - fix code errors found by compiling in IDL 7.1

despike - add into package (CJJ routine to remove extrema from mages, called in zstack_analyze)

extrapolateaa - extrarpolate spectral data (XSpecSim)

genextrap - extrarpolate spectral data (XSpecSim)

parsecomposition - determine elemental composition from AA codes (XSpecSim)

pickfile2 - accomodate calls where defpath is not defined

read_aa_header - read AA spectral file header (XSpecSim)

read_aadata - read AA spectral file (XSpecSim)

read_dm_datacube - update to read in stack parameters from *.txt file written in export from Digital Micrograph

read_energies - read energies from an *.enf file (XSpecSim)

read_lox - get and display energy of image files

read_xrf_spectra - adapted to read hdf files written by XGLabs; fixed errors in read-in of *.dta spectra

read_xrf_stack_hdf5 - reads XGLabs XRF maps

region_analyze - region analysis - using single peaks in spectral domain to identify spatial regions (R. Coulombe)

rstack_analyze - Remy Coulombe version of stack_analyze - most of this is out-dated

sav_aa - sav peptide spectrum generated by X-ray spectral simulator (XSpecSim)

sfconvert - close header definition

stack_fit - fix code errors found by compiling in IDL 7.1

stack_process - update energies in filename_ev_msec list when use E_cal function; replot spectra;
                            - provide direct display without reading *.ncb file (use if stack in memory)

stack_rb - correctly read in stacks written as REALS (not scaled integers)

stack_wb - coreectly write stacks as REALS (-ve scale parameter indicates data is REAL)

write_cts - fixed errors in filename generation

xspecsim - X-ray spectral simulator (XSpecSim)

xspecsim_com - common for X-ray spectral simulator (XSpecSim)

xspecsim_init - initialization of energies and data files for X-ray spectral simulator (XSpecSim)

xspecsim_run - start file for X-ray spectral simulator (XSpecSim)

================================== 21-Jun-10 from (27-Mar-10) ==============================

ax_clear - resets to default color table right after logo loaded so do not need to select a buffer before executing a command for which the tesult is color table sensitivel

pickfile2 - remove 'forcing extension' warning

read_sdf - add no_display option

read_ascii_img - reads image files which are (x,y) ascii data without header

read_APS_xrf_maps - read XRF maps from APS XRF microscopes

read_cls_sgm_srf - read XRF excitation spectra fro CLS SGM beamline

read_xas_xrf_stack - read STXM_control format 4-d stack (XRF at each pixel of a normal stack)

read_xrf_img - improved - deal with situation when Amptek *.mca file does not have calibration info

stack2_rb - reads a 4d data set (XRF stack of stacks) - under development

stack2_wb - writes a 4d data set (XRF stack of stacks) - under development

xas_xrf_extract - extracts absorption stacks from a 4-d array (*.ssb) written by XAS_XRF_STACK and writes them as regular 3D stacks (*.ncb)

xrf_com - common block for xrf_map_selector

xrf_map_selector - used with read_APS_xrf_maps to select maps for each aXis2000 buffer

================================== 27-Mar-10 from (21-feb-10) ============================== - added parameters related to XRD (Inca maps) - enable read-in of multiple *.tsv files - correct for error on missing data tags - reads in stacks written by Gatan Digital Micrograph EELS software - trim to non-zero parts of Inca maps - allow read-in of fill 8095 XRF spectra; - adapt to XRF map files written by STXM_Control from XGLabs data - remove keyword axis in call for ax_sort_mono - converts an aXis binary stack to set of ascii spectra (*.cts) ; suitable for input to PyMCA

================================== 21-Feb-10 from (03-Aug-09) ============================== - changed name to avoid conflict with same common block inside stack_analyze.sav (CJJ) - correct syntax error on include common - correct number of channels in print tag - extend to up to 16 spectra (needed for XRF fitting) - (IDL file - modified its internal common block to avoid conflict) - NEW - converts {*.dta} to (*.cts) and an axis *.ncb XRF stack - NEW - reads interferometer positions and shifts to make a more accurate image (not yet in aXis2000) - ADDED (Twinmic XRF &Transmisison read-in; spectra fix_rollover; grouped power commands in image & spectra; EELS-MSA read-in; XRF (Amtek, XGLabs, Inca) spectra and stacks; DM_datacube readin (GIF EELS stack) - added buttons for new XRF-related read-in and conversions - removed axis_ini_save code to obey IDL 7.x conventions - isolated from to obey IDL 7.x conventions - changed axis_ini_save call from procedure to a function - removed embedded code to obey IDL 7.x conventions - updated to add Elettra, SSRL names and links - isolated from to obey IDL 7.x conventions - corrected read_png for correct orientation and color - isolated from to obey IDL 7.x conventions - NEW - reads in Twinmic format image or spectra - commented out all lines calling a routine '' - isolated from to obey IDL 7.x conventions - fix group ID problem - isolated \from LOADSPEM.PRO to obey IDL 7.x conventions - NEW - read in EELS datacube (exported *.raw file from Gatan Digital Micrograph) and convert to aXis2000 *.ncb binary stack format - add region name to label - NEW reads in XRF images from Twinmic STXM; Inca (Oxford SDD) or Tescan SEM - NEW reads in XGLabs X-ray fluorescence spectra - NEW - read is XRF stack written by STXM_control (*.xrf) or by Oxford Inca (*.raw, *.rpl) files - name changed from sav-hdf (hyphens not allowed) - added read in for EMSA/MSA EELS spectral files (1-column); Amptek (*.mca) and XGLabs (*.dta) XRF spectral - add /silent keyword - check for different numbers of images in the 2 stacks - replace @aligncom with @stack_process_align_com to remove name conflict with same common block inside stack_analyze.sav (CJJ) - filename_ev_list problem fixed - add spatial scale calibration (x-axis - full range) - changed name to remove conflict with stack_align_common in stack_analyze.sav - adapt to reading in stacks written as reals - add real option (for high dynamic range data such as TEM-EELS); add over write protection for *.dat ; add hourglass for large stacks - removed embedded code to obey IDL 7.x conventions - isolated from to obey IDL 7.x conventions - REMOVED axis_com common - changed write_gif procedure to ax_write_gif procedure to work-around the conflict of the named write_gif_common common block in IDL's with that embedded in stack_analyze.sav (CJJ)

================================== 03-Aug-09 from (07-Mar-09) ============================== - changed analcom to stack_process_com (update to stack_process) - changed analcom to stack_process_com (update to stack_process) - add additional paramaters (ScanType, Energy) to GUI widget; i-ring normalization - add stack name to component map; remove 'clip at limits' option; re-arrange menu - add stack name to component map; remove 'clip at limits' option; re-arrange menu - changed analcom to stack_process_com (update to stack_process) - changed analcom to stack_process_com (update to stack_process) - changed analcom to stack_process_com (update to stack_process) - change normalization current to 500 mA (ALS) - improve alphabetization of some menus - changed analcom to stack_process_com (update to stack_process) - write out files if use stretch-shift with different tag (path problem before) - correct error in reading png format files - changed analcom to stack_process_com (update to stack_process) - changed analcom to stack_process_com (update to stack_process) - fixed code error (xsize, ysize) - changed analcom to stack_process_com (update to stack_process) - fix loss-of-energy scale problem (wrong common block)
                            add ScanType and other information from parameter file; i-ring normalization - changed analcom to stack_process_com (update to stack_process) - change sdf_normalize so it adapts to changes in norm_value - changed to short file name feedback (no path) - changed analcom to stack_process_com (update to stack_process) - changed analcom to stack_process_com (update to stack_process) - corrected a problem with filename_ev_list array indices - add stack name to component map; remove 'clip at limits' option; re-arrange menu - changed analcom to stack_process_com (update to stack_process) - auto-transfer name of roi to name of output - changed analcom to stack_process_com (update to stack_process) - changed analcom to stack_process_com (update to stack_process) - changed analcom to stack_process_com (update to stack_process) - changed analcom to stack_process_com (update to stack_process)

zstack_(align, analyze, buildlist, display, plot, profile, readlist, save, spectra, tune).pro
                     - extract all common to external files; change alog10 to alog when computing OD

================================== 07-Mar-09 from (29-dec-08) ============================== - used longer version from later CJJ - modified towork with IDL5.2 (switch) - modified to work with stxm filenames containing letters - allow access to olf CJJ alignment routine (select read_alignment, then cancel) - add read~stacks~(FTIR, PEEM) PEEM routine same as stacks~convert format~peem - add routine to interpolate images using interferometer (x_pos, y_pos) values saved by STXM_control - add xy_correct_flag to identify if interferometric correction is valid - differentiate a stack (option for FTIR stack processing) -(new) routine to change requested (x,y) co-ordinates to interferometric (x,y) co-ordinates for a single image - replace read_mapper with zstack_read_mapper to allow correct reading of all types of *.aln formatted files

zstack_(align, analyze, buildlist, display, plot, profile, readlist, save, spectra, tune).pro - introduce @zstack_common - add binary_filename (to allow auto generation of align file name)

================================== 29-dec-08 from (17-Sep-08) ==============================

axis2000.pdf - updated help file

ax_read_roi - puts ROI image in the current buffer (not buffer 0)

read_ftir - (new) converts FTIR maps (Thermo ver 7) to ncb binary stack files

stack_process - checks for overwrite when writing any type of output

spc_save - remove duplication of overwrite check

read_bessy_stack, read_bessy_stxm, read_bessy_xml - (new) - read in data from old Bessy STXM

ax_name - adapt to work with names containing '.'s

================================== 17-Sep-08 from (15-jun-08) ==============================

tif_convert - allow read in without ring current normalization

read_peem3 - remove ring current normalization if ring current less than 1 mA or absent

stack_analyze.sav - add Jacobsen version (Version 2.6.1, Dec. 9, 2005) - use directly if only have VM

pca_gui.sav - update to Version 1.1.1, Dec. 9, 2005

stack_process - new name for aXis2000 version (old stack_analyze); add check for file overwrite

many files (stack_xx, ax_svd, ax_pc, ax_tomo_read, ax_pol_map, ax_cgo, ax_slicer3, stack_rb, stack_wb) - convert common block name from analcom to stack_process_com to differentiate from analcom block in Jacobsen's stack_analyze.sav

================================== 15-jun-08 from (20-Apr-08) ==============================

axdeltamin - new routine to find minimum spacing between adjacent points in an array

axis_c - add multi-column writing of multiple spectra (over the range displayed) using write~xas single/multiple

ax_write_xas, write_xas - modified to perform multi-column format writes

read_lox- modified to read binned images correctly

plot_buf - now ignores NaN and infnities, so one can visualize spectra or images even when there are divide-by zero errors

================================== 20-Apr-08 from (01-feb-08) ==============================

axis2000 - startup file now auto direct to c:\axis2000 folder in codePath not found

stack_append - isolated form aXis2000 - NB need to preview the first stack for it to work

stack_analyze - overwrite protection implemented for saving spectra; saved in aXis format ( retired)

Zimba package (all files) - modified to have fixxed GUI size on non-windows operating systems (allows use on MacOS)

================================== 01-Feb-08 from (29-Dec-07) ==============================

spectra~convert to. (OD, OD1, IP) - convert to OD   - now uses interpolation so energy spacing in I, Io can differ
                                                                 convert to OD1 - converts spectrum to absolute linear absorbance for 1 nm

================================== 29-Dec-07 from (11-Dec-07) ==============================

stacks~RGB color composite map - new widget (ax_RBG_map) to generate RGB composites with more control
                                                                     (CAUTION: does not work in VM version or pre-IDL 6.3)

images~generate mask~threshold - new widget (ax_select) with lower/upper bounds and more control 
                                                                     (CAUTION: does not work in VM version or pre-IDL 6.3)

ax_histogram - segregated from main routine and corrected

cw_rslider - introduced from IDL share site (Thomas Döring 6/1/2007) - allows lower/upper bounds and move window

plotbuf - removed date/time from the label

================================== 11-Dec-07 from (13-Sep-07) =================================

Remove_zeros - hot and cold spot removal implemented (called from stack_analyse)

Stacks~bin~(*.ncb, lox) - Lox (CLS PEEM) stack files can be read in, binned, and written as *.ncb files

================================== 13-Sep-07 from (01-Jun-07) =================================

Read_peem3 - improve readin routine & adapt to further changes in data format

ax_cimage - clean up images by removing very low and very high values. (from A. Scholl)

================================== 01-Jun-07 from (14-May-07) =================================

Stacks~statistical analysis~pca_gui - Jacobsen's PCA routine accessed as a sav file
                                    - manual at

Read STXM (sdf) - selected images from any channel (bug fix)

Utilities~Write image ascii - corected to write axis images as text not binary (bug fix)

stacks~maps~polarization fit - default values improved
spectra~Curve fit~polarization fit - default values improved

================================== 14-May-07 from (23-Jan-07) =================================

Utilities~compute peptide spectra - new routine to predict peptide and protein spectra from sequences

Read~images~PEEM~ALS PEEM3 - corrected for evolution on file format

Stacks~map~polfit - access to convergence properties added

================= 23-Jan-07 (from 05-Dec-06) ========================================

Linescans~Locate Line - working for SDF files

Stack_analyze (viewer) - multiply by constant, image
                                            - write out inmages in axis format (correct error)

Read~images~PEEM~ALS PEEM3 - new data format for ALS PEEM (on PEEM-2 and PEEM-3)

Stacks~convert format~PEEM - reads new data format for ALS PEEM (on PEEM-2 and PEEM-3)

Read_lox - errors fixed

Spectra~ convert _to_BE - error fixed

================= 05-Dec-06 (from 12-Nov-06) ========================================

axis_dialog - screen scroll set to be implemented only in Windows version (Linux compatibility)

============== 12-Nov-06 (from 10-Oct--06) ===============================
- set user selected ROI to 1, all other pixels =0

images~generate_mask~threshold - set all pixels > user-defined threshold to 1, all other pixels =0 (old code)

stacks~append - append (combine) two stacks

stack_analyze - modified to add ratio~constant - gain adjustment of the z-scale of the stack



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