file: CONTENTS.LST (aph: 30-Aug-20113)

DIRECTORIES		Content 
(NB only AAData, sfdata and logo are in aXsi2000.zip)
*************************************************************
AAData     files of amino acid spectra used by spectral predictor (XSpecSim)
logo		files for aXis2000 logo
sfdata	paramaters to calculate X-ray absorption quantities
***************************************************************
in aXis-doc folder   [not in axis2000.zip]
axis.doc			Word documentation file (source of AXIS.PDF help file) 
\PASS-test-data		example of every data type supported by AXIS 2000
\tutorial			systematic procedures for data analysis

FILE			                 Content
*************************************************************
aa_writeconfig.pro	XSpecSim - write configuration of amino acid files
align.pro			Jacobsen align procedure (for stacks) (CJJ)
als2ncdf.pro		converts ALS format image files to netCDF
als_specin.pro		ALS spectral readin procedure (derived from XAS1)
als_spectra.pro		widget to read in ALS spectra
aph-3dcolor-slicer.txt 	script to convert set of tif's to input to IDL slicer
averageval.pro		averages adjacent data values (convert_to_OD1) (JSO)
ax_angle_stack.pro	generate an angle-stack(tomo) from list of stack folder
ax_bin.pro			bins (2x2 to 1, etc) NetCDF formatfiles (stack smoothing)
ax_binf.pro			bins aXis2000 images (*.axb) (used in Bessy TXM readin) 
ax_cgo.pro			component maps from conjugate gradient optimization fits 
ax_cimage.pro		Cleans up high / low extrema values
ax_clear.pro		clear buffers (current, all, selected)
ax_color.pro		set color tables for independent image/spectra colors
ax_colorbar.pro		Fanning colorbar generator (not object)
ax_conv.pro			convert 1 or a sequence of ALS images to NetCDF format
ax_conv_all.pro		convert "ALL" time-of-flight files to axis binary images
ax_copy.pro			copy data among buffers using ThumbNails for selection
ax_curvfit.pro		curve fit spectrum using CG_OPTIMIZE (STAND ALONE)
ax_deltamin.pro		finds smallest spacing in an array
ax_file_load.pro		widget to select columns of a multi-column ascii file 
                       to read via spc_load
ax_file_protect.pro	routine to check for file overwrite and prompt user if needed
ax_fix_rollover.pro	fix sign/unsigned roll-over from CCD images (ALS peem related problem)
ax_gen_stack.pro		make angle-stack from data in set of folders (tomography data read in)
ax_header_template.pro template for html-oriented standard IDL pro documentation
ax_histogram.pro		generate histoggram of an image
ax_image_add.pro		add two images with matching on (x,y) scales
ax_image_append.pro	append two images with averaging in overlapping (x,y) scales
ax_img_avg.pro		computes mean and standard deviation of user-selected regions
ax_img_del.pro		replace pixels in user-selected region with fixed value
ax_img_line.pro		replaces a user-selected line with another line (default avg adjacent)
ax_imscl.pro		rescale image Z to truncated color table
                        [ax_low_color_index,ax_top_color_index]
ax_interp.pro		re-mesh images or spectra to user specified spacing
ax_load_logo.pro		loads aXis2000 rotating globe/web link access
ax_lox.pro			widget to read in LOX format files (CLS-PEEM)
ax_macro.pro		executes a script of aXis2000 commands
ax_make_html.pro		makes aXis2000 programming manual as an html web document
ax_make_xyz.pro		convert aXis2000 stack to set of (x.y.z) triplets (export format)
ax_mesh.pro			mesh an image to the (x,y) values of another image
ax_name.pro			parse arbitrary filename into path, main, and extension
ax_nc2gif.pro		convert *.nc files to *.gif files
ax_one_pt.pro		delete or add a single point in a spectrum or image
ax_order.pro		enforce increasing x, increasing y ordering of image axes
ax_par_load.pro		load path and names of reference spectral files 
				  (maps, linefits, spectral fits)
ax_par_save.pro		save path and names of reference spectral files 
				  (maps, linefits, spectral fits)
ax_particles.pro		particle size & distribution analyser
ax_pc.pro			principal component analysis of image sequences
ax_peem_com.pro		common block for ALS PEEM read-in
ax_peem_read.pro		widget to read in one or a sequence of ALS PEEM files
ax_pickcolor.pro		adjust color table for hard spectral colors etc (CGZ)
ax_pol_fit.pro		fits an angle dependent signal to determine 
					dichroic angle, constant and magnitude
ax_pol_map.pro		fits a polarization stack to optimize angle and magnitude
ax_prof_rad.pro		radial profile generator
ax_rd_im.pro		converts 1 or a series of ALS images to NetCDF format
ax_read_roi.pro		read ROI data and generate corresponding mask image
ax_read_xas.pro		read CJJ *.xas format, reference spectra files (idl_X1)
ax_regress_spectra.pro	performs linear regression (with constant) on spectra
ax_rgb.pro			generates RGB composite color maps from 3Oimages
ax_rgb_com.pro		common block for ax_rgb
ax_rgb_map.pro		widget to display and manipulate RGB color composite maps (incomplete!)
ax_rgb_widget.pro		flexible RGB color composite maps(lower, upper limits selectable)
ax_rotate.pro		rotate images
ax_sdf.pro			widget to read in self defining format (BL 5.3.2)
ax_select.pro		manually select regions of an image from which to make an ROI file
ax_select_com.pro		common block for ax_select.pro
ax_sep.pro			determines appropriate sub-directory separator for the operating system
ax_shift_all.pro		uses ax_shift_image to rotate and resize a set of images
ax_shift_image.pro	rotate, calibrate and resize an image (part of 3-d chemical map suite)
ax_show_cindex.pro	display color table (CGZ, Fanning)
ax_slicer3.pro		read binary stack into slicer3
ax_sort_mono.pro		sorts (x,y) data sets and forces monotonic (required for INTERPOL)
ax_sort_names.pro		sorts filenames for orderly listing, from various file formats
ax_spec_delete.pro	deletes all data points in a 1-d data set, between user selected limits
ax_strmid.pro		extracts an intermediate part of a string deifned by 2 other strings
ax_stxm4nc.pro		converts NSLS STXM IV image files to *.NC files
ax_svd.pro			singular value decompostion of image sets (STAND-ALONE also)
ax_svd_spectra.pro	performs SVD on a spectrum - NB incomplete as of 20-feb-05
ax_switch.pro		switch buffer viewed on MainImg window using Thumbnail selector
ax_tomo_read.pro		prepares STXM532 tomography files - groups images for different angles
ax_txm_read_demo.pro	trial code to use java to read in Xradia txm data files
ax_wait.pro			turn on or off (/off) the Hourglass cursor
ax_write_gif.pro		writes gif files- IDL code embedded in aXis2000 set
ax_write_xas.pro		write CJJ *.xas format, ref. spectra files (idl_X1) - one or multiple col
ax_xrf_convert.pro	converts XRF {*.dta} files (from XGLabs to *.cts (for PyMCA) and *.ncb
ax_xy_correct.pro		replace requested (x,y) positions with interferometric (x,y) positions
ax_xycal.pro		calibrates image (x,y) scales (1 or 2 points)
ax_xydis.pro		distorts pixel sizes (for Mephisto)
ax_xyscl.pro		sets (x,y) scales of images (same pixels)
ax_zoom_cursor.pro	zoom images within user selected box cursor
ax_zoom_cut.pro		extracts component of an image within user selected box cursor
ax_zoom_pan.pro		pan zooming (adapted from IDL zoom pro)
axb_load.pro		load binary AXIS file
axb_save.pro		save binary AXIS file
aXis2000.ico		Windows icon file for aXis2000 (courtesy Martin Obst)
axis2000.pdf		Adobe portable data format version of manual
aXis2000.prj		project file to build aXis200.sav (IDL6.1 VM version)
axis2000.pro		starting file for aXis2000
aXis2000.sav		SAV file for Virtual Machine use (post IDL6.0)
aXis2000.zip		ZIP file of full code
aXis2000_batch.pro	batch file to execute aXis2000 (for IDL auto start-up)
axis2000_batch_macos.pro   batch file to execute aXis2000 in MAc-OS (unix) operating system
aXis2000_batchs.pro	batch file to execute aXis2000 with spinning logo
axis.bmp			old logo for AXIS (static)
axis.ini			default initialization file (adapt to your system)
axis_add.pro		add two spectra
axis_app.pro		append two spectra
axis_c.pro			MAIN code - menu processing for widget
axis_com.pro		common block for AXIS routines
axis_default.ini		default ini file (for which op sys ?)
axis_dialog.pro		menu dialog (extracted from axis_c)
axis_ini.pro		processes initialization procedure (read-in default parameters)
axis_ini_save.pro		reads and writes default values of paramters from axis.ini
axis_log.pro		writes log of all events (under development)
axis_macos.ini		ini file for Macintosh operating system
axis_options.prc		IDL 5.2 widget GUI builder file for axis_options.pro
axis_options.pro		IDL 5.2 widget to set content of default file
axis_options_eventcb	event processing for axis_options.pro
axis_peem_update.pro	part of axis_peem read in widget
axis_programs.html	html programming documentation file
axis_read_image.pro	reads in a variety of image file types identified by extension
axis_start.prc		GUI panel for start-up dialog - select: AXIS, ZIMBA_STACK, IDL.
axis_start.pro		start-up dialog - select: AXIS, ZIMBA_STACK, IDL.
axis_start_eventcb.pro	even processing for axis_start, start-up dialog
axis_sub.pro		aXis200 start-up through axis_compile
axis_web.pro		manages web links to X-ray microscopy sites
axis_windows.ini		ini file for Windows Op. Sys.
axis-default.ini		default ini file for Windows
axis-MacOS-071002.ini	 possible ini file for MacOS
axis-macOS-safari.ini 	ini file for safari version of Mac-OS
blbl_upd.pro		update label of buffers (separated from thumblbls, Feb2010)
bmp_to_ncb.pro		convert sequence of *.BMP files to binary stack file
bnl_load.pro		load Brookhaven images (ascii format)
box.pro			draws rubber-band boxes (adpated from idl library !!)
box_cursor.pro		corrected (IDL 5.03) version of box_cursor (used by zstack)
bsif_com.pro		common block for BSIF file format
bsif_common.pro		long_name form of common block for BSIF file format
buffer.pro			widget to select 1 buffer
bx_cursor.pro		box cursor for graphical zoom (adapted idl)
capers-scale.pro		set (x,y) scale of CaPeRS (Lox) images
catch_err_example.pro  	TEST program to learn how to use CATCH procedure to trap out IDL error 
                      	messages so can display in aXis2000 log area (not working as of Feb-2010)
catch_error.pro		get IDL run time error message for adding to axis log (NOT WORKING)
cbar-test.pro		color_bar object code
cg_optimize.pro		curve fit using conjugate gradient method (B.Loo)
chkfileblocks.pro		utility to parse multi-block ascii files (JDD, ER)
cimage.pro			replaces extrema (hi, lo) with local averag (A. Scholl)
cindex.pro			view color definitions (Fanning)
clean.pro			routine for Fourier filtering to remove noise (from SGU)
clip.pro			clip images based on user selected intensity range
colorbar.pro		colorbar generator (Fanning code)
contents.lst		this file (list of ALL files in AXIS package)
convert_princeton_header.pro  acceses instrument parameters for Bessy TXM images
copy_bytes.pro		utility for BSIF files
cryo_to_stxm.pro		converts NSLS X1A cryostxm files to old-style stxm (*.nc) (CJJ)
csv.prj			project to make read_csv.pro  (testing IDL 7 version project syntax ??)
cw_rslider.pro		complex widget for  slider with lowe  & hiset points (T. Doering, Jun 2007)
deglitch.pro		deglitch image files by replacing out-of-bounds with local avg (SC)
despike.pro			remove extreme points (spikes) (CJJ)
dindex.pro			converts (x,y) values to closest (i,j) index in images
disp3col.pro		generate RGB composite image, with optional bytescaling
distance.pro		compute distance from 2 co-ordinates
edgegauss.pro		Gaussian edge filter (for stack_align) (CJJ)
elements.dat		file listing element codes for Henke calculations (BL)
en2wvlen.pro		energy to wavelength conversion (Loo)
extrapolateaa.pro		interpolate spectra (specific to XSpecSim)
file2string.pro		(Billy Loo) routine used by SF procedure (Henke)
file.pro			ALS file input routines (text_read, etc)
file_overwrite.pro	handles user dialog and outcome if file exists on a write
filetype_p3b.pro		identifies PEEM3 file type (AS)
GdiPlus.dll			Microsoft graphics driver used by XimageViewer
gen_aa_string.pro		generates AA sequence string for XSpecSim (protein spectral predictor)
gen_read.pro		(Billy Loo) routine used by SF procedure (Henke)
genextrap.pro		extrapolate to match SF (convert_To_OD1) (XSpecSim - JSO)
get_num.pro			widget to input number
get_path.pro		determine correct path for a file
get_text.pro		widget to input text string
Gifinfo.exe			provide information about Gif files (e.g multi-GIF)
h5_read_ptycho.pro	read in ptychography output in HDF5 (data format of Shapiro, Nov 2012) 
idl_startup.pro		loads axis_start.pro (get around system dependent idl @ problems)
idl_version.pro		queries and returns the version ID of the IDL code in use
idlspawn			IDL PIF to allow passing commands to op. sys.
img_algn.pro		aligns image at 1 or 2 points (pre-processing for stacks)
img_asav.pro		saving alignment shifts from image_align processing
img_com.pro			image display common (ER for SPEM images ??)
img_load.pro		loads bmp, gif, tif files
img_warp.pro		use IDL warp routine to align non-linear distorted images
info.pro			reports information about an XPS file (ALS=SPEM)
ini_test.pro		test routine to check ini file functions
init_sd.pro			initialization for BSIF files (X1A files)
install.txt			information on how to install and run AXIS
interp.pro			interpolation routine to set meshing of images & spectra
interspline.pro		interpolation by spline fitting (from JDD math.pro - may not be used)
irmap_load.pro		converts FTIR maps as set of csv spectra files to *.ncb stack,
				     using *.map parameters (hand written) - not in aXis2000 widget
isnumber.pro		checksif a string is a number (ER, separated from file.pro, Aug2009)
join_string.pro		(Billy Loo) utility for SF
jpg_to_ncb.pro		converts set of jpg files to a stack (*.nb)
length.pro			determines difference of 1st and last points in an array (XSpecSim, jso)
line_fit.pro		fits spectra at each point along line - linescan stack-fit
lineclear.pro		erase lines on MainImage
litho_read.pro		read *.xyt format files
litho_save.pro		write *.xyt format files (pattern generation)
ln_add.pro			adding sets of horizontal or vertical lines from images or linescans
ln_align.pro		aligns linescans using a user-defined straight or curved line
ln_load.pro			read in ALS linescan file
ln_locat.pro		plots position of linescan on a displayed image
ln_norm.pro			normalizes a linescan file to Io stored in an AXIs buffer
ln_subsp.pro		subtracts a spectrum from each line of a linescan
load_nex.pro		reads in SPEM sample current NEXAFS spectra
load_spm.pro		reads in SPEM XPS images using loadspem
load_ssv.pro		reads Twinmic STXM image or spectrum file
loadspem.pro		engine for load_spm
look.pro			routine to display XM1 files (ALS TXM)
lox_com.pro			common blocks for Lox format read-in and manipultion
make_square.pro		forces image to have square pixels - interpolates if needed
math.pro			ALS math routines
mbuf.pro			widget to select multiple buffers
mcf_com.pro			common block for AX_FILE_LOAD read-in widget
meter.pro			meter widget - attempt to generate a progress bar(unused)
meter_eventcb.pro		eventcall back for the meter widget
misc.pro			ALS miscellaneous routines (GET_RANGE etc)
multigif.exe		file to generate single file with multiple GIF format images
ncb_to_mpg.pro		convert ncp file to an MPEG via Xinteranimate (GAJ)
ncdf2als.pro		converts 1 or a list of NetCDF files to ALS ascii files (for exchange)
nsrrc_peem_com.pro	common file (include) for NSRRC PEEM stack read-in
nsrrc_spem_com.pro	common file (include) for NSRRC SPEM 16-channel image read-in
obsolete-code.txt		list of obsolete files (in axis-dev\old_code) started Jul-11
parse_sdf.pro		convert string of a structure into a structure (SDF format readin)
parsebytes.pro		(ALS-ER) utility for SPEM readin
parsecomposition.pro	determine number of each element from amino acid string (XSpecSim)
parsestring.pro		(ALS-ER) utility for SPEM readin
pca_gui.sav          	Jacobsen multivariate statistical analysis (PCA, target) (CJJ 17-Sep-08)
PEEMVision.sav		PEEM data processing routine (A. Scholl, Jan 2007 version)
pem_load.pro		read ALS PEEM NEXAFS spectra
photon_conv.pro		(Billy Loo) utility for SF
pickfile2.pro		file selection utility (uses IDL 4.0's pickfile routine
					(replaced by DIALOG_PICKFILE post-IDL 5.2; but still used)
plot2d.pro			ALS 2d plot routine
plot3d.pro			ALS 3d plot routine (not used currently)
plotbuf.pro			routines to plot a single AXIS buffer (of any type of data)
plotsect.pro		plots multiple section data where x-values are repeated (non single valued)
princeton_header_define.pro  defines structure of header for Princeton Inst. files (MR)
print.pro			ALS print routines (pra, prb)
print_sysvar.pro		write to IDL log current values of all IDL global parameters
ptycho_select.prc		GUI for reading ptychgraphy results (Shapiro, Nov 2012 version)
ptycho_select.pro		routine for reading ptychgraphy results (Shapiro, Nov 2012 version)
ptycho_select_com.pro	common (include) file for reading ptychgraphy results (Shapiro, Nov 2012 version)
ptycho_select_eventcb.pro  evencall back file reading ptychgraphy results 
randomfile.pro		generates a random file name, tested to be unique (cjj)
rd_peem.pro			read ALS PEEM images (16-bit tif, white correcting)
rd_spem.pro			read SPEM XPS images (shell around LOADSPEM)
read_a_n.pro		read i noriginal ALS BL7 STXM data files (1995-2000); probably OLD, not-used
read_aa_header.pro	read header of amino acid spectral files (XSpecSim, jso)
read_aadata.pro		read amino acid spectral files (XSpecSim, jso)
read_all.pro		read in an "ALL" time-fo-flight file
read_als.pro		input ALS image (*.img)
read_aps_xrf_maps.pro	read X-ray flluorescence maps from APS (widget)
read_ascii_img.pro	reads img in ascii format (I(x,y)
read_axm.pro		reads MAPPER-type files (*.aln, spectral files for NSLS cryo-stxm)
read_bessy_stack.pro	reads files from old Bessy STXM (image sequence)
read_bessy_stxm.pro	reads files from old Bessy STXM (single images)
read_bessy_txm.pro	reads images (Princeton Instruments camera) from Bessy TXM
read_bessy_xml.pro	reads parameter file from old Bessy STXM
read_bl5.pro		reads early (2000-2001) versions of ALS STXM5322 data files; probably OLD, not-used 
read_bnl.pro		input binary (BSIF format) image file from X1A
read_bsp.pro		input X1A spectrum (BSIF format)
read_cls_sgm_xrf.pro	reads XRF data written by Labview program of CLS SGM beamline
read_cryo.pro		uses read_sxm to convert NSLS cryo-STXM image files to *.nc files
read_csv.pro		reads comma separated variables (csv) format (CJJ)
read_dm_datacube.pro	read in {x,y, I(E)} data cuve exported from Digital micrograph(Gatan)
read_energies.pro		read energies from *.enf spectral files (XSpecSim, jso)
read_ftir.pro		reads Thermo Nicolet (ver 7) *.map FTIR map files (binary)
read_h5_ptycho.pro	reads Shapiro format (N0v 12) ptychography analysis
read_h5_ssrf.pro		reads Shanghai STXM (X-radia) images (using Java bridge)
read_img.pro
read_lox.pro		read Lox format (PEEM) images
read_lox_spectra.pro	read Lox format (PEEM)spectra
read_mapper.pro		reads mapper type file (for stack align info) (CJJ)
read_mef.pro		input Mephisto (CCD 256x256 binary) file
read_mrc_file.pro		reads tomography type file (Imod)  (GAJ)
read_nsrrc_peem.pro	reads NSRRC PEEM stacks
read_nsrrc_spem.pro	reads NSRRC SPEM images
read_nsrrc_spem_gui.pro gui to read in NSRRC SPEM data & define parameters
read_numbers.pro		utility for SPEM readin (ALS-ER)
read_p3b.pro		reads peem 3 image files (AS)
read_p3b_spectrum.pro	 reads peem 3spectral files (AS)
read_peem3.pro		reads peem3 (ALS) data  files using A. Scholl routines
read_phi.pro		input ALS Phi XPS spectrum (1-channel only) (ER)
read_princeton.pro	reads Princeton Instruments camera files (from Mark Rivers)
read_sdf.pro		read file in SDF format (BL 5.3.2)
read_sm.pro			read in NSLS STXM IV format files
read_stxm4.pro		read NSLS stxm IV image files
read_stxm.pro		read_stxm - NSLS read in of images (aph modified)
read_sxm.pro		read nsls *.sxm images from cryo-stxm (CJJ)
read_tof.pro		input McMaster time-of-flight PEPIPICO file
read_tomo.pro		read in files set up for angle-scan tomography
read_until_nochar.pro	(ALS-ER) utility for SPEM readin
read_untilstring.pro	(ALS-ER) utility for SPEM readin
read_uview.pro		read in 16-bit binary files from Elmitec (UView2002)
read_xas.pro		reads NSLS X1A *.xas files (documented spectra)
read_xas_xrf_stack.pro 	reads XRF(x,y,E) stack from STXM_control(amptek, XGLabs)
read_xrf_img.pro		reads in XRF images from Twinmic STXM; Inca (SEM) element maps
read_xrf_spectra.pro	reads in XGLabs X-ray fluorescence spectra (*.dta)
read_xrf_stack.pro	reads in XRF stacks (XRF at each pixel) from STXM_control & Inca
read_xrf_stack_hdf5.pro	reads in XGLabs XRF maps in hdf5 (Dec09 format)
readfileinfo_p3b.pro	header reader for  peem 3 image & spectral files (AS)
readme_sf.txt		information file for (Billy Loo) SF routine
readme-mgif.txt		information about multi-GIF.exe
readstringbig.pro	(	ALS-ER) utility for SPEM readin
readtags.pro		tag reader peem 3 image & spectral files (AS)
readwin.pro			reads window into a byte array (from Window.pro, JDD)
refresh.pro			plots user-defined sequence of buffers (for spectral overplotting)
region_analyze.pro	widget (from stack_analyze) to auto-map regions (RC)
region_analyze_common.pro   common block for region_analyze.pro
regress2.pro		linear regression (curve fit) (from ?? - perhaps IDL share) (XSpecSim)
remove_lines.pro		automatic removal of lines with multiple outliers in an image
remove_zeros.pro		locate and replace zeros with local average (in STXM images)
resetplots.pro		zeros the AXIS buffers
rstack_analyze.pro	Remy Colombe customized stack visualizer and analysis (not active in aXis2000)
sav_aa.pro			stores output of XSpecSim (jso)
sav_als.pro			write ALS format image file
sav_hdf.pro			write HDF format image file
sav_hdfm.pro		write HDFM format image file
sav_nsls.pro		write NSLS X1A type netCDF format image file
SAV-run-problems.txt  	list of buttons in VM version (*.SAV) that do not work (Dec 2008, IDL 6.3)
sdf_com.pro			common block for selfdefining file format(ALS 5.3.2stxm)
sdf_query.txt		description of possible problem with spectral sdf files (29-Jul-01)
set_digits.pro		returns string of a number with the specified number of digits
setgraf.pro			used by AXIS to make various graphic windows active with proper scaling
sf.pro			(Billy Loo) IDL implementation of Henke X-ray absorption calculator
sf_init.pro			(Billy Loo) initialize SF (must call first)
sfconvert.pro		calculates the OD1 spectrum of a compound based on SF and OD data  (JSO)
sm_fixclock.pro		clock correction for stxm IV images (cjj)
sm_ipar.pro			initialization of sm_par structure (for stxm IV files) (cjj)
spc_load.pro		Load AXIS spectra (ascii format)
spc_save.pro		Save AXIS spectra (ascii format)
spectra.pro			routine used in SPEM spectral/image read-in (ALS ER)
split_string.pro		(Billy Loo) utility for SF
splot2d.pro			image plot routine (JDD)
splot3d.pro			volume plot routine (JDD)
splot.pro			spectral plot routine (JDD)
srotate.pro			(ALS ER) routine used in SPEM spectral/image read-in
stack2_rb.pro		reads 'stack-of-stacks' (XRF at each pixel in a set of images) 
stack2_wb.pro		writes 'stack-of-stacks' (XRF at each pixel in a set of images) 
stack_add.pro		add 2 stacks
stack_align.pro		stack align procedure (CJJ)
stack_analyze.sav		stack analyze procedure as a sav file (CJJ. v. 2.6.1, 17-sep-08)
stack_analyze_multi.txt notes on attempt to develop multi-region display (like in Zimba)
stack_analyze_multi.pro	attempt to develop multi region display - code not completed (aph)
stack_analyze-TOF.pro	specialized stack_analyze for time of flight "ALL" sequences
stack_append.pro		append 2 stacks
stack_buildlist.pro	stack build-list procedure (CJJ)
stack_diff.pro		differentiate spectra at each pixel in a stack (for FTIR)
stack_fit.pro		stack fit pixel-by-pixel spectral regression (APH, RK)
stack_list.pro		utility to parse *.sl files from either CJJ or CZ formants;; writes CZ format
stack_make.pro		generate stack as product of image and spectrum
stack_mesh.pro		changes mesh of a stack (to allow appending or adding)
stack_movie.pro		play stack movie (CJJ)
stack_plot_spectrum.pro	 plot stack spectrum (CJJ)
stack_process.pro		stack analyze procedure (derived from CJJ: renamed 17-sep-08)
stack_process_align_com.pro  common block for stack_process_align (remove conflict with aligncom)
stack_process_com.pro		common block for stack_process
stack_psprint.pro		postscript print from stacks (CJJ)
stack_rb.pro		read stack from single binary file (from stack_wb.pro)
stack_readlist.pro	stack read-list procedure (CJJ)
stack_wb.pro		write full stack to single binary file
stack_writelist.pro	write list of files in a stack (CJJ)
stag.pro			utility to check existence of a structure tag (JDD)
str_columns.pro		(Billy Loo) utility for SF
string2file.pro		(Billy Loo) utility for SF
structure.pro		ALS structure manipulation routines
stxm4_ncb.pro		convert NSLS stxm4 image sequences to *.ncb
sxm_acommon.pro		common for cryo-stxm files  (CJJ)
sxm_common.pro		common for cryo-stxm files  (CJJ)
sxm_fileexists.pro	check on file existance     (CJJ)
sxm_ipar.pro		set-up data structure for NSLS (*.sxm) files (CJJ)
sxm_readfile.pro		reads NSLS (*.sxm) files (CJJ)
sxm_strclean.pro		string clean-up for NSLS (*.sxm) files (CJJ)
text_read1.pro		read 1 block of text (ER)
text_read.pro		read multi block text (ER)
thumblbls.pro		thumbnail plotting and label updating
thumbplot.pro		update Bufnum using Thumblbls (separated from thumblbls, Feb2010)
thumbzoom.pro		plots 4 or 9 buffers on MainImg wondiw
tif2ncdf.pro		converts TIF (ALS peem) to NetCDF files
tif_convert.pro		widget to convert 1 or more tif images to axis format (Andy Smith)
tif_convert_com.pro	common for tif_convert.pro
tif_load.pro		load TIF and BMP images
tifrd_im.pro		read in tif for ALS PEEM read in
tri_fit.pro			part of CJJ stack procedures (alignment related)
TVimage.pro			(Fanning) color scale independent image plotting (trial, not implemented)
tweak.pro			image filtering for stxm files (CJJ)
wdivide.pro			set up window for multiple plots (ER)
win2lpr.pro			ALS-based routine to transfer window to printer via a PS file
win2tif.pro			convert window to a tif file (JDD, from window.pro)
win2tiff.pro		convert window to a tif file (JDD, from window.pro)
write_cts.pro		converts an aXis binary stack to set of ascii spectra (*.cts)
					suitable for input to PyMCA
write_mrc_file.pro	writes tomo format file (Imod)  (GAJ)
write_ncdf.pro		write out NSLS NetCDF image file (CJJ version)
write_p3b.pro		writes peem 3 image & spectral files (AS)
write_princeton.pro	writes images in format of Princeton Instruments cameras (MR)
write_sdf.pro		write out image in SDF format
write_spectrum.pro	write out NSLS NetCDF spectral file (CJJ version)
write_stxm.pro		writing NSLS NetCDF format images
write_xas-1col.pro	1-column version od XAS formar writer
write_xas.pro		writes NSLS X1A documented XAS specrtral files
writetags.pro		tag writer peem 3 image & spectral files (AS)
wrstx_ax.pro		(aph version of write_stxm.pro)
wvlen2en.pro		(Loo)utility to convert wavelength to energy
xas1.pro			reads a Beamline 7 STXM X-ray absorption spectral data (1995-98)
xas2.pro			reads I, Io BALS BL7 STXM X-ray absorption spectral data (1995-98)
xas_xrf_extract.pro	extracts X-ray absoprtion stack for range of XRF energies (XRF-yield)
XimageViewer.exe		utility to view STXM (sdf) format images and standard image formats
				(written by Ivo Koprinarov 2003)
xm1_load.pro		read in  XM1 files (ALS TXM) into AXIS
xmload.pro			read in XM1 files (ALS TXM)
xrf_com.pro			common for XRF maps (APS)
xrf_map_selector.pro	selects specific XRF maps from APS data file to read into aXis2000
XSpecSim.pro		XSpecSim spectral simulator - main program
XSpecSim_com.pro		XSpecSim - common block
XSpecSim_init.pro		initialize XSpecSim (jso)
XSpecSim_run.pro		run XspecSim (jso)
xspecsim-readme.txt	documentation for XSpecSim (jso)
zimba_color.pro		CZ stack - set-up co-ordinated image/spectral color table
zimba_run.pro		runs Zimba package from ax_start (start-up)
zstack_align.pro		CZ stack - align images
zstack_align_common.pro	CZ stack - common for zstack_align
zstack_align_images.pro  CZ stack - aling images
zstack_analyze.pro	CZ stack - extract spectra etc
zstack_analyze_common.pro  CZ stack - common for zstack_analyze.pro
zstack_buildlist.pro	CZ stack - set up list of files
zstack_buildlist_common.pro	CZ stack - common for zstack_buildlist.pro
zstack_color.pro		CZ stack - set-up co-ordinated image/spectral color table
zstack_color_common.pro	  CZ stack - common block for color info (APH)
zstack_common.pro		CZ stack - common block for Zstack(APH)
zstack_display.pro	CZ stack - generates zstack_analayze panel
zstack_display_common.pro  CZ stack - common block for color info in zstack (APH)
zstack_pickcolor.pro	CZ stack - select colors for lines etc
zstack_plot.pro		CZ stack - display multiple spectra from stack
zstack_profile.pro	CZ stack - alignment routine
zstack_profile_common.pro	CZ stack - commonf for zstack_profile
zstack_read_mapper.pro	 	CZ stack - read mapper for alignment shifts
zstack_readlist.pro	CZ stack - stack input routine
zstack_save.pro		CZ stack - stack save output routine - aph modified
zstack_save_common.pro	CZ stack - common for zstack_save
zstack_shift.pro		CZ stack - shift images according to &.aln file
zstack_spectra.pro	CZ stack - generate spectra
zstack_spectra_common.pro  CZ stack - common for zstack_spectra
zstack_tune.pro		CZ stack - fine tune stack alignment
zstack_tune_common.pro	CZ stack - common for zstack_tune


************************************************************************
OLD CODE files - date last modified & date retired
************************************************************************
removed from content.lst
-----  Feb-2010-----------------
ax_sdfe.pro		widget to read  EARLY (pre Aug 2001)  5.3.2  SDF format
axis_startup.pro	auto start AXIS from the idl_startup widget
energy_sort.pro		sort and force monotonic energies of spectra & stacks (NOT WORKING)
go.pro			widget to allow selection of AXIS, aXis2000 or IDL on startup
read_lox_pre_15oct05.pro  read Lox format (PEEM) data files prior to 15-oct-05(image, spectra)
				cannot find the file!!
zstack.pro			CZ stack - load files (USE in stand alone mode for greater reliability)
zstack_save-cgz.pro	CZ stack - stack save output routine
------ Jul-2010 ------------------
aligncom.pro		common for align.pro (CJJ) - replaced by stack_process_com
splota.pro			structure plot routines (splot, splot2d, splot3d) - DEAD CODE


Removed from aXis2000 folder
-----  Feb-2010-----------------
ax_sdfe.pro		widget to read  EARLY (pre Aug 2001)  5.3.2  SDF format
axis_startup.pro	auto start AXIS from the idl_startup widget
energy_sort.pro		sort and force monotonic energies of spectra & stacks (NOT WORKING)
go.pro			widget to allow selection of AXIS, aXis2000 or IDL on startup
stack_align-07mar2009.pro 
stack_align-16Aug2009.pro
stack_process-16aug2009.pro
stack_process-19-dec-2008.pro
tifrd_im-test.pro  (4-Apr-07)
zstack_buildlist-with_axis_com-20Aug09.pro
------ Jul-2010 ------------------
aligncom.pro		common for align.pro (CJJ) - replaced by stack_process_com
splota.pro			structure plot routines (splot, splot2d, splot3d) - DEAD CODE
--------- Jul-2011 ------------
axis.pro			loads all pro's and runs AXIS_C.PRO,start_file='c:\axis\axis.ini'
				- conflicts with Eclipse (IDL8.x) procedures
READ_A_N.PRO		read pre-2000 ALS BL7.0 STXM
					replaced by JDD integrated version
READ_BL5.pro		read-in intermediate ALS STXM5322 images
					superceded by READ_SDF.PRO
INIT_STXM_SD.pro	same as INIT_SD so did global replacement (10 files)
AX_GEN_STACK.pro	renamed AX_ANGLE_STACK
XAS1.PRO			reads old ALS BL7.0 STXM (not used)replaced by ALS-specin.pro
XAS2.PRO			reads 2 old ALS BL7.0 STXM (not used)
WT_SPEC.PRO		early version of spc_save (axis2000 format spectra)
					NB - did not exist in the aXis2000 directory ! (oops)
stack_setup.pro		(Stack_setup_update) stack setup procedure (CJJ)
					did not exist in aXis2000 directory

------------ Dec-2011-------
read_img.pro		reads PRISM data (old ALS peem) (JDD, from io.pro - NOT USED)
io.pro			ALS input/output routines (READ_IMG, READ_BIN, WRITE_BIN) - unused 
