updates: pshell import, angle-scans, elog

- pshell import: fix units and data scaling.
- pshell import: support new multi-region scans.
- angle scans: add trim function.
- angle scans: update import_tpi_scan function.
- angle scans: fix scales of check waves in normalization.
- area display: new cursor mode for background selection.
- elog: bugfixes (attachment list, check existing logbook).

README.md

@@ -11,10 +11,12 @@ PEARL Procedures should be installed according to the regular Igor Pro guideline
 
 - Make a `pearl-procs` directory in your private or shared `User Procedures` folder, and copy the PEARL Procedures distribution there.
 - Create shortcuts of the `pearl-arpes.ipf` and `pearl-menu.ipf` files, and move them to the `Igor Procedures` folder next to your `User Procedures` folder.
-- Find the `HDF5.XOP` extension in the `Igor Pro Folder` under `More Extensions/File Loaders`, create a shortcut, and move the shortcut to the `Igor Extensions` folder next to your `User Procedures` folder.
+- Find the `HDF5.XOP` (`HDF5-64.xop` for Igor 7 64-bit) extension in the `Igor Pro Folder` under `More Extensions/File Loaders` (`More Extensions (64-bit)/File Loaders`), create a shortcut, and move the shortcut to the `Igor Extensions` folder next to your `User Procedures` folder.
 - Find the `HDF5 Help.ihf` next to `HDF5.XOP`, create a shortcut, and move the shortcut to the `Igor Help Files` folder next to your `User Procedures` folder.
 
-PEARL Procedures has been tested under Igor Pro version 6.37 (32-bit). Older versions (particularly prior to 6.34) may not be compatible. Please update to the latest Igor Pro version before reporting any problems.
+PEARL Procedures has been tested under Igor Pro version 6.37 (32-bit). Older versions prior to 6.36 are not be compatible. Please update to the latest Igor Pro 6 version before reporting any problems.
+
+PEARL Procedures compiles under Igor 7.00. Some features, in particular 3D graphics, may not work properly.
 
 
 License

pearl/pearl-anglescan-process.ipf

@@ -6,14 +6,14 @@
 #include "pearl-polar-coordinates"
 #include <New Polar Graphs>
 
-// $Id$
-//
-// copyright (c) 2013-15 Paul Scherrer Institut
+// copyright (c) 2013-16 Paul Scherrer Institut
 //
 // Licensed under the Apache License, Version 2.0 (the "License");
 //   you may not use this file except in compliance with the License.
 //   You may obtain a copy of the License at
 //   http:///www.apache.org/licenses/LICENSE-2.0
+//
+// Please acknowledge the use of this code.
 
 /// @file
 /// @brief processing and holographic mapping of angle scanned XPD data.
@@ -64,7 +64,7 @@
 ///
 /// @author matthias muntwiler, matthias.muntwiler@psi.ch
 ///
-/// @copyright 2013-15 Paul Scherrer Institut @n
+/// @copyright 2013-16 Paul Scherrer Institut @n
 /// Licensed under the Apache License, Version 2.0 (the "License"); @n
 ///   you may not use this file except in compliance with the License. @n
 ///   You may obtain a copy of the License at
@@ -79,15 +79,38 @@
 ///
 /// PearlAnglescanProcess is declared in @ref pearl-anglescan-process.ipf.
 
-/// @warning experimental
-function strip_remove_frames(strip, yscale, ylo, yhi)
+
+/// delete a contiguous range of frames from a strip.
+///
+/// this can be used to remove a region of bad frames due to, e.g., measurement problems.
+/// the function operates on 2D intensity data and manipulator coordinates at the same time.
+///
+/// @param[in,out]	strip			2D data, X-axis = analyser angle, Y-axis = arbitrary manipulator scan.
+///								the result is written to the original wave.
+///
+/// @param[in,out]	theta		1D data, manipulator scan.
+///								the result is written to the original wave.
+///
+/// @param[in,out]	tilt			1D data, manipulator scan.
+///								the result is written to the original wave.
+///
+/// @param[in,out]	phi			1D data, manipulator scan.
+///								the result is written to the original wave.
+///
+/// @param[in]		qlo			point index of first frame to delete.
+///
+/// @param[in]		qhi			point index of last frame to delete.
+///								qhi must be greater or equal than qlo.
+///
+function strip_delete_frames(strip, qlo, qhi, theta, tilt, phi)
 	wave strip // 2D data, X-axis = analyser angle, Y-axis = arbitrary manipulator scan
-	wave /z yscale // Y scaling, e.g. ManipulatorPhi
-		// if unassigned, point scaling is assumed
-	variable ylo
-	variable yhi
+	variable qlo
+	variable qhi
+	wave theta
+	wave tilt
+	wave phi
 	
-	if (ylo > yhi)
+	if (qlo > qhi)
 		return -1
 	endif
 	
@@ -95,8 +118,8 @@ function strip_remove_frames(strip, yscale, ylo, yhi)
 	variable snx = dimsize(strip, 0)
 	variable sny = dimsize(strip, 1)
 	variable sq1lo = 0
-	variable sq1hi = max(round((ylo - dimoffset(strip, 1)) / dimdelta(strip, 1)), 0)
-	variable sq2lo = min(round((ylo - dimoffset(strip, 1)) / dimdelta(strip, 1)), sny - 1)
+	variable sq1hi = max(qlo-1, 0)
+	variable sq2lo = min(qhi+1, sny - 1)
 	variable sq2hi = dimsize(strip, 1) - 1
 	
 	// dest indices
@@ -111,10 +134,24 @@ function strip_remove_frames(strip, yscale, ylo, yhi)
 	
 	duplicate /free strip, strip_copy
 	redimension /n=(dnx,dny) strip
-	
 	strip[][dq1lo,dq1hi] = strip_copy[p][q + q1ofs]
 	strip[][dq2lo,dq2hi] = strip_copy[p][q + q2ofs]
 	
+	duplicate /free theta, theta_copy
+	redimension /n=(dny) theta
+	theta[dq1lo,dq1hi] = theta_copy[p + q1ofs]
+	theta[dq2lo,dq2hi] = theta_copy[p + q2ofs]
+	
+	duplicate /free tilt, tilt_copy
+	redimension /n=(dny) tilt
+	tilt[dq1lo,dq1hi] = tilt_copy[p + q1ofs]
+	tilt[dq2lo,dq2hi] = tilt_copy[p + q2ofs]
+	
+	duplicate /free phi, phi_copy
+	redimension /n=(dny) phi
+	phi[dq1lo,dq1hi] = phi_copy[p + q1ofs]
+	phi[dq2lo,dq2hi] = phi_copy[p + q2ofs]
+	
 	return 0
 end
 
@@ -144,6 +181,7 @@ end
 /// @return if check waves are enabled, the following waves are created (overwritten if existing):
 /// @arg check_dist average X distribution
 /// @arg check_smoo smoothed distribution used to normalize the strip
+///
 function normalize_strip_x(strip, [smooth_method, smooth_factor, check])
 	wave strip
 	variable smooth_method
@@ -233,6 +271,7 @@ end
 /// @return if check waves are enabled, the following waves are created (overwritten if existing):
 ///	@arg check_dist average theta distribution
 ///	@arg check_smoo smoothed distribution used to normalize the strip
+///
 function normalize_strip_theta(strip, theta, [theta_offset, smooth_method, smooth_factor, check])
 	wave strip
 	wave theta
@@ -261,6 +300,7 @@ function normalize_strip_theta(strip, theta, [theta_offset, smooth_method, smoot
 	duplicate /free dist, dist_smoo
 	duplicate /free theta, theta_int
 	theta_int = theta - theta_offset
+	setscale /p x theta_int[0], theta_int[1] - theta_int[0], waveunits(theta,-1), dist, dist_smoo
 	variable nx = dimsize(strip, 0)
 	variable ix
 	
@@ -297,6 +337,71 @@ function normalize_strip_theta(strip, theta, [theta_offset, smooth_method, smoot
 	if (check)
 		duplicate /o dist, check_dist
 		duplicate /o dist_smoo, check_smoo
+		setscale /p x dimoffset(dist,0), dimdelta(dist,0), waveunits(dist,0), check_dist, check_smoo
+	endif
+end
+
+/// divide the strip by a two-dimensional normalization function.
+///
+/// @warning experimental. this function is under development.
+///
+/// @param check enable output of intermediate results
+///	@arg 0 (default)  don't create additional waves
+/// 	@arg 1 create check waves in the current folder
+///	@arg 2 calculate check waves only, do not modify strip
+///
+/// @return if check waves are enabled, the following waves are created (overwritten if existing):
+///	@arg check_dist average theta distribution
+///	@arg check_smoo smoothed distribution used to normalize the strip
+///
+function normalize_strip_2d(strip, theta, [theta_offset, smooth_method, smooth_factor, check])
+	wave strip
+	wave theta
+	variable theta_offset
+	variable smooth_method
+	variable smooth_factor
+	variable check
+	
+	if (ParamIsDefault(check))
+		check = 0
+	endif
+	if (ParamIsDefault(theta_offset))
+		theta_offset = 0
+	endif
+	if (ParamIsDefault(smooth_method))
+		smooth_method = 4
+	endif
+	if (ParamIsDefault(smooth_factor))
+		smooth_factor = 0.5
+	endif
+
+	variable nx = dimsize(strip, 0)
+	variable ny = dimsize(strip, 1)
+	
+	duplicate /free strip, dist, alpha_int, theta_int
+	theta_int = theta[q] - theta_offset
+	alpha_int = dimoffset(strip, 0) + p * dimdelta(strip, 0)
+	redimension /n=(nx * ny) dist, alpha_int, theta_int
+	
+	switch(smooth_method)
+		case 4:
+			loess /dest=dist_smoo /smth=(smooth_factor) srcWave=dist, factors={alpha_int, theta_int}
+			redimension /n=(nx, ny) dist_smoo
+			break
+		default:
+			Abort "undefined smooth method"
+			break
+	endswitch
+	
+	// divide
+	if (check != 2)
+		strip /= dist_smoo
+	endif
+	
+	// check
+	if (check)
+		//duplicate /o dist, check_dist
+		duplicate /o dist_smoo, check_smoo
 	endif
 end
 
@@ -705,9 +810,9 @@ function convert_angles_ttpa2polar(theta, tilt, phi, analyser, polar, azi)
 	// this is simply a polar-cartesian mapping, independent of the manipulator
 	// phi=0 is in the polar rotation plane
 	make /n=(3,na) /d /free w_orig_polar, w_orig_cart, w_rot_cart, w_rot_polar
-	w_orig_polar[0] = radius
-	w_orig_polar[1] = analyser[q]
-	w_orig_polar[2] = 0
+	w_orig_polar[0][] = radius
+	w_orig_polar[1][] = analyser[q]
+	w_orig_polar[2][] = 0
 	polar2cart_wave(w_orig_polar, w_orig_cart)
 	// if the angle-dispersive axis was horizontal, we'd need to rotate the detector
 	//rotate_z_wave(w_orig_cart, 90)
@@ -1758,7 +1863,7 @@ function /s display_scanlines(nickname, alpha_lo, alpha_hi, m_theta, m_tilt, m_p
 	make /n=1 /d /free d_polar, d_azi
 	variable n_alpha = round(alpha_hi - alpha_lo) + 1
 	make /n=(n_alpha) /d /free analyser
-	setscale /i x alpha_lo, alpha_hi, "deg", analyser
+	setscale /i x alpha_lo, alpha_hi, "<EFBFBD>", analyser
 	analyser = x
 	
 	convert_angles_ttpa2polar(m_theta, loc_m_tilt, m_phi, analyser, d_polar, d_azi)
@@ -1802,21 +1907,46 @@ function /s display_scanlines(nickname, alpha_lo, alpha_hi, m_theta, m_tilt, m_p
 	return graphname
 end
 
-static constant kProjScaleLinear = 2
+/// @page PageProjections Projections
+///
+/// the functions of the anglescan package support the following map projections.
+/// for a description of the different projections, see, for example,
+/// https://en.wikipedia.org/wiki/Map_projection
+///
+/// | Selector | Projection | Function | Properties |
+/// | :----: | :----: | :----: | :---- |
+/// | kProjDist = 0 | azimuthal equidistant | r = c * theta | radius is proportional to polar angle. |
+/// | kProjStereo = 1 | stereographic | r = c * tan theta/2 | circles on sphere map to circles. |
+/// | kProjArea = 2 | azimuthal equal-area | r = c * sin theta/2 | preserves area measure. |
+/// | kProjGnom = 3 | gnomonic | r = c * tan theta | great circles map to straight lines. |
+/// | kProjOrtho = 4 | orthographic | r = c * sin theta | k-space mapping in ARPES and LEED. |
+///
+/// the projections in this package are defined for 0 <= theta < 90.
+///
+constant kProjDist = 0
+constant kProjStereo = 1
+constant kProjArea = 2
+constant kProjGnom = 3
+constant kProjOrtho = 4
+
+static constant kProjScaleDist = 2
 static constant kProjScaleStereo = 2
-static constant kProjScaleAzim = 2
+static constant kProjScaleArea = 2
 // scaled so that radius(gnom) = radius(stereo) for polar = 88
-static constant kProjScaleGnomonic = 0.06744519021
+static constant kProjScaleGnom = 0.06744519021
+static constant kProjScaleOrtho = 2
 
 /// calculate the projected polar angle
 ///
 /// @param	polar			polar angle in degrees
 ///
-/// @param	projection		mapping function from polar to cartesian coordinates
-///	@arg	0				linear
-///	@arg	1				stereographic (default)
-///	@arg	2				azimuthal
-///	@arg	3				gnomonic (0 <= polar < 90)
+/// @param	projection		mapping function from polar to cartesian coordinates.
+///							see @ref PageProjections for details.
+///	@arg	kProjDist = 0		azimuthal equidistant
+///	@arg	kProjStereo = 1	stereographic (default)
+///	@arg	kProjArea = 2	azimuthal equal-area
+///	@arg	kProjGnom = 3	gnomonic (0 <= polar < 90)
+///	@arg	kProjOrtho = 4	orthographic
 ///
 /// @return projected radius.
 ///	the radius is scaled such that grazing emission maps to 2.
@@ -1830,17 +1960,20 @@ threadsafe function calc_graph_radius(polar, [projection])
 
 	variable radius
 	switch(projection)
-		case 1: // stereographic
+		case kProjStereo: // stereographic
 			radius = kProjScaleStereo * tan(polar / 2 * pi / 180)
 			break
-		case 2: // azimuthal
-			radius = kProjScaleAzim * cos((180 - polar) / 2 * pi / 180)
+		case kProjArea: // equal area
+			radius = kProjScaleArea * sin(polar / 2 * pi / 180)
 			break
-		case 3: // gnomonic
-			radius = polar < 90 ? kProjScaleGnomonic * tan(polar * pi / 180) : inf
+		case kProjGnom: // gnomonic
+			radius = polar < 90 ? kProjScaleGnom * tan(polar * pi / 180) : inf
 			break
-		default: // linear
-			radius = kProjScaleLinear * polar / 90
+		case kProjOrtho: // orthographic
+			radius = kProjScaleOrtho * sin(polar * pi / 180)
+			break
+		default: // equidistant
+			radius = kProjScaleDist * polar / 90
 	endswitch
 	
 	return radius
@@ -1852,10 +1985,13 @@ end
 ///
 /// @param	x, y				projected Cartesian coordinate
 ///
-/// @param	projection		mapping function from polar to cartesian coordinates
-///	@arg	0				linear
-///	@arg	1				stereographic (default)
-///	@arg	2				azimuthal
+/// @param	projection		mapping function from polar to cartesian coordinates.
+///							see @ref PageProjections for details.
+///	@arg	kProjDist = 0		azimuthal equidistant
+///	@arg	kProjStereo = 1	stereographic (default)
+///	@arg	kProjArea = 2	azimuthal equal-area
+///	@arg	kProjGnom = 3	gnomonic (0 <= polar < 90)
+///	@arg	kProjOrtho = 4	orthographic
 ///
 /// @returns polar angle in degrees
 ///
@@ -1873,17 +2009,20 @@ threadsafe function calc_graph_polar(x, y, [projection])
 	
 	radius = sqrt(x^2 + y^2)
 	switch(projection)
-		case 1: // stereographic
+		case kProjStereo: // stereographic
 			polar = 2 * atan(radius / kProjScaleStereo) * 180 / pi
 			break
-		case 2: // azimuthal
-			polar = 180 - 2 * acos(radius / kProjScaleAzim) * 180 / pi
+		case kProjArea: // equal area
+			polar = 2 * asin(radius / kProjScaleArea) * 180 / pi
 			break
-		case 3: // gnomonic
-			polar = atan(radius / kProjScaleGnomonic) * 180 / pi
+		case kProjGnom: // gnomonic
+			polar = atan(radius / kProjScaleGnom) * 180 / pi
 			break
-		default: // linear
-			polar = 90 * radius / kProjScaleLinear
+		case kProjOrtho: // orthographic
+			polar = asin(radius / kProjScaleOrtho) * 180 / pi
+			break
+		default: // equidistant
+			polar = 90 * radius / kProjScaleDist
 	endswitch
 
 	return polar
@@ -1894,10 +2033,13 @@ end
 /// @param	x, y				projected Cartesian coordinate
 ///
 /// @param	projection		mapping function from polar to cartesian coordinates.
-/// 							projections 0-2 have no effect  on the azimuthal coordinate.
-///	@arg	0				linear
-///	@arg	1				stereographic (default)
-///	@arg	2				azimuthal
+///							all supported projections are azimuthal, they have no effect on the azimuthal coordinate.
+///							see @ref PageProjections for details.
+///	@arg	kProjDist = 0		azimuthal equidistant
+///	@arg	kProjStereo = 1	stereographic (default)
+///	@arg	kProjArea = 2	azimuthal equal-area
+///	@arg	kProjGnom = 3	gnomonic (0 <= polar < 90)
+///	@arg	kProjOrtho = 4	orthographic
 ///
 /// @param	zeroAngle		zeroAngleWhere parameter of polar graphs
 ///	@arg	0 (default)		zero is at the 3 o'clock position
@@ -2446,8 +2588,35 @@ end
 
 /// import a hemispherical scan from theta-phi-intensity waves and display it
 ///
-/// @warning EXPERIMENTAL
-/// the interface and behaviour of this function may change
+/// in the tpi format, the hemi scan data is represented
+/// by a triple of flat one-dimensional waves
+/// corresponding to the polar angle (theta), azimuthal angle (phi) and intensity.
+/// no specific sort order is required.
+///
+/// @param	nickname	nick name for output data
+///	@arg in default mode, this will become the name of a child folder containing the output.
+///	@arg in XPDplot mode, this will become a prefix of the generated data in the root folder.
+///
+/// @param	theta		theta angles, 0 = normal emission.
+///
+/// @param	phi			phi angles, 0 = azimuthal origin. size = dimsize(data, 1)
+///
+/// @param	intensity		intensity wave, see requirements above.
+///
+/// @param	npolar		number of polar angles, determines polar and azimuthal step size.
+///						default = 91 (1 degree steps)
+///
+/// @param	folding		rotational averaging.
+///						example: 3 = average to 3-fold symmetry.
+///						default = 1.
+///
+/// @param	nograph		display a new graph window?
+///	@arg	0			(default) display a new polar graph
+///	@arg	1			don't display a new graph
+///
+/// @param	xpdplot		XPDplot compatibility
+///	@arg	0			(default) create waves in child folder $nickname
+///	@arg	1			create waves in root folder (compatible with XPDplot)
 ///
 function import_tpi_scan(nickname, theta, phi, intensity, [folding, npolar, nograph, xpdplot])
 	string nickname
@@ -2482,5 +2651,195 @@ function import_tpi_scan(nickname, theta, phi, intensity, [folding, npolar, nogr
 		fold_phi = fold_phi >= 180 ? fold_phi + 360 / folding - fold_phi : fold_phi + 360 / folding
 	endfor
 
-	display_hemi_scan(nickname)
-end
+	if (nograph==0)
+		display_hemi_scan(nickname)
+	endif
+end
+
+/// trim a hemispherical scan at grazing angle
+///
+/// the function recalaculates the values wave from totals and weights
+/// but sets elements above a given polar angle to nan.
+///
+/// @param nickname		name of the scan dataset.
+///						can be empty if no prefix is used.
+///						the dataset must be in the current datafolder.
+///
+/// @param theta_max	highest polar angle to keep (0...90 degrees).
+///
+function trim_hemi_scan(nickname, theta_max)
+	string nickname
+	variable theta_max
+
+	if (strlen(nickname))
+		string s_prefix = nickname + "_"
+		string s_int = s_prefix + "i"
+	else
+		s_prefix = ""
+		s_int = "values"
+	endif
+	string s_totals = s_prefix + "tot"
+	string s_weights = s_prefix + "wt"
+	string s_polar = s_prefix + "pol"
+
+	wave w_polar = $s_polar
+	wave w_values = $s_int
+	wave w_totals = $s_totals
+	wave w_weights = $s_weights
+
+	w_values = w_polar <= theta_max ? w_totals / w_weights : nan
+end
+
+/// extract a polar cut from a hemispherical scan.
+///
+/// for each polar angle, the function first extracts all azimuthal angles.
+/// the intensity is then interpolated between the nearest neighbours of the given azimuth.
+///
+/// the hemi grid must have been created in the current data folder by the make_hemi_grid function.
+/// correct ordering is required.
+///
+/// @param nickname		name of the scan dataset.
+///						can be empty if no prefix is used.
+///						the dataset must be in the current datafolder.
+///
+/// @param azim			azimuthal angle in degrees
+///
+/// @return				reference of the created wave.
+///						the wave has the same name as the intensity wave of the dataset
+///						with the suffix "_azi" and the azimuthal angle rounded to integer.
+///						it is created in the same datafolder as the original data.
+///
+function /wave hemi_polar_cut(nickname, azim)
+	string nickname
+	variable azim
+
+	if (strlen(nickname))
+		string s_prefix = nickname + "_"
+		string s_int = s_prefix + "i"
+	else
+		s_prefix = ""
+		s_int = "values"
+	endif
+	string s_totals = s_prefix + "tot"
+	string s_weights = s_prefix + "wt"
+	string s_polar = s_prefix + "pol"
+	string s_azim = s_prefix + "az"
+	string s_index = s_prefix + "index"
+	string s_theta = s_prefix + "th"
+	string s_dphi = s_prefix + "dphi"
+	string s_nphis = s_prefix + "nphis"
+	string s_cut
+	sprintf s_cut, "%s_azi%03u", s_int, round(azim)
+
+	wave w_polar = $s_polar
+	wave w_azim = $s_azim
+	wave w_values = $s_int
+	wave w_totals = $s_totals
+	wave w_weights = $s_weights
+	wave w_index = $s_index
+	wave w_theta = $s_theta
+	wave w_dphi = $s_dphi
+	wave w_nphis = $s_nphis
+
+	variable npol = numpnts(w_theta)
+	variable ipol
+	variable pol_st = abs(w_theta[1] - w_theta[0])
+	variable pol
+	variable pol1, pol2
+	variable nsel
+	make /n=(npol) /o $s_cut
+	wave w_cut = $s_cut
+	setscale /i x w_theta[0], w_theta[numpnts(w_theta)-1], "deg", w_cut
+	make /n=1 /free azi_slice
+	make /n=1 /free values_slice
+	
+	for (ipol = 0; ipol < npol; ipol += 1)
+		pol = w_theta[ipol]
+		pol1 = pol - pol_st / 2
+		pol2 = pol + pol_st / 2
+		extract /free /indx w_polar, sel, (pol1 < w_polar) && (w_polar <= pol2)
+		nsel = numpnts(sel)
+		if (nsel > 0)
+			redimension /n=(nsel+2) azi_slice, values_slice
+			azi_slice[1, nsel] = w_azim[sel[p-1]]
+			azi_slice[0] = azi_slice[nsel] - 360
+			azi_slice[nsel+1] = azi_slice[1] + 360
+			values_slice[1, nsel] = w_values[sel[p-1]]
+			values_slice[0] = values_slice[nsel]
+			values_slice[nsel+1] = values_slice[1]
+			w_cut[ipol] = interp(azim, azi_slice, values_slice)
+		else
+			w_cut[ipol] = nan
+		endif
+	endfor
+	return w_cut
+end
+
+/// extract an azimuthal cut from a hemispherical scan
+///
+/// the function extracts all azimuthal angles that are present for the given polar angle.
+///
+/// the hemi grid must have been created in the current data folder by the make_hemi_grid function.
+/// correct ordering is required.
+///
+/// @param nickname		name of the scan dataset.
+///						can be empty if no prefix is used.
+///						the dataset must be in the current datafolder.
+///
+/// @param pol			polar angle in degrees
+///
+/// @return				reference of the created wave.
+///						the wave has the same name as the intensity wave of the dataset
+///						with the suffix "_azi" and the azimuthal angle rounded to integer.
+///						it is created in the same datafolder as the original data.
+///
+function /wave hemi_azi_cut(nickname, pol)
+	string nickname
+	variable pol
+
+	if (strlen(nickname))
+		string s_prefix = nickname + "_"
+		string s_int = s_prefix + "i"
+	else
+		s_prefix = ""
+		s_int = "values"
+	endif
+	string s_totals = s_prefix + "tot"
+	string s_weights = s_prefix + "wt"
+	string s_polar = s_prefix + "pol"
+	string s_azim = s_prefix + "az"
+	string s_index = s_prefix + "index"
+	string s_theta = s_prefix + "th"
+	string s_dphi = s_prefix + "dphi"
+	string s_nphis = s_prefix + "nphis"
+	string s_cut
+	sprintf s_cut, "%s_pol%03u", s_int, round(pol)
+
+	wave w_polar = $s_polar
+	wave w_azim = $s_azim
+	wave w_values = $s_int
+	wave w_totals = $s_totals
+	wave w_weights = $s_weights
+	wave w_index = $s_index
+	wave w_theta = $s_theta
+	wave w_dphi = $s_dphi
+	wave w_nphis = $s_nphis
+
+	variable pol_st = abs(w_theta[1] - w_theta[0])
+	variable pol1, pol2
+	variable nsel
+
+	pol1 = pol - pol_st / 2
+	pol2 = pol + pol_st / 2
+	extract /free /indx w_polar, sel, (pol1 < w_polar) && (w_polar <= pol2)
+	nsel = numpnts(sel)
+	if (nsel > 0)
+		make /n=(nsel) /o $s_cut
+		wave w_cut = $s_cut
+		w_cut = w_values[sel]
+		setscale /i x w_azim[sel[0]], w_azim[sel[nsel-1]], "<22>", w_cut
+		return w_cut
+	else
+		return $""
+	endif
+end

pearl/pearl-anglescan-tracker.ipf

@@ -436,7 +436,7 @@ static function setup_detector()
 	setdatafolder $(package_path)
 
 	make /n=31 /o detector_angle, detector_pol, detector_az, detector_rad
-	setscale /i x -30, 30, "deg", detector_angle, detector_pol, detector_az, detector_rad
+	setscale /i x -30, 30, "°", detector_angle, detector_pol, detector_az, detector_rad
 	detector_angle = x
 	
 	setdatafolder saveDF
@@ -573,7 +573,7 @@ static function update_detector(theta, tilt, phi, range)
 	//m_phi *= -1 // checked 140702
 	
 	wave detector_angle, detector_pol, detector_az, detector_rad
-	setscale /i x -range/2, +range/2, "deg", detector_angle
+	setscale /i x -range/2, +range/2, "°", detector_angle
 	detector_angle = x
 	
 	convert_angles_ttpa2polar(m_theta, m_tilt, m_phi, detector_angle, detector_pol, detector_az)

pearl/pearl-area-display.ipf

@@ -52,6 +52,25 @@
 /// PearlAreaDisplay is declared in @ref pearl-area-display.ipf.
 ///
 
+/// compose a valid and unique graph name from a data folder reference
+static function /s graphname_from_dfref(df, prefix)
+	dfref df
+	string prefix
+
+	string name
+
+	name = GetDataFolder(1, df)
+	name = ReplaceString("root:", name, "")
+	name = name[0, strlen(name) - 2]
+	name = ReplaceString(" ", name, "")
+	name = CleanupName(prefix + name, 0)
+	if (CheckName(name, 6))
+		name = UniqueName(name, 6, 0)
+	endif
+	
+	return name
+end
+
 /// open a new graph window with a 2D image.
 ///
 /// this is essentially <code>display; appendimage</code>.
@@ -72,7 +91,7 @@ function /s ad_display(image)
 
 	string dfname = ReplaceString("root:", GetDataFolder(1, imagedf), "")
 	string graphtitle = dfname + " View"
-	string /g view_graphname = CleanupName("view_" + dfname, 0)
+	string /g view_graphname = graphname_from_dfref(imagedf, "view_")
 	svar graphname = view_graphname
 	display /k=1/n=$graphname as graphtitle
 	graphname = s_name
@@ -104,7 +123,7 @@ function /s ad_display_histogram(image)
 
 	string dfname = ReplaceString("root:", GetDataFolder(1, imagedf), "")
 	string graphtitle = dfname + " Histogram"
-	string /g hist_graphname = CleanupName("hist_" + dfname, 0)
+	string /g hist_graphname = graphname_from_dfref(imagedf, "hist_")
 	svar graphname = hist_graphname
 	display /k=1/n=$graphname as graphtitle
 	graphname = s_name
@@ -177,9 +196,10 @@ function /s ad_display_profiles(image, [filter])
 	view_filter_options = ""
 	variable /g view_filter_smoothing_x = 1
 	variable /g view_filter_smoothing_y = 1
-	string dfname = GetDataFolder(0, imagedf)
-	string graphtitle = dfname + ":" + NameOfWave(image) + " Profiles"
-	string /g prof_graphname = CleanupName("prof_" + dfname, 0)
+	variable /g view_cursor_mode = 0
+	string dfname = ReplaceString("root:", GetDataFolder(1, imagedf), "")
+	string graphtitle = dfname + NameOfWave(image) + " Profiles"
+	string /g prof_graphname = graphname_from_dfref(imagedf, "prof_")
 	svar graphname = prof_graphname
 	variable /g graph_avg // average value in ROI (ROI is defined by the crosshairs A and B)
 	variable /g graph_min // minimum value in ROI
@@ -329,15 +349,88 @@ function ad_update_profiles(image)
 	return 0
 end
 
+/// switch cursors on a profiles graph
+///
+/// the standard cursors allow to select the profiles to display in the profiles panes.
+/// additional cursors are shown in the profiles panes.
+///
+/// in the background selection mode, additional cursors allow the user to select
+/// the limits of the background and peak integration regions.
+/// the meaning of the cursors depends on the particular processing function.
+///
+/// @param	mode			cursor mode.
+///	@arg	0 (default)		standard profile selection. cursors C-F on profile panes.
+///	@arg	1				background selection. cursors A-F on image.
+///
+/// @param	image			image displayed in the graph. 
+///							this is the original image, not the one in the view data folder.
+///
+function ad_profiles_cursor_mode(image, mode)
+	wave image
+	variable mode
+	
+	dfref savedf = GetDataFolderDFR()
+	wave view_image = get_view_image(image)
+	dfref viewdf = GetWavesDataFolderDFR(view_image)
+	svar /sdfr=viewdf graphname = prof_graphname
+	nvar /sdfr=viewdf cursor_mode = view_cursor_mode
+	wave /sdfr=viewdf xprofiles, yprofiles
+	
+	variable dx = DimSize(view_image, 0)
+	variable dy = DimSize(view_image, 1)
+	switch(mode)
+		case 1: // background selection
+			Cursor /w=$graphname /A=0 /P /I /S=2 /H=1 /L=1 A view_image 0, 0
+			Cursor /w=$graphname /A=0 /P /I /S=2 /H=1 /L=1 B view_image dx-1, dy-1
+			Cursor /w=$graphname /A=0 /P /I /S=2 /H=2 /L=1 C view_image round(0.2 * dx) -1, 0
+			Cursor /w=$graphname /A=0 /P /I /S=2 /H=2 /L=1 D view_image round(0.8 * dx) -1, 0
+			Cursor /w=$graphname /A=0 /P /I /S=2 /H=2 /L=1 E view_image round(0.4 * dx) -1, 0
+			Cursor /w=$graphname /A=0 /P /I /S=2 /H=2 /L=1 F view_image round(0.6 * dx) -1, 0
+
+			ShowInfo /w=$graphname /CP=0
+			cursor_mode = mode
+			break
+		default:
+			Cursor /w=$graphname /A=1 /P /I /S=2 /H=1 /L=1 A view_image 0,0
+			Cursor /w=$graphname /A=1 /P /I /S=2 /H=1 /L=1 B view_image dx-1, dy-1
+			variable pcurs
+			pcurs = floor(DimSize(xprofiles, 0) / 3)
+			Cursor /w=$graphname /A=0 /P /S=1 /H=0 C xprofiles#2 pcurs
+			pcurs = floor(DimSize(xprofiles, 0) * 2 / 3)
+			Cursor /w=$graphname /A=0 /P /S=1 /H=0 D xprofiles#2 pcurs
+			pcurs = floor(DimSize(yprofiles, 0) / 3)
+			Cursor /w=$graphname /A=0 /P /S=1 /H=0 E yprofiles#2 pcurs
+			pcurs = floor(DimSize(yprofiles, 0) * 2 / 3)
+			Cursor /w=$graphname /A=0 /P /S=1 /H=0 F yprofiles#2 pcurs
+			ShowInfo /w=$graphname /CP=0
+			cursor_mode = 0
+	endswitch
+	
+	setdatafolder savedf
+	return 0
+end
+
 /// move a cursor to the specified position in a profiles graph.
+///
+/// this function can only set cursors in the image part of the profiles graph.
+///
+/// @param image		image displayed in the graph. 
+///						this is the original image, not the one in the view data folder.
+/// @param cursorname	name of the cursor, e.g. "A" or "B".
+///						other cursors are allowed but need to be activated separately.
+/// @param xa			x-coordinate to move the cursor to.
+///						the position is coerced to the image scale. +/-inf is allowed.
+/// @param ya			y-coordinate to move the cursor to.
+///						the position is coerced to the image scale. +/-inf is allowed.
+/// @param pscale		scaling of the position argument
+///						@arg 0 (default) wave scaling
+///						@arg 1 point scaling
+///
 function ad_profiles_set_cursor(image, cursorname, xa, ya, [pscale])
-	wave image // image displayed in the graph. this is the original image, not the one in the view data folder.
-	string cursorname // name of the cursor. must be "A" or "B".
-	variable xa, ya // position to move the cursor to.
-		// the position is coerced to the image scale. +/-inf is allowed.
-	variable pscale // scaling of the position argument
-		// 0 (default) = wave scaling
-		// 1 = point scaling
+	wave image
+	string cursorname
+	variable xa, ya
+	variable pscale
 	
 	if (ParamIsDefault(pscale))
 		pscale = 0
@@ -1004,7 +1097,7 @@ function /s ad_display_brick(data)
 	setdatafolder viewdf
 	string dfname = ReplaceString("root:", s_datadf, "")
 	string graphtitle = dfname + " Gizmo"
-	string /g gizmo_graphname = CleanupName("giz_" + dfname, 0)
+	string /g gizmo_graphname = graphname_from_dfref(datadf, "giz_")
 	svar graphname = gizmo_graphname
 
 	if ((strlen(graphname) > 0) && (wintype(graphname) == 13))

pearl/pearl-area-import.ipf

@@ -1667,12 +1667,12 @@ function adh5_scale_scienta(data)
 			case 1: // Angular45
 				ALow = -45/2
 				AHigh = +45/2
-				AUnit = "deg"
+				AUnit = "°"
 				break
 			case 2: // Angular60
 				ALow = -60/2
 				AHigh = +60/2
-				AUnit = "deg"
+				AUnit = "°"
 				break
 		endswitch
 	endif

pearl/pearl-data-explorer.ipf

@@ -1,11 +1,14 @@
 #pragma rtGlobals=3		// Use modern global access method and strict wave access.
 #pragma IgorVersion = 6.1
 #pragma ModuleName = PearlDataExplorer
-#pragma version = 1.43
+#pragma version = 1.50
 #include "pearl-area-import"
 #include "pearl-area-profiles"
 #include "pearl-area-display"
 #include "pearl-pshell-import"
+#if exists("MFR_OpenResultFile")
+#include "pearl-matrix-import"
+#endif
 
 // copyright (c) 2013-16 Paul Scherrer Institut
 //
@@ -20,7 +23,10 @@
 ///
 ///
 /// preview and import panel for PEARL data:
-/// scienta analyser, prosilica cameras, s-scans, otf-scans
+/// @arg area detector (HDF5) files from scienta analyser and prosilica cameras (if HDF5.xop is installed).
+/// @arg igor text files from s-scans and otf-scans.
+/// @arg pshell (HDF5) data files (if HDF5.xop is installed).
+/// @arg matrix STM files (if MatrixFileReader.xop is installed).
 
 /// @namespace PearlDataExplorer
 /// @brief preview and import panel for PEARL data
@@ -33,6 +39,7 @@ static strconstant package_path = "root:packages:pearl_explorer:"
 static strconstant ks_filematch_adh5 = "*.h5"
 static strconstant ks_filematch_pshell = "psh*.h5"
 static strconstant ks_filematch_itx = "*.itx"
+static strconstant ks_filematch_mtrx = "*_mtrx"
 
 function pearl_data_explorer()
 	init_package()
@@ -140,31 +147,64 @@ static function load_prefs()
 	return result
 end
 
+/// check whether a file can be imported by this module.
+///
+/// the file type is determined by the extension of the file name.
+///
+/// @return file type
+///	@arg 0	not a recognized file type
+///	@arg 1	PShell file (HDF5, name starts with psh_)
+///	@arg 2	area detector HDF5 file
+///	@arg 3	Igor text (itx) file
+///	@arg 4	Matrix STM file (*_mtrx)
+///
+static function pearl_file_type(filename)
+	string filename
+	
+	if (StringMatch(filename, ks_filematch_pshell))
+		return 1
+	elseif (StringMatch(filename, ks_filematch_adh5))
+		return 2
+	elseif (StringMatch(filename, ks_filematch_itx))
+		return 3
+#if exists("MFR_OpenResultFile")
+	elseif (StringMatch(filename, ks_filematch_mtrx))
+		return 4
+#endif
+	else
+		return 0
+	endif
+end
+
+/// read a list of PEARL files from the file system
+///
+/// wtFiles and wSelectedFiles in the package data folder are updated.
+/// only files for which pearl_file_type() returns non-zero are listed.
+///
 static function update_filelist()
 	dfref saveDF = GetDataFolderDFR()
 
-	string hdf_files, itx_files, all_files
+	string all_files
 	wave /t wtFiles = $(package_path + "wtFiles")
 	wave wSelectedFiles = $(package_path + "wSelectedFiles")
 	variable nn
 	
 	PathInfo pearl_explorer_filepath
 	if (v_flag == 1)
-		hdf_files = IndexedFile(pearl_explorer_filepath, -1, ".h5")
-		itx_files = IndexedFile(pearl_explorer_filepath, -1, ".itx")
-		all_files = hdf_files + itx_files
-		all_files = SortList(hdf_files + itx_files, ";", 4)
+		all_files = IndexedFile(pearl_explorer_filepath, -1, "????")
 		nn = ItemsInList(all_files)
 	else
 		all_files = ""
 		nn = 0
 	endif
 	
-	redimension /n=(nn) wtFiles, wSelectedFiles
-	if (nn > 0)
-		wtFiles = StringFromList(p, all_files)
-		wSelectedFiles = 0
-	endif
+	make /n=(nn) /t /free wtAllFiles
+	wtAllFiles = StringFromList(p, all_files)
+	Extract /o /t wtAllFiles, wtFiles, pearl_file_type(wtAllFiles[p])
+	Sort /A /R wtFiles, wtFiles
+	
+	redimension /n=(numpnts(wtFiles)) wSelectedFiles
+	wSelectedFiles = 0
 	
 	setdatafolder saveDF
 end
@@ -216,14 +256,24 @@ static function preview_file(filename)
 	string filename
 	
 	dfref saveDF = GetDataFolderDFR()
-
-	if (StringMatch(filename, ks_filematch_pshell))
-		wave /z image = preview_pshell_file(filename)
-	elseif (StringMatch(filename, ks_filematch_adh5))
-		wave /z image = preview_hdf_file(filename)
-	elseif (StringMatch(filename, ks_filematch_itx))
-		wave /z image = preview_itx_file(filename)
-	endif
+	
+	variable ft = pearl_file_type(filename)
+	switch(ft)
+		case 1:
+			wave /z image = preview_pshell_file(filename)
+			break
+		case 2:
+			wave /z image = preview_hdf_file(filename)
+			break
+		case 3:
+			wave /z image = preview_itx_file(filename)
+			break
+		case 4:
+			wave /z image = preview_mtrx_file(filename)
+			break
+		default:
+			wave /z image = $""
+	endswitch
 	
 	if (WaveExists(image))
 		string graphname = show_preview_graph(image)
@@ -240,9 +290,10 @@ static function preview_file(filename)
 	endif
 	
 	setdatafolder saveDF
+	return 0
 end
 
-/// load the preview of a PShell HDF5 file (not implemented).
+/// load the preview of a PShell HDF5 file.
 ///
 /// the preview is an arbitrary detector image extracted from the file, see adh5_load_preview().
 /// the preview is loaded to the preview_image wave in the pear_explorer data folder.
@@ -354,6 +405,63 @@ static function /wave preview_itx_file(filename)
 	return preview_image
 end
 
+/// load the preview of a Matrix STM file.
+///
+/// the preview is loaded to the preview_image wave in the pearl_explorer data folder.
+///
+/// the s_file_info string is updated with information about the scan dimensions.
+///
+/// this function requires the MatrixFileReader.xop and pearl-matrix-import.ipf to be loaded.
+/// otherwise it will return an empty wave reference.
+///
+/// @param	filename		name of a file in the directory specified by the pearl_explorer_filepath path object.
+///
+/// @return	wave reference of the preview image.
+///			empty wave reference if the function failed.
+///
+static function /wave preview_mtrx_file(filename)
+	string filename
+
+#if exists("MFR_OpenResultFile")
+	dfref saveDF = GetDataFolderDFR()
+	setdatafolder $package_path
+	variable /g V_MatrixFileReaderOverwrite = 1
+	variable /g V_MatrixFileReaderFolder = 0
+	variable /g V_MatrixFileReaderDouble = 0
+	svar s_preview_file
+	svar s_preview_source
+	string datanames
+	string dataname
+	datanames = mtrx_load_preview("preview", "pearl_explorer_filepath", filename)
+	if (strlen(datanames) > 0)
+		s_preview_file = filename
+
+		dataname = StringFromList(0, datanames)
+		wave data = $dataname
+		duplicate /o $dataname, preview_image
+		s_preview_source = StringByKey("Dataset", note(data), "=", "\r")
+		
+		svar /z s_file_info
+		if (svar_exists(s_file_info))
+			s_file_info = ""
+		endif
+		
+		variable i
+		variable n = ItemsInList(datanames)
+		string s
+		for (i = 0; i < n; i += 1)
+			s = StringFromList(i, datanames)
+			killwaves /z $s
+		endfor
+	endif
+	wave /z preview_image
+	setdatafolder saveDF
+#else
+	wave /z preview_image = $""
+#endif
+	return preview_image
+end
+
 static function extract_preview_image(data, preview)
 	// extracts a preview image from a wave of arbitrary dimension
 	wave data
@@ -862,22 +970,32 @@ static function load_file(filename, [options])
 	
 	dfref saveDF = GetDataFolderDFR()
 
-	if (StringMatch(filename, ks_filematch_pshell))
-		if (ParamIsDefault(options))
-			load_pshell_file(filename)
-		else
-			load_pshell_file(filename, options=options)
-		endif
-	elseif (StringMatch(filename, ks_filematch_adh5))
-		if (ParamIsDefault(options))
-			load_hdf_file(filename)
-		else
-			load_hdf_file(filename, options=options)
-		endif
-	elseif (StringMatch(filename, ks_filematch_itx))
-		load_itx_file(filename)
-	endif
-	
+	variable ft = pearl_file_type(filename)
+	switch(ft)
+		case 1:
+			if (ParamIsDefault(options))
+				load_pshell_file(filename)
+			else
+				load_pshell_file(filename, options=options)
+			endif
+			break
+		case 2:
+			if (ParamIsDefault(options))
+				load_hdf_file(filename)
+			else
+				load_hdf_file(filename, options=options)
+			endif
+			break
+		case 3:
+			load_itx_file(filename)
+			break
+		case 4:
+			load_mtrx_file(filename)
+			break
+		default:
+			break
+	endswitch
+
 	setdatafolder saveDF
 end
 
@@ -972,6 +1090,7 @@ static function /df load_pshell_file(filename, [options])
 				string reduction_params = pref_params
 				if (prompt_func_params(reduction_func, reduction_params) == 0)
 					pref_params = reduction_params
+					print reduction_func, reduction_params
 					psh5_load_reduced(nickname, "pearl_explorer_filepath", filename, $reduction_func, reduction_params)
 					svar s_filepath
 					loaded_filename = s_filepath
@@ -1023,6 +1142,7 @@ static function /df load_hdf_file(filename, [options])
 				string reduction_params = pref_params
 				if (prompt_func_params(reduction_func, reduction_params) == 0)
 					pref_params = reduction_params
+					print reduction_func, reduction_params
 					loaded_filename = adh5_load_reduced(nickname, "pearl_explorer_filepath", filename, $reduction_func, reduction_params)
 				endif
 				break
@@ -1080,6 +1200,32 @@ static function /df load_itx_file(filename, [options])
 	return actDF
 end
 
+/// load a matrix (STM) data file
+///
+///
+static function /df load_mtrx_file(filename, [options])
+	string filename
+	string options
+
+	dfref saveDF = GetDataFolderDFR()
+	dfref dataDF = $""
+
+#if exists("MFR_OpenResultFile")
+	setdatafolder root:
+	string datasets = ""
+	datasets = mtrx_load_file("pearl_explorer_filepath", filename)
+	if (strlen(datasets) > 0)
+		string /g pearl_explorer_import = "load_mtrx_file"
+		string s1 = StringFromList(0, datasets)
+		wave w1 = $s1
+		dataDF = GetWavesDataFolderDFR(w1)
+	endif
+#endif
+	
+	setdatafolder saveDF
+	return dataDF
+end
+
 function /s itx_suggest_foldername(filename, [ignoredate,sourcename,unique])
 	// suggests the name of a data folder based on a file name
 	// if the file name follows the naming convention source-date-index.extension,
@@ -1450,7 +1596,7 @@ static function bp_dataset_folder(ba) : ButtonControl
 				string cmd
 				sprintf cmd, "setdatafolder root:%s", PossiblyQuoteName(dataset)
 				execute /q /z cmd
-				cmd = "setdatafolder :scan_1"
+				cmd = "setdatafolder :scan1"
 				execute /q /z cmd
 				sprintf cmd, "setdatafolder %s", GetDataFolder(1)
 				print cmd

pearl/pearl-elog.ipf

@@ -1,5 +1,5 @@
 #pragma rtGlobals=3		// Use modern global access method and strict wave access.
-#pragma version = 1.31
+#pragma version = 1.40
 #pragma IgorVersion = 6.2
 #pragma ModuleName = PearlElog
 
@@ -16,13 +16,38 @@
 /// @ingroup ArpesPackage
 ///
 ///
-/// the functions in this module support the following work flows:
-/// 1. send a preview of a selected measurement to ELOG.
-/// 2. send any Igor graph to ELOG. (CLI and GUI)
-/// 3. direct access to all ELOG parameters. (CLI only)
+/// the functions in this module support the following ELOG features:
+/// - submit new entries and replies to existing entries.
+/// - text field, list box, and check box attributes.
+/// - attach any Igor graph to ELOG.
+/// - configurable logbook templates for logbooks that share the same configuration.
+/// - common server configurations available on the ELOG command line
+///   (hostname, port, SSL, username, password, sub-directory).
+/// - not specific to the configuration at PEARL.
+///   PEARL code is concentrated in the elog_init_pearl_templates() function.
+/// - the configuration of the ELOG server and logbooks
+///   as well as the most recently used attributes are persisted in the preference file.
 ///
-/// the configuration of the ELOG server and logbooks (except user name and password)
-/// as well as the most recently used attributes are persisted in the preference file.
+/// usage:
+/// 1. the administrator of the ELOG server creates logbook templates
+///    according to the configuration of the logbooks.
+///    the templates are written in Igor code.
+/// 2. the user opens logbooks via the _Open ELOG panel_ menu item.
+///    before first use, select a template and enter a name for the logbook.
+///    the new logbook is written to the preference file,
+///    and can afterwards be opened directly.
+/// 3. if the server requires a user name and password,
+///    click the login button.
+/// 4. edit the message, attributes and attachments as necessary, and submit to ELOG.
+/// 5. log out before saving the experiment to clear the password.
+///
+/// @attention the user name and password are stored in the global data tree of an experiment.
+/// it is not possible to handle passwords safely in Igor.
+/// they can be read by anyone having access to an open Igor experiment or a saved experiment file
+/// (unless the password is reset before saving).
+/// therefore:
+/// - use a password for the ELOG server which is different from your other passwords.
+/// - clear the password (logout button in the panel) before saving an experiment.
 ///
 /// elog command line
 ///@verbatim
@@ -43,12 +68,6 @@
 ///     -m <textfile>] | <text>
 ///@endverbatim
 ///
-/// user name and password are used if configured in the package data folder.
-/// there is currently no separate user interface.
-///
-/// @attention some functions in this module refer specifically to the ELOG configuration at PEARL.
-///
-/// @todo ask for logbook, username and password before opening the panel.
 ///
 /// @author matthias muntwiler, matthias.muntwiler@psi.ch
 ///
@@ -82,7 +101,7 @@ function pearl_elog(logbook)
 		load_prefs()
 		string templates = list_logbooks(templates=1)
 		if (ItemsInList(templates) < 1)
-			init_pearl_templates()
+			elog_init_pearl_templates()
 		endif
 	endif
 	
@@ -95,7 +114,11 @@ function pearl_elog(logbook)
 		if (strlen(WinList(win_name, ";", "")) > 0)
 			DoWindow /F $win_name
 		else
-			PearlElogPanel(logbook)
+			win_name = PearlElogPanel(logbook)
+			STRUCT WMWinHookStruct s
+			s.eventCode = 0
+			s.winName = win_name
+			elog_panel_hook(s)
 		endif
 	endif
 end
@@ -104,6 +127,7 @@ end
 static function IgorBeforeNewHook(igorApplicationNameStr)
 	string igorApplicationNameStr
 	save_prefs()
+	cleanup_temp_files()
 	return 0
 end
 
@@ -111,6 +135,7 @@ end
 static function IgorQuitHook(igorApplicationNameStr)
 	string igorApplicationNameStr
 	save_prefs()
+	cleanup_temp_files()
 	return 0
 end
 
@@ -234,7 +259,7 @@ end
 ///
 /// @remark this function is specific to the setup at PEARL.
 ///
-static function init_pearl_templates()
+function elog_init_pearl_templates()
 	dfref savedf = getdatafolderdfr()
 
 	dfref df_root = get_elog_df("", kdfRoot)
@@ -247,10 +272,10 @@ static function init_pearl_templates()
 	
 	// attributes (persistent)
 	// available attributes
-	string /g attributes = "author;project;sample;source;task;technique;valid;file"
+	string /g attributes = "author;project;sample;source;task;technique;file;valid;"
 	// controls corresponding to attributes
 	// prefix determines the control type: sv_ = setvariable (string), pm_ = popup menu, cb = check box
-	string /g controls = "sv_author;sv_project;sv_sample;pm_source;pm_task;pm_technique;cb_valid;sv_file"
+	string /g controls = "sv_author;sv_project;sv_sample;pm_source;pm_task;pm_technique;sv_file;cb_valid;"
 	// attributes with fixed options, value item declares the options string
 	string /g options = "source=sources;task=tasks;technique=techniques"
 	// attributes which must be defined
@@ -258,8 +283,8 @@ static function init_pearl_templates()
 
 	// option lists
 	string /g sources = "Manual Entry;PShell;Scienta Data;SScan Data;Prosilica Data;OTF Data;Beamline Status;LEED Data;QMS Data;Matrix Data;Igor Pro;Other"
-	string /g tasks = "Measurement;Sample Preparation;Sample Storage;Optimization;Analysis;Development;Maintenance;Test;Comment;Other"
-	string /g techniques = "XPS;UPS;XPD;XAS;XMCD;PhD;ARUPS;LEED;AES;STM;STS;QMS;MBE;Test;Other"
+	string /g tasks = "Measurement;Optimization;Analysis;Sample Preparation;Sample Storage;Comment;Development;Maintenance;Test;Other"
+	string /g techniques = "XPS;UPS;XPD;XAS;XMCD;PhD;ARUPS;STM;STS;LEED;AES;QMS;MBE;Sputter/Anneal;Test;Other"
 
 	// Calculations template
 	setdatafolder df_templates
@@ -267,18 +292,38 @@ static function init_pearl_templates()
 	
 	// attributes (persistent)
 	// available attributes
-	string /g attributes = "author;project;sample;program;revision;machine;job;source path;result path;valid"
+	string /g attributes = "author;project;sample;program;revision;machine;job;experiment;source path;result path;valid"
 	// controls corresponding to attributes
 	// prefix determines the control type: sv_ = setvariable (string), pm_ = popup menu, cb = check box
-	string /g controls = "sv_author;sv_project;sv_sample;pm_program;sv_revision;pm_machine;sv_job;sv_sourcepath;sv_resultpath;cb_valid"
+	string /g controls = "sv_author;sv_project;sv_sample;pm_program;sv_revision;pm_machine;sv_job;sv_experiment;sv_sourcepath;sv_resultpath;cb_valid"
 	// attributes with fixed options, value item declares the options string
 	string /g options = "program=programs;machine=machines"
 	// attributes which must be defined
 	string /g required_attributes = "author;project;sample"
 
 	// option lists
-	string /g programs = "DMSUP;EDAC;MSC;MUFPOT;SSC"
-	string /g machines = "llcx;Merlin;PC"
+	string /g programs = "PMSCO;EDAC;MSC;SSC;MUFPOT;DMSUP;Other"
+	string /g machines = "PC;VM;Ra;Merlin;llcx;Other"
+
+	// System template
+	setdatafolder df_templates
+	newdatafolder /o/s System
+	
+	// attributes (persistent)
+	// available attributes
+	string /g attributes = "author;type;system;source;file"
+	// controls corresponding to attributes
+	// prefix determines the control type: sv_ = setvariable (string), pm_ = popup menu, cb = check box
+	string /g controls = "sv_author;pm_type;pm_system;pm_source;sv_file"
+	// attributes with fixed options, value item declares the options string
+	string /g options = "type=types;system=systems;source=sources"
+	// attributes which must be defined
+	string /g required_attributes = "author;type;system"
+
+	// option lists
+	string /g types = "Installation;Repair;Maintenance;Test;Commissioning;Bakeout;Incident;Cool-down;Warm-up;Storage;Other"
+	string /g systems = "Vacuum;Control System;BL;XA;XP;SA;SP;T;LL;Monochromator;Carving;Scienta;STM;PC-Scienta;PC-Matrix;PC-Console;PC-Console-Win;PC-XP;EPS;LAC;Desiccator"
+	string /g sources = "Manual Entry;PShell;Scienta Data;SScan Data;Prosilica Data;OTF Data;Beamline Status;LEED Data;QMS Data;Matrix Data;Igor Pro;Other"
 
 	setdatafolder savedf
 	return 0
@@ -303,6 +348,11 @@ static function init_volatile_vars()
 	variable nlb = ItemsInList(logbooks)
 	variable ilb
 	
+	SetDataFolder df_volatile_root
+	if (exists("temp_graph_files") != 2)
+		string /g temp_graph_files = ""
+	endif
+
 	for (ilb = 0; ilb < nlb; ilb += 1)
 		logbook = StringFromList(ilb, logbooks)
 		
@@ -322,6 +372,13 @@ static function init_volatile_vars()
 		if (exists("msg_id") != 2)
 			variable /g msg_id = 0
 		endif
+		if (exists("att_list") != 1)
+			make /n=(0,3) /t /o attach_list
+			make /n=(0,3) /i /o attach_sel
+		endif
+		if (exists("url") != 2)
+			string /g url = ""
+		endif
 	endfor
 	
 	SetDataFolder savedf
@@ -347,6 +404,9 @@ end
 /// create a new empty logbook or duplicate from a template.
 ///
 /// @param name				name of the new logbook.
+///							if the logbook exists, the existing logbook folder is killed
+///							and replaced by a new one.
+///							this may fail if a window is still open.
 ///
 /// @param template			name of the template.
 ///							if empty string, a new empty logbook is created.
@@ -366,8 +426,19 @@ function elog_create_logbook(name, [template])
 	dfref df_volatile_root = get_elog_df("", kdfVolatile)
 	dfref df_volatile_parent = df_volatile_root:logbooks
 
+	setdatafolder df_persistent_parent
+	if (CheckName(name, 11) != 0)
+		setdatafolder savedf
+		Abort "invalid logbook name"
+		return -1
+	endif
+	
 	if (strlen(template) > 0)
 		dfref df_template = get_elog_df(template, kdfTemplates)
+		dfref df_existing = get_elog_df(name, kdfPersistent)
+		if (DataFolderRefStatus(df_existing))
+			KillDataFolder /Z df_existing
+		endif
 		DuplicateDataFolder df_template, df_persistent_parent:$name
 	else
 		NewDataFolder /o/s df_persistent_parent:$name
@@ -695,7 +766,6 @@ function elog_create_entry(logbook, attributes, message, [encoding, graphs, repl
 				endif
 				result = -4
 			endif
-			cleanup_temp_files()
 		else
 			if (loglevel >= 2)
 				print "ELOG: failed to create temporary message file."
@@ -759,7 +829,6 @@ function elog_add_attachment(logbook, id, graphs)
 			endif
 			result = -4 // error: elog returned error
 		endif
-		cleanup_temp_files()
 	endif
 	
 	setdatafolder savedf
@@ -817,6 +886,39 @@ static function /s prepare_command_line(logbook)
 	return cmd
 end
 
+/// format the URL for display to the user
+///
+///
+/// @param	logbook	name of the target logbook
+///
+static function /s format_url(logbook)
+	string logbook
+	
+	dfref df_general = get_elog_df("", kdfPersistent)
+	
+	svar /sdfr=df_general hostname
+	nvar /sdfr=df_general port
+	nvar /sdfr=df_general ssl
+	svar /sdfr=df_general subdir
+
+	string cmd = ""
+	if ((nvar_exists(ssl)) && (ssl != 0))
+		cmd += "https://"
+	else
+		cmd += "http://"
+	endif
+	cmd += hostname
+	if ((nvar_exists(port)) && (port > 0))
+		cmd += ":" + num2str(port)
+	endif
+	if ((svar_exists(subdir)) && (strlen(subdir) > 0))
+		cmd += "/" + subdir
+	endif
+	cmd += "/" + logbook
+	
+	return cmd
+end
+
 /// prepare screenshots of graph windows for attachments
 ///
 /// prepares the attachment files from Igor graph windows
@@ -875,13 +977,18 @@ static function /s create_graph_file(graphname, fileindex)
 	string graphname
 	variable fileindex
 	
+	dfref df_volatile_root = get_elog_df("", kdfVolatile)
+	svar /sdfr=df_volatile_root temp_graph_files
+
 	string path = SpecialDirPath("Temporary", 0, 1, 0)
 	string ts = get_timestamp("_")
 	variable len = strlen(path)
 	if (numtype(len) == 0)
 		path += "elog_" + ts + "_" + num2str(fileindex) + ".png"
 		SavePICT /B=72 /E=-5 /M /O /W=(0,0,8,6) /WIN=$graphname /Z as path
-		if (v_flag != 0)
+		if (v_flag == 0)
+			temp_graph_files = AddListItem(path, temp_graph_files, ";", inf)
+		else
 			path = ""
 		endif
 	else
@@ -921,12 +1028,30 @@ static function /s get_log_path()
 	return path
 end
 
-static function /s cleanup_temp_files()
-	string path = SpecialDirPath("Temporary", 0, 1, 0)
-	string cmd
-	sprintf cmd, "del \"%s\elog*.*\"", path
-	//ExecuteScriptText cmd
-	return path
+/// delete temporary files created by the ELOG module.
+///
+/// this deletes all temporary graph files that are referenced by the volatile temp_graph_files list.
+/// temp_graph_files is a semicolon-delimited string.
+/// items are added by create_graph_file().
+///
+/// this function should be called before a new experiment is loaded or igor quits.
+///
+static function cleanup_temp_files()
+	dfref df_volatile_root = get_elog_df("", kdfVolatile)
+	if (DataFolderRefStatus(df_volatile_root))
+		svar /sdfr=df_volatile_root /z temp_graph_files
+		if (SVAR_Exists(temp_graph_files))
+			variable nfi = ItemsInList(temp_graph_files)
+			variable ifi
+			string sfi
+			for (ifi = 0; ifi < nfi; ifi += 1)
+				sfi = StringFromList(ifi, temp_graph_files)
+				DeleteFile /Z sfi
+			endfor
+			temp_graph_files = ""
+		endif
+	endif
+	return 0
 end
 
 static strconstant elog_success_msg = "Message successfully transmitted"
@@ -1048,14 +1173,17 @@ function /s PearlElogPanel(logbook)
 	string win_name = logbook + "ElogPanel"
 	string win_title = "ELOG " + logbook
 	
-	NewPanel /K=1 /N=$win_name /W=(600,200,926,494) as win_title
+	NewPanel /K=1 /N=$win_name /W=(600,200,1200,700) as win_title
 	win_name = s_name
 	ModifyPanel /w=$win_name cbRGB=(52224,52224,65280)
 
 	svar /sdfr=df_persistent attributes
 	svar /sdfr=df_persistent controls
 	svar /sdfr=df_persistent options
-
+	wave /t /sdfr=df_volatile attach_list
+	wave /sdfr=df_volatile attach_sel
+	svar /sdfr=df_volatile url
+	
 	variable iattr
 	variable nattr = ItemsInList(attributes, ";")
 	string s_attr
@@ -1066,35 +1194,28 @@ function /s PearlElogPanel(logbook)
 	string options_path
 	string variable_path
 	variable ypos = 2
+	variable height = 0
 	
-	Button b_login,win=$win_name, pos={264,ypos},size={46,20},proc=PearlElog#bp_login,title="Login"
-	Button b_login,win=$win_name, help={"Enter user name and password."}
-	Button b_login,win=$win_name, fcolor=(56576,60928,47872)
-
-	Button b_logout,win=$win_name, pos={264,ypos},size={46,20},proc=PearlElog#bp_logout,title="Logout"
-	Button b_logout,win=$win_name, help={"Clear user name and password."}
-	Button b_logout,win=$win_name, fcolor=(56576,60928,47872), disable=3
-
 	for (iattr = 0; iattr < nattr; iattr += 1)
 		s_attr = StringFromList(iattr, attributes, ";")
 		s_control = StringFromList(iattr, controls, ";")
 		strswitch(s_control[0,1])
 			case "sv":
-				SetVariable $s_control, win=$win_name, pos={0,ypos}, size={260,16}, bodyWidth=200
+				SetVariable $s_control, win=$win_name, pos={0,ypos}, size={300,16}, bodyWidth=230
 				SetVariable $s_control, win=$win_name, title=s_attr, value= _STR:""
 				SetVariable $s_control, win=$win_name, userdata(attribute)=s_attr
 				ypos += 18
 				break
 			case "pm":
 				options_path = persistent_path + StringByKey(s_attr, options, "=", ";")
-				PopupMenu $s_control, win=$win_name, pos={0,ypos}, size={260,21}, bodyWidth=200
+				PopupMenu $s_control, win=$win_name, pos={0,ypos}, size={300,21}, bodyWidth=230
 				PopupMenu $s_control, win=$win_name, title=s_attr
 				PopupMenu $s_control, win=$win_name, mode=1, popvalue="Test", value= #options_path
 				PopupMenu $s_control, win=$win_name, userdata(attribute)=s_attr
 				ypos += 23
 				break
 			case "cb":
-				CheckBox $s_control, win=$win_name, pos={60,ypos}, size={260,14}
+				CheckBox $s_control, win=$win_name, pos={70,ypos}, size={300,14}
 				CheckBox $s_control, win=$win_name, title=s_attr, value= 1
 				CheckBox $s_control, win=$win_name, userdata(attribute)=s_attr
 				ypos += 17
@@ -1102,48 +1223,81 @@ function /s PearlElogPanel(logbook)
 		endswitch
 	endfor
 
-	PopupMenu pm_attach,win=$win_name, pos={0,ypos},size={260,21},bodyWidth=200,title="Attachment"
-	PopupMenu pm_attach,win=$win_name, mode=1,popvalue="(none)",value=PearlElog#pm_list_attach_items()
-	PopupMenu pm_attach,win=$win_name, help={"Choose any visible Igor graph for attachment."}
-	Button b_select_attach_top,win=$win_name, pos={264,ypos},size={60,20},proc=PearlElog#bp_select_attach_top,title="Top Graph"
-	Button b_select_attach_top,win=$win_name, help={"Select top graph window."}
-	Button b_select_attach_top,win=$win_name, fcolor=(56576,60928,47872)
+	TitleBox t_attach, win=$win_name, pos={308,5}, size={70,14}, title="Attachments", frame=0
+	height = ypos - 21 - 4
+	ListBox lb_attach, win=$win_name, pos={308,21}, size={264,height}
+	ListBox lb_attach, win=$win_name, listWave=attach_list
+	ListBox lb_attach, win=$win_name, mode=1, selWave=attach_sel, selRow=-1
+	ListBox lb_attach, win=$win_name, widths={20,160,80}
+	ListBox lb_attach, win=$win_name, help={"Choose graphs to attach to the message."}
+
+	Button b_attach_top, win=$win_name, pos={420,2}, size={40,18}, title="top"
+	Button b_attach_top, win=$win_name, fcolor=(56576,60928,47872)
+	Button b_attach_top, win=$win_name, proc=PearlElog#bp_attach_top
+	Button b_attach_top, win=$win_name, help={"Select top graph for attachment."}
+	Button b_attach_all, win=$win_name, pos={460,2}, size={40,18}, title="all"
+	Button b_attach_all, win=$win_name, fcolor=(56576,60928,47872)
+	Button b_attach_all, win=$win_name, proc=PearlElog#bp_attach_allnone
+	Button b_attach_all, win=$win_name, help={"Select all graphs for attachment."}
+	Button b_attach_none, win=$win_name, pos={500,2}, size={40,18}, title="none"
+	Button b_attach_none, win=$win_name, fcolor=(56576,60928,47872)
+	Button b_attach_none, win=$win_name, proc=PearlElog#bp_attach_allnone
+	Button b_attach_none, win=$win_name, help={"Deselect all attachments."}
+	Button b_save_graphs, win=$win_name, pos={540,2}, size={40,18}, title="save"
+	Button b_save_graphs, win=$win_name, fcolor=(56576,60928,47872)
+	Button b_save_graphs, win=$win_name, proc=PearlElog#bp_save_graphs
+	Button b_save_graphs, win=$win_name, help={"Save selected graphs as PNG bitmap files."}
+	Button b_attach_up, win=$win_name, pos={576,20}, size={20,20}, title="\\W517"
+	Button b_attach_up, win=$win_name, fcolor=(56576,60928,47872)
+	Button b_attach_up, win=$win_name, proc=PearlElog#bp_attach_updown
+	Button b_attach_up, win=$win_name, help={"Move selected graph up."}
+	Button b_attach_dw, win=$win_name, pos={576,40}, size={20,20}, title="\\W523"
+	Button b_attach_dw, win=$win_name, fcolor=(56576,60928,47872)
+	Button b_attach_dw, win=$win_name, proc=PearlElog#bp_attach_updown
+	Button b_attach_dw, win=$win_name, help={"Move selected graph down."}
 
 	ypos += 246-160
-	Button b_submit,win=$win_name, pos={60,ypos},size={46,20},proc=PearlElog#bp_submit,title="Submit"
+	Button b_submit,win=$win_name, pos={70,ypos},size={46,20},proc=PearlElog#bp_submit,title="Submit"
 	Button b_submit,win=$win_name, help={"Submit form data to ELOG (new entry)."}
 	Button b_submit,win=$win_name, fcolor=(56576,60928,47872)
-	
-	Button b_clear,win=$win_name, pos={110,ypos},size={46,20},proc=PearlElog#bp_clear,title="Clear"
+	Button b_clear,win=$win_name, pos={120,ypos},size={46,20},proc=PearlElog#bp_clear,title="Clear"
 	Button b_clear,win=$win_name, help={"Clear the form fields"}
 	Button b_clear,win=$win_name, fcolor=(56576,60928,47872)
 
 	ypos += 272-246
 	variable_path = volatile_path + "msg_id"
-	SetVariable sv_id,win=$win_name, pos={46,ypos},size={109,16},bodyWidth=94
+	SetVariable sv_id,win=$win_name, pos={51,ypos},size={119,16},bodyWidth=77
 	SetVariable sv_id,win=$win_name, title="ID",value=$variable_path
 	SetVariable sv_id,win=$win_name, help={"ID of last submitted message, or message to attach or reply to."}
 
+	TitleBox t_host, win=$win_name, pos={170,ypos+4}, size={112.00,14.00}, frame=0
+	TitleBox t_host, win=$win_name, variable=url
+
 	ypos += 270-272
-	Button b_attach,win=$win_name, pos={160,ypos},size={48,20},proc=PearlElog#bp_attach,title="Attach"
+	Button b_attach,win=$win_name, pos={170,ypos},size={48,20},proc=PearlElog#bp_attach,title="Attach"
 	Button b_attach,win=$win_name, help={"Attach the selected graph to an existing ELOG entry (correct ID required)."}
 	Button b_attach,win=$win_name, fcolor=(56576,60928,47872)
-	
-	Button b_reply,win=$win_name, pos={210,ypos},size={48,20},proc=PearlElog#bp_submit,title="Reply"
+	Button b_reply,win=$win_name, pos={220,ypos},size={48,20},proc=PearlElog#bp_submit,title="Reply"
 	Button b_reply,win=$win_name, help={"Submit form data to ELOG as a reply to an existing message (correct ID required)."}
 	Button b_reply,win=$win_name, fcolor=(56576,60928,47872)
-
-	ypos += 184-270
-	TitleBox t_message,win=$win_name, pos={0,ypos},size={58,16},fixedSize=1,frame=0,anchor=RT,title="Message"
+	Button b_login,win=$win_name, pos={550,ypos},size={46,20},proc=PearlElog#bp_login,title="Login"
+	Button b_login,win=$win_name, help={"Enter user name and password."}
+	Button b_login,win=$win_name, fcolor=(56576,60928,47872)
+	Button b_logout,win=$win_name, pos={550,ypos},size={46,20},proc=PearlElog#bp_logout,title="Logout"
+	Button b_logout,win=$win_name, help={"Clear user name and password."}
+	Button b_logout,win=$win_name, fcolor=(56576,60928,47872), disable=3
 
 	SetWindow $win_name, hook(elogPanelHook)=PearlElog#elog_panel_hook
 	SetWindow $win_name, userdata(logbook)=logbook
 
-	DefineGuide UGH0={FT,ypos},UGV0={FL,60},UGH1={FB,-52},UGV1={FR,-2}
+	ypos += 160-270
+	TitleBox t_message,win=$win_name, pos={10,ypos},size={58,16},fixedSize=1,frame=0,anchor=RT,title="Message"
+	DefineGuide UGH0={FT,ypos},UGV0={FL,70},UGH1={FB,-52},UGV1={FR,-2}
 	NewNotebook /F=0 /N=Message /OPTS=3 /W=(115,404,345,341)/FG=(UGV0,UGH0,UGV1,UGH1) /HOST=# 
 	Notebook kwTopWin, defaultTab=20, statusWidth=0, autoSave=0
-	Notebook kwTopWin font="Arial", fSize=10, fStyle=0, textRGB=(0,0,0)
+	Notebook kwTopWin fSize=10, fStyle=0, textRGB=(0,0,0)
 	RenameWindow #,Message
+	string nb_name = win_name + "#Message"
 	SetActiveSubwindow ##
 
 	// restore recently used attributes and message
@@ -1155,6 +1309,7 @@ function /s PearlElogPanel(logbook)
 	if (svar_exists(recent_message) && (strlen(recent_message) > 0))
 		set_panel_message(win_name, recent_message)
 	endif
+	Notebook $nb_name selection={startOfFile,startOfFile}, findText={"",1}
 	
 	setdatafolder savedf
 	return win_name
@@ -1166,49 +1321,153 @@ static function elog_panel_hook(s)
 	Variable hookResult = 0
 
 	switch(s.eventCode)
+		case 0: // activate
+			string logbook = GetUserData(s.winName, "", "logbook")
+			if (strlen(logbook) > 0)
+				dfref df_volatile = get_elog_df(logbook, kdfVolatile)
+				svar /sdfr=df_volatile url
+				url = format_url(logbook)
+				update_attach_items(logbook)
+			endif
+			break
 		case 6: // resize
 			// move bottom-aligned controls when the window is resized
 			variable b_top = s.winRect.bottom + 4
-			Button b_submit,pos={60,b_top}
-			Button b_clear,pos={110,b_top}
+			Button b_submit,pos={70,b_top}
+			Button b_clear,pos={120,b_top}
+			TitleBox t_host, pos={170,b_top+4}
 			b_top += 24
-			Button b_attach,pos={160,b_top}
-			Button b_reply,pos={210,b_top}
+			Button b_attach,pos={170,b_top}
+			Button b_reply,pos={220,b_top}
+			Button b_login, pos={550,b_top}
+			Button b_logout, pos={550,b_top}
 			b_top += 2
-			SetVariable sv_id,pos={46,b_top}
+			SetVariable sv_id,pos={51,b_top}
 			break
 	endswitch
 
 	return hookResult		// 0 if nothing done, else 1
 end
 
-/// get a list of graph windows for a popup menu.
-static function /s pm_list_attach_items()
+static constant kAttachColSel = 0
+static constant kAttachColTitle = 1
+static constant kAttachColName = 2
 
-	// get graph names
+/// update the list of attachments
+static function update_attach_items(logbook)
+	string logbook
+
+	dfref savedf = getdatafolderdfr()
+	dfref df_volatile = get_elog_df(logbook, kdfVolatile)
+	wave /t /sdfr=df_volatile attach_list
+	wave /sdfr=df_volatile attach_sel
+
+	if (!waveexists(attach_list))
+		return -1
+	endif
 	string names = WinList("*", ";", "WIN:1;VISIBLE:1")
 	names = SortList(names, ";", 16)
-	
-	// get corresponding graph titles
-	variable nnames = ItemsInList(names, ";")
-	variable iname
-	string name
-	string item
-	string items = ""
-	
-	// format each entry like "name: title"
-	for (iname = 0; iname < nnames; iname += 1)
-		name = StringFromList(iname, names, ";")
-		getwindow /z $name, wtitle
-		if (v_flag == 0)
-			item = ReplaceString(";", s_value, ", ")	// title
-			item = item + " (" + name + ")"
-			items = AddListItem(item, items, ";", inf)
+
+	// remove closed graphs
+	variable i
+	variable k
+	variable n = DimSize(attach_list, 0)
+	string s
+	for (i = n-1; i >= 0; i -= 1)
+		s = attach_list[i][kAttachColName]
+		if (WhichListItem(s, names) < 0)
+			DeletePoints /M=0 i, 1, attach_list, attach_sel
 		endif
 	endfor
 	
-	items = AddListItem("(none)", items, ";")
-	return items
+	// add new graphs
+	n = ItemsInList(names)
+	for (i = 0; i < n; i += 1)
+		s = StringFromList(i, names)
+		FindValue /text=s /txop=4 /z attach_list
+		if (v_value < 0)
+			k = DimSize(attach_list, 0)
+			Redimension /n=(k+1,3) attach_list, attach_sel
+			//InsertPoints /M=0 k, 1, attach_list, attach_sel
+			attach_list[k][kAttachColSel] = ""
+			attach_list[k][kAttachColTitle] = ""
+			attach_list[k][kAttachColName] = s
+			attach_sel[k][kAttachColSel] = 32
+			attach_sel[k][kAttachColTitle] = 0
+			attach_sel[k][kAttachColName] = 0
+		endif
+	endfor
+
+	// update titles
+	n = DimSize(attach_list, 0)
+	for (i = n-1; i >= 0; i -= 1)
+		s = attach_list[i][kAttachColName]
+		getwindow /z $s, wtitle
+		if (v_flag == 0)
+			attach_list[i][kAttachColTitle] = s_value
+		else
+			attach_list[i][kAttachColTitle] = s
+		endif
+	endfor
+	
+	setdatafolder savedf
+	return 0
+end
+
+/// move an attachment item in the list of attachments
+static function move_attach_item(logbook, item, distance)
+	string logbook
+	variable item
+	variable distance
+	
+	dfref savedf = getdatafolderdfr()
+	dfref df_volatile = get_elog_df(logbook, kdfVolatile)
+	wave /t /sdfr=df_volatile attach_list
+	wave /sdfr=df_volatile attach_sel
+	variable n = DimSize(attach_list, 0)
+	variable dest = item + distance
+	
+	if ((item >= 0) && (item < n) && (dest >= 0) && (dest < n))
+		string name = attach_list[item][kAttachColName]
+		variable sel = attach_sel[item][kAttachColSel]
+		DeletePoints /M=0 item, 1, attach_list, attach_sel
+		InsertPoints /M=0 dest, 1, attach_list, attach_sel
+		attach_list[dest][kAttachColName] = name
+		update_attach_items(logbook)
+		attach_sel[dest][kAttachColSel] = sel
+	endif
+end
+
+/// button procedure for the attachment up and down buttons
+static function bp_attach_updown(ba) : ButtonControl
+	STRUCT WMButtonAction &ba
+
+	switch( ba.eventCode )
+		case 2: // mouse up
+			string logbook = GetUserData(ba.win, "", "logbook")
+			ControlInfo /w=$ba.win lb_attach
+			variable row = v_value
+			dfref df = $s_datafolder
+			wave /t /sdfr=df attach_list = $s_value
+			if (cmpstr(ba.ctrlName, "b_attach_up") == 0)
+				// up button
+				if (row >= 1)
+					move_attach_item(logbook, row, -1)
+					ListBox lb_attach, win=$ba.win, selRow=(row-1)
+				endif
+			else
+				// down button
+				if (row < DimSize(attach_list, 0) - 1)
+					move_attach_item(logbook, row, +1)
+					ListBox lb_attach, win=$ba.win, selRow=(row+1)
+				endif
+			endif
+			break
+		case -1: // control being killed
+			break
+	endswitch
+
+	return 0
 end
 
 /// button procedure for the Submit and Reply buttons
@@ -1259,7 +1518,7 @@ static function bp_submit(ba) : ButtonControl
 end
 
 /// select top graph window for attachment
-static function bp_select_attach_top(ba) : ButtonControl
+static function bp_attach_top(ba) : ButtonControl
 	STRUCT WMButtonAction &ba
 
 	switch( ba.eventCode )
@@ -1274,6 +1533,28 @@ static function bp_select_attach_top(ba) : ButtonControl
 	return 0
 end
 
+/// select/deselect all graph windows for attachment
+static function bp_attach_allnone(ba) : ButtonControl
+	STRUCT WMButtonAction &ba
+
+	switch( ba.eventCode )
+		case 2: // mouse up
+			string logbook = GetUserData(ba.win, "", "logbook")
+			dfref df_volatile = get_elog_df(logbook, kdfVolatile)
+			wave /sdfr=df_volatile attach_sel
+			if (cmpstr(ba.ctrlName, "b_attach_all") == 0)
+				attach_sel[][kAttachColSel] = attach_sel[p][kAttachColSel] | 16
+			else
+				attach_sel[][kAttachColSel] = attach_sel[p][kAttachColSel] & ~16
+			endif
+			break
+		case -1: // control being killed
+			break
+	endswitch
+
+	return 0
+end
+
 static function bp_attach(ba) : ButtonControl
 	STRUCT WMButtonAction &ba
 
@@ -1307,6 +1588,34 @@ static function bp_attach(ba) : ButtonControl
 	return 0
 end
 
+static function bp_save_graphs(ba) : ButtonControl
+	STRUCT WMButtonAction &ba
+
+	switch( ba.eventCode )
+		case 2: // mouse up
+			string logbook = GetUserData(ba.win, "", "logbook")
+			string graphs = get_panel_graphs(ba.win)
+			variable ngraphs = ItemsInList(graphs, ";")
+
+			variable igraph
+			string sgraph
+			string graph_path
+			for (igraph = 0; igraph < ngraphs; igraph += 1)
+				sgraph = StringFromList(igraph, graphs, ";")
+				graph_path = create_graph_file(sgraph, igraph)
+				if (strlen(graph_path) > 0)
+					print graph_path
+				endif
+			endfor
+				
+			break
+		case -1: // control being killed
+			break
+	endswitch
+
+	return 0
+end
+
 static function bp_clear(ba) : ButtonControl
 	STRUCT WMButtonAction &ba
 	
@@ -1522,15 +1831,14 @@ end
 
 /// get the names of the graphs selected for attachment
 ///
+/// @param windowname	panel window name
 /// @returns a semicolon-separated list,
 /// or the empty string if the selection is not valid.
 ///
-/// in the current version, the function returns at most one graph.
-/// in future versions, the function may return more than one graph.
-///
 static function /s get_panel_graphs(windowname)
 	string windowname // panel window name
 	
+	dfref savedf = getdatafolderdfr()
 	if (strlen(windowname) == 0)
 		windowname = get_default_panel_name()
 	endif
@@ -1538,24 +1846,38 @@ static function /s get_panel_graphs(windowname)
 		return ""
 	endif
 
-	ControlInfo /W=$windowname pm_attach
-
-	// menu item has the form: "title (name)"
-	string graphname = ReplaceString(")", StringFromList(ItemsInList(s_value, "(") - 1, s_value, "("), "")
+	string logbook = GetUserData(windowname, "", "logbook")
+	dfref df_volatile = get_elog_df(logbook, kdfVolatile)
+	wave /t /sdfr=df_volatile attach_list
+	wave /sdfr=df_volatile attach_sel
 	string graphs = ""
-	string windows = WinList(graphname,  ";", "WIN:1")
-	if (ItemsInList(windows) == 1)
-		graphs = graphname
-	else
-		graphs = ""
-	endif
+	string windows = ""
+	string graphname
+
+	variable n = DimSize(attach_sel, 0)
+	variable i
+	for (i = 0; i < n; i += 1)
+		if (attach_sel[i][kAttachColSel] & 16)
+			graphname = attach_list[i][kAttachColName]
+			windows = WinList(graphname,  ";", "WIN:1")
+			if (ItemsInList(windows) == 1)
+				graphs = AddListItem(graphname, graphs, ";", inf)
+			endif
+		endif
+	endfor
 	
 	return graphs
 end
 
+/// update selection of graphs for attachment
+///
+/// @param windowname		panel window name. looks for default panel if empty.
+///
+/// @param graphs			semicolon-separated list of names of graph windows to select for attachment.
+///
 static function /s set_panel_graphs(windowname, graphs)
-	string windowname // panel window name. looks for default panel if empty.
-	string graphs // name of graph window to select for attachment.
+	string windowname
+	string graphs
 
 	if (strlen(windowname) == 0)
 		windowname = get_default_panel_name()
@@ -1564,23 +1886,21 @@ static function /s set_panel_graphs(windowname, graphs)
 		return ""
 	endif
 
-	// the panel supports only one graph
-	string graph = StringFromList(0, graphs, ";")
-	
-	string items = pm_list_attach_items()
-	string item
-	string itemname
-	variable nitems = ItemsInList(items, ";")
-	variable iitem
-	for (iitem = 0; iitem < nitems; iitem += 1)
-		item = StringFromList(iitem, items, ";")
-		itemname = ReplaceString(")", StringFromList(ItemsInList(item, "(") - 1, item, "("), "")
-		if (cmpstr(graph, itemname) == 0)
-			iitem += 1
-			PopupMenu pm_attach mode=iitem, win=$windowname
-			break
+	string logbook = GetUserData(windowname, "", "logbook")
+	update_attach_items(logbook)
+	dfref df_volatile = get_elog_df(logbook, kdfVolatile)
+	wave /t /sdfr=df_volatile attach_list
+	wave /sdfr=df_volatile attach_sel
+
+	variable n = DimSize(attach_sel, 0)
+	variable i
+	string graphname
+	for (i = 0; i < n; i += 1)
+		graphname = attach_list[i][kAttachColName]
+		if (WhichListItem(graphname, graphs)>= 0)
+			attach_sel[i][kAttachColSel] = 48
+		else
+			attach_sel[i][kAttachColSel] = 32
 		endif
 	endfor
-	
-	return graph
 end

pearl/pearl-fitfuncs.ipf

@@ -454,7 +454,7 @@ function Au4f(w, x): fitfunc
 		vc1 = w[ip] / sqrt(pi) * vc2
 		vc3 = w[ip+1]
 		vc4 = vc2 * w[ip+2] / 2
-		v += vc1 * Voigt(vc2 * (x - vc3), vc4)
+		v += vc1 * VoigtFunc(vc2 * (x - vc3), vc4)
 	endfor
 
 	return v
@@ -491,25 +491,25 @@ function Au4f_2p2(w, x): fitfunc
 	vc1 = w[3] / sqrt(pi) * vc2
 	vc3 = w[4]
 	vc4 = vc2 * w[5] / 2
-	v += vc1 * Voigt(vc2 * (x - vc3), vc4)
+	v += vc1 * VoigtFunc(vc2 * (x - vc3), vc4)
 
 	// 5/2 surface
 	vc1 = w[3] / sqrt(pi) * vc2 * w[9]
 	vc3 = w[4] + w[10]
 	vc4 = vc2 * w[5] / 2
-	v += vc1 * Voigt(vc2 * (x - vc3), vc4)
+	v += vc1 * VoigtFunc(vc2 * (x - vc3), vc4)
 
 	// 7/2 bulk
 	vc1 = w[6] / sqrt(pi) * vc2
 	vc3 = w[7]
 	vc4 = vc2 * w[8] / 2
-	v += vc1 * Voigt(vc2 * (x - vc3), vc4)
+	v += vc1 * VoigtFunc(vc2 * (x - vc3), vc4)
 
 	// 7/2 surface
 	vc1 = w[6] / sqrt(pi) * vc2 * w[9]
 	vc3 = w[7] + w[10]
 	vc4 = vc2 * w[8] / 2
-	v += vc1 * Voigt(vc2 * (x - vc3), vc4)
+	v += vc1 * VoigtFunc(vc2 * (x - vc3), vc4)
 
 	return v
 	
@@ -578,37 +578,37 @@ function Au4f_2p3(w, x): fitfunc
 	vc1 = w[3] / sqrt(pi) * vc2
 	vc3 = w[4]
 	vc4 = vc2 * w[5] / 2
-	v += vc1 * Voigt(vc2 * (x - vc3), vc4)
+	v += vc1 * VoigtFunc(vc2 * (x - vc3), vc4)
 
 	// 5/2 surface
 	vc1 = w[3] / sqrt(pi) * vc2 * w[9]
 	vc3 = w[4] + w[10]
 	vc4 = vc2 * w[5] / 2
-	v += vc1 * Voigt(vc2 * (x - vc3), vc4)
+	v += vc1 * VoigtFunc(vc2 * (x - vc3), vc4)
 
 	// 5/2 2nd layer
 	vc1 = w[3] / sqrt(pi) * vc2 * w[11]
 	vc3 = w[4] + w[12]
 	vc4 = vc2 * w[5] / 2
-	v += vc1 * Voigt(vc2 * (x - vc3), vc4)
+	v += vc1 * VoigtFunc(vc2 * (x - vc3), vc4)
 
 	// 7/2 bulk
 	vc1 = w[6] / sqrt(pi) * vc2
 	vc3 = w[7]
 	vc4 = vc2 * w[8] / 2
-	v += vc1 * Voigt(vc2 * (x - vc3), vc4)
+	v += vc1 * VoigtFunc(vc2 * (x - vc3), vc4)
 
 	// 7/2 surface
 	vc1 = w[6] / sqrt(pi) * vc2 * w[9]
 	vc3 = w[7] + w[10]
 	vc4 = vc2 * w[8] / 2
-	v += vc1 * Voigt(vc2 * (x - vc3), vc4)
+	v += vc1 * VoigtFunc(vc2 * (x - vc3), vc4)
 
 	// 7/2 2nd layer
 	vc1 = w[6] / sqrt(pi) * vc2 * w[11]
 	vc3 = w[7] + w[12]
 	vc4 = vc2 * w[8] / 2
-	v += vc1 * Voigt(vc2 * (x - vc3), vc4)
+	v += vc1 * VoigtFunc(vc2 * (x - vc3), vc4)
 
 	return v
 	

pearl/pearl-matrix-import.ipf

@@ -0,0 +1,900 @@
+#pragma rtGlobals=3
+#pragma version = 1.00
+#pragma IgorVersion = 6.36
+#pragma ModuleName = PearlMatrixImport
+
+// author: matthias.muntwiler@psi.ch
+// Copyright (c) 2016 Paul Scherrer Institut
+
+// Licensed under the Apache License, Version 2.0 (the "License");
+//   you may not use this file except in compliance with the License.
+//   You may obtain a copy of the License at
+//   http://www.apache.org/licenses/LICENSE-2.0
+
+/// @file
+/// @brief data file import for omicron matrix (STM) files
+///
+/// the matrix file import requires the matrix file reader XOP by thomas braun
+/// (http://www.igorexchange.com/project/matrixFileReader)
+/// which in turn requires an installation of vernissage by omicron nanotechnology.
+///
+/// @warning EXPERIMENTAL
+/// the matrix import module and its interface may change radically in future revisions!
+///
+/// @author matthias muntwiler, matthias.muntwiler@psi.ch
+///
+/// @copyright 2016 Paul Scherrer Institut @n
+/// Licensed under the Apache License, Version 2.0 (the "License"); @n
+///   you may not use this file except in compliance with the License. @n
+///   You may obtain a copy of the License at
+///   http://www.apache.org/licenses/LICENSE-2.0
+
+/// @namespace PearlMatrixImport
+/// @brief data file import for omicron matrix (STM) files
+///
+/// PearlMatrixImport is declared in @ref pearl-matrix-import.ipf.
+
+static strconstant package_name = "pearl_matrix_import"
+static strconstant package_path = "root:packages:pearl_matrix_import:"
+
+static strconstant ks_filematch_mtrx = "*_mtrx"
+
+/// initialize the package data folder.
+///
+///
+static function init_package()
+	
+	dfref savedf = getdatafolderdfr()
+	
+	setdatafolder root:
+	newdatafolder /o/s packages
+	newdatafolder /o/s $package_name
+	
+	variable /g loglevel = 3
+	string /g dataFilePath = ""
+	string /g resultFilePath = ""
+	variable /g runCycle = 0
+	variable /g scanCycle = 0
+	string /g channelName = ""
+	variable /g brickletID = 0
+	variable /g V_MatrixFileReaderOverwrite = 1
+	variable /g V_MatrixFileReaderFolder = 0
+	variable /g V_MatrixFileReaderDouble = 0
+
+	setdatafolder savedf
+	return 0
+end
+
+/// check that the package data folder exists
+///
+/// initialize the package if the folder does not exist.
+///
+static function check_package_folder()
+	dfref df_pack = $(package_path)
+	if (DataFolderRefStatus(df_pack))
+		svar /sdfr=df_pack /z resultFilePath
+		if (!svar_exists(resultFilePath))
+			init_package()
+		endif
+	else
+		init_package()
+	endif
+end
+
+/// initialize the package and reload preferences after an experiment is loaded.
+static function AfterFileOpenHook(refNum,file,pathName,type,creator,kind)
+	Variable refNum,kind
+	String file,pathName,type,creator
+	if( (kind >= 1) && (kind <= 2))
+		init_package()
+		//load_prefs()
+	endif
+	return 0
+end
+
+/// open a matrix file that was dropped into Igor.
+///
+/// preliminary implementation.
+/// this should rather load the entire file and display a preview.
+/// graph windows should be reused by subsequent loads.
+/// also decide on a data saving location.
+///
+static function BeforeFileOpenHook(refNum,fileName,path,type,creator,kind)
+	Variable refNum,kind
+	String fileName,path,type,creator
+
+	Variable handledOpen = 0
+	if (StringMatch(fileName, ks_filematch_mtrx))
+		setdatafolder root:
+		newdatafolder /o /s matrix
+		mtrx_load_preview("matrix", path, fileName)
+		handledOpen = 1
+	endif
+	return handledOpen
+End
+
+/// generate elog message from bricklet metadata
+///
+/// @param metadata		two-column text wave
+///
+function /s matrix_format_elog_message(metadata)
+	wave /t metadata
+
+	string key
+	string value
+	variable nkeys = dimsize(metadata, 0)
+	variable ikey
+	string message_keys
+	message_keys = "resultFileName;sampleName;channelName;"
+	message_keys += "XYScanner.Points.value;XYScanner.Raster_Time.value;XYScanner.Raster_Time.unit;XYScanner.Width.value;XYScanner.Width.unit;XYScanner.Height.value;XYScanner.Height.unit;"
+	message_keys += "GapVoltageControl.Voltage.value;GapVoltageControl.Voltage.unit;"
+	message_keys += "Regulator.Loop_Gain_1_I.value;Regulator.Loop_Gain_1_I.unit;Regulator.Setpoint_1.value;Regulator.Setpoint_1.unit;"
+	message_keys += "Spectroscopy.Device_1_Start.value;Spectroscopy.Device_1_Start.unit;Spectroscopy.Spectroscopy_Mode.value;"
+	string message
+	
+	message_keys = ""
+	for (ikey = 0; ikey < nkeys; ikey += 1)
+		key = metadata[ikey][0]
+		value = metadata[ikey][1]
+		if (WhichListItem(key, message_keys) >= 0)
+			message += key + " = " + value + "\r"
+		endif
+	endfor
+end
+
+function matrix_preview_2d(data, metadata)
+	wave data
+	wave /t metadata
+	
+	Display
+	AppendImage data
+	ModifyImage data ctab= {*,*,Mud,0}
+	ModifyGraph margin(left)=30,margin(bottom)=30,margin(top)=5,margin(right)=5,height={Plan,1,left,bottom}
+	ModifyGraph mirror=2
+	ModifyGraph nticks=3
+	ModifyGraph axThick=0.5
+	ModifyGraph btLen=4
+
+end
+
+/// load the preview of a Matrix data file
+///
+/// the preview is loaded to the preview_image wave in the pearl_explorer data folder.
+///
+/// the s_file_info string is updated with information about the scan dimensions.
+///
+/// @param	filename		name of a file in the directory specified by the pearl_explorer_filepath path object.
+///
+/// @return	wave reference of the preview image
+///
+static function /wave preview_matrix_file(filename)
+	string filename
+
+	dfref saveDF = GetDataFolderDFR()
+	setdatafolder $package_path
+	svar s_preview_file
+	svar s_preview_source
+	mtrx_load_preview("preview_image", "pearl_explorer_filepath", filename)
+	s_preview_file = filename
+	s_preview_source = ""
+	wave /z preview_image
+	
+	svar /z s_file_info
+	if (! svar_exists(s_file_info))
+		string /g s_file_info
+	endif
+	if (strlen(s_preview_file) > 0)
+		s_file_info = mtrx_load_info("pearl_explorer_filepath", filename)
+	else
+		s_file_info = ""
+	endif
+	
+	setdatafolder saveDF
+	return preview_image
+end
+
+/// from matrixfilereader help
+Structure errorCode
+	int32	 SUCCESS 
+	int32	 UNKNOWN_ERROR
+	int32	 ALREADY_FILE_OPEN
+	int32	 EMPTY_RESULTFILE
+	int32	 FILE_NOT_READABLE
+	int32	 NO_NEW_BRICKLETS
+	int32	 WRONG_PARAMETER
+	int32	 INTERNAL_ERROR_CONVERTING_DATA
+	int32	 NO_FILE_OPEN
+	int32	 INVALID_RANGE
+	int32	 WAVE_EXIST
+EndStructure
+
+/// from matrixfilereader help
+static Function initStruct(errorCode)
+	Struct errorCode &errorCode
+
+	errorCode.SUCCESS =0
+	errorCode.UNKNOWN_ERROR=10001
+	errorCode.ALREADY_FILE_OPEN=10002
+	errorCode.EMPTY_RESULTFILE=10004
+	errorCode.FILE_NOT_READABLE=10008
+	errorCode.NO_NEW_BRICKLETS=10016
+	errorCode.WRONG_PARAMETER=10032
+	errorCode.INTERNAL_ERROR_CONVERTING_DATA=10064
+	errorCode.NO_FILE_OPEN=10128
+	errorCode.INVALID_RANGE=10256  
+	errorCode.WAVE_EXIST=10512
+	
+end
+
+/// load all data from a Matrix data file.
+///
+function mtrx_load_all()
+
+	struct errorCode errorCode
+	initStruct(errorCode)
+
+#if exists("MFR_OpenResultFile")
+	MFR_OpenResultFile
+	if(V_flag != errorCode.SUCCESS)
+		MFR_GetXOPErrorMessage
+		return -1
+	endif
+
+	MFR_GetBrickletData
+	if(V_flag != errorCode.SUCCESS)
+		MFR_GetXOPErrorMessage
+		return -1
+	endif
+
+	MFR_GetBrickletMetaData
+	if(V_flag != errorCode.SUCCESS)
+		MFR_GetXOPErrorMessage
+		return -1
+	endif
+
+	return 0
+#else
+	return -1
+#endif
+end
+
+/// parse matrix file names
+///
+/// parse matrix file names for result name, run cycle, scan cycle, and channel.
+///
+/// @param fileName			matrix result or data file name (without path).
+///
+/// @param resultFile			(out) base name of the result file.
+///							append "_%04u.mtrx" to get the actual result file.
+///							we do not know the chain link number at this stage.
+///
+/// @param runCycle			(out) run cycle number. necessary to look up the bricklet ID.
+///
+/// @param scanCycle		(out) scan cycle number. necessary to look up the bricklet ID.
+///
+/// @param channel			(out) channel name.
+///
+/// @return file type
+///	@arg 0 result file (logbook)
+///	@arg 1 result data file (bricklet)
+///
+/// result file names look like:
+/// default_2015Apr20-124353_STM-STM_AtomManipulation_0001.mtrx,
+/// default_2015Apr20-124353_STM-STM_AtomManipulation_0002.mtrx, etc.
+/// the function returns the first part up to the experiment name ("AtomManipulation" in the examples).
+/// all other return values set to defaults and must not be regarded.
+///
+/// result data files look like:
+/// default_2015Apr20-124353_STM-STM_AtomManipulation--136_1.Aux1(V)_mtrx,
+/// default_2015Apr20-124353_STM-STM_AtomManipulation--136_1.I(V)_mtrx,
+/// default_2015Apr20-124353_STM-STM_AtomManipulation--14_1.I_mtrx,
+/// default_2015Apr20-124353_STM-STM_AtomManipulation--14_1.Z_mtrx, etc.
+/// the function returns all results as described in the parameter list.
+///
+function mtrx_parse_filename(fileName, resultFile, runCycle, scanCycle, channel)
+	string fileName
+	string &resultFile
+	variable &runCycle
+	variable &scanCycle
+	string &channel
+	
+	variable fileType = 0
+	resultFile = ""
+	channel = ""
+	runCycle = 0
+	scanCycle = 0
+
+	string regexp = ""
+	string index1 = ""
+	string index2 = ""
+	string extension = ""
+	
+	if (StringMatch(fileName, "*.mtrx"))
+		regexp = "(.+)_([[:digit:]]+)\.(.+)"
+		SplitString /E=regexp fileName, resultFile, index1, extension
+		fileType = 0
+	else
+		regexp = "(.+)--([[:digit:]]+)_([[:digit:]]+)\.((.+)_mtrx)"
+		SplitString /E=regexp fileName, resultFile, index1, index2, extension, channel
+		fileType = 1
+		runCycle = str2num(index1)
+		scanCycle = str2num(index2)
+	endif
+	
+	return fileType
+end
+
+/// split a matrix filename and return the first three parts
+///
+/// we assume that the second (third) part contains the date (time).
+/// the parts are separated by dash or underscore.
+///
+function /s mtrx_split_filename(fileName, prefix, datepart, timepart)
+	string fileName
+	string &prefix
+	string &datepart
+	string &timepart
+	
+	string regexp
+	regexp = "([[:alpha:][:digit:]]+)[-_]([[:alpha:][:digit:]]+)[-_]([[:alpha:][:digit:]]+)[-_].+"
+	SplitString /E=regexp fileName, prefix, datepart, timepart
+	return datepart
+end
+
+/// create or look up a data folder based on a matrix file name.
+///
+/// the name of the folder is mtrx_date_time, where date and time are parsed from the file name.
+/// for this to work, the file name must consist of at least three parts that are separated by dash or underscore.
+/// the second (third) part contains the date (time).
+/// date and time are copied as strings.
+///
+/// if the data folder exists, a reference to the existing folder is returned.
+///
+/// @param fileName		name of the result or data file.
+///
+/// @param df_base		(optional) base data folder. 
+///						default: current folder.
+///
+/// @return				reference of the newly created or existing data folder.
+///
+function /df mtrx_create_folder(fileName, [df_base])
+	string fileName
+	dfref df_base
+	
+	if (ParamIsDefault(df_base))
+		df_base = GetDataFolderDFR()
+	endif
+
+	string prefix
+	string datepart
+	string timepart
+	string folderName
+	
+	mtrx_split_filename(fileName, prefix, datepart, timepart)
+	folderName = "mtrx_" + datepart + "_" + timepart
+	folderName = CleanupName(folderName, 0)
+	
+	dfref df_save = GetDataFolderDFR()
+	setdatafolder root:
+	newdatafolder /o /s $foldername
+	dfref df = GetDataFolderDFR()
+
+	setdatafolder df_save
+	return df
+end
+
+/// create a data folder for bricklet data.
+///
+/// the name of the folder is, for example "r23s2" where the first (second) number is the run (scan) cycle.
+/// run cycle and scan cycle numbers are taken from the open matrix file unless overridden by optional arguments.
+///
+/// if the data folder exists, a reference to the existing folder is returned.
+/// if one of the run or scan cycle numbers is lower than 1, the base folder is returned.
+///
+/// @param df_base		(optional) base data folder. 
+///						default: current folder.
+///
+/// @param runCycle		(optional) run cycle number. must be >= 1.
+///						default: from last mtrx_open_file call.
+///
+/// @param scanCycle	(optional) scan cycle number. must be >= 1.
+///						default: from last mtrx_open_file call.
+///
+/// @return				reference of the newly created or existing data folder.
+///
+function /df mtrx_get_cycle_folder([df_base, runCycle, scanCycle])
+	dfref df_base
+	variable runCycle
+	variable scanCycle
+
+	dfref df_save = GetDataFolderDFR()
+	dfref df_pack = $(package_path)
+	if (ParamIsDefault(df_base))
+		df_base = GetDataFolderDFR()
+	endif
+	if (ParamIsDefault(runCycle))
+		nvar /sdfr=df_pack defRunCycle = runCycle
+		runCycle = defRunCycle
+	endif
+	if (ParamIsDefault(scanCycle))
+		nvar /sdfr=df_pack defScanCycle = scanCycle
+		scanCycle = defScanCycle
+	endif
+
+	string dfname
+	if ((runCycle >= 1) && (scanCycle >= 1))
+		sprintf dfname, "r%us%u", runCycle, scanCycle
+		setdatafolder df_base
+		dfref df = $dfname
+		if (DataFolderRefStatus(df) == 0)
+			newdatafolder $dfname
+			dfref df = $dfname
+		endif
+	else
+		dfref df = df_base
+	endif
+	
+	setdatafolder df_save
+	return df
+end
+
+/// find out bricklet ID of a file
+///
+/// @warning EXPERIMENTAL
+/// the code of this function is inefficient.
+/// the function may be removed in a later version.
+///
+/// @param resultFile			base name of result file without chain link number and extension.
+///							as returned by mtrx_parse_filename.
+///
+/// @param runCycle			requested run cycle.
+///							0 = first available.
+///
+/// @param scanCycle		requested scan cycle.
+///							0 = first available.
+///
+/// @param channel			channel name. for example: "I", "Z", "Aux(V)", etc.
+///							empty string: first available.
+///
+/// @return bricklet ID, or -1 if an error occurred.
+///
+function mtrx_file_brickletID(resultFile, runCycle, scanCycle, channel)
+	string resultFile
+	variable runCycle
+	variable scanCycle
+	string channel
+
+	dfref df_overview = NewFreeDataFolder()
+	variable link = 1
+	variable id = -1
+	variable idx = 0
+	
+	string resultFileName
+#if exists("MFR_OpenResultFile")
+	struct errorCode errorCode
+	initStruct(errorCode)
+	do
+		sprintf resultFileName, "%s_%04u.mtrx", resultFile, link
+		MFR_OpenResultFile /K resultFileName
+		if(V_flag != errorCode.SUCCESS)
+			return -1
+		endif
+		MFR_CreateOverviewTable /DEST=df_overview
+		// dimension labels are: brickletID, scanCycleCount, runCycleCount, sequenceID, dimension, channelName
+		wave /t /sdfr=df_overview overviewTable
+		make /n=(dimsize(overviewTable, 0)) /i /u /free runcycles, scancycles, ids, match
+		make /n=(dimsize(overviewTable, 0)) /t /free channels
+		ids = str2num(overviewtable[p][%brickletID])
+		if (runcycle > 0)
+			runcycles = str2num(overviewtable[p][%runCycleCount])
+		else
+			runcycles = runcycle
+		endif
+		if (scancycle > 0)
+			scancycles = str2num(overviewtable[p][%scanCycleCount])
+		else
+			scancycles = scancycle
+		endif
+		if (strlen(channel) > 0)
+			channels = overviewTable[p][%channelName]
+		else
+			channels = channel
+		endif
+		Extract /FREE ids, match_ids, (scancycles == scanCycle) && (runcycles == runCycle) && (cmpstr(channels, channel) == 0)
+		if (numpnts(match_ids) > 0)
+			id = match_ids[0]
+		else
+			link += 1
+		endif
+	while (id < 0)
+#endif
+	return id
+end
+
+/// open a matrix result or data file
+///
+/// this function opens a matrix result file (.mtrx) or data file (.*_mtrx).
+///
+/// if a data file is selected, the function locates the corresponding result file, opens it,
+/// and looks up the bricklet ID of the data file.
+/// if a result file is selected, the function opens it but does not look up bricklet IDs.
+///
+/// the result file remains open and can be accessed using the mtrx_ functions or MFR_ operations.
+/// once a result file is open, you can easily access any bricklets linked to it,
+/// i.e., any run cycle, scan cycle, and channel.
+///
+/// the function stores information about the opened file in a global package data folder.
+/// if the same result file is opened again later, the information is reused and the file not read again.
+/// this may cause problems if the file has been modified in the meantime,
+/// or if the cached data become corrupt for some reason.
+/// the function detects if a data file is not linked in the open result file, and updates the cache.
+/// in other situations it may be necessary to force a reload.
+///
+/// @todo fix possible cache issues, add an option to override the cache.
+///
+/// @param pathName			igor path name or empty string.
+///
+/// @param fileName			file name, with or without path, or empty string.
+///
+/// @return file type
+///	@arg 0 result file (logbook)
+///	@arg 1 result data file (bricklet)
+///	@arg -1 error, no data loaded
+///	@arg -2 matrixfilereader.xop not installed
+///
+function mtrx_open_file(pathName, fileNameOrPath)
+	string pathName
+	string fileNameOrPath
+
+	check_package_folder()
+	dfref df_save = GetDataFolderDFR()
+	dfref df_pack = $(package_path)
+	svar /sdfr=df_pack dataFilePath
+	svar /sdfr=df_pack resultFilePath
+	nvar /sdfr=df_pack runCycle
+	nvar /sdfr=df_pack scanCycle
+	svar /sdfr=df_pack channelName
+	nvar /sdfr=df_pack brickletID
+
+	string loc_resultFileName
+	string loc_resultFilePath
+	variable loc_runCycle
+	variable loc_scanCycle
+	string loc_channelName
+
+	// make sure we have a valid and complete file path
+	GetFileFolderInfo /P=$pathName /Q /Z=2 fileNameOrPath
+	string filePath
+	if ((v_flag == 0) && (v_isFile))
+		filePath = s_path
+	else
+		return -1
+	endif
+
+	// get base file name
+	string fileName
+	string fileDir
+	string baseFileName
+	variable fileType
+	fileName = ParseFilePath(0, filePath, ":", 1, 0)
+	fileDir = ParseFilePath(1, filePath, ":", 1, 0)
+	fileType = mtrx_parse_filename(fileName, baseFileName, loc_runCycle, loc_scanCycle, loc_channelName)
+	
+	variable link = 1
+	variable id = -1
+	variable result = -1
+	variable using_cache = 0
+	
+	struct errorCode errorCode
+	initStruct(errorCode)
+	do
+		sprintf loc_resultFileName, "%s_%04u.mtrx", baseFileName, link
+		loc_resultFilePath = fileDir + loc_resultFileName
+#if exists("MFR_OpenResultFile")
+		if ((strlen(resultFilePath) == 0) || (cmpstr(loc_resultFilePath, resultFilePath) != 0))
+			MFR_OpenResultFile /K loc_resultFilePath
+			if(V_flag != errorCode.SUCCESS)
+				MFR_GetXOPErrorMessage
+				result = -1
+				break
+			endif
+			resultFilePath = loc_resultFilePath
+			if (fileType == 1)
+				dataFilePath = filePath
+			else
+				dataFilePath = ""
+			endif
+			runCycle = 0
+			scanCycle = 0
+			channelName = ""
+			brickletID = 0
+			MFR_CreateOverviewTable /DEST=df_pack
+			if(V_flag != errorCode.SUCCESS)
+				MFR_GetXOPErrorMessage
+				result = -1
+				break
+			endif
+			using_cache = 0
+		else
+			using_cache = 1
+		endif
+#else
+		print "matrixfilereader.xop not installed"
+		result = -2
+		break
+#endif
+		// dimension labels are: brickletID, scanCycleCount, runCycleCount, sequenceID, dimension, channelName
+		wave /t /sdfr=df_pack overviewTable
+		make /n=(dimsize(overviewTable, 0)) /i /u /o df_pack:runCycles, df_pack:scanCycles, df_pack:ids
+		make /n=(dimsize(overviewTable, 0)) /t /o df_pack:channels
+		wave /sdfr=df_pack ids, runCycles, scanCycles
+		wave /t /sdfr=df_pack channels
+		ids = str2num(overviewtable[p][%brickletID])
+		runCycles = str2num(overviewtable[p][%runCycleCount])
+		scanCycles = str2num(overviewtable[p][%scanCycleCount])
+		channels = overviewTable[p][%channelName]
+		result = fileType
+
+		// if a data file is opened, make sure we found the right result file
+		if ((loc_runCycle > 0) && (loc_scanCycle > 0))
+			Extract /FREE ids, match_ids, (runCycles == loc_runCycle) && (scanCycles == loc_scanCycle) && (cmpstr(channels, loc_channelName) == 0)
+			if (numpnts(match_ids) > 0)
+				id = match_ids[0]
+				runCycle = loc_runCycle
+				scanCycle = loc_scanCycle
+				channelName = loc_channelName
+				brickletID = id
+				break
+			elseif (using_cache)
+				resultFilePath = ""
+			else
+				link += 1
+			endif
+		else
+			break
+		endif
+	while (id < 0)
+	
+	return result
+end
+
+/// load a preview image from a Matrix data file.
+///
+/// the data wave is loaded into the current data folder.
+///
+/// @param destName			destination wave name. the wave is created in the current data folder.
+///
+/// @param pathName			igor symbolic path name. can be empty if the path is specified in FileName or a dialog box should be displayed
+///
+/// @param fileName			if empty a dialog box shows up
+///							the file name must adhere to the format
+///							"{prefix}-{date}-{time}-{anything}--{run_cycle}_{scan_cycle}.{extension}".
+///							the first three seperators can alternatively be underscores.
+///							it may be necessary to change the configuration of the Matrix application.
+///
+/// @param traces			(currently not used) semicolon-separated list of preferred traces.
+///							the items of the list are match strings for the Igor StringMatch function.
+///							only the first matching trace is loaded from the file.
+///							default: "*Up;*Down;*ReUp;*ReDown;"
+///
+/// @return					semicolon-separated list of loaded waves including partial path from current data folder.
+///
+function /s mtrx_load_preview(destName, pathName, fileName, [traces])
+	string destName
+	string pathName
+	string fileName
+	string traces
+		
+	if (ParamIsDefault(traces))
+		traces = "*Up;*Down;*ReUp;*ReDown;"
+	endif
+	
+	dfref df_save = GetDataFolderDFR()
+
+	string datanames = ""
+	string datapaths = ""
+	variable filestatus = mtrx_open_file(pathName, fileName)
+	if (filestatus != 1)
+		return ""
+	endif
+
+	dfref df_pack = $(package_path)
+	svar /sdfr=df_pack dataFilePath
+	svar /sdfr=df_pack resultFilePath
+	nvar /sdfr=df_pack runCycle
+	nvar /sdfr=df_pack scanCycle
+	svar /sdfr=df_pack channelName
+	nvar /sdfr=df_pack brickletID
+
+#if exists("MFR_OpenResultFile")
+	dfref df_data = df_save
+	variable /g df_data:V_MatrixFileReaderOverwrite = 1
+	variable /g df_data:V_MatrixFileReaderFolder = 0
+	variable /g df_data:V_MatrixFileReaderDouble = 0
+	struct errorCode errorCode
+	initStruct(errorCode)
+	MFR_GetBrickletData /N=destName /R=(brickletID) /S=2 /DEST=df_data
+	if(V_flag == errorCode.SUCCESS)
+		datanames = S_waveNames
+		variable i
+		variable n = ItemsInList(datanames)
+		string s
+		s = StringFromList(0, datanames)
+		wave data = $s
+		mtrx_scale_dataset(data)
+		if (WaveDims(data) == 2)
+			subtract_line_bg(data)
+		endif
+		datapaths = AddListItem(GetWavesDataFolder(data, 4), datapaths, ";", inf)
+		for (i = 1; i < n; i += 1)
+			s = StringFromList(i, datanames)
+			killwaves /z $s
+		endfor
+	else
+		MFR_GetXOPErrorMessage
+	endif
+	//MFR_GetBrickletMetaData /N=ANickName /R=(brickletID) // /DEST=dfref
+#else
+	print "matrixfilereader.xop not installed"
+#endif
+	
+	setdatafolder df_save
+	return datapaths
+end
+
+/// load all data from a Matrix data file.
+///
+/// the data wave is loaded into a sub-subfolder the current data folder.
+/// the relative path has the format ":mtrx_{date}_{time}:r{run_cycle}s{scan_cycle}",
+/// where the parameters {date}, {time}, {run_cycle} and {scan_cycle} are copied from the file name.
+/// the file name must be formatted according to the specifications set out below.
+///
+/// @param pathName			igor symbolic path name. can be empty if the path is specified in FileName or a dialog box should be displayed
+///
+/// @param fileName			if empty a dialog box shows up
+///							the file name must adhere to the format
+///							"{prefix}-{date}-{time}-{anything}--{run_cycle}_{scan_cycle}.{extension}".
+///							the first three seperators can alternatively be underscores.
+///							it may be necessary to change the configuration of the Matrix application.
+///
+/// @param traces			(currently not used) semicolon-separated list of preferred traces.
+///							the items of the list are match strings for the Igor StringMatch function.
+///							only matching traces are loaded from the file.
+///							default: "*Up;*Down;*ReUp;*ReDown;"
+///
+/// @return					semicolon-separated list of loaded waves including partial path from current data folder.
+///
+function /s mtrx_load_file(pathName, fileName, [traces])
+	string pathName
+	string fileName
+	string traces
+		
+	if (ParamIsDefault(traces))
+		traces = "*Up;*Down;*ReUp;*ReDown;"
+	endif
+	
+	dfref df_save = GetDataFolderDFR()
+
+	string datanames = ""
+	string datapaths = ""
+	variable filestatus = mtrx_open_file(pathName, fileName)
+	if (filestatus != 1)
+		return ""
+	endif
+
+	dfref df_pack = $(package_path)
+	svar /sdfr=df_pack dataFilePath
+	svar /sdfr=df_pack resultFilePath
+	nvar /sdfr=df_pack runCycle
+	nvar /sdfr=df_pack scanCycle
+	svar /sdfr=df_pack channelName
+	nvar /sdfr=df_pack brickletID
+
+#if exists("MFR_OpenResultFile")
+	string resultFileName = ParseFilePath(0, resultFilePath, ":", 1, 0)
+	dfref df_result = mtrx_create_folder(resultFileName, df_base=df_save)
+	dfref df_data = mtrx_get_cycle_folder(df_base = df_result)
+	variable /g df_data:V_MatrixFileReaderOverwrite = 1
+	variable /g df_data:V_MatrixFileReaderFolder = 0
+	variable /g df_data:V_MatrixFileReaderDouble = 0
+	
+	struct errorCode errorCode
+	initStruct(errorCode)
+	string name
+	name = CleanupName(channelName, 0)
+	MFR_GetBrickletData /N=name /R=(brickletID) /DEST=df_data
+	if(V_flag == errorCode.SUCCESS)
+		datanames = S_waveNames
+		variable i
+		variable n = ItemsInList(datanames)
+		string s
+		for (i = 0; i < n; i += 1)
+			s = StringFromList(i, datanames)
+			wave /sdfr=df_data data = $s
+			mtrx_scale_dataset(data)
+			datapaths = AddListItem(GetWavesDataFolder(data, 4), datapaths, ";", inf)
+		endfor
+	else
+		MFR_GetXOPErrorMessage
+	endif
+	//MFR_GetBrickletMetaData /N=ANickName /R=(brickletID) // /DEST=dfref
+#else
+	print "matrixfilereader.xop not installed"
+#endif
+	
+	setdatafolder df_save
+	return datapaths
+end
+
+function mtrx_scale_dataset(data)
+	wave data
+
+	dfref df_pack = $(package_path)
+	nvar /sdfr=df_pack runCycle
+	nvar /sdfr=df_pack scanCycle
+	svar /sdfr=df_pack channelName
+	nvar /sdfr=df_pack brickletID
+
+	string scanDir = StringFromList(2, NameOfWave(data), "_")
+	if (WaveDims(data) == 2)
+		Note data, "AxisLabelX=X"
+		Note data, "AxisLabelY=Y"
+	endif
+	Note data, "AxisLabelD=" + channelName
+	string title
+	sprintf title, "%u-%u %s %s", runCycle, scanCycle, channelName, scanDir
+	Note data, "Dataset=" + title
+end
+
+/// load descriptive info from a Matrix data file.
+///
+/// the info string lists the following information for each scan contained in the file:
+/// - path of the scan group inside the file.
+/// - number of scan positions.
+/// - dataset names of scan positioners.
+/// - dataset names of detectors.
+///
+/// @param APathName		igor symbolic path name. can be empty if the path is specified in AFileName or a dialog box should be displayed
+///
+/// @param AFileName		if empty a dialog box shows up
+///
+/// @return					newline terminated string.
+///
+function /s mtrx_load_info(APathName, AFileName)
+	string APathName
+	string AFileName
+		
+	dfref saveDF = GetDataFolderDFR()
+	dfref fileDF = NewFreeDataFolder()
+	setdatafolder fileDF
+
+	variable fileID
+	string filepath
+	string scanpaths
+	variable nscans
+	variable iscan
+	string scanpath
+	string info = ""
+	  
+	
+	setdatafolder saveDF
+	return info
+end
+
+/// remove linear background line-by-line
+///
+function subtract_line_bg(img)
+	wave img
+	
+	variable nx = dimsize(img, 0)
+	variable ny = dimsize(img, 1)
+	variable iy
+	make /n=(nx) /free line, fit
+	for (iy = 0; iy < ny; iy += 1)
+		line = img[p][iy]
+		if (numtype(sum(line)) == 0)
+			CurveFit /N /Q /NTHR=0 line line /D=fit
+			img[][iy] = line[p] - fit[p]
+		endif
+	endfor
+end

pearl/pearl-scienta-preprocess.ipf

@@ -703,3 +703,99 @@ function scienta_poly_bg(w, e, a): fitfunc
 	
 	return bg * (base + pk1 + pk2 + pk3)
 end
+
+/// parameter dialog for the redim_linbg_reduction() function
+///
+/// @param param	parameter string in a key1=value1;key2=value2;... list.
+///					the parameter string is passed by reference.
+///					see redim_linbg_reduction() for a description of parameters.
+///
+/// @return	zero if the user clicked OK, non-zero if the user clicked Cancel.
+///
+function prompt_redim_linbg_reduction(param)
+	string &param
+
+	variable Lcrop = NumberByKey("Lcrop", param, "=", ";")
+	variable Lsize = NumberByKey("Lsize", param, "=", ";")
+	variable Hcrop = NumberByKey("Hcrop", param, "=", ";")
+	variable Hsize = NumberByKey("Hsize", param, "=", ";")
+	variable Cpos = NumberByKey("Cpos", param, "=", ";")
+	variable Csize = NumberByKey("Csize", param, "=", ";")
+	
+	prompt Lcrop, "Lower cropping region"
+	prompt Hcrop, "Upper cropping region"
+	prompt Lsize, "Lower background region"
+	prompt Hsize, "Upper background region"
+	prompt Cpos, "Center position"
+	prompt Csize, "Center integration region"
+	
+	doprompt "redim_linbg_reduction Parameters", lcrop, hcrop, lsize, hsize, cpos, csize
+	if (v_flag == 0)
+		param = ReplaceNumberByKey("Lcrop", param, Lcrop, "=", ";")
+		param = ReplaceNumberByKey("Lsize", param, Lsize, "=", ";")
+		param = ReplaceNumberByKey("Hcrop", param, Hcrop, "=", ";")
+		param = ReplaceNumberByKey("Hsize", param, Hsize, "=", ";")
+		param = ReplaceNumberByKey("Cpos", param, Cpos, "=", ";")
+		param = ReplaceNumberByKey("Csize", param, Csize, "=", ";")
+	endif
+
+	return v_flag
+end
+
+/// linear background reduction function for incorrectly dimensioned scienta image
+///
+/// if the energy step size does not divide the energy range to an integer number,
+/// the scienta image is exported with the wrong array size.
+/// this can be fixed by redimensioning the array.
+/// 
+/// the current implementation works in the case where dimension 0 needs to be incremented.
+/// the function may be generalized to dimension 1 and/or decrementing by additional parameters.
+/// it is not known yet whether a generalization is needed or whether it can cover all cases.
+///
+/// background subtraction and peak integration is the same as by the int_linbg_reduction() function.
+///
+/// @param source	source wave
+///					Scienta detector image, energy axis along X, angle axis along Y
+///
+/// @param dest1		destination wave 1
+///
+/// @param dest2		destination wave 2
+///					each wave is a one-dimensional intensity distribution
+///					the function may redimension these waves to one of the image dimensions
+///					(it must be clear to the user which dimension this is).
+///					the meaning of dest1 and dest2 is up to the particular function,
+///					e.g. dest1 could hold the mean value and dest2 the one-sigma error,
+///					or dest1 could hold the X-profile, and dest2 the Y-profile.
+///
+/// @param param	parameter string in a key1=value1;key2=value2;... list.
+///					the parameter string is passed by reference.
+///
+/// all region parameters are relative to the image size (0...1).
+/// @arg Lcrop	size of the lower cropping region
+/// @arg Hcrop	size of the upper cropping region
+/// @arg Lsize	size of the lower background integration region
+/// @arg Hsize	size of the upper background integration region
+/// @arg Cpos	center position of the of the peak integration region
+/// @arg Csize	size of the peak integration region
+///	
+/// typical values (peak centered on detector, FWHM ~ 20 % of image)
+/// Lcrop=0.11;Hcrop=0.11;Lsize=0.2;Hsize=0.2;Cpos=0.5;Csize=0.2
+///
+/// @return zero if successful, non-zero if an error occurs.
+///
+threadsafe function redim_linbg_reduction(source, dest1, dest2, param)
+	wave source
+	wave dest1, dest2
+	string &param
+	
+	variable nx = dimsize(source, 0)
+	variable ny = dimsize(source, 1)
+	
+	duplicate /free source, source_redim
+	redimension /n=(nx * ny) source_redim
+	nx += 1
+	redimension /n=(nx, ny) source_redim
+	
+	return int_linbg_reduction(source_redim, dest1, dest2, param)
+end
+