code changes for release 2.2.0
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.gitignore
vendored
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.gitignore
vendored
@ -2,5 +2,6 @@
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~*
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*.bak
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*.ipfT*
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doc/html/*
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doc/latex/*
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18
README.md
18
README.md
@ -14,8 +14,13 @@ PEARL Procedures should be installed according to the regular Igor Pro guideline
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- 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.
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- 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.
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PEARL Procedures are compatible with Igor Pro versions 6.37 and 8.04, 32-bit and 64-bit.
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PEARL Procedures are tested on Igor 8.04, 64-bit.
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Please make sure to use the latest release version.
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While most of the code remains compatible with Igor 6.37, it is not tested and not supported.
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Importing recent PShell data files may requires Igor 8 due to changes in the HDF5 library.
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Igor 7 contains some bugs which affect PEARL Procedures and should not be used.
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As long as no Igor 8 specific features are used (long object names), the produced experiment files remain compatible with Igor 6.
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@ -34,12 +39,16 @@ Matthias Muntwiler, <mailto:matthias.muntwiler@psi.ch>
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Copyright
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---------
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Copyright 2009-2020 by [Paul Scherrer Institut](http://www.psi.ch)
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Copyright 2009-2021 by [Paul Scherrer Institut](http://www.psi.ch)
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Release Notes
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=============
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## rev-distro-2.2.0
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- Updates, bugfixes and performance improvements in angle scan processing.
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## rev-distro-2.1.0
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- Check compatibility of major features with Igor 8.
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@ -53,8 +62,3 @@ Release Notes
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- The interface of data reduction functions has changed to make data reduction more efficient in multi-peak fits. The supplied reduction functions and dialogs have been refactored. If you want to use your own reduction functions written for pre-2.0, you have to adapt them to the new interface.
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## rev-distro-1.1.1
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- If you have upgraded PEARL Procedures from pre-1.1.1 and Igor breaks in pearl-elog.ipf while opening an experiment, please delete the ELOG preferences file `pearl-elog/preferences.pxp`. (Check the Igor Help to find the package preferences folder on your system.)
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2375
pearl/electron-binding-energies.itx
Normal file
2375
pearl/electron-binding-energies.itx
Normal file
File diff suppressed because it is too large
Load Diff
@ -1,3 +1,4 @@
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#pragma TextEncoding = "UTF-8"
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#pragma rtGlobals=3 // Use modern global access method and strict wave access.
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#include "pearl-area-profiles"
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@ -297,24 +298,3 @@ function show_shift(data)
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shift_x += ecenter
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end
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/// calculate the energy resolution of the analyser
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///
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/// @param epass pass energy in eV
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/// @param slit analyser entrance slit in mm
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///
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/// @return energy resolution (FWHM)
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function analyser_energy_resolution(epass, slit)
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variable epass
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variable slit
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variable respow
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if (epass < 4)
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respow = 1110
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elseif (epass < 8)
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respow = 1400
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else
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respow = 1750
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endif
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return epass * max(0.2, slit) / 0.2 / respow
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end
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@ -1,9 +1,12 @@
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#pragma TextEncoding = "UTF-8"
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#pragma rtGlobals=3 // Use modern global access method and strict wave access.
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#pragma version = 1.8
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#pragma IgorVersion = 6.2
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#pragma ModuleName = PearlAnglescanPanel
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#include "pearl-anglescan-process"
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#include "pearl-pmsco-import"
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#include "pearl-scienta-preprocess"
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#include "pearl-area-display"
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// copyright (c) 2018-20 Paul Scherrer Institut
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//
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@ -430,9 +433,9 @@ static function delete_rows(rows, data, theta, tilt, phi)
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extract /free idx, idx, idx >= 0
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variable nx = dimsize(data, 0)
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variable ny = numpnts(idx)
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theta = theta[idx]
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tilt = tilt[idx]
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phi = phi[idx]
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theta[0,ny-1] = theta[idx]
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tilt[0,ny-1] = tilt[idx]
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phi[0,ny-1] = phi[idx]
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redimension /n=(ny) theta, tilt, phi
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duplicate /free data, data_copy
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redimension /n=(nx,ny) data
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@ -1,12 +1,13 @@
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#pragma TextEncoding = "UTF-8"
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#pragma rtGlobals=3 // Use modern global access method and strict wave access.
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#pragma version = 1.8
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#pragma version = 1.9
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#pragma IgorVersion = 6.2
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#pragma ModuleName = PearlAnglescanProcess
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#include "pearl-vector-operations"
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#include "pearl-polar-coordinates"
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#include <New Polar Graphs>
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// copyright (c) 2013-17 Paul Scherrer Institut
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// copyright (c) 2013-21 Paul Scherrer Institut
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//
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// Licensed under the Apache License, Version 2.0 (the "License");
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// you may not use this file except in compliance with the License.
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@ -64,7 +65,7 @@
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///
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/// @author matthias muntwiler, matthias.muntwiler@psi.ch
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///
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/// @copyright 2013-17 Paul Scherrer Institut @n
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/// @copyright 2013-21 Paul Scherrer Institut @n
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/// Licensed under the Apache License, Version 2.0 (the "License"); @n
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/// you may not use this file except in compliance with the License. @n
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/// You may obtain a copy of the License at
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@ -80,6 +81,70 @@
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/// PearlAnglescanProcess is declared in @ref pearl-anglescan-process.ipf.
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/// append an angle scan strip to another one
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///
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/// concatenate two angle scan strips including matching attribute waves
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/// and replace the first strip with the resulting waves.
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/// this is useful if a scan was interrupted and continues in a second data file.
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///
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/// all accompanying 1D waves which have a matching length and exist in both source and destination folders
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/// are concatenated and stored in the destination.
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/// 'accompanying waves' are those in the same folder as the 2D strip wave and those in the :attr sub-folder.
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///
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/// @attention this function modifies all matching waves in the data and attr folders of strip1!
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/// consider a backup before calling the function, or work on a copy of the original data
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/// (cf. Igor's DuplicateDataFolder operation)!
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///
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/// @param[in,out] strip1 2D data, X-axis = analyser angle, Y-axis = arbitrary manipulator scan.
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/// this is the first source wave and destination wave.
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///
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/// @param[in] strip2 2D data, X-axis = analyser angle, Y-axis = arbitrary manipulator scan.
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/// this is the second source wave.
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///
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/// @return (string) semicolon-separated list of modified wave names (without folder path).
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///
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function /s strip_append(strip1, strip2)
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wave strip1
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wave strip2
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dfref df1 = GetWavesDataFolderDFR(strip1)
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dfref df2 = GetWavesDataFolderDFR(strip2)
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variable ny1 = dimsize(strip1, 1)
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variable ny2 = dimsize(strip2, 1)
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concatenate /np=1 {strip2}, strip1
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string modified = AddListItem(NameOfWave(strip1), "")
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variable idf = 0
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do
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variable iw = 0
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do
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wave /z w1 = WaveRefIndexedDFR(df1, iw)
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if (!WaveExists(w1))
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break
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endif
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wave /z w2 = df2:$(NameOfWave(w1))
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if (WaveExists(w1) && WaveExists(w2))
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if ((DimSize(w1, 0) == ny1) && (DimSize(w1, 1) == 0) && (DimSize(w2, 0) == ny2) && (DimSize(w2, 1) == 0))
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concatenate /np=0 {w2}, w1
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modified = AddListItem(NameOfWave(w1), modified, "", Inf)
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endif
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endif
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iw += 1
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while(1)
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df1 = df1:attr
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df2 = df2:attr
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if ((DataFolderRefStatus(df1) != 1) || (DataFolderRefStatus(df2) != 1))
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break
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endif
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idf += 1
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while(idf < 2)
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return modified
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end
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/// delete a contiguous range of frames from a strip.
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///
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/// this can be used to remove a region of bad frames due to, e.g., measurement problems.
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@ -299,7 +364,9 @@ function normalize_strip_phi(strip, theta, phi, [theta_offset, theta_range, chec
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endif
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// average over analyser angles
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wave dist = ad_profile_y(strip, -inf, inf, "")
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duplicate /free strip, strip_copy
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MatrixFilter NanZapMedian strip_copy
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wave dist = ad_profile_y(strip_copy, -inf, inf, "")
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// smooth distribution function
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duplicate /free dist, dist_smoo
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@ -385,7 +452,9 @@ function normalize_strip_theta(strip, theta, [theta_offset, smooth_method, smoot
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endif
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// average over analyser angles
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wave dist = ad_profile_y(strip, -inf, inf, "")
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duplicate /free strip, strip_copy
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MatrixFilter NanZapMedian strip_copy
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wave dist = ad_profile_y(strip_copy, -inf, inf, "")
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// smooth distribution function
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duplicate /free dist, dist_smoo
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@ -484,7 +553,9 @@ function normalize_strip_thetaphi(strip, theta, phi, [theta_offset, smooth_metho
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endif
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// average over analyser angles
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wave dist = ad_profile_y(strip, -inf, inf, "")
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duplicate /free strip, strip_copy
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MatrixFilter NanZapMedian strip_copy
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wave dist = ad_profile_y(strip_copy, -inf, inf, "")
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// smooth distribution function
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duplicate /free dist, dist_smoo
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@ -542,7 +613,9 @@ function normalize_strip_theta_scans(strip, theta, [theta_offset, smooth_method,
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endif
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// average over analyser angles
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wave dist = ad_profile_y(strip, -inf, inf, "")
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duplicate /free strip, strip_copy
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MatrixFilter NanZapMedian strip_copy
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wave dist = ad_profile_y(strip_copy, -inf, inf, "")
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// smooth distribution function
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duplicate /free dist, dist_smoo
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@ -635,6 +708,7 @@ function normalize_strip_2d(strip, theta, [theta_offset, smooth_method, smooth_f
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variable ny = dimsize(strip, 1)
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duplicate /free strip, dist, alpha_int, theta_int
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MatrixFilter NanZapMedian dist
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theta_int = theta[q] - theta_offset
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alpha_int = dimoffset(strip, 0) + p * dimdelta(strip, 0)
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redimension /n=(nx * ny) dist, alpha_int, theta_int
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@ -1955,7 +2029,7 @@ static function /s display_polar_graph(graphname, [angle_offset, do_ticks])
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WMPolarGraphSetVar(graphname, "doAngleTickLabelSubRange", 1)
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WMPolarGraphSetVar(graphname, "angleTickLabelRangeStart", 0)
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WMPolarGraphSetVar(graphname, "angleTickLabelRangeExtent", 90)
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WMPolarGraphSetStr(graphname, "angleTickLabelNotation", "%g°")
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WMPolarGraphSetStr(graphname, "angleTickLabelNotation", "%g°")
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WMPolarGraphSetVar(graphname, "doPolarGrids", 0)
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WMPolarGraphSetVar(graphname, "doRadiusTickLabels", 0)
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@ -2083,9 +2157,9 @@ static function /s draw_hemi_axes(graphname, [do_grids])
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SetDrawEnv /W=$graphname textxjust= 1,textyjust= 2
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SetDrawEnv /W=$graphname save
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radi = calc_graph_radius(30, projection=projection)
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DrawText /W=$graphname radi, -0.1, "30°"
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DrawText /W=$graphname radi, -0.1, "30°"
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radi = calc_graph_radius(60, projection=projection)
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DrawText /W=$graphname radi, -0.1, "60°"
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DrawText /W=$graphname radi, -0.1, "60°"
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endif
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setdatafolder savedf
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@ -2205,7 +2279,7 @@ function /s display_scanlines(nickname, alpha_lo, alpha_hi, m_theta, m_tilt, m_p
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make /n=1 /d /free d_polar, d_azi
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variable n_alpha = round(alpha_hi - alpha_lo) + 1
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make /n=(n_alpha) /d /free analyser
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setscale /i x alpha_lo, alpha_hi, "°", analyser
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setscale /i x alpha_lo, alpha_hi, "°", analyser
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analyser = x
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convert_angles_ttpa2polar(m_theta, loc_m_tilt, m_phi, analyser, d_polar, d_azi)
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@ -2526,50 +2600,78 @@ function set_polar_graph_cursor(nickname, cursorname, polar_angle, azim_angle, [
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endif
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end
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/// add an arbitrary angle scan to a hemispherical scan grid.
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/// add arbitrary angle scan data to a hemispherical scan grid.
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///
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/// the hemi grid must have been created in the current data folder by the make_hemi_grid function.
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/// the function determines the bin size at the given polar angle,
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/// and adds all data points which fall into a bin.
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/// a point which lies exactly on the upper boundary falls into the next bin.
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/// this function does not clear previous values before adding new data.
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/// the function fills the input data into bins defined by the hemi scan grid.
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/// it sums up the values and weights of the data points which fall into each bin,
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/// and adds the results to the totals and weights waves of the existing hemi grid.
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/// finally, it updates the values wave (values divided by weights).
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///
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/// the hemi grid must have been created in the current data folder by the make_hemi_grid() function.
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/// the function does not clear previous values before adding new data.
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/// values are added to the _tot wave, weights to the _wt wave.
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/// the intensity (_i) wave is calculated as _tot / _wt.
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/// the intensity (_i/values) wave is calculated as _tot divided by _wt.
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///
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/// @param nickname name prefix of holo waves.
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/// empty if waves are in current data folder.
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/// @param values counts/intensity values at the positions given in the polara nd azi waves.
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/// one- or two-dimensional.
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/// NaN values are ignored.
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/// @param polar polar angles (in degrees) of each data point.
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/// allowed range 0 <= theta <= 90.
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/// no specific ordering required.
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/// @param azi azimuthal angles (in degrees) of each data point.
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/// allowed range -360 <= phi < +360.
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/// no specific order required.
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/// @param weights weight or accumulation time of each point of values.
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/// weights must be positive. values with weight 0 are ignored.
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/// defaults to 1 if not specified.
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///
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/// the values, weights, polar and azi waves must have the same dimensions (one- or two-dimensional).
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/// no specific order is required, the function sorts (copies of) the arrays internally.
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///
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/// the actual binning is delegated to the thread-safe add_anglescan_worker() function
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/// under Igor's automatic multi-threading facility.
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///
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function hemi_add_anglescan(nickname, values, polar, azi, [weights])
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string nickname // name prefix of holo waves.
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// may be empty.
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wave values // intensity values
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// the wave can be one- or two-dimensional.
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// no specific order required, the function sorts the arrays internally
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wave polar // polar coordinates. allowed range 0 <= theta <= 90
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// dimensions corresponding to value.
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wave azi // azimuthal coordinates. allowed range -360 <= phi < +360
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// dimensions corresponding to value.
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wave weights // total accumulation time of each point of values. default = 1
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string nickname
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wave values
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wave polar
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wave azi
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wave weights
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dfref savedf = GetDataFolderDFR()
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if (ParamIsDefault(weights))
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duplicate /free values, weights
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weights = 1
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endif
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// quick check whether hemi grid is existing
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string s_prefix = ""
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string s_int = "values"
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dfref df = find_hemi_data(nickname, s_prefix, s_int)
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string s_totals = s_prefix + "tot"
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string s_weights = s_prefix + "wt"
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string s_polar = s_prefix + "pol"
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string s_azim = s_prefix + "az"
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string s_index = s_prefix + "index"
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string s_theta = s_prefix + "th"
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wave /sdfr=df /z w_values = $s_int
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wave /sdfr=df /z w_azim = $s_azim
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wave /sdfr=df /z w_polar = $s_polar
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wave /sdfr=df /z w_theta = $s_theta
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if (!waveexists(w_values) || !waveexists(w_azim) || !waveexists(w_polar))
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abort "Missing hemispherical scan grid. Please call make_hemi_grid() first."
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endif
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string s_dphi = s_prefix + "dphi"
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string s_nphis = s_prefix + "nphis"
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// make internal copies, one-dimensional, ordered in theta
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wave /sdfr=df w_polar = $s_polar
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wave /sdfr=df w_azim = $s_azim
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wave /sdfr=df w_values = $s_int
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wave /sdfr=df w_totals = $s_totals
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wave /sdfr=df w_weights = $s_weights
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wave /sdfr=df w_index = $s_index
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wave /sdfr=df w_theta = $s_theta
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wave /sdfr=df w_dphi = $s_dphi
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wave /sdfr=df w_nphis = $s_nphis
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// make internal copies of input, one-dimensional, ordered in theta
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duplicate /free values, values_copy
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duplicate /free polar, polar_copy
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duplicate /free azi, azi_copy
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@ -2577,49 +2679,186 @@ function hemi_add_anglescan(nickname, values, polar, azi, [weights])
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variable nn = dimsize(values, 0) * max(dimsize(values, 1), 1)
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redimension /n=(nn) values_copy, polar_copy, azi_copy, weights_copy
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sort /r polar_copy, polar_copy, azi_copy, values_copy, weights_copy
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make /n=(numpnts(w_theta)) /free /df dfw
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// for debugging: remove the MultiThread keyword and the ThreadSafe keywords of sub-functions
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MultiThread dfw = add_anglescan_worker(p, values_copy, weights_copy, polar_copy, azi_copy, w_polar, w_azim, w_theta, w_index, w_dphi, w_nphis)
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variable pp
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for (pp = 0; pp < numpnts(dfw); pp += 1)
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dfref tdf= dfw[pp]
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wave df_totals = tdf:w_totals
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wave df_weights = tdf:w_weights
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w_totals += df_totals
|
||||
w_weights += df_weights
|
||||
endfor
|
||||
w_values = w_weights > 0 ? w_totals / w_weights : nan
|
||||
|
||||
variable pol
|
||||
SetDataFolder savedf
|
||||
end
|
||||
|
||||
/// thread worker for hemi_add_anglescan
|
||||
///
|
||||
/// this function extracts one azimuthal scan from the input data and adds it to an existing holo scan.
|
||||
/// it should be considered as a part of hemi_add_anglescan and not used elsewhere,
|
||||
/// as its interface may change in the future.
|
||||
///
|
||||
/// the function takes as input the entire input data, an existing hemi grid and the index of a polar angle to work on.
|
||||
/// the results are a w_totals and w_weights wave that can be added to the hemi scan.
|
||||
/// the two waves are returned in a free data folder referenced by the return value of the function.
|
||||
/// the function does not change global data.
|
||||
///
|
||||
threadsafe static function /df add_anglescan_worker(ith, values, weights, polar, azi, w_polar, w_azim, w_theta, w_index, w_dphi, w_nphis)
|
||||
variable ith // index into w_theta
|
||||
wave values // input data: intensity/counts
|
||||
wave weights // input data: weights/dwell time
|
||||
wave polar // input data: polar angles
|
||||
wave azi // input data: azimuthal angles
|
||||
wave w_polar // hemi grid
|
||||
wave w_azim // hemi grid
|
||||
wave w_theta // hemi grid
|
||||
wave w_index // hemi grid
|
||||
wave w_dphi // hemi grid
|
||||
wave w_nphis // hemi grid
|
||||
|
||||
dfref savedf= GetDataFolderDFR()
|
||||
dfref freedf= NewFreeDataFolder()
|
||||
SetDataFolder freedf
|
||||
make /n=(numpnts(w_polar)) /d w_totals, w_weights
|
||||
|
||||
variable pol = w_theta[ith]
|
||||
variable pol_st = abs(w_theta[1] - w_theta[0])
|
||||
variable pol1, pol2
|
||||
variable pol1 = pol - pol_st / 2
|
||||
variable pol2 = pol + pol_st / 2
|
||||
|
||||
extract /free /indx polar, sel, (pol1 < polar) && (polar <= pol2) && (numtype(values) == 0) && (weights > 0)
|
||||
if (numpnts(sel) > 0)
|
||||
duplicate /free /r=[0, numpnts(sel)-1] azi, azi_slice
|
||||
duplicate /free /r=[0, numpnts(sel)-1] values, values_slice
|
||||
duplicate /free /r=[0, numpnts(sel)-1] weights, weights_slice
|
||||
azi_slice = azi[sel]
|
||||
values_slice = values[sel]
|
||||
weights_slice = weights[sel]
|
||||
add_aziscan_core(values_slice, weights_slice, pol, azi_slice, w_theta, w_azim, w_index, w_dphi, w_totals, w_weights)
|
||||
endif
|
||||
|
||||
SetDataFolder savedf
|
||||
return freedf
|
||||
end
|
||||
|
||||
/// thread worker for hemi_add_anglescan and hemi_add_aziscan
|
||||
///
|
||||
/// this function adds one azimuthal scan to an existing holo scan.
|
||||
/// it should be considered as a part of hemi_add_anglescan and hemi_add_aziscan and not used elsewhere,
|
||||
/// as its interface may change in the future.
|
||||
///
|
||||
/// the function takes as input an azimuthal scan and an existing hemi grid.
|
||||
/// the results are added to w_totals and w_weights waves.
|
||||
///
|
||||
/// @attention the function sorts the input arrays by azimuthal angle!
|
||||
/// these waves must not refer to global objects if multi-threading is used!
|
||||
///
|
||||
threadsafe static function add_aziscan_core(values, weights, polar, azi, w_theta, w_azim, w_index, w_dphi, w_totals, w_weights)
|
||||
wave values // input data: intensity/counts
|
||||
wave weights // input data: weights/dwell time
|
||||
variable polar // input data: polar angle
|
||||
wave azi // input data: angle positions of the azimuthal scan
|
||||
// acceptable range: >= -360 and < +360
|
||||
// no specific order required, the function sorts the array in place (!)
|
||||
wave w_theta // hemi grid
|
||||
wave w_azim // hemi grid
|
||||
wave w_index // hemi grid
|
||||
wave w_dphi // hemi grid
|
||||
wave w_totals // output data: total counts in hemi grid order
|
||||
wave w_weights // output data: total weights in hemi grid order
|
||||
|
||||
duplicate /free azi_copy, azi_slice
|
||||
duplicate /free values_copy, values_slice
|
||||
duplicate /free weights_copy, weights_slice
|
||||
for (pol = 90; pol >= 0; pol -= pol_st)
|
||||
pol1 = pol - pol_st / 2
|
||||
pol2 = pol + pol_st / 2
|
||||
extract /free /indx polar_copy, sel, (pol1 < polar_copy) && (polar_copy <= pol2)
|
||||
if (numpnts(sel) > 0)
|
||||
redimension /n=(numpnts(sel)) azi_slice, values_slice, weights_slice
|
||||
azi_slice = azi_copy[sel]
|
||||
values_slice = values_copy[sel]
|
||||
weights_slice = weights_copy[sel]
|
||||
hemi_add_aziscan(nickname, values_slice, pol, azi_slice, weights=weights_slice)
|
||||
// destination slice coordinates
|
||||
variable ipol = BinarySearch(w_theta, polar)
|
||||
if (ipol < 0)
|
||||
return -1
|
||||
endif
|
||||
|
||||
variable d1, d2
|
||||
if (ipol >= 1)
|
||||
d1 = w_index[ipol - 1]
|
||||
else
|
||||
d1 = 0
|
||||
endif
|
||||
d2 = w_index[ipol] - 1
|
||||
variable nd = d2 - d1 + 1
|
||||
variable dphi = w_dphi[ipol]
|
||||
make /n=(nd+1) /free bin_index
|
||||
setscale /i x w_azim[d1] - dphi/2, w_azim[d2] + dphi/2, "deg", bin_index
|
||||
|
||||
// source slice coordinates
|
||||
// order the slice from -dphi/2 to 360-dphi/2
|
||||
azi = azi < 0 ? azi + 360 : azi
|
||||
azi = azi >= 360 - dphi/2 ? azi - 360 : azi
|
||||
sort azi, values, weights, azi
|
||||
setscale /p x 0, 1, "", values, weights, azi
|
||||
|
||||
bin_index = BinarySearch(azi, x) + 1
|
||||
bin_index = bin_index == -2 ? 0 : bin_index[p]
|
||||
bin_index = bin_index == -1 ? numpnts(azi) : bin_index[p]
|
||||
bin_index[nd] = numpnts(azi)
|
||||
|
||||
// loop over destination
|
||||
variable id
|
||||
variable v1, v2, w1, w2
|
||||
for (id = 0; id < nd; id += 1)
|
||||
if (bin_index[id+1] > bin_index[id])
|
||||
v1 = w_totals[d1 + id]
|
||||
w1 = w_weights[d1 + id]
|
||||
if ((numtype(v1) == 2) || (w1 <= 0))
|
||||
v1 = 0
|
||||
w1 = 0
|
||||
endif
|
||||
v2 = sum(values, bin_index[id], bin_index[id+1] - 1)
|
||||
w2 = sum(weights, bin_index[id], bin_index[id+1] - 1)
|
||||
w_totals[d1 + id] = v1 + v2
|
||||
w_weights[d1 + id] = w1 + w2
|
||||
endif
|
||||
endfor
|
||||
end
|
||||
|
||||
/// add an azimuthal scan to a hemispherical scan grid.
|
||||
/// add azimuthal data to a hemispherical scan grid.
|
||||
///
|
||||
/// the hemi grid must have been created in the current data folder by the make_hemi_grid function.
|
||||
/// the hemi grid must have been created in the current data folder by the make_hemi_grid() function.
|
||||
/// the function determines the bin size at the given polar angle,
|
||||
/// and calculates the mean values of the data points which fall into a bin.
|
||||
/// a point which lies exactly on the upper boundary falls into the next bin.
|
||||
/// sums up the values and weights of the data points which fall into each bin,
|
||||
/// and adds the results to the totals and weights waves of the existing hemi grid.
|
||||
/// finally, it updates the values wave (values divided by weights).
|
||||
///
|
||||
/// @param nickname name prefix of holo waves.
|
||||
/// empty if waves are in current data folder.
|
||||
/// @param values counts/intensity values of the azimuthal scan at the positions given in the azi parameter.
|
||||
/// @param polar polar angle (in degrees) where to add the azi scan.
|
||||
/// @param azi angle positions of the azimuthal scan.
|
||||
/// acceptable range: >= -360 and < +360.
|
||||
/// no specific order required, the function sorts the array internally.
|
||||
/// @param weights weight or accumulation time of each point of values.
|
||||
/// defaults to 1 if not specified.
|
||||
///
|
||||
/// the actual binning is delegated to the thread-safe add_aziscan_core() function shared with hemi_add_anglescan().
|
||||
///
|
||||
function hemi_add_aziscan(nickname, values, polar, azi, [weights])
|
||||
string nickname // name prefix of holo waves.
|
||||
// may be empty.
|
||||
wave values // intensity values of the azimuthal scan at the positions given in the azi parameter
|
||||
variable polar // polar angle where to add the azi scan
|
||||
wave azi // angle positions of the azimuthal scan
|
||||
// acceptable range: >= -360 and < +360
|
||||
// no specific order required, the function sorts the array internally
|
||||
wave weights // total accumulation time of each point of values. default = 1
|
||||
string nickname
|
||||
wave values
|
||||
variable polar
|
||||
wave azi
|
||||
wave weights
|
||||
|
||||
dfref savedf = GetDataFolderDFR()
|
||||
|
||||
duplicate /free values, values_copy
|
||||
duplicate /free azi, azi_copy
|
||||
if (ParamIsDefault(weights))
|
||||
duplicate /free values, weights
|
||||
weights = 1
|
||||
duplicate /free values, weights_copy
|
||||
weights_copy = 1
|
||||
else
|
||||
duplicate /free weights, weights_copy
|
||||
endif
|
||||
|
||||
|
||||
// hemi grid waves
|
||||
string s_prefix = ""
|
||||
string s_int = "values"
|
||||
@ -2644,56 +2883,11 @@ function hemi_add_aziscan(nickname, values, polar, azi, [weights])
|
||||
wave /sdfr=df w_dphi = $s_dphi
|
||||
wave /sdfr=df w_nphis = $s_nphis
|
||||
|
||||
// destination slice coordinates
|
||||
//polar = round(polar)
|
||||
//variable ipol = 90 - polar
|
||||
variable ipol = BinarySearch(w_theta, polar)
|
||||
if (ipol < 0)
|
||||
abort "assertion failed in hemi_add_aziscan(): polar angle not found in grid."
|
||||
endif
|
||||
|
||||
variable d1, d2
|
||||
if (ipol >= 1)
|
||||
d1 = w_index[ipol - 1]
|
||||
else
|
||||
d1 = 0
|
||||
endif
|
||||
d2 = w_index[ipol] - 1
|
||||
variable nd = d2 - d1 + 1
|
||||
variable dphi = w_dphi[ipol]
|
||||
variable az1, az2
|
||||
|
||||
// source slice coordinates
|
||||
// order the slice from -dphi/2 to 360-dphi/2
|
||||
azi = azi < 0 ? azi + 360 : azi
|
||||
azi = azi >= 360 - dphi/2 ? azi - 360 : azi
|
||||
duplicate /free values, sel_values
|
||||
duplicate /free weights, sel_weights
|
||||
|
||||
// loop over destination
|
||||
variable id
|
||||
variable v1, v2, w1, w2
|
||||
for (id = 0; id < nd; id += 1)
|
||||
az1 = (id - 0.5) * dphi
|
||||
az2 = (id + 0.5) * dphi
|
||||
extract /free /indx azi, sel, (az1 <= azi) && (azi < az2)
|
||||
if (numpnts(sel) > 0)
|
||||
redimension /n=(numpnts(sel)) sel_values, sel_weights
|
||||
sel_values = values[sel]
|
||||
sel_weights = weights[sel]
|
||||
v1 = w_totals[d1 + id]
|
||||
w1 = w_weights[d1 + id]
|
||||
if ((numtype(v1) == 2) || (w1 <= 0))
|
||||
v1 = 0
|
||||
w1 = 0
|
||||
endif
|
||||
v2 = sum(sel_values)
|
||||
w2 = sum(sel_weights)
|
||||
w_totals[d1 + id] = v1 + v2
|
||||
w_weights[d1 + id] = w1 + w2
|
||||
endif
|
||||
endfor
|
||||
w_values[d1, d1 + nd - 1] = w_totals[p] / w_weights[p]
|
||||
add_aziscan_core(values_copy, weights_copy, polar, azi_copy, w_theta, w_azim, w_index, w_dphi, w_totals, w_weights)
|
||||
|
||||
w_values = w_weights > 0 ? w_totals / w_weights : nan
|
||||
|
||||
SetDataFolder savedf
|
||||
end
|
||||
|
||||
/// interpolate a hemispherical scan onto a rectangular grid
|
||||
@ -3011,8 +3205,9 @@ function import_tpi_scan(nickname, theta, phi, intensity, [folding, npolar, nogr
|
||||
variable ifold
|
||||
duplicate /free phi, fold_phi
|
||||
for (ifold = 0; ifold < folding; ifold += 1)
|
||||
fold_phi = fold_phi >= 360 ? fold_phi - 360 : fold_phi
|
||||
hemi_add_anglescan(nickname, intensity, theta, fold_phi)
|
||||
fold_phi = fold_phi >= 180 ? fold_phi + 360 / folding - fold_phi : fold_phi + 360 / folding
|
||||
fold_phi += 360 / folding
|
||||
endfor
|
||||
|
||||
if (nograph==0)
|
||||
@ -3199,7 +3394,7 @@ function /wave hemi_azi_cut(nickname, pol)
|
||||
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]], "°", w_cut
|
||||
setscale /i x w_azim[sel[0]], w_azim[sel[nsel-1]], "°", w_cut
|
||||
setdatafolder savedf
|
||||
return w_cut
|
||||
else
|
||||
@ -3209,23 +3404,37 @@ function /wave hemi_azi_cut(nickname, pol)
|
||||
setdatafolder savedf
|
||||
end
|
||||
|
||||
static function check_contrast(values, pcmin, pcmax, vmin, vmax)
|
||||
static function check_contrast(values, pcmin, pcmax, vmin, vmax, sym)
|
||||
wave values
|
||||
variable pcmin
|
||||
variable pcmax
|
||||
variable &vmin
|
||||
variable &vmax
|
||||
variable sym
|
||||
|
||||
dfref save_df = GetDataFolderDFR()
|
||||
dfref dfr = NewFreeDataFolder()
|
||||
setdatafolder dfr
|
||||
StatsQuantiles /inan /iw /q /z values
|
||||
wave index = w_quantilesindex
|
||||
variable imin = round(numpnts(index) * pcmin / 100)
|
||||
variable imax = round(numpnts(index) * (100 - pcmax) / 100)
|
||||
vmin = values[index[imin]]
|
||||
vmax = values[index[imax]]
|
||||
wave /z index = w_quantilesindex
|
||||
setdatafolder save_df
|
||||
|
||||
if (waveexists(index))
|
||||
variable imin = round(numpnts(index) * pcmin / 100)
|
||||
variable imax = round(numpnts(index) * (100 - pcmax) / 100)
|
||||
vmin = values[index[imin]]
|
||||
vmax = values[index[imax]]
|
||||
if (sym)
|
||||
variable d = vmax - vmin
|
||||
if ((vmax >= d/4) && (-vmin >= d/4))
|
||||
vmax = min(abs(vmin), abs(vmax))
|
||||
vmin = -vmax
|
||||
endif
|
||||
endif
|
||||
else
|
||||
vmin = wavemin(values)
|
||||
vmax = wavemax(values)
|
||||
endif
|
||||
end
|
||||
|
||||
/// set the pseudocolor contrast by percentile.
|
||||
@ -3243,12 +3452,21 @@ end
|
||||
/// @param pcmax percentile above the maximum color (0-100).
|
||||
/// @param graphname name of graph. default: top graph.
|
||||
/// @param colortable name of new colortable. default: keep current table.
|
||||
/// @param reversecolors reverse colors of new colorable.
|
||||
/// takes effect only if colortable argument is defined.
|
||||
/// @arg 0 (default) normal colors,
|
||||
/// @arg 1 reverse color table
|
||||
/// @param symmetric make scale symmetric about zero (for modulation functions, e.g.).
|
||||
/// @arg 0 (default) do not enforce symmetry.
|
||||
/// @arg 1 try symmetric scale if "reasonable".
|
||||
///
|
||||
function set_contrast(pcmin, pcmax, [graphname, colortable])
|
||||
function set_contrast(pcmin, pcmax, [graphname, colortable, reversecolors, symmetric])
|
||||
variable pcmin
|
||||
variable pcmax
|
||||
string graphname
|
||||
string colortable
|
||||
variable reversecolors
|
||||
variable symmetric
|
||||
|
||||
if (ParamIsDefault(graphname))
|
||||
graphname = ""
|
||||
@ -3256,6 +3474,12 @@ function set_contrast(pcmin, pcmax, [graphname, colortable])
|
||||
if (ParamIsDefault(colortable))
|
||||
colortable = ""
|
||||
endif
|
||||
if (ParamIsDefault(reversecolors))
|
||||
reversecolors = 0
|
||||
endif
|
||||
if (ParamIsDefault(symmetric))
|
||||
symmetric = 0
|
||||
endif
|
||||
|
||||
dfref save_df = GetDataFolderDFR()
|
||||
|
||||
@ -3285,9 +3509,12 @@ function set_contrast(pcmin, pcmax, [graphname, colortable])
|
||||
rev = str2num("0" + StringFromList(4, info, ","))
|
||||
if (strlen(colortable) > 0)
|
||||
ctab = colortable
|
||||
rev = reversecolors
|
||||
endif
|
||||
check_contrast(w, pcmin, pcmax, vmin, vmax, symmetric)
|
||||
if (vmax > vmin)
|
||||
ModifyGraph /w=$graphname zColor($objname)={w, vmin, vmax, $ctab, rev}
|
||||
endif
|
||||
check_contrast(w, pcmin, pcmax, vmin, vmax)
|
||||
ModifyGraph /w=$graphname zColor($objname)={w, vmin, vmax, $ctab, rev}
|
||||
endif
|
||||
endif
|
||||
endfor
|
||||
@ -3307,9 +3534,12 @@ function set_contrast(pcmin, pcmax, [graphname, colortable])
|
||||
rev = str2num("0" + StringFromList(3, info, ","))
|
||||
if (strlen(colortable) > 0)
|
||||
ctab = colortable
|
||||
rev = reversecolors
|
||||
endif
|
||||
check_contrast(w, pcmin, pcmax, vmin, vmax, symmetric)
|
||||
if (vmax > vmin)
|
||||
ModifyImage /w=$graphname $objname ctab={vmin, vmax, $ctab, rev}
|
||||
endif
|
||||
check_contrast(w, pcmin, pcmax, vmin, vmax)
|
||||
ModifyImage /w=$graphname $objname ctab={vmin, vmax, $ctab, rev}
|
||||
endif
|
||||
endif
|
||||
endfor
|
||||
|
||||
@ -1,3 +1,4 @@
|
||||
#pragma TextEncoding = "Windows-1252"
|
||||
#pragma rtGlobals=3
|
||||
#pragma version = 1.4
|
||||
#pragma IgorVersion = 6.2
|
||||
|
||||
@ -1,8 +1,10 @@
|
||||
#pragma TextEncoding = "UTF-8"
|
||||
#pragma rtGlobals=3 // Use modern global access method and strict wave access.
|
||||
#pragma IgorVersion = 6.2
|
||||
#pragma ModuleName = PearlAreaDisplay
|
||||
#pragma version = 1.04
|
||||
#include "pearl-compat"
|
||||
#include "pearl-area-profiles"
|
||||
|
||||
/// @file
|
||||
/// @brief visualization tools for 2D and 3D data.
|
||||
|
||||
@ -1,3 +1,4 @@
|
||||
#pragma TextEncoding = "Windows-1252"
|
||||
#pragma rtGlobals=3 // Use modern global access method and strict wave access.
|
||||
#pragma IgorVersion = 6.2
|
||||
#pragma ModuleName = PearlAreaImport
|
||||
@ -5,7 +6,7 @@
|
||||
#include "pearl-compat"
|
||||
#include "pearl-gui-tools"
|
||||
|
||||
// copyright (c) 2013-18 Paul Scherrer Institut
|
||||
// copyright (c) 2013-20 Paul Scherrer Institut
|
||||
//
|
||||
// Licensed under the Apache License, Version 2.0 (the "License");
|
||||
// you may not use this file except in compliance with the License.
|
||||
@ -26,7 +27,7 @@
|
||||
///
|
||||
/// @author matthias muntwiler, matthias.muntwiler@psi.ch
|
||||
///
|
||||
/// @copyright 2013-18 Paul Scherrer Institut @n
|
||||
/// @copyright 2013-20 Paul Scherrer Institut @n
|
||||
/// Licensed under the Apache License, Version 2.0 (the "License"); @n
|
||||
/// you may not use this file except in compliance with the License. @n
|
||||
/// You may obtain a copy of the License at
|
||||
@ -1331,7 +1332,7 @@ function adh5_reduce_brick(source, reduction_func, reduction_param, result_prefi
|
||||
for (iw = 0; iw < func_result; iw += 1)
|
||||
sw = "redw_" + num2str(iw)
|
||||
wave profile = dfr:$sw
|
||||
sw = "ReducedData" + num2str(iw+1)
|
||||
sw = result_prefix + num2str(iw+1)
|
||||
make /n=(dimsize(profile, 0), nz, nt) /d /o $sw
|
||||
wave data = $sw
|
||||
setdimlabel 0, -1, $getdimlabel(profile, 0, -1), data
|
||||
|
||||
@ -1,3 +1,4 @@
|
||||
#pragma TextEncoding = "UTF-8"
|
||||
#pragma rtGlobals=3 // Use modern global access method and strict wave access.
|
||||
#pragma IgorVersion = 6.1
|
||||
#pragma ModuleName = PearlAreaProfiles
|
||||
|
||||
@ -1,3 +1,4 @@
|
||||
#pragma TextEncoding = "UTF-8"
|
||||
#pragma rtGlobals=3 // Use modern global access method and strict wave access.
|
||||
#pragma IgorVersion = 6.1
|
||||
#pragma ModuleName = PearlArpes
|
||||
@ -18,7 +19,7 @@
|
||||
#include "pearl-epics" // EPICS access under Igor
|
||||
#include "pearl-arpes-scans" // run ARPES scans under Igor
|
||||
#include "pearl-sample-tracker" // live tracking and adjustment of sample position
|
||||
#include "pearl-scienta-countrate"
|
||||
#include "pearl-scienta-live"
|
||||
#endif
|
||||
|
||||
/// @file
|
||||
@ -84,4 +85,4 @@ end
|
||||
function UnloadPearlArpesPackage()
|
||||
execute /p/q/z "DELETEINCLUDE \"pearl-arpes\""
|
||||
execute /p/q/z "COMPILEPROCEDURES "
|
||||
end
|
||||
end
|
||||
|
||||
@ -1,3 +1,4 @@
|
||||
#pragma TextEncoding = "UTF-8"
|
||||
#pragma rtGlobals=3 // Use modern global access method and strict wave access.
|
||||
#pragma IgorVersion = 6.1
|
||||
#pragma ModuleName = PearlCompat
|
||||
|
||||
@ -1,7 +1,8 @@
|
||||
#pragma TextEncoding = "UTF-8"
|
||||
#pragma rtGlobals=3 // Use modern global access method and strict wave access.
|
||||
#pragma IgorVersion = 6.1
|
||||
#pragma IgorVersion = 6.36
|
||||
#pragma ModuleName = PearlDataExplorer
|
||||
#pragma version = 1.50
|
||||
#pragma version = 1.60
|
||||
#include "pearl-area-import"
|
||||
#include "pearl-area-profiles"
|
||||
#include "pearl-area-display"
|
||||
@ -11,7 +12,7 @@
|
||||
#include "pearl-matrix-import"
|
||||
#endif
|
||||
|
||||
// copyright (c) 2013-16 Paul Scherrer Institut
|
||||
// copyright (c) 2013-20 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.
|
||||
@ -258,6 +259,9 @@ static function preview_file(filename)
|
||||
string filename
|
||||
|
||||
dfref saveDF = GetDataFolderDFR()
|
||||
dfref previewDF = $package_path
|
||||
|
||||
killStrings /z authors, pgroup, proposal, proposer, sample
|
||||
|
||||
variable ft = pearl_file_type(filename)
|
||||
switch(ft)
|
||||
@ -288,6 +292,35 @@ static function preview_file(filename)
|
||||
sprintf cmd, "PearlElog#set_panel_graphs(\"\", \"%s\")", graphname
|
||||
execute /Q/Z cmd
|
||||
endif
|
||||
svar /sdfr=previewDF /z authors
|
||||
if (svar_Exists(authors))
|
||||
if (strlen(authors)>=1)
|
||||
sprintf cmd, "PearlElog#set_panel_attributes(\"\", \"author=%s\")", authors
|
||||
execute /Q/Z cmd
|
||||
endif
|
||||
endif
|
||||
svar /sdfr=previewDF /z pgroup
|
||||
if (svar_Exists(pgroup))
|
||||
if (strlen(pgroup)>=1)
|
||||
sprintf cmd, "PearlElog#set_panel_attributes(\"\", \"p-group=%s\")", pgroup
|
||||
execute /Q/Z cmd
|
||||
endif
|
||||
endif
|
||||
svar /sdfr=previewDF /z proposal
|
||||
if (svar_Exists(proposal))
|
||||
if (strlen(proposal)>=1)
|
||||
sprintf cmd, "PearlElog#set_panel_attributes(\"\", \"project=%s\")", proposal
|
||||
execute /Q/Z cmd
|
||||
endif
|
||||
endif
|
||||
svar /sdfr=previewDF /z proposer
|
||||
svar /sdfr=previewDF /z sample
|
||||
if (svar_Exists(sample))
|
||||
if (strlen(sample)>=1)
|
||||
sprintf cmd, "PearlElog#set_panel_attributes(\"\", \"sample=%s\")", sample
|
||||
execute /Q/Z cmd
|
||||
endif
|
||||
endif
|
||||
endif
|
||||
endif
|
||||
|
||||
@ -337,6 +370,8 @@ static function /wave preview_pshell_file(filename)
|
||||
|
||||
if (strlen(s_preview_file) > 0)
|
||||
s_file_info = psh5_load_info("pearl_explorer_filepath", filename)
|
||||
setdatafolder previewDF
|
||||
psh5_load_general_group("pearl_explorer_filepath", filename)
|
||||
else
|
||||
s_file_info = ""
|
||||
endif
|
||||
@ -960,15 +995,22 @@ static function /s display_preview_trace(xtrace, ytrace)
|
||||
lab = "X"
|
||||
endif
|
||||
Label /w=$graphname bottom lab + " (\\U)"
|
||||
lab = StringByKey("AxisLabelD", labels, "=", "\r")
|
||||
lab = StringByKey("Dataset", labels, "=", "\r")
|
||||
if (!strlen(lab))
|
||||
lab = "value"
|
||||
endif
|
||||
Label /w=$graphname left lab + " (\\U)"
|
||||
|
||||
|
||||
return s_name
|
||||
end
|
||||
|
||||
/// load the selected files
|
||||
///
|
||||
/// load the files that are selected in the data explorer panel.
|
||||
/// the files are loaded using the load_file() function.
|
||||
///
|
||||
/// @note this function may change the current data folder!
|
||||
///
|
||||
static function load_selected_files([options])
|
||||
string options
|
||||
|
||||
@ -981,6 +1023,7 @@ static function load_selected_files([options])
|
||||
variable ii
|
||||
for (ii = 0; ii < nn; ii += 1)
|
||||
if (wSelectedFiles[ii])
|
||||
setdatafolder saveDF
|
||||
if (ParamIsDefault(options))
|
||||
load_file(wtFiles[ii])
|
||||
else
|
||||
@ -990,15 +1033,19 @@ static function load_selected_files([options])
|
||||
endfor
|
||||
|
||||
update_datasets()
|
||||
setdatafolder saveDF
|
||||
end
|
||||
|
||||
/// load one file
|
||||
///
|
||||
/// this can be a PShell, HDF5, ITX or MTRX file.
|
||||
/// (HDF5 and MTRX files require the corresponding XOP to be loaded - cf. file documentation)
|
||||
///
|
||||
/// @note this function may change the current data folder!
|
||||
///
|
||||
static function load_file(filename, [options])
|
||||
string filename
|
||||
string options
|
||||
|
||||
dfref saveDF = GetDataFolderDFR()
|
||||
|
||||
variable ft = pearl_file_type(filename)
|
||||
switch(ft)
|
||||
case 1:
|
||||
@ -1024,8 +1071,6 @@ static function load_file(filename, [options])
|
||||
default:
|
||||
break
|
||||
endswitch
|
||||
|
||||
setdatafolder saveDF
|
||||
end
|
||||
|
||||
static function prompt_hdf_options(options)
|
||||
@ -1087,6 +1132,27 @@ function prompt_func_params(func_name, func_param)
|
||||
endif
|
||||
end
|
||||
|
||||
/// load a pshell file
|
||||
///
|
||||
/// load a pshell hdf5 file (complete or reduced).
|
||||
///
|
||||
/// if options is not specified, the complete file is loaded.
|
||||
/// if options is an empty string, the package default options are used.
|
||||
///
|
||||
/// the only supported options is `mode:load_reduced`.
|
||||
/// in this case, the name of the reduction function must also be given under the `reduction_func` key.
|
||||
/// the reduction parameters are prompted for if a prompt function for the reduction function is found.
|
||||
/// the default reduction parameters are the most recent parameters `s_reduction_params` stored in the package data folder.
|
||||
///
|
||||
/// @param options `key:value;` list of load options.
|
||||
/// by default, load complete, using psh5_load_complete().
|
||||
/// empty string, use options from `s_hdf_options.
|
||||
/// @arg `mode:load_reduced` load reduced, using psh5_load_reduced().
|
||||
/// @arg `reduction_func:...` name of the reduction function.
|
||||
///
|
||||
/// @note after the function returns,
|
||||
/// the current data folder points to the loaded data (scan1).
|
||||
///
|
||||
static function /df load_pshell_file(filename, [options])
|
||||
string filename
|
||||
string options
|
||||
@ -1122,7 +1188,7 @@ static function /df load_pshell_file(filename, [options])
|
||||
print reduction_func, reduction_params
|
||||
psh5_load_reduced(nickname, "pearl_explorer_filepath", filename, $reduction_func, reduction_params)
|
||||
svar s_filepath
|
||||
loaded_filename = s_filepath
|
||||
loaded_filename = filename
|
||||
endif
|
||||
break
|
||||
endswitch
|
||||
@ -1132,10 +1198,12 @@ static function /df load_pshell_file(filename, [options])
|
||||
if (strlen(loaded_filename) > 0)
|
||||
setdatafolder $("root:" + nickname)
|
||||
dataDF = GetDataFolderDFR()
|
||||
setdatafolder $(":scan1")
|
||||
string /g pearl_explorer_import = "load_pshell_file"
|
||||
else
|
||||
setdatafolder saveDF
|
||||
endif
|
||||
|
||||
setdatafolder saveDF
|
||||
return dataDF
|
||||
end
|
||||
|
||||
@ -1183,9 +1251,10 @@ static function /df load_hdf_file(filename, [options])
|
||||
setdatafolder $("root:" + nickname)
|
||||
dataDF = GetDataFolderDFR()
|
||||
string /g pearl_explorer_import = "load_hdf_file"
|
||||
else
|
||||
setdatafolder saveDF
|
||||
endif
|
||||
|
||||
setdatafolder saveDF
|
||||
return dataDF
|
||||
end
|
||||
|
||||
|
||||
@ -1,10 +1,11 @@
|
||||
#pragma TextEncoding = "UTF-8"
|
||||
#pragma rtGlobals=3 // Use modern global access method and strict wave access.
|
||||
#pragma version = 1.41
|
||||
#pragma IgorVersion = 6.2
|
||||
#pragma version = 1.50
|
||||
#pragma IgorVersion = 6.36
|
||||
#pragma ModuleName = PearlElog
|
||||
|
||||
// author: matthias.muntwiler@psi.ch
|
||||
// Copyright (c) 2013-17 Paul Scherrer Institut
|
||||
// Copyright (c) 2013-20 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.
|
||||
@ -71,7 +72,7 @@
|
||||
///
|
||||
/// @author matthias muntwiler, matthias.muntwiler@psi.ch
|
||||
///
|
||||
/// @copyright 2013-17 Paul Scherrer Institut @n
|
||||
/// @copyright 2013-20 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
|
||||
@ -272,14 +273,14 @@ function elog_init_pearl_templates()
|
||||
|
||||
// attributes (persistent)
|
||||
// available attributes
|
||||
string /g attributes = "author;project;p-group;sample;source;task;technique;file;valid;"
|
||||
string /g attributes = "author;project;pgroup;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_pgroup;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
|
||||
string /g required_attributes = "author;project;p-group;sample;source;task;technique;valid"
|
||||
string /g required_attributes = "author;project;pgroup;sample;source;task;technique;valid"
|
||||
|
||||
// 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"
|
||||
@ -292,7 +293,7 @@ function elog_init_pearl_templates()
|
||||
|
||||
// attributes (persistent)
|
||||
// available attributes
|
||||
string /g attributes = "author;project;p-group;sample;program;revision;machine;job;experiment;source path;result path;valid"
|
||||
string /g attributes = "author;project;pgroup;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_pgroup;sv_sample;pm_program;sv_revision;pm_machine;sv_job;sv_experiment;sv_sourcepath;sv_resultpath;cb_valid"
|
||||
|
||||
@ -1,3 +1,4 @@
|
||||
#pragma TextEncoding = "UTF-8"
|
||||
#pragma rtGlobals=3 // Use modern global access method and strict wave access.
|
||||
#pragma IgorVersion = 6.2
|
||||
#pragma ModuleName = PearlFitFuncs
|
||||
@ -124,6 +125,51 @@ threadsafe function DoubletGaussLinBG_AO(pw, yw, xw) : FitFunc
|
||||
yw += pw[2] * pw[3] * exp( -( (xw[p] - pw[4] + pw[5] /2) / pw[6] / pw[7] )^2 )
|
||||
end
|
||||
|
||||
/// two doublet gaussian peaks on a linear background fit function (all at once).
|
||||
///
|
||||
/// this fits four gaussian peaks.
|
||||
/// peak positions are specified by center, splitting and shift rather than individually.
|
||||
/// amplitudes are specified as absolute values for peaks 1 and 3,
|
||||
/// and relative values for peaks 2 and 4.
|
||||
///
|
||||
/// can be used if a spin-orbit doublet is split by a chemical shift
|
||||
/// which affects both spin-orbit peaks equally.
|
||||
///
|
||||
/// @note FWHM = width * 2 * sqrt(ln(2)) = width * 1.665
|
||||
///
|
||||
/// @param pw shape parameters.
|
||||
/// @arg pw[0] = constant coefficient of background
|
||||
/// @arg pw[1] = linear coefficient of background
|
||||
/// @arg pw[2] = amplitude of peak 1
|
||||
/// @arg pw[3] = amplitude of peak 2
|
||||
/// @arg pw[4] = amplitude of peak 3, relative to peak 1
|
||||
/// @arg pw[5] = amplitude of peak 4, relative to peak 2
|
||||
/// @arg pw[6] = position of peak 1
|
||||
/// @arg pw[7] = splitting (distance between peaks 1 and 3)
|
||||
/// @arg pw[8] = shift (distance between peaks 1 and 2)
|
||||
/// @arg pw[9] = width of peaks 1 and 3
|
||||
/// @arg pw[10] = width of peaks 2 and 4
|
||||
///
|
||||
/// @param yw y (dependent) values.
|
||||
///
|
||||
/// @param xw x (independent) independent values.
|
||||
///
|
||||
threadsafe function DblDoubletGaussLinBG_AO(pw, yw, xw) : FitFunc
|
||||
wave pw
|
||||
wave yw
|
||||
wave xw
|
||||
|
||||
yw = pw[0] + xw[p] * pw[1]
|
||||
// peak 1
|
||||
yw += pw[2] * exp( -( (xw[p] - pw[6]) / pw[9] )^2 )
|
||||
// peak 2
|
||||
yw += pw[3] * exp( -( (xw[p] - pw[6] - pw[8]) / pw[10] )^2 )
|
||||
// peak 3
|
||||
yw += pw[2] * pw[4] * exp( -( (xw[p] - pw[6] - pw[7]) / pw[9] )^2 )
|
||||
// peak 4
|
||||
yw += pw[3] * pw[5] * exp( -( (xw[p] - pw[6] - pw[7] - pw[8]) / pw[10] )^2 )
|
||||
end
|
||||
|
||||
//------------------------------------------------------------------------------
|
||||
// Voigt shapes
|
||||
//------------------------------------------------------------------------------
|
||||
@ -141,7 +187,7 @@ end
|
||||
/// @arg w[5 + (i-1) * 4] = shape of peak i
|
||||
/// @param x independent variable
|
||||
///
|
||||
function MultiVoigtLinBG(w,x) : FitFunc
|
||||
threadsafe function MultiVoigtLinBG(w,x) : FitFunc
|
||||
wave w
|
||||
variable x
|
||||
|
||||
@ -156,6 +202,39 @@ function MultiVoigtLinBG(w,x) : FitFunc
|
||||
return v
|
||||
end
|
||||
|
||||
/// multiple voigt peaks on a linear background fit function.
|
||||
///
|
||||
///
|
||||
/// this is the all-at-once version of @ref MultiVoigtLinBG.
|
||||
/// it runs slightly faster compared to the point-by-point function.
|
||||
///
|
||||
/// @param pw shape parameters.
|
||||
/// the length of the wave defines the number of peaks.
|
||||
/// @arg pw[0] = constant coefficient of background
|
||||
/// @arg pw[1] = linear coefficient of background
|
||||
/// @arg pw[2 + (i-1) * 4] = amplitude of peak i
|
||||
/// @arg pw[3 + (i-1) * 4] = position of peak i
|
||||
/// @arg pw[4 + (i-1) * 4] = width of peak i
|
||||
/// @arg pw[5 + (i-1) * 4] = shape of peak i
|
||||
///
|
||||
/// @param yw y (dependent) values.
|
||||
///
|
||||
/// @param xw x (independent) independent values.
|
||||
///
|
||||
threadsafe function MultiVoigtLinBG_AO(pw, yw, xw) : FitFunc
|
||||
wave pw
|
||||
wave yw
|
||||
wave xw
|
||||
|
||||
variable np = numpnts(pw)
|
||||
variable ip
|
||||
|
||||
yw = pw[0] + xw[p] * pw[1]
|
||||
for (ip = 2; ip < np; ip += 4)
|
||||
yw += pw[ip] * VoigtFunc((xw[p] - pw[ip+1]) / pw[ip+2], pw[ip+3])
|
||||
endfor
|
||||
end
|
||||
|
||||
|
||||
//------------------------------------------------------------------------------
|
||||
// Doniach-Sunjic shapes
|
||||
@ -198,7 +277,7 @@ end
|
||||
/// @arg w[5 + (i-1) * 4] = singularity index (0...1) of peak i
|
||||
/// @param x independent variable
|
||||
///
|
||||
function MultiDoniachSunjicLinBG(w,x) : FitFunc
|
||||
threadsafe function MultiDoniachSunjicLinBG(w,x) : FitFunc
|
||||
wave w
|
||||
variable x
|
||||
|
||||
|
||||
@ -1,3 +1,4 @@
|
||||
#pragma TextEncoding = "UTF-8"
|
||||
#pragma rtGlobals=3 // Use modern global access method and strict wave access.
|
||||
#pragma IgorVersion = 6.1
|
||||
#pragma ModuleName = PearlGuiTools
|
||||
|
||||
@ -1,3 +1,4 @@
|
||||
#pragma TextEncoding = "UTF-8"
|
||||
#pragma rtGlobals=3
|
||||
#pragma version = 1.00
|
||||
#pragma IgorVersion = 6.36
|
||||
|
||||
@ -1,3 +1,4 @@
|
||||
#pragma TextEncoding = "UTF-8"
|
||||
#pragma rtGlobals=1 // Use modern global access method.
|
||||
#pragma ModuleName = PearlMenu
|
||||
#pragma version = 1.02
|
||||
|
||||
@ -1,3 +1,4 @@
|
||||
#pragma TextEncoding = "UTF-8"
|
||||
#pragma rtGlobals=3 // Use modern global access method and strict wave access.
|
||||
#pragma IgorVersion = 6.2
|
||||
#pragma ModuleName = PearlPmscoImport
|
||||
@ -174,6 +175,137 @@ static function /s save_scan_helper(destname, value, template, destdfr, wavename
|
||||
return wavenames
|
||||
end
|
||||
|
||||
/// load a PMSCO scan file into the current data folder.
|
||||
///
|
||||
/// the function loads all columns from the file.
|
||||
/// the waves are named with two-letter names according to the file extension.
|
||||
/// existing waves are overwritten.
|
||||
///
|
||||
/// the file extension must be `etpais` or a subset of it, e.g., `etpi`.
|
||||
/// the wave names will be `en` (energy), `th` (theta), `ph` (phi), `al` (alpha),
|
||||
/// `in` (intensity) or `mo` (modulation), and `si` (sigma).
|
||||
///
|
||||
/// @param pathname name of igor symbolic path to destination folder.
|
||||
/// prompt user if empty.
|
||||
///
|
||||
/// @param filename requested file name.
|
||||
/// prompt user if empty.
|
||||
/// the extension must be a string of characters indicating the data of each column.
|
||||
/// it must be "etpais" or any substring of it, and the columns must be ordered accordingly.
|
||||
/// if the name contains `.modf`, the intensity wave is named as `mo` rather than `in`.
|
||||
/// this behaviour can be overridden by the `is_modulation` flag.
|
||||
///
|
||||
/// @param is_modulation select whether the intensity column is named `mo` rather than `in`.
|
||||
/// @arg 0 (default) decide based on existens of `.modf` in the file name.
|
||||
/// @arg > 0 use `mo` regardless of file name.
|
||||
/// @arg < 0 use `in` regardless of file name.
|
||||
///
|
||||
/// @param quiet (optional)
|
||||
/// @arg 0 (default) print the file name and wave names to the history.
|
||||
/// @arg 1 do not print messages to the history.
|
||||
///
|
||||
function /s load_pmsco_scan(pathname, filename, [is_modulation, quiet])
|
||||
string pathname // name of a symbolic path
|
||||
string filename
|
||||
variable is_modulation
|
||||
variable quiet
|
||||
|
||||
if (ParamIsDefault(quiet))
|
||||
quiet = 0
|
||||
endif
|
||||
|
||||
loadwave /p=$pathname /a /g /o /q filename
|
||||
|
||||
if (ParamIsDefault(is_modulation))
|
||||
is_modulation = StringMatch(s_filename, "*.modf.*")
|
||||
else
|
||||
is_modulation = is_modulation > 0
|
||||
endif
|
||||
|
||||
string fileext
|
||||
string waves = ""
|
||||
if (v_flag > 0)
|
||||
fileext = StringFromList(ItemsInList(s_filename, ".") - 1, s_filename, ".")
|
||||
variable nw = ItemsInList(s_wavenames)
|
||||
variable iw
|
||||
string sw1, sw2
|
||||
for (iw = 0; iw < nw; iw += 1)
|
||||
sw1 = StringFromlist(iw, s_wavenames)
|
||||
strswitch(fileext[iw])
|
||||
case "e":
|
||||
sw2 = "en"
|
||||
break
|
||||
case "t":
|
||||
sw2 = "th"
|
||||
break
|
||||
case "p":
|
||||
sw2 = "ph"
|
||||
break
|
||||
case "a":
|
||||
sw2 = "al"
|
||||
break
|
||||
case "i":
|
||||
if (is_modulation)
|
||||
sw2 = "mo"
|
||||
else
|
||||
sw2 = "in"
|
||||
endif
|
||||
break
|
||||
case "s":
|
||||
sw2 = "si"
|
||||
break
|
||||
endswitch
|
||||
duplicate /o $sw1, $sw2
|
||||
killwaves /z $sw1
|
||||
waves = AddListItem(sw2, waves, ",", inf)
|
||||
endfor
|
||||
|
||||
// Sort {en,th,ph, al} en,th,ph,al,int,sig
|
||||
|
||||
if (!quiet)
|
||||
print "load_pmsco_scan ", s_filename, ": ", waves
|
||||
endif
|
||||
|
||||
return s_filename
|
||||
else
|
||||
return ""
|
||||
endif
|
||||
end
|
||||
|
||||
/// load a PMSCO result file into the current data folder.
|
||||
///
|
||||
/// result files have the extension dat or tasks.dat.
|
||||
/// this will overwrite existing waves.
|
||||
/// the function loads all columns.
|
||||
///
|
||||
/// @param pathname name of a symbolic path
|
||||
/// @param filename file name
|
||||
/// @param quiet (optional) @arg 0 (default) print the file name and wave names to the history.
|
||||
/// @arg 1 do not print messages to the history.
|
||||
///
|
||||
function /s load_pmsco_result(pathname, filename, [quiet])
|
||||
string pathname // name of a symbolic path
|
||||
string filename
|
||||
variable quiet
|
||||
|
||||
if (ParamIsDefault(quiet))
|
||||
quiet = 0
|
||||
endif
|
||||
|
||||
if (quiet)
|
||||
loadwave /p=$pathname /a /w /g /o /q filename
|
||||
else
|
||||
loadwave /p=$pathname /a /w /g /o filename
|
||||
endif
|
||||
|
||||
if (v_flag > 0)
|
||||
return s_filename
|
||||
else
|
||||
return ""
|
||||
endif
|
||||
end
|
||||
|
||||
|
||||
/// load an xyz cluster file
|
||||
///
|
||||
/// load an xyz cluster file into the current data folder
|
||||
|
||||
@ -1,3 +1,4 @@
|
||||
#pragma TextEncoding = "UTF-8"
|
||||
#pragma rtGlobals=3
|
||||
#pragma version = 1.1
|
||||
#pragma IgorVersion = 6.1
|
||||
|
||||
@ -1,12 +1,14 @@
|
||||
#pragma TextEncoding = "UTF-8"
|
||||
#pragma rtGlobals=3 // Use modern global access method and strict wave access.
|
||||
#pragma IgorVersion = 6.36
|
||||
#pragma ModuleName = PearlPShellImport
|
||||
#pragma version = 1.11
|
||||
#include <HDF5 Browser>
|
||||
#include "pearl-compat"
|
||||
#include "pearl-gui-tools"
|
||||
#include "pearl-area-import"
|
||||
|
||||
// copyright (c) 2013-18 Paul Scherrer Institut
|
||||
// copyright (c) 2013-21 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.
|
||||
@ -50,7 +52,7 @@
|
||||
///
|
||||
/// @author matthias muntwiler, matthias.muntwiler@psi.ch
|
||||
///
|
||||
/// @copyright 2013-18 Paul Scherrer Institut @n
|
||||
/// @copyright 2013-21 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
|
||||
@ -75,7 +77,7 @@ strconstant kScanDimLabel = "scan"
|
||||
strconstant kDataDimLabel = "data"
|
||||
|
||||
/// List of preferred datasets to load for preview
|
||||
strconstant kPreviewDatasets = "ScientaImage;ScientaSpectrum;ImageAngleDistribution;ImageEnergyDistribution;Counts;SampleCurrent;"
|
||||
strconstant kPreviewDatasets = "ImageEnergyDistribution;ScientaSpectrum;ScientaImage;Counts;SampleCurrent;"
|
||||
|
||||
/// List of datasets that must be loaded to determine the axis scaling of a Scienta image
|
||||
strconstant kScientaScalingDatasets = "LensMode;ScientaChannelBegin;ScientaChannelEnd;ScientaSliceBegin;ScientaSliceEnd;"
|
||||
@ -336,6 +338,81 @@ function /s psh5_load_preview(APathName, AFileName, [load_data, load_attr, pref_
|
||||
return dataname
|
||||
end
|
||||
|
||||
/// load organizational metadata from the general group.
|
||||
///
|
||||
/// the general group contains the following datasets:
|
||||
/// authors, pgroup, proposal, proposer, sample.
|
||||
///
|
||||
/// data is loaded into the current data folder.
|
||||
/// all items are loaded into strings, authors is a comma-separated list.
|
||||
/// missing items default to empty strings.
|
||||
///
|
||||
/// @param APathName igor symbolic path name. can be empty if the path is specified in FileName or a dialog box should be displayed
|
||||
///
|
||||
/// @param AFileName if empty a dialog box shows up
|
||||
///
|
||||
/// @return semicolon-separated list of the objects.
|
||||
///
|
||||
function /s psh5_load_general_group(APathName, AFileName)
|
||||
string APathName
|
||||
string AFileName
|
||||
|
||||
variable fileID
|
||||
|
||||
HDF5OpenFile /P=$APathName /R /Z fileID as AFileName
|
||||
if (v_flag == 0)
|
||||
string obj_names = "authors;pgroup;proposal;proposer;sample;"
|
||||
variable nn = ItemsInList(obj_names, ";")
|
||||
variable ii
|
||||
string name
|
||||
|
||||
for (ii = 0; ii < nn; ii += 1)
|
||||
name = StringFromList(ii, obj_names, ";")
|
||||
psh_load_general_string(fileID, name)
|
||||
endfor
|
||||
|
||||
return obj_names
|
||||
else
|
||||
return ""
|
||||
endif
|
||||
end
|
||||
|
||||
/// load a string from the general group.
|
||||
///
|
||||
/// the general group contains the following datasets:
|
||||
/// authors, pgroup, proposal, proposer, sample.
|
||||
///
|
||||
/// data is loaded into a global string in the current data folder.
|
||||
/// arrays with multiple items are loaded into a comma-separated list.
|
||||
/// a missing item defaults to the empty string.
|
||||
///
|
||||
/// @param fileID ID of open HDF5 file from psh5_open_file().
|
||||
///
|
||||
/// @return comma-separated list of values.
|
||||
///
|
||||
function /s psh_load_general_string(fileID, name)
|
||||
variable fileID
|
||||
string name
|
||||
|
||||
string path = "/general/" + name
|
||||
HDF5LoadData /O /Q /Z /N=wt_load_general /TYPE=1 fileID, path
|
||||
string values = ""
|
||||
if (!v_flag)
|
||||
wave /t wt_load_general
|
||||
variable nn = numpnts(wt_load_general)
|
||||
variable ii
|
||||
for (ii = 0; ii < nn; ii += 1)
|
||||
values = AddListItem(wt_load_general[ii], values, ",", inf)
|
||||
endfor
|
||||
killwaves /z wt_load_general
|
||||
if (strlen(values) >= 1)
|
||||
values = values[0,strlen(values)-2]
|
||||
endif
|
||||
endif
|
||||
string /g $name = values
|
||||
return values
|
||||
end
|
||||
|
||||
/// load all data of a selected scan from a PShell data file.
|
||||
///
|
||||
/// data is loaded into the current data folder.
|
||||
@ -1667,13 +1744,13 @@ function ps_detect_scale(ax, lo, hi, un)
|
||||
case "Angular45":
|
||||
lo[%$kAngleDimLabel] = -45/2
|
||||
hi[%$kAngleDimLabel] = +45/2
|
||||
un[%$kAngleDimLabel] = "°"
|
||||
un[%$kAngleDimLabel] = "°"
|
||||
ax[%$kAngleDimLabel] = "angle"
|
||||
break
|
||||
case "Angular60":
|
||||
lo[%$kAngleDimLabel] = -60/2
|
||||
hi[%$kAngleDimLabel] = +60/2
|
||||
un[%$kAngleDimLabel] = "°"
|
||||
un[%$kAngleDimLabel] = "°"
|
||||
ax[%$kAngleDimLabel] = "angle"
|
||||
break
|
||||
case "Transmission":
|
||||
@ -1719,12 +1796,12 @@ function ps_detect_scale(ax, lo, hi, un)
|
||||
un[%$kScanDimLabel] = "mm"
|
||||
break
|
||||
case "ExitSlit":
|
||||
un[%$kScanDimLabel] = "µm"
|
||||
un[%$kScanDimLabel] = "µm"
|
||||
break
|
||||
case "ManipulatorTheta":
|
||||
case "ManipulatorTilt":
|
||||
case "ManipulatorPhi":
|
||||
un[%$kScanDimLabel] = "°"
|
||||
un[%$kScanDimLabel] = "°"
|
||||
break
|
||||
case "FocusXRot":
|
||||
case "FocusYRot":
|
||||
@ -1890,6 +1967,11 @@ end
|
||||
///
|
||||
/// @param reduction_param parameter string for the reduction function.
|
||||
///
|
||||
/// @param dataset name of dataset to load, optionally including group path relative to scan (scan 1).
|
||||
/// by default, the function looks for a ScientaImage dataset.
|
||||
/// in a multi-region scan, this will be region 1.
|
||||
/// to select region 2, e.g., use `dataset="region2/ScientaImage"`.
|
||||
///
|
||||
/// @param progress progress window.
|
||||
/// @arg 1 (default) show progress window
|
||||
/// @arg 0 do not show progress window
|
||||
@ -1908,12 +1990,13 @@ end
|
||||
///
|
||||
/// @return global string s_scanpaths in new data folder contains a list of scan groups inside the file.
|
||||
///
|
||||
function /s psh5_load_reduced(ANickName, APathName, AFileName, reduction_func, reduction_param, [progress, nthreads])
|
||||
function /s psh5_load_reduced(ANickName, APathName, AFileName, reduction_func, reduction_param, [dataset, progress, nthreads])
|
||||
string ANickName
|
||||
string APathName
|
||||
string AFileName
|
||||
funcref adh5_default_reduction reduction_func
|
||||
string reduction_param
|
||||
string dataset
|
||||
variable progress
|
||||
variable nthreads
|
||||
|
||||
@ -1972,7 +2055,9 @@ function /s psh5_load_reduced(ANickName, APathName, AFileName, reduction_func, r
|
||||
|
||||
setdatafolder dataDF
|
||||
string datasets = psh5_list_scan_datasets(fileID, scanpath, include_regions=1)
|
||||
string dataset = select_dataset(datasets, "ScientaImage")
|
||||
if (ParamIsDefault(dataset))
|
||||
dataset = select_dataset(datasets, "ScientaImage")
|
||||
endif
|
||||
wavenames = psh5_load_dataset_reduced(fileID, scanpath, dataset, reduction_func, reduction_param, progress=progress, nthreads=nthreads)
|
||||
|
||||
psh5_close_file(fileID)
|
||||
@ -2503,3 +2588,48 @@ static function /s wave2list(w, format, sep)
|
||||
|
||||
return list
|
||||
end
|
||||
|
||||
/// kill any waves matching a pattern in the experiment
|
||||
///
|
||||
/// this may be used to kill big waves of original data before saving
|
||||
///
|
||||
function /s kill_matching_waves(dfr, pattern, recurse, [killed])
|
||||
DFREF dfr
|
||||
string pattern
|
||||
variable recurse
|
||||
string killed
|
||||
|
||||
if (ParamIsDefault(killed))
|
||||
killed = ""
|
||||
endif
|
||||
|
||||
string s
|
||||
string r
|
||||
variable index = 0
|
||||
do
|
||||
Wave/Z w = WaveRefIndexedDFR(dfr, index)
|
||||
if (!WaveExists(w))
|
||||
break
|
||||
endif
|
||||
|
||||
s = NameOfWave(w)
|
||||
if (stringmatch(s, pattern))
|
||||
killwaves /z w
|
||||
killed = AddListItem(s, killed, ";", Inf)
|
||||
endif
|
||||
|
||||
index += 1
|
||||
while(1)
|
||||
|
||||
if (recurse)
|
||||
Variable numChildDataFolders = CountObjectsDFR(dfr, 4)
|
||||
Variable i
|
||||
for(i=0; i<numChildDataFolders; i+=1)
|
||||
String childDFName = GetIndexedObjNameDFR(dfr, 4, i)
|
||||
DFREF childDFR = dfr:$childDFName
|
||||
killed = kill_matching_waves(childDFR, pattern, 1, killed=killed)
|
||||
endfor
|
||||
endif
|
||||
|
||||
return killed
|
||||
End
|
||||
|
||||
@ -1,6 +1,7 @@
|
||||
#pragma TextEncoding = "UTF-8"
|
||||
#pragma rtGlobals=3 // Use modern global access method and strict wave access.
|
||||
#pragma IgorVersion = 6.35
|
||||
#pragma ModuleName = PearlScientaCountrate
|
||||
#pragma ModuleName = PearlScientaLive
|
||||
#include "pearl-area-display"
|
||||
|
||||
// Copyright (c) 2019 Paul Scherrer Institut
|
||||
@ -11,10 +12,13 @@
|
||||
// http://www.apache.org/licenses/LICENSE-2.0
|
||||
|
||||
/// @file
|
||||
/// @brief count rate functions for Scienta detector images.
|
||||
/// @brief utility functions for operating the Scienta analyser.
|
||||
/// @ingroup ArpesPackage
|
||||
///
|
||||
/// this procedure contains functions for working with true count rates.
|
||||
/// this procedure contains various utility functions for working with the Scienta analyser, e.g.
|
||||
///
|
||||
/// - statistical analysis of true count rates
|
||||
/// - estimate energy and angle resolution
|
||||
///
|
||||
/// @author matthias muntwiler, matthias.muntwiler@psi.ch
|
||||
///
|
||||
@ -24,10 +28,10 @@
|
||||
/// You may obtain a copy of the License at
|
||||
/// http://www.apache.org/licenses/LICENSE-2.0
|
||||
|
||||
/// @namespace PearlScientaCountrate
|
||||
/// @brief count rate functions for Scienta detector images.
|
||||
/// @namespace PearlScientaLive
|
||||
/// @brief utility functions for operating the Scienta analyser.
|
||||
///
|
||||
/// PearlScientaCountrate is declared in @ref pearl-scienta-countrate.ipf.
|
||||
/// PearlScientaLive is declared in @ref pearl-scienta-live.ipf.
|
||||
|
||||
/// open live display of most recent scienta measurement
|
||||
///
|
||||
@ -211,3 +215,25 @@ function check_exposure_opt(image, outmask, dwelltime, [calc_df])
|
||||
|
||||
SetDataFolder save_df
|
||||
end
|
||||
|
||||
/// calculate the energy resolution of the analyser
|
||||
///
|
||||
/// @param epass pass energy in eV
|
||||
/// @param slit analyser entrance slit in mm
|
||||
///
|
||||
/// @return energy resolution (FWHM)
|
||||
function analyser_energy_resolution(epass, slit)
|
||||
variable epass
|
||||
variable slit
|
||||
|
||||
variable respow
|
||||
if (epass < 4)
|
||||
respow = 1110
|
||||
elseif (epass < 8)
|
||||
respow = 1400
|
||||
else
|
||||
respow = 1750
|
||||
endif
|
||||
|
||||
return epass * max(0.2, slit) / 0.2 / respow
|
||||
end
|
||||
@ -1,7 +1,9 @@
|
||||
#pragma TextEncoding = "UTF-8"
|
||||
#pragma rtGlobals=3 // Use modern global access method and strict wave access.
|
||||
#pragma IgorVersion = 6.1
|
||||
#pragma ModuleName = PearlScientaPreprocess
|
||||
#include "pearl-fitfuncs"
|
||||
#include "pearl-area-import"
|
||||
|
||||
// Copyright (c) 2013-18 Paul Scherrer Institut
|
||||
//
|
||||
@ -804,6 +806,7 @@ threadsafe function /wave gauss4_reduction(source, param)
|
||||
p1 -= ceil((ybox - 1) / 2)
|
||||
endif
|
||||
variable V_FitNumIters
|
||||
variable V_FitError
|
||||
|
||||
for (pp = p0; pp <= p1; pp += 1)
|
||||
// box average
|
||||
@ -820,10 +823,11 @@ threadsafe function /wave gauss4_reduction(source, param)
|
||||
wmax = wavemax(xprof)
|
||||
w_coef[0] = wmin
|
||||
w_coef[1] = 0
|
||||
|
||||
for (ipk=0; ipk < npeaks; ipk += 1)
|
||||
w_coef[2 + ipk*3] = wmax - wmin
|
||||
endfor
|
||||
|
||||
V_FitError = 0
|
||||
FuncFit /H=hold /Q /NTHR=1 /N /W=2 MultiGaussLinBG_AO w_coef xprof[pl,ph] /C={cmat, cvec} /I=1 /W=xprof_sig[pl,ph]
|
||||
wave w_sigma
|
||||
|
||||
@ -948,6 +952,237 @@ function /s find_gauss4_reduction_params(spectrum, peakpos)
|
||||
return param
|
||||
end
|
||||
|
||||
/// fit horizontal cuts of an image with up to four voigtian peaks on a linear background
|
||||
///
|
||||
/// the function fits each horizontal profile (EDC) with four voigtian peaks on a linear background.
|
||||
/// the position, width and shape of the peaks is kept fixed according to input parameters.
|
||||
/// the peak amplitude is constrained to positive value.
|
||||
///
|
||||
/// the width and shape parameters are defined as in Igor's VoigtFunc:
|
||||
/// width is the width of the gaussian component,
|
||||
/// shape * width is the width of the lorentzian component.
|
||||
///
|
||||
/// @param source source wave.
|
||||
/// two-dimensional distribution of counts.
|
||||
/// for correct weighting and error estimation it is important
|
||||
/// that the source wave contains actual counts (Poisson statistics).
|
||||
///
|
||||
/// @param param (in, out) semicolon-separated key=value list of processing parameters.
|
||||
/// this is a pass-by-reference argument.
|
||||
/// the following parameters are required.
|
||||
/// position, width and limit parameters are on the x (energy) scale.
|
||||
/// @arg rngl low limit of fit interval
|
||||
/// @arg rngh high limit of fit interval
|
||||
/// @arg pos1 position of peak 1
|
||||
/// @arg wid1 width of peak 1
|
||||
/// @arg shp1 shape of peak 1
|
||||
/// @arg pos2 position of peak 2
|
||||
/// @arg wid2 width of peak 2
|
||||
/// @arg shp2 shape of peak 2
|
||||
/// @arg pos3 position of peak 3
|
||||
/// @arg wid3 width of peak 3
|
||||
/// @arg shp3 shape of peak 3
|
||||
/// @arg pos4 position of peak 4
|
||||
/// @arg wid4 width of peak 4
|
||||
/// @arg shp4 shape of peak 4
|
||||
/// @arg npeaks number of peaks to fit: 1...4
|
||||
/// the others are held at amplitude 0.
|
||||
///
|
||||
/// @return free wave containing references of the result waves.
|
||||
/// the number of waves is two times the number of peaks that are fit.
|
||||
/// the first npeaks waves contain the peak amplitudes,
|
||||
/// the second npeaks waves the corresponding error estimates.
|
||||
///
|
||||
threadsafe function /wave voigt4_reduction(source, param)
|
||||
wave source
|
||||
string ¶m
|
||||
|
||||
dfref orig_dfr = GetDataFolderDFR()
|
||||
|
||||
variable nx = dimsize(source, 0)
|
||||
variable ny = dimsize(source, 1)
|
||||
|
||||
// read parameters
|
||||
variable rngl = NumberByKey("rngl", param, "=", ";")
|
||||
variable rngh = NumberByKey("rngh", param, "=", ";")
|
||||
variable pos1 = NumberByKey("pos1", param, "=", ";")
|
||||
variable wid1 = NumberByKey("wid1", param, "=", ";")
|
||||
variable shp1 = NumberByKey("shp1", param, "=", ";")
|
||||
variable pos2 = NumberByKey("pos2", param, "=", ";")
|
||||
variable wid2 = NumberByKey("wid2", param, "=", ";")
|
||||
variable shp2 = NumberByKey("shp2", param, "=", ";")
|
||||
variable pos3 = NumberByKey("pos3", param, "=", ";")
|
||||
variable wid3 = NumberByKey("wid3", param, "=", ";")
|
||||
variable shp3 = NumberByKey("shp3", param, "=", ";")
|
||||
variable pos4 = NumberByKey("pos4", param, "=", ";")
|
||||
variable wid4 = NumberByKey("wid4", param, "=", ";")
|
||||
variable shp4 = NumberByKey("shp4", param, "=", ";")
|
||||
variable npeaks = NumberByKey("npeaks", param, "=", ";")
|
||||
|
||||
// prepare curve fit
|
||||
variable ipk
|
||||
make /free xprof
|
||||
adh5_setup_profile(source, xprof, 0)
|
||||
duplicate /free xprof, xprof_sig
|
||||
variable pl = max(x2pnt(xprof, rngl), 0)
|
||||
variable ph = min(x2pnt(xprof, rngh), numpnts(xprof) - 1)
|
||||
|
||||
make /free /n=(npeaks) peak_coef
|
||||
variable coef_per_peak = 4
|
||||
peak_coef = p * coef_per_peak + 2
|
||||
variable n_coef = npeaks * coef_per_peak + 2
|
||||
make /free /d /n=18 w_coef, W_sigma
|
||||
w_coef[0] = {0, 0, 1, pos1, wid1, shp1, 1, pos2, wid2, shp2, 1, pos3, wid3, shp3, 1, pos4, wid4, shp4}
|
||||
redimension /n=(n_coef) w_coef, w_sigma
|
||||
|
||||
// text constraints cannot be used in threadsafe functions.
|
||||
// the following matrix-vector formulation enforces all peak amplitudes to be positive.
|
||||
make /free /n=(npeaks, numpnts(w_coef)) cmat
|
||||
make /free /n=(npeaks) cvec
|
||||
cmat = 0
|
||||
cvec = 0
|
||||
|
||||
string hold = "00"
|
||||
for (ipk=0; ipk < npeaks; ipk += 1)
|
||||
hold += "0111"
|
||||
cmat[ipk][2 + ipk * coef_per_peak] = -1
|
||||
endfor
|
||||
|
||||
// prepare output
|
||||
make /free /n=(npeaks * 2) /wave result_waves
|
||||
string s_note
|
||||
for (ipk = 0; ipk < npeaks; ipk += 1)
|
||||
make /free /n=0 pk_int
|
||||
adh5_setup_profile(source, pk_int, 1)
|
||||
pk_int = nan
|
||||
sprintf s_note, "AxisLabelD=peak %u integral", ipk+1
|
||||
Note pk_int, s_note
|
||||
sprintf s_note, "KineticEnergy=%.3f", w_coef[3 + ipk * coef_per_peak]
|
||||
Note pk_int, s_note
|
||||
result_waves[ipk] = pk_int
|
||||
|
||||
make /free /n=0 pk_sig
|
||||
adh5_setup_profile(source, pk_sig, 1)
|
||||
pk_sig = nan
|
||||
sprintf s_note, "AxisLabelD=peak %u sigma", ipk+1
|
||||
Note pk_sig, s_note
|
||||
sprintf s_note, "KineticEnergy=%.3f", w_coef[3 + ipk * coef_per_peak]
|
||||
Note pk_sig, s_note
|
||||
result_waves[ipk + npeaks] = pk_sig
|
||||
|
||||
waveclear pk_int, pk_sig
|
||||
endfor
|
||||
|
||||
// loop over angle scale
|
||||
variable p0 = 0
|
||||
variable p1 = dimsize(source, 1) - 1
|
||||
variable pp
|
||||
variable wmin
|
||||
variable wmax
|
||||
variable V_FitNumIters
|
||||
variable V_FitError
|
||||
|
||||
for (pp = p0; pp <= p1; pp += 1)
|
||||
xprof = source[p][pp]
|
||||
xprof_sig = max(sqrt(xprof), 1)
|
||||
|
||||
// generate guess
|
||||
wmin = wavemin(xprof)
|
||||
wmax = wavemax(xprof)
|
||||
w_coef[0] = wmin
|
||||
w_coef[1] = 0
|
||||
|
||||
for (ipk=0; ipk < npeaks; ipk += 1)
|
||||
w_coef[2 + ipk * coef_per_peak] = wmax - wmin
|
||||
endfor
|
||||
|
||||
V_FitError = 0
|
||||
FuncFit /H=hold /Q /N /W=2 MultiVoigtLinBG_AO w_coef xprof[pl,ph] /C={cmat, cvec} /I=1 /W=xprof_sig[pl,ph]
|
||||
wave w_sigma
|
||||
|
||||
// retrieve results, leave them at nan if the fit did not converge
|
||||
if (V_FitNumIters < 40)
|
||||
for (ipk = 0; ipk < npeaks; ipk += 1)
|
||||
wave val = result_waves[ipk]
|
||||
wave sig = result_waves[ipk + npeaks]
|
||||
val[pp] = max(w_coef[peak_coef[ipk]], 0)
|
||||
sig[pp] = max(w_sigma[peak_coef[ipk]], 0)
|
||||
endfor
|
||||
endif
|
||||
endfor
|
||||
|
||||
SetDataFolder orig_dfr
|
||||
return result_waves
|
||||
end
|
||||
|
||||
|
||||
/// prompt for the voigt4_reduction parameters
|
||||
///
|
||||
///
|
||||
function prompt_voigt4_reduction(param)
|
||||
string ¶m
|
||||
|
||||
variable rngl = NumberByKey("rngl", param, "=", ";")
|
||||
variable rngh = NumberByKey("rngh", param, "=", ";")
|
||||
variable pos1 = NumberByKey("pos1", param, "=", ";")
|
||||
variable wid1 = NumberByKey("wid1", param, "=", ";")
|
||||
variable shp1 = NumberByKey("shp1", param, "=", ";")
|
||||
variable pos2 = NumberByKey("pos2", param, "=", ";")
|
||||
variable wid2 = NumberByKey("wid2", param, "=", ";")
|
||||
variable shp2 = NumberByKey("shp2", param, "=", ";")
|
||||
variable pos3 = NumberByKey("pos3", param, "=", ";")
|
||||
variable wid3 = NumberByKey("wid3", param, "=", ";")
|
||||
variable shp3 = NumberByKey("shp3", param, "=", ";")
|
||||
variable pos4 = NumberByKey("pos4", param, "=", ";")
|
||||
variable wid4 = NumberByKey("wid4", param, "=", ";")
|
||||
variable shp4 = NumberByKey("shp4", param, "=", ";")
|
||||
variable npeaks = NumberByKey("npeaks", param, "=", ";")
|
||||
variable dummy = nan
|
||||
|
||||
prompt rngl, "range low"
|
||||
prompt rngh, "range high"
|
||||
prompt pos1, "position 1"
|
||||
prompt wid1, "width 1"
|
||||
prompt shp1, "shape 1"
|
||||
prompt pos2, "position 2"
|
||||
prompt wid2, "width 2"
|
||||
prompt shp2, "shape 2"
|
||||
prompt pos3, "position 3"
|
||||
prompt wid3, "width 3"
|
||||
prompt shp3, "shape 3"
|
||||
prompt pos4, "position 4"
|
||||
prompt wid4, "width 4"
|
||||
prompt shp4, "shape 4"
|
||||
prompt npeaks, "number of peaks"
|
||||
prompt dummy, "(not used)"
|
||||
|
||||
doprompt "voigt4_reduction reduction parameters (1/2)", rngl, rngh, npeaks, dummy, pos1, pos2, pos3, pos4
|
||||
if (v_flag == 0)
|
||||
param = ReplaceNumberByKey("rngl", param, rngl, "=", ";")
|
||||
param = ReplaceNumberByKey("rngh", param, rngh, "=", ";")
|
||||
param = ReplaceNumberByKey("npeaks", param, npeaks, "=", ";")
|
||||
param = ReplaceNumberByKey("pos1", param, pos1, "=", ";")
|
||||
param = ReplaceNumberByKey("pos2", param, pos2, "=", ";")
|
||||
param = ReplaceNumberByKey("pos3", param, pos3, "=", ";")
|
||||
param = ReplaceNumberByKey("pos4", param, pos4, "=", ";")
|
||||
|
||||
doprompt "voigt4_reduction reduction parameters (2/2)", wid1, shp1, wid2, shp2, wid3, shp3, wid4, shp4
|
||||
if (v_flag == 0)
|
||||
param = ReplaceNumberByKey("wid1", param, wid1, "=", ";")
|
||||
param = ReplaceNumberByKey("shp1", param, shp1, "=", ";")
|
||||
param = ReplaceNumberByKey("wid2", param, wid2, "=", ";")
|
||||
param = ReplaceNumberByKey("shp2", param, shp2, "=", ";")
|
||||
param = ReplaceNumberByKey("wid3", param, wid3, "=", ";")
|
||||
param = ReplaceNumberByKey("shp3", param, shp3, "=", ";")
|
||||
param = ReplaceNumberByKey("wid4", param, wid4, "=", ";")
|
||||
param = ReplaceNumberByKey("shp4", param, shp4, "=", ";")
|
||||
endif
|
||||
endif
|
||||
|
||||
return v_flag
|
||||
end
|
||||
|
||||
|
||||
/// apply the Shockley_anglefit function to a single image
|
||||
///
|
||||
/// useful for testing or manual processing
|
||||
|
||||
@ -1,3 +1,4 @@
|
||||
#pragma TextEncoding = "UTF-8"
|
||||
#pragma rtGlobals=3 // Use modern global access method and strict wave access.
|
||||
#pragma version = 1.00
|
||||
#pragma IgorVersion = 6.2
|
||||
|
||||
@ -1,9 +1,10 @@
|
||||
#pragma TextEncoding = "UTF-8"
|
||||
#pragma rtGlobals=3
|
||||
#pragma version = 2.1
|
||||
#pragma version = 2.2
|
||||
#pragma IgorVersion = 6.1
|
||||
#pragma ModuleName = PearlVectorOperations
|
||||
|
||||
// copyright (c) 2011-17 Paul Scherrer Institut
|
||||
// copyright (c) 2011-21 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.
|
||||
@ -21,7 +22,7 @@
|
||||
///
|
||||
/// @author matthias muntwiler, matthias.muntwiler@psi.ch
|
||||
///
|
||||
/// @copyright 2011-17 Paul Scherrer Institut @n
|
||||
/// @copyright 2011-21 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
|
||||
@ -176,16 +177,17 @@ function rotate_x_wave(inout, angle)
|
||||
wave inout
|
||||
variable angle
|
||||
|
||||
wave m_rotation_x = create_rotation_matrix_free()
|
||||
make /n=3/d/free w_temp_rotate_x
|
||||
variable ivec, nvec
|
||||
nvec = max(DimSize(inout, 1), 1)
|
||||
for (ivec = 0; ivec < nvec; ivec += 1)
|
||||
set_rotation_x(m_rotation_x, angle)
|
||||
w_temp_rotate_x = inout[p][ivec]
|
||||
matrixop /free w_temp_rotate_x_result = m_rotation_x x w_temp_rotate_x
|
||||
inout[0,2][ivec] = w_temp_rotate_x_result[p]
|
||||
wave m_rotation = create_rotation_matrix_free()
|
||||
set_rotation_x(m_rotation, angle)
|
||||
|
||||
duplicate /free inout, out
|
||||
out = 0
|
||||
variable j
|
||||
for (j = 0; j < 3; j += 1)
|
||||
out += m_rotation[p][j] * inout[j][q]
|
||||
endfor
|
||||
|
||||
inout = out
|
||||
end
|
||||
|
||||
/// rotates a wave of 3-vectors about the y axis
|
||||
@ -204,16 +206,17 @@ function rotate_y_wave(inout, angle)
|
||||
wave inout
|
||||
variable angle
|
||||
|
||||
wave m_rotation_y = create_rotation_matrix_free()
|
||||
make /n=3/d/free w_temp_rotate_y
|
||||
variable ivec, nvec
|
||||
nvec = max(DimSize(inout, 1), 1)
|
||||
for (ivec = 0; ivec < nvec; ivec += 1)
|
||||
set_rotation_y(m_rotation_y, angle)
|
||||
w_temp_rotate_y = inout[p][ivec]
|
||||
matrixop /free w_temp_rotate_y_result = m_rotation_y x w_temp_rotate_y
|
||||
inout[0,2][ivec] = w_temp_rotate_y_result[p]
|
||||
endfor
|
||||
wave m_rotation = create_rotation_matrix_free()
|
||||
set_rotation_y(m_rotation, angle)
|
||||
|
||||
duplicate /free inout, out
|
||||
out = 0
|
||||
variable j
|
||||
for (j = 0; j < 3; j += 1)
|
||||
out += m_rotation[p][j] * inout[j][q]
|
||||
endfor
|
||||
|
||||
inout = out
|
||||
end
|
||||
|
||||
/// rotates a wave of 3-vectors about the z axis
|
||||
@ -232,14 +235,15 @@ function rotate_z_wave(inout, angle)
|
||||
wave inout
|
||||
variable angle
|
||||
|
||||
wave m_rotation_z = create_rotation_matrix_free()
|
||||
make /n=3/d/free w_temp_rotate_z
|
||||
variable ivec, nvec
|
||||
nvec = max(DimSize(inout, 1), 1)
|
||||
for (ivec = 0; ivec < nvec; ivec += 1)
|
||||
set_rotation_z(m_rotation_z, angle)
|
||||
w_temp_rotate_z = inout[p][ivec]
|
||||
matrixop /free w_temp_rotate_z_result = m_rotation_z x w_temp_rotate_z
|
||||
inout[0,2][ivec] = w_temp_rotate_z_result[p]
|
||||
endfor
|
||||
wave m_rotation = create_rotation_matrix_free()
|
||||
set_rotation_z(m_rotation, angle)
|
||||
|
||||
duplicate /free inout, out
|
||||
out = 0
|
||||
variable j
|
||||
for (j = 0; j < 3; j += 1)
|
||||
out += m_rotation[p][j] * inout[j][q]
|
||||
endfor
|
||||
|
||||
inout = out
|
||||
end
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user