code changes for release 3.0.0: new PShell import
This commit is contained in:
@ -1,12 +1,15 @@
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#pragma TextEncoding = "Windows-1252"
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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 IgorVersion = 6.2
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#pragma IgorVersion = 6.36
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#pragma ModuleName = PearlAreaImport
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#pragma version = 1.13
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#if IgorVersion() < 9.00
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#include <HDF5 Browser>
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#endif
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#include "pearl-compat"
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#include "pearl-gui-tools"
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// copyright (c) 2013-20 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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@ -1195,6 +1198,7 @@ end
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/// a numeric index is appended to distinguish the results.
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/// the index starts at 1. existing waves are overwritten.
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///
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/// @return result code: 0 for success, < 0 for error
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///
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function adh5_reduce_brick(source, reduction_func, reduction_param, result_prefix, [progress, nthreads])
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wave source
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@ -1211,7 +1215,10 @@ function adh5_reduce_brick(source, reduction_func, reduction_param, result_prefi
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if (ParamIsDefault(nthreads))
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nthreads = -1
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endif
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dfref base_df = GetDataFolderDFR()
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variable result = 0
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string wavenames = ""
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// nx and nz are the image dimensions
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variable nx, ny, nz, nt
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@ -1219,10 +1226,9 @@ function adh5_reduce_brick(source, reduction_func, reduction_param, result_prefi
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ny = dimsize(source, 1)
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nz = dimsize(source, 2)
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// force 4th dimension to singleton (ad_extract_slab handles 3 dimensions only)
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nt = 0
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nt = 1
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variable nzt = max(nz, 1) * max(nt, 1)
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variable izt
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// set up multi threading
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if (nthreads < 0)
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@ -1239,133 +1245,159 @@ function adh5_reduce_brick(source, reduction_func, reduction_param, result_prefi
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endif
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if (progress)
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display_progress_panel("data reduction", "extracting data (step 1 of 2)...", nzt)
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display_progress_panel("Reduction", "Processing data...", nzt)
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endif
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variable iz, it
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variable n_sent = 0
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variable n_recvd = 0
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variable tmo = 0
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string dfname
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dfref dfr
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variable iw, nw
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string sw
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make /n=0 /free /wave result_waves
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iz = 0
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it = 0
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izt = 0
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for (iz = 0; iz < max(nz, 1); iz += 1)
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for (it = 0; it < max(nt, 1); it += 1)
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dfname = "processing_" + num2str(izt)
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newdatafolder /s $dfname
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ad_extract_slab(source, nan, nan, nan, nan, iz, iz, "image", pscale=1)
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wave image
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do
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// fill the processing queue up to a maximum number of folders
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if (n_sent < max(1, nthreads) * 10 + n_recvd)
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if (iz < nz)
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if (it < nt)
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// load a slab into a temporary folder
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dfname = "processing_" + num2str(n_sent)
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NewDataFolder /s $dfname
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ad_extract_slab(source, nan, nan, nan, nan, iz, iz, "image", pscale=1)
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wave image
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variable /g r_index = iz
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variable /g s_index = it
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string /g func_param = reduction_param
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// send to processing queue
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variable /g r_index = iz
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variable /g s_index = it
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string /g func_param = reduction_param
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if (nthreads > 0)
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WaveClear image
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ThreadGroupPutDF threadGroupID, :
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else
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processing_folders[izt] = GetDataFolderDFR()
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string param = reduction_param
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wave /wave reduced_waves = reduction_func(image, param)
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variable /g func_result = numpnts(reduced_waves)
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adh5_get_result_waves(reduced_waves, "redw_", 0)
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WaveClear image, reduced_waves
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setdatafolder ::
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endif
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izt += 1
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// progress window
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if (progress)
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if (update_progress_panel(izt))
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result = -4 // user abort
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break
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endif
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endif
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endfor
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endfor
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if (progress)
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update_progress_panel(0, message="processing data (step 2 of 2)...")
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endif
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dfref dfr
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for (izt = 0; (izt < nzt) && (result == 0); izt += 1)
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if (nthreads > 0)
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do
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dfr = ThreadGroupGetDFR(threadGroupID, 1000)
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if (DatafolderRefStatus(dfr) != 0)
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break
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endif
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if (progress)
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if (update_progress_panel(izt))
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result = -4 // user abort
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break
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if (nthreads > 0)
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// send to thread group
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WaveClear image
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ThreadGroupPutDF threadGroupID, :
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else
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// process immediately in single-thread mode
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processing_folders[n_sent] = GetDataFolderDFR()
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string param = func_param
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wave /wave reduced_waves = reduction_func(image, param)
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variable /g func_result = numpnts(reduced_waves)
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adh5_get_result_waves(reduced_waves, "redw_", 0)
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WaveClear image, reduced_waves
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setdatafolder ::
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endif
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endif
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while (1)
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else
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dfr = processing_folders[izt]
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if (progress)
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if (update_progress_panel(izt))
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result = -4 // user abort
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break
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iz += 1
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n_sent += 1
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tmo = 0
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else
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iz += 1
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it = 0
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endif
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endif
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else
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// throttle the loop if processing is slow
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tmo = min(100, tmo + 10)
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endif
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if (result != 0)
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break
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endif
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nvar rr = dfr:r_index
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nvar ss = dfr:s_index
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nvar func_result = dfr:func_result
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if (func_result < 1)
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result = -3 // dimension reduction error
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// receive a slab from the processing queue
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if (n_recvd < nzt)
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if (nthreads > 0)
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dfr = ThreadGroupGetDFR(threadGroupID, tmo)
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else
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dfr = processing_folders[n_recvd]
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processing_folders[n_recvd] = $""
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endif
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if (DatafolderRefStatus(dfr) != 0)
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// access results folder
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nvar rr = dfr:r_index
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nvar ss = dfr:s_index
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nvar func_result = dfr:func_result
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if (func_result < 1)
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print "error during data reduction."
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result = -3
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break
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endif
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// initialize result waves just once
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if (numpnts(result_waves) == 0)
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redimension /n=(func_result) result_waves
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for (iw = 0; iw < func_result; iw += 1)
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sw = "redw_" + num2str(iw)
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wave profile = dfr:$sw
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sw = "ReducedData" + num2str(iw+1)
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make /n=(dimsize(profile, 0), nz, nt) /d /o $sw
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wave data = $sw
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setdimlabel 0, -1, $getdimlabel(profile, 0, -1), data
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setscale /p x dimoffset(profile, 0), dimdelta(profile, 0), waveunits(profile, 0), data
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setscale /p y dimoffset(source, 2), dimdelta(source, 2), waveunits(source, 2), data
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setscale /p z dimoffset(source, 3), dimdelta(source, 3), waveunits(source, 3), data
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setscale d 0, 0, waveunits(profile, -1), data
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note data, note(profile)
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result_waves[iw] = data
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endfor
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endif
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// copy results
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for (iw = 0; iw < func_result; iw += 1)
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sw = "redw_" + num2str(iw)
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wave profile = dfr:$sw
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wave data = result_waves[iw]
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data[][rr][ss] = profile[p]
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endfor
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n_recvd += 1
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KillDataFolder /Z dfr
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endif
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else
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// processing complete
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break
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endif
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if (numpnts(result_waves) == 0)
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redimension /n=(func_result) result_waves
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for (iw = 0; iw < func_result; iw += 1)
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sw = "redw_" + num2str(iw)
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wave profile = dfr:$sw
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sw = result_prefix + num2str(iw+1)
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make /n=(dimsize(profile, 0), nz, nt) /d /o $sw
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wave data = $sw
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setdimlabel 0, -1, $getdimlabel(profile, 0, -1), data
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setscale /p x dimoffset(profile, 0), dimdelta(profile, 0), waveunits(profile, 0), data
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setscale /p y dimoffset(source, 2), dimdelta(source, 2), waveunits(source, 2), data
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setscale /p z dimoffset(source, 3), dimdelta(source, 3), waveunits(source, 3), data
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setscale d 0, 0, waveunits(profile, -1), data
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result_waves[iw] = data
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endfor
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// update progress window
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if (progress)
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if (update_progress_panel(n_recvd))
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print "user abort"
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result = -4
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break
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endif
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endif
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for (iw = 0; iw < func_result; iw += 1)
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sw = "redw_" + num2str(iw)
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wave profile = dfr:$sw
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wave data = result_waves[iw]
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data[][rr][ss] = profile[p]
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endfor
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endfor
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while ((n_recvd < nzt) && (result == 0))
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// clean up
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if (nthreads > 0)
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variable tstatus = ThreadGroupRelease(threadGroupID)
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if (tstatus == -2)
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result = -5 // thread did not terminate properly
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print "error: thread did not terminate properly."
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result = -5
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endif
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else
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for (izt = 0; izt < nzt; izt += 1)
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KillDataFolder /Z processing_folders[izt]
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endfor
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endif
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// finalize results
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nw = numpnts(result_waves)
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wavenames = ""
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for (iw = 0; iw < nw; iw += 1)
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wave /z data = result_waves[iw]
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if (WaveExists(data))
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if (nz == 1)
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redimension /n=(-1, 0, 0) data
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elseif (nt == 1)
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redimension /n=(-1, nz, 0) data
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endif
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wavenames += nameofwave(data) + ";"
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endif
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endfor
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if (progress)
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kill_progress_panel()
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endif
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setdatafolder base_df
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return result
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end
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@ -1979,12 +2011,12 @@ function adh5_scale_scienta(data)
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case 1: // Angular45
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ALow = -45/2
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AHigh = +45/2
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AUnit = "<EFBFBD>"
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AUnit = "°"
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break
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case 2: // Angular60
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ALow = -60/2
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AHigh = +60/2
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AUnit = "<EFBFBD>"
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AUnit = "°"
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break
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endswitch
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endif
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File diff suppressed because it is too large
Load Diff
@ -273,14 +273,14 @@ function elog_init_pearl_templates()
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// attributes (persistent)
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// available attributes
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string /g attributes = "author;project;pgroup;sample;source;task;technique;file;valid;"
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string /g attributes = "author;project;p-group;sample;source;task;technique;file;valid;"
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// controls corresponding to attributes
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// prefix determines the control type: sv_ = setvariable (string), pm_ = popup menu, cb = check box
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string /g controls = "sv_author;sv_project;sv_pgroup;sv_sample;pm_source;pm_task;pm_technique;sv_file;cb_valid;"
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// attributes with fixed options, value item declares the options string
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string /g options = "source=sources;task=tasks;technique=techniques"
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// attributes which must be defined
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string /g required_attributes = "author;project;pgroup;sample;source;task;technique;valid"
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string /g required_attributes = "author;project;sample;source;task;technique;valid"
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// option lists
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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"
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@ -293,7 +293,7 @@ function elog_init_pearl_templates()
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// attributes (persistent)
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// available attributes
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string /g attributes = "author;project;pgroup;sample;program;revision;machine;job;experiment;source path;result path;valid"
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string /g attributes = "author;project;p-group;sample;program;revision;machine;job;experiment;source path;result path;valid"
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// controls corresponding to attributes
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// prefix determines the control type: sv_ = setvariable (string), pm_ = popup menu, cb = check box
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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"
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File diff suppressed because it is too large
Load Diff
@ -853,6 +853,148 @@ threadsafe function /wave gauss4_reduction(source, param)
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return result_waves
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end
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threadsafe function /wave gauss6_reduction(source, param)
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wave source
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string ¶m
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variable nx = dimsize(source, 0)
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variable ny = dimsize(source, 1)
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// read parameters
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variable rngl = NumberByKey("rngl", param, "=", ";")
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variable rngh = NumberByKey("rngh", param, "=", ";")
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variable pos1 = NumberByKey("pos1", param, "=", ";")
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variable wid1 = NumberByKey("wid1", param, "=", ";")
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variable pos2 = NumberByKey("pos2", param, "=", ";")
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variable wid2 = NumberByKey("wid2", param, "=", ";")
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variable pos3 = NumberByKey("pos3", param, "=", ";")
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variable wid3 = NumberByKey("wid3", param, "=", ";")
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variable pos4 = NumberByKey("pos4", param, "=", ";")
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variable wid4 = NumberByKey("wid4", param, "=", ";")
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variable pos5 = NumberByKey("pos5", param, "=", ";")
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variable wid5 = NumberByKey("wid5", param, "=", ";")
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variable pos6 = NumberByKey("pos6", param, "=", ";")
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variable wid6 = NumberByKey("wid6", param, "=", ";")
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variable npeaks = NumberByKey("npeaks", param, "=", ";")
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variable ybox = NumberByKey("ybox", param, "=", ";")
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// prepare curve fit
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variable ipk
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make /free xprof
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adh5_setup_profile(source, xprof, 0)
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duplicate /free xprof, xprof_sig
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variable pl = max(x2pnt(xprof, rngl), 0)
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variable ph = min(x2pnt(xprof, rngh), numpnts(xprof) - 1)
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make /free /n=(npeaks) peak_coef
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peak_coef = p * 3 + 2
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variable n_coef = npeaks * 3 + 2
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make /free /d /n=(n_coef) w_coef, W_sigma
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w_coef[0] = {0, 0, 1, pos1, wid1, 1, pos2, wid2, 1, pos3, wid3, 1, pos4, wid4, 1, pos5, wid5, 1, pos6, wid6}
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redimension /n=(n_coef) w_coef, w_sigma
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// text constraints cannot be used in threadsafe functions.
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// the following matrix-vector forumlation is equivalent to:
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// make /free /T /N=6 constraints
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// constraints[0] = {"K2 >= 0", "K5 >= 0", "K8 >= 0", "K11 >= 0", "K1 <= 0", "K0 => 0"}
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make /free /n=(npeaks + 2, numpnts(w_coef)) cmat
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make /free /n=(npeaks + 2) cvec
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cmat = 0
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cmat[0][0] = -1
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cmat[1][1] = 1
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cvec = 0
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string hold = "00"
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for (ipk=0; ipk < npeaks; ipk += 1)
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hold += "011"
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cmat[2 + ipk][2 + ipk*3] = -1
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endfor
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// prepare output
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make /free /n=(npeaks * 2) /wave result_waves
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string s_note
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for (ipk = 0; ipk < npeaks; ipk += 1)
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make /free /n=0 pk_int
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adh5_setup_profile(source, pk_int, 1)
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pk_int = nan
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sprintf s_note, "AxisLabelD=peak %u integral", ipk+1
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Note pk_int, s_note
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sprintf s_note, "KineticEnergy=%.3f", w_coef[3 + ipk * 3]
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Note pk_int, s_note
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result_waves[ipk] = pk_int
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make /free /n=0 pk_sig
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adh5_setup_profile(source, pk_sig, 1)
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pk_sig = nan
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sprintf s_note, "AxisLabelD=peak %u sigma", ipk+1
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Note pk_sig, s_note
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sprintf s_note, "KineticEnergy=%.3f", w_coef[3 + ipk * 3]
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Note pk_sig, s_note
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result_waves[ipk + npeaks] = pk_sig
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waveclear pk_int, pk_sig
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endfor
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||||
// loop over angle scale
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variable p0 = 0
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||||
variable p1 = dimsize(source, 1) - 1
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variable pp
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||||
variable wmin
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variable wmax
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if (ybox > 1)
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p0 += ceil((ybox - 1) / 2)
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p1 -= ceil((ybox - 1) / 2)
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endif
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variable V_FitNumIters
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variable V_FitError
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||||
for (pp = p0; pp <= p1; pp += 1)
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||||
// box average
|
||||
xprof = source[p][pp]
|
||||
if (ybox > 1)
|
||||
xprof += source[p][pp-1] + source[p][pp+1]
|
||||
endif
|
||||
xprof_sig = max(sqrt(xprof), 1)
|
||||
xprof /= ybox
|
||||
xprof_sig /= ybox
|
||||
|
||||
// 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*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
|
||||
|
||||
// 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
|
||||
|
||||
// calculate integral
|
||||
for (ipk = 0; ipk < npeaks; ipk += 1)
|
||||
wave val = result_waves[ipk]
|
||||
wave sig = result_waves[ipk + npeaks]
|
||||
val *= w_coef[peak_coef[ipk] + 2] * sqrt(pi)
|
||||
sig *= w_coef[peak_coef[ipk] + 2] * sqrt(pi)
|
||||
endfor
|
||||
|
||||
return result_waves
|
||||
end
|
||||
|
||||
|
||||
|
||||
|
||||
/// find peak positions for the gauss-fit reduction function
|
||||
///
|
||||
|
||||
Reference in New Issue
Block a user