igor 8 compatibility
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@ -2,6 +2,7 @@
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#pragma IgorVersion = 6.2
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#pragma ModuleName = PearlAreaImport
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#include <HDF5 Browser>
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#include "pearl-compat"
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#include "pearl-gui-tools"
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// copyright (c) 2013-18 Paul Scherrer Institut
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@ -46,7 +47,7 @@ static function BeforeFileOpenHook(refNum,fileName,path,type,creator,kind)
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//PathInfo $path
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//string FilePath = s_path + filename
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string NickName = CleanupName(ParseFilePath(3, FileName, ":", 0, 0), 0)
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string NickName = PearlCleanupName(ParseFilePath(3, FileName, ":", 0, 0))
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string FileExt = LowerStr(ParseFilePath(4, FileName, ":", 0, 0))
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string result = ""
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@ -149,7 +150,7 @@ function /s ad_suggest_foldername(filename, [ignoredate,sourcename,unique])
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sprintf nickname, "%s_%s_%s", sourcename, datepart, indexpart
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endif
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else
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nickname = CleanupName(basename, 0)
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nickname = PearlCleanupName(basename)
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endif
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if (unique && CheckName(nickname, 11))
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@ -1175,6 +1176,243 @@ function /s adh5_test_reduction_func(source, reduction_func, reduction_param, re
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return reduction_param
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end
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/// reduce a three-dimensional intensity distribution
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///
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/// this function reduces a three-dimensional intensity distribution
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/// to a two-dimensional intensity map.
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/// the given reduction function is applied once on each Z section.
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///
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/// @param source source wave.
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/// three-dimensional intensity distribution (image).
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/// the scales are carried over to the result waves.
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///
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/// @param reduction_func name of the reduction function to apply to the source data.
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///
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/// @param reduction_param string with reduction parameters as required by the specific reduction function.
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///
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/// @param result_prefix name prefix of result waves.
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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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///
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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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funcref adh5_default_reduction reduction_func
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string reduction_param
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string result_prefix
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variable progress
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variable nthreads
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if (ParamIsDefault(progress))
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progress = 1
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endif
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if (ParamIsDefault(nthreads))
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nthreads = -1
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endif
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variable result = 0
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// nx and nz are the image dimensions
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variable nx, ny, nz, nt
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nx = dimsize(source, 0)
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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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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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nthreads = ThreadProcessorCount
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endif
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if (nthreads > 0)
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variable threadGroupID = ThreadGroupCreate(nthreads)
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variable ithread
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for (ithread = 0; ithread < nthreads; ithread += 1)
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ThreadStart threadGroupID, ithread, reduce_slab_worker(reduction_func)
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endfor
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else
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make /n=(nzt) /df /free processing_folders
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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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endif
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variable iz, it
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string dfname
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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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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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// 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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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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endif
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endif
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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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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 = "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, $getdimlabel(profile, 0, -1), data
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setscale /p x dimoffset(profile, 0), dimdelta(profile, 0), waveunits(profile, 0), data
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setscale /p y dimoffset(source, 2), dimdelta(source, 2), waveunits(source, 2), data
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setscale /p z dimoffset(source, 3), dimdelta(source, 3), waveunits(source, 3), data
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setscale d 0, 0, waveunits(profile, -1), data
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result_waves[iw] = data
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endfor
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endif
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for (iw = 0; iw < func_result; iw += 1)
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sw = "redw_" + num2str(iw)
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wave profile = dfr:$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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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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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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if (progress)
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kill_progress_panel()
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endif
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return result
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end
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/// thread worker for adh5_reduce_brick
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///
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/// this function polls job data folders from thread group 0
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/// and calls the reduction function on their contents.
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/// the result waves have prefix "redw_" and are saved in the job folder.
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///
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threadsafe static function reduce_brick_worker(reduction_func)
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funcref adh5_default_reduction reduction_func
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do
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// wait for job from main thread
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do
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dfref dfr = ThreadGroupGetDFR(0, 1000)
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if (DataFolderRefStatus(dfr) == 0)
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if (GetRTError(2))
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return 0 // no more jobs
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endif
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else
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break
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endif
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while (1)
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// get input data
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wave image = dfr:image
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svar func_param = dfr:func_param
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nvar rr = dfr:r_index
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nvar ss = dfr:s_index
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// do the work
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newdatafolder /s outDF
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variable /g r_index = rr
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variable /g s_index = ss
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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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// send output to queue and clean up
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adh5_get_result_waves(reduced_waves, "redw_", 0)
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WaveClear image, reduced_waves
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ThreadGroupPutDF 0, :
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KillDataFolder dfr
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while (1)
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return 0
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end
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/// copy waves from wave reference wave into current data folder
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///
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/// this function copies waves that are referenced in a wave reference wave into the current data folder.
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