#pragma rtGlobals=3 // Use modern global access method and strict wave access. #pragma IgorVersion = 6.2 #pragma ModuleName = PearlAreaImport #pragma version = 1.06 #include #include "pearl-gui-tools" // copyright (c) 2013-16 Paul Scherrer Institut // // Licensed under the Apache License, Version 2.0 (the "License"); // you may not use this file except in compliance with the License. // You may obtain a copy of the License at // http:///www.apache.org/licenses/LICENSE-2.0 /// @file /// @brief HDF5 file import from EPICS area detectors /// @ingroup ArpesPackage /// /// /// HDF5 file import from EPICS area detectors /// such as CCD cameras, 2D electron analysers /// /// as of Igor 6.3, Igor can open datasets of up to rank 4. /// i.e. the extra dimension Y of the file plugin cannot be used. /// the extra dimensions N and X are supported. /// @namespace PearlAreaImport /// @brief HDF5 file import from EPICS area detectors /// /// PearlAreaImport is declared in @ref pearl-area-import.ipf. /// callback function for drag&drop of HDF5 files into Igor. /// static function BeforeFileOpenHook(refNum,fileName,path,type,creator,kind) variable refNum, kind string fileName, path, type, creator variable handledOpen = 0 //PathInfo $path //string FilePath = s_path + filename string NickName = CleanupName(ParseFilePath(3, FileName, ":", 0, 0), 0) string FileExt = LowerStr(ParseFilePath(4, FileName, ":", 0, 0)) string result = "" // override nickname with custom setting svar /z cnn = gsCustomNickName if (svar_exists(cnn)) if (exists("gvNickNameIndex") != 2) variable/g gvNickNameIndex = 1 endif nvar nni = gvNickNameIndex NickName = cnn + num2str(nni) nni += 1 endif if (stringmatch(FileExt, "h5") == 1) result = adh5_load_complete(NickName, path, FileName) endif string/g s_latest_datafile = result string/g s_latest_nickname = nickname handledOpen = strlen(result) > 0 if (handledOpen) close refnum endif return handledOpen // 1 tells Igor not to open the file End /// generate the name of a data folder based on a file name. /// /// if the file name follows the naming convention source-date-index.extension, /// the function tries to generate the nick name as source_date_index. /// otherwise it's just a cleaned up version of the file name. /// /// date must be in yyyymmdd or yymmdd format and is clipped to the short yymmdd format. /// index should be a running numeric index of up to 6 digits, or the time encoded as hhmmss. /// however, in the current version index can be any string that can be a valid Igor folder name. /// /// @param filename file name, including extension. can also include a folder path (which is ignored). /// the extension is currently ignored, but may be used to select the parent folder in a later version. /// @param ignoredate if non-zero, the nick name will not include the date part. /// defaults to zero. /// @param sourcename nick name of the data source. /// by default, the function tries to detect the source from the file name. /// this option can be used to override auto-detection. /// the automatic source names are: /// sci (scienta by area detector), /// psh (pshell), /// sl (optics slit camera by area detector), /// es (end station camera by area detector), /// xy (unidentified). /// @param unique if non-zero, the resulting name is made a unique data folder name in the current data folder /// defaults to zero. /// function /s ad_suggest_foldername(filename, [ignoredate,sourcename,unique]) string filename variable ignoredate string sourcename variable unique if (ParamIsDefault(ignoredate)) ignoredate = 0 endif if (ParamIsDefault(unique)) unique = 0 endif string basename = ParseFilePath(3, filename, ":", 0, 0) string extension = ParseFilePath(4, filename, ":", 0, 0) string nickname string autosource if (strsearch(basename, "scienta", 0, 2) >= 0) autosource = "sci" elseif (strsearch(basename, "pshell", 0, 2) >= 0) autosource = "psh" elseif (strsearch(basename, "OP-SL", 0, 2) >= 0) autosource = "sl" elseif (strsearch(basename, "ES-PS", 0, 2) >= 0) autosource = "es" else autosource = "xy" endif if (ParamIsDefault(sourcename)) sourcename = autosource endif variable nparts = ItemsInList(basename, "-") if (nparts >= 3) string datepart = StringFromList(1, basename, "-") variable l_datepart = strlen(datepart) if (l_datepart == 8) datepart = datepart[l_datepart-6, l_datepart-1] endif string indexpart = StringFromList(2, basename, "-") if (ignoredate) sprintf nickname, "%s_%s", sourcename, indexpart else sprintf nickname, "%s_%s_%s", sourcename, datepart, indexpart endif else nickname = CleanupName(basename, 0) endif if (unique && CheckName(nickname, 11)) nickname = UniqueName(nickname + "_", 11, 0) endif return nickname end /// load area detector data files selected in a file dialog window /// /// @param APathName Igor symbolic path name. /// if empty, Igor will choose a folder on its own function ad_load_dialog(APathName) string APathName variable refNum string message = "Select data files" string filepaths string filefilters = "Area Detector HDF5 Files (*.h5):.h5;" filefilters += "All Files:.*;" PathInfo /S $APathName Open /D /R /F=filefilters /M=message /MULT=1 refNum filepaths = S_fileName dfref saveDF = GetDataFolderDFR() setdatafolder root: if (strlen(filepaths) > 0) variable nfiles = ItemsInList(filepaths, "\r") variable ifile for(ifile = 0; ifile < nfiles; ifile += 1) String path = StringFromList(ifile, filepaths, "\r") string nickname = ad_suggest_foldername(path) adh5_load_complete(nickname, "", path) endfor endif setdatafolder saveDF end /// import everything from a HDF5 file created by the Area Detector software. /// /// if the data is from the electron analyser driver and some special attributes are included, /// the function will set the scales of the image dimensions. /// /// @param ANickName destination folder name (top level under root) /// @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 /// @param load_data 1 (default): load data; 0: do not load data /// @param load_attr 1 (default): load attributes; 0: do not load attributes /// for proper wave scaling, the attributes must be loaded function /s adh5_load_complete(ANickName, APathName, AFileName, [load_data, load_attr]) string ANickName string APathName string AFileName variable load_data variable load_attr if (ParamIsDefault(load_data)) load_data = 1 endif if (ParamIsDefault(load_attr)) load_attr = 1 endif dfref saveDF = GetDataFolderDFR() setdatafolder root: newdatafolder /s/o $("root:" + ANickName) // open file variable fileID string instrumentpath = "/entry/instrument/" string detectorpath = instrumentpath + "detector/" string attributespath = instrumentpath + "NDAttributes/" string datasetname string datawavename // performance monitoring variable timerRefNum variable /g adh5_perf_secs timerRefNum = startMSTimer // avoid compilation error if HDF5 XOP has not been loaded #if Exists("HDF5OpenFile") HDF5OpenFile /P=$APathName/R fileID as AFileName if (v_flag == 0) AFileName = s_path + s_filename print "loading " + s_filename + "\r" if (load_data) adh5_load_detector_slabs(fileID, detectorpath) endif if (load_attr) newdatafolder /o/s attr adh5_loadattr_all(fileID, attributespath) setdatafolder :: endif wave /z data if (waveexists(data)) //adh5_redim(data) // not to be used with adh5_load_detector_slabs adh5_scale(data) endif HDF5CloseFile fileID else AFileName = "" endif #else Abort "HDF5 XOP not loaded." #endif if (timerRefNum >= 0) adh5_perf_secs = stopMSTimer(timerRefNum) / 1e6 endif setdatafolder saveDF return AFileName end /// load and reduce a dataset from a HDF5 file created by the Area Detector software. /// /// the resulting dataset is reduced in one image dimension by a user-defined reduction function, /// e.g. by region-of-interest integration, curve fitting, etc. /// /// the function loads the dataset image by image using the hyperslab option /// and applies a custom reduction function to each image. /// the results from the reduction function are composed into one result wave. /// the raw data are discarded. /// /// if the data is from the electron analyser driver and some special attributes are included, /// the function will set the scales of the image dimensions. /// /// @param ANickName destination folder name (top level under root) /// @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 /// /// @param reduction_func custom reduction function /// (any user-defined function which has the same parameters as adh5_default_reduction()) /// @param reduction_param parameter string for the reduction function /// /// @param load_data 1 (default): load data; 0: do not load data /// @param load_attr 1 (default): load attributes; 0: do not load attributes /// for proper wave scaling, the attributes must be loaded /// @param progress 1 (default): show progress window; 0: do not show progress window /// function /s adh5_load_reduced(ANickName, APathName, AFileName, reduction_func, reduction_param, [load_data, load_attr, progress]) string ANickName string APathName string AFileName funcref adh5_default_reduction reduction_func string reduction_param variable load_data variable load_attr variable progress if (ParamIsDefault(load_data)) load_data = 1 endif if (ParamIsDefault(load_attr)) load_attr = 1 endif if (ParamIsDefault(progress)) progress = 1 endif dfref saveDF = GetDataFolderDFR() setdatafolder root: newdatafolder /s/o $("root:" + ANickName) // open file variable fileID string instrumentpath = "/entry/instrument/" string detectorpath = instrumentpath + "detector/" string attributespath = instrumentpath + "NDAttributes/" string datasetname string datawavename // performance monitoring variable timerRefNum variable /g adh5_perf_secs timerRefNum = startMSTimer // avoid compilation error if HDF5 XOP has not been loaded #if Exists("HDF5OpenFile") HDF5OpenFile /P=$APathName/R fileID as AFileName if (v_flag == 0) AFileName = s_path + s_filename print "loading " + s_filename + "\r" if (load_attr) newdatafolder /o/s attr adh5_loadattr_all(fileID, attributespath) setdatafolder :: endif if (load_data) adh5_load_reduced_detector(fileID, detectorpath, reduction_func, reduction_param, progress=progress) endif HDF5CloseFile fileID else AFileName = "" endif #else Abort "HDF5 XOP not loaded." #endif if (timerRefNum >= 0) adh5_perf_secs = stopMSTimer(timerRefNum) / 1e6 endif setdatafolder saveDF return AFileName end /// load a single image from a HDF5 file created by the Area Detector software. /// /// the data wave is loaded into the current data folder. /// attributes are loaded into the attr subfolder. existing waves in attr are deleted. /// /// @warning EXPERIMENTAL /// this function uses the root:pearl_area:preview data folder. existing data there may be deleted! /// /// @param ANickName destination wave name. the wave is created in the current data folder. /// @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 /// @param load_data 1 (default): load data; 0: do not load data /// @param load_attr 1 (default): load attributes; 0: do not load attributes /// note: for correct scaling of the image, the attributes need to be loaded function /s adh5_load_preview(ANickName, APathName, AFileName, [load_data, load_attr]) string ANickName string APathName string AFileName variable load_data variable load_attr if (ParamIsDefault(load_data)) load_data = 1 endif if (ParamIsDefault(load_attr)) load_attr = 1 endif dfref saveDF = GetDataFolderDFR() setdatafolder root: newdatafolder /o/s pearl_area newdatafolder /o/s preview // open file variable fileID string instrumentpath = "/entry/instrument/" string detectorpath = instrumentpath + "detector/" string attributespath = instrumentpath + "NDAttributes/" string datasetname string datawavename // performance monitoring variable timerRefNum variable /g adh5_perf_secs timerRefNum = startMSTimer // avoid compilation error if HDF5 XOP has not been loaded #if Exists("HDF5OpenFile") HDF5OpenFile /P=$APathName/R/Z fileID as AFileName if (v_flag == 0) AFileName = s_path + s_filename // detector data datasetname = detectorpath + "data" STRUCT HDF5DataInfo di // Defined in HDF5 Browser.ipf. InitHDF5DataInfo(di) variable err = HDF5DatasetInfo(fileID, datasetname, 0, di) if (err != 0) print "error accessing detector/data" return "" endif if (di.ndims < 2) print "error: rank of dataset < 2" return "" endif variable dim2start = 0, dim2count = 1, dim3start = 0, dim3count = 1 if (di.ndims >= 3) dim2start = floor(di.dims[di.ndims - 3] / 2) dim2count = 1 endif if (di.ndims >= 4) dim3start = floor(di.dims[di.ndims - 4] / 2) dim3count = 1 endif if (load_data) adh5_load_detector_image(fileID, detectorpath, dim2start, dim2count, dim3start, dim3count) wave /z data string destpath = GetDataFolder(1, saveDF) + ANickName if (waveexists(data)) duplicate /o data, $destpath wave /z data = $destpath endif endif if (load_attr) setdatafolder saveDF newdatafolder /o/s attr killwaves /a/z adh5_loadattr_all(fileID, attributespath) setdatafolder :: if (waveexists(data)) adh5_scale(data) endif endif HDF5CloseFile fileID else print "error opening file " + AFileName AFileName = "" endif #else Abort "HDF5 XOP not loaded." #endif if (timerRefNum >= 0) adh5_perf_secs = stopMSTimer(timerRefNum) / 1e6 endif setdatafolder saveDF return AFileName end /// load descriptive info from a HDF5 file created by the Area Detector software. /// /// the information returned is the array size and active scans /// /// @attention EXPERIMENTAL /// this function should be merged with adh5_load_preview /// /// @param APathName igor symbolic path name. can be empty if the path is specified in FileName or a dialog box should be displayed /// @param AFileName if empty a dialog box shows up /// function /s adh5_load_info(APathName, AFileName) string APathName string AFileName dfref saveDF = GetDataFolderDFR() // open file variable fileID string instrumentpath = "/entry/instrument/" string detectorpath = instrumentpath + "detector/" string attributespath = instrumentpath + "NDAttributes/" string datasetname string datawavename string s_info = "" string s variable idim // avoid compilation error if HDF5 XOP has not been loaded #if Exists("HDF5OpenFile") HDF5OpenFile /P=$APathName/R/Z fileID as AFileName if (v_flag == 0) AFileName = s_path + s_filename // detector data datasetname = detectorpath + "data" STRUCT HDF5DataInfo di // Defined in HDF5 Browser.ipf. InitHDF5DataInfo(di) variable err = HDF5DatasetInfo(fileID, datasetname, 0, di) if (err != 0) print "error accessing detector/data" return "" endif for (idim = 0; idim < di.ndims; idim += 1) sprintf s, "dim %u: %u points", idim, di.dims[idim] if (strlen(s_info) > 0) s_info = s_info + "\r" + s else s_info = s endif endfor dfref df = NewFreeDataFolder() setdatafolder df adh5_loadattr_all(fileID, attributespath) for (idim = 1; idim < 5; idim += 1) sprintf s, "Scan%uActive", idim wave /z w = $s if (waveexists(w) && (numpnts(w) > 0) && (w[0] > 0)) sprintf s, "Scan%uPositioner1", idim wave /t wt = $s sprintf s, "scan %u: %s", idim, wt[0] if (strlen(s_info) > 0) s_info = s_info + "\r" + s else s_info = s endif endif endfor HDF5CloseFile fileID else print "error opening file " + AFileName AFileName = "" endif #else Abort "HDF5 XOP not loaded." #endif setdatafolder saveDF return s_info end /// load the detector dataset from the open HDF5 file. /// /// the function loads the whole dataset at once /// and redimensions it so that the image dimensions are X and Y /// /// @param fileID ID of open HDF5 file from HDF5OpenFile /// @param detectorpath path to detector group in the HDF5 file /// function adh5_load_detector(fileID, detectorpath) variable fileID string detectorpath // avoid compilation error if HDF5 XOP has not been loaded #if Exists("HDF5LoadData") string datasetname string datawavename // detector data datasetname = detectorpath + "data" STRUCT HDF5DataInfo di // Defined in HDF5 Browser.ipf. InitHDF5DataInfo(di) variable err = HDF5DatasetInfo(fileID, datasetname, 0, di) if (err != 0) print "error accessing detector/data" return -1 endif if (di.ndims < 2) print "error: rank of dataset < 2" return -2 endif HDF5LoadData /O /Q /Z fileID, datasetname wave data #else Abort "HDF5 XOP not loaded." #endif end /// redimension a multi-dimensional area detector array loaded from HDF5. /// /// so that the image dimensions are X and Y /// singleton dimensions are removed (most common cases only) /// /// in the redimensioned array, the original dimension type is noted in the dimension label: /// AD_Dim0 = first image dimension /// AD_Dim1 = second image dimension /// AD_DimN = frame sequence /// AD_DimX = extra dimension X /// AD_DimY = extra dimension Y (cannot be loaded in Igor) /// /// @param data area detector data loaded from HDF5 to be redimensioned /// function adh5_redim(data) wave data duplicate /free data, tempdata variable nd = wavedims(tempdata) variable nx = dimsize(tempdata, nd - 1) variable ny = dimsize(tempdata, nd - 2) variable nz = dimsize(tempdata, nd - 3) variable nt = dimsize(tempdata, nd - 4) switch (nd) case 2: if (nx <= 1) redimension /n=(ny) data setdimlabel 0, -1, AD_Dim1, data data = tempdata[p][0] elseif (ny <= 1) redimension /n=(nx) data setdimlabel 0, -1, AD_Dim0, data data = tempdata[0][p] else redimension /n=(nx,ny) data setdimlabel 0, -1, AD_Dim0, data setdimlabel 1, -1, AD_Dim1, data data = tempdata[q][p] endif break case 3: if (nx <= 1) redimension /n=(ny,nz) data setdimlabel 0, -1, AD_Dim1, data setdimlabel 1, -1, AD_DimN, data multithread data = tempdata[q][p][0] elseif (ny <= 1) redimension /n=(nx,nz) data setdimlabel 0, -1, AD_Dim0, data setdimlabel 1, -1, AD_DimN, data multithread data = tempdata[q][0][p] elseif (nz <= 1) redimension /n=(nx,ny) data setdimlabel 0, -1, AD_Dim0, data setdimlabel 1, -1, AD_Dim1, data multithread data = tempdata[0][q][p] else redimension /n=(nx,ny,nz) data setdimlabel 0, -1, AD_Dim0, data setdimlabel 1, -1, AD_Dim1, data setdimlabel 2, -1, AD_DimN, data multithread data = tempdata[r][q][p] endif break case 4: if (nz <= 1) // singleton "frame number" dimension redimension /n=(nx,ny,nt) data setdimlabel 0, -1, AD_Dim0, data setdimlabel 1, -1, AD_Dim1, data setdimlabel 2, -1, AD_DimX, data multithread data = tempdata[r][0][q][p] else redimension /n=(nx,ny,nz,nt) data setdimlabel 0, -1, AD_Dim0, data setdimlabel 1, -1, AD_Dim1, data setdimlabel 2, -1, AD_DimN, data setdimlabel 3, -1, AD_DimX, data multithread data = tempdata[s][r][q][p] endif break endswitch end /// find the attributes data folder of an area detector dataset. /// /// since version 1.04 attributes should be stored in a subfolder named attr. /// earlier versions had the attributes in the same data folder as the actual dataset. /// /// @param data wave containing the main dataset. /// /// @return data folder reference of the attributes folder. /// the reference may be invalid (and default to root) if the folder cannot be found, /// cf. built-in DataFolderRefStatus function. static function /DF GetAttrDataFolderDFR(data) wave data dfref dataDF = GetWavesDataFolderDFR(data) dfref attrDF = dataDF:attr if (DataFolderRefStatus(attrDF) == 0) attrDF = dataDF endif return attrDF end /// set the dimension scales of an area detector dataset. /// /// the intrinsic dimensions 0 and 1 are scaled according to the data source /// (currently supported: Prosilica cameras, Scienta electron analyser). /// the extra dimensions are scaled according to the scan. /// the latter requires that the positioner names and position values are available. /// function adh5_scale(data,[source]) wave data string source dfref saveDF = GetDataFolderDFR() dfref dataDF = GetWavesDataFolderDFR(data) dfref attrDF = GetAttrDataFolderDFR(data) if (ParamIsDefault(source)) // is the source a Scienta analyser? wave /SDFR=attrDF /Z AcquisitionMode wave /SDFR=attrDF /T /Z Manufacturer source = "unknown" if (waveexists(Manufacturer) && (numpnts(Manufacturer) >= 1)) strswitch(Manufacturer[0]) case "VG Scienta": source = "scienta" break case "Prosilica": source = "prosilica" break endswitch elseif (waveexists(AcquisitionMode) && (numpnts(AcquisitionMode) >= 1)) if (stringmatch(note(AcquisitionMode), "*SCIENTA*")) source = "scienta" endif endif endif strswitch(source) case "prosilica": // pixel scale - nothing to do break case "scienta": adh5_scale_scienta(data) break endswitch setdatafolder saveDF end /// load the detector dataset from the open HDF5 file. /// /// the function loads the dataset image by image using the hyperslab option. /// this function gives the same result as adh5_load_detector. /// it is about 5% slower, and it depends on HDF5 Browser code. /// but it does not choke on large datasets (as long as the final wave fits into memory). /// /// @param fileID ID of open HDF5 file from HDF5OpenFile. /// @param detectorpath path to detector group in the HDF5 file. /// @param progress 1 (default): show progress window; 0: do not show progress window. /// /// @return 0 if successful, non-zero if an error occurred. /// function adh5_load_detector_slabs(fileID, detectorpath, [progress]) variable fileID string detectorpath variable progress if (ParamIsDefault(progress)) progress = 1 endif variable result = 0 // avoid compilation error if HDF5 XOP has not been loaded #if Exists("HDF5LoadData") string datasetname string datawavename // detector data datasetname = detectorpath + "data" STRUCT HDF5DataInfo di // Defined in HDF5 Browser.ipf. InitHDF5DataInfo(di) variable err = HDF5DatasetInfo(fileID, datasetname, 0, di) if (err != 0) print "error accessing detector/data" return -1 endif if (di.ndims < 2) print "error: rank of dataset < 2" return -2 endif // nx and nz are the image dimensions variable idx, idy, idz, idt, izt idx = di.ndims - 1 idy = di.ndims - 2 idz = -1 idt = -1 variable nx, ny, nz, nt, nzt nx = di.dims[idx] ny = di.dims[idy] nz = 1 nt = 1 make /n=(nx,ny,nz,nt) /o data string dim_labels = "AD_Dim0;AD_Dim1;AD_DimN;AD_DimX;AD_DimY" string dim_label dim_label = StringFromList(0, dim_labels, ";") setdimlabel 0, -1, $dim_label, data dim_labels = RemoveFromList(dim_label, dim_labels, ";") dim_label = StringFromList(0, dim_labels, ";") setdimlabel 1, -1, $dim_label, data dim_labels = RemoveFromList(dim_label, dim_labels, ";") // find additional dimensions, ignore singletons variable id for (id = idy - 1; (id >= 0) && (nz == 1); id -= 1) if (di.dims[id] > 1) idz = id nz = di.dims[id] dim_label = StringFromList(0, dim_labels, ";") setdimlabel 2, -1, $dim_label, data endif dim_labels = RemoveListItem(0, dim_labels, ";") endfor for (id = idz - 1; (id >= 0) && (nt == 1); id -= 1) if (di.dims[id] > 1) idt = id nt = di.dims[id] dim_label = StringFromList(0, dim_labels, ";") setdimlabel 3, -1, $dim_label, data endif dim_labels = RemoveListItem(0, dim_labels, ";") endfor redimension /n=(nx,ny,nz,nt) data // default values if dimensions are not present in dataset if (idz < 0) idz = idx + 1 idt = idz + 1 elseif (idt < 0) idt = idx + 1 endif nzt = nz * nt izt = 0 if (progress) display_progress_panel("HDF5 Import", "Loading data...", nzt) endif // load data image by image HDF5MakeHyperslabWave(GetDataFolder(1) + "slab", max(di.ndims, 4)) wave slab slab[][%Start] = 0 slab[][%Stride] = 1 slab[][%Count] = 1 slab[][%Block] = 1 slab[idx][%Block] = nx slab[idy][%Block] = ny variable iz, it for (iz = 0; iz < nz; iz += 1) for (it = 0; it < nt; it += 1) slab[idz][%Start] = iz slab[idt][%Start] = it HDF5LoadData /O /Q /Z /SLAB=slab /N=slabdata fileID, datasetname wave slabdata // 2D, 3D, or 4D with singletons switch (WaveDims(slabdata)) case 2: data[][][iz][it] = slabdata[q][p] break case 3: data[][][iz][it] = slabdata[0][q][p] break case 4: data[][][iz][it] = slabdata[0][0][q][p] break endswitch // progress window izt += 1 if (progress) if (update_progress_panel(izt)) result = -4 // user abort break endif endif endfor if (result < 0) break endif endfor if (nz == 1) redimension /n=(nx,ny) data elseif (nt == 1) redimension /n=(nx,ny,nz) data endif if (progress) kill_progress_panel() endif #else Abort "HDF5 XOP not loaded." #endif return result end /// load a single image from the detector dataset of the open HDF5 file /// /// the function can average over a region in the extra dimensions. /// /// @param fileID ID of open HDF5 file from HDF5OpenFile /// @param detectorpath path to detector group in the HDF5 file /// @param dim2start 2nd dimension coordinate of the first image /// note that the order of dimensions is reversed in the file /// 2nd dimension = N dimension in area detector = dimension 0 of the three-dimensional HDF dataset /// set to 0 if dimension may not be present /// @param dim2count number of subsequent images to average /// set to 1 if dimension may not be present /// @param dim3start 3rd dimension coordinate of the first image /// note that the order of dimensions is reversed in the file /// 3rd dimension = extra X dimension in area detector = dimension 0 of the four-dimensional HDF dataset /// set to 0 if dimension may not be present /// @param dim3count number of subsequent images to average /// set to 1 if dimension may not be present /// function adh5_load_detector_image(fileID, detectorpath, dim2start, dim2count, dim3start, dim3count) variable fileID string detectorpath variable dim2start variable dim2count variable dim3start variable dim3count // avoid compilation error if HDF5 XOP has not been loaded #if Exists("HDF5LoadData") string datasetname string datawavename // detector data datasetname = detectorpath + "data" STRUCT HDF5DataInfo di // Defined in HDF5 Browser.ipf. InitHDF5DataInfo(di) variable err = HDF5DatasetInfo(fileID, datasetname, 0, di) if (err != 0) print "error accessing detector/data" return -1 endif if (di.ndims < 1) print "error: rank of dataset < 1" return -2 endif // nx and nz are the image dimensions variable idx, idy, idz, idt idx = di.ndims - 1 idy = di.ndims >= 2 ? di.ndims - 2 : 1 idz = di.ndims >= 3 ? di.ndims - 3 : 2 idt = di.ndims >= 4 ? di.ndims - 4 : 3 variable nx, ny nx = di.dims[idx] ny = di.ndims >= 2 ? di.dims[idy] : 1 variable dim2end = dim2start + dim2count - 1 variable dim3end = dim3start + dim3count - 1 // the slab wave is at least 4-dimensional // it will also load lower-dimensional datasets HDF5MakeHyperslabWave(GetDataFolder(1) + "slab", max(di.ndims, 4)) wave slab slab[][%Start] = 0 slab[][%Stride] = 1 slab[][%Count] = 1 slab[][%Block] = 1 slab[idx][%Block] = nx slab[idy][%Block] = ny make /n=(nx,ny)/o/d data data = 0 variable iz, it variable navg = 0 for (iz = dim2start; iz <= dim2end; iz += 1) for (it = dim3start; it <= dim3end; it += 1) slab[idz][%Start] = iz slab[idt][%Start] = it HDF5LoadData /O /Q /Z /SLAB=slab /N=slabdata fileID, datasetname wave slabdata // 2D, 3D, or 4D with singletons switch (WaveDims(slabdata)) case 1: data += slabdata[p] navg += 1 break case 2: data += slabdata[q][p] navg += 1 break case 3: data += slabdata[0][q][p] navg += 1 break case 4: data += slabdata[0][0][q][p] navg += 1 break endswitch endfor endfor data /= navg setdimlabel 0, -1, AD_Dim0, data setdimlabel 1, -1, AD_Dim1, data #else Abort "HDF5 XOP not loaded." #endif end /// get a list of functions which can be used as reduction functions. /// /// the function evaluates only the function arguments, /// it may thus include functions which are not suitable as reduction functions. /// function /s adh5_list_reduction_funcs() string all_funcs = FunctionList("*", ";", "KIND:6,NPARAMS:4,VALTYPE:1") string result = "" variable ii variable nn = ItemsInList(all_funcs, ";") string funcname string info variable nparams variable accept for (ii = 0; ii < nn; ii += 1) funcname = StringFromList(ii, all_funcs, ";") info = FunctionInfo(funcname) accept = (NumberByKey("RETURNTYPE", info, ":", ";") == 0x0004) accept = accept && (cmpstr(StringByKey("THREADSAFE", info, ":", ";"), "yes") == 0) accept = accept && (NumberByKey("N_PARAMS", info, ":", ";") == 4) accept = accept && (NumberByKey("N_OPT_PARAMS", info, ":", ";") == 0) if (accept) // 3 numeric waves and one pass-by-reference string accept = accept && (NumberByKey("PARAM_0_TYPE", info, ":", ";") == 0x4002) accept = accept && (NumberByKey("PARAM_1_TYPE", info, ":", ";") == 0x4002) accept = accept && (NumberByKey("PARAM_2_TYPE", info, ":", ";") == 0x4002) accept = accept && (NumberByKey("PARAM_3_TYPE", info, ":", ";") == 0x3000) endif if (accept) result = AddListItem(funcname, result, ";") endif endfor result = SortList(result, ";", 4) return result end /// function prototype for adh5_load_reduced_detector /// /// derived functions reduce a two-dimensional dataset to a one-dimensional dataset, /// e.g. by ROI-integration, curve fitting, etc. // the resulting wave must have the same size as either dimension of the source image. /// /// each destination wave is a one-dimensional intensity distribution. /// the function must redimension each of these waves to one of the image dimensions /// by calling the adh5_setup_profile() function. /// this function will also copy the scale information and dimension labels, /// which is important for the proper scaling of the result. /// /// the meaning of the data in dest1 and dest2 is up to the particular function, /// e.g. dest1 could hold the mean value and dest2 the one-sigma error, /// or dest1 could hold the X-profile, and dest2 the Y-profile. /// /// @param source source wave /// two-dimensional intensity distribution (image) /// @param dest1, dest2 destination waves /// @param param string with optional parameters, shared between calls. /// this is a pass-by-reference argument, /// the function may modify the string /// /// @return zero if successful, non-zero if an error occurs. /// threadsafe function adh5_default_reduction(source, dest1, dest2, param) wave source wave dest1, dest2 string ¶m // demo code // integrate along the dimensions adh5_setup_profile(source, dest1, 0) ad_profile_x_w(source, 0, -1, dest1) adh5_setup_profile(source, dest2, 1) ad_profile_y_w(source, 0, -1, dest2) return 0 end /// set up a one-dimensional wave for a line profile based on a 2D original wave. /// /// redimensions the profile wave to the given dimension. /// copies the scale and dimension label of the given dimension. /// threadsafe function adh5_setup_profile(image, profile, dim) wave image // prototype wave profile // destination wave variable dim // which dimension to keep: 0 = X, 1 = Y redimension /n=(dimsize(image, dim)) profile setscale /p x dimoffset(image, dim), dimdelta(image, dim), waveunits(image, dim), profile setscale d 0, 0, waveunits(image, -1), profile setdimlabel 0, -1, $getdimlabel(image, dim, -1), profile end /// wrapper function for testing reduction functions from the command line. /// /// Igor does not allow global variables as pass-by-reference parameter for reduction_param. /// function /s adh5_test_reduction_func(source, dest1, dest2, reduction_func, reduction_param) wave source wave dest1 wave dest2 funcref adh5_default_reduction reduction_func string reduction_param reduction_func(source, dest1, dest2, reduction_param) return reduction_param end /// load a reduced detector dataset from the open HDF5 file. /// /// the function loads the dataset image by image using the hyperslab option /// and applies a custom reduction function to each image. /// the results from the reduction function are composed into one result wave. /// the raw data are discarded. /// /// by default, the reduction function is called in separate threads to reduce the total loading time. /// (see the global variable adh5_perf_secs which reports the total run time of the function.) /// the effect varies depending on the balance between file loading (image size) /// and data processing (complexity of the reduction function). /// for debugging the reduction function, multi-threading can be disabled. /// /// @param fileID ID of open HDF5 file from HDF5OpenFile /// @param detectorpath path to detector group in the HDF5 file /// @param reduction_func custom reduction function /// (any user-defined function which has the same parameters as adh5_default_reduction()) /// @param reduction_param parameter string for the reduction function /// @param progress 1 (default): show progress window; 0: do not show progress window /// @param nthreads -1 (default): use as many threads as there are processor cores (in addition to main thread) /// 0: use main thread only (e.g. for debugging the reduction function) /// >= 1: use a fixed number of (additional) threads function adh5_load_reduced_detector(fileID, detectorpath, reduction_func, reduction_param, [progress, nthreads]) variable fileID string detectorpath funcref adh5_default_reduction reduction_func string reduction_param variable progress variable nthreads if (ParamIsDefault(progress)) progress = 1 endif if (ParamIsDefault(nthreads)) nthreads = -1 endif variable result = 0 // avoid compilation error if HDF5 XOP has not been loaded #if Exists("HDF5LoadData") string datasetname string datawavename // detector data datasetname = detectorpath + "data" STRUCT HDF5DataInfo di // Defined in HDF5 Browser.ipf. InitHDF5DataInfo(di) variable err = HDF5DatasetInfo(fileID, datasetname, 0, di) if (err != 0) print "error accessing detector/data" return -1 endif if (di.ndims < 2) print "error: rank of dataset < 2" return -2 endif // nx and nz are the image dimensions variable idx, idy, idz, idt idx = di.ndims - 1 idy = di.ndims - 2 idz = -1 idt = -1 variable nx, ny, nz, nt nx = di.dims[idx] ny = di.dims[idy] nz = 1 nt = 1 // find additional dimensions, ignore singletons variable id for (id = idy - 1; (id >= 0) && (nz == 1); id -= 1) if (di.dims[id] > 1) idz = id nz = di.dims[id] endif endfor for (id = idz - 1; (id >= 0) && (nt == 1); id -= 1) if (di.dims[id] > 1) idt = id nt = di.dims[id] endif endfor // default values if dimensions are not present in dataset if (idz < 0) idz = idx + 1 idt = idz + 1 elseif (idt < 0) idt = idx + 1 endif variable nzt = nz * nt variable izt // load data image by image HDF5MakeHyperslabWave(GetDataFolder(1) + "slab", max(di.ndims, 4)) wave slab slab[][%Start] = 0 slab[][%Stride] = 1 slab[][%Count] = 1 slab[][%Block] = 1 slab[idx][%Block] = nx slab[idy][%Block] = ny // set up multi threading if (nthreads < 0) nthreads = ThreadProcessorCount endif if (nthreads > 0) variable threadGroupID = ThreadGroupCreate(nthreads) variable ithread for (ithread = 0; ithread < nthreads; ithread += 1) ThreadStart threadGroupID, ithread, reduce_slab_worker(reduction_func) endfor else make /n=(nzt) /df /free processing_folders endif if (progress) display_progress_panel("HDF5 Import", "Loading data (step 1 of 2)...", nzt) endif make /n=(nx,ny)/d image_template setdimlabel 0, -1, AD_Dim0, image_template setdimlabel 1, -1, AD_Dim1, image_template adh5_scale(image_template) variable iz, it string dfname izt = 0 for (iz = 0; iz < nz; iz += 1) for (it = 0; it < nt; it += 1) // load hyperslab slab[idz][%Start] = iz slab[idt][%Start] = it dfname = "processing_" + num2str(izt) newdatafolder /s $dfname HDF5LoadData /O /Q /Z /SLAB=slab /N=slabdata fileID, datasetname // send to processing queue duplicate image_template, image variable /g r_index = iz variable /g s_index = it string /g func_param = reduction_param if (nthreads > 0) WaveClear image ThreadGroupPutDF threadGroupID, : else processing_folders[izt] = GetDataFolderDFR() make /n=1/d profile1, profile2 wave slabdata variable /g func_result func_result = reduce_slab_image(slabdata, image, profile1, profile2, reduction_func, func_param) WaveClear slabdata, image, profile1, profile2 setdatafolder :: endif izt += 1 // progress window if (progress) if (update_progress_panel(izt)) result = -4 // user abort break endif endif endfor endfor killwaves /z slab, image_template if (progress) update_progress_panel(0, message="Processing data (step 2 of 2)...") endif dfref dfr for (izt = 0; (izt < nzt) && (result == 0); izt += 1) if (nthreads > 0) do dfr = ThreadGroupGetDFR(threadGroupID, 1000) if (DatafolderRefStatus(dfr) != 0) break endif if (progress) if (update_progress_panel(izt)) result = -4 // user abort break endif endif while (1) else dfr = processing_folders[izt] if (progress) if (update_progress_panel(izt)) result = -4 // user abort break endif endif endif if (result != 0) break endif nvar rr = dfr:r_index nvar ss = dfr:s_index nvar func_result = dfr:func_result wave profile1 = dfr:profile1 wave profile2 = dfr:profile2 if (func_result == 0) if (izt == 0) make /n=(dimsize(profile1, 0), nz, nt)/d/o data1 make /n=(dimsize(profile2, 0), nz, nt)/d/o data2 setdimlabel 0, -1, $getdimlabel(profile1, 0, -1), data1 setdimlabel 0, -1, $getdimlabel(profile2, 0, -1), data2 setscale /p x dimoffset(profile1, 0), dimdelta(profile1, 0), waveunits(profile1, 0), data1 setscale /p x dimoffset(profile2, 0), dimdelta(profile2, 0), waveunits(profile2, 0), data2 setscale d 0, 0, waveunits(profile1, -1), data1 setscale d 0, 0, waveunits(profile2, -1), data2 endif data1[][rr][ss] = profile1[p] data2[][rr][ss] = profile2[p] else result = -3 // dimension reduction error break endif endfor if (nthreads > 0) variable tstatus = ThreadGroupRelease(threadGroupID) if (tstatus == -2) result = -5 // thread did not terminate properly endif else for (izt = 0; izt < nzt; izt += 1) KillDataFolder /Z processing_folders[izt] endfor endif if (result == 0) if (nz == 1) redimension /n=(dimsize(data1,0)) data1 redimension /n=(dimsize(data2,0)) data2 elseif (nt == 1) redimension /n=(dimsize(data1,0),nz) data1 redimension /n=(dimsize(data2,0),nz) data2 setdimlabel 1, -1, AD_DimN, data1 setdimlabel 1, -1, AD_DimN, data2 else setdimlabel 1, -1, AD_DimN, data1 setdimlabel 1, -1, AD_DimN, data2 setdimlabel 2, -1, AD_DimX, data1 setdimlabel 2, -1, AD_DimX, data2 endif endif if (progress) kill_progress_panel() endif #else Abort "HDF5 XOP not loaded." #endif return result end threadsafe static function reduce_slab_worker(reduction_func) funcref adh5_default_reduction reduction_func do // wait for job from main thread do dfref dfr = ThreadGroupGetDFR(0, 1000) if (DataFolderRefStatus(dfr) == 0) if (GetRTError(2)) return 0 // no more jobs endif else break endif while (1) // get input data wave slabdata = dfr:slabdata wave image = dfr:image svar func_param = dfr:func_param nvar rr = dfr:r_index nvar ss = dfr:s_index // do the work newdatafolder /s outDF make /n=1/d profile1, profile2 variable /g r_index = rr variable /g s_index = ss variable /g func_result func_result = reduce_slab_image(slabdata, image, profile1, profile2, reduction_func, func_param) // send output to queue and clean up WaveClear slabdata, image, profile1, profile2 ThreadGroupPutDF 0, : KillDataFolder dfr while (1) return 0 end threadsafe static function reduce_slab_image(slabdata, image, profile1, profile2, reduction_func, reduction_param) wave slabdata wave image wave profile1 wave profile2 funcref adh5_default_reduction reduction_func string reduction_param switch (WaveDims(slabdata)) case 2: image = slabdata[q][p] break case 3: image = slabdata[0][q][p] break case 4: image = slabdata[0][0][q][p] break endswitch return reduction_func(image, profile1, profile2, reduction_param) end /// load an NDAttributes group from an open HDF5 file into the current data folder. /// /// datasets contained in the group are loaded as waves. /// if a dataset contains only one data point, it is added to the IN, ID, IV, IU waves, /// where IN = EPICS channel name, ID = attribute name, IV = value, IU = unit /// (units are left empty as they are not saved in HDF5). /// attributes of the NDAttributes group are added to the IN, ID, IV, IU waves, /// however, IN and IU are left empty as this information is not saved in the HDF5 file. /// /// @param fileID ID of open HDF5 file from HDF5OpenFile /// @param attributespath path to NDAttributes group in the HDF5 file /// function adh5_loadattr_all(fileID, attributespath) variable fileID string attributespath string datasetname string datawavename // avoid compilation error if HDF5 XOP has not been loaded #if Exists("HDF5LoadData") // datasets in NDAttributes group HDF5ListGroup /F /TYPE=2 fileID, attributespath string h5datasets = S_HDF5ListGroup HDF5ListAttributes /TYPE=1 /Z fileID, attributespath string h5attributes = S_HDF5ListAttributes variable nds = ItemsInList(h5datasets, ";") variable na = ItemsInList(h5attributes, ";") variable ids variable idest = 0 variable n_attr string s_attr string s_source make /n=(nds+na) /t /o IN, ID, IV, IU for (ids = 0; ids < nds; ids += 1) datasetname = StringFromList(ids, h5datasets, ";") HDF5LoadData /O/Q fileID, datasetname if (v_flag == 0) datawavename = StringFromList(0, s_wavenames) else datawavename = "" endif HDF5LoadData /A="source"/O/Q/TYPE=2 fileID, datasetname if (v_flag == 0) wave /t source s_source = source[0] else s_source = "" endif read_attribute_info(datawavename, s_source, idest) endfor // attributes of NDAttributes group if (v_flag == 0) nds = ItemsInList(h5attributes, ";") else nds = 0 endif for (ids = 0; ids < nds; ids += 1) datasetname = StringFromList(ids, h5attributes, ";") HDF5LoadData /A=datasetname/O/Q/TYPE=1 fileID, attributespath if (v_flag == 0) datawavename = StringFromList(0, s_wavenames) read_attribute_info(datawavename, "", idest) // we don't get the source of these attributes endif endfor redimension /n=(idest) IN, ID, IV, IU sort {IN, ID}, IN, ID, IV, IU killwaves /z source #else Abort "HDF5 XOP not loaded." #endif end /// sub-function of adh5_loadattr_all. /// /// reads one attribute from a wave which was loaded from an HDF5 file into the info waves IN, ID, IV, IU. /// the attribute is read only if the input wave contains exactly one item, /// i.e. either the measurement is a single image, or the attribute has string type. /// /// @param datawavename name of the attribute wave in the current folder. /// can be text or numeric. /// @param source source identifier (EPICS name) of the attribute. /// @param idest destination index in IN, ID, IV, IU where the results are written. /// the variable is incremented if data was written, otherwise it is left unchanged. /// make sure IN, ID, IV, IU have at least idest + 1 elements. /// static function read_attribute_info(datawavename, source, idest) string datawavename // name of the attribute wave in the current folder. // can be text or numeric. string source // source identifier (EPICS name) of the attribute. variable &idest // destination index in IN, ID, IV, IU where the results are written. // the variable is incremented if data was written, otherwise it is left unchanged. // make sure IN, ID, IV, IU have at least idest + 1 elements. wave /t IN wave /t ID wave /t IV wave /t IU variable n_attr string s_attr if (exists(datawavename) == 1) if (strlen(source) > 0) Note $datawavename, "PV=" + source endif switch(WaveType($datawavename, 1)) case 1: // numeric wave w_attr = $datawavename n_attr = numpnts(w_attr) sprintf s_attr, "%.12g", w_attr[0] break case 2: // text wave /t wt_attr = $datawavename n_attr = numpnts(wt_attr) s_attr = wt_attr[0] break default: // unknown n_attr = 0 endswitch if (n_attr == 1) IN[idest] = source ID[idest] = datawavename IV[idest] = s_attr IU[idest] = "" // we don't get the units idest += 1 endif endif end /// set the energy and angle scales of an area detector dataset from the Scienta analyser. /// /// the dimension labels of the energy and angle scales must be set correctly: /// AD_Dim0 = energy dimension; AD_Dim1 = angle dimension. /// these dimensions must be the first two dimensions of a multi-dimensional dataset. /// normally, AD_Dim0 is the X dimension, and AD_Dim1 the Y dimension. /// function adh5_scale_scienta(data) wave data dfref saveDF = GetDataFolderDFR() dfref dataDF = GetWavesDataFolderDFR(data) dfref attrDF = GetAttrDataFolderDFR(data) wave /SDFR=attrDF LensMode wave /SDFR=attrDF /Z ChannelBegin, ChannelEnd wave /SDFR=attrDF /Z SliceBegin, SliceEnd variable EDim, ADim variable ELow, EHigh, ALow, AHigh string EUnit, AUnit // which dimension is angle and which one is energy? strswitch(GetDimLabel(data, 0, -1)) case "AD_Dim0": EDim = 0 break case "AD_Dim1": EDim = 1 break default: EDim = -1 endswitch strswitch(GetDimLabel(data, 1, -1)) case "AD_Dim0": ADim = 0 break case "AD_Dim1": ADim = 1 break default: ADim = -1 endswitch // defaults (point scaling) if (EDim >= 0) ELow = dimoffset(data, EDim) EHigh = dimoffset(data, EDim) + dimdelta(data, EDim) * (dimsize(data, EDim) - 1) EUnit = "eV" endif if (ADim >= 0) ALow = dimoffset(data, ADim) AHigh = dimoffset(data, ADim) + dimdelta(data, ADim) * (dimsize(data, ADim) - 1) AUnit = "arb." endif // lens mode can give more detail if (waveexists(LensMode) && (numpnts(LensMode) >= 1)) switch(LensMode[0]) case 1: // Angular45 ALow = -45/2 AHigh = +45/2 AUnit = "°" break case 2: // Angular60 ALow = -60/2 AHigh = +60/2 AUnit = "°" break endswitch endif // best option if scales are explicit in separate waves if (waveexists(ChannelBegin) && waveexists(ChannelEnd) && (numpnts(ChannelBegin) >= 1) && (numpnts(ChannelEnd) >= 1)) ELow = ChannelBegin[0] EHigh = ChannelEnd[0] endif if (waveexists(SliceBegin) && waveexists(SliceEnd) && (numpnts(SliceBegin) >= 1) && (numpnts(SliceEnd) >= 1)) ALow = SliceBegin[0] AHigh = SliceEnd[0] endif // apply new scales switch(EDim) case 0: setscale /i x ELow, EHigh, EUnit, data break case 1: setscale /i y ELow, EHigh, EUnit, data break endswitch switch(ADim) case 0: setscale /i x ALow, AHigh, AUnit, data break case 1: setscale /i y ALow, AHigh, AUnit, data break endswitch setscale d 0, 0, "arb.", data setdatafolder saveDF end /// scales the extra dimensions of an area detector dataset according to the EPICS scan /// /// the scan positioner name and its values must be available /// /// @todo incomplete /// function adh5_scale_scan(data) wave data dfref saveDF = GetDataFolderDFR() dfref dataDF = GetWavesDataFolderDFR(data) wave /SDFR=dataDF AcquisitionMode, DetectorMode, EnergyMode wave /SDFR=dataDF /z Scan1Active, Scan2Active wave /SDFR=dataDF /t /z Scan1Positioner1, Scan1Readback1 wave /SDFR=dataDF /t /z Scan1Positioner2, Scan1Readback2 wave /SDFR=dataDF /t /z Scan2Positioner1, Scan2Readback1 wave /SDFR=dataDF /t /z Scan2Positioner2, Scan2Readback2 // TODO : search the data folder for positioner waves, // i.e. waves with the PV name corresponding to Scan1Positioner1 in their wave note. wave /z zscale strswitch(GetDimLabel(data, 0, -1)) case "AD_DimN": setscale /i x zscale[0], zscale[numpnts(zscale)-1], "", data break endswitch strswitch(GetDimLabel(data, 1, -1)) case "AD_DimN": setscale /i y zscale[0], zscale[numpnts(zscale)-1], "", data break endswitch strswitch(GetDimLabel(data, 2, -1)) case "AD_DimN": setscale /i z zscale[0], zscale[numpnts(zscale)-1], "", data break endswitch setdatafolder saveDF end