updates: igor 7, map projections, hemi cuts, longitudinal section
- pearl procedures compile under igor 7. some features may not work, e.g. 3D graphics with gizmo. - add orthographic map projection to angle scans. - add functions for azimuthal and polar cuts through hemispherical scan. - add function to load longitudinal section from pshell data file.
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@ -676,6 +676,56 @@ function /s psh5_load_dataset(fileID, scanpath, datasetname, [set_scale])
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return dataname
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end
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/// select the preferred dataset from a list of available datasets.
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///
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/// @param file_datasets semicolon-separated list of datasets that are available in the file.
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///
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/// @param pref_datasets semicolon-separated list of preferred datasets.
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/// the items of the list are match strings for the Igor StringMatch function.
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/// the first matching dataset is loaded from the file.
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/// if no match is found, the first file dataset is selected.
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///
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/// @return name of selected dataset.
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///
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static function /s select_dataset(file_datasets, pref_datasets)
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string file_datasets
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string pref_datasets
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variable index
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variable nds = ItemsInList(file_datasets)
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variable ids
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string sds = ""
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variable np = ItemsInList(pref_datasets)
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variable ip
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string sp
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variable found = 0
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if (nds > 0)
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for (ip = 0; ip < np; ip += 1)
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for (ids = 0; ids < nds; ids += 1)
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sds = StringFromList(ids, file_datasets)
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index = ItemsInList(sds, "/") - 1
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sds = StringFromList(index, sds, "/")
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sp = StringFromList(ip, pref_datasets)
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if (StringMatch(sds, sp))
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found = 1
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break
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endif
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endfor
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if (found)
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break
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endif
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endfor
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if (!found)
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ids = 0
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sds = StringFromList(ids, file_datasets)
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index = ItemsInList(sds, "/") - 1
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sds = StringFromList(index, sds, "/")
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endif
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endif
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return sds
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end
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/// load a preview dataset from an open PShell HDF5 file.
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///
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/// if the dataset has a maximum of two dimensions, the function loads it at once.
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@ -686,9 +736,6 @@ end
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///
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/// @param scanpath path to the scan group in the HDF5 file, e.g. "/scan 1".
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///
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/// @param dataset name of the dataset.
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/// the name of the loaded wave is a cleaned up version of the dataset name.
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///
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/// @param set_scale by default, the function tries to set the wave scaling if the attributes have been loaded.
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/// if multiple datasets are loaded from a file,
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/// it is more efficient to set the scaling of all loaded datasets at the end by calling ps_scale_datasets().
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@ -720,45 +767,11 @@ function /s psh5_load_scan_preview(fileID, scanpath, [set_scale, pref_datasets])
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dfref dataDF = saveDF
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string datasets = psh5_list_scan_datasets(fileID, scanpath)
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variable index
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variable nds = ItemsInList(datasets)
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variable ids
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string sds
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variable np = ItemsInList(pref_datasets)
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variable ip
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string sp
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variable found = 0
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if (nds > 0)
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for (ip = 0; ip < np; ip += 1)
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for (ids = 0; ids < nds; ids += 1)
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sds = StringFromList(ids, datasets)
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index = ItemsInList(sds, "/") - 1
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sds = StringFromList(index, sds, "/")
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sp = StringFromList(ip, pref_datasets)
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if (StringMatch(sds, sp))
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found = 1
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break
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endif
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endfor
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if (found)
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break
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endif
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endfor
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if (!found)
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ids = 0
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sds = StringFromList(ids, datasets)
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index = ItemsInList(sds, "/") - 1
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sds = StringFromList(index, sds, "/")
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endif
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else
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return ""
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endif
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string datasetname = select_dataset(datasets, pref_datasets)
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string datasetpath
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string datasetname = sds
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datasetpath = scanpath + "/" + datasetname
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datasetpath = ReplaceString("//", datasetpath, "/")
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STRUCT HDF5DataInfo di // Defined in HDF5 Browser.ipf.
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InitHDF5DataInfo(di)
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variable err = HDF5DatasetInfo(fileID, datasetpath, 0, di)
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@ -824,6 +837,153 @@ function /s psh5_load_scan_preview(fileID, scanpath, [set_scale, pref_datasets])
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return dataname
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end
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/// load a longitudinal section of a scan from an open PShell HDF5 file.
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///
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/// the dataset must have three dimensions.
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///
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///
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/// @param fileID ID of open HDF5 file from psh5_open_file().
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///
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/// @param scanpath path to the scan group in the HDF5 file, e.g. "/scan 1".
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///
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/// @param dim reserved, must be 0.
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///
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/// @param set_scale by default, the function tries to set the wave scaling if the attributes have been loaded.
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/// if multiple datasets are loaded from a file,
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/// it is more efficient to set the scaling of all loaded datasets at the end by calling ps_scale_datasets().
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/// @arg 1 (default) set the wave scaling.
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/// @arg 0 do not set the wave scaling.
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///
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/// @param pref_datasets semicolon-separated list of preferred datasets.
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/// the items of the list are match strings for the Igor StringMatch function.
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/// the first matching dataset is loaded from the file.
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/// if no match is found, the first dataset listed in the file is loaded.
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/// if empty, a hard-coded default preference list is used.
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///
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/// @return name of loaded wave if successful. empty string otherwise.
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///
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/// @warning EXPERIMENTAL: this function is under development.
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///
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function /s psh5_load_scan_section(fileID, scanpath, dim, [set_scale, pref_datasets])
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variable fileID
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string scanpath
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variable dim
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variable set_scale
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string pref_datasets
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// select first dimension (future argument)
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// 0 = first dimension is x axis (energy of scienta image)
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dim = 0
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if (ParamIsDefault(set_scale))
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set_scale = 1
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endif
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if (ParamIsDefault(pref_datasets) || (strlen(pref_datasets) == 0))
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pref_datasets = kPreviewDatasets
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endif
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dfref saveDF = GetDataFolderDFR()
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dfref dataDF = saveDF
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string datasets = psh5_list_scan_datasets(fileID, scanpath)
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string datasetname = select_dataset(datasets, pref_datasets)
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string datasetpath
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datasetpath = scanpath + "/" + datasetname
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datasetpath = ReplaceString("//", datasetpath, "/")
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string dataname = StringFromList(ItemsInList(datasetpath, "/") - 1, datasetpath, "/")
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string destname = dataname[0,29] + num2str(dim)
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STRUCT HDF5DataInfo di // Defined in HDF5 Browser.ipf.
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InitHDF5DataInfo(di)
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variable err = HDF5DatasetInfo(fileID, datasetpath, 0, di)
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if (err != 0)
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print "error accessing detector/data"
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return ""
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elseif (di.ndims != 3)
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print "error: rank of dataset != 3"
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return ""
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endif
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variable idx, idy, idz, idt
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variable transpose = WhichListItem(dataname, kTransposedDatasets) >= 0
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if (transpose)
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idx = 1
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idy = 0
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else
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idx = 0
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idy = 1
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endif
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idz = 2
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idt = 3
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variable nx, ny, nz
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nx = di.dims[idx]
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ny = di.dims[idy]
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nz = di.dims[idz]
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HDF5MakeHyperslabWave(GetDataFolder(1) + "slab", max(di.ndims, 4))
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wave slab
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slab[][%Start] = 0
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slab[][%Stride] = 1
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slab[][%Count] = 1
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slab[][%Block] = 1
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if (dim == 0)
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slab[idy][%Start] = floor(ny / 2)
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slab[idx][%Block] = nx
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make /n=(nx,nz) /o $destname
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else
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slab[idx][%Start] = floor(nx / 2)
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slab[idy][%Block] = ny
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make /n=(ny,nz) /o $destname
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endif
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slab[idz][%Block] = nz
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wave data = $destname
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data = 0
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HDF5LoadData /O /Q /Z /SLAB=slab /N=slabdata fileID, datasetpath
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if (!v_flag)
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wave slabdata
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if (transpose)
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data += slabdata[0][p][q][0]
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else
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data += slabdata[p][0][q][0]
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endif
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endif
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killwaves /z slab, slabdata
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if (set_scale)
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make /n=(1,1,1) /free dummy
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ps_set_dimlabels2(dummy, dataname)
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setdimlabel 0, -1, $GetDimLabel(dummy, dim, -1), data
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setdimlabel 1, -1, $kScanDimLabel, data
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setdatafolder dataDF
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string positioners
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string positioner
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string positionerpath
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positioners = psh5_load_scan_meta(fileID, scanpath)
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wave /t /z ScanWritables
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if (waveexists(ScanWritables) && (numpnts(ScanWritables) >= 1))
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positioner = ScanWritables[0]
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if (strlen(positioner) > 0)
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positionerpath = scanpath + "/" + positioner
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positionerpath = ReplaceString("//", positionerpath, "/")
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HDF5LoadData /O /Q /Z fileID, positionerpath
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endif
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endif
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setdatafolder dataDF
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newdatafolder /o/s attr
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killwaves /a/z
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psh5_load_scan_attrs(fileID, scanpath, attr_sets=2)
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setdatafolder dataDF
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ps_scale_dataset(data)
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endif
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return destname
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end
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/// load metadata of a PShell dataset.
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///
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/// "metadata" are the HDF5 attributes attached to the scan dataset.
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@ -1136,9 +1296,27 @@ end
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function ps_set_dimlabels(data)
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wave data
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string name = NameOfWave(data)
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variable dummy
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ps_set_dimlabels2(data, NameOfWave(data))
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end
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/// set dimension labels according to the axis type
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///
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/// same as ps_set_dimlabels() except that the dimension labels are set
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/// according to a separate name argument instead of the wave name.
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///
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/// @param data data wave as loaded from PShell file.
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///
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/// @param name original name of the dataset in the PShell file.
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///
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/// @return @arg 0 all labels set successfully.
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/// @arg 1 unidentified data source.
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/// @arg 2 wave does not contain data.
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///
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function ps_set_dimlabels2(data, name)
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wave data
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string name
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variable dummy
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try
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// intrinsic dimensions
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strswitch(name)
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