bugfixes in pshell import and preview
changes: - fix null string exception in preview - fix transposition of two-dimensional datasets
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@ -66,6 +66,15 @@ strconstant kScanDimLabel = "scan"
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/// This label may be used to store the parameters for the `setscale d` operation.
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strconstant kDataDimLabel = "data"
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/// List of preferred datasets to load for preview
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strconstant kPreviewDatasets = "ScientaImage;ScientaSpectrum;ImageAngleDistribution;ImageEnergyDistribution;Counts;SampleCurrent;"
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/// List of datasets that must be loaded to determine the axis scaling of a Scienta image
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strconstant kScientaScalingDatasets = "LensMode;ScientaChannelBegin;ScientaChannelEnd;ScientaSliceBegin;ScientaSliceEnd;"
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/// List of datasets that should be transposed upon loading
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strconstant kTransposedDatasets = "ScientaImage;"
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/// open a HDF5 file created by the PShell data acquisition program and prepare the data folder.
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///
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/// the function opens a specified or interactively selected HDF5 file,
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@ -301,21 +310,25 @@ function /s psh5_load_preview(ANickName, APathName, AFileName, [load_data, load_
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endif
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sg = StringFromList(ig, scanpaths)
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dataname = psh5_load_scan_preview(fileID, sg, set_scale=load_attr, pref_datasets=pref_datasets)
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endif
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wave /z data = $dataname
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string destpath = GetDataFolder(1, saveDF) + ANickName
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if (waveexists(data))
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duplicate /o data, $destpath
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wave /z data = $destpath
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endif
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if (load_attr)
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setdatafolder saveDF
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newdatafolder /o/s attr
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killwaves /a/z
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psh5_load_scan_attrs(fileID, sg)
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setdatafolder ::
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wave /z data = $dataname
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string destpath = GetDataFolder(1, saveDF) + ANickName
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if (waveexists(data))
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duplicate /o data, $destpath
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wave /z data = $destpath
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else
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print "no data found in file " + AFileName
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endif
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if (load_attr)
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setdatafolder saveDF
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newdatafolder /o/s attr
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killwaves /a/z
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psh5_load_scan_attrs(fileID, sg)
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setdatafolder ::
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endif
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else
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print "no scans found in file " + AFileName
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endif
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HDF5CloseFile fileID
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@ -510,17 +523,21 @@ function /s psh5_load_scan_attrs(fileID, scanpath, [attr_sets])
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endif
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endif
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variable ids
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variable nds
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string sds
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if (attr_sets & 2)
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attr_list = AddListItem("LensMode", attr_list, ";", inf)
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attr_list = AddListItem("ScientaChannelBegin", attr_list, ";", inf)
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attr_list = AddListItem("ScientaChannelEnd", attr_list, ";", inf)
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attr_list = AddListItem("ScientaSliceBegin", attr_list, ";", inf)
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attr_list = AddListItem("ScientaSliceEnd", attr_list, ";", inf)
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nds = ItemsInList(kScientaScalingDatasets, ";")
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for (ids = 0; ids < nds; ids += 1)
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sds = StringFromList(ids, kScientaScalingDatasets)
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if (WhichListItem(sds, attr_list) < 0)
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attr_list = AddListItem(sds, attr_list, ";", inf)
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endif
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endfor
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endif
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variable ids
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variable nds = ItemsInList(attr_list, ";")
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string sds
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nds = ItemsInList(attr_list, ";")
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string wavenames = ""
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for (ids = 0; ids < nds; ids += 1)
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sds = StringFromList(ids, attr_list, ";")
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@ -529,6 +546,7 @@ function /s psh5_load_scan_attrs(fileID, scanpath, [attr_sets])
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wavenames = AddListItem(s_wavenames, wavenames, ";", inf)
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endif
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endfor
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wavenames = ReplaceString(";;", wavenames, ";")
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return wavenames
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end
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@ -695,7 +713,7 @@ function /s psh5_load_scan_preview(fileID, scanpath, [set_scale, pref_datasets])
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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 = "ScientaImage;ScientaSpectrum;ImageAngleDistribution;ImageEnergyDistribution;Counts;SampleCurrent"
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pref_datasets = kPreviewDatasets
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endif
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dfref saveDF = GetDataFolderDFR()
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@ -880,9 +898,6 @@ end
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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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/// @todo images are transposed in the first two dimensions.
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/// this is useful for Scienta images but may not be appropriate for other sources.
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///
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function /s psh5_load_dataset_slabs(fileID, datapath, datasetname, [progress])
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variable fileID
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string datapath
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@ -910,11 +925,19 @@ function /s psh5_load_dataset_slabs(fileID, datapath, datasetname, [progress])
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if (di.ndims < 2)
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print "error: rank of dataset < 2"
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return ""
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elseif (di.ndims < 3)
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progress = 0
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endif
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variable idx, idy, idz, idt, izt
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idx = 1
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idy = 0
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variable transpose = WhichListItem(datawavename, 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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@ -951,7 +974,11 @@ function /s psh5_load_dataset_slabs(fileID, datapath, datasetname, [progress])
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slab[idt][%Start] = it
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HDF5LoadData /O /Q /Z /SLAB=slab /N=slabdata fileID, datasetpath
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wave slabdata // 2D, 3D, or 4D with singletons
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data[][][iz][it] = slabdata[q][p][0][0]
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if (transpose)
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data[][][iz][it] = slabdata[q][p][0][0]
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else
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data[][][iz][it] = slabdata[p][q][0][0]
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endif
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// progress window
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izt += 1
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@ -1007,9 +1034,6 @@ end
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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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/// @todo images are transposed in the first two dimensions.
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/// this is useful for Scienta images but may not be appropriate for other data sources.
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///
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function /s psh5_load_dataset_slab(fileID, datapath, datasetname, dim2start, dim2count, dim3start, dim3count)
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variable fileID
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string datapath
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@ -1038,8 +1062,14 @@ function /s psh5_load_dataset_slab(fileID, datapath, datasetname, dim2start, dim
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endif
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variable idx, idy, idz, idt
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idx = 1
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idy = 0
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variable transpose = WhichListItem(datawavename, 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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@ -1070,7 +1100,11 @@ function /s psh5_load_dataset_slab(fileID, datapath, datasetname, dim2start, dim
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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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data += slabdata[q][p][0][0]
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if (transpose)
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data += slabdata[q][p][0][0]
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else
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data += slabdata[p][q][0][0]
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endif
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navg += 1
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endif
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endfor
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@ -1570,11 +1604,19 @@ function /s psh5_load_dataset_reduced(fileID, scanpath, datasetname, reduction_f
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print "error: rank of dataset < 2"
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result = -2
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return wavenames
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elseif (di.ndims < 3)
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progress = 0
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endif
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variable idx, idy, idz, idt
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idx = 1
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idy = 0
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variable transpose = WhichListItem(datawavename, 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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