updates: scaling of pshell data, matrix preview, elog panel
- elog panel supports multiple attachments - matrix (omicron STM) data file preview in data explorer - various improvements for the scaling of pshell data
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@ -1,11 +1,14 @@
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#pragma rtGlobals=3 // Use modern global access method and strict wave access.
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#pragma IgorVersion = 6.1
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#pragma ModuleName = PearlDataExplorer
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#pragma version = 1.43
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#pragma version = 1.50
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#include "pearl-area-import"
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#include "pearl-area-profiles"
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#include "pearl-area-display"
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#include "pearl-pshell-import"
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#if exists("MFR_OpenResultFile")
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#include "pearl-matrix-import"
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#endif
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// copyright (c) 2013-16 Paul Scherrer Institut
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//
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@ -20,7 +23,10 @@
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///
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///
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/// preview and import panel for PEARL data:
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/// scienta analyser, prosilica cameras, s-scans, otf-scans
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/// @arg area detector (HDF5) files from scienta analyser and prosilica cameras (if HDF5.xop is installed).
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/// @arg igor text files from s-scans and otf-scans.
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/// @arg pshell (HDF5) data files (if HDF5.xop is installed).
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/// @arg matrix STM files (if MatrixFileReader.xop is installed).
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/// @namespace PearlDataExplorer
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/// @brief preview and import panel for PEARL data
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@ -33,6 +39,7 @@ static strconstant package_path = "root:packages:pearl_explorer:"
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static strconstant ks_filematch_adh5 = "*.h5"
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static strconstant ks_filematch_pshell = "psh*.h5"
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static strconstant ks_filematch_itx = "*.itx"
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static strconstant ks_filematch_mtrx = "*_mtrx"
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function pearl_data_explorer()
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init_package()
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@ -140,31 +147,64 @@ static function load_prefs()
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return result
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end
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/// check whether a file can be imported by this module.
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///
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/// the file type is determined by the extension of the file name.
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///
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/// @return file type
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/// @arg 0 not a recognized file type
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/// @arg 1 PShell file (HDF5, name starts with psh_)
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/// @arg 2 area detector HDF5 file
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/// @arg 3 Igor text (itx) file
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/// @arg 4 Matrix STM file (*_mtrx)
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///
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static function pearl_file_type(filename)
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string filename
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if (StringMatch(filename, ks_filematch_pshell))
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return 1
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elseif (StringMatch(filename, ks_filematch_adh5))
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return 2
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elseif (StringMatch(filename, ks_filematch_itx))
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return 3
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#if exists("MFR_OpenResultFile")
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elseif (StringMatch(filename, ks_filematch_mtrx))
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return 4
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#endif
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else
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return 0
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endif
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end
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/// read a list of PEARL files from the file system
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///
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/// wtFiles and wSelectedFiles in the package data folder are updated.
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/// only files for which pearl_file_type() returns non-zero are listed.
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///
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static function update_filelist()
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dfref saveDF = GetDataFolderDFR()
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string hdf_files, itx_files, all_files
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string all_files
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wave /t wtFiles = $(package_path + "wtFiles")
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wave wSelectedFiles = $(package_path + "wSelectedFiles")
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variable nn
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PathInfo pearl_explorer_filepath
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if (v_flag == 1)
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hdf_files = IndexedFile(pearl_explorer_filepath, -1, ".h5")
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itx_files = IndexedFile(pearl_explorer_filepath, -1, ".itx")
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all_files = hdf_files + itx_files
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all_files = SortList(hdf_files + itx_files, ";", 4)
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all_files = IndexedFile(pearl_explorer_filepath, -1, "????")
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nn = ItemsInList(all_files)
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else
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all_files = ""
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nn = 0
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endif
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redimension /n=(nn) wtFiles, wSelectedFiles
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if (nn > 0)
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wtFiles = StringFromList(p, all_files)
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wSelectedFiles = 0
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endif
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make /n=(nn) /t /free wtAllFiles
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wtAllFiles = StringFromList(p, all_files)
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Extract /o /t wtAllFiles, wtFiles, pearl_file_type(wtAllFiles[p])
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Sort /A /R wtFiles, wtFiles
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redimension /n=(numpnts(wtFiles)) wSelectedFiles
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wSelectedFiles = 0
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setdatafolder saveDF
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end
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@ -216,14 +256,24 @@ static function preview_file(filename)
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string filename
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dfref saveDF = GetDataFolderDFR()
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if (StringMatch(filename, ks_filematch_pshell))
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wave /z image = preview_pshell_file(filename)
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elseif (StringMatch(filename, ks_filematch_adh5))
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wave /z image = preview_hdf_file(filename)
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elseif (StringMatch(filename, ks_filematch_itx))
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wave /z image = preview_itx_file(filename)
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endif
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variable ft = pearl_file_type(filename)
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switch(ft)
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case 1:
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wave /z image = preview_pshell_file(filename)
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break
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case 2:
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wave /z image = preview_hdf_file(filename)
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break
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case 3:
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wave /z image = preview_itx_file(filename)
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break
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case 4:
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wave /z image = preview_mtrx_file(filename)
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break
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default:
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wave /z image = $""
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endswitch
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if (WaveExists(image))
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string graphname = show_preview_graph(image)
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@ -240,9 +290,10 @@ static function preview_file(filename)
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endif
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setdatafolder saveDF
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return 0
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end
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/// load the preview of a PShell HDF5 file (not implemented).
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/// load the preview of a PShell HDF5 file.
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///
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/// the preview is an arbitrary detector image extracted from the file, see adh5_load_preview().
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/// the preview is loaded to the preview_image wave in the pear_explorer data folder.
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@ -354,6 +405,63 @@ static function /wave preview_itx_file(filename)
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return preview_image
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end
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/// load the preview of a Matrix STM file.
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///
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/// the preview is loaded to the preview_image wave in the pearl_explorer data folder.
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///
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/// the s_file_info string is updated with information about the scan dimensions.
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///
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/// this function requires the MatrixFileReader.xop and pearl-matrix-import.ipf to be loaded.
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/// otherwise it will return an empty wave reference.
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///
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/// @param filename name of a file in the directory specified by the pearl_explorer_filepath path object.
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///
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/// @return wave reference of the preview image.
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/// empty wave reference if the function failed.
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///
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static function /wave preview_mtrx_file(filename)
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string filename
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#if exists("MFR_OpenResultFile")
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dfref saveDF = GetDataFolderDFR()
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setdatafolder $package_path
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variable /g V_MatrixFileReaderOverwrite = 1
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variable /g V_MatrixFileReaderFolder = 0
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variable /g V_MatrixFileReaderDouble = 0
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svar s_preview_file
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svar s_preview_source
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string datanames
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string dataname
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datanames = mtrx_load_preview("preview", "pearl_explorer_filepath", filename)
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if (strlen(datanames) > 0)
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s_preview_file = filename
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dataname = StringFromList(0, datanames)
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wave data = $dataname
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duplicate /o $dataname, preview_image
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s_preview_source = StringByKey("Dataset", note(data), "=", "\r")
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svar /z s_file_info
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if (svar_exists(s_file_info))
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s_file_info = ""
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endif
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variable i
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variable n = ItemsInList(datanames)
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string s
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for (i = 0; i < n; i += 1)
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s = StringFromList(i, datanames)
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killwaves /z $s
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endfor
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endif
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wave /z preview_image
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setdatafolder saveDF
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#else
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wave /z preview_image = $""
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#endif
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return preview_image
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end
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static function extract_preview_image(data, preview)
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// extracts a preview image from a wave of arbitrary dimension
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wave data
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@ -862,22 +970,32 @@ static function load_file(filename, [options])
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dfref saveDF = GetDataFolderDFR()
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if (StringMatch(filename, ks_filematch_pshell))
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if (ParamIsDefault(options))
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load_pshell_file(filename)
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else
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load_pshell_file(filename, options=options)
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endif
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elseif (StringMatch(filename, ks_filematch_adh5))
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if (ParamIsDefault(options))
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load_hdf_file(filename)
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else
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load_hdf_file(filename, options=options)
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endif
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elseif (StringMatch(filename, ks_filematch_itx))
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load_itx_file(filename)
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endif
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variable ft = pearl_file_type(filename)
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switch(ft)
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case 1:
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if (ParamIsDefault(options))
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load_pshell_file(filename)
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else
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load_pshell_file(filename, options=options)
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endif
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break
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case 2:
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if (ParamIsDefault(options))
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load_hdf_file(filename)
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else
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load_hdf_file(filename, options=options)
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endif
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break
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case 3:
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load_itx_file(filename)
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break
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case 4:
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load_mtrx_file(filename)
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break
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default:
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break
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endswitch
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setdatafolder saveDF
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end
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@ -1080,6 +1198,32 @@ static function /df load_itx_file(filename, [options])
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return actDF
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end
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/// load a matrix (STM) data file
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///
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///
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static function /df load_mtrx_file(filename, [options])
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string filename
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string options
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dfref saveDF = GetDataFolderDFR()
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dfref dataDF = $""
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#if exists("MFR_OpenResultFile")
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setdatafolder root:
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string datasets = ""
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datasets = mtrx_load_file("pearl_explorer_filepath", filename)
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if (strlen(datasets) > 0)
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string /g pearl_explorer_import = "load_mtrx_file"
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string s1 = StringFromList(0, datasets)
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wave w1 = $s1
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dataDF = GetWavesDataFolderDFR(w1)
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endif
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#endif
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setdatafolder saveDF
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return dataDF
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end
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function /s itx_suggest_foldername(filename, [ignoredate,sourcename,unique])
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// suggests the name of a data folder based on a file name
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// if the file name follows the naming convention source-date-index.extension,
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