code changes for release 2.2.0
This commit is contained in:
@ -1,12 +1,14 @@
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#pragma TextEncoding = "UTF-8"
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#pragma rtGlobals=3 // Use modern global access method and strict wave access.
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#pragma IgorVersion = 6.36
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#pragma ModuleName = PearlPShellImport
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#pragma version = 1.11
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#include <HDF5 Browser>
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#include "pearl-compat"
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#include "pearl-gui-tools"
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#include "pearl-area-import"
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// copyright (c) 2013-18 Paul Scherrer Institut
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// copyright (c) 2013-21 Paul Scherrer Institut
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//
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// Licensed under the Apache License, Version 2.0 (the "License");
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// you may not use this file except in compliance with the License.
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@ -50,7 +52,7 @@
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///
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/// @author matthias muntwiler, matthias.muntwiler@psi.ch
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///
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/// @copyright 2013-18 Paul Scherrer Institut @n
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/// @copyright 2013-21 Paul Scherrer Institut @n
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/// Licensed under the Apache License, Version 2.0 (the "License"); @n
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/// you may not use this file except in compliance with the License. @n
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/// You may obtain a copy of the License at
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@ -75,7 +77,7 @@ strconstant kScanDimLabel = "scan"
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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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strconstant kPreviewDatasets = "ImageEnergyDistribution;ScientaSpectrum;ScientaImage;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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@ -336,6 +338,81 @@ function /s psh5_load_preview(APathName, AFileName, [load_data, load_attr, pref_
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return dataname
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end
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/// load organizational metadata from the general group.
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///
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/// the general group contains the following datasets:
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/// authors, pgroup, proposal, proposer, sample.
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///
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/// data is loaded into the current data folder.
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/// all items are loaded into strings, authors is a comma-separated list.
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/// missing items default to empty strings.
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///
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/// @param APathName igor symbolic path name. can be empty if the path is specified in FileName or a dialog box should be displayed
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///
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/// @param AFileName if empty a dialog box shows up
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///
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/// @return semicolon-separated list of the objects.
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///
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function /s psh5_load_general_group(APathName, AFileName)
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string APathName
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string AFileName
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variable fileID
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HDF5OpenFile /P=$APathName /R /Z fileID as AFileName
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if (v_flag == 0)
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string obj_names = "authors;pgroup;proposal;proposer;sample;"
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variable nn = ItemsInList(obj_names, ";")
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variable ii
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string name
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for (ii = 0; ii < nn; ii += 1)
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name = StringFromList(ii, obj_names, ";")
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psh_load_general_string(fileID, name)
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endfor
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return obj_names
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else
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return ""
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endif
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end
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/// load a string from the general group.
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///
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/// the general group contains the following datasets:
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/// authors, pgroup, proposal, proposer, sample.
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///
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/// data is loaded into a global string in the current data folder.
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/// arrays with multiple items are loaded into a comma-separated list.
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/// a missing item defaults to the empty string.
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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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/// @return comma-separated list of values.
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///
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function /s psh_load_general_string(fileID, name)
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variable fileID
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string name
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string path = "/general/" + name
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HDF5LoadData /O /Q /Z /N=wt_load_general /TYPE=1 fileID, path
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string values = ""
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if (!v_flag)
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wave /t wt_load_general
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variable nn = numpnts(wt_load_general)
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variable ii
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for (ii = 0; ii < nn; ii += 1)
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values = AddListItem(wt_load_general[ii], values, ",", inf)
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endfor
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killwaves /z wt_load_general
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if (strlen(values) >= 1)
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values = values[0,strlen(values)-2]
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endif
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endif
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string /g $name = values
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return values
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end
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/// load all data of a selected scan from a PShell data file.
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///
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/// data is loaded into the current data folder.
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@ -1667,13 +1744,13 @@ function ps_detect_scale(ax, lo, hi, un)
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case "Angular45":
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lo[%$kAngleDimLabel] = -45/2
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hi[%$kAngleDimLabel] = +45/2
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un[%$kAngleDimLabel] = "<EFBFBD>"
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un[%$kAngleDimLabel] = "°"
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ax[%$kAngleDimLabel] = "angle"
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break
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case "Angular60":
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lo[%$kAngleDimLabel] = -60/2
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hi[%$kAngleDimLabel] = +60/2
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un[%$kAngleDimLabel] = "<EFBFBD>"
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un[%$kAngleDimLabel] = "°"
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ax[%$kAngleDimLabel] = "angle"
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break
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case "Transmission":
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@ -1719,12 +1796,12 @@ function ps_detect_scale(ax, lo, hi, un)
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un[%$kScanDimLabel] = "mm"
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break
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case "ExitSlit":
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un[%$kScanDimLabel] = "<EFBFBD>m"
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un[%$kScanDimLabel] = "µm"
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break
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case "ManipulatorTheta":
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case "ManipulatorTilt":
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case "ManipulatorPhi":
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un[%$kScanDimLabel] = "<EFBFBD>"
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un[%$kScanDimLabel] = "°"
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break
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case "FocusXRot":
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case "FocusYRot":
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@ -1890,6 +1967,11 @@ end
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///
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/// @param reduction_param parameter string for the reduction function.
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///
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/// @param dataset name of dataset to load, optionally including group path relative to scan (scan 1).
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/// by default, the function looks for a ScientaImage dataset.
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/// in a multi-region scan, this will be region 1.
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/// to select region 2, e.g., use `dataset="region2/ScientaImage"`.
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///
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/// @param progress progress window.
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/// @arg 1 (default) show progress window
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/// @arg 0 do not show progress window
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@ -1908,12 +1990,13 @@ end
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///
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/// @return global string s_scanpaths in new data folder contains a list of scan groups inside the file.
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///
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function /s psh5_load_reduced(ANickName, APathName, AFileName, reduction_func, reduction_param, [progress, nthreads])
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function /s psh5_load_reduced(ANickName, APathName, AFileName, reduction_func, reduction_param, [dataset, progress, nthreads])
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string ANickName
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string APathName
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string AFileName
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funcref adh5_default_reduction reduction_func
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string reduction_param
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string dataset
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variable progress
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variable nthreads
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@ -1972,7 +2055,9 @@ function /s psh5_load_reduced(ANickName, APathName, AFileName, reduction_func, r
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setdatafolder dataDF
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string datasets = psh5_list_scan_datasets(fileID, scanpath, include_regions=1)
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string dataset = select_dataset(datasets, "ScientaImage")
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if (ParamIsDefault(dataset))
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dataset = select_dataset(datasets, "ScientaImage")
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endif
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wavenames = psh5_load_dataset_reduced(fileID, scanpath, dataset, reduction_func, reduction_param, progress=progress, nthreads=nthreads)
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psh5_close_file(fileID)
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@ -2503,3 +2588,48 @@ static function /s wave2list(w, format, sep)
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return list
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end
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/// kill any waves matching a pattern in the experiment
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///
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/// this may be used to kill big waves of original data before saving
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///
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function /s kill_matching_waves(dfr, pattern, recurse, [killed])
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DFREF dfr
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string pattern
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variable recurse
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string killed
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if (ParamIsDefault(killed))
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killed = ""
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endif
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string s
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string r
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variable index = 0
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do
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Wave/Z w = WaveRefIndexedDFR(dfr, index)
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if (!WaveExists(w))
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break
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endif
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s = NameOfWave(w)
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if (stringmatch(s, pattern))
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killwaves /z w
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killed = AddListItem(s, killed, ";", Inf)
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endif
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index += 1
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while(1)
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if (recurse)
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Variable numChildDataFolders = CountObjectsDFR(dfr, 4)
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Variable i
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for(i=0; i<numChildDataFolders; i+=1)
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String childDFName = GetIndexedObjNameDFR(dfr, 4, i)
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DFREF childDFR = dfr:$childDFName
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killed = kill_matching_waves(childDFR, pattern, 1, killed=killed)
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endfor
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endif
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return killed
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End
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