new features: data reduction, angle scan panel
- new data reduction interface for more efficient multi-peak fitting. the new interface breaks compatibility with pre-2.0 data reduction functions. user-defined functions must be adapted to the new interface. - new angle scan processing panel for interactive data analysis.
This commit is contained in:
@ -1,12 +1,11 @@
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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 = 1.03
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#include <HDF5 Browser>
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#include "pearl-gui-tools"
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#include "pearl-area-import"
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// copyright (c) 2013-16 Paul Scherrer Institut
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// copyright (c) 2013-18 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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@ -47,6 +46,14 @@
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/// - psh5_list_scan_datasets()
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/// - psh5_load_scan_meta()
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/// - psh5_load_scan_attrs()
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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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/// 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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/// http://www.apache.org/licenses/LICENSE-2.0
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/// @namespace PearlPShellImport
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/// @brief import data from PShell
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@ -1728,6 +1735,12 @@ end
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/// @arg `lo[%%scan]` scan dimension.
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/// @arg `lo[%%data]` data dimension.
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///
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/// if the data dimension labels and units are at their defaults ("value" and "arb.", respectively),
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/// the function tries to read them from the existing wave note ("AxisLabelD" and "AxisUnitD"),
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/// or based on the wave name if the name is one of the known measurement variables:
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/// "ScientaImage", "ImageAngleDistribution", "ScientaAngleDistribution", "ScientaSpectrum", "ImageEnergyDistribution", "ScientaEnergyDistribution",
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/// "SampleCurrent", "RefCurrent", "AuxCurrent", "MachineCurrent".
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///
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/// @param data data wave to be scaled.
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/// dimension labels (index -1) must be set to match the limit waves.
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///
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@ -1754,28 +1767,45 @@ function ps_scale_dataset_2(data, ax, lo, hi, un)
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wave hi
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wave /t un
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string snote = note(data)
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string sdim
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sdim = GetDimLabel(data, 0, -1)
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if (strlen(sdim))
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setscale /i x lo[%$sdim], hi[%$sdim], un[%$sdim], data
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Note data, "AxisLabelX=" + ax[%$sdim]
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snote = ReplaceStringByKey("AxisLabelX", snote, ax[%$sdim], "=", "\r")
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endif
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sdim = GetDimLabel(data, 1, -1)
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if (strlen(sdim))
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setscale /i y lo[%$sdim], hi[%$sdim], un[%$sdim], data
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Note data, "AxisLabelY=" + ax[%$sdim]
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snote = ReplaceStringByKey("AxisLabelY", snote, ax[%$sdim], "=", "\r")
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endif
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sdim = GetDimLabel(data, 2, -1)
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if (strlen(sdim))
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setscale /i z lo[%$sdim], hi[%$sdim], un[%$sdim], data
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Note data, "AxisLabelZ=" + ax[%$sdim]
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snote = ReplaceStringByKey("AxisLabelZ", snote, ax[%$sdim], "=", "\r")
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endif
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string data_unit = un[%$kDataDimLabel]
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string data_label = ax[%$kDataDimLabel]
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if (cmpstr(data_unit, "arb.") == 0)
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string s
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variable def = (cmpstr(data_unit, "arb.") == 0) && (cmpstr(data_label, "value") == 0)
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if (def)
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s = StringByKey("AxisLabelD", snote, "=", "\r")
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if (strlen(s) > 0)
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data_label = s
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def = 0
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endif
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s = StringByKey("AxisUnitD", snote, "=", "\r")
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if (strlen(s) > 0)
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data_unit = s
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def = 0
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endif
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endif
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if (def)
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strswitch(NameOfWave(data))
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case "ScientaImage":
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case "ImageAngleDistribution":
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@ -1786,28 +1816,35 @@ function ps_scale_dataset_2(data, ax, lo, hi, un)
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data *= kDetectorSensitivity
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data_unit = "counts"
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data_label = "intensity"
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def = 0
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break
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case "SampleCurrent":
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case "RefCurrent":
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case "AuxCurrent":
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data_unit = "A"
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data_label = "current"
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def = 0
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break
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case "MachineCurrent":
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data_unit = "mA"
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data_label = "current"
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def = 0
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break
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endswitch
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endif
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setscale d 0, 0, data_unit, data
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Note data, "AxisLabelD=" + data_label
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Note data, "Dataset=" + NameOfWave(data)
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snote = ReplaceStringByKey("AxisLabelD", snote, data_label, "=", "\r")
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snote = ReplaceStringByKey("AxisUnitD", snote, data_unit, "=", "\r")
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snote = ReplaceStringByKey("Dataset", snote, NameOfWave(data), "=", "\r")
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note /k data, snote
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end
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/// load and reduce the ScientaImage dataset of the first scan of a PShell data file.
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///
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/// the resulting dataset is reduced in one image dimension by a user-defined reduction function,
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/// e.g. by region-of-interest integration, curve fitting, etc.
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/// cf. @ref adh5_default_reduction for further details.
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///
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/// the function loads the dataset image by image using the hyperslab option
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/// and applies a custom reduction function to each image.
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@ -1817,14 +1854,21 @@ end
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/// if the data is from the electron analyser driver and some special attributes are included,
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/// the function will set the scales of the image dimensions.
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///
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/// by default, the reduction function is called in separate threads to reduce the total loading time.
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/// (see the global variable psh5_perf_secs which reports the total run time of the function.)
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/// the effect varies depending on the balance between file loading (image size)
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/// and data processing (complexity of the reduction function).
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/// for debugging the reduction function, multi-threading can be disabled.
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///
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/// @param ANickName destination folder name (top level under root).
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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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/// @param reduction_func custom reduction function
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/// (any user-defined function which has the same parameters as adh5_default_reduction())
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/// @param reduction_func custom data reduction function.
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/// this can be any user-defined function which has the same parameters as @ref adh5_default_reduction.
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/// some reduction functions are predefined in the @ref PearlScientaPreprocess module.
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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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@ -1832,8 +1876,13 @@ end
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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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///
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/// @return semicolon-separated list of the loaded waves,
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/// `ReducedData1` and `ReducedData2` if successful.
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/// @param nthreads
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/// @arg -1 (default) use as many threads as there are processor cores (in addition to main thread).
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/// @arg 0 use main thread only (for debugging and profiling).
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/// @arg >= 1 use a fixed number of (additional) threads.
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///
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/// @return semicolon-separated list of the loaded dataset `ReducedData1`, `ReducedData2`, etc. if successful.
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/// auxiliary waves, scan positions, attributes are loaded but not listed in the string.
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/// empty string if an error occurred.
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/// error messages are printed to the history.
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///
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@ -1841,20 +1890,22 @@ 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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/// @todo load scan positions.
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///
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function /s psh5_load_reduced(ANickName, APathName, AFileName, reduction_func, reduction_param, [progress])
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function /s psh5_load_reduced(ANickName, APathName, AFileName, reduction_func, reduction_param, [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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variable progress
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variable nthreads
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if (ParamIsDefault(progress))
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progress = 1
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endif
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if (ParamIsDefault(nthreads))
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nthreads = -1
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endif
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dfref saveDF = GetDataFolderDFR()
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// performance monitoring
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@ -1904,7 +1955,7 @@ 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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wavenames = psh5_load_dataset_reduced(fileID, scanpath, dataset, reduction_func, reduction_param, progress=progress)
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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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endif
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@ -1922,7 +1973,7 @@ end
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///
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/// the function loads the dataset image by image using the hyperslab option
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/// and applies a custom reduction function to each image.
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/// the results from the reduction function are written to the `ReducedData1` and `ReducedData2` waves.
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/// the results from the reduction function are written to the `ReducedData1`, `ReducedData2`, etc. waves.
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/// the raw data are discarded.
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///
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/// by default, the reduction function is called in separate threads to reduce the total loading time.
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@ -1946,8 +1997,9 @@ end
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/// the name can include the region name as a relative path, e.g. "region1/ScientaImage".
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/// in this case, the dataset is loaded into a sub-folder named "region1".
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///
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/// @param reduction_func custom reduction function
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/// (any user-defined function which has the same parameters as adh5_default_reduction()).
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/// @param reduction_func custom data reduction function.
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/// this can be any user-defined function which has the same parameters as @ref adh5_default_reduction.
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/// some reduction functions are predefined in the @ref PearlScientaPreprocess module.
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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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@ -1957,11 +2009,11 @@ end
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///
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/// @param nthreads
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/// @arg -1 (default) use as many threads as there are processor cores (in addition to main thread).
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/// @arg 0 use main thread only (e.g. for debugging the reduction function).
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/// @arg 0 use main thread only (for debugging and profiling).
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/// @arg >= 1 use a fixed number of (additional) threads.
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///
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/// @return semicolon-separated list of the loaded waves,
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/// `ReducedData1` and `ReducedData2` if successful.
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/// @return semicolon-separated list of the loaded dataset `ReducedData1`, `ReducedData2`, etc. if successful.
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/// auxiliary waves, scan positions, attributes are loaded but not listed in the string.
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/// empty string if an error occurred.
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/// error messages are printed to the history.
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///
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@ -2079,6 +2131,10 @@ function /s psh5_load_dataset_reduced(fileID, scanpath, datasetname, reduction_f
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variable iz, it, izt
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string dfname
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variable iw, nw
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string sw
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make /n=0 /free /wave result_waves
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izt = 0
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for (iz = 0; iz < nz; iz += 1)
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for (it = 0; it < nt; it += 1)
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@ -2102,9 +2158,10 @@ function /s psh5_load_dataset_reduced(fileID, scanpath, datasetname, reduction_f
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processing_folders[izt] = GetDataFolderDFR()
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make /n=1/d profile1, profile2
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wave slabdata
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variable /g func_result
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func_result = reduce_slab_image(slabdata, image, profile1, profile2, reduction_func, func_param)
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WaveClear slabdata, image, profile1, profile2
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wave /wave reduced_waves = reduce_slab_image(slabdata, image, reduction_func, func_param)
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variable /g func_result = numpnts(reduced_waves)
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adh5_get_result_waves(reduced_waves, "redw_", 0)
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WaveClear slabdata, image, reduced_waves
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setdatafolder ::
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endif
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@ -2159,31 +2216,36 @@ function /s psh5_load_dataset_reduced(fileID, scanpath, datasetname, reduction_f
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nvar rr = dfr:r_index
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nvar ss = dfr:s_index
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nvar func_result = dfr:func_result
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wave profile1 = dfr:profile1
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wave profile2 = dfr:profile2
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if (func_result == 0)
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if (izt == 0)
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make /n=(dimsize(profile1, 0), nz, nt) /d /o ReducedData1
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make /n=(dimsize(profile2, 0), nz, nt) /d /o ReducedData2
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setdimlabel 0, -1, $getdimlabel(profile1, 0, -1), ReducedData1
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setdimlabel 0, -1, $getdimlabel(profile2, 0, -1), ReducedData2
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setdimlabel 1, -1, $kScanDimLabel, ReducedData1
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setdimlabel 1, -1, $kScanDimLabel, ReducedData2
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ps_scale_dataset(ReducedData1)
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ps_scale_dataset(ReducedData2)
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setscale /p x dimoffset(profile1, 0), dimdelta(profile1, 0), waveunits(profile1, 0), ReducedData1
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setscale /p x dimoffset(profile2, 0), dimdelta(profile2, 0), waveunits(profile2, 0), ReducedData2
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setscale d 0, 0, waveunits(profile1, -1), ReducedData1
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setscale d 0, 0, waveunits(profile2, -1), ReducedData2
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endif
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ReducedData1[][rr][ss] = profile1[p]
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ReducedData2[][rr][ss] = profile2[p]
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else
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if (func_result < 1)
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print "error during data reduction."
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result = -3
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break
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endif
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if (numpnts(result_waves) == 0)
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redimension /n=(func_result) result_waves
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for (iw = 0; iw < func_result; iw += 1)
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sw = "redw_" + num2str(iw)
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wave profile = dfr:$sw
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sw = "ReducedData" + num2str(iw+1)
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make /n=(dimsize(profile, 0), nz, nt) /d /o $sw
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wave data = $sw
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setdimlabel 0, -1, $getdimlabel(profile, 0, -1), data
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setdimlabel 1, -1, $kScanDimLabel, data
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note data, note(profile)
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ps_scale_dataset(data)
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setscale /p x dimoffset(profile, 0), dimdelta(profile, 0), waveunits(profile, 0), data
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setscale d 0, 0, waveunits(profile, -1), data
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result_waves[iw] = data
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endfor
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endif
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for (iw = 0; iw < func_result; iw += 1)
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sw = "redw_" + num2str(iw)
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wave profile = dfr:$sw
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wave data = result_waves[iw]
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data[][rr][ss] = profile[p]
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endfor
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endfor
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if (nthreads > 0)
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@ -2199,14 +2261,17 @@ function /s psh5_load_dataset_reduced(fileID, scanpath, datasetname, reduction_f
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endif
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if (result == 0)
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if (nz == 1)
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redimension /n=(-1, 0, 0) ReducedData1
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redimension /n=(-1, 0, 0) ReducedData2
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elseif (nt == 1)
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redimension /n=(-1, nz, 0) ReducedData1
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redimension /n=(-1, nz, 0) ReducedData2
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endif
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wavenames = "ReducedData1;ReducedData2;"
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nw = numpnts(result_waves)
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wavenames = ""
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for (iw = 0; iw < nw; iw += 1)
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wave data = result_waves[iw]
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if (nz == 1)
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redimension /n=(-1, 0, 0) data
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elseif (nt == 1)
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redimension /n=(-1, nz, 0) data
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endif
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wavenames += nameofwave(data) + ";"
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endfor
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endif
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if (progress)
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kill_progress_panel()
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@ -2240,14 +2305,14 @@ threadsafe static function reduce_slab_worker(reduction_func)
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// do the work
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newdatafolder /s outDF
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make /n=1/d profile1, profile2
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variable /g r_index = rr
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variable /g s_index = ss
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variable /g func_result
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func_result = reduce_slab_image(slabdata, image, profile1, profile2, reduction_func, func_param)
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wave /wave reduced_waves = reduce_slab_image(slabdata, image, reduction_func, func_param)
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variable /g func_result = numpnts(reduced_waves)
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// send output to queue and clean up
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WaveClear slabdata, image, profile1, profile2
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adh5_get_result_waves(reduced_waves, "redw_", 0)
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WaveClear slabdata, image, reduced_waves
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ThreadGroupPutDF 0, :
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KillDataFolder dfr
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while (1)
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@ -2255,18 +2320,16 @@ threadsafe static function reduce_slab_worker(reduction_func)
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return 0
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end
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threadsafe static function reduce_slab_image(slabdata, image, profile1, profile2, reduction_func, reduction_param)
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threadsafe static function /wave reduce_slab_image(slabdata, image, reduction_func, reduction_param)
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wave slabdata
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wave image
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wave profile1
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wave profile2
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funcref adh5_default_reduction reduction_func
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string reduction_param
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// the multiplication by detector sensitivity assumes that we are loading a ScientaImage.
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image = slabdata[q][p][0][0] * kDetectorSensitivity
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return reduction_func(image, profile1, profile2, reduction_param)
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return reduction_func(image, reduction_param)
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end
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/// load descriptive info from a PShell data file.
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