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:
@ -1,11 +1,10 @@
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#pragma rtGlobals=3 // Use modern global access method and strict wave access.
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#pragma IgorVersion = 6.2
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#pragma ModuleName = PearlAreaImport
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#pragma version = 1.06
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#include <HDF5 Browser>
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#include "pearl-gui-tools"
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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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@ -23,6 +22,14 @@
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/// as of Igor 6.3, Igor can open datasets of up to rank 4.
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/// i.e. the extra dimension Y of the file plugin cannot be used.
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/// the extra dimensions N and X are supported.
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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 PearlAreaImport
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/// @brief HDF5 file import from EPICS area detectors
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@ -1031,7 +1038,7 @@ end
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/// it may thus include functions which are not suitable as reduction functions.
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///
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function /s adh5_list_reduction_funcs()
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string all_funcs = FunctionList("*", ";", "KIND:6,NPARAMS:4,VALTYPE:1")
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string all_funcs = FunctionList("*", ";", "KIND:6,NPARAMS:2,VALTYPE:8")
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string result = ""
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variable ii
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@ -1045,16 +1052,14 @@ function /s adh5_list_reduction_funcs()
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for (ii = 0; ii < nn; ii += 1)
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funcname = StringFromList(ii, all_funcs, ";")
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info = FunctionInfo(funcname)
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accept = (NumberByKey("RETURNTYPE", info, ":", ";") == 0x0004)
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accept = (NumberByKey("RETURNTYPE", info, ":", ";") == 0x4000)
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accept = accept && (cmpstr(StringByKey("THREADSAFE", info, ":", ";"), "yes") == 0)
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accept = accept && (NumberByKey("N_PARAMS", info, ":", ";") == 4)
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accept = accept && (NumberByKey("N_PARAMS", info, ":", ";") == 2)
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accept = accept && (NumberByKey("N_OPT_PARAMS", info, ":", ";") == 0)
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if (accept)
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// 3 numeric waves and one pass-by-reference string
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// one numeric wave and one pass-by-reference string
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accept = accept && (NumberByKey("PARAM_0_TYPE", info, ":", ";") == 0x4002)
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accept = accept && (NumberByKey("PARAM_1_TYPE", info, ":", ";") == 0x4002)
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accept = accept && (NumberByKey("PARAM_2_TYPE", info, ":", ";") == 0x4002)
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accept = accept && (NumberByKey("PARAM_3_TYPE", info, ":", ";") == 0x3000)
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accept = accept && (NumberByKey("PARAM_1_TYPE", info, ":", ";") == 0x3000)
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endif
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if (accept)
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result = AddListItem(funcname, result, ";")
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@ -1067,9 +1072,18 @@ end
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/// function prototype for adh5_load_reduced_detector
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///
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/// derived functions reduce a two-dimensional dataset to a one-dimensional dataset,
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/// e.g. by ROI-integration, curve fitting, etc.
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// the resulting wave must have the same size as either dimension of the source image.
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/// this is a prototype of custom functions that convert (reduce) a two-dimensional detector image
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/// into one or more one-dimensional waves.
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/// data processing can be tuned with a set of parameters.
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///
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/// reduction functions have a fixed signature (function arguments) so that the file import functions
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/// can call them efficiently on a series of detector images.
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/// pearl procedures comes with a number of pre-defined reduction functions
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/// but you may as well implement your own functions.
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/// if you write your own function, you must use the same declaration and arguments
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/// as this function except for the function name.
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/// you can do many things in a reduction function,
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/// e.g. integration over a region of interest, curve fitting, etc.
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///
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/// each destination wave is a one-dimensional intensity distribution.
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/// the function must redimension each of these waves to one of the image dimensions
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@ -1077,32 +1091,38 @@ end
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/// this function will also copy the scale information and dimension labels,
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/// which is important for the proper scaling of the result.
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///
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/// the meaning of the data in dest1 and dest2 is up to the particular function,
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/// the meaning of the data in the result waves is up to the particular function,
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/// e.g. dest1 could hold the mean value and dest2 the one-sigma error,
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/// or dest1 could hold the X-profile, and dest2 the Y-profile.
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///
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/// @param source source wave
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/// two-dimensional intensity distribution (image)
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/// @param dest1, dest2 destination waves
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/// @param param string with optional parameters, shared between calls.
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/// @param source source wave.
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/// two-dimensional intensity distribution (image).
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/// the scales are carried over to the result waves.
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///
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/// @param param string with optional parameters, shared between calls.
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/// this is a pass-by-reference argument,
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/// the function may modify the string
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/// the function may modify the string.
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///
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/// @return zero if successful, non-zero if an error occurs.
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/// @return a free wave containing references of the result waves.
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/// the result waves should as well be free waves.
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/// if an error occurred, the reference wave is empty.
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///
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threadsafe function adh5_default_reduction(source, dest1, dest2, param)
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threadsafe function /wave adh5_default_reduction(source, param)
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wave source
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wave dest1, dest2
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string ¶m
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// demo code
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// integrate along the dimensions
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// integrate along the dimensions
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make /n=0 /free dest1, dest2
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adh5_setup_profile(source, dest1, 0)
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ad_profile_x_w(source, 0, -1, dest1)
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adh5_setup_profile(source, dest2, 1)
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ad_profile_y_w(source, 0, -1, dest2)
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return 0
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make /n=2 /free /wave results
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results[0] = dest1
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results[1] = dest2
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return results
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end
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/// set up a one-dimensional wave for a line profile based on a 2D original wave.
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@ -1123,20 +1143,66 @@ end
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/// wrapper function for testing reduction functions from the command line.
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///
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/// Igor does not allow global variables as pass-by-reference parameter for reduction_param.
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/// reduction functions cannot be used on the command line because they require
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/// a pass-by-reference argument and return free waves.
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/// this function expects the reduction parameters in a normal string
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/// and copies the results into the current data folder.
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/// the prefix of the result names can be specified.
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///
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function /s adh5_test_reduction_func(source, dest1, dest2, reduction_func, reduction_param)
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/// @param source source wave.
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/// two-dimensional intensity distribution (image).
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/// the scales are carried over to the result waves.
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///
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/// @param reduction_func name of the reduction function to apply to the source data.
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///
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/// @param reduction_param string with reduction parameters as required by the specific reduction function.
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///
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/// @param result_prefix name prefix of result waves.
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/// a numeric index is appended to distinguish the results.
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/// the index starts at 1. existing waves are overwritten.
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///
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/// @return a copy of the reduction_param string, possibly modified by the reduction function.
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///
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function /s adh5_test_reduction_func(source, reduction_func, reduction_param, result_prefix)
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wave source
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wave dest1
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wave dest2
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funcref adh5_default_reduction reduction_func
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string reduction_param
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string result_prefix
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reduction_func(source, dest1, dest2, reduction_param)
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wave /wave results = reduction_func(source, reduction_param)
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adh5_get_result_waves(results, result_prefix, 1)
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return reduction_param
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end
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/// copy waves from wave reference wave into current data folder
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///
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/// this function copies waves that are referenced in a wave reference wave into the current data folder.
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/// the destination waves get new names consisting of a prefix and a numeric index.
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/// the index is the array index of the wave in results plus a chosen offset.
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///
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/// @param results a wave reference wave pointing to result waves from data reduction.
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/// the waves can be free or regular waves.
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/// results can be a free or regular wave.
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///
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/// @param result_prefix name prefix of the copied waves.
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///
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/// @param start_index start index (offset) of the copied waves.
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///
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threadsafe function adh5_get_result_waves(results, result_prefix, start_index)
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wave /wave results
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string result_prefix
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variable start_index
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variable nw = numpnts(results)
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variable iw
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string sw
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for (iw = 0; iw < nw; iw += 1)
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sw = result_prefix + num2str(iw + start_index)
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duplicate /o results[iw], $sw
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endfor
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end
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/// load a reduced detector dataset from the open HDF5 file.
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///
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/// the function loads the dataset image by image using the hyperslab option
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@ -1266,6 +1332,10 @@ function adh5_load_reduced_detector(fileID, detectorpath, reduction_func, reduct
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variable iz, it
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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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@ -1287,11 +1357,11 @@ function adh5_load_reduced_detector(fileID, detectorpath, reduction_func, reduct
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ThreadGroupPutDF threadGroupID, :
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else
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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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@ -1343,26 +1413,32 @@ function adh5_load_reduced_detector(fileID, detectorpath, reduction_func, reduct
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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 data1
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make /n=(dimsize(profile2, 0), nz, nt)/d/o data2
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setdimlabel 0, -1, $getdimlabel(profile1, 0, -1), data1
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setdimlabel 0, -1, $getdimlabel(profile2, 0, -1), data2
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setscale /p x dimoffset(profile1, 0), dimdelta(profile1, 0), waveunits(profile1, 0), data1
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setscale /p x dimoffset(profile2, 0), dimdelta(profile2, 0), waveunits(profile2, 0), data2
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setscale d 0, 0, waveunits(profile1, -1), data1
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setscale d 0, 0, waveunits(profile2, -1), data2
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endif
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data1[][rr][ss] = profile1[p]
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data2[][rr][ss] = profile2[p]
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else
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if (func_result < 1)
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result = -3 // dimension reduction error
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break
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endif
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if (numpnts(result_waves) == 0)
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redimension /n=(func_result) result_waves
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for (iw = 0; iw < func_result; iw += 1)
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sw = "redw_" + num2str(iw)
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wave profile = dfr:$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, $getdimlabel(profile, 0, -1), data
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setscale /p x dimoffset(profile, 0), dimdelta(profile, 0), waveunits(profile, 0), data
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setscale d 0, 0, waveunits(profile, -1), data
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result_waves[iw] = data
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endfor
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endif
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for (iw = 0; iw < func_result; iw += 1)
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sw = "redw_" + num2str(iw)
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wave profile = dfr:$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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@ -1377,20 +1453,19 @@ function adh5_load_reduced_detector(fileID, detectorpath, reduction_func, reduct
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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=(dimsize(data1,0)) data1
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redimension /n=(dimsize(data2,0)) data2
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elseif (nt == 1)
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redimension /n=(dimsize(data1,0),nz) data1
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redimension /n=(dimsize(data2,0),nz) data2
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setdimlabel 1, -1, AD_DimN, data1
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setdimlabel 1, -1, AD_DimN, data2
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else
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setdimlabel 1, -1, AD_DimN, data1
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setdimlabel 1, -1, AD_DimN, data2
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setdimlabel 2, -1, AD_DimX, data1
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setdimlabel 2, -1, AD_DimX, data2
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endif
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nw = numpnts(result_waves)
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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=(dimsize(data, 0)) data
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elseif (nt == 1)
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redimension /n=(dimsize(data, 0),nz) data
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setdimlabel 1, -1, AD_DimN, data
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else
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setdimlabel 1, -1, AD_DimN, data
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setdimlabel 2, -1, AD_DimX, data
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endif
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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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@ -1426,14 +1501,14 @@ 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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@ -1441,11 +1516,9 @@ 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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@ -1461,7 +1534,7 @@ threadsafe static function reduce_slab_image(slabdata, image, profile1, profile2
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break
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endswitch
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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 an NDAttributes group from an open HDF5 file into the current data folder.
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@ -1667,12 +1740,12 @@ function adh5_scale_scienta(data)
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case 1: // Angular45
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ALow = -45/2
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AHigh = +45/2
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AUnit = "°"
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AUnit = "<EFBFBD>"
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break
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case 2: // Angular60
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ALow = -60/2
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AHigh = +60/2
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AUnit = "°"
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AUnit = "<EFBFBD>"
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break
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endswitch
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endif
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