minor updates and bug fixes in angle scan processing and data explorer
This commit is contained in:
@@ -537,7 +537,7 @@ end
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/// calculate the output using all enabled processing filters.
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///
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/// the diffractogram is calculated, to display the graph, call @ref asp_display_graph.
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/// the diffractogram is calculated, to display the graph, call @ref asp_display_output.
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///
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function asp_calculate_output()
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dfref saveDF = GetDataFolderDFR()
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@@ -552,6 +552,7 @@ function asp_calculate_output()
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nvar folding=output_folding
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nvar horizon=output_horizon
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nvar graph_mode
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do_init_process(0)
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do_crop_alpha(0)
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@@ -569,25 +570,57 @@ function asp_calculate_output()
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values = pol <= horizon ? values : nan
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endif
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interpolate_hemi_scan("")
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SetDataFolder saveDF
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end
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/// display the output diffractogram in a new graph
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/// display the output diffractogram
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///
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function asp_display_output()
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dfref df = $(package_path)
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/// this function either displays the current working data from the angle scan panel data folder,
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/// or hologram data from a specified other data folder.
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/// in either case, the graph is displayed using the current projection, mode, color table and contrast settings of the angle scan panel.
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///
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/// @param data_df data folder where the diffractogram data is located.
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/// default: the folder of the angle scan panel package.
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///
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/// @param data_name name of the diffractogram data.
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/// this is normally the name of a sub-folder that contains the data.
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/// default: the name specified in the output_name variable in the package data folder.
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///
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function /s asp_display_output([data_df, data_name])
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dfref data_df
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string data_name
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dfref pkg_df = $(package_path)
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svar /sdfr=pkg_df output_name
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svar /sdfr=pkg_df output_graphname
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nvar /sdfr=pkg_df graph_projection
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nvar /sdfr=pkg_df graph_mode
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svar /sdfr=pkg_df graph_colortable
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nvar /sdfr=pkg_df graph_contrast
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svar /sdfr=df output_name
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svar /sdfr=df output_graphname
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nvar /sdfr=df graph_projection
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nvar /sdfr=df graph_mode
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if (ParamIsDefault(data_df))
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dfref data_df = pkg_df
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endif
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if (ParamIsDefault(data_name))
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data_name = output_name
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endif
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dfref saveDF = GetDataFolderDFR()
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setdatafolder $(package_path)
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output_graphname = output_name
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output_graphname = display_hemi_scan(output_name, projection=graph_projection, graphtype=graph_mode, graphname=output_graphname)
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setdatafolder data_df
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string graphname = data_name
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graphname = display_hemi_scan(data_name, projection=graph_projection, graphtype=graph_mode, graphname=graphname)
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if (ParamIsDefault(data_df))
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output_graphname = graphname
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endif
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SetDataFolder saveDF
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asp_update_graph()
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if (strlen(graphname) && (wintype(graphname) == 1))
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set_contrast(graph_contrast, graph_contrast, graphname=graphname, colortable=graph_colortable)
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endif
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return graphname
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end
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/// update graphs with new color table or contrast
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@@ -647,9 +680,19 @@ end
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/// the destination folder does not need to exist.
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/// existing data in the destination folder is overwritten.
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///
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function asp_duplicate_output(dest_name)
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/// @param do_graph switch to duplicate the graph window as well (1).
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/// default: 0 (do not create a graph)
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///
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/// @return name of the graph window
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///
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function /s asp_duplicate_output(dest_name, [do_graph])
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string dest_name
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variable do_graph
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if (ParamIsDefault(do_graph))
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do_graph = 0
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endif
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dfref df = $(package_path)
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svar /sdfr=df source_path
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svar /sdfr=df output_name
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@@ -657,14 +700,20 @@ function asp_duplicate_output(dest_name)
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wave raw_data = $source_path
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dfref saveDF = GetDataFolderDFR()
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dfref dest_df = GetWavesDataFolderDFR(raw_data)
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setdatafolder dest_df
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dfref raw_df = GetWavesDataFolderDFR(raw_data)
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setdatafolder raw_df
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newdatafolder /o /s $dest_name
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dfref dest_df = GetDataFolderDFR()
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setdatafolder df
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duplicate_hemi_scan(output_name, dest_df, "")
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string graphname = ""
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if (do_graph)
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graphname = asp_display_output(data_df=raw_df, data_name=dest_name)
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endif
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SetDataFolder saveDF
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return graphname
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end
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/// save the output diffractogram to an igor text file
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@@ -777,12 +826,14 @@ function asp_show_panel()
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return 0
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endif
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NewPanel /K=1 /N=anglescan_panel /W=(200,100,479,1027) as "angle scan processing"
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NewPanel /K=1 /N=anglescan_panel /W=(200,100,479,854) as "angle scan processing"
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panel_name = s_name
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GroupBox gb_source, title="data source"
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Button b_source_select, size={50,20},proc=PearlAnglescanPanel#bp_source_select,title="select..."
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Button b_source_select, help={"select the source wave, e.g. ReducedData1. it must be in the original scan data folder along with the attr folder and the manipulator positions."}
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Button b_source_select, help={"select the source wave, e.g. ReducedData1. it must be in the scan or region data folder. the attr folder with the manipulator waves must be in the same folder or one level up."}
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Button b_source_update, size={50,20},proc=PearlAnglescanPanel#bp_source_update,title="update"
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Button b_source_update, help={"reload the process data from the previous source (link displayed below)"}
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TitleBox tb_source_path, size={240,21}
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TitleBox tb_source_path,variable= root:packages:pearl_anglescan_panel:source_path
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@@ -799,6 +850,10 @@ function asp_show_panel()
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SetVariable sv_alpha_offset, size={90,16},bodyWidth=60,title="alpha"
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SetVariable sv_alpha_offset,value= root:packages:pearl_anglescan_panel:alpha_offset
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SetVariable sv_alpha_offset, help={"alpha value that corresponds to normal emission (if the sample normal is properly aligned)."}
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Button b_save_prefs, size={80,20},proc=PearlAnglescanPanel#bp_save_prefs,title="save prefs"
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Button b_save_prefs, help={"save settings as preferences."}
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Button b_load_prefs, size={80,20},proc=PearlAnglescanPanel#bp_load_prefs,title="load prefs"
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Button b_load_prefs, help={"load settings from preferences."}
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GroupBox gb_crop_alpha, title="crop alpha"
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CheckBox cb_crop_alpha_enable, size={50,14}, title="enable"
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@@ -878,8 +933,8 @@ function asp_show_panel()
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PopupMenu pm_graph_projection, mode=2, popvalue="stereographic", value= #"\"equidistant;stereographic;equal area;gnomonic;orthographic;\""
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PopupMenu pm_graph_projection, help={"projection (theta mapping) mode"}
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PopupMenu pm_graph_mode, size={129,21}, bodyWidth=100, proc=PearlAnglescanPanel#pmp_graph_mode,title="mode"
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PopupMenu pm_graph_mode, mode=2, popvalue="polar plot", value= #"\"none;polar plot;none;image;\""
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PopupMenu pm_graph_mode, help={"graph mode"}
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PopupMenu pm_graph_mode, mode=2, popvalue="dots", value= #"\"none;dots;none;image;\""
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PopupMenu pm_graph_mode, help={"graph type: dots = coloured dots on circles; image = interpolated matrix"}
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Button b_output_calc, size={80,20}, proc=PearlAnglescanPanel#bp_output_calc, title="calc + display"
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Button b_output_calc, help={"execute data processing with the enabled filters and display the diffractogram."}
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Button b_output_duplicate, size={80,20}, proc=PearlAnglescanPanel#bp_output_duplicate, title="duplicate ..."
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@@ -910,9 +965,9 @@ static function arrange_controls()
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svar /sdfr=df panel_name
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variable gb_space = 2
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variable gb_internal_top = 20
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variable gb_internal_bot = 8
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variable line_space = 26
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variable gb_internal_top = 16
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variable gb_internal_bot = 4
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variable line_space = 22
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variable cb_adj = 2
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variable sv_adj = 2
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@@ -933,6 +988,7 @@ static function arrange_controls()
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GroupBox gb_source,pos={4,gb_top}
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gb_ht = gb_internal_top
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Button b_source_select,pos={17, gb_top + gb_ht + b_adj},size={50,20}
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Button b_source_update, pos={67, gb_top + gb_ht + b_adj},size={50,20}
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gb_ht += line_space
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TitleBox tb_source_path,pos={18, gb_top + gb_ht + tb_adj},size={240,21}
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gb_ht += line_space
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@@ -943,8 +999,10 @@ static function arrange_controls()
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GroupBox gb_offsets,pos={4,gb_top}
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gb_ht = gb_internal_top
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SetVariable sv_theta_offset,pos={46, gb_top + gb_ht + sv_adj},size={88,16}
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Button b_save_prefs,pos={186, gb_top + gb_ht + b_adj},size={80,20}
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gb_ht += line_space
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SetVariable sv_tilt_offset,pos={60, gb_top + gb_ht + sv_adj},size={74,16}
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Button b_load_prefs,pos={186, gb_top + gb_ht + b_adj},size={80,20}
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gb_ht += line_space
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SetVariable sv_phi_offset,pos={56, gb_top + gb_ht + sv_adj},size={78,16}
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gb_ht += line_space
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@@ -1047,6 +1105,9 @@ static function arrange_controls()
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gb_ht += line_space
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gb_ht += gb_internal_bot
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GroupBox gb_graph, size={272,gb_ht}
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gb_top += gb_ht + gb_space
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//MoveWindow 200, 100, 479, 100 + gb_top
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end
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/// update the popup menus to reflect the values of the global variables
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@@ -1077,6 +1138,34 @@ static function update_menus()
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endif
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end
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static function bp_load_prefs(ba) : ButtonControl
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STRUCT WMButtonAction &ba
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switch( ba.eventCode )
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case 2: // mouse up
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load_prefs()
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break
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case -1: // control being killed
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break
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endswitch
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return 0
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End
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static function bp_save_prefs(ba) : ButtonControl
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STRUCT WMButtonAction &ba
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switch( ba.eventCode )
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case 2: // mouse up
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save_prefs()
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break
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case -1: // control being killed
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break
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endswitch
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return 0
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End
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static function bp_source_select(ba) : ButtonControl
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STRUCT WMButtonAction &ba
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@@ -1103,6 +1192,27 @@ static function bp_source_select(ba) : ButtonControl
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return 0
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End
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static function bp_source_update(ba) : ButtonControl
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STRUCT WMButtonAction &ba
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switch( ba.eventCode )
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case 2: // mouse up
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dfref packdf = $package_path
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svar /sdfr=packdf source_path
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wave /z w = $source_path
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if (waveexists(w))
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asp_import_raw(w)
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else
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DoAlert 0, "can't find source data."
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endif
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break
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case -1: // control being killed
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break
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endswitch
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return 0
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End
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static function bp_norm_alpha_check(ba) : ButtonControl
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STRUCT WMButtonAction &ba
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@@ -1250,10 +1360,12 @@ static function bp_output_duplicate(ba) : ButtonControl
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switch( ba.eventCode )
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case 2: // mouse up
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string dest_folder
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variable do_graph = 1
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prompt dest_folder, "destination folder name (relative to data source)"
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doprompt "duplicate", dest_folder
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prompt do_graph, "duplicate graph (yes = 1, no = 0)"
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doprompt "duplicate", dest_folder, do_graph
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if (!v_flag)
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asp_duplicate_output(dest_folder)
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asp_duplicate_output(dest_folder, do_graph=do_graph)
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endif
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break
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case -1: // control being killed
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@@ -160,6 +160,8 @@ end
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/// this is a simple way to remove the effect of the angle-dependence of the analyser transmission function.
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/// the strip is normalized in place, previous data is overwritten.
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///
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/// the function can handle sparse NaNs.
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///
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/// @param[in,out] strip 2D data, X-axis = analyser angle, Y-axis = arbitrary manipulator scan
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///
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/// @param[in] smooth_method smoothing method
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@@ -205,12 +207,20 @@ function normalize_strip_x(strip, [smooth_method, smooth_factor, check])
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endif
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// average over all scan positions
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wave dist = ad_profile_x(strip, -inf, inf, "")
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wave raw_dist = ad_profile_x(strip, -inf, inf, "")
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// remove nans
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extract /free /indx raw_dist, clean_index, numtype(raw_dist) == 0
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duplicate /free raw_dist, dist, dist_x
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redimension /n=(numpnts(clean_index)) dist, dist_x
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dist = raw_dist[clean_index[p]]
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dist_x = pnt2x(raw_dist, clean_index[p])
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variable div = mean(dist)
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dist /= div
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if (check)
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duplicate /o dist, check_dist
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duplicate /o raw_dist, check_dist
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check_dist = numtype(raw_dist) == 0 ? interp(x, dist_x, dist) : nan
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endif
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// smooth distribution function
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@@ -223,21 +233,24 @@ function normalize_strip_x(strip, [smooth_method, smooth_factor, check])
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break
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case 3:
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make /n=1 /d /free fit_params
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fit_scienta_ang_transm(dist, fit_params)
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fit_scienta_ang_transm(raw_dist, fit_params)
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duplicate /free raw_dist, dist, dist_x
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dist_x = x
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dist = scienta_ang_transm(fit_params, x)
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break
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case 4:
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loess /smth=(smooth_factor) srcWave=dist
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loess /smth=(smooth_factor) srcWave=dist, factors={dist_x}
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break
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endswitch
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if (check)
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duplicate /o dist, check_smoo
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duplicate /o raw_dist, check_smoo
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check_smoo = interp(x, dist_x, dist)
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endif
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// divide
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if (check != 2)
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strip /= dist[p]
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strip /= interp(x, dist_x, dist)
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endif
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end
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@@ -1660,6 +1673,17 @@ function /s display_hemi_scan(nickname, [projection, graphtype, do_ticks, do_gri
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endif
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string s_trace
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DoWindow $graphname
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if (v_flag)
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if (str2num(GetUserData(graphname, "", "graphtype")) == graphtype)
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// graph exists and will update automatically - do not recreate
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graphtype = 0
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else
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// graph exists - but needs recreating
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killwindow $graphname
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endif
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endif
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switch(graphtype)
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case 1:
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graphname = display_polar_graph(graphname, angle_offset=azim_offset, do_ticks=do_ticks)
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@@ -1673,6 +1697,7 @@ function /s display_hemi_scan(nickname, [projection, graphtype, do_ticks, do_gri
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ColorScale /W=$graphname /C /N=text0 nticks=2, minor=1, tickLen=4.00, tickThick=0.50
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SetWindow $graphname, userdata(projection)=num2str(projection)
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SetWindow $graphname, userdata(graphtype)=num2str(graphtype)
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draw_hemi_axes(graphname, do_grids=do_grids)
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break
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case 3:
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@@ -1687,6 +1712,7 @@ function /s display_hemi_scan(nickname, [projection, graphtype, do_ticks, do_gri
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ColorScale /W=$graphname /C /N=text0 nticks=2, minor=1, tickLen=4.00, tickThick=0.50
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SetWindow $graphname, userdata(projection)=num2str(projection)
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SetWindow $graphname, userdata(graphtype)=num2str(graphtype)
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draw_hemi_axes(graphname, do_grids=do_grids)
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break
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endswitch
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@@ -79,7 +79,7 @@ static function init_package()
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string /g s_reduction_params = "" // recently used reduction parameters
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string /g s_preview_pvs = "" // semicolon-separated list of EPICS PVs to display in preview.
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// the list items can contain wildcards for StringMatch
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s_preview_pvs = "*OP:CURRENT*;*Stats*Total*;*CADC*"
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s_preview_pvs = "*OP:CURRENT*;*Stats*Total*;*KEITHLEY*READOUT;*CADC*"
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// non-persistent strings and variables
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string /g s_preview_file = "" // file or folder name of the current preview
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@@ -392,6 +392,25 @@ static function /wave preview_hdf_file(filename)
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return preview_image
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end
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/// load the preview of a general ITX file.
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///
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/// the function is designed for PEARL OTF and EPICS scan data converted from MDA files.
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/// the function picks the first wave whose PV note matches one from the global string s_preview_pvs
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/// (see @ref preview_datafolder and @ref init_package).
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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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/// the s_file_info string is updated with information about the scan dimensions.
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///
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/// @note: the ITX files should load their waves into the current data folder (a "free" data folder).
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/// some early versions of PEARL ITX data files created a data folder of their own.
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/// both ways are allowed, while the first one is preferred.
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/// on return, the current data folder must point to either the original free folder or the newly created one.
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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 trace.
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/// empty wave reference if the function failed.
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///
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static function /wave preview_itx_file(filename)
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string filename
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@@ -401,10 +420,6 @@ static function /wave preview_itx_file(filename)
|
||||
svar s_preview_source
|
||||
wave preview_image
|
||||
|
||||
// note: some versions of PEARL data files save data to a new data folder,
|
||||
// and leave the newly created folder as the current folder.
|
||||
// the free data folder is used by those files which don't create their own data folder.
|
||||
// this is the new recommended behaviour
|
||||
dfref dataDF = newfreedatafolder()
|
||||
setdatafolder dataDF
|
||||
LoadWave /t/p=pearl_explorer_filepath/q filename
|
||||
|
||||
@@ -90,6 +90,40 @@ threadsafe function MultiGaussLinBG_AO(pw, yw, xw) : FitFunc
|
||||
endfor
|
||||
end
|
||||
|
||||
/// doublet gaussian peaks on a linear background fit function (all at once).
|
||||
///
|
||||
/// this fits two gaussian peaks.
|
||||
/// peak positions are specified by center and distance rather than individually.
|
||||
/// amplitude and width are specified as absolute values for the upper peak (in x),
|
||||
/// and relative values for the lower peak.
|
||||
///
|
||||
/// @note FWHM = width * 2 * sqrt(ln(2)) = width * 1.665
|
||||
///
|
||||
/// @param pw shape parameters.
|
||||
/// the length of the wave defines the number of peaks.
|
||||
/// @arg pw[0] = constant coefficient of background
|
||||
/// @arg pw[1] = linear coefficient of background
|
||||
/// @arg pw[2] = amplitude of peak 1 (higher x)
|
||||
/// @arg pw[3] = amplitude of peak 2 relative to peak 1
|
||||
/// @arg pw[4] = center position
|
||||
/// @arg pw[5] = distance between peaks (splitting)
|
||||
/// @arg pw[6] = width of peak 1 (see note)
|
||||
/// @arg pw[7] = width of peak 2 relative to peak 1
|
||||
///
|
||||
/// @param yw y (dependent) values.
|
||||
///
|
||||
/// @param xw x (independent) independent values.
|
||||
///
|
||||
threadsafe function DoubletGaussLinBG_AO(pw, yw, xw) : FitFunc
|
||||
wave pw
|
||||
wave yw
|
||||
wave xw
|
||||
|
||||
yw = pw[0] + xw[p] * pw[1]
|
||||
yw += pw[2] * exp( -( (xw[p] - pw[4] - pw[5] /2) / pw[6] )^2 )
|
||||
yw += pw[2] * pw[3] * exp( -( (xw[p] - pw[4] + pw[5] /2) / pw[6] / pw[7] )^2 )
|
||||
end
|
||||
|
||||
//------------------------------------------------------------------------------
|
||||
// Voigt shapes
|
||||
//------------------------------------------------------------------------------
|
||||
@@ -581,7 +615,7 @@ function Au4f(w, x): fitfunc
|
||||
// otherwise only the constant background.
|
||||
variable x
|
||||
|
||||
variable np = 15
|
||||
variable np = numpnts(w)
|
||||
variable ip, ip0
|
||||
|
||||
variable bg = w[0]
|
||||
|
||||
Reference in New Issue
Block a user