Added import and plot for flow data that is now logged for the MFC
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@@ -1,3 +1,4 @@
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.gitignore
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# Autosave files
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*.asv
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*.m~
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@@ -31,3 +32,15 @@ codegen/
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# Cloud based storage dotfile
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.MATLABDriveTag
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# MacOS system files
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.DS_Store
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lopap/3.Skripte/.DS_Store
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# error messages
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utils/distFig_Error.mat
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utils\\distFig_Update.txt
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beamtime/clean_file.p
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beamtime/requirements.txt
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@@ -0,0 +1,104 @@
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function tbl = issFlowImportData(fullFileName)
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%FLOWIMPORTDATA Import the MFC flow-log channels from a new-format LabView file.
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%
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% tbl = flowImportData(fullFileName) reads the mid-2026 LabView chamber log
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% (tab-delimited, 2 header lines, ISO-8859-1) and returns a table of the
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% 7 MFC flow channels:
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% datetime - absolute time (date + time columns)
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% MFC4 .. MFC10 - one column per mass-flow controller, named by its
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% physical MFC number (as on the gas panel).
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% MFC4 [l/min] - cryo cooling flow (the old "flow cryo" channel)
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% MFC5..MFC10 [sccm] - dosing/carrier gas flows (the old flow1..flow6)
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%
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% MFC <-> COLUMN MAPPING
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% The file's header line 1 names 7 controllers in order (MFC4..MFC10,
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% with a gas type each), and the data columns log 7 flow channels in the
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% same order (flow-cryo, then flow1..flow6). This function maps them
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% 1:1 by that shared order:
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% MFC4 <- "flow cryo (l/min)" (col 9)
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% MFC5 <- "flow1 (sccm)" (col 11)
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% MFC6 <- "flow2 (sccm)" (col 12)
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% MFC7 <- "flow3 (sccm)" (col 13)
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% MFC8 <- "flow4 (sccm)" (col 14)
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% MFC9 <- "flow5 (sccm)" (col 15)
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% MFC10 <- "flow6 (sccm)" (col 16)
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% This is an ORDER-MATCH inference (the file does not literally print
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% "flow3 = MFC7"), so double-check it once against the gas panel /
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% LabView front panel if in doubt. The parsed gas type per MFC (from the
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% header) is stored in tbl.Properties.UserData.mfcMap for that check.
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%
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% OUTPUT
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% tbl.Properties.UserData.mfcMap - table with MFC, SourceColumn, Gas,
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% Unit, MfcVarName for all 7 channels
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% (for verification and lookup)
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%
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% EXAMPLE
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% tbl = flowImportData('01-07-2026_11-28datafile.txt');
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% tbl.Properties.UserData.mfcMap % inspect / verify the mapping
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% ax = plotFlowData(tbl, [4 7 10]); % plot by MFC number
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% ax = plotFlowData(tbl, 'flow3'); % or by the raw logged tag
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%
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% See also PLOTFLOWDATA, LABVIEW_IMPORTDATA
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lines = readlines(fullFileName, 'Encoding', 'ISO-8859-1');
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lines = lines(strlength(lines) > 0); % drop trailing blank from final CRLF
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if numel(lines) < 3
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error('flowImportData:tooShort', 'File does not look like a valid log.');
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end
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hdr1 = lines(1); % gas name line
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hdr2 = lines(2); % column names
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data = lines(3:end);
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if ~contains(hdr2, 'pressure_cell') && ~contains(hdr1, 'gas name')
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error('flowImportData:wrongFormat', ...
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'This does not look like the new-format LabView file (no "gas name"/"pressure_cell" header found).');
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end
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%--- Parse gas names/types from header line 1: "gas name MFCn:Gas" ---
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tok = regexp(hdr1, 'gas name (MFC\d+):(\S+)', 'tokens');
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mfcNum = cellfun(@(t) str2double(erase(t{1},'MFC')), tok);
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gasType = cellfun(@(t) string(t{2}), tok);
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[mfcNum, order] = sort(mfcNum);
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gasType = gasType(order);
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if numel(mfcNum) ~= 7
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warning('flowImportData:unexpectedMfcCount', ...
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'Expected 7 named MFCs in the header, found %d. Mapping may be wrong.', numel(mfcNum));
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end
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%--- Parse the data rows ---
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parts = split(data, sprintf('\t'));
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if size(parts, 2) < 16
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error('flowImportData:tooFewColumns', 'Fewer columns than expected in data rows.');
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end
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dateStr = parts(:,1);
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timeStr = parts(:,2);
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dt = datetime(strcat(dateStr, timeStr), 'InputFormat', 'dd.MM.yyyyHH:mm:ss');
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flowCryo = str2double(parts(:,9)); % "flow cryo (l/min)"
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flowN = str2double(parts(:,11:16)); % flow1..flow6 (sccm)
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%--- Order-matched MFC <-> column mapping ---
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columnData = [{flowCryo}, num2cell(flowN,1)]; % 1x7 cell of column vectors
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columnNames = {'flowCryo','flow1','flow2','flow3','flow4','flow5','flow6'};
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columnUnits = [{'l/min'}, repmat({'sccm'}, 1, 6)];
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tbl = table(dt, 'VariableNames', {'datetime'});
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nCh = min(7, numel(mfcNum));
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mfcVarNames = strings(1, nCh);
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for k = 1:nCh
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varName = sprintf('MFC%d', mfcNum(k));
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tbl.(varName) = columnData{k};
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mfcVarNames(k) = varName;
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end
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mfcMap = table(mfcNum(1:nCh)', columnNames(1:nCh)', gasType(1:nCh)', columnUnits(1:nCh)', ...
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'VariableNames', {'MFC','SourceColumn','Gas','Unit'});
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mfcMap.MfcVarName = cellstr(mfcVarNames(:));
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tbl.Properties.VariableUnits = [{''}, columnUnits(1:nCh)];
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tbl.Properties.UserData = struct('mfcMap', mfcMap);
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end
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@@ -0,0 +1,183 @@
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function sp = issPlotFlowData(tbl, channels, options)
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%PLOTFLOWDATA Stacked plot of selected MFC flow channels vs lab time.
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%
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% sp = plotFlowData(tbl)
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% sp = plotFlowData(tbl, channels)
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% sp = plotFlowData(tbl, channels, TimeWindow=timeWindow)
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% sp = plotFlowData(tbl, channels, MfcNames=mfcNames)
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% sp = plotFlowData(tbl, channels, TimeWindow=timeWindow, MfcNames=mfcNames)
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%
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% Plots one stacked panel per selected MFC flow channel (via stackedplot),
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% all sharing a linked lab-time x-axis. Each panel keeps its own y-scale,
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% so channels in different units (l/min vs sccm) sit cleanly on their own
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% axis without needing yyaxis.
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%
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% TimeWindow and MfcNames are name-value arguments (order-independent,
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% optional, with autocomplete/tooltips in the Editor and Live Script).
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%
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% INPUTS
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% tbl table from flowImportData (columns MFC4..MFC10)
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% channels which channel(s) to plot. Any of:
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% * [] -> all channels present (default)
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% * MFC numbers, e.g. [4 7 10] or 7 (physical MFC number)
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% * flow tags, e.g. {'flow1','flow2'} or 'flow3'
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% * MFC names, e.g. {'MFC4','MFC9'} or 'MFC7'
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% * YOUR custom names from MfcNames, e.g. 'Water dosing'
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% or {'Cryo cooling (LN2)','Water dosing'} — only
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% resolvable if MfcNames is also supplied in this call.
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% All selection styles resolve to the same underlying
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% channel — pick whichever is most convenient. Pass multiple
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% as a CELL ARRAY of char, e.g. {'flow1','flow2'} — NOT
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% ['flow1','flow2'], which MATLAB concatenates into the
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% single char 'flow1flow2'.
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%
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% NAME-VALUE ARGUMENTS
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% TimeWindow date-string window as a 2-element cell/string array,
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% {'2026-07-01 11:30:00','2026-07-01 18:30:00'}. Default: the
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% full available range.
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% MfcNames your own display names for the panels (and, per above,
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% usable to SELECT channels too), as a containers.Map keyed
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% by MFC NUMBER (double), e.g.:
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% mfcNames = containers.Map('KeyType','double','ValueType','char');
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% mfcNames(4) = 'Cryo cooling (LN2)';
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% mfcNames(7) = 'Water dosing';
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% Panel labels always show the MFC identifier for
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% traceability, e.g. "MFC7: Water dosing [sccm]". Channels
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% without an entry fall back to "MFC7 (N2) [sccm]" using the
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% gas type parsed from the file header.
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%
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% OUTPUT
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% sp the StackedLineChart object. To further customize (e.g. the x-axis
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% tick format, since stackedplot is a chart, not a plain axes):
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% axs = findobj(sp.NodeChildren, 'Type', 'Axes');
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% axs(end).XAxis.TickLabelFormat = 'dd-MMM HH:mm'; % bottom panel
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%
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% EXAMPLE
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% tbl = flowImportData('01-07-2026_11-28datafile.txt');
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% tbl.Properties.UserData.mfcMap % check the mapping once
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%
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% mfcNames = containers.Map('KeyType','double','ValueType','char');
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% mfcNames(4) = 'Cryo cooling (LN2)';
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% mfcNames(7) = 'Water dosing';
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%
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% sp = plotFlowData(tbl, 'Water dosing', MfcNames=mfcNames); % by custom name
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% sp = plotFlowData(tbl, {'flow1','flow2'}, MfcNames=mfcNames);
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% sp = plotFlowData(tbl, {'MFC4','MFC9'}); % by MFC name
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% sp = plotFlowData(tbl, [4 7], ...
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% TimeWindow={'2026-07-01 11:30:00','2026-07-01 18:30:00'}, ...
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% MfcNames=mfcNames);
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%
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% See also FLOWIMPORTDATA
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arguments
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tbl table
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channels = []
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options.TimeWindow = []
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options.MfcNames containers.Map = containers.Map('KeyType','double','ValueType','char')
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end
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mfcMap = tbl.Properties.UserData.mfcMap; % MFC, SourceColumn, Gas, Unit, MfcVarName
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mfcNames = options.MfcNames;
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%--- Resolve requested channels into MfcVarName column names ---
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if isempty(channels)
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selVars = mfcMap.MfcVarName;
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elseif isnumeric(channels)
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selVars = arrayfun(@(n) resolveByMfcNumber(mfcMap, n), channels, 'UniformOutput', false);
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elseif ischar(channels)
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selVars = {resolveChannel(mfcMap, mfcNames, channels)};
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elseif iscellstr(channels) || isstring(channels) %#ok<ISCLSTR>
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c = cellstr(channels);
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selVars = cellfun(@(v) resolveChannel(mfcMap, mfcNames, v), c, 'UniformOutput', false);
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else
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error('plotFlowData:badChannels', ...
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'channels must be [] , MFC numbers, or flow/MFC/custom name(s).');
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end
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selVars = cellstr(string(selVars));
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%--- Resolve the time window (date strings) ---
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if isempty(options.TimeWindow)
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tStart = min(tbl.datetime);
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tEnd = max(tbl.datetime);
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else
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tw = cellstr(options.TimeWindow);
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if numel(tw) ~= 2
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error('plotFlowData:badTimeWindow', ...
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'TimeWindow must be a 2-element cell/string array {start, end}.');
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end
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tStart = datetime(tw{1});
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tEnd = datetime(tw{2});
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end
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mask = tbl.datetime >= tStart & tbl.datetime <= tEnd;
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tblSub = tbl(mask, [{'datetime'}, selVars]);
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%--- Panel labels: always "MFCn: <name>" or "MFCn (<gas>)" as fallback ---
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labels = cellfun(@(v) labelFor(mfcMap, mfcNames, v), selVars, 'UniformOutput', false);
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%--- Units per panel, for the y-axis label ---
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units = cellfun(@(v) mfcMap.Unit{strcmp(mfcMap.MfcVarName, v)}, selVars, 'UniformOutput', false);
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dispLabels = cellfun(@(l,u) sprintf('%s [%s]', l, u), labels, units, 'UniformOutput', false);
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%--- Stacked plot ---
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figure;
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sp = stackedplot(tblSub, selVars, 'XVariable', 'datetime', ...
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'DisplayLabels', dispLabels);
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sp.Title = 'MFC flow channels';
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sp.GridVisible = 'on';
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sp.XLimits = [tStart tEnd];
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% Format the shared x-axis date ticks (stackedplot is a chart object,
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% so its axes are reached via NodeChildren)
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axs = findobj(sp.NodeChildren, 'Type', 'Axes');
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if ~isempty(axs)
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axs(end).XAxis.TickLabelFormat = 'dd-MMM HH:mm';
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end
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end
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% -------------------------------------------------------------------------
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function varName = resolveByMfcNumber(mfcMap, n)
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idx = find(mfcMap.MFC == n, 1);
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if isempty(idx)
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error('plotFlowData:unknownMFC', 'MFC%d not found in this table.', n);
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end
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varName = mfcMap.MfcVarName{idx};
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end
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% -------------------------------------------------------------------------
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function varName = resolveChannel(mfcMap, mfcNames, v)
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v = char(v);
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% 1) MFC var name, e.g. 'MFC7'
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idx = find(strcmpi(mfcMap.MfcVarName, v), 1);
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if ~isempty(idx), varName = mfcMap.MfcVarName{idx}; return; end
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% 2) raw source column tag, e.g. 'flow3', 'flowCryo'
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idx = find(strcmpi(mfcMap.SourceColumn, v), 1);
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if ~isempty(idx), varName = mfcMap.MfcVarName{idx}; return; end
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% 3) your custom display name, e.g. 'Water dosing' (only if MfcNames given)
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if mfcNames.Count > 0
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ks = cell2mat(keys(mfcNames));
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vs = values(mfcNames);
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idxName = find(strcmpi(vs, v), 1);
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if ~isempty(idxName)
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mfcNum = ks(idxName);
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idx = find(mfcMap.MFC == mfcNum, 1);
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if ~isempty(idx), varName = mfcMap.MfcVarName{idx}; return; end
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end
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end
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error('plotFlowData:unknownChannel', ...
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'Channel "%s" not recognized as an MFC name, flow tag, or custom name in MfcNames.', v);
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end
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% -------------------------------------------------------------------------
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function s = labelFor(mfcMap, mfcNames, varName)
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idx = find(strcmp(mfcMap.MfcVarName, varName), 1);
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mfcNum = mfcMap.MFC(idx);
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if isKey(mfcNames, mfcNum)
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s = sprintf('%s: %s', varName, mfcNames(mfcNum));
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else
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s = sprintf('%s (%s)', varName, mfcMap.Gas(idx));
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end
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end
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