first Jeti plotting function

beamtime/commit.md

@@ -1,42 +0,0 @@
-feat: Major refactor - generic model architecture with full Shirley background support
-
-BREAKING CHANGES:
-- Single-spectrum fitting only (enforces exactly one row selected)
-- Gauss fitting now uses FWHM parameter instead of Gaussian width sigma
-- Removed multi-row batch processing capability
-
-NEW FEATURES:
-- Generic model architecture: arbitrary number of peaks (determined by length of FitParameter.peakArea)
-- Full Shirley background support for both Gaussian and Pseudo-Voigt peak shapes
-- Comprehensive parameter validation system with detailed error messages
-- Support for shared vs per-peak Shirley K parameters
-- New fitting modes: 'positionShirley', 'widthShirley', 'widthPositionShirley'
-- New custom mode: 'TwoSpinOrbitDoubletPseudoVoigtShirley'
-- Automatic field name typo correction ('Bond' → 'Bound')
-- Enhanced results export: now includes peakEta and peakShirleyK columns
-
-REFACTORING:
-- Centralized peak and background equations in helper functions
-  - gaussPeak(), lorentzPeak(), pseudoVoigtPeak()
-  - linearBackground(), activeShirleyBackgroundFwhm()
-  - fwhm2w() conversion utility
-- Extracted model generation to genericModelGenerator()
-- Modular validation helpers: checkFieldDimension(), checkBoundsPair()
-- Standardized parameter vector layouts documented for all mode/background/peak-type combinations
-- Improved column resizing logic with resizeColumnHelper()
-- Enhanced plotting integration with nappPlot.m and nappAddFitToPlot.m
-
-ARCHITECTURE:
-- Unified parameter extraction for all fitting modes in centralized switch-case structure
-- Consistent FWHM-based width parameterization across all peak types
-- Mode-specific Shirley K sizing (scalar for shared modes, array for per-peak modes)
-- Comprehensive inline documentation of parameter vector layouts (50+ combinations)
-
-IMPROVEMENTS:
-- Backward compatibility for 'gauss' width mode (auto-converts to FWHM)
-- Robust bounds checking with detailed diagnostic messages
-- Enhanced figure generation: residuals plot + fit visualization in tiledlayout
-- Better error handling for empty/malformed data structures
-- NaN-padded result arrays for variable peak counts
-
-FILE SIZE: ~73KB → ~152KB (107% increase due to comprehensive documentation and generic architecture)

import/importJeti.m

@@ -1,14 +1,14 @@
 function dataTable = importJeti(filename)
-%IMPORTFILE Import JETI SPECBOS irradiance data (CSV or TXT format)
-%  DATATABLE = IMPORTFILE(FILENAME) reads data from text file FILENAME.
+%IMPORTJETI Import JETI SPECBOS irradiance data (CSV or TXT format)
+%  DATATABLE = IMPORTJETI(FILENAME) reads data from text file FILENAME.
 %
-%  Supports two formats:
+%  Supports:
 %  1. CSV: Semicolon-separated with header metadata
 %  2. isd: txt-style format with [sections] and tab-separated data
 %
 %  Example:
-%    table = importfile("20251212_1606_Jeti.csv");
-%    table = importfile("spectrum_#2.isd");
+%    table = importJeti("20251212_1606_Jeti.csv");
+%    table = importJeti("spectrum_#2.isd");
 
 %% Determine file type and route accordingly
 [~, ~, ext] = fileparts(filename);
@@ -47,8 +47,8 @@ while true
     end
     lineIdx = lineIdx + 1;
 
-    % Detect start of data
-    if contains(thisLine, 'Wavelength [nm];Spectral Irradiance [W/(sqm*nm)]')
+    % Detect start of data header line
+    if contains(thisLine, 'Wavelength [nm]')
         dataHeaderLineIdx = lineIdx;
         break
     end
@@ -89,10 +89,27 @@ end
 firstDataLineInFile = dataHeaderLineIdx + 1;
 fclose(fid);
 
-% Derive number of columns
-if isnan(metadata.numDatasets)
-    error('Number of datasets not found in header.');
+% Derive number of columns:
+% If 'Number of datasets' is present: use it.
+% Otherwise infer from the header line (new Spec1/Spec2 format).[file:1]
+fid = fopen(filename, 'r');
+if fid == -1
+    error('Cannot reopen file: %s', filename);
 end
+headerLine = '';
+for k = 1:dataHeaderLineIdx
+    headerLine = fgetl(fid);
+end
+fclose(fid);
+
+headerParts = strsplit(headerLine, ';');
+nHeaderCols = numel(headerParts);
+
+if isnan(metadata.numDatasets)
+    % New format: first column is wavelength, remaining are datasets
+    metadata.numDatasets = nHeaderCols - 1;
+end
+
 numCols = 1 + metadata.numDatasets;
 
 % Build dataLines
@@ -119,8 +136,9 @@ if ~isempty(metadata.Date) && ~isempty(metadata.Time)
         tstr = strtrim(metadata.Time{k});
 
         try
+            % JETI CSV: e.g. 12/18/2025 and 10:40:14 for 12h clock.[file:1]
             dt = datetime([dstr ' ' tstr], ...
-                'InputFormat', 'MM/dd/yyyy hh:mm:ssa');
+                'InputFormat', 'MM/dd/yyyy HH:mm:ss');
             timestr = datestr(dt, 'yyyymmdd_HHMMss');
         catch
             timestr = sprintf('dataset%02d', k);