[ehennestad]

Summary

Batch R1 from the module review: correctness fixes, stacked on #1. Two commits: the readrawfile rewrite with the INI reader, and the rest.

readrawfile rewritten from scratch

The old function built its arrays through eval, changed its loop index inside the loop, opened a file dialog when called without a path, and stopped at the end of the file by catching fread errors. The new one has an arguments block (Channel, SkipFrames, NumFrames), derives the frame count from the file size, reads with one fread per request (a block-skip for a single channel), raises typed errors for a missing .ini, an unsupported file.format, no recorded channels and an invalid channel, and warns when fewer frames are available than requested. Output layout is unchanged: x-by-y-by-frames(-by-channels) in the file's sample type. readinivar is now the single INI reader (the static method on SciScanRaw delegates to it): it matches whole variable names at line start, returns logicals for TRUE/FALSE and doubles for numbers, and evaluates nothing. SciScanRawFileTest covers both sample types, channel selection, skip and count, truncation, the error paths and the INI typing. The function has no callers in NANSEN or the module today; it is kept as a public utility.

Other fixes

• eval on file content. getParameterValueFromString parses the literal subset ScanImage writes (numbers, strings, logicals, bracketed arrays, cell arrays, zeros(1,0)-style constructors) and returns anything else as text with a warning, so a TIFF tag can no longer execute code. ScanImageParameterParsingTest covers 25 literal forms and the fallbacks.
• Mixin contract. TwoPhotonRecording documents that its host must be a VirtualArray and which members it uses. Declaring them abstract in the mixin is not possible: MATLAB rejects an abstract declaration of a property that another superclass defines with a type constraint.
• Unreachable code. Removed the never-taken branches in MotionCorrection (statistics are always computed up front; updating the reference image after drift correction is not implemented, now stated in a comment), the abandoned frame-count algorithm behind a return in ScanImageTiff, the if 1 / else in both suite2p segmentation functions, and FluFinder's debug plotting blocks, the unused showDetectedEdges function and a try/catch that printed 'a'.
• Unset outputs. improveRoiMasks drops its never-implemented second output. SciScanRaw loses an empty readFrameSet placeholder (readFrames is the base-class API).
• Deleted, no callers. roi.stats.roiEdgyness was a template stub whose function was named computeRoi; roi.extractDff was error('Deprecated') over a commented-out body.

Not changed: the ScanImage getScanParameters warning-state item from the review was a false positive of my scan; that function restores the state. The cnmf and legacy extract/ImviewerPlugin sites flagged by the analyzer are dead code for the deletion batch.

🤖 Generated with Claude Code

[github-actions]

Test Results

78 tests   77 ✅  5s ⏱️
 8 suites   1 💤
 1 files     0 ❌

Results for commit 6c5040b.