APIS v0.1.4

APIS v0.1.4 Release Notes

Summary

This release updates the XPL calibration/search workflow so APIS can handle film that is not centered vertically, and tightens the app UI around the sequence controls.

Changed Since v0.1.3

• Local XPL search now checks both background ROIs during the coarse scan:
  • bottom ROI: x=700, y=1000, width=700, height=80 px
  • top ROI: x=700, y=0, width=700, height=80 px
• Fine XPL search and confirmation now focus on whichever ROI produced the darker signal.
• XPL confirmation now requires ROI mean <=65 and <=1.2x of the selected scan minimum.
• Polarizer calibration now uses the same adaptive local XPL search path as sequence capture.
• Polarizer calibration now uses one calibration exposure setting instead of separate coarse/fine exposure settings.
• Calibration metadata and CSV logs now include structured detail for top/bottom ROI readings, selected ROI, and confirmation results.
• Sequence XPL capture starts from HOME, moves the sample stage to 0 deg, runs adaptive XPL search, then keeps the selected polarizer angle fixed while imaging.
• Sequence cleanup returns the sample stage to 0 deg without homing/resetting the polarizer.
• Long calibration/status messages no longer resize the app window; full text remains available through the log and tooltip.
• Sequence control button sizing was adjusted so labels such as START SEQUENCE do not clip at the default window size.

Validation

• python -m compileall app apis scripts
• python -m unittest tests.test_ximea_raw16_sequence
• .\build\build.ps1 -Version 0.1.4

Notes

• Sequence capture remains RAW16 only.
• RAW16 preview conversion remains available inside the APIS app.
• Reusing the same SampleID may append to the existing CSV log.

APIS v0.1.3

Summary

This release updates the polarization workflow around PPL/XPL, adds a reusable polarizer calibration baseline, and sets validated default acquisition exposures for routine PPL/XPL imaging.

Added

• Polarization mode naming is now standardized to PPL / XPL across the app, sequence flow, and documentation.
• Polarizer-angle calibration now performs a coarse scan plus a fine scan around the darkest XPL angle.
• Calibrated polarizer baseline values are saved and restored on later app launches.
• Reachable orthogonal-angle handling for PPL derivation from the calibrated XPL angle.
• scripts/analyze_xpl_exposure_sweep.py for reviewing RAW16 XPL exposure-sweep datasets.
• Release packaging now stages files before zipping to avoid transient file-lock failures during archive creation.

Changed

• Default validated acquisition baseline:
  • PPL: 18000 us at polarizer 5 deg
  • XPL: 400000 us at polarizer 95 deg
• Default polarizer calibration exposure:
  • 200000 us
• PPL is no longer chosen from a brightness search; it is derived from the reachable orthogonal angle relative to XPL.
• Sequence output folders now use ppl and xpl.
• Distribution and implementation docs now match the current PPL/XPL baseline and calibration flow.

Sequence Behavior

• Live camera preview is paused before sequence capture and restored afterward.
• Sequence capture remains XI_RAW16 only.
• Sequence images are saved as Bayer RAW uint16 TIFF.
• Sequence outputs include:
  • {SampleID}_log.csv
  • {SampleID}_metadata.json
• CSV logs now include calibration signal metrics used during XPL-angle selection.

Polarizer Calibration

• The calibration scan searches for the darkest XPL angle first.
• A coarse scan identifies the minimum region, then a fine scan refines the result around that angle.
• PPL is assigned as XPL + 90 deg or XPL - 90 deg, whichever stays inside the reachable polarizer range.
• The resulting baseline is saved for reuse on later runs.

Conversion Tool

• Converts saved RAW16 TIFF datasets into RGB preview images.
• Processes the selected folder and its immediate child folders.
• Saves results into a sibling _rgb folder.
• Uses demosaic plus fixed white balance plus gamma for preview generation.

Validation

• python -m py_compile apis\\config.py apis\\io.py apis\\sequence.py apis\\utils.py app\\main.py app\\workers.py scripts\\analyze_xpl_exposure_sweep.py tests\\test_ximea_raw16_sequence.py
• python -m unittest tests.test_ximea_raw16_sequence tests.test_mock_serial
• .\build\build.ps1 -Version 0.1.3

Notes

• Sequence capture is still RAW16-only in this release.
• Live view and Snapshot behavior are unchanged.
• Reusing the same SampleID may append to the existing CSV log.

APIS v0.1.2

Summary

This release adds a RAW16-based XIMEA sequence workflow for quantitative imaging while keeping live view and normal snapshot behavior unchanged.

Added

• XIMEA sequence capture in XI_RAW16
• Per-sequence JSON metadata output
• RAW16 to RGB8 preview conversion tool
• Automated tests for RAW16 sequence, cleanup, metadata, and conversion

Changed

• Live view remains XI_RGB24
• Snapshot remains preview RGB TIFF
• Camera gamma is fixed to 1.0
• Sequence capture enforces gain = 0 dB
• Default validated sequence exposures:
  • Normal / PPL: 18000 us
  • Crosspol / XPL: 50000 us

Sequence behavior

• Live camera thread is stopped before sequence capture and restored afterward
• Sequence images are saved as Bayer RAW uint16 TIFF
• Sequence outputs now include:
  • {SampleID}_log.csv
  • {SampleID}_metadata.json

Conversion tool

• Converts saved RAW16 TIFF datasets into RGB8 preview images
• Processes the selected folder and its immediate child folders
• Saves results into a sibling _rgb folder
• Uses demosaic + fixed white balance + gamma for preview generation

Validation

• Unit tests passed
• Hardware validation confirmed:
  • RAW16 TIFF output
  • JSON metadata generation
  • Live-view recovery after sequence
  • Exposure baseline validation for PPL/XPL

Notes

• Sequence capture is RAW16-only in this release
• RAW Snapshot is not included
• Reusing the same SampleID may append to the existing CSV log

APIS v0.1.1

Highlights

• Calibration-based stage-angle handling in Python for both polarizer and sample axes
• Calibrated software limit set to 169 deg per stage while keeping the standard 0-180 Arduino servo command path
• Fixed XIMEA acquisition baseline for more consistent Normal/Crosspol comparison
  • Auto white balance disabled during capture
  • Fixed white balance: R=1.40, G=1.00, B=1.20
  • Default exposures: Normal 12000 us, Crosspol 50000 us
• Added hardware documentation for full system reproduction
  • Hardware implementation guide (wiring, calibration, verification)
  • Hardware assembly guide (printed parts, bearings, gears, stack-up)
• Added STL part set for the current mechanical build
• Documented current mechanical build details including M3 screws and heat-set brass inserts

Distribution

• [APIS-win64-v0.1.1.zip]
  • APIS/ (GUI app)
  • check_hardware/ (console tool)
  • [README.txt]
  • [prereq_checklist.md]

Prerequisites

• XIMEA Windows Software Package (drivers + xiAPI) must be installed
• Arduino firmware must be flashed ([APIS_Firmware.ino])

Notes

• Keep the APIS folder intact; do not move APIS.exe out of it
• Current sequence convention:
  • Crosspol = polarizer 90 deg
  • Normal = polarizer 0 deg
• The current build uses calibrated stage-angle mapping with a software max of 169 deg per stage
• If the camera is not detected, verify XIMEA drivers and device recognition first
• Hardware reproduction details are documented in:
  • docs/implementation_guide.md
  • docs/hardware_assembly_guide.md

APIS v0.1.0

Highlights

• PyQt6 GUI with live view, manual control, and automated sequence capture
• Safe state handling (LATCHED/ARMED) with ESTOP / RESET / HOME
• Crosspol/Normal sequence modes with custom angles
• Snapshot capture with metadata logging
• Hardware check tool (check_hardware) included for quick Arduino/ESTOP validation

Distribution

• [APIS-win64-v0.1.0.zip]
  • APIS/ (GUI app)
  • check_hardware/ (console tool)
  • [README.txt]
  • [prereq_checklist.md]

Prerequisites

• XIMEA Windows Software Package (drivers + xiAPI) must be installed

• Arduino firmware must be flashed ([APIS_Firmware.ino])

Notes

• Keep the APIS folder intact; do not move [APIS.exe] out of it
• If camera is not detected, verify drivers and device recognition first