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Changelog

Source: NEWS.md

OpenSpecy 1.7.1

  • Added auditable prune_lib() and recipe-selective build_lib(prune = ...) support for reference-library QA/QC. Generic classes are reassigned only to eligible same-technique candidates, then classes are processed largest first with bounded correlation blocks, deterministic ties, and protected minimum sizes. The official workflow prunes derivative and nobaseline libraries before medoid/model creation while leaving raw unpruned.
  • Harmonized reviewed metadata aliases and made build_lib() lookup keys explicitly selectable, with optional fallback-key merging and fill-only lookup values. The official workflow coalesces username into a missing organization before one type join and verifies complete library/spectrum types. The curated reference tables now separate polyamides from polyacrylamides, classify adipate polymers as polyesters, correct PA, aramid, Nomex, duplicate, and common-name mappings, and cover reviewed organization plus exact user-source fallbacks.
  • Added predict_class_reference() for reviewable class-table curation. Flexible patterns now live in a separate regex reference, run only after the exact lookup, and fill only blank materials when every match agrees. Exact overlaps are allowed and reported; distinct-material clashes stay blank.
  • build_lib() now removes recognizable paths and every read_any()-supported trailing file extension from spectrum_identity before exact metadata lookup. Numeric OPUS suffixes include any terminal period followed only by digits, such as .10. It records an audit attribute and normalizes exact lookup keys the same way. The compressed exact class table no longer carries extension-only aliases, and the source table records all observed spectrum techniques, including MBARI as Raman.
  • Accelerated reference-library Savitzky-Golay derivatives with compiled convolution and polynomial baseline subtraction with reusable QR fits. The retained benchmark compares the former implementations and enforces tight same-output tolerances.
  • Added the opt-in compact map Specs 0.2 format for ENVI/H5/ZIP inputs. Regular coordinates and repeated metadata use validated descriptors, while optional S/N background suppression retains foreground values and maps every rejected source to an exact virtual zero spectrum with auditable reasons. Weighted PCA/K-means and foreground Hilbert transforms preserve full-source multiplicity without expanding compact pixels. The bundled app now stages one local direct path or one hosted WORKERFS mount, reads only after Run, and offers the compact transformed map as an RDS download.
  • automate_particle_analysis() now treats both S/N threshold extremes as valid outcomes. Removing every map pixel emits a message and returns an empty analysis before library matching; retaining every pixel emits a message and continues, allowing connected collapse to identify and measure the full map as one particle per source.
  • Reduced default read_envi() peak memory without changing its public API or returned OpenSpecy format. BIP, BIL, and BSQ files are now read in bounded blocks directly into the final band-by-pixel matrix instead of constructing and permuting multiple complete arrays; spectral_smooth = TRUE retains its existing three-dimensional smoothing path.
  • Reduced read_zip() peak memory for two-member ENVI HDR+DAT archives by streaming the compressed binary directly into the same blockwise band-by-pixel reader. This avoids retaining a complete extracted DAT beside the final matrix in WebAssembly while preserving the returned OpenSpecy data and the existing extraction path for other ZIP layouts and smoothed ENVI reads.
  • Fixed collapsed analysis settings requiring a separate maximize click: the Preprocessing, Identification, Advanced, and Quantification tabs now expand the card and activate the chosen tab with the same click. Run, Recalculate Preview, and download actions again schedule the central loading overlay directly from the browser click, before a blocking local or WebAssembly R task can delay server phase messages. The overlay now follows Shiny’s real idle lifecycle instead of being dismissed after the first reactive flush, which could precede lazy identification and rendering work.
  • Changed the default assess_spec() silent region to 2420–2550 cm-1 and the high-tail/CO2 detection and automatic-correction ratio from 3x to 2x. Explicit caller values remain unchanged.
  • Removed speculative RAM forecasting from the Shiny app. Jobs now proceed until the real read, allocation, or processing operation succeeds or fails, with elapsed-phase recovery guidance while retaining the 10 GiB input limit.
  • The hosted Shinylive app can mount browser-selected files into webR WORKERFS and pass their paths to the ordinary read_any() pipeline, avoiding the copying multipart/R-raw upload bridge while still fully materializing an in-memory OpenSpecy object. Shinylive now presents only that mounted-file picker, while local Shiny presents only its native upload. Hosted mount and read/materialization status appears in the central progress popup instead of explanatory/status text below the picker. Mounted text spectra are read through fread()’s text parser to avoid its unsupported 32-bit WORKERFS file memory map while retaining delimiter/type inference and output structure.
  • WebAssembly repository builds now reuse a verified dependency-only CRAN-like cache locally and in GitHub Actions. Every reuse evicts and rebuilds OpenSpecy, refreshes changed dependency versions, regenerates the VFS image, and retains exact commit/artifact checks.
  • Fixed active-spectrum quality findings for collapsed maps: retained units and rejected clicked pixels now use the same one-spectrum object as the plotted trace, and SNR is calculated directly from that object instead of indexing a dataset/heatmap vector. Rejected pixels are labeled and no longer assessed as synthetic zero spectra.
  • Fixed Spatial Smooth running its (potentially expensive) convolution immediately on every toggle/Spatial Standard Deviation change, before Run was ever clicked. An always-on observer that keeps the heatmap’s selection marker in sync with clicks was reading the spatially-smoothed object purely for pixel x/y coordinates, which smoothing never changes, and that incidentally forced the real computation to run live.
  • Changed Remove Isolated Spikes, Flatten Region, and Range Selection to default off. Whether their toggles are on or off, the viewed spectrum’s Warnings/Successes now always include a spike/CO2-region/high-tail/ saturation check (previously these four were only ever reported as part of “Automatic Corrections Made,” which stayed silent when the matching toggle was off, and a leftover filter separately hid them from Warnings/ Successes even after being computed), so turning automatic correction off never hides whether the spectrum actually has the issue. Every one of these checks now also has its own specific success message (e.g. “No isolated single-point spikes were detected”) instead of a generic “check passed” placeholder. A Low Signal/Noise check was considered but left out as redundant with the app’s existing separate SNR Threshold finding.
  • Filled the Warnings/Successes buttons with their semantic color (amber/ green) instead of a thin border on a neutral background, so they read as clickable like the app’s other buttons; Automatic Corrections Made keeps its rainbow identity as a permanent fill (previously only a border shown when something had actually been applied), with a glow ring added to still flag when a correction was actually applied.
  • Fixed the Thresholded Particles download’s Particle Unit and Match ID heatmap images always drawing a legend, even though both are per-particle identifiers with too many categories for a legend to be useful.
  • Fixed a selection feedback loop that snapped a manual heatmap click on a multi-pixel collapsed particle back to that particle’s first/representative pixel instead of staying on the pixel actually clicked: syncing the sidebar metadata table’s selection to match a heatmap click echoed back through the table’s own selection-change handler, which was indistinguishable from a genuine row click.
  • Fixed the Top Matches table staying empty whenever Library type = AI model, even though the Top Matches download and the Selection Metadata table already showed AI predictions. AI mode has one prediction per spectrum rather than a ranked candidate list, so the table now shows that single prediction for the selected spectrum instead of erroring/staying blank.
  • Clicking Run, Recalculate Preview, or a download now shows busy feedback immediately instead of after a multi-second delay (dominated, for Run, by an unannounced whole-map signal-to-noise scan that ran ahead of the first progress message; Recalculate Preview previously had no progress signal at all in its default configuration). Run and Recalculate Preview also get an instant client-side busy indicator on click, and downloads show the same indicator consistently in both the local Shiny app and the hosted Shinylive build.
  • Fixed clicking a row in the Uploaded Metadata table jumping to an unrelated or unchanged map location instead of that particle’s first (lowest raw pixel index) location: the handler treated the table row’s particle/unit index as if it were a raw pixel index, and separately skipped updating the selection whenever the clicked unit happened to already equal the current selection’s default – most visibly on the very first row click, since the app’s initial selection defaults to unit 1. It now resolves both the selected pixel and unit directly, unconditionally, matching the heatmap click handler.
  • Changed the Summary panel’s “Good Signal”/“Good Match Values”/“Good Identifications” bars to show the underlying pixel counts (e.g. “142 / 331,180”) alongside the percentage: shinyWidgets::progressBar() rounds its displayed percentage to the nearest whole number, so a real but small share of passing pixels on a large, sparse map could read as a misleading “0%”.
  • Moved the Signal/Noise Recalculate Preview button out of the histogram card it previously shared with the plot: that card dims when the preview is stale, which was dimming the one control needed to un-dim it. The button now uses the same green (“would change the result”)/dark navy (“already current”) convention as the main Run button, and the histogram itself now visibly resets to blank (instead of freezing on the previous dataset’s chart) when a new file is uploaded.
  • Fixed a bug in canonical_state_gate’s Run-gated result where return() inside tryCatch() exits the enclosing reactive directly, silently skipping the settings snapshot the previous entry’s fixes attached after the tryCatch() call – on every code path except one (collapse with Threshold Correlation on and a successful result), canonical_state()’s settings were NULL, so the heatmap/plot/download fixes below were silently inert whenever Threshold Correlation was off. Settings are now attached at every actual return point instead. This also fixes the particle-size histogram never rendering when collapsed (its req() on the missing settings blocked it silently) and the Map Color selector/ particle-summary gating for the same reason.
  • Added a Signal/Noise Basis choice (Raw / Spatially Smoothed, the previous default; or Fully Processed, which also applies every other enabled preprocessing step to each pixel before scoring it) that decides which pixels are eligible for particle collapsing. The Signal/Noise histogram preview no longer recomputes live on every settings change (which could re-run spatial smoothing or, with Fully Processed, full preprocessing, before Run was ever clicked); it now only updates on Run or a new Recalculate Preview button in the Threshold Signal/Noise box, and dims when the basis, Spatial Smooth, or thresholding settings have changed since its last computation. The memory preflight advisory no longer runs a live spatial smooth either (uses the raw upload’s dimensions only, which is all it ever needed).
  • Fixed a filter_spec() “zero spectra” error when clicking a collapse-rejected/background pixel: the raw-spectrum overlay reactive had no fallback for an invalid selection (unlike the processed-spectrum reactive, which already flat-lines correctly); it now does the same.
  • Fixed the Run-gated reactivity the previous entry introduced: the heatmap, particle/material plots, correlation and signal/noise histograms, download type list, and progress-bar summaries now read only the settings captured at the last Run instead of live checkboxes, so toggling Collapse Particle Spectra, Spatial Smooth, Threshold Signal/Noise, or Threshold Correlation no longer recomputes or re-renders anything before Run is clicked. Added an on/off switch to the Identification Strategy box (default on) that fully skips identification, and one Turn All On/Off button per settings tab that has switches. Processed spectra now flat-line below the enabled signal/noise threshold whether or not Collapse Particle Spectra is on (previously only when it was on). Fixed a race between the six Run-triggered result caches that could leave quantification, quality reports, and other Run-gated results silently stuck at their pre-Run value; results are now populated in an explicit, deterministic order. Fixed the Map Color selector defaulting to Signal/Noise and never updating once Material Class/Match ID/Match Value became available. The Run button’s default (nothing-to-run) color is now the app’s dark background color instead of light blue, and the Spectra card has visible space above it. Vectorized residual spike detection across every spectrum in a map/batch upload at once instead of one small allocation per spectrum per correction pass (same output; see benchmarks/spike_correction.R), and raised the identification blockwise match size from 100 to 1,000 query spectra per block (same output, less chunking overhead). The memory preflight estimate no longer runs the actual spatial smooth as a side effect of estimating memory. Fixed a duplicate id="columns_selected" between the Top Matches column-choice uiOutput wrapper and its inner selectInput.
  • Added a single Run button as the sole trigger for the app’s analysis tranche, replacing the four per-tab owner switches; the button turns bright green whenever a new dataset is uploaded or a setting changes, and returns to the app’s normal accent color once Run has produced current results. Uploading a new dataset now also resets the heatmap, spectrum plot, and quality/automatic-correction reports back to a “click Run” state instead of continuing to show the previous dataset’s results. “Collapse Particle Spectra” and “Spatial Smooth” are silently ignored for a single uploaded spectrum instead of erroring. Fixed a crash (“wasn’t able to determine range of domain”) when a heatmap’s selected color metric has no finite values for any pixel (for example, when no uploaded spectrum clears the correlation threshold).
  • Replaced the Preserve Uploaded Wavenumbers advanced switch with a Mean Up conformation technique (the new default). Mean Up only resamples the uploaded spectra to the selected Wavenumber Resolution when that resolution is finer than what was actually uploaded; otherwise it leaves the uploaded axis untouched and conforms the reference library onto it instead, exactly as the removed switch did.
  • Rebuilt the bundled app around one in-memory OpenSpecy workflow with a unified 10 GiB upload ceiling and best-effort resident/peak-memory guidance. Identification now ranks bounded query blocks and retains only a shared Top N result (10 by default) for the match table and download. Particle analysis calculates signal/noise after optional spatial smoothing but before other processing. Spectral cluster modes now fit source-scoped PCA/K-means first, identify collapsed clusters once, and either retain them as non-spatial particles or project their identities into a second connected same-material spatial collapse without re-identification. Correlation thresholds reuse that first pass. All heatmaps black out rejected pixels, omit inline legends, and expose a formatted legend modal (or a >30-category explanation); rejected clicks return no match and a flat processed trace. Threshold histograms remain on-theme, and only caught errors open alert dialogs. The default-on uploaded-axis option conforms the reference library onto the exact uploaded axis with memory-bounded mean_up averaging/interpolation, and particle ZIPs restore the summary table, both histograms, every heatmap, material summary, and size distribution.
  • Corrected package automate_particle_analysis() partitioning so connected units and source-scoped PCA/K-means clusters never cross source maps or H5 regions; return stable pixel-to-unit membership and aligned unit IDs/metadata; and apply the minimum pixel area inclusively. Connected units retain recomputed shape and signal summaries, while specs_centers remains the public K policy and non-default specs_steps now fails clearly instead of being silently ignored.
  • Added experimental, package-only FileSpecs descriptors for read-only H5 and ENVI maps. They fingerprint immutable sources, keep derived generations in a separate atomic cache, provide bounded decompress_spec() selections and lightweight region views, stream complete rectangular views to new atomic float64 ENVI pairs without wavelength-axis truncation, and fail early for unsupported matrix-only operations while preserving legacy matrix-backed Specs behavior. The first direct large-map workflow streams region-wise S/N and exact particle means through automate_particle_analysis(), retains one exact best match, and lazily caches registered regional H5 mosaics for particle images; it intentionally requires the collapse strategy, mean, and non-entropy S/N. spectral_smooth = TRUE now streams a halo-padded 3-D Gaussian smooth (matching mmand::gaussianSmooth() exactly) instead of erroring, without ever materializing a full region. H5 mosaics retain region, local and stage coordinates, unique pixels, and intersecting image tiles. These APIs remain available to package users but are no longer routed through the app.
  • automate_particle_analysis()/automate_particle_filespecs() now return queryable plot data (particle_image, particle_heatmap, particle_heatmap_thresholded, cor_heatmap, sn_histogram, cor_histogram; each a list with grid/histogram values and a type, or type = "empty" with a reason when nothing passed filtering) instead of stored recordedplot objects; this is a breaking change to the field names and shape of automate_particle_analysis()’s per-sample result. plot() still draws any of these with base graphics, and the app renders them with Plotly for on-theme, interactive maps. Advanced no longer disables its own controls while off, matching the other top-level switches. The Thresholded Particles download drops the duplicative Raw Map object choice, defaults to itself once a particle result exists, and now zips every selected content type including an explanatory details/summary when no particles passed filtering. The redundant “No regions passing threshold” popup is removed in favor of the existing quality warning/success indicators.
  • Unified the app’s numeric, categorical, and particle heatmaps into one Plotly renderer with hover tooltips, an on-demand modal legend, and a selection marker kept in sync via a cheap trace restyle; this replaces the separate base-graphics heatmap, its click/brush handlers, and the metadata popover. Material-class colors are resolved from one shared palette across the heatmap, particle summary, and particle_image(). The Advanced switch and its correlation threshold default on. The Uploaded Metadata tab moves x/y/z and other per-pixel columns to the front for every source, and for sources over 100,000 spectra shows only those columns, dropping duplicated file-level metadata. automate_particle_analysis() now accepts a character vector of file paths, reading and processing each one in turn. Base-graphics particle-plot legends (plot(), particle_image()) now draw in the margin outside the plotted data instead of overlapping it. The as_OpenSpecy() data.table-to-matrix conversion notice is silent when called internally.
  • Added correct_spike() with a conservative wavenumber-aware residual method and the manual and automated prominence/FWHM methods described by Coca-Lopez (2024). Corrections are transactional, preserve the OpenSpecy axis and metadata alignment, avoid boundary extrapolation, and retain auditable accepted/rejected-region diagnostics. Safe correction now repeats while the correctable count decreases, retaining successful passes when later candidates are newly exposed and leaving no-progress candidates unchanged with their safeguard reason.
  • Added opt-in spike and saturation checks plus report = "all" status output to assess_spec(), exact sorted-amplitude breakpoint_snr support to sig_noise(), and optional spike correction at the start of process_spec(). restrict_range() can now remove one guarded union of hard saturation intervals from a whole batch, with irregular-axis coverage accounting and a conservative rollback when the proposed loss exceeds 70% or leaves too few points.
  • Added a default-on app control for isolated spikes and an opt-in saturation control, separated automatic-correction details from warning/success results for the active spectrum, an external adaptive spectrum legend, and bright colorblind-accessible heatmap palettes. Numeric map legends sit horizontally above the plot, default Match Name maps no longer flash a numeric metric, categorical Match Name colors are shared with the material summary, and map selection updates its marker without rebuilding the heatmap. Hosted WebAssembly downloads now use a same-frame validated Blob handoff while local Shiny retains its native download handler; browser smoke tests require genuine CSV and ZIP files from real clicks.
  • Added a dark, accessible static landing page at the hosted-site root with the embedded app, navigation guidance, search and social metadata, tutorial, publications, contacts, and funding context. Conventional README-driven pkgdown documentation now lives at /pkgdown/; the app remains at /app/. Pew-Gerstner Fellowship in Ocean Plastics Research and Walking Softer are credited as Thriving monetary partners.
  • Added a reusable workflow for compressing hyperspectral images with PCA and K-means (k = 100) and plotting pixel cluster groups with heatmap_spec().
  • Fixed bundled Shiny app startup when another attached package caused R to resolve dashboard box() calls to graphics::box().
  • Restored the empty spectrum canvas and made uploaded spectra render before reference matching completes. Replaced redundant native progress popups with one central status display showing the active phase, elapsed time, and a staged progress bar without fragile completion-time estimates. Spectral, heatmap, and diagnostic plots now use a cohesive bordered dark theme.
  • Added ratio-based CO2 and high-tail quality checks that avoid flagging unstructured noise. flatten_range() and restrict_range() can now assess and correct those issues automatically, with guarded batch-wide tail cropping. The bundled app enables both corrections and identification by default, gates reference results on an uploaded spectrum, and prioritizes downloads according to the current upload and identification state. In the app, ordinary preprocessing now runs before range/CO2 assessment, and an automatic correction is retained only when it strictly increases the number of passing spectra; the bundled Test Map exercises both corrections.
  • Fixed Test Data, Test Map, Processed Spectra, and Top Matches downloads by restoring the native Shiny download link and validating every generated payload. Added an always-available, timestamped User Metadata CSV containing the current analysis inputs for manual reproducibility, without adding a settings-import compatibility contract. Top Match options are collapsed by default.
  • Refined the bundled app workspace with collapsed-by-default settings and download cards, tab-triggered settings expansion, selection-specific download labels, responsive gap-free summary layouts, and one dark navy/cyan theme for the app chrome, cards, controls, tables, progress widgets, and plots.
  • Added named area-under-band ratio indices, explicit custom area-ratio composition, peak_ratio() for nearest-point or linearly interpolated point ratios, point_intensity() for non-ratio point measurements, and 4S Fill Peaks baseline correction. The app’s Quantification tab now defaults off and lets users save ratios, individual band areas, and individual point intensities from precise numeric inputs. Custom Ratios and Single Measurements now share the single Quantification owner without a redundant child switch. The app calculates any combination from the exact final processed spectra displayed in the app and includes exact definitions, values, and processed-spectrum provenance in Processed Spectra and Top Matches downloads.
  • Made the representative medoid library the interactive app default and cache reference-library preparation by the final processed axis. The complete library remains an explicit local-app option for users who accept its longer initial calculation.
  • Reimplemented 4S Fill Peaks smoothing and suppression in base R, removing the compiled baseline runtime dependency so the same correction works in local R and the hosted WebAssembly app.
  • Made the contextual download action fill its card, changed uploaded spectrum traces to white, standardized enabled switches to green and white, validated all informational disclosures, and restored the historical donation choices in an on-demand right-side header dialog. Removed the inactive help and dark-mode header toggles, aligned the full-width Spectra and Summary cards, and kept disabled child settings inert until their owning analysis switch is enabled. Automatic tail mode now visibly disables its manual bounds and explains that assessment uses the full processed axis. Processing disclosures now explain each spike and saturation input, success findings omit empty interpretation and action fields, and automatic details report the ranges actually corrected by spike, saturation, CO2, and high-tail operations.
  • Streamlined the app to one analysis workspace with Preprocessing, Identification, and Advanced tabs; moved independent thresholds and map controls to Advanced, removed Google Translate and the informational sidebar, and moved community, partner, and contract information to the hosted landing source.
  • Embedded the hosted Shinylive app on the static landing page with real Shiny readiness feedback and a viewport app mode that persists through upload/download dialogs. GitHub retains a normal README, and brief reactive updates no longer flash the app’s processing overlay. Relative app/ and pkgdown/ routes keep GitHub project and hosting-fork deployments portable.
  • Added source manifests, app configuration, and GitHub Actions for building a hosted Shinylive/WebAssembly app from inst/shiny/. The hosted app is pinned to a versioned wasm CRAN-like repository containing OpenSpecy and the app dependency closure, stages the small medoid/model libraries, and keeps full library support available in the local bundled app.
  • Bundled the action-built, commit-pinned wasm library image into Shinylive so the app loads the package version in DESCRIPTION without waiting for the floating webR package repository. Deployment now smoke-tests the package version, upload, identification, download, and public GitHub Pages endpoint.
  • Fixed hosted-app startup by including hard dependencies from R’s recommended packages (including Matrix, survival, and their closure), skipping the unavailable Google Translate connectivity probe in WebAssembly mode, and exercising the Shinylive iframe/selectize controls in the browser smoke test.
  • Consolidated GitHub Pages publication into one native deployment containing the static landing page, conventional pkgdown docs, and the self-contained Shinylive app. The complete wasm package repository is now retained as a pinned Actions build artifact and embedded in the app instead of accumulating public wasm/<commit> trees.
  • Bundled the Shiny app in inst/shiny/ from wincowgerDEV/OpenSpecy-shiny commit 60d1bdefff90affcda3353d7c389ea8f3748ca56; run_app() now launches the installed app by default instead of downloading app files from GitHub.
  • Added bundled-app path, asset, source-parse, YAML-removal, and app helper regression tests; optimized/pruned Shiny app static assets and fixed app sample-data loading for the current matrix-backed OpenSpecy spectra format.
  • Fixed bundled Shiny app smoke-test issues: startup no longer opens a blocking donation modal, bundled UI no longer auto-loads remote image assets, and identification uses existing package/app cached reference libraries before attempting a download.
  • Removed built-in YAML read/write support and the YAML example fixture; read_spec() and write_spec() now support JSON, RDS, and CSV formats.
  • Removed runtime signal and cluster dependencies by using internal Savitzky-Golay filtering and PAM medoid selection in package workflows.
  • Made internal PAM medoid return order deterministic in tied cases so reduce_lib(return = "ids") is stable across platforms.
  • Aligned automate_particle_analysis() collapse exports with legacy analyze_features() particle details, summaries, raw maps, and processed particle objects; returned list item names now mirror export filenames and formats.
  • Added automate_particle_analysis() image return/export support for particle heatmaps, thresholded particle heatmaps, and correlation heatmaps. Requested image outputs are returned as recorded base-graphics plots, and are written to matching image files when output_dir is supplied.
  • Fixed automate_particle_analysis(particle_id_strategy = "all_cell_id") so cell-level match joins preserve x/y map coordinates, collapsed particle spectra are processed to the library wavenumber axis before final matching, H5 mosaic coregistration can drive complete edge-tolerant particle color extraction, and single-class character feature labels define one class instead of erroring.
  • particle_image() now leaves particle labels off by default and uses the attached visual image’s full map extent when overlaying collapsed particle results. Particle maps are now drawn as categorical rasters with transparent background cells rather than point markers.
  • Added a signal/noise heatmap legend, enlarged the correlation heatmap legend, and made automate_particle_analysis(spectral_smooth = TRUE) smooth already-loaded OpenSpecy/Specs maps as well as file-backed maps.
  • Fixed visual-image BMP reading without relying on the unavailable grDevices::readbitmap() helper.
  • Fixed .xyz text-map reading so coordinate metadata and spectra are aligned.

OpenSpecy 1.7.0

  • Improved run_app functionality to allow for version control.
  • Added automate_particle_analysis() for package-native batch particle detection, matching, summaries, and optional file output based on OpenSpecy/Specs workflows.
  • Added visual-image helpers (add_visual_image(), visual_image(), and detect_image_origin()) so spectral maps can carry aligned visual imagery for feature color extraction and base graphics overlays.
  • Added particle_image() for dependency-light particle map plotting with the package material color defaults.
  • Added crowd_lookup(), recovery_rate(), minimum_detectable_amount(), and batch_detection_limit() for generalized particle-size crowding, spike recovery, MDA, and single-blank BDL summaries.
  • read_h5() now defaults to raw per-region/pixel spectra instead of collapsing by particle, preserves region and stage-position metadata, parses scalar H5 metadata where possible, and attaches mosaic imagery when present.
  • Faster ENVI file reading.
  • Add area under band calculation.
  • Added library-builder helpers for creating lookup templates, auditing metadata joins, reducing libraries with PAM medoids, and training model libraries.
  • Expanded build_lib() into the standard end-to-end library workflow with full-range resolution-6 merging, lookup-triggered metadata and material hierarchy joins, editable metadata-name cleanup, automatic NA-aware recipes, signal-to-noise, processing attributes, and optional assess_spec() metadata summaries.
  • build_lib() now converts declared reflectance and transmittance sources to absorbance before merging. The intensity_unit object attribute takes precedence over per-spectrum intensity_units metadata, and conversion can be disabled with convert_intensity = FALSE.
  • build_lib() now accepts file paths, one OpenSpecy, or a list of OpenSpecy objects. Each RDS path may contain either one object or a list, while other formats continue through read_any(). Named progress stages and elapsed time are reported by default and can be disabled with progress = FALSE. It also accepts optional restrict_range_args before library recipes. Large same-axis source lists are bulk-prepared to avoid repeated legacy object coercion.
  • Automatic build_lib() metadata lookups now infer the single shared column with overlapping values and unique lookup keys, skip lookups with no usable shared key, remain strict when multiple usable keys are ambiguous, and coalesce curated lookup values back into existing metadata columns.
  • Added optional metadata value normalization with build_lib(clean_metadata_values = TRUE) and lib_clean_metadata(clean_values = TRUE), used by the reference workflow to trim/lowercase metadata values before joins.
  • Fixed NA-aware process_spec() dispatch so downstream arguments such as baseline or intensity type reach the intended processing function. NA-aware processing now groups leading/trailing missing-value ranges and bulk-processes complete spectra where possible.
  • Optimized sig_noise() for matrix-native signal/noise summaries, including the default run signal-to-noise calculation used by build_lib().
  • build_lib() now generates reference-library sample_name hashes at the source stage using the legacy cleanup recipe and removes exclude_ids against both sample_name and sample_name_old, preserving compatibility with the curated bad-ID hash list.
  • filter_spec() now treats NA values in logical filters as FALSE and checks logical filter length, preventing spectra/metadata misalignment when filtering metadata columns that contain missing values.
  • Added a tracked, package-build-excluded workflows/OpenSpecy_reference_library.R workflow composed only from existing package operations, with canonical lookup and exclusion CSVs under workflows/data/. Repeated filtering, reduction, assessment, model building, and artifact writing are applied across named library lists.
  • The reference workflow now prunes legacy raw-source technical metadata using a versioned metadata-drop CSV while retaining modern canonical metadata names.
  • Exported metadata-name cleaning helpers with automatic underscore and terminal-s matching, extensible exact aliases, and ambiguity-checked regular expression rules.
  • as_Specs() now supports an end-to-end compressed Specs workflow. By default it fits PCA and then Hilbert-encodes the scores into exact high/low 64-bit code rows; K-means can be placed before, between, or after those steps. Hilbert Specs objects can be decoded, decompressed back to approximate OpenSpecy spectra, subset-decompressed by numeric index for plotting, and matched with fast Hilbert-code distance.

OpenSpecy 1.5.0

Major

  • Update to vignettes for new functionality.
  • Improved plots
  • Improved tests for Open Specy format.
  • Improved reading of csv files.
  • Improved reading of spa files.
  • Extended options for library version downloads.
  • Simpler function calling
  • Extended baseline fitting options.

OpenSpecy 1.3.0

Major

  • added 2 new libraries a nobaseline and derivative version of medioid and model
  • Created new function for spatial smooth without reading envi files
  • Allow adj_intens to work on vectors or Open Specy objects

Minor

  • fixed bug with mac reading libraries

OpenSpecy 1.2.0

CRAN release: 2024-09-14

Potentially Breaking

  • Removed share data options in all functions. They just weren’t useful to users at all and were more of an administrative thing. Keeping them forced us to be incompatible with webR.

Major

  • added support for siMPle files.
  • added support for xyz files.
  • added support for img files.
  • improved interactive plot popups.
  • changed how libraries are downloaded to avoid osfr pacakage.
  • increased support for options when collapsing maps.
  • avoid forcing min-max relative plots in interactive mode.
  • create static map option.

OpenSpecy 1.1.0

CRAN release: 2024-06-13

Minor Improvements

  • updated links

OpenSpecy 1.0.9

Minor Improvements

  • more closing and flexibility options

OpenSpecy 1.0.8

CRAN release: 2024-03-14

Minor Improvements

  • updated manage_na, spec_res, read_any for easier flow with the app

OpenSpecy 1.0.7

CRAN release: 2024-03-11

Minor Improvements

  • Modified manage_na.R
  • Added to NAMESPACE

OpenSpecy 1.0.6

CRAN release: 2023-11-25

Minor Improvements

  • Add attributes to OpenSpecy objects
  • More flexible sig_noise()
  • Simpler matching

OpenSpecy 1.0.5

CRAN release: 2023-10-31

Minor Improvements

  • Support .tsv files

Bug Fixes

  • Flip xy coordinates in ENVI files

OpenSpecy 1.0.4

CRAN release: 2023-10-02

Minor Improvements

  • More contributors
  • showlegend argument for interactive plots

Bug Fixes

  • Fixes a fatal error in match_spec() probably causing incorrect identifications

OpenSpecy 1.0.3

CRAN release: 2023-09-13

Minor Improvements

OpenSpecy 1.0.2

CRAN release: 2023-09-05

Bug Fixes

  • Set data.table threads to 2 for (CRAN) checks

OpenSpecy 1.0.1

Bug Fixes

  • Fixed spelling mistakes
  • Reduced example and test run times for CRAN

OpenSpecy 1.0.0

New Features

  • Complete package, app, and SOP overhaul!
  • The Shiny app has been outsourced to an own GitHub repository: https://github.com/wincowgerDEV/OpenSpecy-shiny
  • Spectra are now stored in dedicated OpenSpecy objects, which can be managed with a set of new functions including c_spec() for concatenating spectra or converting them back to tables
  • Various functions have been renamed and improved, for instance, to facilitate reading (and writing) spectral files
  • New functions include def_features() to identify microplastics in spectral maps and ai_classify() to use AI for matching/identifying spectra

Minor Improvements

  • Added pkgdown documentation
  • Added code coverage tests

OpenSpecy 0.9.5

CRAN release: 2022-07-06

Bug Fixes

  • Fixed outdated links and redirects

OpenSpecy 0.9.4

Minor Improvements

  • UI improvements
  • Gitter support

Bug Fixes

  • Fixed invalid regex failing CRAN checks

OpenSpecy 0.9.3

CRAN release: 2021-10-13

Minor Improvements

  • Better error handling for .csv formats
  • Add funders and goals
  • Updated package citation
  • CI testing for Mac

Bug Fixes

  • Fixed testthat routines occasionally failing CRAN checks

OpenSpecy 0.9.2

CRAN release: 2021-05-20

New Features

  • Manual baseline corrections
  • Citable technical note

Minor Improvements

  • More generic .spa file reading
  • Added funding

Bug Fixes

  • UI improvements

OpenSpecy 0.9.1

CRAN release: 2021-04-11

Bug Fixes

  • Checks fail gracefully if api.osf.io is not reachable
  • Adjust UI selectors to comply with inverse axis and not exceed ranges

OpenSpecy 0.9.0

CRAN release: 2021-04-09

New Features

  • UI overhaul
  • Give more control to the user when starting via run_app()

Minor Improvements

  • Reverse spectral axes to comply with most wavenumber scales
  • Let users select metadata license
  • Improved data sharing and logging capabilities
  • Google Analytics removed

Bug Fixes

  • Use tempdir for unit tests and examples

OpenSpecy 0.8.2

CRAN release: 2021-03-31

Minor Improvements

  • Compliance with CRAN style guide
  • More references with DOIs
  • Better error/warning messages during Shiny file input

Bug Fixes

  • Fixed bug with Shiny reactive values

OpenSpecy 0.8.1

Bug Fixes

  • Fix redirecting URLs

OpenSpecy 0.8.0

New Features

  • Use external Open Specy libraries from OSF
  • read_asp() for reading Agilent .asp files
  • GUI overhaul
  • Comprehensive package vignette and function documentation
  • Unit testing for main functions

Minor Improvements

  • Better error handling
  • Stripped down dependencies

OpenSpecy 0.7.0

  • Transferred code base from openspecy.org to this R package