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Merge pull request #36 from dipterix/dragndrop
Multiple update (see commit comments and `CHANGELOG`)
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,100 @@ | ||
| ## Changes since last CRAN release | ||
| * `e1dfba0f (HEAD -> dragndrop)` [_`dipterix`_]: Color look-up table can be set with arbitrary single color (in `HexString`, indicating that all values should be rendered with such color; Drag & Drop volumes can change to single colors | ||
| * `c04d7783` [_`dipterix`_]: Remembers to state when switching volumes (`datacube2`) | ||
| * `d7cab685 (origin/dragndrop)` [_`dipterix`_]: Allowed prototype contact colors to be fixed; Prototype control points displays channel information (provided control points are channels) Added color (`randomColor`, `testColorString`) and file-name utility functions; Soft removed `addColorCoat` and using `ElectrodeMaterial`, this results in massive code improvement in electrode instance; Allow to set default electrode colors if a contact is not rendered with values nor fixed color; Fixed `NamedLut` color error when a value range is zero; Prototype electrode click information displays the channel number; Fixed `RShinyDriver` issue when object does not have construction parameters (using `getThreeBrainInstance` instead); | ||
| * `1ed4b5b4` [_`dipterix`_]: Scrolling on side canvas is faster now | ||
| * `b4cd7dbf` [_`dipterix`_]: Drag & drop file names is sanitized to avoid displaying issues; Electrode contacts (`instancedMesh`) are now click-able; Dispose is cleaner now, it also fires events; Added `makeClickable` and `removeClickable` to replace previous `add_clickable` function; Renamed `register_object` to `registerToMap`; Fixed `UV` mapping issue in sphere electrode geometry; Better ways to sanitize `datacube`; | ||
| * `e0437d6c` [_`dipterix`_]: Improved `datacube` overlay texture, including using `clamp-to-border` instead `clamp-to-edge`; Fixed `shader` issue when transparency is set to negative (treated as 1) | ||
| * `7a196ff4` [_`dipterix`_]: Ray-casting electrode prototypes with `instancedMesh` now works under `contact-only` mode; Show electrode prototype with contacts by default | ||
| * `28f3af8d` [_`dipterix`_]: Changed drag & drop default color mode; changing global opacity also affects the `Voxel Opacity` under volume settings; `AbstractThreeBrainObject` now inherits `EventDispatcher` (from `three`) so events can be registered to instances directly; Color changes to `datacube2` will notify the underlay `datacube` via event dispatcher; For each color keyword added, a reversed version is also registered; Fixed discrete volume treated as continuous map when overlaid | ||
| * `5f068018` [_`dipterix`_]: Added color modes for uploaded images; using `NIfTI` headers to get calculated color intensities before applying heuristic approach; removed `normalize` method (replaced by `getNormalizedImage`) from `NiftiImage` and `MGHImage` | ||
| * `bb1e6150` [_`dipterix`_]: Using script to generate change log automatically from Git commits | ||
| * `1eea71c6` [_`dipterix`_]: Added news | ||
| * `6f3ceefe` [_`dipterix`_]: bump version | ||
| * `a9d0c8f6` [_`dipterix`_]: rename electrode prototypes: (type-company-version.json) | ||
| * `bb3adf85` [_`dipterix`_]: minor fix | ||
| * `01ed4695` [_`dipterix`_]: Added campass to side cameras when slice mode is not canonical; dragndrop changes folders; removed UV for sphere electrodes; added model-up for segmented electrodes shaft; fixed a bug when slice instance is missing but controller tries to set overlay; voxel threshold is async now; changed default to some controller; added broadcast() to more controllers; atlas number will be displayed so users don't need to search for lut; added global debug flag; js source map is hidden so browser won't complain about missing map; | ||
| * `fa4fe3f6` [_`dipterix`_]: viewer can be seen in quarto/rmarkdown/knitr now | ||
| * `e7cdff72` [_`dipterix`_]: added default prototypes | ||
| * `60f0dddd` [_`dipterix`_]: added functions to create seeg prototypes | ||
| * `2096eb4c` [_`dipterix`_]: added electrode "up", allowing electrode to rotate along direction | ||
| * `6a53d729` [_`dipterix`_]: dnd surface granted with USER_ALL_SIDE_CAMERA_4; implemented slice overlay; splited render distance into Frustum near and far; added model2vox to datacube and datacube2; no more timeout for workers; fixed sEEG-16 UV mapping | ||
| * `0c466378` [_`dipterix`_]: dynamic async workers; support dnd gii and colormap; added snap-to-electrode mode; dnd surface infer space from filename (BIDS); no voxel matching for subcortical surfaces; | ||
| * `d64ae335` [_`dipterix`_]: added support for electrode directions; prototypes are loaded from system by default to allow updating certain params | ||
| * `a9275a43` [_`dipterix`_]: fixed prototype channel number not set when set from list | ||
| * `3dc98c5e` [_`dipterix`_]: added options to enable/disable cache; used better file loader with options to use js workers | ||
| * `0ef6c1c3` [_`dipterix`_]: fixed UV issues in prototype | ||
| * `2c1f30e4` [_`dipterix`_]: allow contact to be fixed (anchor); reduced number of control points to 2; removed `flattern=FALSE` for prototypes; fixed prototype transform issue | ||
| * `4351cc4b` [_`dipterix`_]: default surface colors | ||
| * `ad4b4299` [_`dipterix`_]: Implemented drag N drop | ||
| * `7fe52479 (origin/master, origin/HEAD, master)` [_`dipterix`_]: added remotes | ||
| * `b53c0725 (origin/custom-electrode-geom, custom-electrode-geom)` [_`dipterix`_]: using instancedMesh to represent electrode contacts when prototype is used | ||
| * `4cacfd41` [_`dipterix`_]: Multi-representation of electrode | ||
| * `e3bb38c0` [_`dipterix`_]: added mapToTemplate back | ||
| * `d5416c4e` [_`dipterix`_]: early stop when webgl2 is unavailable | ||
| * `4b71dee7` [_`dipterix`_]: no render if webgl2 is disabled | ||
| * `fa11027f` [_`dipterix`_]: Fixing win again | ||
| * `fe2cc379` [_`dipterix`_]: recompile | ||
| * `2313b0a5` [_`dipterix`_]: changed pial surface material depthwrite when transparent | ||
| * `cf2f1905` [_`dipterix`_]: fixed the electrode values when prototype is used | ||
| * `88e10f8d` [_`dipterix`_]: js fix | ||
| * `a6d61c23` [_`dipterix`_]: Added support for QRCode; using flags instead of function to hard update contact positions (may not ready) | ||
| * `f77c8ee0` [_`dipterix`_]: docs, always docs | ||
| * `b498b613` [_`dipterix`_]: avoid auto-load geometries; added type string to prototype; added set_matrix_world to set transform of an object | ||
| * `6e91dba8` [_`dipterix`_]: added custom electrode shape support | ||
| * `fe5f2c84` [_`dipterix`_]: added news; cran-comments; allowed plot_slices to be additive | ||
| * `ca56af1b (origin/win-fix, win-fix)` [_`dipterix`_]: fixing the crash issue on windows | ||
| * `ba3f975b` [_`dipterix`_]: removed shader cache in surface shader (may cause window crash | ||
| * `8904130d` [_`dipterix`_]: updated readme | ||
| * `48ea5ea6` [_`dipterix`_]: adjust the implementation of background color and arcball radius; removed additional unsed params from material call; added zindex base to side canvas; added defaultColor to electrodes; fixed localization electrodes color not set correctly issues; completely removed composer effects | ||
| * `9785b05d` [_`dipterix`_]: trackball uses longer side instead of shorter side as arc radius; mouse position in the canvas is caluclated every mouse down instead of every resizing | ||
| * `85bffcbf` [_`dipterix`_]: internalize col2hexstr | ||
| * `9a5d74ad` [_`dipterix`_]: Added brain$electrodes$fix_electrode_color to fix contacts to a color for given clip names; added electrode visibility mode: use threshold only to show contacts that pass threhsold but have no values | ||
| * `467eac5d` [_`dipterix`_]: more robust controller.load | ||
| * `34727c80` [_`dipterix`_]: textsprite depth fix | ||
| * `c4365bad` [_`dipterix`_]: changed default controllers | ||
| * `78acc14a` [_`dipterix`_]: upgraded threejs to v160 with significant light fix + removed outline pass (using clearcoat instead) | ||
| * `56f0e000` [_`dipterix`_]: atlas label also returns atlas IDs | ||
| * `f0712167` [_`dipterix`_]: if user name rave_slices under fs folder, use it to display T1 slices | ||
| * `b28a22f5` [_`dipterix`_]: auto adjust T1 brightness when ploting slices | ||
| * `28767b24` [_`dipterix`_]: adjust title position | ||
| * `77a28c2f` [_`dipterix`_]: Added plot_slices to brain class | ||
| * `58c66337` [_`dipterix`_]: mesh clipping | ||
| * `c6f90fee` [_`dipterix`_]: Fixed download template subject URL query | ||
| * `e4092702` [_`dipterix`_]: dev bump | ||
| * `10524a4c` [_`dipterix`_]: Added default rave_slices in case users want to choose their own slices in the 3D viewer | ||
| * `a4cac580` [_`dipterix`_]: Allow slices to change gamma | ||
| * `ff842861` [_`dipterix`_]: make voxel IJK starting from 0 | ||
| * `c139b53c` [_`dipterix`_]: Fixed brain electrode mapping; added atlas guesser | ||
| * `16defcdb` [_`dipterix`_]: Added space transform for electrodes class; set controllers (setFromDictionary) uses try-catch clauses now | ||
| * `176e7746` [_`dipterix`_]: Partition datauri so the datauri size does not exceed 65529 | ||
| * `21e12b51` [_`dipterix`_]: bump version | ||
| * `a12128c4` [_`dipterix`_]: updated citation | ||
| * `06a99127` [_`dipterix`_]: truly standalone viewer | ||
| * `a5746ca2` [_`dipterix`_]: animation uses new cmap | ||
| * `af2d2c76` [_`dipterix`_]: added png to dep | ||
| * `bb773fcb` [_`dipterix`_]: Added ACPC alignment, new tubegeom for customized electrode types | ||
| * `1b37825a` [_`dipterix`_]: allows additional geoms to viewer in brain$plot | ||
| * `75e77aec` [_`dipterix`_]: using new mac command | ||
| * `14f53797` [_`dipterix`_]: plot_slices is column-major | ||
| * `0d43840d` [_`dipterix`_]: minor patch | ||
| * `3503ee49` [_`dipterix`_]: minor patch | ||
| * `19a0c0bc` [_`dipterix`_]: line-of-sight view (js) and plot_slices (R) | ||
| * `d019c899` [_`dipterix`_]: bump version | ||
| * `b121553a` [_`dipterix`_]: Fixing CT matrix in js when s/qforms are inconsistent (the coregistration matrix in sform and original matrix in qform) | ||
| * `aea5c03f` [_`dipterix`_]: improved way of calc spacing offsets | ||
| * `8be639fa` [_`dipterix`_]: Fixed bugs on interpolation with spacing | ||
| * `74a871e7` [_`dipterix`_]: specify spacing for inter/extrapolation; removed old interpolation logic; added distanceRatio to prevent large shift (auto adjust) | ||
| * `73685b8a` [_`dipterix`_]: localization: Outlines are on | ||
| * `1da0aa4f` [_`dipterix`_]: Update to match the yael paper | ||
| * `60b014c3` [_`dipterix`_]: fixing incorrect subcortical label | ||
| * `1c98fa37` [_`dipterix`_]: Disabled old format; as_subcortical_label generates correct wm labels | ||
| * `a909a73f` [_`dipterix`_]: let electrodes to be opaque on main but transparent on side canvas | ||
| * `3591520e` [_`dipterix`_]: added initialization condition | ||
| * `0d538d85` [_`dipterix`_]: Let subcortical surfaces to display by default | ||
| * `258a7cda` [_`dipterix`_]: added get_ijk2ras to get Norig (sform) and Torig (tkr) | ||
| * `289153c2` [_`dipterix`_]: minor bug fix and bump | ||
| * `a48ca697` [_`dipterix`_]: using pial surface center as trackball center | ||
| * `1c44190d` [_`dipterix`_]: added support for showing subcortical surfaces; fixed depth issues when showing electrodes in side viewers | ||
| * `bb0fb968` [_`dipterix`_]: fixed freesurfer_lut | ||
| * `bd75f4e8` [_`dipterix`_]: Dithering the datacube2 to make rendering "smooth"; added `target` arg to pre_render so pre_render also applies to side canvas |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,7 @@ | ||
| Package: threeBrain | ||
| Type: Package | ||
| Title: Your Advanced 3D Brain Visualization | ||
| Version: 1.0.1.9200 | ||
| Version: 1.1.0 | ||
| Authors@R: c( | ||
| person("Zhengjia", "Wang", email = "[email protected]", role = c("aut", "cre", "cph")), | ||
| person("John", "Magnotti", email = "[email protected]", role = c("aut", "res")), | ||
|
|
@@ -18,7 +18,7 @@ Description: A fast, interactive cross-platform, and easy to share | |
| a web browser with 'WebGL2' support (for example, 'Chrome', 'Firefox', | ||
| 'Safari'), and can be inserted into any websites. The 'R-shiny' | ||
| support allows the 3D viewer to be dynamically generated from reactive user | ||
| inputs. Please check the publication by Wang, Magnoti, Zhang, | ||
| inputs. Please check the publication by Wang, Magnotti, Zhang, | ||
| and Beauchamp (2023, <doi:10.1523/ENEURO.0328-23.2023>) for electrode | ||
| localization. This viewer has been fully adopted by 'RAVE' | ||
| <https://openwetware.org/wiki/RAVE>, an interactive toolbox to | ||
|
|
@@ -41,6 +41,7 @@ Imports: | |
| xml2, | ||
| servr, | ||
| png, | ||
| knitr, | ||
| shiny (>= 1.2.0), | ||
| digest (>= 0.6.22), | ||
| freesurferformats (>= 0.1.7), | ||
|
|
@@ -51,7 +52,6 @@ Imports: | |
| gifti (>= 0.7.5), | ||
| oro.nifti (>= 0.9.1) | ||
| Suggests: | ||
| knitr, | ||
| rmarkdown, | ||
| DT, | ||
| ravetools, | ||
|
|
||
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