• core

  • add Task to create screenshots on the gallery
  • scan
    • rename hdf5tomoscan.HDF5TomoScan to nxtomoscan.NXtomoScan (PR 609)

• gui

  • propose colormap histogram by default (PR 642)
  • improve handling of eisting Qt path (PR 704)
  • improve vignettes: users can now ask for a specific number of column (PRs 622, 636)

• orangecanvas

  • rename 'datas' link to 'serie' (PR 654)

• axis (aka axis of rotation finder)

  • allow user to enter a value from the bottom QLineEdit (PR 655)
  • notify from background color if a line waits to be validate (PR 655)
  • provide access to latest nabu algorithm (fourier-angles and octave accurate) (PR 689)
  • extend access to near parameter
  • add an alias 'near' to the 'composite-coarse-to-fine' algorithm
  • improve +180 angle. Look now on both side: -180 and +180 (PR 621)

• cast-volume

  • move default output to uint16

• data-list

  • allow the user to select between two display mode (short or full url) PR 648

• data-viewer

  • use 'histogram' display mode to colormap dialog by default

• future-supervisor

  • fix job conversion (PR 696)

• nabu slice

  • allow reconstruction over different place (PR 683)
  • add Vo and mean-subtraction / division deringer
  • allow slice to be reconstructed over different plane (PR 683)

• icat

  • add a first prototype to publish to processed data to icat. Not accessible from orangecanvas for now. (PR 647)

• saaxis (aka multi-cor )

  • use nabu-multicor instead of nabu (PR 593)
  • remove 'tomo-consistency' score to speed up
  • rename 'multi-cor' in orange (PR 838)
  • add processing wheel when computation is on-going (PRs 531, 838)
  • rename default output folder to multi_cor_results (PR 703)

• sadeltabeta (aka multi-delta-beta)

  • rename default output folder to multi_delta_beta_results (PR 703)

• slurm

  • add a proposed configuration for stitching (PR 640)
  • allow user to provide the value of sbatch '--export' parameter (PR 638)
  • allow user to load module instead of sourcing a virtual environment (PR 638)
  • allow user to ask for a specific gpu (PR 645)

• stitching

  • first official prototype for stitching. Only accessible form the standalone application for now. (PRs 618, 630, 656, 690)

• volume-viewer

  • load non-hdf5 volumes into dedicated thread - avoid gui-freeze - (PR 676)
  • add processing wheel when a volume is being loaded (PR 676)

• misc

  • move to silx 2.0 (PR 531)
  • replace HDF5TomoScan by NXtomoScan
  • move to nxtomomill 1.0 and tomoscan 2.0
  • fix colored logs
  • rework doc and move to sphinx-pydata-theme (PRs 673, 682, 684, 686, 705)
  • provide generic output (RAW_DATA, PROCESSED_DATA...) to several widgets (PR 867)
  • add webhooks to trigger readthedoc documetation on tag vx.y.z

• app

  • deprecate dark-ref application in favor of reduce-dark-flat (PR 587)
  • reduce-dark-flat: move processing to a thread
  • deprecate dark-ref-patch application in favor of patch-raw-dark-flat (PR 587)
  • add tomwer z-stitching application (as an early prototype)
  • axis: remove radio1 and radio2 options, add optional 'entry' input (PR 530)

• core

  • several class deprecation
    • tomwer.core.process.reconstruction.sadeltabeta.SAdeltaBetaProcess in favor of tomwer.core.process.reconstruction.sadeltabeta.SADeltaBetaTask
    • tomwer.core.process.reconstruction.saaxis.SAAxisProcess in favor of tomwer.core.process.reconstruction.saaxis.SAAxisTask
    • tomwer.core.process.reconstruction.NabuSlices in favor of tomwer.core.process.reconstruction.NabuSlicesTask
    • tomwer.core.process.reconstruction.NabuVolume in favor of tomwer.core.process.reconstruction.NabuVolumeTask
    • tomwer.core.process.reconstruction.darkref.darkrefs.DarkRefs in favor of tomwer.core.process.reconstruction.darkref.darkrefs.DarkRefsTask
    • tomwer.core.process.reconstruction.lamino.tofu.LaminoReconstruction in favor of tomwer.core.process.reconstruction.lamino.tofu.LaminoReconstructionTask
    • tomwer.core.process.reconstruction.axis.AxisProcess in favor of tomwer.core.process.reconstruction.axis.AxisTask
    • tomwer.core.process.control.volumesymlink.VolumeSymbolicLinkProcess in favor of tomwer.core.process.control.volumesymlink.VolumeSymbolicLinkTask
    • tomwer.core.process.control.scantransfer.ScanTransfer in favor of tomwer.core.process.control.scantransfer.ScanTransferTask
    • tomwer.core.process.conditions.filters.FileNameFilter in favor of tomwer.core.process.conditions.filters.FileNameFilterTask
    • tomwer.core.process.edit.darkflatpatch.DarkFlatPatch in favor of tomwer.core.process.edit.darkflatpatch.DarkFlatPatchTask
    • tomwer.core.process.edit.imagekeyeditor.ImageKeyUpgrader in favor of tomwer.core.process.edit.imagekeyeditor.ImageKeyUpgraderTask
    • tomwer.core.process.edit.imagekeyeditor.ImageKeyEditor in favor of tomwer.core.process.edit.imagekeyeditor.ImageKeyEditorTask

• canvas

  • add a 'helpdesk' button to trigger esrf jira ticket web page (PR 580)
  • add more examples directly on the canvas (PR 564, 510)

• control

  • add scan discovery widget: search for scans (NXtomo, EDF, raw-bliss scan) contained under a root directory (recursive - one-time- search) (PR 511)
  • add NXtomo concatenate widget (PR 548)
  • add 'tomoobjshub' widget (PR 590)
  • data listener: activate it by default when added to the canvas (PR 562)
  • add an email notification widget (PR 581)
  • 'data' lists: now handle copy and paste of a list of tomo object (instead of a single one previously) (PR !596)

• edition

  • NXtomo editor
    • add an option to automate edition (PR 524)
    • add a warning if edit a link (external or soft) (PR 545)

• slurm

  • add slurm job logs collection (PR 509)
  • add found partition to 'slurm cluster configuration' gui (PR 523)
  • provide a set of pre-defined slurm configuration (PR 582)

• reconstruction

  • axis
    • rework deduction of projections (PR 537)
    • when 'other' angles is selected: try to automatically propose coherent angles (PR 572)
  • cast-volume: add input for compression-ratios (PR 544)
  • add 'reduce-dark-flat-selector' widget (PR 597)

• visualization

  • metadata
    • benefit from tomoscan volumes to display slice (data viewer) and volume (volume viewer) metadata for all file format (and not only .hdf5)
    • extend metadata to non-hdf5 volumes (PR 543) - raw volume still not display any metadata
  • diffviewer: minor improvements (PR 525)
  • scan overview: append 'scan range' to the metadata (PR 526)
  • add action to display a frame in full screen (PR 529)
  • volume viewer: fix: avoid loading all the data in memory when possible (PR 541)

• helical

  • preparing helical
    • add 'nabu-helical-prepare-weights-double' widget (PR 547)

• doc

  • reference beamlines tutorials
  • add examples on user corner (PR 574, 594)
  • add more examples directly on the canvas (PR 564, 510)

• stitching

  • add first prototype for stitching (PR 463, 551, 595)
  • add NXtomo concatenate widget (PR 548)

• misc

  • add possibility to cancel some jobs (PR 486)
  • replace multiprocessing lock by flufl.lock for file locking (PR 555)
  • rework future supervisor column management (PR 579)
  • improve opening with ImageJ (PR 567)

• add NXtomo editor and viewer (PR 474)

• add management of serie and definition of a serie (PR 375)

• improve slurm job submission (using sluurp and updating GUI / future handling) - (PR 469)

• nabu

  • integrate CTF (PR 410)
  • add management of centered_axis (PR 475)

• axis

  • add an option to avoid cropping images (PR 478)

• cast volume improvements

  • allow users to provide data_min and data_max (PR 464)

• data viewer

  • add display of reduced darks and flats

• darkref

  • use FrameReduced from tomoscan (PR 465)

• semi automated widgets

  • improve connection with other widgets: can process nabu directly now (PR 479)
  • add an option to save a screenshot for all reconstructed slices (PR 479)

• notifier: add a signal tone (PR 490)

• misc:

  • add pylint to CI (PR 462)
  • use ewoks dockers images for CI
  • add a tutorial to use ewoks convert and ewoks execute
  • remove distutils for packaging (PR 480)
  • Improve management of output directory (PR 488)
  • Remove tomwer.web module (PR 501)
  • update default file to source for slurm-clsuter (now this is '/scisoft/tomotools/activate.sh stable')

• integrate volumes from tomoscan (PR 394). Now user can handle a volume and process it.

• visualization

  • remove old data validator and data viewer (deprecated since 0.5)

• control

  • add edf2nx widget (PR 393)
  • add image_key_upgrader (PR 396)
  • add VolumeSelector related gui (and orange widget) (PR 396)
  • upgrade datawatcher to allow research of bliss scan and NXtomo (PR 406)
  • add 'single tomo obj' widget (PR 409)
  • data listener: add option to filter file name (PR 426)

• reconstruction

  • dark and ref
    • update copy to fit new 'reduced frames' policy using tomoscan (PR 396)
    • add 'channel' for the user to provide reduced dark and flat (PR 409)
  • rework volume cast to call nabu volume casting and use the new VolumeBase class (PR 394)
  • output file format can now be redefined from NabuVolumeOW (PR 403)
  • nabu
    • slice: user can now provide 'angles_file'
    • volume: user can now redefine output location and output file format from advanced settings
    • add shepp-logan, cosine, hamming, hann, tukey, lanczos, hilbert to filter kernels (PR 421)
    • add management of sino_rings_options (PR 420)
    • add management of tilt correction (PR 437)
  • axis:
    • fix loading cor value when saved in the .ows and bug with manual mode beeing locked in some cases (PR 450)
    • add a '+180' button to find automatically the associated angle when radio angles defined manually (PR 455)
    • fix relative position cast to absolute (PR 457)
  • sadelta-beta
    • fix bug when slice computation fails (PR 447)

• slurm

  • replace dask-jobqueue by the 'tomwer.slurm' module (PR 405)

• other

  • update python widget to handle a volume
  • allow several input for some widgets (PR 446)

• misc:

  • Remove pyhst binding
  • first version with some widgets 'fully' handled by ewoksorange

CHANGELOG

• core
  • use latest tomoscan dark and flat definition ([scan]_flats.hdf5:flats and [scan]_darks.hdf5:darks) (PR674)
  • add normalization process to apply user defined normalization to frames and provide this one to nabu
• gui
  • add normalization gui
  • nabu volume: active histogram request to nabu by default
  • axis:
    • rework possible algorithm. If an algorithm can be done with sinogram or radios propose two values (instead of one and a sinogram vs radios option previously)
    • move parameters to a QScrollArea (#688)
    • allow users to define the angle value manually (PR702)
    • move input side by side with calculation to ease readibility (PR705)
    • fix issue with scrolling (PR706)
  • data list
    • fix remove item (PR707)
• orangecontrib
  • fix slice stack (PR708)

• app

  • canvas:remove dependency on the orange3 project and replace it by dependency on orange-canvas-core and orange-widget-base. fork has been created to access the 'processing wheel' but this is an optionnal feature (https://github.com/payno/orange-widget-base, https://github.com/payno/orange-canvas-core) (!350)

• core

  • adapt all 'core process' to ewoks Task. Insure low level compatibility with ewoks (!340).
  • reconstructions
    • add option to trigger reconstruction on slurm cluster (!349)
  • add a cast process to convert nabu volume to other file format
  • slurm cluster: rework to provide port dynamically
  • darkref: now save dark / flat also in darks.hdf5 and flats.hdf5 for hdf5 acquisition

• gui

  • add future supervisor interface
  • add slurm cluster interface
  • nabu
    • add interface to set the rings removal method
    • connect "composite-to-fine" algorithm
    • add the "None" method to the pahse method in order to allow user to use other options
  • diffviewer
    • add widget to shift second image

• orangecontrib

  • add cluster group with SlurmclusterOW and FutureSupervisorOW
  • add a "cast volume" widget to cast nabu volume

• doc

  • provide description of canvas objects
  • add streamline videos

• app

  • add scan viewer: allow user to display contain of a scan and browse on it

• gui

  • dataviewer: add tab contains information on scan (number of dark / flat...)
  • axis: several minor ug fix with the color map and reset zoom
  • improve diff frame

• orangecontrib

  • widgets
    • add SADeltaBetaOW to compute a score from several delta / beta values
    • patch-nx add a configuration entry (!346)

• Miscellaneous:

  • move doc to autosumary
  • move to setup.cfg
  • move to pytest