Changelog#

1.4.1: 2024/12/12#

  • remove ‘tomwer_processes’ and dependency on flufl (PR 869).

1.4.0: 2024/12/11#

  • cluster

    • future supervisor ewoksify the FutureSupervisorOW (PR 883, 906)

    • slurm

      • add walltime to the GUI (PR 904)

      • add warning for op[i]dXX users (PR 881)

  • control

    • dark/flat: add an option to clear cache (PR 791)

    • data listener: add time stamp to the ‘observation tab’ (PR 863)

    • data list

      • replace ‘send all’ button by ‘select all’ (PR 864, 911)

      • bliss data list: filter by default the .nx file (PR 920)

    • nxtomomill improve settings loading (PR 892)

  • edit

    • ewoksify ‘ImageKeyEditor’ (PR 777)

    • NXtomo editor

      • better handling of ‘unknown’ field (PR 795)

      • ewoksify the widget (PR 844)

  • reconstruction

    • gpu: add an option to select the gpu to be used (if local processing) (PR 841)

    • axis

      • Refactor GUI and remove internal layer to call directly nabu ‘estimate_cor’ function (PR 899).

      • Reworked ‘read’ to read metadata from the scan and removed reads from a third-party .txt file. Was useful (PR 789).

    • output nabu slice will now reconstruct in ‘reconstructed_slices’ and nabu volume in ‘reconstructed_volumes’. Better for publication to drac (PR 787)

    • cast volume

      • avoid advancement on the given task task input instead of only on volume (PR 1294)

      • fix setting loading (PR 889)

    • nabu slice

      • ‘phase’ section is no more checkable (PR 915)

      • expose ‘exclude_projections’ field (PR 879)

    • axis

      • handle ‘instrument.detector.y_rotation_axis_pixel_position’ instead of ‘estimated_cor’

  • tomwer canvas

    • Forced the process supervisor to always be visible when the ‘canvas’ application is launched.

    • Fully removed volume symbolic link.

    • Update software stack version (PR 918)

  • visualization

    • slice stack: rework inputs. Now user can provide path to a reconstructed slice directly (PR 805, 806 886)

    • image stack (widget used in slice stack or data viewer): add an option to filter urls (PR 885).

    • data viewer fix volume metadata setting (PR 907)

  • drac

    • rework drac publication (PR 811, 902, 890)

  • application

    • add a standalone application for y-stitching (pre-processing only)

    • improve slice stack CLI inputs (PR 806)

  • Documentation

    • Improve documentation readability (PR 853).

    • Update documentation to publish reconstructed volumes to drac

  • misc

    • remove code related to ‘add symbolic link’ task (PR 804)

    • now relies on ewoksnotify (PR 753)

    • move to __future__.annotations (PR 824)

    • move to tqdm (PR 838)

    • move to pyunitsystem >= 2.0

    • add an example on how to process volume cast on slurm (PR 913)

    • remove drepreacted ‘value_ref_nabu’ and ‘value_ref_tomwer’

1.3.21: 2024/10/08#

  • slurm settings

    • fix updating of the ‘–export’ option (PR 871)

1.3.13: 2024/06/06#

  • dark-flat copy

    • Improved copy behavior: removed any existing reduced dark/flat if they exist before copying (PR 799).

    • GUI: Added a ‘clear cache’ button (PR 791).

1.3.0: 2024/02/28#

  • core

    • Added Task to create screenshots in the gallery.

  • scan

    • Renamed hdf5tomoscan.HDF5TomoScan to nxtomoscan.NXtomoScan (PR 609).

  • gui

    • Default colormap histogram proposed (PR 642).

    • Improved handling of existing Qt paths (PR 704).

    • Improved vignettes: users can now request a specific number of columns (PRs 622, 636).

  • orangecanvas

    • Renamed ‘datas’ link to ‘series’ (PR 654).

  • axis (aka axis of rotation finder)

    • Allowed user input from the bottom QLineEdit (PR 655).

    • Notified with background color if a line is waiting for validation (PR 655).

    • Provided access to the latest Nabu algorithm (Fourier-angles and Octave-accurate) (PR 689).

    • Extended access to the ‘near’ parameter.

    • Added alias ‘near’ to the ‘composite-coarse-to-fine’ algorithm.

    • Improved +180 angle detection: now checks both -180 and +180 angles (PR 621).

  • cast-volume

    • Changed default output to uint16.

  • data-list

    • Allowed user to select between two display modes (short or full URL) (PR 648).

  • data-viewer

    • Set ‘histogram’ display mode to colormap dialog by default.

  • future-supervisor

    • Fixed job conversion (PR 696).

  • nabu slice

    • Allowed reconstruction over different planes (PR 683).

    • Added Vo and mean-subtraction/division deringer options.

    • Supported slice reconstruction over different planes (PR 683).

  • data portal

    • Added first prototype for publishing processed data to the data portal. Not yet accessible from Orangecanvas (PR 647).

  • saaxis (aka multi-cor)

    • Used Nabu-multicor instead of Nabu (PR 593).

    • Removed ‘tomo-consistency’ score to speed up processing.

    • Renamed ‘multi-cor’ in Orange (PR 838).

    • Added processing wheel when computation is ongoing (PRs 531, 838).

    • Renamed default output folder to multi_cor_results (PR 703).

  • sadeltabeta (aka multi-delta-beta)

    • Renamed default output folder to multi_delta_beta_results (PR 703).

  • slurm

    • Added proposed configuration for stitching (PR 640).

    • Allowed user to specify the value for the sbatch –export parameter (PR 638).

    • Allowed user to load modules instead of sourcing a virtual environment (PR 638).

    • Allowed user to request a specific GPU (PR 645).

  • stitching

    • First official prototype for stitching, currently accessible only via the standalone application (PRs 618, 630, 656, 690).

  • volume-viewer

    • Loaded non-HDF5 volumes in a dedicated thread to avoid GUI freezing (PR 676).

    • Added processing wheel when a volume is loading (PR 676).

  • misc

    • Moved to silx 2.0 (PR 531).

    • Replaced HDF5TomoScan with NXtomoScan.

    • Transitioned to nxtomomill 1.0 and tomoscan 2.0.

    • Fixed colored logs.

    • Reworked documentation and migrated to sphinx-pydata-theme (PRs 673, 682, 684, 686, 705).

    • Provided generic output (e.g., RAW_DATA, PROCESSED_DATA) to several widgets (PR 867).

    • Added webhooks to trigger ReadTheDocs documentation updates on tag vx.y.z.

1.2.0: 2023/09/29#

  • app

    • Deprecated dark-ref application in favor of reduce-dark-flat (PR 587).

    • reduce-dark-flat: Moved processing to a thread.

    • Deprecated dark-ref-patch application in favor of patch-raw-dark-flat (PR 587).

    • Added tomwer z-stitching application (early prototype).

    • axis: Removed radio1 and radio2 options, added optional ‘entry’ input (PR 530).

  • core
    • Multiple class deprecations:

      • tomwer.core.process.reconstruction.sadeltabeta.SAdeltaBetaProcess -> tomwer.core.process.reconstruction.sadeltabeta.SADeltaBetaTask.

      • tomwer.core.process.reconstruction.saaxis.SAAxisProcess -> tomwer.core.process.reconstruction.saaxis.SAAxisTask.

      • tomwer.core.process.reconstruction.NabuSlices -> tomwer.core.process.reconstruction.NabuSlicesTask.

      • tomwer.core.process.reconstruction.NabuVolume -> tomwer.core.process.reconstruction.NabuVolumeTask.

      • tomwer.core.process.reconstruction.darkref.darkrefs.DarkRefs -> tomwer.core.process.reconstruction.darkref.darkrefs.DarkRefsTask.

      • tomwer.core.process.reconstruction.lamino.tofu.LaminoReconstruction -> tomwer.core.process.reconstruction.lamino.tofu.LaminoReconstructionTask.

      • tomwer.core.process.reconstruction.axis.AxisProcess -> tomwer.core.process.reconstruction.axis.AxisTask.

      • tomwer.core.process.control.volumesymlink.VolumeSymbolicLinkProcess -> tomwer.core.process.control.volumesymlink.VolumeSymbolicLinkTask.

      • tomwer.core.process.control.scantransfer.ScanTransfer -> tomwer.core.process.control.scantransfer.ScanTransferTask.

      • tomwer.core.process.conditions.filters.FileNameFilter -> tomwer.core.process.conditions.filters.FileNameFilterTask.

      • tomwer.core.process.edit.darkflatpatch.DarkFlatPatch -> tomwer.core.process.edit.darkflatpatch.DarkFlatPatchTask.

      • tomwer.core.process.edit.imagekeyeditor.ImageKeyUpgrader -> tomwer.core.process.edit.imagekeyeditor.ImageKeyUpgraderTask.

      • tomwer.core.process.edit.imagekeyeditor.ImageKeyEditor -> tomwer.core.process.edit.imagekeyeditor.ImageKeyEditorTask.

  • canvas

    • Added ‘helpdesk’ button to trigger ESRF Jira ticket page (PR 580).

    • Added more examples directly on the canvas (PR 564, 510).

  • control

    • Added scan discovery widget: Search for scans (NXtomo, EDF, raw-bliss) in a root directory (recursive, one-time search) (PR 511).

    • Added NXtomo concatenate widget (PR 548).

    • Added ‘tomoobjshub’ widget (PR 590).

    • data listener: Activated by default when added to the canvas (PR 562).

    • Added email notification widget (PR 581).

    • data lists: Now supports copy and paste of a list of tomo objects (previously only single items) (PR 596).

  • edition
    • NXtomo editor

      • Added an option to automate edition (PR 524).

      • Added a warning when editing a link (external or soft) (PR 545).

  • slurm

    • Added slurm job log collection (PR 509).

    • Added found partition to ‘slurm cluster configuration’ GUI (PR 523).

    • Provided a set of pre-defined slurm configurations (PR 582).

  • reconstruction
    • axis

      • Reworked projection deduction (PR 537).

      • Automatically propose coherent angles when ‘other’ angles are selected (PR 572).

    • cast-volume: Added input for compression ratios (PR 544).

    • Added reduce-dark-flat-selector widget (PR 597).

  • visualization
    • metadata

      • Leveraged tomoscan volumes to display slice (data viewer) and volume (volume viewer) metadata for all file formats (not just .hdf5).

      • Extended metadata support to non-hdf5 volumes (PR 543) – raw volumes still don’t display metadata.

    • diffviewer: Minor improvements (PR 525).

    • scan overview: Appended ‘scan range’ to metadata (PR 526).

    • Added action to display a frame in full-screen mode (PR 529).

    • volume viewer: Fixed issue to avoid loading all data in memory when possible (PR 541).

  • helical
    • Preparing for helical:

      • Added nabu-helical-prepare-weights-double widget (PR 547).

  • doc

    • Added reference beamline tutorials.

    • Added examples to the user corner (PR 574, 594).

    • Added more examples directly on the canvas (PR 564, 510).

  • stitching

    • Added first prototype for stitching (PR 463, 551, 595).

    • Added NXtomo concatenate widget (PR 548).

  • misc

    • Added the ability to cancel jobs (PR 486).

    • Replaced multiprocessing lock with flufl.lock for file locking (PR 555).

    • Reworked future supervisor column management (PR 579).

    • Improved opening with ImageJ (PR 567).

1.1.0: 2023/03/24#

  • NXtomo editor and viewer

    • Added NXtomo editor and viewer (PR 474).

  • series management

    • Added management of series and the definition of a series (PR 375).

  • slurm

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

  • nabu

    • Integrated CTF (PR 410).

    • Added management of centered_axis (PR 475).

  • axis

    • Added an option to avoid cropping images (PR 478).

  • cast volume
    • Improvements:

      • Allowed users to provide data_min and data_max (PR 464).

  • data viewer

    • Added display of reduced darks and flats.

  • darkref

    • Used FrameReduced from tomoscan (PR 465).

  • semi-automated widgets

    • Improved connection with other widgets: can now process Nabu directly (PR 479).

    • Added an option to save a screenshot for all reconstructed slices (PR 479).

  • notifier

    • Added a signal tone (PR 490).

  • miscellaneous

    • Added pylint to CI (PR 462).

    • Used ewoks docker images for CI.

    • Added a tutorial for using ewoks convert and ewoks execute.

    • Removed distutils for packaging (PR 480).

    • Improved management of the output directory (PR 488).

    • Removed tomwer.web module (PR 501).

    • Updated the default file to source for slurm-cluster (now /scisoft/tomotools/activate.sh stable).

1.0.4: 2023/02/08#

  • data transfer

    • Avoided updating the created scan object (was freezing the GUI with EDF and GPFS - 5a7a8548).

  • fixes

    • Fixed layout and Qt parenting issues (e0b65c63 & 589c8d1f).

1.0.3: 2023/01/12#

  • volume integration

    • Integrated .vol volume to allow existing post-processing to work (ID16B).

1.0.2: 2022/12/20#

  • notification widget

    • Added a ‘notification’ widget.

  • data transfer

    • Moved processing to threads.

    • Rebased Nabu configuration file paths that are expected to be moved.

  • fixes
    • data watcher:

      • Added a try-catch on TomoScanBase.update, which could fail when encountering an empty file (due to Fabio’s new behavior).

      • Copied .xml and .info files to the scan directory if in /data instead of /lbsram/data.

    • darkref:

      • Fixed notification when a new ref (dark or flat) is set.

1.0.0: 2022/11/08#

  • integration

    • Integrated volumes from tomoscan (PR 394). Users can now handle a volume and process it.

  • visualization

    • Removed old data validator and data viewer (deprecated since 0.5).

  • control

    • Added edf2nx widget (PR 393).

    • Added image_key_upgrader (PR 396).

    • Added VolumeSelector GUI and orange widget (PR 396).

    • Upgraded datawatcher to allow searching for bliss scan and NXtomo (PR 406).

    • Added ‘single tomo obj’ widget (PR 409).

    • data listener: Added option to filter file names (PR 426).

  • reconstruction
    • dark and ref

      • Updated copy to fit new ‘reduced frames’ policy using tomoscan (PR 396).

      • Added ‘channel’ for the user to provide reduced dark and flat (PR 409).

    • Reworked volume casting to call Nabu volume casting and used the new VolumeBase class (PR 394).

    • output file format: Can now be redefined from NabuVolumeOW (PR 403).

    • nabu

      • slice: Users can now provide angles_file.

      • volume: Output location and file format can be redefined from advanced settings.

      • Added Shepp-Logan, Cosine, Hamming, Hann, Tukey, Lanczos, Hilbert filter kernels (PR 421).

      • Added management of sino_rings_options (PR 420).

      • Added management of tilt correction (PR 437).

    • axis

      • Fixed loading of cor value when saved in the .ows and bug with manual mode being locked in some cases (PR 450).

      • Added a +180 button to automatically find the associated angle when radio angles are defined manually (PR 455).

      • Fixed relative position casting to absolute (PR 457).

    • sadelta-beta

      • Fixed bug when slice computation fails (PR 447).

  • slurm

    • Replaced dask-jobqueue with the tomwer.slurm module (PR 405).

  • other

    • Updated Python widget to handle a volume.

    • Allowed several inputs for some widgets (PR 446).

  • miscellaneous

    • Removed pyhst binding.

    • First version with some widgets fully handled by ewoksorange.

0.10.0: 2022/06/27#

  • core

    • Used the latest tomoscan dark and flat definitions ([scan]_flats.hdf5:flats and [scan]_darks.hdf5:darks) (!674).

    • Added normalization process to apply user-defined normalization to frames and provide them to Nabu.

  • gui

    • Added normalization GUI.

    • nabu volume: Activated histogram request to Nabu by default.

    • axis:

      • Reworked possible algorithms. If an algorithm can be done with sinogram or radios, proposed two values (instead of one with a sinogram vs. radios option previously).

      • Moved parameters to a QScrollArea (!688).

      • Allowed users to define the angle value manually (!702).

      • Moved input side-by-side with calculation to improve readability (!705).

      • Fixed issue with scrolling (!706).

    • data list:

      • Fixed item removal (!707).

  • orangecontrib

    • Fixed slice stack (!708).

0.9.0: 2022/01/17#

  • app

    • canvas: Removed dependency on the orange3 project and replaced it with dependency on orange-canvas-core and orange-widget-base.

    • A fork was created to access the ‘processing wheel’ as an optional feature (payno/orange-widget-base, payno/orange-canvas-core) (!350).

  • core

    • Adapted all ‘core process’ to ewoks Task. Ensured low-level compatibility with ewoks (!340).

    • reconstructions

      • Added option to trigger reconstruction on the slurm cluster (!349).

      • Added a cast process to convert Nabu volume to other file formats.

    • slurm cluster: Reworked to provide ports dynamically.

    • darkref: Now saves darks/flats in darks.hdf5 and flats.hdf5 for HDF5 acquisition.

  • gui

    • Added future supervisor interface.

    • Added slurm cluster interface.

    • nabu:

      • Added interface to set the rings removal method.

      • Connected “composite-to-fine” algorithm.

      • Added the “None” method to the phase method to allow users to use other options.

    • diffviewer:

      • Added widget to shift the second image.

  • orangecontrib

    • Added cluster group with SlurmclusterOW and FutureSupervisorOW.

    • Added a “cast volume” widget to cast Nabu volume.

  • doc

    • Provided descriptions of canvas objects.

    • Added streamline videos.

0.8.0: 2021/08/31#

  • app

    • Added scan viewer: allows the user to display the contents of a scan and browse through it.

  • gui
    • dataviewer:

      • Integrated an instance of the ‘scanoverview’ widget to display information regarding the scan (e.g., number of darks/flats, energy).

      • Provided access to darks and flats.

    • axis: Fixed several minor issues with the color map and reset zoom.

    • Improved diff frame.

  • orangecontrib
    • widgets:

      • Added SADeltaBetaOW to compute a score from several delta/beta values.

      • patch-nx: Added a configuration entry (!346).

  • miscellaneous

    • Moved doc to autosummary.

    • Migrated to setup.cfg.

    • Moved to pytest.

0.7.0: 2021/05/20#

  • orangecontrib
    • widgets:

      • Added AdvancementOW: Displays the advancement of all processes.

      • Added SAAxisOW: Semi-automatic axis widget.

    • Integrated processview.

  • core
    • process:

      • Added manager module to observe SuperviseProcess and display processes’ advancement.

    • Axis:

      • AxisProcess: Integrated the latest Nabu algorithm based on sinogram.

      • AxisRP: Deprecated value_ref_tomwer and value_ref_nabu in favor of absolute_value and relative_value.

    • SAAxis:

      • Added process to compute several centers of rotation for the same slice and Nabu reconstruction parameters, providing a score for each slice (scores include standard deviation and total variation).

    • Integrated processview.

    • Nabu:

      • Fixed file retrieval when .tif was requested.

    • scan:

      • Benefited from tomoscan HDF5 sinogram speed-up.

  • gui
    • DataList:

      • Allowed copying of text (e.g., scan directory, master file).

    • Axis:

      • Improved speed (removed the reset_scan).

      • Added Nabu algorithm using sinogram.

        • Updated the ‘Input’ tab: Users can now select from radio or sinogram and provide the sinogram line and subsampling.

      • When manual mode is activated, pressing ‘validate’ forces validation and ensures the displayed value is set to the scan.

      • Changed QLabel for displaying cor values to QLineEdit (read-only) to allow copying/pasting the cor value.

    • nabu:

      • Saved processing log to the processview.

    • volume viewer:

      • Integrated reconstruction parameters.

  • synctools

    • FIFO is now a SuperviseProcess.

0.6.0: 2020/12/15#

  • app
    • canvas:
      • Added edit submodule:

        • Added ImageKeyEditorOW: Allows invalidating some frames or changing their ‘frame type’.

        • Added DarkFlatPatchOW: Allows adding dark and/or flat to a NXtomo entry.

      • Added debug submodule (!289):

        • Added random data generator.

        • Added tomwer object viewer.

      • control:

        • Added volume symbolic link widget.

        • data listener: Added file conversion on a thread to avoid GUI freeze.

    • darkref:

      • Added a –no-gui option and options to define the calculation method for dark and ref from the command line (!299).

    • Added image-key-editor.

    • Added dark-ref-patch.

  • control
    • nxtomomill:

      • Added an option to retain the last parameter provided by the user (e.g., energy, overwrite files). This will be cleared between two calls to the converter (!296).

      • Attempted to filter non-bliss files from user input (!296).

    • datalistener:

      • Ensured that only one instance is active on the PC. Otherwise, displayed a dialog to notify the user.

    • utils:

      • Reworked isOnLbsRam to handle either a TomwerScanBase or a str.

  • reconstruction
    • axis:

      • Added ‘global’ algorithm from Nabu. Works for both half-acquisition and standard acquisition (!295).

      • GUI update:

        • Avoided reset zoom (!295).

        • Avoided validation when pressing ‘enter’ after manual cor editing (!295).

        • Sped up radio shift (!295).

        • Displayed both absolute and relative cor (!295).

    • nabu (!303):
      • slices:

        • Added subsampling.

        • Removed margins.

      • volume:

        • Added option to compute histograms.

      • Slices to be reconstructed are now always set to ‘middle’. The value is no longer loaded, as it confused users (commit 947d475b31d2).

    • dark-ref:

      • Added first and last options to select the first or last frame from a series of dark/ref frames (!299).

      • Automated settings for half-field/standard tomography (!294).

  • visualization
    • viewer:

      • Added an ‘open with ImageJ’ button (!298).

      • Reduced memory usage by limiting the number of images in cache (!289).

    • Added diff viewer prototype (!286).

  • miscellaneous

    • Adopted black coding style.

    • tomwer.core.process:

      • Moved timer, datalistener, datawatcher, scanvalidator, datalist, and datatransfert to control submodule.

0.5.3: 2020/10/19#

  • core
    • axis:

      • Renamed ‘accurate’ to ‘centered’.

      • Added global algorithm.

  • orangecanvas

    • Fixed issues (commit 8a368fd7).

  • miscellaneous

    • Reworked logs (!292).

0.5.2: 2020/09/02#

  • core

    • Added volume reconstruction from Nabu.

    • nabu:

      • Renamed Nabu to NabuSlices.

      • Caught Nabu logs (!273).

      • Managed .tiff and .jp2 file formats.

  • gui

    • Added a new data viewer [prototype].

    • Added a volume viewer for Nabu volume reconstruction (!275).

    • axis: Fixed display of shifted images (#424).

    • viewers: Added timestamp (!279).

    • darkref: Fixed issue when adding a widget to Orange canvas, removing it, and adding it again (!265).

  • orangecontrib

    • Deprecated old data viewer.

    • Added new DataViewerOW [prototype].

    • Added VolumeViewerOW.

    • Added NabuVolumeOW.

  • app
    • nabu:

      • Added interface to give cor (!280).

      • Added display button to browse reconstructed slices and projections (!280).

    • Added process application: run a .ows within pypushflow in a GUI-free environment [prototype] (!277).

    • Added ows-to-script application: translates a .ows file into a Python script [prototype] (!278).

  • web

    • Fixed Graypy new API (!270).

  • miscellaneous

    • Added dependency on pypushflow.

    • Managed HDF5_USE_FILE_LOCKING when reading or writing files using tomoscan.io.HDF5File.

    • Fixed some utilities using BaseProcess._get_process_nodes.

0.5.0: 2020/06/30#

  • core

    • Completed compatibility with HDF5.

    • Added datalistener process: listens to a Tango device to retrieve the acquisition status. Also starts synchronization between lbsram and nice if on the lbsram system.

    • Added nabu process: calls Nabu to reconstruct slices and create .conf files for full-volume reconstruction.

    • settings:

      • Added BEAMLINE_NAME, TANGO_PORT, BLISS_SESSION_NAMES, DEFAULT_BLISS_SESSION_NAME, and MAKE_OAR_PYST2_PATH.

      • Added management of PyHST2_* environment variables.

    • scan:

      • Added dependency on tomoscan.

    • utils:

      • Added HDF5Mock.

    • data transfer: Deactivated for HDF5.

  • gui

    • Added interfaces for Nabu, data listener, and sinogram viewer.

    • axis: Updated interface.

    • viewer: Added prototype of the next data viewer.

  • orangecontrib

    • Added sinogram widget: used to compute a sinogram from an EDF or HDF5 (NXtomo) acquisition.

    • Added data listener widget: connects to a Tango device to retrieve information.

    • Added Nabu widget: used to reconstruct using the Nabu library.

    • Added nxtomomill widget: converts a Bliss HDF5 acquisition to a (NXTomo) .nx acquisition.

    • Added prototype of the DataViewer.

    • Added prototype of the new DataValidator (moved previous one to OldDataValidatorOW).

  • app

    • Added Nabu application: GUI for calling Nabu or creating a Nabu configuration file.

    • Added sinogram viewer utility: computes a sinogram from an EDF or HDF5 (NXtomo) acquisition.

    • Added canvas application.

  • examples

    • Added nabu_flow.py example, presenting a default workflow with Nabu.

  • miscellaneous

    • Dropped Python 3.4 support.

    • Alpha version released on 2020/04/30.

0.4.0: 2020/03/06#

  • core

    • Started compatibility with HDF5.

    • scan folder:

      • Added TomoScan, EDFScan, and HDF5Scan. These objects are all serializable (using from_dict, to_dict functions).

    • reconstruction:
      • process:

        • All processes now return a serializable object (TomoScan).

        • ftseries:

          • Removed dependency on Fastomo, using pyhstcaller instead.

        • Added pyhstcaller: generates .par and .rec files.

        • lamino:

          • Reworked and checked calls to Tofu with Lukas.

          • Added pre-processing and stitching for half-acquisition.

        • darkref: Adapted to TomoScan object.

        • axis: New process to compute the center of rotation.

      • reconsparam: Replaced the previous ReconsParamRegistry with a set of classes (FTReconsParams, AxisReconsParams, etc.).

    • utils:

      • Added scanrange file.

  • gui
    • reconstruction:

      • Reworked lamino widget.

      • Added AxisWidget (stack requested axis).

    • Updated datawatcher:

      • Removed pop-up windows and embedded them in the same widget.

      • Checked acquisition type (HDF5 or EDF).

  • orangecontrib

    • Links now use TomoScan objects instead of str.

    • widgets:

      • Added axis widget.

  • app

    • Added Axis application: computes the center of rotation from a scan directory or some files.

    • Added Rsync application: synchronizes a folder containing a scan with another folder. The user can specify a ‘point of advancement’ in the scan’s lifecycle, so only files created at that stage will be synchronized.

  • examples

    • Added orangeworkflow example: common orange workflow with datawatcher, axis, darkref, ftseries, datavalidator, and datatransfer widgets.

    • Added datawatcher example: simple instantiation of datawatcher with automatic acquisition generation.

  • luigi

    • Removed prototype.

0.3.0: 2019/01/08#

  • core

    • Added simple Python binding for launching Tofu (currently only available for Python 2).

    • conditions: Introduced a new package to include conditions (e.g., folder names) on a workflow.

    • ftseries:

      • Duplicated octave outputs to octave.log.

      • Enabled running multiple Paganin reconstructions with different parameters.

    • Created different nodes for loading image stacks.

    • data transfer: Added pre-transfer operations.

    • Created tomwer.core.scan package to include different types of scans (e.g., edfscan, hdf5scan) with specific treatment and interfaces for each.

  • gui

    • lamino: Added TofuWidget to call lamino reconstruction from Tofu.

    • compare images: Used the comparison tool from silx if silx >= 0.9.

    • data list:

      • Added a ‘remove all’ button.

      • Enabled handling of mouse drag-and-drop.

    • Added widgets radio stack and slice stack to record all radios or slices passing through the widget, allowing users to browse through them.

    • live slice: Embedded live slice into an Orange widget (if installed).

    • Added GUI for the new conditions process.

    • Separated tomwer’s Orange add-on widgets into three parts: control, reconstruction, and visualization.

    • data validator: Added three different options for loading images (just-in-time, on-demand, and load-as-soon-as-possible).

  • doc

    • Added automatic screenshots for documentation generation.

  • luigi

    • Added the first prototype (not functional yet).

0.2.0: 2018/07/16#

  • dark & flat fields:

    • Added a process to manage dark and flat field creation (creates the median of the mean).

    • Managed copying of dark and flat fields if they don’t already exist in the repository.

  • refactoring:

    • Moved tomwer core functions and Qt base widgets to the tomwer package.

    • The orangecontrib subpackage now only contains the Orange add-on.

  • ftseries:

    • Removed the octave version previously read and loaded.

  • data watcher:

    • Enabled parallel observations.

    • Skipped acquisition folders containing a .abo file (treated as if no data was available).

    • GUI refactoring.

  • scan validator:

    • Added a GUI as a stack, allowing users to browse through it.

  • Added group slice to display all reconstructed slices received.

  • Added data selector: a simple GUI to select a scan from a list.

  • sample moved: Interface to display ‘key radios’ and check if the sample moved during acquisition.

  • Added applications:

    • darkref

    • ftseries

    • samplemoved

    • slicestack

0.1.0: 2017/09/28#

  • core features:

    • tomodir: (aka data watcher) Detects when an acquisition is finished and synchronizes data with the destination directory as soon as possible if the system is on lbsram.

    • ftseries: Interface for fastomo3 (Octave).

  • orange add-on:

    • ftseries widget.

    • scan validator: Validates a scan or requests reconstruction with changed parameters.

    • data watcher.

    • data viewer.

    • data list.

    • data transfer.