Implementing web UI #144

…homepage Redirect README to docs/index

Build docs on circle ci

…er it

Fix readme

Adding codecov to CI

… a new tag

Fixing codecov

Configuring pytest coverage output

…e the main branch is now protected

Replacing auto-generate GITHUB_TOKEN with Personal Access Token, since the main branch is protected

Add spellchecker to NDK

Adding label enforcer to CI

…se_job Only running publish release if a new version was generated

Removing empty lines to test version bump

…n_to_push_release Adding Personal Access Token to push release

…o_docs Adding troubleshooting section

* Add pyright integration * Fixing warnings discovered by pyright * Linting * Fixing pyright warnings * Fixing pyright catches * Fix linting issues * Linting, fixing pyright issues * Installing napari on lint job * Replacing 'if' with assertion * Fixing docstrings * Removing all usages of typing.cast * Disabling pyright reportGeneralTypeIssues for the whole project --------- Co-authored-by: Florin Pop <[email protected]>

…set (#30) * Printing a warning when the DEVITO_ARCH environment variable was not set * update warning message --------- Co-authored-by: Diogo de Lucena <[email protected]>

…rt with upper case

…rendering Fixing docstrings to make API rendering correct

* Adding process section to 'Contributing' * updating PR template to mention the labels * add comment about redirects not available --------- Co-authored-by: Diogo de Lucena <[email protected]>

…cts_url Adding job to display a link to the PR generated documentation

… docs

…cts_redirect Updating contributing guide for generated documentation

* Adding phased array source example to gallery * Extending phased array gallery example * Moving docs around * Increase circleCI resources * Adding missing images * small format changes * fix typo --------- Co-authored-by: Diogo de Lucena <[email protected]>

* Adding plots * add note about development. * fix note syntax --------- Co-authored-by: d-lucena <[email protected]>

* Adding example of save and load results * change file extension to match new format * add note about development * fix text --------- Co-authored-by: d-lucena <[email protected]>

* Adding GPU support documentation * add warning about gpu memory for large simulations --------- Co-authored-by: d-lucena <[email protected]>

* Adding gallery example with multiple sources * update file name and add note about development --------- Co-authored-by: d-lucena <[email protected]>

* Moving local installation to its own page * Adding local installation page * add note about docker in installation menu * fix file name * update text and links --------- Co-authored-by: d-lucena <[email protected]>

* Storing results into a tarball together with a VERSION file * Adding test for the tz VERSION check * Adding docstrings * Replacing shutil.rmtree with os.remove * Removing version from unit test check * add details to docstring * fix linting --------- Co-authored-by: d-lucena <[email protected]>

…on_instructions Split installation methods in docs

* Caching in CI

* Fixing CI cache folder * Changing poetry config for linting job

* Adding pulsed simulation to gallery * Adding code required to store a mp4 file with the simulation animation * Installing ffmpeg dependency * Replacing experimental code with production code in the pulsed plot * Improving docs * Adding ffmpeg to github workflow * update text * update text --------- Co-authored-by: Diogo de Lucena <[email protected]>

* Removing abstract function. Exposing util functions from scenarios module. * Adding full scenario to gallery * Exposing API documentation to functions made available for external usage * Test extra step to generate gallery * Revert "Test extra step to generate gallery" This reverts commit 5fb37e9. * add note on development --------- Co-authored-by: Diogo de Lucena <[email protected]>

* Adding download-notebooks script to NDK * Adding pooch as dependency * Updating dockerfile to generate example notebooks and to print the http address of the jupyter server * Updating docker test * Replacing download_notebook script with a link to download the zip file with the example notebooks * Removing pooch from main dependencies * Not generating the gallery examples into the docker container anymore * Downloading gallery to the docker image * Updating docs to run ndk in a docker container * Adding jupyter lab links to documentation * update text --------- Co-authored-by: Diogo de Lucena <[email protected]>

)

* Using generated gallery as cache for making docs * Applying changes from test workflow to official workflow

…out cache (#69) * Adding cronjob triggering circleCI to build the gallery examples without cache * Replacing cron to test workflow * Running job every Monday at 7am

* Moving local installation to its own page * Adding local installation page * Adding linux installation instructions * Extending linux installation docs * separate pre and post installation instructions * fix text * Fixing typo * Update installation.md fixing typo --------- Co-authored-by: d-lucena <[email protected]>

* Adding Windows installation instructions * Adding command to download and extract the notebook packages

* Adding 3d example to gallery * Downloading results from simulation in the 3d example * Adding neurotechdevkit URL to plot_3d example * Adding hash of results file, Removing 3d from usage * Improving wording * change example name * add link to napari --------- Co-authored-by: Diogo de Lucena <[email protected]>

* Adding integration test to CI * Adding step to install gcc on mac

…73)

* updated text * fix typo

* Testing ndk with python 3.11 * Using fork with stride fix for python3.11 * Replacing NewtonSander stride repo with trustimage

* Using circleCI to build gh-pages

* Adding code spellchecker

* Improving docs for ARM MacOS * Updating contributing page removing duplication * Removing duplicated steps * Pointing to new installation.md page location

…#82) * Allowing customization of the center frequency and of material layers * Removing docstring mentions of the fixed 500kHz frequency * Making materials dynamic, allowing the absorption calculation based on center frequency * Adding algorithm to calculate the material absorption based on the frequency * Defining fixed material properties to the scenarios to match the paper --------- Co-authored-by: Diogo de Lucena <[email protected]>

* Update napari install instructions to Qt6 on Mac M1 * lint code * improve error message Co-authored-by: Diogo de Lucena <[email protected]> --------- Co-authored-by: Diogo de Lucena <[email protected]>

* Adding resource estimation for pulsed simulations

…124)

* Not adding default labels if PR is already labeled * Triggering CI * Fixing labeler condition * Trigger CI * Reverting changes

* Add PointSources that have no direction or aperture * Draft time-reverse simulation to calculate delays * Update comment on point source * Enable math latex rendering with Arithmatex * Update docs/examples/plot_time_reverse.py Co-authored-by: Diogo de Lucena <[email protected]> * Fix up documentation - address PR comments * Include target error calculation in plot_time_reverse.py * lint/spellcheck * Consolidate flags for source rendering type into a single Enum * Add Enum to dictionary * Fix spellcheck error / typo * Add thought exercise for time reverse simulation * Rename SourceType to SourceRenderType to be more specific --------- Co-authored-by: Diogo de Lucena <[email protected]>

* Implementing new API for NDK * Updating gallery examples to use the new API * Updating 3d scenario result * Cleaning up scenario __init__ * Updating api docs * Compiling problem explicitly * Small fixes to plot full scenario * Creating NDK's own Problem class * Removing 'scenario_id' attribute * Cleaning up * Fixing docs * Decoupling render layout from compile problem * Moving grid creation to its own class * Moving center_frequency to the scenario root * Cleaning up * Cleaning up code. Invalidating grid and compiled problem when center_frequency is changed * Adapting documentation * Updating plot full scenario to use the procedural approach * Updating API docs adding the Grid and Problem pages * Fixing bug with 3D example * Improving docs, updating hash of 3d results file * Improving docs * Small improvements to notebook * Addressing review suggestion: replacing enum with subdirectory containing the built in scenarios * Update src/neurotechdevkit/grid.py Co-authored-by: charles <[email protected]> * Addressing review suggestion * Fixing issue with commited PR suggestion * Fixing bug * Removing layer_ids from problem creation. Removing need of creating material_layers, using material_masks keys instead * Fixing print * Replacing numpy arrays with plain lists for simple attributes like position, origin and direction * Refactoring * Refactoring * Fixing hash of results file * Simplifying API * Setting center_frequency in built_in scenarios * Adding SliceAxis to spellcheck's whitelist * Adding unit tests and cleaning up code * Adding predefined target options * Fix typo * Showing how the predefined targt options can be used * Improving plot full scenario masks creation * Addressing review suggestions * Fixing spellchecking error by removing unnecessary types from docstrings * Updating 3d file hash * update docstrings --------- Co-authored-by: charles <[email protected]> Co-authored-by: d-lucena <[email protected]>

…r benchmark 8 (#138)

…equencies (#132) * Resample scenario2 mask to the appropriate grid size * Add unit tests for initializing and compiling default scenarios * Add voxel to the dictionary * Remove the center_frequency=1e6 test because it is very slow for Scenario2_3D * Fix Scenario0 resizing bug * Port scenario 2 changes to new file

…tallation error on Python 3.11 (#150)

* Allowing any scenario to be saved * Fixing bug when loading parameters from file * Updating file hash * Fixing issue with 2d/3d parameters * Updating filename of 3d plot * Removing duplicated test and marking built in scenario testd as integration tests --------- Co-authored-by: Kyle McGraw <[email protected]> Co-authored-by: d-lucena <[email protected]>

* initial port of ultrasound imaging experiment * Match _scenario_3.py to update functional API * Update in order to render layout properly * Port notebook up to point of simulate_pulse * Bugfix for receiver locations * Run poetry update * add xarray as dependency for beamforming code * Add jupyter widgets to allow use of tqdm.notebook * Scan-line notebook now enabled, with the workaround-method for recording * Move receiver config from scenario special subclass to _base.py * Port multi-plane imaging to new API * Add comments for fields * Run the notebooks to generate output * Lint code * Some mypy type-hint fixes * Fix mypy type hint error * Fix type-hint warnings: variable reassignment, xarray vs numpy ufunc etc * Suppress type error where can't infer type * Fix linting issues * Add test for beamform and demodulate * Add Scenario3 to built-in tests and mark as integration test similar to test_compilation * Rename _shots.py internal function properly * Fix test_base to work with new receiver_coords argument * Fix test_shots to accomodate new receiver_coords parameter * Lint code * Fix spelling errors * Refactor optimize_f_number into its own function * Add args docstring for delay_and_sum_matrix function * Clean up redundant variable * Swap labeling of x/z dimension order: fix * Refactor time-of-flight calculation to its own function * Refactor out aperture angle of view calculation * Split out interp weights to its own helper function * Lint test_beamform.py * Refactor out sparse matrix indexing code * fix spelling * minor fixes * Convert ipynb jupyter notebooks to ipython scripts for gallery on CI * Fix lint and mypy errors * Fix mkdocs format, which requires standard Python docstring * Fix documentation formatting * Update minor text formatting --------- Co-authored-by: d-lucena <[email protected]>

* Add method to slice 3d result * Add warning for metrics * Change target warning to use try/except * Change target getter, add checks for None target * Revert target getter, remove checks, add tests * Fix slicing alternate source types * Add suggestions, alter validate function * Drop duplicate _validate_slice_args

* Add link check workflow action file * Added link checker config to ignore linked files * Fix config patterns * Fix link check config patterns * Fixed config file path * Switched link checker to handle linked files

…h settings coming from the client

…ngs to scenario

…ss variables

…nario

Adding support to point source transducer Showing scenario names instead of scenario ids Displaying transducer type titles instead of transducer types

This reverts commit 02ed489.

…display

…terface

* Move webpage.html files into their own folder, as they are done in local MacOS build * Revert "Move webpage.html files into their own folder, as they are done in local MacOS build" This reverts commit a9b2e4a. * Remove mkdocs offline plugin, which conflicts with how the gallery examples link to images * no need to pass in OFFLINE environment variable since it is no longer used * Revert "no need to pass in OFFLINE environment variable since it is no longer used" This reverts commit 208318e. * Revert "Remove mkdocs offline plugin, which conflicts with how the gallery examples link to images" This reverts commit ca4a389. * Add mkdocs-offline-links-plugin as a dependency and include as a mkdocs.yml plugin * Update mkdocs-offline plugin to new home at agencyenterprise * Update poetry.lock

* Add Scenario2 variant that mirrors Benchmark 7 of Aubry et al. (2022) * Fix spellcheck

* Pin stride version in all the places we specify pip install * Fix dead link

* Adding CT loading functionality to web * Fixing issues with ct loading * Adding support to load zipped dicom CTs * Spellcheck * Adding absorption to shaped grid * Exposing CT scan info to the FE, so that we can make FE validations * Constraining the distance from origin based on the CT size * Removing unused pynrrd lib * Small refactoring * Refactoring * Using voxels spacing when creating the grid * Adding dependency * Reverting the X/Y swap * Removing gunicorn and replacing the make tarket web with web-development * Pin stride version in all the places we specify pip install (#163) * Pin stride version in all the places we specify pip install * Fix dead link * Poetry version updated * Add focal pressure, focal volume, and FWHM to results metrics (#152) * Poetry version updated --------- Co-authored-by: newton sander <[email protected]> Co-authored-by: charles <[email protected]> Co-authored-by: d-lucena <[email protected]>

…ml forms

Commits on May 31, 2023

change hyperlink

d-lucena committed May 31, 2023

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Commits on Jun 23, 2023

Trigger gallery

NewtonSander committed Jun 23, 2023

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Commits on Jul 5, 2023

Renaming circle_ci job (#103 )

NewtonSander authored Jul 5, 2023

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Commits on Aug 22, 2023

Fixing issue with load from disk

NewtonSander committed Aug 22, 2023

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Implementing web UI #144

Implementing web UI #144

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