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Major Version Update- BTEP Presentations #121
Commits on May 29, 2024
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It wasn't forcing a key reset, it was just that I hadn't updated the …
…plot chart key; now the reset button works as expected, but the chart still resets its zoom if anything such as selection or slider changing etc. modifies the selected region. If I pursue this as users probably want, it would require the original idea of toggling the plotly box selection between a zoom, i.e. manually setting it, and the actual histogram region selection functionality which is already implemented
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Add radio to select the function of the box selection, whether select…
…ion of positive region of the histogram(s) or the x axis zoom
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Initialize relevant histogram-zoom-related settings every time the co…
…lumn for filtering is changed
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Add too-global fixes in comments to force MAWA to use just a single C…
…PU when Squidpy is selected since it commandeers threads; in future we'll need to limit just the significance calculations to a single thread if Squidpy is selected
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Commits on Jun 1, 2024
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Add functionality for robust image filtering using new selectable dat…
…aframes in Streamlit, to replace previous image filters such as in the multiaxial gater and probably in the plotter-based pages such as the scatter plotter and the draft radial profiles page
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Commits on Jun 3, 2024
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Commits on Jun 4, 2024
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Commits on Jun 5, 2024
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Commits on Jun 6, 2024
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Commits on Jun 7, 2024
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Commits on Jun 10, 2024
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Merge pull request #120 from ncats/improvement_suggestions
Removing Neighborhood Profiles checkpointing
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Andrew intended to make the default condition for the umap subset to be true. The change in this commit will make the intention true
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Something weird is going on with palantir library. Taking this out for the time being
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Commits on Jun 11, 2024
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Commits on Jun 12, 2024
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Commits on Jun 13, 2024
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Commits on Jun 14, 2024
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Merge pull request #122 from ncats/improvement_suggestions
QoL changes for MAWA/Neighborhood Profiles
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Commits on Jun 17, 2024
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Merge pull request #125 from ncats/improvement_suggestions
Hard setting cpu_pool_size = 3 for clustering
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Commits on Jun 18, 2024
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Add box plot to scatter plotter as a check that the phenotyping was p…
…erformed as expected
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Only want this to run when its toggle_clust_diff and when its also a appro_feat
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This only solves half the problem. I think I can make the rest of it work too
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Allow the user to specify the mean and std to be used for the thresho…
…ld calculation for the box and whisker plots. This allows e.g. to use T=0 mean and std in the plots for the entire dataset
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Removing calls to callback function
Didnt solve all my problems. Making a simple variable to check for the kind of clustering being completed
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Merge pull request #127 from ncats/improvement_suggestions
Adding mp_start_method to match utils.execute_data_parallelism_potentially
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Trying a direct call of the utils function
I think this is what Andrew wanted. Lets give this a go
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Merge pull request #128 from ncats/improvement_suggestions
Trying a direct call of the utils function
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Commits on Jun 19, 2024
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About to try to debug why going to the next image scrolls page back u…
…p to the plot in the radial profiles app but not in the scatter plotter
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Fix issue with page automatically scrolling back to the top when some…
…thing updates a plotly figure by rendering some output (st.toggle() works too) after the plotly figure is rendered
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Commits on Jun 20, 2024
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Commits on Jun 21, 2024
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Unify the unit coordinates by temporarily converting the coordinates …
…since we currently did not perform the conversion in the unifier
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Commits on Jun 22, 2024
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Pin Streamlit to v1.35 due to st_pages breaking in v1.36
Automatically calculate the midpoint of each image Calculate evenly spaced radii from the midpoint to at most include the largest possible radius Plot the radii on the image In the scatter plotter, exit cleanly if the input dataset does not exist
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Commits on Jun 24, 2024
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Percent positivities appear to be correctly calculated based on curso…
…ry visual inspection
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Fixing an issue with slider val and plotting
Too many calls to a function and things got lost along the way
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Commits on Jun 25, 2024
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Put analysis inside its own function and cleaned up code, all still s…
…eems to be good, 6M cells take 20 sec to run
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Start to intelligently and in a user friendly way calculate the means…
… and CIs of a selected set of images; basically just have to do plotting now, no more calculations
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Use annuli out to the rectangle corners instead of the edges and crea…
…te a single function that detects the radial bin for each cell
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Commits on Jun 26, 2024
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Improved method for checking the values within a column and determining if we can split it before clustering
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Merge pull request #130 from ncats/improvement_suggestions
Adding Feature separation for difference clustering
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Commits on Jun 27, 2024
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Commits on Jun 28, 2024
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Merge pull request #131 from ncats/improvement_suggestions
Fixing a bug related to drawing 0 values on log scale
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Don't throw red error box if no file has been opened if the user imme…
…diately tries to use the scatter plotter
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Delete streamlit=1.35.0 in pip section of environment.yml, should hav…
…e been == anyway I believe
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Also delete pinned Streamlit version in .hooks/startup.sh, note there…
…'s no longer a red error though you have to hit 'r' to reload the page and then the sidebar loads correctly
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Commits on Jul 2, 2024
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Address bug where if you set a custom phenotype name to unassigned in…
… order to ignore it, the phenotyping in the spatial interaction tool won't die on an assertion error
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Refactor and clean up the code, didn't implement parallelization but …
…doesn't seem to be needed when applying the thresholds to each individual group as likely makes the most sense
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Rename pages to something else since we get a warning with the new mu…
…ltipage functionality
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Try porting to Streamlit's new multipage functionality since we have …
…to significantly change the .toml file anyway
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Remove reference to pages directory, which the new Streamlit multipag…
…e functionality says to not use or else issues might crop up, hence the rename to pages2
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Move code from radial_bins_plots.py to the new pages adaptive_phenoty…
…ping.py and preprocessing.py
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Commits on Jul 8, 2024
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Use lambda functions in callbacks to simplify key deletion from sessi…
…on state Remove any dependence of adaptive phenotyping on radial bins analysis... it's completely general Make categorical column determination a function in utils.py
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Add calculation and plotting of significant differents of the means b…
…etween two groups
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Commits on Jul 15, 2024
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Disabled unsupervised phenotyping workflow so app works while Andrei …
…sees if he can fix it Saved edits back to main dataframe in session state in adaptive phenotyper Add warning that preprocessing may have already been done so exit preprocessing function cleanly Broaden ImageJ preprocessing to accommodate newest dataset
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Allow user to select confidence level for determination of significan…
…ce difference in the means
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Commits on Jul 18, 2024
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No idea they were in this order. I think these changes came after we had finished working with Will and group.
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Merge pull request #132 from ncats/improvement_suggestions
Improvement suggestions
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Gracefully give warning if data isn't loaded before clicking on radia…
…l profiles analysis
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Don't stop rest of Unifier from running until ROI definition button h…
…as been pressed Don't let robust scatter plotter die if the dataframe of interest contains lists in a column (unhashable error) Fix Squidpy from dying with cryptic error 'TypeError: No matching definition for argument type(s) readonly array(uint32, 1d, C), array(uint32, 1d, C), array(uint32, 1d, C)' by basically removing n_jobs=1
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Clear datafile unifier data when new files are combined
Implement taking the intersection of columns instead of forcing the user to use datafiles with all the same columns Detect null values in the data Turn off plotting once min/max settings are changed
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Merge pull request #135 from ncats/improvement_suggestions
Fixing an issue with feature separation
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In null row detection in the unifier, display only the rows with null…
… values; also, if basic_phenotyper_lib.init_pheno_cols() null rows are found, delete them automatically and render a warning to the user
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Get kdtree working to match the previous cdist implementation in the …
…SIT, although it may suffer from: (1) generating many trees, and (2) not taking memory issues into consideration as is done using kdtree in neighborhood profiles
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Reverting to cdist method accounting for OOM. Refactoring the SIT to …
…use kdtree efficiently involves the following considerations: (1) many trees are generated in the version just implemented so it'd be tempting to generate one per center phenotype and neighbor phenotype where there are fewer possible centers than neighbors due to edge effects, (2) the metrics calculation includes the number of neighbors in lambda, (3) using utils.fast_neighbors_counts_for_block2() would be tempting which suggests to use one df per ROI but don't forget edge effects, (4) it could also be best to just take into account memory considerations in the new kdtree counts method implemented today, (5) there could be more considerations. Basically, we'd need to balance the considerations in utils.fast_neighbors_counts_for_block2() with many nuances most of which are touched upon in this commit message, so refactoring to use kdtree efficiently for the SIT is far from trivial and probably not worth it at this time
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Merge pull request #136 from ncats/andrei_develop
Andrei develop
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Merge pull request #137 from ncats/andrei_develop
normalization methods and variable features selection
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Merge pull request #145 from ncats/andrei_develop
Andrei develop
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Allow for .zip files to be loaded in which the user has potentially a…
…dded a bunch more periods than expected
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Add instructions imploring user to always delete null rows in the Dat…
…afile Unifier. This is in response to a user running the SIT when using a unified datafile where null values weren't deleted, so the SIT crashed with df[marker_cols] = df[marker_cols].map(lambda x: {'+': 1, '-': 0}[x[-1]])
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Don't allow length mismatches in e.g. the line df_paths['slide'] = co…
…rresp_slide_filename
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Update missing ROI heatmap data message
Account for missing average slide heatmap data in the plots
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Remove unit conversion in the file opener since the conversion should…
… always be done in the unifier
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Add demo of forking issue that doesn't seem to be present in a clean …
…multipage instance
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Merge pull request #146 from ncats/andrew-dev
Bunch of changes mainly to address issues with user's dataset and settings
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Fix occassional 'Stopping...' error by forcing the forkserver start m…
…ethod to get set since it never was since it was being set in the name==main block, which is never called by Multiplex_Analysis_Web_Apps.py
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Pare down Multiplex_Analysis_Web_Apps.py keeping only 'st.set_page_co…
…nfig(layout=wide)'; the problem still occurs: 2024-09-23 13:38:45.780 WARNING streamlit.runtime.scriptrunner_utils.script_run_context: Thread 'MainThread': missing ScriptRunContext! This warning can be ignored when running in bare mode.
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Putting back in 'st.set_page_config(layout=wide)' to find this is wha…
…t causes the problem to occur, at least in the MAWA code stack
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Fix the problem by moving the wide layout command to inside the main(…
…) function. It was previously outside it above the import statements because at least one of those scripts contained calls to streamlit (well, to st) outside functions, which can't be called before the layout command
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Put back in all the imports... no conflicts with the layout function …
…are detected so there must be no more streamlit calls before layout is called in the main() function in Multiplex_Analysis_Web_Apps.py. However, running the forking test still executes slowly with seconds of overhead.
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Note which modules whose imports cause the forking test to have a lar…
…ge amount of overhead
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Switch back to my original forking test which is more representative …
…of how parallel calls are made in MAWA. The slow imports still occur the same way, we probably just need to fix those scripts
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Show that only if both nidap_dashboard_lib.py and basic_phenotyper_li…
…b.py are commented out that speed goes back to normal (note in my last commit I still had one of those mistakenly commented out)
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It's fast again having commented out the import of the thresholded ph…
…enotyper, will address that later
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Find that not only is umap slow, but also something in 'from neighbor…
…hood_profiles import NeighborhoodProfiles, UMAPDensityProcessing' in nidap_dashboard_lib.py is slow
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The culprit seems to be the import of umap in neighborhood_profiles.p…
…y... so it seems that umap is what makes anything in nidap_dashboard_lib.py and basic_phenotyper_lib.py slow
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The culprit seems to be the import of umap in neighborhood_profiles.p…
…y... so it seems that umap is what makes anything in nidap_dashboard_lib.py and basic_phenotyper_lib.py slow
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Start uncommenting things out, carefully ensuring the threading issue…
… still doesn't pop up due to setting the wide layout in the main() function now
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Finish fixing threading problem by moving wide layout and assessing s…
…peed of module imports and their effects on the forking testing
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Merge pull request #147 from ncats/check_ubuntu_installation
Check ubuntu installation + Andrew's additions
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This seems to be working for both published and unpublished dashboard…
…s, though I'm a bit nervous about the consistency of the installation of 'annoy'. But the last two times it worked. This adds Python-based installation of packages after environment.yml/startup.sh have been used to set up the environments.
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Merge pull request #148 from ncats/package_setup_using_old_methods
Update live installation of packages so that both unpublished workspaces and published dashboards work
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Don't resample without replacement if the requested sample size is sm…
…aller than the dataframe size; if so, then essentially just return the whole dataframe
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Allow the user to manually re-extract the columns from the dataset of…
… interest in case they have changed and haven't updated through the app
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Even if ROI name have spaces in them, ensure ALL images generated by …
…SIT replace them with underscores; until now, just some of them did, like those in single_roi_outlines_on_whole_slides
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Parsing image names is proving really hard to generalize; trying a mu…
…ch cleaner way, basically undoing most of the changes from the last commit; compare to the commit before that
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Clean up a little better and note that the commit I meant to say to c…
…ompare the previous one to is 64bac4e
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Since we are maintaining that images get generated without the spaces…
…, in order to not change many things at once, then make sure we respect that when getting the correct paths for the ROIs
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