Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

warn annotation loss with resolution change #977

Merged
merged 7 commits into from
Feb 13, 2024
Merged

warn annotation loss with resolution change #977

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
14d61a7
warn annotation loss with resolution change
alexvpickering Jan 31, 2024
d740156
explicit step
alexvpickering Jan 31, 2024
72816ab
redo logic
alexvpickering Jan 31, 2024
622baee
revert old changes
alexvpickering Jan 31, 2024
daae0d4
fix tests
alexvpickering Jan 31, 2024
b0399ac
move save to funs
alexvpickering Feb 13, 2024
69f0bcb
Merge branch 'master' into warn-annotation-loss
alexvpickering Feb 13, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
14 changes: 13 additions & 1 deletion src/__test__/redux/actions/pipelines/__snapshots__/runQC.test.js.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,19 @@ exports[`runQC action Dispatches events properly 2`] = `

exports[`runQC action Dispatches status error if loading fails 1`] = `[]`;

exports[`runQC action Runs only the embedding if only changed filter was configureEmbedding 1`] = `
exports[`runQC action Runs only clustering if only changed filter was clusteringSettings 1`] = `
[
{
"payload": {},
"type": "experimentSettings/discardChangedQCFilters",
},
{
"type": "cellSets/clusteringUpdating",
},
]
`;

exports[`runQC action Runs only the embedding if only changed filter was embeddingSettings 1`] = `
[
{
"payload": {},
Expand Down
35 changes: 31 additions & 4 deletions src/__test__/redux/actions/pipelines/runQC.test.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,8 @@ import {
EXPERIMENT_SETTINGS_DISCARD_CHANGED_QC_FILTERS,
} from 'redux/actionTypes/experimentSettings';

import { CELL_SETS_CLUSTERING_UPDATING } from 'redux/actionTypes/cellSets';

import { EMBEDDINGS_LOADING } from 'redux/actionTypes/embeddings';

import { runQC } from 'redux/actions/pipeline';
Expand Down Expand Up @@ -46,6 +48,7 @@ const initialState = {
},
},
},
cellSets: {},
backendStatus: {
[experimentId]: {
status: {
Expand Down Expand Up @@ -102,15 +105,15 @@ describe('runQC action', () => {
expect(actions).toMatchSnapshot();
});

it('Runs only the embedding if only changed filter was configureEmbedding', async () => {
it('Runs only the embedding if only changed filter was embeddingSettings', async () => {
fetchMock.resetMocks();

saveProcessingSettings.mockImplementation(() => () => Promise.resolve());

const onlyConfigureEmbeddingChangedState = _.cloneDeep(initialState);
onlyConfigureEmbeddingChangedState.experimentSettings.processing.meta.changedQCFilters = new Set(['configureEmbedding']);
const onlyEmbeddingSettingsChangedState = _.cloneDeep(initialState);
onlyEmbeddingSettingsChangedState.experimentSettings.processing.meta.changedQCFilters = new Set(['embeddingSettings']);

const store = mockStore(onlyConfigureEmbeddingChangedState);
const store = mockStore(onlyEmbeddingSettingsChangedState);
await store.dispatch(runQC(experimentId));

await waitForActions(
Expand All @@ -125,4 +128,28 @@ describe('runQC action', () => {

expect(actions).toMatchSnapshot();
});

it('Runs only clustering if only changed filter was clusteringSettings', async () => {
fetchMock.resetMocks();

saveProcessingSettings.mockImplementation(() => () => Promise.resolve());

const onlyClusteringSettingsChangedState = _.cloneDeep(initialState);
onlyClusteringSettingsChangedState.experimentSettings.processing.meta.changedQCFilters = new Set(['clusteringSettings']);

const store = mockStore(onlyClusteringSettingsChangedState);
await store.dispatch(runQC(experimentId));

await waitForActions(
store,
[EXPERIMENT_SETTINGS_DISCARD_CHANGED_QC_FILTERS, CELL_SETS_CLUSTERING_UPDATING],
);

const actions = store.getActions();

expect(actions[0].type).toEqual(EXPERIMENT_SETTINGS_DISCARD_CHANGED_QC_FILTERS);
expect(actions[1].type).toEqual(CELL_SETS_CLUSTERING_UPDATING);

expect(actions).toMatchSnapshot();
});
});
66 changes: 14 additions & 52 deletions src/components/data-processing/ConfigureEmbedding/CalculationConfig.jsx
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
import React, {
useState, useEffect, useCallback,
useState, useEffect,
} from 'react';
import _ from 'lodash';
import { useDispatch, useSelector } from 'react-redux';
Expand All @@ -9,9 +9,8 @@ import {
import PropTypes from 'prop-types';
import { QuestionCircleOutlined } from '@ant-design/icons';

import { updateFilterSettings, saveProcessingSettings } from 'redux/actions/experimentSettings';
import { updateFilterSettings } from 'redux/actions/experimentSettings';

import { runCellSetsClustering } from 'redux/actions/cellSets';
import PreloadContent from '../../PreloadContent';

import SliderWithInput from '../../SliderWithInput';
Expand All @@ -32,7 +31,7 @@ const EMBEDD_METHOD_TEXT = 'Reducing the dimensionality does lose some informati
+ 't-SNE and UMAP are stochastic and very much dependent on choice of parameters (t-SNE even more than UMAP) and can yield very different results in different runs. ';

const CalculationConfig = (props) => {
const { experimentId, onConfigChange, disabled } = props;
const { onConfigChange, disabled } = props;
const FILTER_UUID = 'configureEmbedding';
const dispatch = useDispatch();

Expand All @@ -46,41 +45,19 @@ const CalculationConfig = (props) => {
const { umap: umapSettings, tsne: tsneSettings } = data?.embeddingSettings.methodSettings || {};
const { louvain: louvainSettings } = data?.clusteringSettings.methodSettings || {};

const debouncedClustering = useCallback(
_.debounce((resolution) => {
dispatch(runCellSetsClustering(experimentId, resolution));
}, 1500),
[],
);

const [resolution, setResolution] = useState(null);
const [minDistance, setMinDistance] = useState(null);

useEffect(() => {
if (!resolution && louvainSettings) {
setResolution(louvainSettings.resolution);
}
}, [louvainSettings]);

useEffect(() => {
if (!minDistance && umapSettings) {
setMinDistance(umapSettings.minimumDistance);
}
}, [umapSettings]);

const dispatchDebounce = useCallback(_.debounce((f) => {
dispatch(f);
}, 1500), []);

const updateSettings = (diff) => {
if (diff.embeddingSettings) {
// If this is an embedding change, indicate to user that their changes are not
// applied until they hit Run.
onConfigChange();
} else {
// If it's a clustering change, debounce the save process at 1.5s.
dispatchDebounce(saveProcessingSettings(experimentId, FILTER_UUID));
}
// updates to configure embedding run on worker if they are the only changes
// need to know if change was to embedding or clustering settings
const settingType = Object.keys(diff)[0];
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Why only the first changed from the diff and not the whole Object.keys(diff)?

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Each of the diffs is a single object where the top level key is either going to be embeddingSettings or clusteringSettings. This just extracts that key.

onConfigChange(settingType);

dispatch(updateFilterSettings(
FILTER_UUID,
Expand All @@ -98,8 +75,6 @@ const CalculationConfig = (props) => {
},
},
});

onConfigChange();
};
const setDistanceMetric = (value) => {
updateSettings({
Expand All @@ -111,8 +86,6 @@ const CalculationConfig = (props) => {
},
},
});

onConfigChange();
};

const setLearningRate = (value) => {
Expand All @@ -125,8 +98,6 @@ const CalculationConfig = (props) => {
},
},
});

onConfigChange();
};
const setPerplexity = (value) => {
updateSettings({
Expand All @@ -138,8 +109,6 @@ const CalculationConfig = (props) => {
},
},
});

onConfigChange();
};

const renderUMAPSettings = () => (
Expand Down Expand Up @@ -395,21 +364,14 @@ const CalculationConfig = (props) => {
max={10}
step={0.1}
disabled={disabled}
value={resolution}
onUpdate={(value) => {
if (value === resolution) { return; }

setResolution(value);
updateSettings({
clusteringSettings: {
methodSettings: {
louvain: { resolution: value },
},
value={louvainSettings.resolution}
onUpdate={(value) => updateSettings({
clusteringSettings: {
methodSettings: {
louvain: { resolution: value },
},
});

debouncedClustering(value);
}}
},
})}
/>
</Form.Item>
</Form>
Expand Down
6 changes: 5 additions & 1 deletion src/pages/experiments/[experimentId]/data-processing/index.jsx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -329,7 +329,7 @@ const DataProcessingPage = ({ experimentId, experimentData }) => {
<ConfigureEmbedding
experimentId={expId}
key={key}
onConfigChange={() => onConfigChange(key)}
onConfigChange={(settingType) => onConfigChange(settingType)}
stepHadErrors={getStepHadErrors(key)}
/>
),
Expand Down Expand Up @@ -695,6 +695,10 @@ const DataProcessingPage = ({ experimentId, experimentData }) => {
Your navigation within Cellenics will be restricted during this time.
Do you want to start?
</p>
<Alert
message='Note that you will lose all of your annotated cell sets.'
type='warning'
/>
</Modal>
)
)}
Expand Down
45 changes: 37 additions & 8 deletions src/redux/actions/pipeline/runQC.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,10 +9,10 @@ import {
import { saveProcessingSettings } from 'redux/actions/experimentSettings';
import { loadBackendStatus } from 'redux/actions/backendStatus';
import { loadEmbedding } from 'redux/actions/embedding';
import { runCellSetsClustering } from 'redux/actions/cellSets';

const runOnlyConfigureEmbedding = async (experimentId, embeddingMethod, dispatch) => {
await dispatch(saveProcessingSettings(experimentId, 'configureEmbedding'));

dispatch({
type: EXPERIMENT_SETTINGS_DISCARD_CHANGED_QC_FILTERS,
payload: {},
Expand All @@ -28,6 +28,22 @@ const runOnlyConfigureEmbedding = async (experimentId, embeddingMethod, dispatch
);
};

const runOnlyClustering = async (experimentId, resolution, dispatch) => {
await dispatch(saveProcessingSettings(experimentId, 'configureEmbedding'));
dispatch({
type: EXPERIMENT_SETTINGS_DISCARD_CHANGED_QC_FILTERS,
payload: {},
});

// Only configure embedding was changed so we run loadEmbedding
dispatch(
runCellSetsClustering(
experimentId,
resolution,
),
);
};

// Question for review, I thought of implementing this function for all the URLs here
// (extracting all the URLs into one single place and using constants to
// define which url I am trying to access)
Expand All @@ -42,12 +58,26 @@ const runQC = (experimentId) => async (dispatch, getState) => {
const { processing } = getState().experimentSettings;
const { changedQCFilters } = processing.meta;

if (changedQCFilters.size === 1 && changedQCFilters.has('configureEmbedding')) {
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

With changedQCFilters.size === 1 removed, now that means that if there's more than one changed filter, running it with changed embedding or clustering in the last step will discard them all and run only embedding / clustering?

Copy link
Contributor Author

@alexvpickering alexvpickering Feb 13, 2024 •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

changedQCFilters.size === 1 is removed because we will now be looking for either exactly embeddingSettings , clusteringSettings, or both. If both are changed but nothing else we also need to run this conditional block (so size is no longer a good way to distinguish).

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Sorry I cant test in staging because i dont have an hms account but what i see is that now this will be run even if there are other changedQCFilters from previous steps. There is a return on line 81, so that means qc wont be triggered.
What will happen if i change for example the mitochondrial content filter and then go to configure embedding and change clustering / embedding there? I think mitochondrial filter changes will be discarded and clustering / embedding will be ran right?

Copy link
Contributor Author

@alexvpickering alexvpickering Feb 13, 2024 •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

If you send me an email I'll create an account for you to test. Here is why it doesn't run if there are other steps changed:

const otherChanged = [...changedQCFilters].some((value) => value !== 'embeddingSettings' && value !== 'clusteringSettings');

This checks to see if there are other settings changed. If there are not, then the below conditional block runs. See added comments to hopefully clarify:

if (!otherChanged) {

// this runs because exactly embedding or clustering or both has changed (but nothing else)
await dispatch(saveProcessingSettings(experimentId, 'configureEmbedding'));

if (embeddingChanged) {
      runOnlyConfigureEmbedding(
        experimentId,
        processing.configureEmbedding.embeddingSettings.method,
        dispatch,
      );
    }
    if (clusteringChanged) {
      runOnlyClustering(
        experimentId,
        processing.configureEmbedding.clusteringSettings.methodSettings.louvain.resolution,
        dispatch,
      );
    }
    // we return because we are in the !otherChanged block so nothing else changed and we don't re-run QC
    return;
}

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

oh alright sorry

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Not at all -- thank you -- always good to have a careful review :)

runOnlyConfigureEmbedding(
experimentId,
processing.configureEmbedding.embeddingSettings.method,
dispatch,
);
const embeddingChanged = changedQCFilters.has('embeddingSettings');
const clusteringChanged = changedQCFilters.has('clusteringSettings');
const otherChanged = [...changedQCFilters].some((value) => value !== 'embeddingSettings' && value !== 'clusteringSettings');

// if only embedding or clustering changed
if (!otherChanged) {
if (embeddingChanged) {
runOnlyConfigureEmbedding(
experimentId,
processing.configureEmbedding.embeddingSettings.method,
dispatch,
);
}
if (clusteringChanged) {
runOnlyClustering(
experimentId,
processing.configureEmbedding.clusteringSettings.methodSettings.louvain.resolution,
dispatch,
);
}

return;
}
Expand All @@ -57,7 +87,6 @@ const runQC = (experimentId) => async (dispatch, getState) => {
const stepConfig = processing[stepKey];
processingConfigDiff[stepKey] = stepConfig;
});

try {
// We are only sending the configuration that we know changed
// with respect to the one that is already persisted in dynamodb
Expand Down
Loading