4578689396

Build Type

github

Committed by GitHub

Commit Message

Merge ddb425c30 into 6a993cb7a

Pull Request Pull Request #436: Model training overhaul: SNGP model, uncertainty visualization, and custom embedding support

Run Details

462 of 1163 branches covered (39.72%)

Branch coverage included in aggregate %.

20 of 628 new or added lines in 27 files covered. (3.18%)

76 existing lines in 5 files now uncovered.

3248 of 5431 relevant lines covered (59.8%)

543.49 hits per line

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0.0

/frontend/src/Project/EditControls/CellTypeControls/TrainingUI/LearnTab.js

import { Box, Button, MenuItem, TextField } from '@mui/material';
import Grid from '@mui/material/Grid';
import { useSelector } from '@xstate/react';
import { useState } from 'react';
import { useChannelExpression } from '../../../ProjectContext';
import AddRemoveCancel from '../ChannelExpressionUI/AddRemoveCancel';
import CalculateWholeToggle from '../ChannelExpressionUI/CalculateWholeToggle';
import EmbeddingColorMapToggle from './EmbeddingColorMapToggle';
import EmbeddingPlot from './EmbeddingPlot';
import TrainingButtons from './TrainingButtons';

function LearnTab() {
  const [embedding, setEmbedding] = useState(0);
  const channelExpression = useChannelExpression();
  const imported = useSelector(channelExpression, (state) => state.context.embeddings);
  const embeddingPlotted = useSelector(channelExpression, (state) => state.context.reduction);
  const quantities = imported
    ? ['Position', 'Mean', 'Total', 'Imported']
    : ['Position', 'Mean', 'Total'];

  const handleVisualize = () => {
    if (quantities[embedding] === 'Position') {
      channelExpression.send({ type: 'CALCULATE', stat: quantities[embedding] });
    } else {
      channelExpression.send({ type: 'CALCULATE_UMAP', stat: quantities[embedding], whole: true });
    }
  };

  return (
    <>
      <Grid item display='flex'>
        <TextField
          select
          size='small'
          value={embedding}
          label='Embedding'
          onChange={(evt) => setEmbedding(evt.target.value)}
          sx={{ width: '47%' }}
        >
          {quantities.map((opt, index) => (
            <MenuItem key={index} value={index}>
              {opt}
            </MenuItem>
          ))}
        </TextField>
        <Box sx={{ marginLeft: '1%' }}>
          <CalculateWholeToggle />
        </Box>
      </Grid>
      <Grid item>
        <Button sx={{ width: '97%' }} variant='contained' onClick={handleVisualize}>
          Visualize
        </Button>
      </Grid>
      <TrainingButtons />
      {embeddingPlotted ? (
        <>
          <EmbeddingColorMapToggle />
          <EmbeddingPlot embedding={embeddingPlotted} />
          <AddRemoveCancel />
        </>
      ) : null}
    </>
  );
}

export default LearnTab;

1	import { Box, Button, MenuItem, TextField } from '@mui/material';
2	import Grid from '@mui/material/Grid';
3	import { useSelector } from '@xstate/react';
4	import { useState } from 'react';
5	import { useChannelExpression } from '../../../ProjectContext';
6	import AddRemoveCancel from '../ChannelExpressionUI/AddRemoveCancel';
7	import CalculateWholeToggle from '../ChannelExpressionUI/CalculateWholeToggle';
8	import EmbeddingColorMapToggle from './EmbeddingColorMapToggle';
9	import EmbeddingPlot from './EmbeddingPlot';
10	import TrainingButtons from './TrainingButtons';
11
12	function LearnTab() {
13	const [embedding, setEmbedding] = useState(0);	×
14	const channelExpression = useChannelExpression();	×
NEW 15	const imported = useSelector(channelExpression, (state) => state.context.embeddings);	×
NEW 16	const embeddingPlotted = useSelector(channelExpression, (state) => state.context.reduction);	×
NEW 17	const quantities = imported	×
18	? ['Position', 'Mean', 'Total', 'Imported']
19	: ['Position', 'Mean', 'Total'];
20
21	const handleVisualize = () => {	×
22	if (quantities[embedding] === 'Position') {	×
23	channelExpression.send({ type: 'CALCULATE', stat: quantities[embedding] });	×
24	} else {
25	channelExpression.send({ type: 'CALCULATE_UMAP', stat: quantities[embedding], whole: true });	×
26	}
27	};
28
29	return (	×
30	<>
31	<Grid item display='flex'>
32	<TextField
33	select
34	size='small'
35	value={embedding}
36	label='Embedding'
37	onChange={(evt) => setEmbedding(evt.target.value)}	×
38	sx={{ width: '47%' }}
39	>
40	{quantities.map((opt, index) => (
41	<MenuItem key={index} value={index}>	×
42	{opt}
43	</MenuItem>
44	))}
45	</TextField>
46	<Box sx={{ marginLeft: '1%' }}>
47	<CalculateWholeToggle />
48	</Box>
49	</Grid>
50	<Grid item>
51	<Button sx={{ width: '97%' }} variant='contained' onClick={handleVisualize}>
52	Visualize
53	</Button>
54	</Grid>
55	<TrainingButtons />
56	{embeddingPlotted ? (	×
57	<>
58	<EmbeddingColorMapToggle />
59	<EmbeddingPlot embedding={embeddingPlotted} />
60	<AddRemoveCancel />
61	</>
62	) : null}
63	</>
64	);
65	}
66
67	export default LearnTab;

vanvalenlab / deepcell-label / 4578689396

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