9.) graph based decoding #1613
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9.) graph based decoding #1613
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Codecov Report
@@ Coverage Diff @@
## saxelrod-delete-old-detect-code #1613 +/- ##
===================================================================
+ Coverage 89.87% 90.24% +0.37%
===================================================================
Files 219 221 +2
Lines 8117 8550 +433
===================================================================
+ Hits 7295 7716 +421
- Misses 822 834 +12
Continue to review full report at Codecov.
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ttung
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Oct 25, 2019
| @@ -122,6 +126,449 @@ def _build_intensity_table( | |||
| return intensity_table | |||
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| def _build_spot_traces_per_round( | |||
| round_dataframes: Dict[int, pd.DataFrame], | |||
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| round_dataframes: Dict[int, pd.DataFrame], | |
| round_dataframes: Mapping[int, pd.DataFrame], |
if you're not going to modify, might as well make it immutable.
| def _build_spot_traces_per_round( | ||
| round_dataframes: Dict[int, pd.DataFrame], | ||
| channels: Sequence[int], | ||
| rounds: Sequence[int] |
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does round_dataframes.keys() contain the same data?
| for i in range(len(conn_comps)): | ||
| df_tmp = df.loc[conn_comps[i], :] | ||
| kdT_tmp = KDTree(df_tmp.loc[:, [Axes.ZPLANE.value, Axes.Y.value, Axes.X.value]].values) | ||
| # Check if all spots whitin a conn component are at most 1 pixels away |
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| # Check if all spots whitin a conn component are at most 1 pixels away | |
| # Check if all spots within a connected component are at most 1 pixels away |
| intensity_tables : Dict[int, IntensityTable] | ||
| Output from _merge_spots_by_round, contains mapping of intensity tables | ||
| from each round to all the spots detected in them. | ||
| channels, rounds : Sequence[int] |
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| search_radius : int | ||
| Euclidean distance in pixels over which to search for spots in subsequent rounds. | ||
| search_radius_max : int | ||
| The maximum (euclidian) distance in pixels allowed between nodes belonging | ||
| to the same sequence |
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kind of surprised these aren't floats
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hey @mattcai can you review this PR? it would be nice to get it in to 0.3.0 if its ready |
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Codecov ReportAttention: Patch coverage is
❗ Your organization needs to install the Codecov GitHub app to enable full functionality. Additional details and impacted files@@ Coverage Diff @@
## saxelrod-delete-old-detect-code #1613 +/- ##
===================================================================
+ Coverage 89.87% 90.24% +0.37%
===================================================================
Files 219 221 +2
Lines 8117 8550 +433
===================================================================
+ Hits 7295 7716 +421
- Misses 822 834 +12 ☔ View full report in Codecov by Sentry. |
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This PR takes the work done by @gapartel in #1482 and modifies it to exist within the new spot finding modules.
h_maxwas missing from out existing collection so I added it as well as tests for it.build_traces_graph_based()instead ofdecode_spots()PerRoundMaxwith the parameterTraceBuildingStrategies.GRAPH. Some examples can be shown in the notebookgraph_decoding.py