Merge pull request #119 from CBroz1/qc

Add QC dashboard

Author: kushalbakshi

.gitignore

@@ -123,3 +123,6 @@ docker-compose.y*ml
 # vscode settings
 .vscode
 *.code-workspace
+
+# exports/notes
+temp*

CHANGELOG.md

@@ -8,6 +8,7 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 + Update - clustering step, update duration for "median_subtraction" step
 + Bugfix - handles single probe recording in "Neuropix-PXI" format
 + Update - safeguard in creating/inserting probe types upon probe activation
++ Add - quality control metric dashboard
 
 ## [0.2.0] - 2022-10-28
 

element_array_ephys/ephys_report.py

@@ -1,8 +1,10 @@
-import pathlib
 import datetime
-import datajoint as dj
+import pathlib
 import typing as T
-import json
+from uuid import UUID
+
+import datajoint as dj
+from element_interface.utils import dict_to_uuid
 
 schema = dj.schema()
 
@@ -92,18 +94,18 @@ class UnitLevelReport(dj.Computed):
     definition = """
     -> ephys.CuratedClustering.Unit
     ---
-    cluster_quality_label   : varchar(100) 
-    waveform_plotly         : longblob  
+    cluster_quality_label   : varchar(100)
+    waveform_plotly         : longblob
     autocorrelogram_plotly  : longblob
     depth_waveform_plotly   : longblob
     """
 
     def make(self, key):
 
         from .plotting.unit_level import (
-            plot_waveform,
             plot_auto_correlogram,
             plot_depth_waveforms,
+            plot_waveform,
         )
 
         sampling_rate = (ephys.EphysRecording & key).fetch1(
@@ -136,6 +138,94 @@ def make(self, key):
         )
 
 
+@schema
+class QualityMetricCutoffs(dj.Lookup):
+    definition = """
+    cutoffs_id                    : smallint
+    ---
+    amplitude_cutoff_maximum=null : float # Defualt null, no cutoff applied
+    presence_ratio_minimum=null   : float # Defualt null, no cutoff applied
+    isi_violations_maximum=null   : float # Defualt null, no cutoff applied
+    cutoffs_hash: uuid
+    unique index (cutoffs_hash)
+    """
+
+    contents = [
+        (0, None, None, None, UUID("5d835de1-e1af-1871-d81f-d12a9702ff5f")),
+        (1, 0.1, 0.9, 0.5, UUID("f74ccd77-0b3a-2bf8-0bfd-ec9713b5dca8")),
+    ]
+
+    @classmethod
+    def insert_new_cutoffs(
+        cls,
+        cutoffs_id: int = None,
+        amplitude_cutoff_maximum: float = None,
+        presence_ratio_minimum: float = None,
+        isi_violations_maximum: float = None,
+    ):
+        if cutoffs_id is None:
+            cutoffs_id = (dj.U().aggr(cls, n="max(cutoffs_id)").fetch1("n") or 0) + 1
+
+        param_dict = {
+            "amplitude_cutoff_maximum": amplitude_cutoff_maximum,
+            "presence_ratio_minimum": presence_ratio_minimum,
+            "isi_violations_maximum": isi_violations_maximum,
+        }
+        param_hash = dict_to_uuid(param_dict)
+        param_query = cls & {"cutoffs_hash": param_hash}
+
+        if param_query:  # If the specified cutoff set already exists
+            existing_paramset_idx = param_query.fetch1("cutoffs_id")
+            if (
+                existing_paramset_idx == cutoffs_id
+            ):  # If the existing set has the same id: job done
+                return
+            # If not same name: human err, adding the same set with different name
+            else:
+                raise dj.DataJointError(
+                    f"The specified param-set already exists"
+                    f" - with paramset_idx: {existing_paramset_idx}"
+                )
+        else:
+            if {"cutoffs_id": cutoffs_id} in cls.proj():
+                raise dj.DataJointError(
+                    f"The specified cuttoffs_id {cutoffs_id} already exists,"
+                    f" please pick a different one."
+                )
+            cls.insert1(
+                {"cutoffs_id": cutoffs_id, **param_dict, "cutoffs_hash": param_hash}
+            )
+
+
+@schema
+class QualityMetricSet(dj.Manual):
+    definition = """
+    -> ephys.QualityMetrics
+    -> QualityMetricCutoffs
+    """
+
+
+@schema
+class QualityMetricReport(dj.Computed):
+    definition = """
+    -> QualityMetricSet
+    ---
+    plot_grid : longblob
+    """
+
+    def make(self, key):
+        from .plotting.qc import QualityMetricFigs
+
+        cutoffs = (QualityMetricCutoffs & key).fetch1()
+        qc_key = ephys.QualityMetrics & key
+
+        self.insert1(
+            key.update(
+                dict(plot_grid=QualityMetricFigs(qc_key, **cutoffs).get_grid().to_json)
+            )
+        )
+
+
 def _make_save_dir(root_dir: pathlib.Path = None) -> pathlib.Path:
     if root_dir is None:
         root_dir = pathlib.Path().absolute()