From 30df6e63942b5169c0642cf1695ef4ae4652faa5 Mon Sep 17 00:00:00 2001
From: Anton Rau <anton.rau@gmail.com>
Date: Fri, 4 Jun 2021 16:55:11 +0200
Subject: [PATCH] Per-channel normalization option in segmentation
 preprocessing.

---
 backend/histocat/core/segmentation/dto.py           |  1 +
 .../processors/acquisition_processor.py             | 13 +++++++++----
 frontend/src/modules/segmentation/models.ts         |  1 +
 .../segmentation/SegmentationSettingsView.vue       |  7 +++++++
 4 files changed, 18 insertions(+), 4 deletions(-)

diff --git a/backend/histocat/core/segmentation/dto.py b/backend/histocat/core/segmentation/dto.py
index adb92470..f005f640 100644
--- a/backend/histocat/core/segmentation/dto.py
+++ b/backend/histocat/core/segmentation/dto.py
@@ -6,6 +6,7 @@
 class SegmentationPreprocessingSettingsDto(BaseModel):
     """Segmentation preprocessing settings model."""
 
+    channels_normalization: Optional[str]
     threshold: Optional[bool]
     percentile: Optional[float]
     normalize: bool
diff --git a/backend/histocat/worker/segmentation/processors/acquisition_processor.py b/backend/histocat/worker/segmentation/processors/acquisition_processor.py
index 2781e7fa..282a2f90 100644
--- a/backend/histocat/worker/segmentation/processors/acquisition_processor.py
+++ b/backend/histocat/worker/segmentation/processors/acquisition_processor.py
@@ -41,11 +41,16 @@ def process_acquisition(
     acquisition_data = parser.get_acquisition_data()
 
     nuclei_channels = acquisition_data.get_image_stack_by_names(params.nuclei_channels)
-    # nuclei_channels = normalize_by_zscore(nuclei_channels)
-    nuclei_channels = np.nanmean(nuclei_channels, axis=0)
-
     cytoplasm_channels = acquisition_data.get_image_stack_by_names(params.cytoplasm_channels)
-    # cytoplasm_channels = normalize_by_zscore(cytoplasm_channels)
+
+    if params.preprocessing.channels_normalization == "minmax":
+        nuclei_channels = normalize_by_minmax(nuclei_channels)
+        cytoplasm_channels = normalize_by_minmax(cytoplasm_channels)
+    elif params.preprocessing.channels_normalization == "zscore":
+        nuclei_channels = normalize_by_zscore(nuclei_channels)
+        cytoplasm_channels = normalize_by_zscore(cytoplasm_channels)
+
+    nuclei_channels = np.nanmean(nuclei_channels, axis=0)
     cytoplasm_channels = np.nanmean(cytoplasm_channels, axis=0)
 
     # Combined together and expand to 4D
diff --git a/frontend/src/modules/segmentation/models.ts b/frontend/src/modules/segmentation/models.ts
index 3dbf8bc7..122dcec0 100644
--- a/frontend/src/modules/segmentation/models.ts
+++ b/frontend/src/modules/segmentation/models.ts
@@ -1,4 +1,5 @@
 export interface ISegmentationPreprocessingSettings {
+  channels_normalization?: string;
   threshold?: boolean;
   percentile?: number;
   normalize: boolean;
diff --git a/frontend/src/views/group/project/segmentation/SegmentationSettingsView.vue b/frontend/src/views/group/project/segmentation/SegmentationSettingsView.vue
index 1e733ee2..24e78011 100644
--- a/frontend/src/views/group/project/segmentation/SegmentationSettingsView.vue
+++ b/frontend/src/views/group/project/segmentation/SegmentationSettingsView.vue
@@ -23,6 +23,11 @@
           <v-text-field label="Dataset Description" hint="Resulting dataset description" v-model="datasetDescription" />
         </v-tab-item>
         <v-tab-item>
+          <v-radio-group v-model="channelsNormalization" label="Per-channel normalization" dense>
+            <v-radio label="None" value="none" />
+            <v-radio label="Min-Max" value="minmax" />
+            <v-radio label="Z-score" value="zscore" />
+          </v-radio-group>
           <v-switch v-model="threshold" label="Threshold" inset class="ml-1" dense />
           <v-text-field
             label="Percentile"
@@ -173,6 +178,7 @@ export default class SegmentationSettingsView extends Vue {
   modelId: number | null = null;
   compartment = "whole-cell";
 
+  channelsNormalization = "none";
   threshold = true;
   percentile = 99.9;
   normalize = true;
@@ -214,6 +220,7 @@ export default class SegmentationSettingsView extends Vue {
       }
 
       const preprocessingParams = {
+        channels_normalization: this.channelsNormalization,
         threshold: this.threshold,
         percentile: this.percentile,
         normalize: this.normalize,