From ecf30b90b47b1ab9842ffec0900d0c8d121edc70 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sophia=20M=C3=A4dler?=
 <15019107+sophiamaedler@users.noreply.github.com>
Date: Tue, 4 Jun 2024 13:59:21 +0200
Subject: [PATCH 1/2] add function to get downsampling parameters

---
 src/sparcscore/pipeline/workflows.py | 25 +++++++++++--------------
 1 file changed, 11 insertions(+), 14 deletions(-)

diff --git a/src/sparcscore/pipeline/workflows.py b/src/sparcscore/pipeline/workflows.py
index b61b28d0..665c2130 100644
--- a/src/sparcscore/pipeline/workflows.py
+++ b/src/sparcscore/pipeline/workflows.py
@@ -1057,6 +1057,7 @@ def _finalize_segmentation_results(self, size_padding):
             channels = np.stack(required_maps).astype(np.uint16)
 
         _seg_size = self.maps["nucleus_segmentation"].shape
+
         self.log(
             f"Segmentation size after downsampling before resize to original dimensions: {_seg_size}"
         )
@@ -1064,28 +1065,24 @@ def _finalize_segmentation_results(self, size_padding):
         # rescale downsampled segmentation results to original size by repeating pixels
         _, x, y = size_padding
 
+        N, smoothing_kernel_size = _get_downsampling_parameters()
+
         nuc_seg = self.maps["nucleus_segmentation"]
-        nuc_seg = nuc_seg.repeat(self.config["downsampling_factor"], axis=0).repeat(
-            self.config["downsampling_factor"], axis=1
-        )
+        nuc_seg = nuc_seg.repeat(N, axis=0).repeat(N, axis=1)
 
         cyto_seg = self.maps["cytosol_segmentation"]
-        cyto_seg = cyto_seg.repeat(self.config["downsampling_factor"], axis=0).repeat(
-            self.config["downsampling_factor"], axis=1
-        )
+        cyto_seg = cyto_seg.repeat(N, axis=0).repeat(N, axis=1)
 
         # perform erosion and dilation for smoothing
-        nuc_seg = erosion(nuc_seg, footprint=disk(self.config["smoothing_kernel_size"]))
+        nuc_seg = erosion(nuc_seg, footprint=disk(smoothing_kernel_size))
         nuc_seg = dilation(
-            nuc_seg, footprint=disk(self.config["smoothing_kernel_size"])
-        )
+            nuc_seg, footprint=disk(smoothing_kernel_size + 1)
+        )  # dilate 1 more than eroded to ensure that we do not lose any pixels
 
-        cyto_seg = erosion(
-            cyto_seg, footprint=disk(self.config["smoothing_kernel_size"])
-        )
+        cyto_seg = erosion(cyto_seg, footprint=disk(smoothing_kernel_size))
         cyto_seg = dilation(
-            cyto_seg, footprint=disk(self.config["smoothing_kernel_size"])
-        )
+            cyto_seg, footprint=disk(smoothing_kernel_size + 1)
+        )  # dilate 1 more than eroded to ensure that we do not lose any pixels
 
         # combine masks into one stack
         segmentation = np.stack([nuc_seg, cyto_seg]).astype(np.uint32)

From 643960d2a059445ea1ac168f78f5f8245233960b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sophia=20M=C3=A4dler?=
 <15019107+sophiamaedler@users.noreply.github.com>
Date: Tue, 4 Jun 2024 14:00:28 +0200
Subject: [PATCH 2/2] implement sanity check to catch cases #4

---
 src/sparcscore/pipeline/workflows.py | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/src/sparcscore/pipeline/workflows.py b/src/sparcscore/pipeline/workflows.py
index 665c2130..ee0dacd6 100644
--- a/src/sparcscore/pipeline/workflows.py
+++ b/src/sparcscore/pipeline/workflows.py
@@ -1068,9 +1068,13 @@ def _finalize_segmentation_results(self, size_padding):
         N, smoothing_kernel_size = _get_downsampling_parameters()
 
         nuc_seg = self.maps["nucleus_segmentation"]
+        n_nuclei = len(
+            np.unique(nuc_seg)[0]
+        )  # get number of objects in mask for sanity checking
         nuc_seg = nuc_seg.repeat(N, axis=0).repeat(N, axis=1)
 
         cyto_seg = self.maps["cytosol_segmentation"]
+        n_cytosols = len(np.unique(cyto_seg)[0])
         cyto_seg = cyto_seg.repeat(N, axis=0).repeat(N, axis=1)
 
         # perform erosion and dilation for smoothing
@@ -1084,6 +1088,23 @@ def _finalize_segmentation_results(self, size_padding):
             cyto_seg, footprint=disk(smoothing_kernel_size + 1)
         )  # dilate 1 more than eroded to ensure that we do not lose any pixels
 
+        # sanity check to make sure that smoothing does not remove masks
+        if len(np.unique(nuc_seg)[0]) != n_nuclei:
+            self.log(
+                "Error. Number of nuclei in segmentation mask changed after smoothing. This should not happen. Ensure that you have chosen adequate smoothing parameters or use the defaults."
+            )
+            sys.exit(
+                "Error. Number of nuclei in segmentation mask changed after smoothing. This should not happen. Ensure that you have chosen adequate smoothing parameters or use the defaults."
+            )
+
+        if len(np.unique(cyto_seg)[0]) != n_cytosols:
+            self.log(
+                "Error. Number of cytosols in segmentation mask changed after smoothing. This should not happen. Ensure that you have chosen adequate smoothing parameters or use the defaults."
+            )
+            sys.exit(
+                "Error. Number of cytosols in segmentation mask changed after smoothing. This should not happen. Ensure that you have chosen adequate smoothing parameters or use the defaults."
+            )
+
         # combine masks into one stack
         segmentation = np.stack([nuc_seg, cyto_seg]).astype(np.uint32)
         del cyto_seg, nuc_seg