From a16c54d2dbb540aebe9df439283b7a00871b4513 Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Wed, 14 Feb 2024 18:03:13 +0000
Subject: [PATCH 1/3] Update raw image processing in scan

This matches recent commits in labthings-picamera2
---
 src/openflexure_microscope_server/things/smart_scan.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/openflexure_microscope_server/things/smart_scan.py b/src/openflexure_microscope_server/things/smart_scan.py
index b03c2d93..807e869a 100644
--- a/src/openflexure_microscope_server/things/smart_scan.py
+++ b/src/openflexure_microscope_server/things/smart_scan.py
@@ -549,8 +549,8 @@ class SmartScanThing(Thing):
             Cb = np.array(lst["Cb"])
             gr, gb = cam.colour_gains
             G = 1/lum
-            R = 1/lum/Cr/gr
-            B = 1/lum/Cb/gb
+            R = G/Cr/gr*np.min(Cr)  # The extra /np.max(Cr) emulates the quirky handling of Cr in
+            B = G/Cb/gb*np.min(Cb)   # the picamera2 pipeline
             white_norm_lores = np.stack([R, G, B], axis=2)
             zoom_factors = [i/n for i, n in zip(rgb[...,:3].shape, white_norm_lores.shape)]
             white_norm = zoom(white_norm_lores, zoom_factors, order=1)[:rgb.shape[0], :rgb.shape[1], :]  # Could use some work

From 82e2a250fcd1492e6f50c0ac1ca2b9b0b3b77a94 Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Thu, 15 Feb 2024 16:38:15 +0000
Subject: [PATCH 2/3] Include colour correction matrix and gamma in saved
 images

I've replicated more of the camera pipeline in the images
saved during scans - in particular, I've added the colour
correction matrix (increases saturation) and the contrast
agorithm (implements gamma correction).

This slows down saving to ~0.5-2 seconds, but that's still less time than it takes to move.
---
 .../things/smart_scan.py                              | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/src/openflexure_microscope_server/things/smart_scan.py b/src/openflexure_microscope_server/things/smart_scan.py
index 807e869a..3c9d3be6 100644
--- a/src/openflexure_microscope_server/things/smart_scan.py
+++ b/src/openflexure_microscope_server/things/smart_scan.py
@@ -12,6 +12,7 @@ from PIL import Image
 from pydantic import BaseModel
 from scipy.stats import norm
 from scipy.ndimage import zoom
+from scipy.interpolate import interp1d
 from copy import deepcopy
 from datetime import datetime
 from subprocess import CompletedProcess, Popen, PIPE, SubprocessError, run
@@ -554,6 +555,14 @@ class SmartScanThing(Thing):
             white_norm_lores = np.stack([R, G, B], axis=2)
             zoom_factors = [i/n for i, n in zip(rgb[...,:3].shape, white_norm_lores.shape)]
             white_norm = zoom(white_norm_lores, zoom_factors, order=1)[:rgb.shape[0], :rgb.shape[1], :]  # Could use some work
+            colour_correction_matrix = np.array(cam.colour_correction_matrix).reshape((3,3))
+            contrast_algorithm = cam.tuning["algorithms"][9]["rpi.contrast"]
+            gamma = np.array(contrast_algorithm["gamma_curve"]).reshape((-1,2))
+            gamma_8bit = interp1d(gamma[:, 0]/255, gamma[:, 1]/255)
+            def process_raw_image(img):
+                normed = img/white_norm
+                corrected = np.dot(colour_correction_matrix, normed.reshape((-1, 3)).T).T.reshape(normed.shape)
+                return gamma_8bit(corrected)
             logger.info(
                 f"Generated normalisation image with shape {white_norm.shape}, "
                 f"max {white_norm.max(axis=(0,1))}, min {white_norm.min(axis=(0,1))}"
@@ -579,7 +588,7 @@ class SmartScanThing(Thing):
                     # Save the raw image
                     np.savez(os.path.join(raw_images_folder, name + ".npz"), raw_image=raw_image, **norm_inputs)
                     # Process it into 8 bit RGB
-                    processed = rggb2rgb(raw2rggb(raw_image)) / white_norm
+                    processed = process_raw_image(rggb2rgb(raw2rggb(raw_image)))
                     processed[processed > 255] = 255
                     processed[processed < 0] = 0
                     img = Image.fromarray(processed.astype(np.uint8), mode="RGB")

From 41f03958c6bb38093f3c1bab7ea583af40f86b9e Mon Sep 17 00:00:00 2001
From: Richard Bowman <richard.bowman@cantab.net>
Date: Thu, 15 Feb 2024 17:34:29 +0000
Subject: [PATCH 3/3] Save images with saturated pixels

If any pixels in the manually processed raw image end up
saturated (>255), this causes an error. I've now manually
clamped the values between 0 and 255 to fix this.

It would probably be a good idea to warn when this happens,
as it does mean we're losing data.
---
 src/openflexure_microscope_server/things/smart_scan.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/openflexure_microscope_server/things/smart_scan.py b/src/openflexure_microscope_server/things/smart_scan.py
index 3c9d3be6..bd61e7ff 100644
--- a/src/openflexure_microscope_server/things/smart_scan.py
+++ b/src/openflexure_microscope_server/things/smart_scan.py
@@ -562,6 +562,8 @@ class SmartScanThing(Thing):
             def process_raw_image(img):
                 normed = img/white_norm
                 corrected = np.dot(colour_correction_matrix, normed.reshape((-1, 3)).T).T.reshape(normed.shape)
+                corrected[corrected < 0] = 0
+                corrected[corrected > 255] = 255
                 return gamma_8bit(corrected)
             logger.info(
                 f"Generated normalisation image with shape {white_norm.shape}, "