From 2db895a1fc4cd3df4157648b4a5e15af4d6cb36b Mon Sep 17 00:00:00 2001 From: Joe Knapper Date: Tue, 3 Dec 2024 11:16:27 +0000 Subject: [PATCH] Defocus and realign simulation axes --- .../things/camera/simulation.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/src/openflexure_microscope_server/things/camera/simulation.py b/src/openflexure_microscope_server/things/camera/simulation.py index 51ae32e0..1e87a4fe 100644 --- a/src/openflexure_microscope_server/things/camera/simulation.py +++ b/src/openflexure_microscope_server/things/camera/simulation.py @@ -17,6 +17,7 @@ import time import cv2 import numpy as np import piexif +from scipy.ndimage import gaussian_filter from labthings_fastapi.utilities import get_blocking_portal from labthings_fastapi.decorators import thing_action, thing_property @@ -95,15 +96,15 @@ class SimulatedCamera(BaseCamera): int(y) - h // 2 : int(y) - h // 2 + h, ] -= self.sprites[int(sprite)] - def generate_image(self, pos: tuple[int, int]): + def generate_image(self, pos: tuple[int, int, int]): """Generate an image with blobs based on supplied coordinates""" cw, ch, _ = self.canvas_shape w, h, _ = self.shape tl = (int(pos[0]) - w // 2 - cw // 2, int(pos[1]) - h // 2 - ch // 2) - image = self.canvas[ + image = gaussian_filter(self.canvas[ tuple(slice(tl[i], tl[i] + self.shape[i]) for i in range(2)) + (slice(None),) - ] + ], sigma = np.abs(pos[2])/5, axes = (0,1)) if image.shape != self.shape: raise ValueError( f"Image shape {image.shape} does not match intended shape {self.shape}" @@ -125,8 +126,8 @@ class SimulatedCamera(BaseCamera): pos = self.get_stage_position() except Exception as e: print(f"Failed to get stage position: {e}") - pos = {"x": 0, "y": 0} - return self.generate_image((pos["x"] / 10, pos["y"] / 10)) + pos = {"x": 0, "y": 0, "z": 0} + return self.generate_image((pos["y"]/10, pos["x"]/10, pos["z"]/10)) def __enter__(self): self._capture_enabled = True