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Fix to CSM scaling for Fiji config as images are now captured at double width

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This commit is contained in:
Joe Knapper 2024-01-13 14:29:34 +00:00
parent d1908eb29a
commit c2f1b591b1
1 changed files with 4 additions and 3 deletions
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7
src/openflexure_microscope_server/things/smart_scan.py
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@ -148,6 +148,8 @@ def generate_config(folder_path: str, positions: list, names: list, camera_to_sa
positions = np.array(positions) positions = np.array(positions)
mean_loc = np.mean(positions, axis = 0) mean_loc = np.mean(positions, axis = 0)
#TODO: positions from recent scans need to be 2x bigger - change to CSM res?
camera_to_sample_matrix = scale_csm(camera_to_sample_matrix, csm_calibration_width, img_width) camera_to_sample_matrix = scale_csm(camera_to_sample_matrix, csm_calibration_width, img_width)
with open(os.path.join(folder_path, 'TileConfiguration.txt'), 'w') as fp: with open(os.path.join(folder_path, 'TileConfiguration.txt'), 'w') as fp:
@ -422,9 +424,6 @@ class SmartScanThing(Thing):
# camera and stage may not be aligned). # camera and stage may not be aligned).
CSM = csm.image_to_stage_displacement_matrix CSM = csm.image_to_stage_displacement_matrix
csm_calibration_width = csm.last_calibration["image_resolution"][1] csm_calibration_width = csm.last_calibration["image_resolution"][1]
# TODO: this downsampling by two is to deal with a camera issue
img_width = int(arr.shape[1] / 2)
overlap = self.overlap overlap = self.overlap
@ -540,6 +539,8 @@ class SmartScanThing(Thing):
width, height = img.size width, height = img.size
img = img.resize((int(width*0.5), int(height*0.5))) img = img.resize((int(width*0.5), int(height*0.5)))
img_width, _ = img.size
logger.info(f"Saving {name}") logger.info(f"Saving {name}")
img.save( img.save(
os.path.join(images_folder, name), os.path.join(images_folder, name),