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DAQ-find_xtal.py error messages

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appleb_m
2025-11-18 17:38:29 +01:00
parent 192e290a67
commit e7b4d12f58
1 changed files with 23 additions and 18 deletions
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common/src/aaredaqlib/find_xtal.py
+23 -18
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@@ -5,7 +5,9 @@ from scipy import ndimage
from aaredaqlib.models import CrystalSize
from aaredaqlib.raster_grid import RasterGridRequest
from aaredaqlib.logger_config import setup_logger
logger = setup_logger('aareDAQ')
def identify_crystal_raster(result, r: RasterGridRequest):
images = result.images
@@ -23,25 +25,25 @@ def identify_crystal_raster(result, r: RasterGridRequest):
and (img.spots_ice / img.spots_low_res) != 1]
if indexed_images:
print(f"Find image by maximum number of spots indexed")
logger.debug(f"Find image by maximum number of spots indexed")
max_image = max(images, key=lambda img: img.spots_indexed)
max_spots = max_image.spots_indexed
max_images = [img for img in images if img.spots_indexed == max_spots]
max_image = max_images[len(max_images) // 2]
print(f"Image with maximum spots_low_res: {max_image}")
print(f"Maximum spots_indexed value: {max_image.spots_indexed}")
print(f"Maximum spots_low_res value: {max_image.spots_low_res}")
logger.debug(f"Image with maximum spots_low_res: {max_image}")
logger.debug(f"Maximum spots_indexed value: {max_image.spots_indexed}")
logger.debug(f"Maximum spots_low_res value: {max_image.spots_low_res}")
else:
print(f"Find image by maximum number of low resolution spots")
logger.debug(f"Find image by maximum number of low resolution spots")
max_image = max(images, key=lambda img: img.spots_low_res)
print(f"Image with maximum spots_low_res: {max_image}")
print(f"Maximum spots_low_res value: {max_image.spots_low_res}")
logger.debug(f"Image with maximum spots_low_res: {max_image}")
logger.debug(f"Maximum spots_low_res value: {max_image.spots_low_res}")
grid_mm_x = max_image.nx * r.grid_size_mm.x
grid_mm_y = max_image.ny * r.grid_size_mm.y
print(f"Grid coordinates in mm: ({grid_mm_x}, {grid_mm_y})")
logger.debug(f"Grid coordinates in mm: ({grid_mm_x}, {grid_mm_y})")
return grid_mm_x, grid_mm_y
else:
@@ -76,6 +78,7 @@ def rebuild_array_from_scan_results(scan_results: List,
values.append(float(value))
if not positions:
logger.error("No valid positions found in scan results")
raise ValueError("No valid positions found in scan results")
# Determine array shape
@@ -195,26 +198,28 @@ def get_xtal_size(crystal_size, result_array, r:RasterGridRequest):
index=range(1, num_objects + 1))
largest_idx = int(np.argmax(areas)) + 1 # +1 because labels start at 1
largest_area = int(areas[largest_idx - 1])
print(f"Largest object label: {largest_idx}, area (px): {largest_area}")
logger.info(f"Largest object label: {largest_idx}, area (px): {largest_area}")
object_mask = labeled_array == largest_idx
rows = np.any(object_mask, axis=1)
cols = np.any(object_mask, axis=0)
row_min, row_max = np.where(rows)[0][[0, -1]]
col_min, col_max = np.where(cols)[0][[0, -1]]
print(f"Largest bbox: width={col_max - col_min}, height={row_max - row_min}")
print(
logger.info(f"Largest bbox: width={col_max - col_min}, height={row_max - row_min}")
logger.info(
f"Largest bbox: width={(col_max - col_min) * r.grid_size_mm.x}, y={(row_max - row_min) * r.grid_size_mm.y}")
if r.n_x == 1:
logger.debug("calculating z")
crystal_size = CrystalSize(x=crystal_size.x, y=crystal_size.y,
z=(col_max - col_min) * r.grid_size_mm.y * 1000)
else:
logger.debug("calculating x and y")
crystal_size = CrystalSize(x=(row_max - row_min) * r.grid_size_mm.x * 1000,
y=(col_max - col_min) * r.grid_size_mm.y * 1000,
z=crystal_size.z)
except ValueError as e:
print(f"error calculating xtal size: {e}")
logger.error(f"error calculating xtal size: {e}")
crystal_size = CrystalSize(x=0,y=0,z=0)
return crystal_size
@@ -228,7 +233,7 @@ def get_best_b_factor(result_list: List):
default=None)
if best_b_factor is None:
return None
print(f"Best b: {best_b_factor.b}")
logger.info(f"Best b: {best_b_factor.b}")
return best_b_factor.b
def get_best_res(result_list: List):
@@ -237,7 +242,7 @@ def get_best_res(result_list: List):
best_res = min((img for img in result_list if img.res is not None),
key=lambda img: img.res,
default=None)
print(f"Best res: {best_res.res}")
logger.info(f"Best res: {best_res.res}")
return best_res.res
def com_nan_check(com):
@@ -252,7 +257,7 @@ def get_result_list_from_com(images, com):
cy, cx = com[::-1]
start_x, end_x = round(cx - 1), round(cx + 1)
start_y, end_y = round(cy - 1), round(cy + 1)
print(f"range x {start_x} {end_x}, y {start_y} {end_y}")
logger.info(f"range x {start_x} {end_x}, y {start_y} {end_y}")
result_list = [img for img in images
if start_x <= img.nx <= end_x and start_y <= img.ny <= end_y]
return result_list
@@ -260,7 +265,7 @@ def get_result_list_from_com(images, com):
def get_com_image_number(com, images):
for image in images:
if image.nx == round(com[0]) and image.ny == round(com[1]):
print(f"com found for image: {image.number}")
logger.info(f"com found for image: {image.number}")
return
def get_grid_mm_from_com(com, r:RasterGridRequest):
@@ -276,9 +281,9 @@ def get_grid_mm_from_com(com, r:RasterGridRequest):
def raster_centre_of_mass(result_array, r:RasterGridRequest):
print('horizontal scan')
logger.debug('horizontal scan')
com = ndimage.center_of_mass(result_array)
print(f"Center of mass: {com}")
logger.info(f"Center of mass: {com}")
grid_mm_x, grid_mm_y = get_grid_mm_from_com(com, r)
return grid_mm_x, grid_mm_y, com