From d962a3de02c7617a3936e312da386d65cdf775d9 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Sun, 22 Oct 2023 09:47:06 +0200
Subject: [PATCH] Merged in pixel scale property
---
model_server/accessors.py | 17 +++++++----------
tests/test_accessors.py | 3 ++-
2 files changed, 9 insertions(+), 11 deletions(-)
diff --git a/model_server/accessors.py b/model_server/accessors.py
index caec8ddf..1bb5b6b4 100644
--- a/model_server/accessors.py
+++ b/model_server/accessors.py
@@ -48,7 +48,7 @@ class GenericImageDataAccessor(ABC):
@property
def pixel_scale_in_micrometers(self):
- return None
+ return {}
@property
def dtype(self):
@@ -176,15 +176,12 @@ class CziImageFileAccessor(GenericImageFileAccessor):
@property
def pixel_scale_in_micrometers(self):
- meta_sc_str = self.czifile.metadata(raw=False)['ImageDocument']['Metadata']['ImageScaling']['ImagePixelSize']
- meta_mags = self.czifile.metadata(raw=False)['ImageDocument']['Metadata']['ImageScaling']['ScalingComponent']
- sc_xy = list(map(
- float,
- meta_sc_str.split(',')
- ))
- assert sc_xy[0] == sc_xy[1]
- mags = [float(m['Magnification']) for m in meta_mags]
- return sc_xy[0] / np.product(mags)
+ scale_meta = self.czifile.metadata(raw=False)['ImageDocument']['Metadata']['Scaling']['Items']['Distance']
+ sc = {}
+ for m in scale_meta:
+ if m['DefaultUnitFormat'].encode() == b'\xc2\xb5m' and m['Id'] in self.shape_dict.keys(): # literal mu-m
+ sc[m['Id']] = m['Value'] * 1e6
+ return sc
def write_accessor_data_to_file(fpath: Path, accessor: GenericImageDataAccessor, mkdir=True) -> bool:
diff --git a/tests/test_accessors.py b/tests/test_accessors.py
index 1a465dfb..557970ea 100644
--- a/tests/test_accessors.py
+++ b/tests/test_accessors.py
@@ -114,4 +114,5 @@ class TestCziImageFileAccess(unittest.TestCase):
def test_read_in_pixel_scale_from_czi(self):
cf = CziImageFileAccessor(czifile['path'])
- self.assertAlmostEqual(cf.pixel_scale_in_micrometers, czifile['um_per_pixel'], places=3)
\ No newline at end of file
+ pxs = cf.pixel_scale_in_micrometers
+ self.assertAlmostEqual(pxs['X'], czifile['um_per_pixel'], places=3)
\ No newline at end of file
--
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