From 977038556cb28fbcea09e00fa421c612c38ff71d Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Sun, 22 Oct 2023 09:28:48 +0200
Subject: [PATCH] Querying image scale in workflow output, but hitting error
---
conf/testing.py | 1 +
extensions/chaeo/util.py | 1 +
extensions/chaeo/workflows.py | 1 +
model_server/accessors.py | 21 +++++++++++++++++++--
tests/test_accessors.py | 6 +++++-
5 files changed, 27 insertions(+), 3 deletions(-)
diff --git a/conf/testing.py b/conf/testing.py
index f2df5040..3c52b95c 100644
--- a/conf/testing.py
+++ b/conf/testing.py
@@ -10,6 +10,7 @@ czifile = {
'h': 1274,
'c': 5,
'z': 1,
+ 'um_per_pixel': 1/3.9881,
}
filename = 'rgb.png'
diff --git a/extensions/chaeo/util.py b/extensions/chaeo/util.py
index b127d937..e966ce3e 100644
--- a/extensions/chaeo/util.py
+++ b/extensions/chaeo/util.py
@@ -7,6 +7,7 @@ import pandas as pd
from model_server.accessors import InMemoryDataAccessor, write_accessor_data_to_file
def autonumber_new_directory(where: str, prefix: str) -> str:
+ Path(where).mkdir(parents=True, exist_ok=True)
yyyymmdd = strftime('%Y%m%d', localtime())
idx = 0
diff --git a/extensions/chaeo/workflows.py b/extensions/chaeo/workflows.py
index 5e1b4e3c..dab8215d 100644
--- a/extensions/chaeo/workflows.py
+++ b/extensions/chaeo/workflows.py
@@ -175,6 +175,7 @@ def export_patches_from_multichannel_zstack(
'pixel_model_id': px_model.model_id,
'input_filepath': input_file_path,
'number_of_objects': len(zmask_meta),
+ 'pixeL_scale_in_micrometers': stack.pixel_scale_in_micrometers,
'success': True,
'timer_results': ti.events,
'dataframe': df,
diff --git a/model_server/accessors.py b/model_server/accessors.py
index b6e5da1f..caec8ddf 100644
--- a/model_server/accessors.py
+++ b/model_server/accessors.py
@@ -37,13 +37,19 @@ class GenericImageDataAccessor(ABC):
if self._data.dtype == 'bool':
return True
elif self._data.dtype == 'uint8':
- return np.all(np.unique(self._data) == [0, 255])
+ unique = np.unique(self._data)
+ if unique.shape[0] == 2 and np.all(unique == [0, 255]):
+ return True
return False
def get_one_channel_data (self, channel: int):
c = int(channel)
return InMemoryDataAccessor(self.data[:, :, c:(c+1), :])
+ @property
+ def pixel_scale_in_micrometers(self):
+ return None
+
@property
def dtype(self):
return self.data.dtype
@@ -163,12 +169,23 @@ class CziImageFileAccessor(GenericImageFileAccessor):
[cf.axes.index(ch) for ch in idx],
[0, 1, 2, 3]
)
-
self._data = self.conform_data(yxcz.reshape(yxcz.shape[0:4]))
def __del__(self):
self.czifile.close()
+ @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)
+
def write_accessor_data_to_file(fpath: Path, accessor: GenericImageDataAccessor, mkdir=True) -> bool:
if mkdir:
diff --git a/tests/test_accessors.py b/tests/test_accessors.py
index f7a4341d..1a465dfb 100644
--- a/tests/test_accessors.py
+++ b/tests/test_accessors.py
@@ -110,4 +110,8 @@ class TestCziImageFileAccess(unittest.TestCase):
def test_read_zstack_mono_mask(self):
acc = generate_file_accessor(monozstackmask['path'])
- self.assertTrue(acc.is_mask())
\ No newline at end of file
+ self.assertTrue(acc.is_mask())
+
+ 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
--
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