From 87fb235032b9fdeff6944fdb587e528d794c37dc Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Mon, 16 Oct 2023 11:46:25 +0200
Subject: [PATCH] Accomodate mono TIFs; support 'uint8' binary masks
---
conf/testing.py | 10 ++++++++++
model_server/accessors.py | 20 +++++++++++++++-----
tests/test_accessors.py | 8 ++++++--
3 files changed, 31 insertions(+), 7 deletions(-)
diff --git a/conf/testing.py b/conf/testing.py
index 5f95b5ca..f2df5040 100644
--- a/conf/testing.py
+++ b/conf/testing.py
@@ -42,6 +42,16 @@ tifffile = {
'z': 7,
}
+filename = 'mono_zstack_mask.tif'
+monozstackmask = {
+ 'filename': filename,
+ 'path': root / filename,
+ 'w': 256,
+ 'h': 256,
+ 'c': 1,
+ 'z': 85
+}
+
ilastik = {
'pixel_classifier': 'demo_px.ilp',
'object_classifier': 'demo_obj.ilp',
diff --git a/model_server/accessors.py b/model_server/accessors.py
index bd6cc11e..8ef4059e 100644
--- a/model_server/accessors.py
+++ b/model_server/accessors.py
@@ -34,7 +34,11 @@ class GenericImageDataAccessor(ABC):
return True if self.shape_dict['Z'] > 1 else False
def is_mask(self):
- return self._data.dtype == 'bool'
+ if self._data.dtype == 'bool':
+ return True
+ elif self._data.dtype == 'uint8':
+ return np.all(np.unique(self._data) == [0, 255])
+ return False
def get_one_channel_data (self, channel: int):
c = int(channel)
@@ -101,12 +105,18 @@ class TifSingleSeriesFileAccessor(GenericImageFileAccessor):
raise DataShapeError(f'Expect only one series in {fpath}')
se = tf.series[0]
- sd = {ch: se.shape[se.axes.index(ch)] for ch in se.axes}
- idx = {k: sd[k] for k in ['Y', 'X', 'C', 'Z']}
+ order = ['Y', 'X', 'C', 'Z']
+ axs = [a for a in se.axes if a in order]
+ da = se.asarray()
+
+ if 'C' not in axs:
+ axs.append('C')
+ da = np.expand_dims(da, len(da.shape))
+
yxcz = np.moveaxis(
- se.asarray(),
- [se.axes.index(ch) for ch in idx],
+ da,
+ [axs.index(k) for k in order],
[0, 1, 2, 3]
)
diff --git a/tests/test_accessors.py b/tests/test_accessors.py
index 4e1e7817..f7a4341d 100644
--- a/tests/test_accessors.py
+++ b/tests/test_accessors.py
@@ -2,7 +2,7 @@ import unittest
import numpy as np
-from conf.testing import czifile, output_path, monopngfile, rgbpngfile, tifffile
+from conf.testing import czifile, output_path, monopngfile, rgbpngfile, tifffile, monozstackmask
from model_server.accessors import CziImageFileAccessor, DataShapeError, generate_file_accessor, InMemoryDataAccessor, PngFileAccessor, write_accessor_data_to_file, TifSingleSeriesFileAccessor
class TestCziImageFileAccess(unittest.TestCase):
@@ -106,4 +106,8 @@ class TestCziImageFileAccess(unittest.TestCase):
self.assertEqual(acc.nz, 1)
def test_read_mono_png(self):
- return self.test_read_png(pngfile=monopngfile)
\ No newline at end of file
+ return self.test_read_png(pngfile=monopngfile)
+
+ def test_read_zstack_mono_mask(self):
+ acc = generate_file_accessor(monozstackmask['path'])
+ self.assertTrue(acc.is_mask())
\ No newline at end of file
--
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