From a857e683e5deb2701522a3f7ede1dbef17b5f5c0 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 12 Oct 2023 16:29:22 +0200
Subject: [PATCH] Support mono PNG too
---
conf/testing.py | 14 ++++++++++++--
model_server/accessors.py | 5 ++++-
tests/test_accessors.py | 9 ++++++---
3 files changed, 22 insertions(+), 6 deletions(-)
diff --git a/conf/testing.py b/conf/testing.py
index 59d642b8..5f95b5ca 100644
--- a/conf/testing.py
+++ b/conf/testing.py
@@ -12,8 +12,8 @@ czifile = {
'z': 1,
}
-filename = 'test_img.png'
-pngfile = {
+filename = 'rgb.png'
+rgbpngfile = {
'filename': filename,
'path': root / filename,
'w': 64,
@@ -22,6 +22,16 @@ pngfile = {
'z': 1
}
+filename = 'mono.png'
+monopngfile = {
+ 'filename': filename,
+ 'path': root / filename,
+ 'w': 64,
+ 'h': 128,
+ 'c': 1,
+ 'z': 1
+}
+
filename = 'zmask-test-stack.tif'
tifffile = {
'filename': filename,
diff --git a/model_server/accessors.py b/model_server/accessors.py
index 84d29708..bd6cc11e 100644
--- a/model_server/accessors.py
+++ b/model_server/accessors.py
@@ -124,7 +124,10 @@ class PngFileAccessor(GenericImageFileAccessor):
except Exception:
FileAccessorError(f'Unable to access data in {fpath}')
- self._data = np.expand_dims(arr, 3)
+ if len(arr.shape) == 3: # rgb
+ self._data = np.expand_dims(arr, 3)
+ else: # mono
+ self._data = np.expand_dims(arr, (2, 3))
class CziImageFileAccessor(GenericImageFileAccessor):
"""
diff --git a/tests/test_accessors.py b/tests/test_accessors.py
index 426afa07..4e1e7817 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, pngfile, tifffile
+from conf.testing import czifile, output_path, monopngfile, rgbpngfile, tifffile
from model_server.accessors import CziImageFileAccessor, DataShapeError, generate_file_accessor, InMemoryDataAccessor, PngFileAccessor, write_accessor_data_to_file, TifSingleSeriesFileAccessor
class TestCziImageFileAccess(unittest.TestCase):
@@ -99,8 +99,11 @@ class TestCziImageFileAccess(unittest.TestCase):
fh_shape_dict = {se.axes[i]: se.shape[i] for i in range(0, len(se.shape))}
self.assertEqual(fh_shape_dict, acc.shape_dict, 'Axes are not preserved in TIF output')
- def test_read_rgb_png(self):
+ def test_read_png(self, pngfile=rgbpngfile):
acc = PngFileAccessor(pngfile['path'])
self.assertEqual(acc.hw, (pngfile['h'], pngfile['w']))
- self.assertEqual(acc.chroma, 3)
+ self.assertEqual(acc.chroma, pngfile['c'])
self.assertEqual(acc.nz, 1)
+
+ def test_read_mono_png(self):
+ return self.test_read_png(pngfile=monopngfile)
\ No newline at end of file
--
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