From 655fbb6275e5e83c2a12de2bc696e44966849752 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Mon, 3 Jun 2024 15:35:55 +0200
Subject: [PATCH] RoiSet can now return and export two-channel images as both
TIFs and PNGs
---
model_server/base/roiset.py | 2 +-
tests/test_roiset.py | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index df00d2b1..11deff15 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -427,7 +427,7 @@ class RoiSet(object):
def _export_patch(roi):
patch = InMemoryDataAccessor(roi.patch)
- ext = 'tif' if make_3d or patch.chroma > 3 else 'png'
+ ext = 'tif' if make_3d or patch.chroma > 3 or kwargs.get('force_tif') else 'png'
fname = f'{prefix}-la{roi.label:04d}-zi{roi.zi:04d}.{ext}'
if patch.dtype is np.dtype('uint16'):
diff --git a/tests/test_roiset.py b/tests/test_roiset.py
index 326d874d..24078720 100644
--- a/tests/test_roiset.py
+++ b/tests/test_roiset.py
@@ -304,7 +304,7 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
self.assertEqual(result.chroma, 1)
def test_multichannel_to_color_2d_patches(self):
- chs = [0, 2, 4, 1]
+ chs = [0, 2,]
where = output_path / 'multichannel' / 'color_2d_patches'
self.assertGreater(self.roiset.acc_raw.chroma, 1)
patches_acc = self.roiset.get_patches_acc(channels=chs)
@@ -316,11 +316,11 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
draw_bounding_box=True,
expanded=True,
pad_to=256,
+ force_tif=True,
)
result = generate_file_accessor(where / df_res.patch_path.iloc[0])
self.assertEqual(result.chroma, len(chs))
-
def test_multichannnel_to_mono_2d_patches_rgb_bbox(self):
where = output_path / 'multichannel' / 'mono_2d_patches_rgb_bbox'
df_res = self.roiset.export_patches(
--
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