From 889870f8a7eb26f81c9a295d79b05c94d853d694 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Mon, 19 Feb 2024 17:35:06 +0100
Subject: [PATCH] Folded remaining tests into base
---
.../extensions/chaeo/tests/test_accessors.py | 73 -------------------
model_server/extensions/ilastik/validators.py | 5 --
tests/test_accessors.py | 72 +++++++++++++++++-
3 files changed, 71 insertions(+), 79 deletions(-)
delete mode 100644 model_server/extensions/chaeo/tests/test_accessors.py
delete mode 100644 model_server/extensions/ilastik/validators.py
diff --git a/model_server/extensions/chaeo/tests/test_accessors.py b/model_server/extensions/chaeo/tests/test_accessors.py
deleted file mode 100644
index c51f31ca..00000000
--- a/model_server/extensions/chaeo/tests/test_accessors.py
+++ /dev/null
@@ -1,73 +0,0 @@
-import unittest
-
-import numpy as np
-
-from model_server.conf.testing import monozstackmask
-from base.accessors import PatchStack, make_patch_stack_from_file, FileNotFoundError
-
-
-class TestMultipositionCziImageFileAccess(unittest.TestCase):
- def setUp(self) -> None:
- pass
-
- def test_make_patch_stack_from_3d_array(self):
- w = 256
- h = 512
- n = 4
- acc = PatchStack(np.random.rand(n, h, w, 1, 1))
- self.assertEqual(acc.count, n)
- self.assertEqual(acc.hw, (h, w))
- self.assertEqual(acc.pyxcz.shape, (n, h, w, 1, 1))
-
- def test_make_patch_stack_from_list(self):
- w = 256
- h = 512
- n = 4
- acc = PatchStack([np.random.rand(h, w, 1, 1) for _ in range(0, n)])
- self.assertEqual(acc.count, n)
- self.assertEqual(acc.hw, (h, w))
- self.assertEqual(acc.pyxcz.shape, (n, h, w, 1, 1))
- return acc
-
-
- def test_make_patch_stack_from_file(self):
- h = monozstackmask['h']
- w = monozstackmask['w']
- c = monozstackmask['c']
- n = monozstackmask['z']
-
- acc = make_patch_stack_from_file(monozstackmask['path'])
- self.assertEqual(acc.hw, (h, w))
- self.assertEqual(acc.count, n)
- self.assertEqual(acc.pyxcz.shape, (n, h, w, c, 1))
-
- def test_raises_filenotfound(self):
- with self.assertRaises(FileNotFoundError):
- acc = make_patch_stack_from_file('c:/fake/file/name.tif')
-
- def test_make_3d_patch_stack_from_nonuniform_list(self):
- w = 256
- h = 512
- c = 1
- nz = 5
- n = 4
-
- patches = [np.random.rand(h, w, c, nz) for _ in range(0, n)]
- patches.append(np.random.rand(h, 2 * w, c, nz))
- acc = PatchStack(patches)
- self.assertEqual(acc.count, n + 1)
- self.assertEqual(acc.hw, (h, 2 * w))
- self.assertEqual(acc.chroma, c)
- self.assertEqual(acc.iat(0).shape, (h, 2 * w, c, nz))
- self.assertEqual(acc.iat_yxcz(0).shape, (h, 2 * w, c, nz))
-
- def test_pczyx(self):
- w = 256
- h = 512
- n = 4
- nz = 15
- nc = 2
- acc = PatchStack(np.random.rand(n, h, w, nc, nz))
- self.assertEqual(acc.count, n)
- self.assertEqual(acc.pczyx.shape, (n, nc, nz, h, w))
- self.assertEqual(acc.hw, (h, w))
diff --git a/model_server/extensions/ilastik/validators.py b/model_server/extensions/ilastik/validators.py
deleted file mode 100644
index 28d92c15..00000000
--- a/model_server/extensions/ilastik/validators.py
+++ /dev/null
@@ -1,5 +0,0 @@
-from model_server.base.accessors import GenericImageDataAccessor
-
-def is_object_map(img: GenericImageDataAccessor):
- # TODO: implement
- pass
\ No newline at end of file
diff --git a/tests/test_accessors.py b/tests/test_accessors.py
index 3bad0c96..d622a368 100644
--- a/tests/test_accessors.py
+++ b/tests/test_accessors.py
@@ -2,6 +2,9 @@ import unittest
import numpy as np
+from base.accessors import PatchStack, make_patch_stack_from_file, FileNotFoundError
+from conf.testing import monozstackmask
+
from model_server.conf.testing import czifile, output_path, monopngfile, rgbpngfile, tifffile, monozstackmask
from model_server.base.accessors import CziImageFileAccessor, DataShapeError, generate_file_accessor, InMemoryDataAccessor, PngFileAccessor, write_accessor_data_to_file, TifSingleSeriesFileAccessor
@@ -115,4 +118,71 @@ class TestCziImageFileAccess(unittest.TestCase):
def test_read_in_pixel_scale_from_czi(self):
cf = CziImageFileAccessor(czifile['path'])
pxs = cf.pixel_scale_in_micrometers
- self.assertAlmostEqual(pxs['X'], czifile['um_per_pixel'], places=3)
\ No newline at end of file
+ self.assertAlmostEqual(pxs['X'], czifile['um_per_pixel'], places=3)
+
+
+class TestPatchStackAccessor(unittest.TestCase):
+ def setUp(self) -> None:
+ pass
+
+ def test_make_patch_stack_from_3d_array(self):
+ w = 256
+ h = 512
+ n = 4
+ acc = PatchStack(np.random.rand(n, h, w, 1, 1))
+ self.assertEqual(acc.count, n)
+ self.assertEqual(acc.hw, (h, w))
+ self.assertEqual(acc.pyxcz.shape, (n, h, w, 1, 1))
+
+ def test_make_patch_stack_from_list(self):
+ w = 256
+ h = 512
+ n = 4
+ acc = PatchStack([np.random.rand(h, w, 1, 1) for _ in range(0, n)])
+ self.assertEqual(acc.count, n)
+ self.assertEqual(acc.hw, (h, w))
+ self.assertEqual(acc.pyxcz.shape, (n, h, w, 1, 1))
+ return acc
+
+
+ def test_make_patch_stack_from_file(self):
+ h = monozstackmask['h']
+ w = monozstackmask['w']
+ c = monozstackmask['c']
+ n = monozstackmask['z']
+
+ acc = make_patch_stack_from_file(monozstackmask['path'])
+ self.assertEqual(acc.hw, (h, w))
+ self.assertEqual(acc.count, n)
+ self.assertEqual(acc.pyxcz.shape, (n, h, w, c, 1))
+
+ def test_raises_filenotfound(self):
+ with self.assertRaises(FileNotFoundError):
+ acc = make_patch_stack_from_file('c:/fake/file/name.tif')
+
+ def test_make_3d_patch_stack_from_nonuniform_list(self):
+ w = 256
+ h = 512
+ c = 1
+ nz = 5
+ n = 4
+
+ patches = [np.random.rand(h, w, c, nz) for _ in range(0, n)]
+ patches.append(np.random.rand(h, 2 * w, c, nz))
+ acc = PatchStack(patches)
+ self.assertEqual(acc.count, n + 1)
+ self.assertEqual(acc.hw, (h, 2 * w))
+ self.assertEqual(acc.chroma, c)
+ self.assertEqual(acc.iat(0).shape, (h, 2 * w, c, nz))
+ self.assertEqual(acc.iat_yxcz(0).shape, (h, 2 * w, c, nz))
+
+ def test_pczyx(self):
+ w = 256
+ h = 512
+ n = 4
+ nz = 15
+ nc = 2
+ acc = PatchStack(np.random.rand(n, h, w, nc, nz))
+ self.assertEqual(acc.count, n)
+ self.assertEqual(acc.pczyx.shape, (n, nc, nz, h, w))
+ self.assertEqual(acc.hw, (h, w))
--
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