From 7961492a17f1d5118e6e5581a0e064ad02a300fd Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Fri, 5 Jul 2024 12:29:36 +0200
Subject: [PATCH] Call test data in a big dictionary
---
tests/base/_conf.py | 107 -----------------------------------
tests/base/conf.py | 106 ++++++++++++++++++++++++++++++++++
tests/base/test_accessors.py | 52 +++++++++--------
3 files changed, 133 insertions(+), 132 deletions(-)
delete mode 100644 tests/base/_conf.py
create mode 100644 tests/base/conf.py
diff --git a/tests/base/_conf.py b/tests/base/_conf.py
deleted file mode 100644
index 8af41966..00000000
--- a/tests/base/_conf.py
+++ /dev/null
@@ -1,107 +0,0 @@
-import json
-import os
-from os import environ
-from pathlib import Path
-
-# places to look for test data
-data_paths = [
- environ.get('UNITTEST_DATA_ROOT'),
- Path.home() / 'model_server' / 'testing',
- os.getcwd(),
-]
-dd = {}
-root = None
-
-# look for first instance of summary.json
-for dp in data_paths:
- if dp is None:
- continue
- sf = (Path(dp) / 'summary.json')
- if sf.exists():
- with open(sf, 'r') as fh:
- dd = json.load(fh)
- root = Path(dp)
- break
-
-if root is None:
- raise Exception('Could not find test data, try setting environmental variable UNITTEST_DATA_ROOT.')
-
-op_ev = environ.get('UNITTEST_OUTPUT', (root / 'test_output').__str__())
-output_path = Path(op_ev)
-output_path.mkdir(parents=True, exist_ok=True)
-
-# TODO: organize this as a dict
-# TODO: assert paths exist
-# TODO: separate out ilastik stuff
-
-
-filename = 'D3-selection-01.czi'
-czifile = {
- 'filename': filename,
- 'path': root / filename,
- 'w': 1274,
- 'h': 1274,
- 'c': 5,
- 'z': 1,
- 'um_per_pixel': 1/3.9881,
-}
-
-filename = 'rgb.png'
-rgbpngfile = {
- 'filename': filename,
- 'path': root / filename,
- 'w': 64,
- 'h': 128,
- 'c': 3,
- '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,
- 'path': root / filename,
- 'w': 512,
- 'h': 512,
- 'c': 2,
- 'z': 7,
-}
-
-filename = 'mono_zstack_mask.tif'
-monozstackmask = {
- 'filename': filename,
- 'path': root / filename,
- 'w': 256,
- 'h': 256,
- 'c': 1,
- 'z': 85
-}
-
-roiset_test_data = {
- 'multichannel_zstack': {
- 'path': root / 'zmask-test-stack-chlorophyl.tif',
- 'w': 512,
- 'h': 512,
- 'c': 5,
- 'z': 7,
- 'mask_path': root / 'zmask-test-stack-mask.tif',
- 'mask_path_3d': root / 'zmask-test-stack-mask-3d.tif',
- },
- 'pipeline_params': {
- 'segmentation_channel': 0,
- 'patches_channel': 4,
- 'pxmap_channel': 0,
- 'pxmap_threshold': 0.6,
- },
- 'pixel_classifier': root / 'zmask' / 'AF405-bodies_boundaries.ilp',
-}
-
diff --git a/tests/base/conf.py b/tests/base/conf.py
new file mode 100644
index 00000000..44bc1ceb
--- /dev/null
+++ b/tests/base/conf.py
@@ -0,0 +1,106 @@
+import json
+import os
+from os import environ
+from pathlib import Path
+
+# places to look for test data
+data_paths = [
+ environ.get('UNITTEST_DATA_ROOT'),
+ Path.home() / 'model_server' / 'testing',
+ os.getcwd(),
+]
+root = None
+
+# look for first instance of summary.json
+for dp in data_paths:
+ if dp is None:
+ continue
+ sf = (Path(dp) / 'summary.json')
+ if sf.exists():
+ with open(sf, 'r') as fh:
+ meta = json.load(fh)
+ root = Path(dp)
+ break
+
+if root is None:
+ raise Exception('Could not find test data, try setting environmental variable UNITTEST_DATA_ROOT.')
+
+op_ev = environ.get('UNITTEST_OUTPUT', (root / 'test_output').__str__())
+output_path = Path(op_ev)
+output_path.mkdir(parents=True, exist_ok=True)
+
+# resolve paths in test image files
+imgs = meta['image_files']
+for k in imgs.keys():
+ imgs[k]['path'] = root / imgs[k]['name']
+
+# filename = 'D3-selection-01.czi'
+# czifile = {
+# 'filename': filename,
+# 'path': root / filename,
+# 'w': 1274,
+# 'h': 1274,
+# 'c': 5,
+# 'z': 1,
+# 'um_per_pixel': 1/3.9881,
+# }
+#
+# filename = 'rgb.png'
+# rgbpngfile = {
+# 'filename': filename,
+# 'path': root / filename,
+# 'w': 64,
+# 'h': 128,
+# 'c': 3,
+# '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,
+# 'path': root / filename,
+# 'w': 512,
+# 'h': 512,
+# 'c': 2,
+# 'z': 7,
+# }
+#
+# filename = 'mono_zstack_mask.tif'
+# monozstackmask = {
+# 'filename': filename,
+# 'path': root / filename,
+# 'w': 256,
+# 'h': 256,
+# 'c': 1,
+# 'z': 85
+# }
+#
+# roiset_test_data = {
+# 'multichannel_zstack': {
+# 'path': root / 'zmask-test-stack-chlorophyl.tif',
+# 'w': 512,
+# 'h': 512,
+# 'c': 5,
+# 'z': 7,
+# 'mask_path': root / 'zmask-test-stack-mask.tif',
+# 'mask_path_3d': root / 'zmask-test-stack-mask-3d.tif',
+# },
+# 'pipeline_params': {
+# 'segmentation_channel': 0,
+# 'patches_channel': 4,
+# 'pxmap_channel': 0,
+# 'pxmap_threshold': 0.6,
+# },
+# 'pixel_classifier': root / 'zmask' / 'AF405-bodies_boundaries.ilp',
+# }
+
diff --git a/tests/base/test_accessors.py b/tests/base/test_accessors.py
index f0d98183..f28a03a2 100644
--- a/tests/base/test_accessors.py
+++ b/tests/base/test_accessors.py
@@ -4,9 +4,11 @@ import numpy as np
from model_server.base.accessors import PatchStack, make_patch_stack_from_file, FileNotFoundError
-from tests.base._conf import czifile, output_path, monopngfile, rgbpngfile, tifffile, monozstackmask
+from tests.base.conf import meta, output_path
from model_server.base.accessors import CziImageFileAccessor, DataShapeError, generate_file_accessor, InMemoryDataAccessor, PngFileAccessor, write_accessor_data_to_file, TifSingleSeriesFileAccessor
+data = meta['image_files']
+
def _random_int(*args):
return np.random.randint(0, 2 ** 8, size=args, dtype='uint8')
@@ -16,27 +18,27 @@ class TestCziImageFileAccess(unittest.TestCase):
pass
def test_tiffile_is_correct_shape(self):
- tf = generate_file_accessor(tifffile['path'])
+ tf = generate_file_accessor(data['tifffile']['path'])
self.assertIsInstance(tf, TifSingleSeriesFileAccessor)
- self.assertEqual(tf.shape_dict['Y'], tifffile['h'])
- self.assertEqual(tf.shape_dict['X'], tifffile['w'])
- self.assertEqual(tf.chroma, tifffile['c'])
+ self.assertEqual(tf.shape_dict['Y'], data['tifffile']['h'])
+ self.assertEqual(tf.shape_dict['X'], data['tifffile']['w'])
+ self.assertEqual(tf.chroma, data['tifffile']['c'])
self.assertTrue(tf.is_3d())
self.assertEqual(len(tf.data.shape), 4)
- self.assertEqual(tf.shape[0], tifffile['h'])
- self.assertEqual(tf.shape[1], tifffile['w'])
+ self.assertEqual(tf.shape[0], data['tifffile']['h'])
+ self.assertEqual(tf.shape[1], data['tifffile']['w'])
self.assertEqual(tf.get_axis('x'), 1)
def test_czifile_is_correct_shape(self):
- cf = CziImageFileAccessor(czifile['path'])
- self.assertEqual(cf.shape_dict['Y'], czifile['h'])
- self.assertEqual(cf.shape_dict['X'], czifile['w'])
- self.assertEqual(cf.chroma, czifile['c'])
+ cf = CziImageFileAccessor(data['czifile']['path'])
+ self.assertEqual(cf.shape_dict['Y'], data['czifile']['h'])
+ self.assertEqual(cf.shape_dict['X'], data['czifile']['w'])
+ self.assertEqual(cf.chroma, data['czifile']['c'])
self.assertFalse(cf.is_3d())
self.assertEqual(len(cf.data.shape), 4)
- self.assertEqual(cf.shape[0], czifile['h'])
- self.assertEqual(cf.shape[1], czifile['w'])
+ self.assertEqual(cf.shape[0], data['czifile']['h'])
+ self.assertEqual(cf.shape[1], data['czifile']['w'])
def test_get_single_channel_from_zstack(self):
w = 256
@@ -60,7 +62,7 @@ class TestCziImageFileAccess(unittest.TestCase):
def test_write_single_channel_tif(self):
ch = 4
- cf = CziImageFileAccessor(czifile['path'])
+ cf = CziImageFileAccessor(data['czifile']['path'])
mono = cf.get_mono(ch)
self.assertTrue(
write_accessor_data_to_file(
@@ -73,7 +75,7 @@ class TestCziImageFileAccess(unittest.TestCase):
def test_write_two_channel_png(self):
from model_server.base.process import resample_to_8bit
- cf = CziImageFileAccessor(czifile['path'])
+ cf = CziImageFileAccessor(data['czifile']['path'])
acc = cf.get_channels([0, 1])
opa = output_path / f'{cf.fpath.stem}_2ch.png'
acc_out = acc.apply(resample_to_8bit)
@@ -129,23 +131,23 @@ 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_png(self, pngfile=rgbpngfile):
+ def test_read_png(self, pngfile=data['rgbpngfile']):
acc = PngFileAccessor(pngfile['path'])
self.assertEqual(acc.hw, (pngfile['h'], pngfile['w']))
self.assertEqual(acc.chroma, pngfile['c'])
self.assertEqual(acc.nz, 1)
def test_read_mono_png(self):
- return self.test_read_png(pngfile=monopngfile)
+ return self.test_read_png(pngfile=data['monopngfile'])
def test_read_zstack_mono_mask(self):
- acc = generate_file_accessor(monozstackmask['path'])
+ acc = generate_file_accessor(data['monozstackmask']['path'])
self.assertTrue(acc.is_mask())
def test_read_in_pixel_scale_from_czi(self):
- cf = CziImageFileAccessor(czifile['path'])
+ cf = CziImageFileAccessor(data['czifile']['path'])
pxs = cf.pixel_scale_in_micrometers
- self.assertAlmostEqual(pxs['X'], czifile['um_per_pixel'], places=3)
+ self.assertAlmostEqual(pxs['X'], data['czifile']['um_per_pixel'], places=3)
class TestPatchStackAccessor(unittest.TestCase):
@@ -175,12 +177,12 @@ class TestPatchStackAccessor(unittest.TestCase):
def test_make_patch_stack_from_file(self):
- h = monozstackmask['h']
- w = monozstackmask['w']
- c = monozstackmask['c']
- n = monozstackmask['z']
+ h = data['monozstackmask']['h']
+ w = data['monozstackmask']['w']
+ c = data['monozstackmask']['c']
+ n = data['monozstackmask']['z']
- acc = make_patch_stack_from_file(monozstackmask['path'])
+ acc = make_patch_stack_from_file(data['monozstackmask']['path'])
self.assertEqual(acc.hw, (h, w))
self.assertEqual(acc.count, n)
self.assertEqual(acc.pyxcz.shape, (n, h, w, c, 1))
--
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