Implemented some unit tests

conf/server.py

@@ -8,7 +8,7 @@ paths = {
     'images': {
         'inbound': root / 'images' / 'inbound',
         'outbound': root / 'images' / 'outbound',
-    }
+    },
     'ilastik' : {
         'projects' : root / 'ilastik'
     }

conf/testing.py

+from pathlib import Path
+
+root = Path('c:/Users/rhodes/projects/proj0015-model-server/resources')
+
+paths = {
+    'czifile': root / 'testdata' / 'Selection--W0000--P0001-T0001.czi'
+}
+
+czifile_attr = {
+    'w': 1024,
+    'h': 1024,
+    'c': 4,
+    'z': 1,
+}
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model_server/image.py

@@ -11,7 +11,7 @@ class GenericImageFileAccessor(object):
 
 class CziImageFileAccessor(GenericImageFileAccessor):
     def __init__(self, fpath: Path):
-        super(CziImageFileAccessor).__init__(fpath)
+        super().__init__(fpath)
         self.fpath = fpath
         try:
             cf = czifile.CziFile(fpath)

model_server/models.py → model_server/model.py

@@ -2,7 +2,7 @@ from math import floor
 
 import numpy as np
 
-from image import GenericImageFileAccessor
+from model_server.image import GenericImageFileAccessor
 
 class Model(object):
     def load(self):
@@ -16,7 +16,7 @@ class Model(object):
 
 class ImageToImageModel(Model): # receives an image and returns an image of the same size
     def infer(self, img, channel=None) -> (np.ndarray, dict):
-        super(DummyImageToImageModel).infer(img, channel)
+        super().infer(img, channel)
 
 class IlastikImageToImageModel(ImageToImageModel):
     pass
@@ -26,12 +26,12 @@ class DummyImageToImageModel(Model):
         self.loaded = True
 
     def infer(self, img, channel=None) -> (np.ndarray, dict):
-        super(DummyImageToImageModel).infer(img, channel)
+        super().infer(img, channel)
         w = img.shape_dict['X']
         h = img.shape_dict['Y']
         result = np.zeros([h, w], dtype='uint8')
         result[floor(0.25 * h) : floor(0.75 * h), floor(0.25 * w) : floor(0.75 * w)] = 255
-        return result
+        return (result, {'success': True})
 
 class Error(Exception):
     pass

model_server/session.py

@@ -47,6 +47,7 @@ class Session(object):
         self.logfile = create_session_log()
 
     def register_inference(self, record):
+        # TODO: same this to file
         self.manifest.append(record)
 
 class Error(Exception):

model_server/share.py

@@ -5,13 +5,13 @@ def validate_directory_exists(path):
 
 class SharedImageDirectory(object):
 
-    def __init__(self, path): # create at session startup, validate
+    def __init__(self, path):
         self.path = path
+        self.is_memory_mapped = False
 
         if not validate_directory_exists(path):
             raise InvalidDirectoryError(f'Invalid directory:\n{path}')
 
-
 class InvalidDirectoryError(Exception):
     pass
 

tests/test_image.py

+import unittest
+from conf.testing import czifile_attr, paths
+from model_server.image import CziImageFileAccessor
+
+class TestCziImageFileAccess(unittest.TestCase):
+    def setUp(self) -> None:
+        pass
+
+    def test_czifile_is_correct_shape(self):
+        cf = CziImageFileAccessor(paths['czifile'])
+        self.assertEqual(cf.shape_dict['Y'], czifile_attr['h'])
+        self.assertEqual(cf.shape_dict['X'], czifile_attr['w'])
+        self.assertEqual(cf.chroma, czifile_attr['c'])
+        self.assertFalse(cf.is_3d)
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tests/test_model.py

+import unittest
+from conf.testing import paths
+from model_server.image import CziImageFileAccessor
+from model_server.model import DummyImageToImageModel
+
+class TestCziImageFileAccess(unittest.TestCase):
+    def setUp(self) -> None:
+        self.cf = CziImageFileAccessor(paths['czifile'])
+
+    def test_czifile_is_correct_shape(self):
+        model = DummyImageToImageModel()
+        model.infer(self.cf, channel=1)
+
+    # TODO: check that result is a white rectangle
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