Merge pull request #3 from rosalindfranklininstitute/bug-issue001

Bugfix: Issue #2

src/quoll/io/tiles.py

@@ -97,7 +97,10 @@ def create_patches(Image, tile_size, tiles_output, pad=True):
         os.mkdir(tiles_output)
     if len(os.listdir(tiles_output)) != 0:
         for f in list(os.listdir(tiles_output)):
-            os.remove(os.path.join(tiles_output, f) )
+            try:
+                os.remove(os.path.join(tiles_output, f))
+            except:
+                print(f"Could not remove {f}")
     for i, tile in enumerate(tiles):
         tile_fn = os.path.join(tiles_output, f"{i:03}.tif")
         tifffile.imwrite(

tests/test_frc_oneimg_cli_mock.py

@@ -0,0 +1,81 @@
+# Copyright 2022 Rosalind Franklin Institute
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND,
+# either express or implied. See the License for the specific
+# language governing permissions and limitations under the License.
+
+
+from unittest import mock
+import unittest
+import shutil
+import os
+import sys
+from quoll.ui import frc_oneimg_ui
+
+class OneImgFRCCLIMockTest(unittest.TestCase):
+    """
+    Tests the one image FRC CLI
+    Test image = ChargeSuppression/SerialFIB-79, Tile 42
+    """
+
+    @mock.patch(
+        'sys.argv',
+        ["oneimgfrc",
+        "./data/042.tif",
+        "3.3724",
+        "--save_csv"],
+    )
+    def test_oneimgfrc_notiles_savecsv(self):
+        frc_oneimg_ui.oneimgfrc()
+        self.assertTrue(os.path.exists("./data/042_oneimgfrc.csv"))
+        os.remove("./data/042_oneimgfrc.csv")
+
+    @mock.patch(
+        'sys.argv',
+        ["oneimgFRC",
+         "./data/SerialFIB57_2048x2048.tif",
+         "3.3724",
+         "-ts",
+         "512",
+         "-td",
+         "./data/tiles",
+         "--save_csv"
+         ]
+    )
+    def test_oneimgfrc_tiles_savecsv(self):
+        frc_oneimg_ui.oneimgfrc()
+        self.assertTrue(os.path.exists("./data/SerialFIB57_2048x2048_oneimgfrc.csv"))
+        os.remove("./data/SerialFIB57_2048x2048_oneimgfrc.csv")
+        shutil.rmtree("./data/tiles", ignore_errors=True)
+
+    @mock.patch(
+        'sys.argv',
+        ["oneimgFRC",
+         "./data/SerialFIB57_2048x2048.tif",
+         "3.3724",
+         "-ts",
+         "512",
+         "-td",
+         "./data/tiles",
+         "--save_heatmap",
+         "--save_overlay",]
+    )
+    def test_oneimgfrc_tiles_saveplots(self):
+        frc_oneimg_ui.oneimgfrc()
+        self.assertTrue(os.path.exists("./data/SerialFIB57_2048x2048_overlay.svg"))
+        self.assertTrue(os.path.exists("./data/SerialFIB57_2048x2048_heatmap.tif"))
+        os.remove("./data/SerialFIB57_2048x2048_overlay.svg")
+        os.remove("./data/SerialFIB57_2048x2048_heatmap.tif")
+        shutil.rmtree("./data/tiles", ignore_errors=True)
+
+
+if __name__ == "__main__":
+    unittest.main()

tests/test_imports.py

@@ -16,6 +16,7 @@
 # Utility imports
 import unittest
 import sys
+import os
 import quoll
 
 
@@ -29,6 +30,13 @@ def test_quoll_version_string(self):
         Tests that the version string can be correctly accessed from the root of the quoll project.
         """
         self.assertTrue("quoll" in sys.modules.keys())
+
+    def test_frc_oneimg_entrypoint(self):
+        """
+        Tests that the entry point for oneimgfrc works
+        """
+        exit_status = os.system("oneimgfrc -h")
+        self.assertEqual(exit_status, 0)
 
 
 if __name__ == '__main__':