Template.py: make filter warnings conditional and allow for no ctf_pa…

…rams (#98) * Make filter warning template.py conditional * allow default for ctf_params * add test for logging * use proper call to assertEqual * this is why we test logging * no space after but a comma * restructure based on Marten's comments, only warn if overriding a set frequency * Update src/pytom_tm/template.py Co-authored-by: Marten <[email protected]> --------- Co-authored-by: Marten <[email protected]>
SBC-Utrecht · Feb 12, 2024 · 3f963fc · 3f963fc
1 parent bc1fced
commit 3f963fc
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Showing 2 changed files with 27 additions and 4 deletions.
diff --git a/src/pytom_tm/template.py b/src/pytom_tm/template.py
@@ -20,7 +20,7 @@ def generate_template_from_map(
         input_map: npt.NDArray[float],
         input_spacing: float,
         output_spacing: float,
-        ctf_params: dict,
+        ctf_params: Optional[dict] = None,
         center: bool = False,
         filter_to_resolution: Optional[float] = None,
         output_box_size: Optional[int] = None,
@@ -36,9 +36,13 @@ def generate_template_from_map(
             mode='edge'
         )
 
-    if filter_to_resolution is None or filter_to_resolution < (2 * output_spacing):
-        logging.warning(f'Filter resolution is either not specified (in which case you can ignore this warning) '
-                        f'or too low, changing to {2 * output_spacing}A (2 * output voxel size)')
+    if filter_to_resolution is None:
+        # Set to nyquist resolution
+        filter_to_resolution = 2 * output_spacing
+    elif filter_to_resolution < (2 * output_spacing):
+        warning_text = (f"Filter resolution is too low,"
+                        f" setting to {2 * output_spacing}A (2 * output voxel size)")
+        logging.warning(warning_text)
         filter_to_resolution = 2 * output_spacing
 
     # extend volume to the desired output size before applying convolutions!

diff --git a/tests/test_logging.py b/tests/test_logging.py
@@ -0,0 +1,19 @@
+import unittest
+import numpy as np
+from pytom_tm.template import generate_template_from_map
+
+class TestLogging(unittest.TestCase):
+    def test_lowpass_resolution(self):
+        template = np.zeros((13, 13, 13), dtype=np.float32)
+
+        # Test too low filter resolution
+        with self.assertLogs(level='WARNING') as cm:
+            _ = generate_template_from_map(template, 1., 1., filter_to_resolution=1.5)
+        self.assertEqual(len(cm.output), 1)
+        self.assertIn('Filter resolution', cm.output[0])
+        self.assertIn('too low', cm.output[0])
+
+        # Test working filter resolution
+        with self.assertNoLogs(level='WARNING'):
+            _ = generate_template_from_map(template, 1., 1., filter_to_resolution=2.5)
+