From 3f963fc9bc56c0a62a08a8e6992382b5e15ff41b Mon Sep 17 00:00:00 2001
From: Sander Roet <sanderroet@hotmail.com>
Date: Mon, 12 Feb 2024 16:11:59 +0100
Subject: [PATCH] Template.py: make filter warnings conditional and allow for
 no ctf_params (#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 <58044494+McHaillet@users.noreply.github.com>

---------

Co-authored-by: Marten <58044494+McHaillet@users.noreply.github.com>
---
 src/pytom_tm/template.py | 12 ++++++++----
 tests/test_logging.py    | 19 +++++++++++++++++++
 2 files changed, 27 insertions(+), 4 deletions(-)
 create mode 100644 tests/test_logging.py

diff --git a/src/pytom_tm/template.py b/src/pytom_tm/template.py
index db6bed66..dbe4b448 100644
--- 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
new file mode 100644
index 00000000..e2bbabae
--- /dev/null
+++ 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)
+