add check on tomo mask shape (#210)

* add check on tomo mask shape

* make f-string and add test also in extraction

* add tests for the errors

* update tooltips to mention that the dimensions should be in pixels

* use correct input name

src/pytom_tm/entry_points.py

@@ -436,7 +436,7 @@ def extract_candidates(argv=None):
         type=pathlib.Path,
         required=False,
         action=CheckFileExists,
-        help="Here you can provide a mask for the extraction with dimensions equal to "
+        help="Here you can provide a mask for the extraction with dimensions (in pixels) equal to "
         "the tomogram. All values in the mask that are smaller or equal to 0 will be "
         "removed, all values larger than 0 are considered regions of interest. It can "
         "be used to extract annotations only within a specific cellular region."
@@ -687,7 +687,7 @@ def match_template(argv=None):
         type=pathlib.Path,
         required=False,
         action=CheckFileExists,
-        help="Here you can provide a mask for matching with dimensions equal to "
+        help="Here you can provide a mask for matching with dimensions (in pixels) equal to "
         "the tomogram. If a subvolume only has values <= 0 for this mask it will be skipped.",
     )
 

src/pytom_tm/extract.py

@@ -216,6 +216,11 @@ def extract_particles(
         tomogram_mask = read_mrc(job.tomogram_mask)
 
     if tomogram_mask is not None:
+        if tomogram_mask.shape != job.tomo_shape:
+            raise ValueError(
+                "Tomogram mask does not have the same number of pixels as the tomogram.\n"
+                f"Tomogram mask shape: {tomogram_mask.shape}, tomogram shape: {job.tomo_shape}"
+            )
         slices = [
             slice(origin, origin + size)
             for origin, size in zip(job.search_origin, job.search_size)

src/pytom_tm/tmjob.py

@@ -371,6 +371,11 @@ def __init__(
         self.tomogram_mask = tomogram_mask
         if tomogram_mask is not None:
             temp = read_mrc(tomogram_mask)
+            if temp.shape != self.tomo_shape:
+                raise ValueError(
+                    "Tomogram mask does not have the same number of pixels as the tomogram.\n"
+                    f"Tomogram mask shape: {temp.shape}, tomogram shape: {self.tomo_shape}"
+                )
             if np.all(temp <= 0):
                 raise ValueError(
                     f"No values larger than 0 found in the tomogram mask: {tomogram_mask}"

tests/test_tmjob.py

@@ -20,6 +20,7 @@
 TEST_DATA_DIR = pathlib.Path(__file__).parent.joinpath("test_data")
 TEST_TOMOGRAM = TEST_DATA_DIR.joinpath("tomogram.mrc")
 TEST_BROKEN_TOMOGRAM_MASK = TEST_DATA_DIR.joinpath("broken_tomogram_mask.mrc")
+TEST_WRONG_SIZE_TOMO_MASK = TEST_DATA_DIR.joinpath("wrong_size_tomogram_mask.mrc")
 TEST_EXTRACTION_MASK_OUTSIDE = TEST_DATA_DIR.joinpath("extraction_mask_outside.mrc")
 TEST_EXTRACTION_MASK_INSIDE = TEST_DATA_DIR.joinpath("extraction_mask_inside.mrc")
 TEST_TEMPLATE = TEST_DATA_DIR.joinpath("template.mrc")
@@ -124,10 +125,17 @@ def setUpClass(cls) -> None:
         broken_tomogram_mask = np.zeros(TOMO_SHAPE, dtype=np.float32)
         write_mrc(TEST_BROKEN_TOMOGRAM_MASK, broken_tomogram_mask, 1.0)
 
+        # write wrong size tomogram mask
+        size = list(TOMO_SHAPE)
+        size[0] += 1
+        wrong_size_tomogram_mask = np.ones(tuple(size), dtype=np.float32)
+        write_mrc(TEST_WRONG_SIZE_TOMO_MASK, wrong_size_tomogram_mask, 1.0)
+
     @classmethod
     def tearDownClass(cls) -> None:
         TEST_MASK.unlink()
         TEST_BROKEN_TOMOGRAM_MASK.unlink()
+        TEST_WRONG_SIZE_TOMO_MASK.unlink()
         TEST_EXTRACTION_MASK_OUTSIDE.unlink()
         TEST_EXTRACTION_MASK_INSIDE.unlink()
         TEST_TEMPLATE.unlink()
@@ -251,6 +259,19 @@ def test_tm_job_errors(self):
                 voxel_size=1.0,
                 tomogram_mask=TEST_BROKEN_TOMOGRAM_MASK,
             )
+        # Test wrong size template mask
+        with self.assertRaisesRegex(ValueError, str(TOMO_SHAPE)):
+            TMJob(
+                "0",
+                10,
+                TEST_TOMOGRAM,
+                TEST_TEMPLATE,
+                TEST_MASK,
+                TEST_DATA_DIR,
+                angle_increment=ANGULAR_SEARCH,
+                voxel_size=1.0,
+                tomogram_mask=TEST_WRONG_SIZE_TOMO_MASK,
+            )
 
     def test_tm_job_copy(self):
         copy = self.job.copy()
@@ -680,3 +701,24 @@ def test_extraction(self):
             msg="We expected a detected particle with a extraction mask that "
             "covers the object.",
         )
+
+        # test mask that is the wrong size raises an error
+        with self.assertRaisesRegex(ValueError, str(TOMO_SHAPE)):
+            _, _ = extract_particles(
+                job,
+                5,
+                100,
+                tomogram_mask_path=TEST_WRONG_SIZE_TOMO_MASK,
+                create_plot=False,
+            )
+
+        # Also test the raise if it somehow got attached to the job
+        job = self.job.copy()
+        job.tomogram_mask = TEST_WRONG_SIZE_TOMO_MASK
+        with self.assertRaisesRegex(ValueError, str(TOMO_SHAPE)):
+            _, _ = extract_particles(
+                job,
+                5,
+                100,
+                create_plot=False,
+            )