Add save_scitiff method

Author: damskii9992

src/easyimaging/measurement/measurement.py

@@ -16,6 +16,7 @@
 from scipp import DimensionError
 from scipp import UnitError
 from scitiff import load_scitiff
+from scitiff import save_scitiff
 
 from ..utils import _is_notebook
 from ..utils import _to_edges
@@ -178,6 +179,33 @@ def from_tiff_stack(
         instance = cls(data_array=data_array, unique_name=unique_name, display_name=display_name)
         return instance
 
+    def save_scitiff(self, filename: str | Path) -> None:
+        """
+        Save the measurement data to a SciTIFF file with its time-of-flight and physical coordinate information.
+        Note that it is the rebinned data array that is saved if rebinning has been applied.
+
+        Parameters
+        ----------
+        filename : str | Path
+            Path to the output SciTIFF file.
+        """
+        if not isinstance(filename, (str, Path)):
+            raise TypeError('filename must be a string or Path object.')
+        try:
+            nan_mask = self._data_array.masks.pop('non_finite')
+            if str(self._data_array.dtype)=='float64':
+                warnings.warn(
+                    "The data array is of type float64, which is not directly supported by the SciTIFF format. "
+                    "It will be downcast to float32 when saving, which may result in loss of precision. "
+                )
+                save_scitiff(self._data_array.astype('float32'), filename)
+            else:
+                save_scitiff(self._data_array, filename)
+        except Exception as e:
+            raise RuntimeError(f"Failed to save SciTIFF file '{filename}': {e}") from e
+        finally:
+            self._data_array.masks['non_finite'] = nan_mask  # Ensure mask is restored
+
     @property
     def _data_array(self) -> sc.DataArray:
         """

tests/unit_tests/measurement/test_measurement.py

@@ -1,3 +1,4 @@
+import warnings
 from copy import copy
 from pathlib import Path
 from typing import MutableSequence
@@ -21,7 +22,7 @@ def valid_data_array(self):
         tof = sc.arange('t', 0, 10, 1, unit='s')
         x = sc.arange('x', 0, 7, 1, unit='m')
         y = sc.arange('y', 0, 7, 1, unit='m')
-        data = sc.ones(dims=['y', 'x', 't'], shape=[6, 6, 10])
+        data = sc.ones(dims=['t', 'y', 'x'], shape=[10, 6, 6])
         return sc.DataArray(
             data=data,
             coords={
@@ -34,15 +35,9 @@ def valid_data_array(self):
     @pytest.fixture
     def valid_data_array_no_xy_coords(self):
         tof = sc.arange('t', 0, 10, 1, unit='s')
-        data = sc.zeros(dims=('y', 'x', 't'), shape=(6, 6, 10))
+        data = sc.zeros(dims=('t', 'y', 'x'), shape=(10, 6, 6))
         return sc.DataArray(data=data, coords={'tof': tof})
 
-    # @pytest.fixture(autouse=True)
-    # def _reset_mpl_defaults(self):
-    #     matplotlib.rcdefaults()
-    #     matplotlib.use('Agg')
-    #     pp.backends.reset()
-
     @pytest.fixture(autouse=True)
     def _close_figures(self):
         """
@@ -456,6 +451,68 @@ def test_from_tiff_stack_invalid_y_positions(self, coord, error, expected_messag
                 y_positions=coord,
             )
 
+    def test_save_scitiff_downcast(self, valid_data_array, tmp_path):
+        # When
+        measurement = Measurement(data_array=valid_data_array)
+        # Then Expect
+        with pytest.warns(UserWarning, match="The data array is of type float64, which is not directly supported by the SciTIFF format. It will be downcast to float32 when saving, which may result in loss of precision."):  # noqa: E501
+            measurement.save_scitiff(tmp_path / 'test.tiff')
+        assert 'non_finite' in measurement._data_array.masks
+
+    def test_save_scitiff(self, valid_data_array, tmp_path):
+        # When
+        data_array = valid_data_array.astype('float32')
+        measurement = Measurement(data_array=data_array)
+        # Then Expect
+        with warnings.catch_warnings():
+            warnings.simplefilter("error")  # Ensure no warnings are raised for valid data type
+            measurement.save_scitiff(tmp_path / 'test.tiff')
+        assert 'non_finite' in measurement._data_array.masks
+
+    def test_save_scitiff_path_object(self, valid_data_array, tmp_path):
+        # When
+        data_array = valid_data_array.astype('float32')
+        measurement = Measurement(data_array=data_array)
+        path = Path(tmp_path) / 'test.tiff'
+        # Then Expect
+        with warnings.catch_warnings():
+            warnings.simplefilter("error")  # Ensure no warnings are raised for valid data type
+            measurement.save_scitiff(path)
+        assert 'non_finite' in measurement._data_array.masks
+
+    def test_save_scitiff_invalid_filename_type(self, valid_data_array):
+        # When
+        measurement = Measurement(data_array=valid_data_array)
+        # Then Expect
+        with pytest.raises(TypeError, match='filename must be a string or Path object.'):
+            measurement.save_scitiff(12345)
+        assert 'non_finite' in measurement._data_array.masks
+
+    def test_save_scitiff_non_existent_directory(self, valid_data_array):
+        # When
+        measurement = Measurement(data_array=valid_data_array)
+        # Then Expect
+        with pytest.raises(RuntimeError, match="Failed to save SciTIFF file 'non_existent_directory/test.tiff'"):
+            measurement.save_scitiff('non_existent_directory/test.tiff')
+        assert 'non_finite' in measurement._data_array.masks
+
+    def test_save_scitiff_rebinned_data_array(self, valid_data_array, tmp_path):
+        # When
+        data_array = valid_data_array.astype('float32')
+        measurement = Measurement(data_array=data_array)
+        measurement.rebin(dimensions={'x': 2, 'y': 2})
+        # Then
+        measurement.save_scitiff(tmp_path / 'test.tiff')
+        loaded_measurement = Measurement.from_scitiff(tmp_path / 'test.tiff')
+        # Expect
+        assert sc.identical(loaded_measurement._data_array.coords['x_pixels'], sc.arange('x', 0, 4, 1))
+        assert sc.identical(loaded_measurement._data_array.coords['y_pixels'], sc.arange('y', 0, 4, 1))
+        loaded_measurement._data_array.coords.pop('x_pixels')
+        loaded_measurement._data_array.coords.pop('y_pixels')
+        measurement._data_array.coords.pop('x_pixels')
+        measurement._data_array.coords.pop('y_pixels')
+        assert sc.identical(loaded_measurement._data_array, measurement._data_array)
+
     @pytest.mark.parametrize('coordinate', ['x_positions', 'y_positions'], ids=['x_coordinate', 'y_coordinate'])
     def test_positions(self, valid_data_array, coordinate):
         # When