move tests of the deprecated code

src/depiction/calibration/deprecated/tests/test_calibrate_image_integration.py

@@ -0,0 +1,74 @@
+import os
+import unittest
+from tempfile import TemporaryDirectory
+
+import numpy as np
+
+from depiction.calibration.deprecated.calibrate_image import CalibrateImage
+from tests.integration.integration_test_utils import IntegrationTestUtils
+from depiction.parallel_ops.parallel_config import ParallelConfig
+from depiction.persistence import ImzmlModeEnum, ImzmlReadFile, ImzmlWriteFile
+
+
+class TestCalibrateImageIntegration(unittest.TestCase):
+    def setUp(self):
+        self.tmp_dir = TemporaryDirectory()
+        self.addCleanup(self.tmp_dir.cleanup)
+        self.mock_input_file_path = os.path.join(self.tmp_dir.name, "input.imzML")
+        self.mock_output_file_path = os.path.join(self.tmp_dir.name, "output.imzML")
+
+    def test_calibrate_image(self):
+        mz_list = np.linspace(100, 110, 23)
+        mz_list_outlier = mz_list.copy()
+        mz_list_outlier[10] += 0.3
+        mz_ref = mz_list[2::5]
+
+        mz_arr_list = np.array([mz_list, mz_list + 0.1, mz_list - 0.2, mz_list_outlier])
+        int_arr_list = np.full_like(mz_arr_list, 1.0)
+        int_arr_list[..., 2::5] = 10.0
+
+        IntegrationTestUtils.populate_test_file(
+            path=self.mock_input_file_path,
+            mz_arr_list=mz_arr_list,
+            int_arr_list=int_arr_list,
+            imzml_mode=ImzmlModeEnum.PROCESSED,
+        )
+
+        read_file = ImzmlReadFile(self.mock_input_file_path)
+        write_file = ImzmlWriteFile(self.mock_output_file_path, imzml_mode=ImzmlModeEnum.PROCESSED)
+
+        calibrate = CalibrateImage(
+            reference_mz=mz_ref,
+            model_type="linear",
+            parallel_config=ParallelConfig(n_jobs=2, task_size=None),
+            output_store=None,
+        )
+        calibrate.calibrate_image(read_file=read_file, write_file=write_file)
+
+        # read the results
+        with ImzmlReadFile(self.mock_output_file_path).reader() as reader:
+            spectra = reader.get_spectra([0, 1, 2, 3])
+            self.assertEqual(ImzmlModeEnum.PROCESSED, reader.imzml_mode)
+
+        for i_spectrum in range(4):
+            mz_arr = spectra[0][i_spectrum]
+            int_arr = spectra[1][i_spectrum]
+
+            mz_peak = mz_arr[int_arr == 10.0]
+            # TODO ideally this would be as close to zero as possible:
+            print(mz_peak - mz_ref)
+            # but in practice it currently is not.
+            # it needs to be checked why this is the case...
+
+        print()
+        # check the delta from the input
+        print(spectra[0])
+        print()
+        print(spectra[1])
+        delta = mz_arr_list - spectra[0]
+        print(delta)
+        self.assertFalse(True)
+
+
+if __name__ == "__main__":
+    unittest.main()