Switch everywhere to use InstrumentLog

mantidimaging/core/data/imagestack.py

@@ -19,7 +19,7 @@
 from mantidimaging.core.utility.leak_tracker import leak_tracker
 
 if TYPE_CHECKING:
-    from mantidimaging.core.utility.imat_log_file_parser import IMATLogFile
+    from mantidimaging.core.io.instrument_log import InstrumentLog
 
 
 class ImageStack:
@@ -55,7 +55,7 @@ def __init__(self,
         self._is_sinograms = sinograms
 
         self._proj180deg: Optional[ImageStack] = None
-        self._log_file: Optional[IMATLogFile] = None
+        self._log_file: InstrumentLog | None = None
         self._projection_angles: Optional[ProjectionAngles] = None
 
         if name is None:
@@ -286,11 +286,11 @@ def is_sinograms(self) -> bool:
         return self._is_sinograms
 
     @property
-    def log_file(self):
+    def log_file(self) -> InstrumentLog | None:
         return self._log_file
 
     @log_file.setter
-    def log_file(self, value: IMATLogFile):
+    def log_file(self, value: InstrumentLog | None) -> None:
         if value is not None:
             self.metadata[const.LOG_FILE] = str(value.source_file)
         elif value is None:

mantidimaging/core/data/test/fake_logfile.py

@@ -3,10 +3,11 @@
 from __future__ import annotations
 from pathlib import Path
 
-from mantidimaging.core.utility.imat_log_file_parser import CSVLogParser, IMATLogFile, TextLogParser
+from mantidimaging.core.io.instrument_log import InstrumentLog
+from mantidimaging.core.utility.imat_log_file_parser import CSVLogParser, TextLogParser
 
 
-def generate_txt_logfile() -> IMATLogFile:
+def generate_txt_logfile() -> InstrumentLog:
     data = [
         TextLogParser.EXPECTED_HEADER_FOR_IMAT_TEXT_LOG_FILE,  # checked if exists, but skipped
         "",  # skipped when parsing
@@ -22,10 +23,10 @@ def generate_txt_logfile() -> IMATLogFile:
         "Sun Feb 10 00:26:29 2019   Projection:  8  angle: 2.5216   Monitor 3 before:  5786535   Monitor 3 after:  5929002",  # noqa: E501
         "Sun Feb 10 00:27:02 2019   Projection:  9  angle: 2.8368   Monitor 3 before:  5938142   Monitor 3 after:  6078866",  # noqa: E501
     ]
-    return IMATLogFile(data, Path("/tmp/fake"))
+    return InstrumentLog(data, Path("/tmp/fake.txt"))
 
 
-def generate_csv_logfile() -> IMATLogFile:
+def generate_csv_logfile() -> InstrumentLog:
     data = [
         CSVLogParser.EXPECTED_HEADER_FOR_IMAT_CSV_LOG_FILE,
         "Sun Feb 10 00:22:04 2019,Projection,0,angle: 0.0,Monitor 3 before: 4577907,Monitor 3 after:  4720271",
@@ -39,4 +40,4 @@ def generate_csv_logfile() -> IMATLogFile:
         "Sun Feb 10 00:26:29 2019,Projection,8,angle: 2.5216,Monitor 3 before: 5786535,Monitor 3 after:  5929002",
         "Sun Feb 10 00:27:02 2019,Projection,9,angle: 2.8368,Monitor 3 before: 5938142,Monitor 3 after:  6078866",
     ]
-    return IMATLogFile(data, Path("/tmp/fake"))
+    return InstrumentLog(data, Path("/tmp/fake.csv"))

mantidimaging/core/data/test/image_stack_test.py

@@ -6,6 +6,7 @@
 from pathlib import Path
 from unittest import mock
 
+from mantidimaging.core.io.instrument_log import InstrumentLog
 from mantidimaging.core.utility.data_containers import ProjectionAngles
 import unittest
 
@@ -15,7 +16,6 @@
 from mantidimaging.core.data.test.fake_logfile import generate_csv_logfile, generate_txt_logfile
 from mantidimaging.core.operations.crop_coords import CropCoordinatesFilter
 from mantidimaging.core.operation_history import const
-from mantidimaging.core.utility.imat_log_file_parser import IMATLogFile
 from mantidimaging.core.utility.sensible_roi import SensibleROI
 from mantidimaging.test_helpers.unit_test_helper import generate_images
 
@@ -73,7 +73,7 @@ def test_loading_metadata_preserves_existing(self):
     def test_loading_metadata_preserves_existing_log(self):
         json_file = io.StringIO('{"pixel_size": 30.0, "log_file": "/old/logfile"}')
         mock_log_path = Path("/aaa/bbb")
-        mock_log_file = mock.create_autospec(IMATLogFile, source_file=mock_log_path)
+        mock_log_file = mock.create_autospec(InstrumentLog, source_file=mock_log_path)
 
         imgs = ImageStack(np.asarray([1]))
         self.assertEqual({}, imgs.metadata)

mantidimaging/core/io/loader/loader.py

@@ -11,10 +11,10 @@
 import astropy.io.fits as fits
 from tifffile import tifffile
 
+from mantidimaging.core.io.instrument_log import InstrumentLog
 from mantidimaging.core.io.loader import img_loader
 from mantidimaging.core.io.utility import find_first_file_that_is_possibly_a_sample
 from mantidimaging.core.utility.data_containers import Indices, FILE_TYPES, ProjectionAngles
-from mantidimaging.core.utility.imat_log_file_parser import IMATLogFile
 from mantidimaging.core.io.filenames import FilenameGroup
 
 if TYPE_CHECKING:
@@ -91,9 +91,9 @@ def read_image_dimensions(file_path: Path) -> Tuple[int, int]:
     return img.shape
 
 
-def load_log(log_file: Path) -> IMATLogFile:
+def load_log(log_file: Path) -> InstrumentLog:
     with open(log_file, 'r') as f:
-        return IMATLogFile(f.readlines(), log_file)
+        return InstrumentLog(f.readlines(), log_file)
 
 
 def load_stack_from_group(group: FilenameGroup, progress: Optional[Progress] = None) -> ImageStack:

mantidimaging/core/io/loader/test/loader_test.py

@@ -7,11 +7,11 @@
 import numpy as np
 
 from mantidimaging.core.io.filenames import FilenameGroup
+from mantidimaging.core.io.instrument_log import InstrumentLog
 from mantidimaging.core.io.loader.loader import (DEFAULT_PIXEL_DEPTH, DEFAULT_PIXEL_SIZE, DEFAULT_IS_SINOGRAM,
                                                  create_loading_parameters_for_file_path, get_loader, load, _imread)
 
 from mantidimaging.core.utility.data_containers import FILE_TYPES, ProjectionAngles
-from mantidimaging.core.utility.imat_log_file_parser import IMATLogFile
 from mantidimaging.test_helpers.unit_test_helper import FakeFSTestCase
 
 
@@ -81,7 +81,7 @@ def test_load_with_golden_angles(self, mock_execute: mock.Mock, mock_load_log: m
         mock_filename_group.all_files.return_value = filenames
         mock_filename_group.first_file.return_value = filenames[0]
 
-        mock_log_data = mock.create_autospec(IMATLogFile)
+        mock_log_data = mock.create_autospec(InstrumentLog)
         mock_log_data.projection_angles.return_value = ProjectionAngles(np.deg2rad(angles))
 
         mock_load_log.return_value = mock_log_data

mantidimaging/gui/windows/image_load_dialog/test/presenter_test.py

@@ -7,7 +7,7 @@
 from unittest import mock
 
 from mantidimaging.core.io.filenames import FilenameGroup
-from mantidimaging.core.utility.imat_log_file_parser import IMATLogFile
+from mantidimaging.core.io.instrument_log import InstrumentLog
 from mantidimaging.gui.windows.image_load_dialog.field import Field
 from mantidimaging.gui.windows.image_load_dialog.presenter import LoadPresenter
 from mantidimaging.core.utility.data_containers import FILE_TYPES, Indices
@@ -165,7 +165,7 @@ def test_ensure_sample_log_consistency_matching(self, mock_load_log):
         """
         Test behaviour when the number of projection angles and files matches
         """
-        mock_log = mock.create_autospec(IMATLogFile)
+        mock_log = mock.create_autospec(InstrumentLog)
         mock_load_log.return_value = mock_log
         file_name = "file_name"
         field = mock.MagicMock()
@@ -182,7 +182,7 @@ def test_ensure_sample_log_consistency_matching(self, mock_load_log):
 
     @mock.patch("mantidimaging.gui.windows.image_load_dialog.presenter.load_log")
     def test_ensure_sample_log_consistency_exits_when_none_or_empty_str(self, mock_load_log):
-        mock_log = mock.create_autospec(IMATLogFile)
+        mock_log = mock.create_autospec(InstrumentLog)
         mock_load_log.return_value = mock_log
         file_name = None
         field = mock.MagicMock()

mantidimaging/gui/windows/main/model.py

@@ -139,12 +139,13 @@ def raise_error_when_parent_dataset_not_found(self, images_id: uuid.UUID) -> NoR
     def raise_error_when_parent_strict_dataset_not_found(self, images_id: uuid.UUID) -> NoReturn:
         raise RuntimeError(f"Failed to find strict dataset containing ImageStack with ID {images_id}")
 
-    def add_log_to_sample(self, images_id: uuid.UUID, log_file: Path):
+    def add_log_to_sample(self, images_id: uuid.UUID, log_file: Path) -> None:
         images = self.get_images_by_uuid(images_id)
         if images is None:
             raise RuntimeError
         log = loader.load_log(log_file)
-        log.raise_if_angle_missing(images.filenames)
+        if images.filenames is not None:
+            log.raise_if_angle_missing(images.filenames)
         images.log_file = log
 
     def _remove_dataset(self, dataset_id: uuid.UUID):