Merge pull request #733 from mantidproject/702_see_if_logs_loaded

Adds source file path to IMATLogFile, shows it in metadata

mantidimaging/core/data/images.py

@@ -272,6 +272,10 @@ def log_file(self):
 
     @log_file.setter
     def log_file(self, value: IMATLogFile):
+        if value is not None:
+            self.metadata[const.LOG_FILE] = value.source_file
+        elif value is None:
+            del self.metadata[const.LOG_FILE]
         self._log_file = value
 
     def projection_angles(self, max_angle: float = 360.0):

mantidimaging/core/data/test/fake_logfile.py

@@ -50,4 +50,4 @@ def generate_logfile() -> IMATLogFile:
             "Monitor 3 after:  6078866"
         ]
     ]
-    return IMATLogFile(data)
+    return IMATLogFile(data, "/tmp/fake")

mantidimaging/core/data/test/images_test.py

@@ -198,3 +198,8 @@ def test_get_projection_angles_no_logfile(self):
         actual = images.projection_angles(275.69)
         self.assertEqual(10, len(actual.value))
         self.assertAlmostEqual(np.deg2rad(275.69), actual.value[-1], places=4)
+
+    def test_metadata_gets_updated_with_logfile(self):
+        images = generate_images()
+        images.log_file = generate_logfile()
+        self.assertEqual(images.log_file.source_file, images.metadata[const.LOG_FILE])

mantidimaging/core/io/loader/loader.py

@@ -97,13 +97,13 @@ def read_in_file_information(input_path,
     return fi
 
 
-def load_log(log_file) -> IMATLogFile:
+def load_log(log_file: str) -> IMATLogFile:
     data = []
     with open(log_file, 'r') as f:
         for line in f:
             data.append(line.strip().split("   "))
 
-    return IMATLogFile(data)
+    return IMATLogFile(data, log_file)
 
 
 def load_p(parameters: ImageParameters, dtype, progress) -> Images:

mantidimaging/core/operation_history/const.py

@@ -7,6 +7,7 @@
 OPERATION_KEYWORD_ARGS = 'kwargs'
 OPERATION_DISPLAY_NAME = 'display_name'
 PIXEL_SIZE = 'pixel_size'
+LOG_FILE = 'log_file'
 
 OPERATION_NAME_COR_TILT_FINDING = 'cor_tilt_finding'
 COR_TILT_ROTATION_CENTRE = 'rotation_centre'

mantidimaging/core/utility/imat_log_file_parser.py

@@ -24,7 +24,8 @@ class IMATLogColumn(Enum):
 
 
 class IMATLogFile:
-    def __init__(self, data: List[List[str]]):
+    def __init__(self, data: List[List[str]], source_file: str):
+        self._source_file = source_file
         self._data: Dict[IMATLogColumn, List] = {
             IMATLogColumn.TIMESTAMP: [],
             IMATLogColumn.IMAGE_TYPE_IMAGE_COUNTER: [],
@@ -46,6 +47,10 @@ def __init__(self, data: List[List[str]]):
             self._data[IMATLogColumn.COUNTS_BEFORE].append(line[2])
             self._data[IMATLogColumn.COUNTS_AFTER].append(line[3])
 
+    @property
+    def source_file(self) -> str:
+        return self._source_file
+
     def projection_numbers(self):
         proj_nums = numpy.zeros(len(self._data[IMATLogColumn.IMAGE_TYPE_IMAGE_COUNTER]), dtype=numpy.uint32)
         for i, angle_str in enumerate(self._data[IMATLogColumn.IMAGE_TYPE_IMAGE_COUNTER]):

mantidimaging/core/utility/test/imat_log_file_parser_test.py

@@ -11,7 +11,7 @@ def test_parsing_log_file():
         EXPECTED_HEADER_FOR_IMAT_LOG_FILE, ["ignored line"],
         ["timestamp", "Projection:  0  angle: 0.1", "counts before: 12345", "counts_after: 45678"]
     ]
-    logfile = IMATLogFile(test_input)
+    logfile = IMATLogFile(test_input, "/tmp/fake")
     assert len(logfile.projection_angles().value) == 1
     assert logfile.projection_angles().value[0] == np.deg2rad(0.1), f"Got: {logfile.projection_angles().value[0]}"
     assert logfile.counts().value[0] == (45678 - 12345)
@@ -25,7 +25,7 @@ def test_counts():
         ["timestamp", "Projection:  1  angle: 0.1", "counts before: 45678", "counts_after: 84678"],
         ["timestamp", "Projection:  2  angle: 0.2", "counts before: 84678", "counts_after: 124333"],
     ]
-    logfile = IMATLogFile(test_input)
+    logfile = IMATLogFile(test_input, "/tmp/fake")
     assert len(logfile.counts().value) == 3
     assert logfile.counts().value[0] == 45678 - 12345
     assert logfile.counts().value[1] == 84678 - 45678
@@ -50,7 +50,7 @@ def test_find_missing_projection_number():
         ["timestamp", "Projection:  1  angle: 0.1", "counts before: 12345", "counts_after: 45678"],
         ["timestamp", "Projection:  2  angle: 0.2", "counts before: 12345", "counts_after: 45678"],
     ]
-    logfile = IMATLogFile(test_input)
+    logfile = IMATLogFile(test_input, "/tmp/fake")
     assert len(logfile.projection_numbers()) == 3
     # nothing missing
     logfile.raise_if_angle_missing(["file_000.tif", "file_001.tif", "file_002.tif"])
@@ -60,3 +60,15 @@ def test_find_missing_projection_number():
     assert_raises(RuntimeError, logfile.raise_if_angle_missing, ["file_000.tif", "file_001.tif"])
     assert_raises(RuntimeError, logfile.raise_if_angle_missing,
                   ["file_000.tif", "file_001.tif", "file_002.tif", "file_003.tif"])
+
+
+def test_source_file():
+    test_input = [
+        EXPECTED_HEADER_FOR_IMAT_LOG_FILE,
+        ["ignored line"],
+        ["timestamp", "Projection:  0  angle: 0.0", "counts before: 12345", "counts_after: 45678"],
+        ["timestamp", "Projection:  1  angle: 0.1", "counts before: 12345", "counts_after: 45678"],
+        ["timestamp", "Projection:  2  angle: 0.2", "counts before: 12345", "counts_after: 45678"],
+    ]
+    logfile = IMATLogFile(test_input, "/tmp/fake")
+    assert logfile.source_file == "/tmp/fake"

mantidimaging/gui/windows/main/model.py

@@ -162,12 +162,21 @@ def have_active_stacks(self) -> bool:
         return len(self.active_stacks) > 0
 
     def add_log_to_sample(self, stack_name: str, log_file: str):
-        stack = self.get_stack_by_name(stack_name).widget()  # type: ignore
-        stack.presenter.images.log_file = loader.load_log(log_file)
-        stack.presenter.images.log_file.raise_if_angle_missing(stack.presenter.images.filenames)
+        stack_dock = self.get_stack_by_name(stack_name)
+        if stack_dock is None:
+            raise RuntimeError(f"Failed to get stack with name {stack_name}")
+
+        stack: StackVisualiserView = stack_dock.widget()  # type: ignore
+        log = loader.load_log(log_file)
+        log.raise_if_angle_missing(stack.presenter.images.filenames)
+        stack.presenter.images.log_file = log
 
     def add_180_deg_to_stack(self, stack_name, _180_deg_file):
-        stack = self.get_stack_by_name(stack_name).widget()  # type: ignore
+        stack_dock = self.get_stack_by_name(stack_name)
+        if stack_dock is None:
+            raise RuntimeError(f"Failed to get stack with name {stack_name}")
+
+        stack: StackVisualiserView = stack_dock.widget()  # type: ignore
         _180_deg = loader.load(file_names=[_180_deg_file])
         stack.presenter.images.proj180deg = _180_deg.sample
         return _180_deg

mantidimaging/gui/windows/main/test/model_test.py

@@ -238,6 +238,21 @@ def test_add_log_to_sample(self, load_log: mock.Mock):
         stack_mock.return_value.widget.return_value.presenter.images.log_file.raise_if_angle_missing \
             .assert_called_once_with(stack_mock.return_value.widget.return_value.presenter.images.filenames)
 
+    @mock.patch('mantidimaging.core.io.loader.load_log')
+    def test_add_log_to_sample_no_stack(self, load_log: mock.Mock):
+        """
+        Test in add_log_to_sample when get_stack_by_name returns None
+        """
+        log_file = "Log file"
+        stack_name = "stack name"
+        stack_mock = mock.MagicMock()
+        self.model.get_stack_by_name = stack_mock
+        stack_mock.return_value = None
+
+        self.assertRaises(RuntimeError, self.model.add_log_to_sample, stack_name=stack_name, log_file=log_file)
+
+        stack_mock.assert_called_with(stack_name)
+
     @mock.patch('mantidimaging.core.io.loader.load')
     def test_add_180_deg_to_stack(self, load: mock.Mock):
         _180_file = "180 file"
@@ -251,6 +266,20 @@ def test_add_180_deg_to_stack(self, load: mock.Mock):
         stack_mock.assert_called_with(stack_name)
         self.assertEqual(_180_stack, stack_mock.return_value.widget.return_value.presenter.images.proj180deg)
 
+    @mock.patch('mantidimaging.core.io.loader.load')
+    def test_add_180_deg_to_stack_no_stack(self, load: mock.Mock):
+        """
+        Test in add_180_deg_to_stack when get_stack_by_name returns None
+        """
+        _180_file = "180 file"
+        stack_name = "stack name"
+        stack_mock = mock.MagicMock()
+        self.model.get_stack_by_name = stack_mock
+        stack_mock.return_value = None
+
+        self.assertRaises(RuntimeError, self.model.add_180_deg_to_stack, stack_name=stack_name, _180_deg_file=_180_file)
+        stack_mock.assert_called_with(stack_name)
+
 
 if __name__ == '__main__':
     unittest.main()

mantidimaging/gui/windows/operations/view.py

@@ -252,6 +252,7 @@ def toggle_average_images(images_):
         toggle_show_averaged_image = QAction("Toggle show averaged image", menu)
         toggle_show_averaged_image.triggered.connect(lambda: toggle_average_images(images))
         menu.addAction(toggle_show_averaged_image)
+        menu.addSeparator()
         self.roi_view.imageItem.menu = menu
 
         self.roi_view.setImage(images.data)

mantidimaging/gui/windows/stack_visualiser/view.py

@@ -121,21 +121,25 @@ def roi_changed_callback(self, roi: SensibleROI):
         self.roi_updated.emit(roi)
 
     def build_context_menu(self) -> QMenu:
-        actions = [("Set ROI", self.set_roi), ("Copy ROI to clipboard", self.copy_roi_to_clipboard),
-                   ("Toggle show averaged image", lambda: self.presenter.notify(SVNotification.TOGGLE_IMAGE_MODE)),
-                   ("Create sinograms from stack", lambda: self.presenter.notify(SVNotification.SWAP_AXES)),
+        actions = [("Show history and metadata", self.show_image_metadata),
                    ("Duplicate whole data", lambda: self.presenter.notify(SVNotification.DUPE_STACK)),
                    ("Duplicate current ROI of data", lambda: self.presenter.notify(SVNotification.DUPE_STACK_ROI)),
-                   ("Show history", self.show_image_metadata), ("Mark as projections/sinograms", self.mark_as_),
+                   ("Mark as projections/sinograms", self.mark_as_), ("", None),
+                   ("Toggle show averaged image", lambda: self.presenter.notify(SVNotification.TOGGLE_IMAGE_MODE)),
+                   ("Create sinograms from stack", lambda: self.presenter.notify(SVNotification.SWAP_AXES)),
+                   ("Set ROI", self.set_roi), ("Copy ROI to clipboard", self.copy_roi_to_clipboard), ("", None),
                    ("Change window name", self.change_window_name_clicked), ("Goto projection", self.goto_projection),
                    ("Goto angle", self.goto_angle)]
 
         menu = QMenu(self)
 
         for (menu_text, func) in actions:
-            action = QAction(menu_text, menu)
-            action.triggered.connect(func)
-            menu.addAction(action)
+            if func is None:
+                menu.addSeparator()
+            else:
+                action = QAction(menu_text, menu)
+                action.triggered.connect(func)
+                menu.addAction(action)
 
         return menu