Merge Rits export to main (#1954)

.github/workflows/conda.yml

@@ -6,9 +6,6 @@ on:
     - 'main'
     - 'release-*'
   pull_request:
-    branches:
-      - 'main'
-      - 'release-*'
   release:
   merge_group:
 

.github/workflows/cos7_testing.yml

@@ -6,9 +6,6 @@ on:
     - 'main'
     - 'release-*'
   pull_request:
-    branches:
-      - 'main'
-      - 'release-*'
   merge_group:
 
 jobs:

.github/workflows/docs.yml

@@ -6,9 +6,6 @@ on:
     - 'main'
     - 'release-*'
   pull_request:
-    branches:
-      - 'main'
-      - 'release-*'
   release:
   merge_group:
 

.github/workflows/license_check.yaml

@@ -6,9 +6,6 @@ on:
     - 'main'
     - 'release-*'
   pull_request:
-    branches:
-      - 'main'
-      - 'release-*'
   merge_group:
 
 jobs:

.github/workflows/u18_testing.yml

@@ -6,9 +6,6 @@ on:
     - 'main'
     - 'release-*'
   pull_request:
-    branches:
-      - 'main'
-      - 'release-*'
   merge_group:
 
 jobs:

.github/workflows/windows.yml

@@ -6,9 +6,6 @@ on:
     - 'main'
     - 'release-*'
   pull_request:
-    branches:
-      - 'main'
-      - 'release-*'
   release:
   merge_group:
 

docs/release_notes/next/dev-1932-RITS_export_backend

@@ -0,0 +1 @@
+#1932 : RITS Export Backend

docs/release_notes/next/feature-1941-rits-gui

@@ -0,0 +1,2 @@
+#1941 : Spectrum viewer tab for exporting to RITS
+

mantidimaging/core/io/saver.py

@@ -7,6 +7,7 @@
 from typing import List, Union, Optional, Dict, Callable, Tuple, TYPE_CHECKING
 
 import h5py
+from pathlib import Path
 import numpy as np
 from tifffile import tifffile
 
@@ -411,7 +412,7 @@ def generate_names(name_prefix: str,
     return names
 
 
-def make_dirs_if_needed(dirname: Optional[str] = None, overwrite_all: bool = False):
+def make_dirs_if_needed(dirname: Optional[str] = None, overwrite_all: bool = False) -> None:
     """
     Makes sure that the directory needed (for example to save a file)
     exists, otherwise creates it.
@@ -428,3 +429,31 @@ def make_dirs_if_needed(dirname: Optional[str] = None, overwrite_all: bool = Fal
     elif os.listdir(path) and not overwrite_all:
         raise RuntimeError("The output directory is NOT empty:{0}\nThis can be "
                            "overridden by specifying 'Overwrite on name conflict'.".format(path))
+
+
+def create_rits_format(tof: np.ndarray, transmission: np.ndarray, transmission_error: np.ndarray) -> str:
+    """
+    create a RITS format ready for exporting to a .dat file
+
+    :param tof: time of flight
+    :param transmission: transmission value
+    :param transmission_error: transmission_error value
+    :return: RITS format ascii
+
+    """
+    return '\n'.join(
+        ['\t'.join([str(x) for x in row]) for row in zip(tof, transmission, transmission_error, strict=True)])
+
+
+def export_to_dat_rits_format(rits_formatted_data: str, path: Path) -> None:
+    """
+    export a RITS formatted data to a .dat file
+
+    :param rits_formatted_data: RITS formatted data
+    :param path: path to save the .dat file
+    :return: None
+
+    """
+    with open(path, 'w', encoding='utf-8') as f:
+        f.write(rits_formatted_data)
+    LOG.info('RITS formatted data saved to: {}'.format(path))

mantidimaging/core/io/test/io_test.py

@@ -483,6 +483,14 @@ def test_convert_float_to_int(self):
             close_arr = np.isclose(conv[i] / factors[i], float_arr[i], rtol=1e-5)
             self.assertTrue(np.count_nonzero(close_arr) >= len(close_arr) * 0.75)
 
+    def test_create_rits_format(self):
+        tof = np.array([1, 2, 3])
+        transmission = np.array([4, 5, 6])
+        absorption = np.array([7, 8, 9])
+        rits_formatted_data = saver.create_rits_format(tof, transmission, absorption)
+        expected = '1\t4\t7\n2\t5\t8\n3\t6\t9'
+        self.assertEqual(rits_formatted_data, expected)
+
 
 if __name__ == '__main__':
     unittest.main()

mantidimaging/gui/windows/spectrum_viewer/model.py

@@ -8,13 +8,17 @@
 
 import numpy as np
 
+from logging import getLogger
 from mantidimaging.core.data import ImageStack
 from mantidimaging.core.io.csv_output import CSVOutput
+from mantidimaging.core.io import saver
 from mantidimaging.core.utility.sensible_roi import SensibleROI
 
 if TYPE_CHECKING:
     from mantidimaging.gui.windows.spectrum_viewer.presenter import SpectrumViewerWindowPresenter
 
+LOG = getLogger(__name__)
+
 
 class SpecType(Enum):
     SAMPLE = 1
@@ -183,6 +187,28 @@ def save_csv(self, path: Path, normalized: bool) -> None:
             csv_output.write(outfile)
             self.save_roi_coords(self.get_roi_coords_filename(path))
 
+    def save_rits(self, path: Path, normalized: bool) -> None:
+        """
+        Saves the spectrum for one ROI to a RITS file.
+
+        @param path: The path to save the CSV file to.
+        @param normalized: Whether to save the normalized spectrum.
+        """
+        if self._stack is None:
+            raise ValueError("No stack selected")
+
+        # Default_roi will likely need updating once UI is implemented
+        default_roi = self.default_roi_list[0]
+        tof = np.arange(self._stack.data.shape[0])
+        transmission_error = np.zeros_like(tof)
+        if normalized:
+            if self._normalise_stack is None:
+                raise RuntimeError("No normalisation stack selected")
+            transmission = self.get_spectrum(default_roi, SpecType.SAMPLE_NORMED)
+            self.export_spectrum_to_rits(path, tof, transmission, transmission_error)
+        else:
+            LOG.error("Data is not normalised to open beam. This will not export to a valid RITS format")
+
     def get_roi_coords_filename(self, path: Path) -> Path:
         """
         Get the path to save the ROI coordinates to.
@@ -209,6 +235,13 @@ def save_roi_coords(self, path: Path) -> None:
                     "Y Max": coords.bottom
                 })
 
+    def export_spectrum_to_rits(self, path: Path, tof, transmission, absorption) -> None:
+        """
+        Export spectrum to RITS format
+        """
+        rits_data = saver.create_rits_format(tof, transmission, absorption)
+        saver.export_to_dat_rits_format(rits_data, path)
+
     def remove_roi(self, roi_name) -> None:
         """
         Remove the selected ROI from the model

mantidimaging/gui/windows/spectrum_viewer/presenter.py

@@ -1,8 +1,11 @@
 # Copyright (C) 2023 ISIS Rutherford Appleton Laboratory UKRI
 # SPDX - License - Identifier: GPL-3.0-or-later
 from __future__ import annotations
+
+from enum import Enum
 from typing import TYPE_CHECKING, Optional
 
+from logging import getLogger
 from mantidimaging.core.data.dataset import StrictDataset
 from mantidimaging.gui.mvp_base import BasePresenter
 from mantidimaging.gui.windows.spectrum_viewer.model import SpectrumViewerWindowModel, SpecType
@@ -13,6 +16,14 @@
     from mantidimaging.core.data import ImageStack
     from uuid import UUID
 
+LOG = getLogger(__name__)
+
+
+class ExportMode(Enum):
+    # Needs to match GUI tab order
+    ROI_MODE = 0
+    IMAGE_MODE = 1
+
 
 class SpectrumViewerWindowPresenter(BasePresenter):
     """
@@ -26,13 +37,15 @@ class SpectrumViewerWindowPresenter(BasePresenter):
     spectrum_mode: SpecType = SpecType.SAMPLE
     current_stack_uuid: Optional['UUID'] = None
     current_norm_stack_uuid: Optional['UUID'] = None
+    export_mode: ExportMode
 
     def __init__(self, view: 'SpectrumViewerWindowView', main_window: 'MainWindowView'):
         super().__init__(view)
 
         self.view = view
         self.main_window = main_window
         self.model = SpectrumViewerWindowModel(self)
+        self.export_mode = ExportMode.ROI_MODE
 
     def handle_sample_change(self, uuid: Optional['UUID']) -> None:
         if uuid == self.current_stack_uuid:
@@ -50,7 +63,6 @@ def handle_sample_change(self, uuid: Optional['UUID']) -> None:
         if uuid is None:
             self.model.set_stack(None)
             self.view.clear()
-            self.handle_button_enabled()
             return
 
         self.model.set_stack(self.main_window.get_stack(uuid))
@@ -65,7 +77,6 @@ def handle_sample_change(self, uuid: Optional['UUID']) -> None:
         self.do_add_roi()
         self.view.set_normalise_error(self.model.normalise_issue())
         self.show_new_sample()
-        self.handle_button_enabled()
 
     def handle_normalise_stack_change(self, normalise_uuid: Optional['UUID']) -> None:
         if normalise_uuid == self.current_norm_stack_uuid:
@@ -144,9 +155,15 @@ def do_set_roi_alpha(self, name: str, alpha: float) -> None:
 
     def handle_button_enabled(self) -> None:
         """
-        Enable the export button if the current stack is not None
+        Enable the export button if the current stack is not None and normalisation is valid
         """
-        self.view.set_export_button_enabled(self.model.has_stack())
+        has_stack = self.model.has_stack()
+        normalisation_on = self.view.normalisation_enabled()
+        normalisation_no_error = (normalisation_on and self.model.normalise_issue() == "") or not normalisation_on
+
+        self.view.exportButton.setEnabled(has_stack and normalisation_no_error)
+        self.view.exportButtonRITS.setEnabled(has_stack and normalisation_on and normalisation_no_error)
+        self.view.addBtn.setEnabled(has_stack)
 
     def handle_export_csv(self) -> None:
         path = self.view.get_csv_filename()
@@ -158,6 +175,18 @@ def handle_export_csv(self) -> None:
 
         self.model.save_csv(path, self.spectrum_mode == SpecType.SAMPLE_NORMED)
 
+    def handle_rits_export(self) -> None:
+        """
+        Handle the export of the current spectrum to a RITS file format
+        """
+        path = self.view.get_rits_export_filename()
+        if path is None:
+            LOG.debug("No path selected, aborting export")
+            return
+        if path.suffix != ".dat":
+            path = path.with_suffix(".dat")
+        self.model.save_rits(path, self.spectrum_mode == SpecType.SAMPLE_NORMED)
+
     def handle_enable_normalised(self, enabled: bool) -> None:
         if enabled:
             self.spectrum_mode = SpecType.SAMPLE_NORMED
@@ -220,3 +249,7 @@ def do_remove_roi(self, roi_name=None) -> None:
             self.view.spectrum.remove_roi(roi_name)
             self.view.set_spectrum(roi_name, self.model.get_spectrum(roi_name, self.spectrum_mode))
             self.model.remove_roi(roi_name)
+
+    def handle_export_tab_change(self, index: int) -> None:
+        self.export_mode = ExportMode(index)
+        self.view.on_visibility_change()

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

@@ -6,6 +6,7 @@
 from pathlib import Path
 from unittest import mock
 
+from PyQt5.QtWidgets import QPushButton
 from parameterized import parameterized
 
 from mantidimaging.core.data.dataset import StrictDataset, MixedDataset
@@ -27,6 +28,9 @@ def setUp(self) -> None:
         self.view.current_dataset_id = uuid.uuid4()
         mock_spectrum_roi_dict = mock.create_autospec(dict)
         self.view.spectrum = mock.create_autospec(SpectrumWidget, roi_dict=mock_spectrum_roi_dict)
+        self.view.exportButton = mock.create_autospec(QPushButton)
+        self.view.exportButtonRITS = mock.create_autospec(QPushButton)
+        self.view.addBtn = mock.create_autospec(QPushButton)
         self.presenter = SpectrumViewerWindowPresenter(self.view, self.main_window)
 
     def test_get_dataset_id_for_stack_no_stack_id(self):
@@ -74,7 +78,6 @@ def test_handle_sample_change_no_new_stack(self):
         self.view.try_to_select_relevant_normalise_stack.assert_not_called()
         self.assertIsNone(self.view.current_dataset_id)
         self.presenter.show_new_sample.assert_not_called()
-        self.view.set_export_button_enabled.assert_called_once_with(False)
 
     def test_handle_sample_change_dataset_unchanged(self):
         initial_dataset_id = self.view.current_dataset_id
@@ -86,7 +89,6 @@ def test_handle_sample_change_dataset_unchanged(self):
         self.presenter.handle_sample_change(uuid.uuid4())
         self.presenter.main_window.get_dataset.assert_not_called()
         self.assertEqual(self.view.current_dataset_id, initial_dataset_id)
-        self.view.set_export_button_enabled.assert_called_once_with(True)
 
     def test_handle_sample_change_to_MixedDataset(self):
         self.presenter.get_dataset_id_for_stack = mock.Mock(return_value=uuid.uuid4())
@@ -112,6 +114,45 @@ def test_handle_sample_change_no_flat(self):
         self.presenter.main_window.get_dataset.assert_called_once()
         self.view.try_to_select_relevant_normalise_stack.assert_not_called()
 
+    @mock.patch("mantidimaging.gui.windows.spectrum_viewer.model.SpectrumViewerWindowModel.has_stack")
+    def test_WHEN_no_stack_THEN_buttons_disabled(self, has_stack):
+        has_stack.return_value = False
+        self.presenter.handle_button_enabled()
+        self.view.exportButton.setEnabled.assert_called_once_with(False)
+        self.view.exportButtonRITS.setEnabled.assert_called_once_with(False)
+        self.view.addBtn.setEnabled.assert_called_once_with(False)
+
+    @mock.patch("mantidimaging.gui.windows.spectrum_viewer.model.SpectrumViewerWindowModel.has_stack")
+    def test_WHEN_has_stack_no_norm_THEN_buttons_set(self, has_stack):
+        has_stack.return_value = True
+        self.view.normalisation_enabled.return_value = False
+        self.presenter.handle_button_enabled()
+        self.view.exportButton.setEnabled.assert_called_once_with(True)
+        self.view.exportButtonRITS.setEnabled.assert_called_once_with(False)  # RITS export needs norm
+        self.view.addBtn.setEnabled.assert_called_once_with(True)
+
+    @mock.patch("mantidimaging.gui.windows.spectrum_viewer.model.SpectrumViewerWindowModel.has_stack")
+    @mock.patch("mantidimaging.gui.windows.spectrum_viewer.model.SpectrumViewerWindowModel.normalise_issue")
+    def test_WHEN_has_stack_has_good_norm_THEN_buttons_set(self, normalise_issue, has_stack):
+        has_stack.return_value = True
+        normalise_issue.return_value = ""
+        self.view.normalisation_enabled.return_value = True
+        self.presenter.handle_button_enabled()
+        self.view.exportButton.setEnabled.assert_called_once_with(True)
+        self.view.exportButtonRITS.setEnabled.assert_called_once_with(True)
+        self.view.addBtn.setEnabled.assert_called_once_with(True)
+
+    @mock.patch("mantidimaging.gui.windows.spectrum_viewer.model.SpectrumViewerWindowModel.has_stack")
+    @mock.patch("mantidimaging.gui.windows.spectrum_viewer.model.SpectrumViewerWindowModel.normalise_issue")
+    def test_WHEN_has_stack_has_bad_norm_THEN_buttons_set(self, normalise_issue, has_stack):
+        has_stack.return_value = True
+        normalise_issue.return_value = "Something wrong"
+        self.view.normalisation_enabled.return_value = True
+        self.presenter.handle_button_enabled()
+        self.view.exportButton.setEnabled.assert_called_once_with(False)
+        self.view.exportButtonRITS.setEnabled.assert_called_once_with(False)
+        self.view.addBtn.setEnabled.assert_called_once_with(True)
+
     def test_WHEN_show_sample_call_THEN_add_range_set(self):
         self.presenter.model.tof_range = (0, 9)
         self.presenter.show_new_sample()
@@ -146,6 +187,18 @@ def test_handle_export_csv(self, path_name: str, mock_save_csv: mock.Mock):
         self.view.get_csv_filename.assert_called_once()
         mock_save_csv.assert_called_once_with(Path("/fake/path.csv"), False)
 
+    @parameterized.expand(["/fake/path", "/fake/path.dat"])
+    @mock.patch("mantidimaging.gui.windows.spectrum_viewer.model.SpectrumViewerWindowModel.save_rits")
+    def test_handle_rits_export(self, path_name: str, mock_save_rits: mock.Mock):
+        self.view.get_rits_export_filename = mock.Mock(return_value=Path(path_name))
+
+        self.presenter.model.set_stack(generate_images())
+
+        self.presenter.handle_rits_export()
+
+        self.view.get_rits_export_filename.assert_called_once()
+        mock_save_rits.assert_called_once_with(Path("/fake/path.dat"), False)
+
     def test_WHEN_do_add_roi_called_THEN_new_roi_added(self):
         self.presenter.model.set_stack(generate_images())
         self.presenter.do_add_roi()