Add save option on analysis (#114)

* Add save option on analysis

* Add (broken) save test

* Update tracks test

* update testing

* Add sleep to fix tests

* Update test data

* Add remaining save tests

* set layer editability later to prevent it being reset

* sleep for longer to see if tests pass on windows/macos

* rename tests

* increase sleep

brainreg_segment/layout/gui_constants.py

@@ -14,6 +14,8 @@
     "left"  # Alignment of text in pushbuttons in methods chooser panel
 )
 
+SAVE_DEFAULT = False
+
 POINT_SIZE = 100
 SPLINE_SIZE = 50
 NUM_COLORS = 10

brainreg_segment/segment.py

@@ -451,10 +451,9 @@ def initialise_loaded_data(self):
             ]
             self.hemispheres_data = self.hemispheres_layer.data
 
-        self.prevent_layer_edit()
-
         self.initialise_segmentation_interface()
         self.status_label.setText("Ready")
+        self.prevent_layer_edit()
 
     def collate_widget_layers(self):
         """
@@ -486,6 +485,7 @@ def collate_widget_layers(self):
         ]
 
     def prevent_layer_edit(self):
+        print("Preventing layer edit")
         self.collate_widget_layers()
         for layer in self.non_editable_widget_layers:
             layer.editable = False
@@ -568,18 +568,21 @@ def save(self, override=True):
             else:
                 choice = True  # for debugging
             if choice:
-                print("Saving")
-                worker = save_all(
-                    self.paths.regions_directory,
-                    self.paths.tracks_directory,
-                    self.label_layers,
-                    self.track_layers,
-                    track_file_extension=TRACK_FILE_EXT,
-                )
-                worker.start()
+                self.run_save()
             else:
                 print('Not saving because user chose "Cancel" \n')
 
+    def run_save(self):
+        print("Saving")
+        worker = save_all(
+            self.paths.regions_directory,
+            self.paths.tracks_directory,
+            self.label_layers,
+            self.track_layers,
+            track_file_extension=TRACK_FILE_EXT,
+        )
+        worker.start()
+
     def export_to_brainrender(self, override=False):
         if not override:
             choice = display_warning(

brainreg_segment/segmentation_panels/regions.py

@@ -7,6 +7,7 @@
     COLUMN_WIDTH,
     IMAGE_FILE_EXT,
     NUM_COLORS,
+    SAVE_DEFAULT,
     SEGM_METHODS_PANEL_ALIGN,
     SUMMARIZE_VOLUMES_DEFAULT,
 )
@@ -34,6 +35,7 @@ def __init__(
         parent,
         calculate_volumes_default=CALCULATE_VOLUMES_DEFAULT,
         summarise_volumes_default=SUMMARIZE_VOLUMES_DEFAULT,
+        save_default=SAVE_DEFAULT,
         brush_size=BRUSH_SIZE,
         image_file_extension=IMAGE_FILE_EXT,
         num_colors=NUM_COLORS,
@@ -43,6 +45,7 @@ def __init__(
 
         self.calculate_volumes_default = calculate_volumes_default
         self.summarise_volumes_default = summarise_volumes_default
+        self.save_default = save_default
 
         # Brushes / ...
         self.brush_size_default = BRUSH_SIZE  # Keep track of default
@@ -60,7 +63,7 @@ def add_region_panel(self, row):
             "Add new region",
             region_layout,
             self.add_new_region,
-            row=2,
+            row=3,
             column=0,
             tooltip="Create a new empty segmentation layer "
             "to manually segment a new region.",
@@ -70,7 +73,7 @@ def add_region_panel(self, row):
             "Analyse regions",
             region_layout,
             self.run_region_analysis,
-            row=2,
+            row=3,
             column=1,
             tooltip="Analyse the spatial distribution of the "
             "segmented regions.",
@@ -79,7 +82,7 @@ def add_region_panel(self, row):
             "Add region from selected layer",
             region_layout,
             self.add_region_from_existing_layer,
-            row=3,
+            row=4,
             column=0,
             tooltip="Adds a region from a selected labels layer (e.g. "
             "from another plugin). Make sure this region "
@@ -105,6 +108,13 @@ def add_region_panel(self, row):
             tooltip="Summarise each segmented region "
             "(e.g. center, volume etc.).",
         )
+        self.save_checkbox = add_checkbox(
+            region_layout,
+            self.save_default,
+            "Save segmentation",
+            row=2,
+            tooltip="Save the segmentation layers during analysis.",
+        )
 
         region_layout.setColumnMinimumWidth(1, COLUMN_WIDTH)
         self.region_panel.setLayout(region_layout)
@@ -204,6 +214,9 @@ def run_region_analysis(self, override=False):
                 choice = True  # for debugging
 
             if choice:
+                if self.save_checkbox.isChecked():
+                    self.parent.run_save()
+
                 print("Running region analysis")
 
                 if check_segmentation_in_correct_space(

brainreg_segment/segmentation_panels/tracks.py

@@ -9,6 +9,7 @@
     COLUMN_WIDTH,
     FIT_DEGREE_DEFAULT,
     POINT_SIZE,
+    SAVE_DEFAULT,
     SEGM_METHODS_PANEL_ALIGN,
     SPLINE_POINTS_DEFAULT,
     SPLINE_SIZE,
@@ -47,6 +48,7 @@ def __init__(
         spline_smoothing_default=SPLINE_SMOOTHING_DEFAULT,
         fit_degree_default=FIT_DEGREE_DEFAULT,
         summarise_track_default=SUMMARISE_TRACK_DEFAULT,
+        save_default=SAVE_DEFAULT,
     ):
         super(TrackSeg, self).__init__()
         self.parent = parent
@@ -62,6 +64,7 @@ def __init__(
         self.spline_size = spline_size  # Initialise
         self.spline_smoothing_default = spline_smoothing_default
         self.fit_degree_default = fit_degree_default
+        self.save_default = save_default
 
         # File formats
         self.track_file_extension = track_file_extension
@@ -78,7 +81,7 @@ def add_track_panel(self, row):
             "Add track",
             track_layout,
             self.add_track,
-            row=5,
+            row=6,
             column=0,
             tooltip="Create a new empty segmentation layer "
             "to manually annotate a new track.",
@@ -88,7 +91,7 @@ def add_track_panel(self, row):
             "Trace tracks",
             track_layout,
             self.run_track_analysis,
-            row=5,
+            row=6,
             column=1,
             tooltip="Join up the points using a spline fit "
             "and save the distribution of the track in "
@@ -99,7 +102,7 @@ def add_track_panel(self, row):
             "Add track from selected layer",
             track_layout,
             self.add_track_from_existing_layer,
-            row=6,
+            row=7,
             column=0,
             tooltip="Adds a track from a selected points layer (e.g. "
             "from another plugin). Make sure this track "
@@ -111,7 +114,7 @@ def add_track_panel(self, row):
             "Add surface points",
             track_layout,
             self.add_surface_points,
-            row=6,
+            row=7,
             column=1,
             tooltip="Add an additional first point at the surface of the "
             "brain. Selecting this option will add an additional "
@@ -128,14 +131,21 @@ def add_track_panel(self, row):
             "each part of the interpolated track "
             "(determined by the number of spline points). ",
         )
+        self.save_checkbox = add_checkbox(
+            track_layout,
+            self.save_default,
+            "Save tracing",
+            row=1,
+            tooltip="Save the traced layers during analysis.",
+        )
 
         self.fit_degree = add_int_box(
             track_layout,
             self.fit_degree_default,
-            1,
+            2,
             5,
             "Fit degree",
-            row=1,
+            row=2,
             tooltip="Degree of polynomial to fit to the track.",
         )
 
@@ -146,7 +156,7 @@ def add_track_panel(self, row):
             1,
             "Spline smoothing",
             0.1,
-            row=2,
+            row=3,
             tooltip="How closely or not to fit the points "
             "(lower numbers fit more closely, for "
             "a less smooth interpolation).",
@@ -158,7 +168,7 @@ def add_track_panel(self, row):
             1,
             10000,
             "Spline points",
-            row=3,
+            row=4,
             tooltip="How many points are sampled from the "
             "interpolation (used for the summary).",
         )
@@ -294,6 +304,9 @@ def run_track_analysis(self, override=False):
                 choice = True  # for debugging
 
             if choice:
+                if self.save_checkbox.isChecked():
+                    self.parent.run_save()
+
                 print("Running track analysis")
                 self.splines, self.spline_names = track_analysis(
                     self.parent.viewer,

tests/conftest.py

@@ -27,8 +27,15 @@ def segmentation_widget(make_napari_viewer):
     return widget
 
 
-@pytest.fixture
+@pytest.fixture(scope="function")
 def segmentation_widget_with_data_atlas_space(tmp_path, segmentation_widget):
+    """
+    Fixture to load a brainreg directory into the segmentation widget.
+    Data is copied to tmpdir so that when it's loaded, so all the paths
+    are set correctly.
+    The manual segmentation data is then deleted so that saving/export
+    can be properly tested
+    """
     tmp_input_dir = tmp_path / "brainreg_output"
     shutil.copytree(brainreg_dir, tmp_input_dir)
     segmentation_widget.standard_space = True
@@ -37,4 +44,6 @@ def segmentation_widget_with_data_atlas_space(tmp_path, segmentation_widget):
     )
     segmentation_widget.directory = Path(tmp_input_dir)
     segmentation_widget.load_brainreg_directory()
+    # delete manual segmentation data to ensure it's saved correctly in tests
+    shutil.rmtree(segmentation_widget.paths.main_directory)
     return segmentation_widget

tests/data/brainreg_output/manual_segmentation/standard_space/regions/summary.csv

@@ -1,2 +1,2 @@
 region,volume_mm3,axis_0_min_um,axis_1_min_um,axis_2_min_um,axis_0_max_um,axis_1_max_um,axis_2_max_um,axis_0_center_um,axis_1_center_um,axis_2_center_um
-test_region,1.95,123,29,46,142,65,80,132,46,62
+test_region,1.95,6150.0,1450.0,2300.0,7100.0,3250.0,4000.0,6600.0,2329.8173076923076,3141.2339743589746

tests/tests/test_integration/test_gui/test_regions.py → tests/tests/test_integration/test_gui/test_region_ui_functionality.py

@@ -1,8 +1,11 @@
 from filecmp import cmp
 from pathlib import Path
+from time import sleep
 
+import numpy as np
 import pandas as pd
 import pytest
+from tifffile import imread
 
 brainreg_dir = Path.cwd() / "tests" / "data" / "brainreg_output"
 validate_regions_dir = (
@@ -11,8 +14,8 @@
 
 
 @pytest.fixture
-def test_regions_dir(tmpdir):
-    tmp_input_dir = tmpdir / "brainreg_output"
+def test_regions_dir(tmp_path):
+    tmp_input_dir = tmp_path / "brainreg_output"
     test_regions_dir = (
         tmp_input_dir / "manual_segmentation" / "standard_space" / "regions"
     )
@@ -59,23 +62,57 @@ def test_add_existing_region(
     assert len(segmentation_widget_with_data_atlas_space.label_layers) == 2
 
 
-def test_region_analysis(
+def test_region_analysis_without_save(
     segmentation_widget_with_data_atlas_space, test_regions_dir
 ):
+    segmentation_widget_with_data_atlas_space.region_seg.calculate_volumes_checkbox.setChecked(
+        True
+    )
+    segmentation_widget_with_data_atlas_space.region_seg.summarise_volumes_checkbox.setChecked(
+        True
+    )
     segmentation_widget_with_data_atlas_space.region_seg.run_region_analysis(
         override=True
     )
-    region_csv_validate = pd.read_csv(validate_regions_dir / "test_region.csv")
-    region_csv_test = pd.read_csv(test_regions_dir / "test_region.csv")
-    pd.testing.assert_frame_equal(region_csv_test, region_csv_validate)
 
-    summary_csv_validate = pd.read_csv(validate_regions_dir / "summary.csv")
-    summary_csv_test = pd.read_csv(test_regions_dir / "summary.csv")
-    pd.testing.assert_frame_equal(summary_csv_test, summary_csv_validate)
+    # ensure data is saved before it is loaded again
+    sleep(8)
+    check_analysis(test_regions_dir, validate_regions_dir)
+
+    # check saving didn't happen (default)
+    test_saved_region = Path(test_regions_dir / "test_region.tiff")
+    assert test_saved_region.exists() is False
+
+
+def test_region_analysis_with_save(
+    segmentation_widget_with_data_atlas_space, test_regions_dir
+):
+    segmentation_widget_with_data_atlas_space.region_seg.calculate_volumes_checkbox.setChecked(
+        True
+    )
+    segmentation_widget_with_data_atlas_space.region_seg.summarise_volumes_checkbox.setChecked(
+        True
+    )
+    segmentation_widget_with_data_atlas_space.region_seg.save_checkbox.setChecked(
+        True
+    )
+    segmentation_widget_with_data_atlas_space.region_seg.run_region_analysis(
+        override=True
+    )
+
+    # ensure data is saved before it is loaded again
+    sleep(8)
+    check_analysis(test_regions_dir, validate_regions_dir)
+    check_saving(test_regions_dir, validate_regions_dir)
 
 
-def test_region_save(segmentation_widget_with_data_atlas_space):
+def test_region_save(
+    segmentation_widget_with_data_atlas_space, test_regions_dir
+):
     segmentation_widget_with_data_atlas_space.save(override=True)
+    # ensure data is saved before it is loaded again
+    sleep(8)
+    check_saving(test_regions_dir, validate_regions_dir)
 
 
 def test_region_export(
@@ -84,7 +121,26 @@ def test_region_export(
     segmentation_widget_with_data_atlas_space.export_to_brainrender(
         override=True
     )
+
+    # ensure data is saved before it is loaded again
+    sleep(8)
     cmp(
         validate_regions_dir / "test_region.obj",
         test_regions_dir / "test_region.obj",
     )
+
+
+def check_analysis(test_regions_dir, validate_regions_dir):
+    region_csv_validate = pd.read_csv(validate_regions_dir / "test_region.csv")
+    region_csv_test = pd.read_csv(test_regions_dir / "test_region.csv")
+    pd.testing.assert_frame_equal(region_csv_test, region_csv_validate)
+
+    summary_csv_validate = pd.read_csv(validate_regions_dir / "summary.csv")
+    summary_csv_test = pd.read_csv(test_regions_dir / "summary.csv")
+    pd.testing.assert_frame_equal(summary_csv_test, summary_csv_validate)
+
+
+def check_saving(test_regions_dir, validate_regions_dir):
+    image_validate = imread(validate_regions_dir / "test_region.tiff")
+    image_test = imread(test_regions_dir / "test_region.tiff")
+    np.testing.assert_array_equal(image_test, image_validate)