Add roi_creator test to test creating an ROI

Author: damskii9992

examples/plotting.ipynb

@@ -18,7 +18,7 @@
    "source": [
     "import scipp as sc\n",
     "\n",
-    "from easyimaging import Measurement\n"
+    "from easyimaging import Measurement"
    ]
   },
   {
@@ -36,7 +36,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "measurement = Measurement.from_scitiff(filename = '../small_scitiff.tiff')"
+    "measurement = Measurement.from_scitiff(filename='../small_scitiff.tiff')"
    ]
   },
   {
@@ -56,9 +56,9 @@
    "source": [
     "measurement = Measurement.from_tiff_stack(\n",
     "    filename='../small_tiff.tiff',\n",
-    "    time_of_flights=sc.arange('t', 0, 240, 1, unit='s'), # mandatory\n",
-    "    #x_positions=sc.arange('x', 0, 50, 1, unit='mm'), # optional\n",
-    "    #y_positions=sc.arange('y', 0, 50, 1, unit='mm'), # optional\n",
+    "    time_of_flights=sc.arange('t', 0, 240, 1, unit='s'),  # mandatory\n",
+    "    # x_positions=sc.arange('x', 0, 50, 1, unit='mm'), # optional\n",
+    "    # y_positions=sc.arange('y', 0, 50, 1, unit='mm'), # optional\n",
     ")"
    ]
   },
@@ -99,8 +99,8 @@
    "outputs": [],
    "source": [
     "tof = sc.arange('t', 0, 10, 1, unit='s')\n",
-    "x = sc.arange('x', 0, 7, 1, unit='m') # optional\n",
-    "y = sc.arange('y', 0, 7, 1, unit='m') # optional\n",
+    "x = sc.arange('x', 0, 7, 1, unit='m')  # optional\n",
+    "y = sc.arange('y', 0, 7, 1, unit='m')  # optional\n",
     "data = sc.ones(dims=['x', 'y', 't'], shape=[6, 6, 10])\n",
     "scipp_array = sc.DataArray(data=data, coords={'tof': tof, 'x': x, 'y': y})"
    ]
@@ -160,8 +160,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "display(measurement.x_positions) # If available\n",
-    "display(measurement.y_positions) # If available\n",
+    "display(measurement.x_positions)  # If available\n",
+    "display(measurement.y_positions)  # If available\n",
     "display(measurement.time_of_flights)"
    ]
   },
@@ -220,7 +220,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "measurement.rebin(dimensions={'x':2, 'y':2})"
+    "measurement.rebin(dimensions={'x': 2, 'y': 2})"
    ]
   },
   {
@@ -386,11 +386,11 @@
    "outputs": [],
    "source": [
     "roi = RectROI(\n",
-    "    x_pixel_range=(15, 35), # mandatory\n",
-    "    y_pixel_range=(15, 35), # mandatory\n",
-    "    x_range=(sc.scalar(-0.05, unit='m'), sc.scalar(0.05, unit='m')), # optional\n",
-    "    y_range=(sc.scalar(-0.05, unit='m'), sc.scalar(0.05, unit='m')), # optional\n",
-    "    unique_name='center_roi' # custom name for the ROI, optional, has to be unique in computer memory\n",
+    "    x_pixel_range=(15, 35),  # mandatory\n",
+    "    y_pixel_range=(15, 35),  # mandatory\n",
+    "    x_range=(sc.scalar(-0.05, unit='m'), sc.scalar(0.05, unit='m')),  # optional\n",
+    "    y_range=(sc.scalar(-0.05, unit='m'), sc.scalar(0.05, unit='m')),  # optional\n",
+    "    unique_name='center_roi',  # custom name for the ROI, optional, has to be unique in computer memory\n",
     ")"
    ]
   },
@@ -517,7 +517,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "measurement.regions_of_interest[1].unique_name = 'best_roi' # Requires that an ROI was drawn using the roi_creator tool."
+    "measurement.regions_of_interest[1].unique_name = 'best_roi'  # Requires that an ROI was drawn using the roi_creator tool."
    ]
   },
   {

pixi.lock

@@ -464,11 +464,13 @@ def slicer_plot(self, **kwargs) -> None:
             See https://scipp.github.io/plopp/generated/plopp.slicer.html for options.
         """
         slicer_kwargs_defaults = self._plot_defaults()
-        slicer_kwargs_defaults.update({
-            'title': self.display_name + ' - Time of Flight Slicer',
-            'keep': ['x_pixels', 'y_pixels'] if not self._has_physical_coords else ['x', 'y'],
-            'mode': 'single'
-        })
+        slicer_kwargs_defaults.update(
+            {
+                'title': self.display_name + ' - Time of Flight Slicer',
+                'keep': ['x_pixels', 'y_pixels'] if not self._has_physical_coords else ['x', 'y'],
+                'mode': 'single',
+            }
+        )
         slicer_kwargs_defaults['coords'].append('tof')
 
         # Overwrite defaults with any user-provided kwargs
@@ -494,14 +496,16 @@ def spectrum_inspector(self, **kwargs) -> None:
         """
         inspector_kwargs_defaults = self._plot_defaults()
         inspector_kwargs_defaults['ymax'] = inspector_kwargs_defaults['cmax']
-        inspector_kwargs_defaults.update({
-            'title': self.display_name + ' - Spectrum Inspector',
-            'ymin': 0.0,
-            'dim': 't',
-            'orientation': 'vertical',
-            'operation': 'mean',
-            'mode': 'point',
-        })
+        inspector_kwargs_defaults.update(
+            {
+                'title': self.display_name + ' - Spectrum Inspector',
+                'ymin': 0.0,
+                'dim': 't',
+                'orientation': 'vertical',
+                'operation': 'mean',
+                'mode': 'point',
+            }
+        )
         # Overwrite defaults with any user-provided kwargs
         inspector_kwargs_defaults.update(kwargs)
 
@@ -535,21 +539,20 @@ def roi_creator(self, **kwargs) -> None:
 
         roi_selector_kwargs_defaults = self._plot_defaults()
         roi_selector_kwargs_defaults['ymax'] = roi_selector_kwargs_defaults['cmax']
-        roi_selector_kwargs_defaults.update({
-            'title': self.display_name + ' - ROI Creator',
-            'ymin': 0.0,
-            'dim': 't',
-            'orientation': 'vertical',
-            'operation': 'mean',
-            'mode': 'rectangle',
-        })
+        roi_selector_kwargs_defaults.update(
+            {
+                'title': self.display_name + ' - ROI Creator',
+                'ymin': 0.0,
+                'dim': 't',
+                'orientation': 'vertical',
+                'operation': 'mean',
+                'mode': 'rectangle',
+            }
+        )
         # Overwrite defaults with any user-provided kwargs
         roi_selector_kwargs_defaults.update(kwargs)
-            
-        plots = pp.inspector(
-            self._data_array, 
-            **roi_selector_kwargs_defaults
-            )
+
+        plots = pp.inspector(self._data_array, **roi_selector_kwargs_defaults)
 
         # -------------------------------------------------------------------------------------------------
         # -------------------------- Plot the existing ROIs on the plot -----------------------------------
@@ -574,11 +577,13 @@ def roi_creator(self, **kwargs) -> None:
                 x_end = roi.x_pixel_end
                 y_end = roi.y_pixel_end
             plots[0].toolbar['inspect']._tool.start()
-            plots[0].toolbar['inspect']._tool.click(x=x_start, y=y_start, button=1) # button 1 is left-click
+            plots[0].toolbar['inspect']._tool.click(x=x_start, y=y_start, button=1)  # button 1 is left-click
             plots[0].toolbar['inspect']._tool.click(x=x_end, y=y_end, button=1)
             plots[0].toolbar['inspect']._tool.stop()
             if hasattr(roi, '_rect_ids'):
-                roi._rect_ids.append(plots[0].toolbar['inspect']._tool.children[-1].id)  # Store the rectangle ID for reference when dragging corners  # noqa: E501
+                roi._rect_ids.append(
+                    plots[0].toolbar['inspect']._tool.children[-1].id
+                )  # Store the rectangle ID for reference when dragging corners  # noqa: E501
             else:
                 roi._rect_ids = [plots[0].toolbar['inspect']._tool.children[-1].id]
 
@@ -622,27 +627,20 @@ def delete_rectangle_roi(rect, roi_list):
         # -------------------------- Connect the callbacks to the RectangleTool ---------------------------
         # -------------------------------------------------------------------------------------------------
 
-        plots[0].toolbar['inspect']._tool.on_create(partial(
-            create_rectangle_roi, 
-            roi_list=self.regions_of_interest, 
-            data_array=self._data_array
-            ))
-        
-        plots[0].toolbar['inspect']._tool.on_change(partial(
-            edit_rectangle_roi, 
-            roi_list=self.regions_of_interest,
-            data_array=self._data_array
-            ))
-        
-        plots[0].toolbar['inspect']._tool.on_remove(partial(
-            delete_rectangle_roi,
-            roi_list=self.regions_of_interest
-            ))
+        plots[0].toolbar['inspect']._tool.on_create(
+            partial(create_rectangle_roi, roi_list=self.regions_of_interest, data_array=self._data_array)
+        )
+
+        plots[0].toolbar['inspect']._tool.on_change(
+            partial(edit_rectangle_roi, roi_list=self.regions_of_interest, data_array=self._data_array)
+        )
+
+        plots[0].toolbar['inspect']._tool.on_remove(partial(delete_rectangle_roi, roi_list=self.regions_of_interest))
 
         plots[0].toolbar['inspect'].tooltip = 'Activate ROI creator tool'
 
         return plots
-        
+
     def spectrum(self, roi: RectROI | str | None = None) -> sc.DataArray:
         """
         Extract the spectrum (intensity vs. time-of-flight) for a specified region of interest (ROI).
@@ -752,11 +750,13 @@ def _validate_provided_coord(
         return coord
 
     @staticmethod
-    def _ranges_from_rectangle(rect, data_array: sc.DataArray) -> tuple[tuple[int, int], None] | tuple[tuple[int, int], tuple[sc.Variable, sc.Variable]]:  # noqa: E501
-        # To be used in the roi_selector method to convert the rectangle vertices to pixel and 
+    def _ranges_from_rectangle(
+        rect, data_array: sc.DataArray
+    ) -> tuple[tuple[int, int], None] | tuple[tuple[int, int], tuple[sc.Variable, sc.Variable]]:  # noqa: E501
+        # To be used in the roi_selector method to convert the rectangle vertices to pixel and
         # physical coordinate ranges for the new ROI.
         x_vertex_list, y_vertex_list = rect.vertices
-        if 'x' not in data_array.coords: # If 'x' exists, so does 'y' due to our constructor.
+        if 'x' not in data_array.coords:  # If 'x' exists, so does 'y' due to our constructor.
             x_pixel_range = (int(min(x_vertex_list)), int(max(x_vertex_list)))
             y_pixel_range = (int(min(y_vertex_list)), int(max(y_vertex_list)))
             x_range = None
@@ -768,7 +768,7 @@ def _ranges_from_rectangle(rect, data_array: sc.DataArray) -> tuple[tuple[int, i
             x_range = (sc.scalar(min(x_vertex_list), unit=x_unit), sc.scalar(max(x_vertex_list), unit=x_unit))
             y_range = (sc.scalar(min(y_vertex_list), unit=y_unit), sc.scalar(max(y_vertex_list), unit=y_unit))
 
-            sliced_data_array = data_array['x', x_range[0]:x_range[1]]['y', y_range[0]:y_range[1]]
+            sliced_data_array = data_array['x', x_range[0] : x_range[1]]['y', y_range[0] : y_range[1]]
 
             sliced_x_pixels = sliced_data_array.coords['x_pixels'].values
             sliced_y_pixels = sliced_data_array.coords['y_pixels'].values
@@ -784,8 +784,8 @@ def _plot_defaults(self):
             'cmin': 0.0,
             'cmax': min(3.0, float(self._data_array.max().value * 1.1)),
             'mask_color': 'red',
-            'coords' : ['x_pixels', 'y_pixels'] if not self._has_physical_coords else ['x', 'y'],
+            'coords': ['x_pixels', 'y_pixels'] if not self._has_physical_coords else ['x', 'y'],
         }
 
     def __repr__(self):
-        return f"{self.display_name} with shape {self._data_array.shape} and regions of interest: {[roi.display_name for roi in self.regions_of_interest]}"  # noqa: E501
+        return f'{self.display_name} with shape {self._data_array.shape} and regions of interest: {[roi.display_name for roi in self.regions_of_interest]}'  # noqa: E501

src/easyimaging/measurement/measurement.py

@@ -51,11 +51,7 @@ def __init__(
         else:
             raise ValueError('Both x_range and y_range must be provided together or not at all.')
 
-    def set_pixel_coord_range(
-            self, 
-            x_pixel_range: Sequence[int], 
-            y_pixel_range: Sequence[int]
-            ) -> None:
+    def set_pixel_coord_range(self, x_pixel_range: Sequence[int], y_pixel_range: Sequence[int]) -> None:
         """Set the pixel coordinate ranges for the ROI.
         Parameters:
             x_pixel_range (Sequence[int]): The start and end pixel coordinates in the x direction.
@@ -69,11 +65,7 @@ def set_pixel_coord_range(
         self._x_pixel_start, self._x_pixel_end = sc.array(values=x_pixel_range, dims='x')
         self._y_pixel_start, self._y_pixel_end = sc.array(values=y_pixel_range, dims='y')
 
-    def set_physical_coord_range(
-        self, 
-        x_range: Sequence[sc.Variable], 
-        y_range: Sequence[sc.Variable]
-    ) -> None:
+    def set_physical_coord_range(self, x_range: Sequence[sc.Variable], y_range: Sequence[sc.Variable]) -> None:
         """Set the physical coordinate ranges for the ROI.
         Parameters:
             x_range (Sequence[sc.Variable]): The start and end physical coordinates in the x direction.
@@ -263,22 +255,14 @@ def to_dict(self, skip: List[str] | None = None) -> Dict[str, Any]:
         out_dict['x_pixel_range'] = [int(self.x_pixel_start), int(self.x_pixel_end)]
         out_dict['y_pixel_range'] = [int(self.y_pixel_start), int(self.y_pixel_end)]
         if self._has_physical_coords:
-            out_dict['x_range'] = [{'@module': 'scipp',
-                                    '@version': sc.__version__,
-                                    '@class' : 'scalar',
-                                    'dict' : sc.to_dict(self.x_start)}, 
-                                    {'@module': 'scipp',
-                                    '@version': sc.__version__,
-                                    '@class' : 'scalar',
-                                    'dict' : sc.to_dict(self.x_end)}]
-            out_dict['y_range'] = [{'@module': 'scipp',
-                                    '@version': sc.__version__,
-                                    '@class' : 'scalar',
-                                    'dict' : sc.to_dict(self.y_start)}, 
-                                    {'@module': 'scipp',
-                                    '@version': sc.__version__,
-                                    '@class' : 'scalar',
-                                    'dict' : sc.to_dict(self.y_end)}]
+            out_dict['x_range'] = [
+                {'@module': 'scipp', '@version': sc.__version__, '@class': 'scalar', 'dict': sc.to_dict(self.x_start)},
+                {'@module': 'scipp', '@version': sc.__version__, '@class': 'scalar', 'dict': sc.to_dict(self.x_end)},
+            ]
+            out_dict['y_range'] = [
+                {'@module': 'scipp', '@version': sc.__version__, '@class': 'scalar', 'dict': sc.to_dict(self.y_start)},
+                {'@module': 'scipp', '@version': sc.__version__, '@class': 'scalar', 'dict': sc.to_dict(self.y_end)},
+            ]
         return out_dict
 
     @classmethod

src/easyimaging/measurement/regions.py

@@ -1,4 +1,3 @@
-
 def _is_notebook() -> bool:
     """
     Check if the code is running in a Jupyter notebook environment.
@@ -13,4 +12,3 @@ def _is_notebook() -> bool:
             return False  # Other type (possibly other IDE)
     except NameError:
         return False  # Probably standard Python interpreter
-    

src/easyimaging/utils/jupyter_notebook_utilities.py

@@ -13,4 +13,4 @@ def _to_edges(centers: sc.Variable) -> sc.Variable:
             2 * centers[-1] - interior_edges[-1],
         ],
         dim=centers.dim,
-    )
+    )