Merge pull request #68 from pr4deepr/master

Add support for importing ellipse and freehand ROIs from ImageJ

docs/source/user_guides/viewer/modules/roi_manager.rst

@@ -44,7 +44,7 @@ Add ROI button              Add Polygon ROI (Manual mode)
 Show all                    Show all ROIs in the viewer
 Live plot                   Live update of the curve plot with changes (Manual mode)
 Plot                        Plot the curves (Manual mode)
-Import from ImageJ          Import ROIs from an ImageJ ROIs zip file (Manual mode)
+Import from ImageJ          Import ROIs from an ImageJ ROIs zip file (Manual mode). Freehand ROIs are downsampled by 5.
 Switch to manual ...        Switch to Manual mode. Clears CNMF(E) ROIs.
 
 ROIs list                   Color-coded list of ROIs.

mesmerize/viewer/modules/roi_manager_modules/managers.py

@@ -21,7 +21,7 @@
 from matplotlib import cm as matplotlib_color_map
 from tqdm import tqdm
 import logging
-
+from itertools import product as iter_product
 
 if HAS_CAIMAN:
     from caiman.utils.visualization import get_contours as caiman_get_contours
@@ -178,11 +178,32 @@ def import_from_imagej(self, path: str):
         """
         ij_roi = read_imagej(path)
         for k in ij_roi.keys():
-            xs = ij_roi[k]['x']
-            ys = ij_roi[k]['y']
-            ps = list(zip(xs, ys))
-
-            roi = ManualROI.from_positions(positions=ps,
+            if ij_roi[k]['type'] in ('oval', 'rectangle'):
+                width=ij_roi[k]['width']
+                height=ij_roi[k]['height']
+                left=ij_roi[k]['left']
+                top=ij_roi[k]['top']
+                if ij_roi[k]['type'] == 'oval':
+                    x_bottom=left
+                    y_bottom=top+height
+                    ps=[x_bottom,y_bottom,width,height]
+                    roi= ManualROI.from_ellipse(positions=ps,
+                                           curve_plot_item=self.get_plot_item(),
+                                           view_box=self.vi.viewer.getView())
+                else:
+                    ps=list(iter_product((left,left+width),(top,top+height)))
+                    ps[2],ps[3]=ps[3],ps[2] #swap coordinates so it draws coordinates in sequence 
+            elif (ij_roi[k]['type']=='freehand'):
+                #freehand ROIs have large number of datapoints, so reducing it by a fifth
+                xs = ij_roi[k]['x'][::5]
+                ys = ij_roi[k]['y'][::5]
+                ps = list(zip(xs, ys))
+            else:
+                xs = ij_roi[k]['x']
+                ys = ij_roi[k]['y']
+                ps = list(zip(xs, ys))                                      
+            if ij_roi[k]['type'] != 'oval':
+                roi = ManualROI.from_positions(positions=ps,
                                            curve_plot_item=self.get_plot_item(),
                                            view_box=self.vi.viewer.getView())
             self.roi_list.append(roi)

mesmerize/viewer/modules/roi_manager_modules/roi_types.py

@@ -386,6 +386,16 @@ def from_positions(cls, curve_plot_item: pg.PlotDataItem, view_box: pg.ViewBox,
         roi_graphics_object = pg.PolyLineROI(positions=positions, closed=True, removable=True)
         return cls(curve_plot_item=curve_plot_item, roi_graphics_object=roi_graphics_object, view_box=view_box)
 
+    @classmethod
+    def from_ellipse(cls, curve_plot_item: pg.PlotDataItem, view_box: pg.ViewBox, positions: list):
+        """
+        Create an ellipse from a list of positions when importing ImageJ ROIs.
+
+        :param positions:  [origin_bottom_x, origin_bottom_y, width, height]
+        """
+
+        roi_graphics_object = pg.EllipseROI(pos=[positions[0], positions[1]], size=[int(positions[2]), int(positions[3])], removable=True)
+        return cls(curve_plot_item=curve_plot_item, roi_graphics_object=roi_graphics_object, view_box=view_box)
 
 class ScatterROI(BaseROI):
     """A class for unmoveable ROIs drawn using scatter points"""