feat(export): export traces as ImageJ .roi files

Author: quasiTriestino

PyReconstruct/modules/backend/exports/roi_export.py

@@ -0,0 +1,54 @@
+"""ImageJ .roi file exporter."""
+
+from pathlib import Path
+from typing import Union, List, Tuple
+
+from roifile import ImagejRoi, ROI_TYPE
+
+from PyReconstruct.modules.datatypes import Trace
+
+
+coordinates = List[Tuple[float, float]]
+filepath = Union[str, Path]
+
+
+class RoiExporter:
+
+    def __init__(self, trace: Trace, mag: float, img_height: int):
+
+        self.trace = trace
+        self.coords = self.get_coords(mag, img_height)
+        self.roi = self.get_roi()
+
+    def export_roi(self, directory: filepath) -> None:
+        """Export an ImageJ .roi file to a directory."""
+
+        if not isinstance(directory, Path):
+            directory = Path(directory)
+
+        ## Assume each trace uniquely named for now
+        output_fp = directory / f"{self.trace.name}-exported.roi"
+
+        self.roi.tofile(output_fp)
+
+        return None
+
+    def get_roi(self) -> ImagejRoi:
+        """Get an ImageJ roi object."""
+
+        roi = ImagejRoi.frompoints(self.coords)
+        
+        roi.roitype = ROI_TYPE.POLYGON if self.trace.closed else ROI_TYPE.FREEHAND
+        roi.name = self.trace.name
+
+        return roi
+
+    def get_coords(self, mag, img_height) -> coordinates:
+        """Get coordinates as pixels."""
+
+        coords = self.trace.asPixels(mag, img_height, subpix=True)
+
+        return [
+            (round(x, 3), round(y, 3)) for x, y in coords
+        ]
+

PyReconstruct/modules/backend/imports/imagej_roi.py

@@ -24,7 +24,7 @@ def __init__(self, roi_fp):
     def trace_closed_p(self) -> bool:
         """Return true if trace closed else false."""
 
-        roi_closed_types = [0, 1, 2, 3, 9, 10]
+        roi_closed_types = [0, 1, 2, 3, 7, 9, 10]
 
         if self.roi.roitype in roi_closed_types:
             return True

PyReconstruct/modules/calc/image.py

@@ -24,22 +24,33 @@ def getImgDims(img_fp: Union[str, Path]) -> Tuple[height, width]:
         return img.shape
 
 
-def point_2_pix(coordinate: Sequence[float], mag: float, height: height) -> Tuple[int, int]:
+def point_2_pix(
+        coordinate: Sequence[float],
+        mag: float, height: height,
+        subpix: bool=False
+) -> Union[Tuple[float, float], Tuple[int, int]]:
             """Convert a single point to pixels."""
 
-            x = int(coordinate[0] // mag)
-            y = int(height - (coordinate[1] // mag))
+            x = coordinate[0] / mag
+            y = height - (coordinate[1] / mag)
+
+            if not subpix:
+                
+                x = int(x)
+                y = int(y)
 
             return x, y
 
 
 def point_list_2_pix(
         points: List[Tuple[int, int]],
         mag: float,
-        height: int) -> List[Tuple[int, int]]:
+        height: int,
+        subpix: bool=False
+) -> List[Tuple[int, int]]:
     """Convert a points list to pixels."""
 
-    mapped_points = map(lambda x: point_2_pix(x, mag, height), points)
+    mapped_points = map(lambda x: point_2_pix(x, mag, height, subpix), points)
     return list(mapped_points)
 
 

PyReconstruct/modules/datatypes/trace.py

@@ -75,10 +75,10 @@ def add(self, point : tuple):
         """
         self.points.append(point)
 
-    def asPixels(self, mag: float, img_height: int):
+    def asPixels(self, mag: float, img_height: int, subpix: bool=False):
         """Return points as a list of (x, y) pixels on an image."""
 
-        return point_list_2_pix(self.points, mag, img_height)
+        return point_list_2_pix(self.points, mag, img_height, subpix)
 
     def isSameTrace(self, other) -> bool:
         """Check if traces have the same name, color, and points.
@@ -568,7 +568,7 @@ def smooth(self, window: int, spacing: Union[int, float]) -> None:
             smoothed = smoothed[:-1]
 
         self.points = smoothed
-    
+
     @staticmethod
     def get_scale_bar():
         """Return a scale bar trace object."""

PyReconstruct/modules/gui/main/main_imports.py

@@ -116,6 +116,8 @@
     Roi
 )
 
+from PyReconstruct.modules.backend.exports.roi_export import RoiExporter
+
 from PyReconstruct.modules.backend.remote import (
     download_vol_as_tifs
 )

PyReconstruct/modules/gui/main/main_window.py

@@ -1180,11 +1180,22 @@ def exportSectionPNG(self):
     def exportROIFiles(self):
         """Export traces as ImageJ .roi files."""
 
-        #notify("Traces exported as .roi files.")
+        directory = FileDialog.get("dir", self, "Select directory to export .roi files.")
 
-        notify("This feature is still being implemented! Stay tuned!")
+        if not directory:
+            return
+
+        h, _ = self.field.section.img_dims
+        mag = self.field.section.mag
+
+        contours = self.field.section.contours
+
+        for _, contour in contours.items():
+            for trace in contour.traces:
+                exporter = RoiExporter(trace, mag, h)
+                exporter.export_roi(directory)
 
-        pass
+        notify("Traces exported as .roi files.")
 
     def downloadExample(self):
         """Download example kharris2015 images to local machine."""

PyReconstruct/modules/gui/main/menubar.py

@@ -225,9 +225,9 @@ def return_section_menu(self):
                 "text": "Export",
                 "opts":
                 [
-                    ("exportsvg_act", "As svg...", "", self.exportSectionSVG),
-                    ("exportpng_act", "As png...", "", self.exportSectionPNG),
-                    ("exportroi_act", "As png...", "", self.exportROIFiles)
+                    ("exportsvg_act", "As .svg...", "", self.exportSectionSVG),
+                    ("exportpng_act", "As .png...", "", self.exportSectionPNG),
+                    ("exportroi_act", "As .roi...", "", self.exportROIFiles)
                 ]
             }
         ]