From 9c4c39fb39a651a5ab32eeec5fc9b143c1200386 Mon Sep 17 00:00:00 2001
From: Martin Laasmaa <martin@sysbio.ioc.ee>
Date: Fri, 12 Dec 2025 23:52:34 +0200
Subject: [PATCH] Adding image converter

---
 src/utils/image_converters.py | 122 ++++++++++++++++++++++++++++++++++
 1 file changed, 122 insertions(+)
 create mode 100644 src/utils/image_converters.py

diff --git a/src/utils/image_converters.py b/src/utils/image_converters.py
new file mode 100644
index 0000000..17b52eb
--- /dev/null
+++ b/src/utils/image_converters.py
@@ -0,0 +1,122 @@
+import numpy as np
+
+from roifile import ImagejRoi
+from tifffile import TiffFile, TiffWriter
+from pathlib import Path
+
+
+class UT:
+    """
+    Docstring for UT
+
+    Operetta files along with rois drawn in ImageJ
+    """
+
+    def __init__(self, roifile_fn: Path):
+        self.roifile_fn = roifile_fn
+        self.rois = ImagejRoi.fromfile(self.roifile_fn)
+        self.stem = self.roifile_fn.stem.strip("-RoiSet")
+        self.image, self.image_props = self._load_images()
+
+    def _load_images(self):
+        """Loading sequence of tif files
+        array sequence is CZYX
+        """
+        print(self.roifile_fn.parent, self.stem)
+        fns = list(self.roifile_fn.parent.glob(f"{self.stem}*.tif*"))
+        stems = [fn.stem.split(self.stem)[-1] for fn in fns]
+        n_ch = len(set([stem.split("-ch")[-1].split("t")[0] for stem in stems]))
+        n_p = len(set([stem.split("-")[0] for stem in stems]))
+        n_t = len(set([stem.split("t")[1] for stem in stems]))
+        print(n_ch, n_p, n_t)
+
+        with TiffFile(fns[0]) as tif:
+            img = tif.asarray()
+            w, h = img.shape
+            dtype = img.dtype
+            self.image_props = {
+                "channels": n_ch,
+                "planes": n_p,
+                "tiles": n_t,
+                "width": w,
+                "height": h,
+                "dtype": dtype,
+            }
+
+        image_stack = np.zeros((n_ch, n_p, w, h), dtype=dtype)
+        for fn in fns:
+            with TiffFile(fn) as tif:
+                img = tif.asarray()
+                stem = fn.stem.split(self.stem)[-1]
+                ch = int(stem.split("-ch")[-1].split("t")[0])
+                p = int(stem.split("-")[0].lstrip("p"))
+                t = int(stem.split("t")[1])
+                print(fn.stem, "ch", ch, "p", p, "t", t)
+                image_stack[ch - 1, p - 1] = img
+
+        print(image_stack.shape)
+
+        return image_stack, self.image_props
+
+    @property
+    def width(self):
+        return self.image_props["width"]
+
+    @property
+    def height(self):
+        return self.image_props["height"]
+
+    @property
+    def nchannels(self):
+        return self.image_props["channels"]
+
+    @property
+    def nplanes(self):
+        return self.image_props["planes"]
+
+    def export_rois(
+        self,
+        path: Path,
+        subfolder: str = "labels",
+        class_index: int = 0,
+    ):
+        """Export rois to a file"""
+        with open(path / subfolder / f"{self.stem}.txt", "w") as f:
+            for roi in self.rois:
+                # TODO add image coordinates normalization
+                coords = ""
+                for x, y in roi.subpixel_coordinates:
+                    coords += f"{x/self.width} {y/self.height}"
+                f.write(f"{class_index} {coords}\n")
+
+        return
+
+    def export_image(
+        self,
+        path: Path,
+        subfolder: str = "images",
+        plane_mode: str = "max projection",
+        channel: int = 0,
+    ):
+        """Export image to a file"""
+
+        if plane_mode == "max projection":
+            self.image = np.max(self.image[channel], axis=0)
+            print(self.image.shape)
+
+        with TiffWriter(path / subfolder / f"{self.stem}.tif") as tif:
+            tif.write(self.image)
+
+
+if __name__ == "__main__":
+    import argparse
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument("input", type=Path)
+    parser.add_argument("output", type=Path)
+    args = parser.parse_args()
+
+    for rfn in args.input.glob("*.zip"):
+        ut = UT(rfn)
+        ut.export_rois(args.output, class_index=0)
+        ut.export_image(args.output, plane_mode="max projection", channel=0)