Initial commit

pyproject.toml

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+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "ploc"
+version = "0.1.0"
+description = "Localizing particles in 3D."
+readme = "README.md"
+requires-python = ">=3.12"
+license = { text = "GPL-3.0-or-later" }
+authors = [{ name = "Martin Laasmaa", email = "martin@sysbio.ioc.ee" }]
+
+dependencies = [
+    "numpy",
+    "scipy",
+    "matplotlib",
+    "tifffile",
+    "czifile",
+    "roifile",
+    "xmltodict",
+    "imagecodecs",
+    "xlsxwriter",
+    "openpyxl",
+]
+
+[project.optional-dependencies]
+dev = ["pytest", "black", "flake8"]
+
+[project.scripts]
+ploc-gui = "ploc.ploc_app:main"
+
+[tool.setuptools]
+package-dir = { "" = "src" }
+
+[tool.setuptools.packages.find]
+where = ["ploc"]
+
+
+[tool.black]
+line-length = 140
+target-version = ['py310']

src/ploc/io/image.py

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+from pathlib import Path
+from ploc.io.read_zeiss import ZeissData
+
+
+class Image:
+    def __init__(self, filename: Path):
+        self.filename = filename
+        if filename.suffix == ".czi":
+            self._read_czi()
+        elif filename.suffix == ".tif":
+            self._read_tif()
+        else:
+            raise ValueError(f"Unsupported file format: {filename.suffix}")
+
+    def _read_czi(self):
+        pass
+
+    def _read_tif(self):
+        pass

src/ploc/io/read_zeiss.py

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+import numpy as np
+
+import czifile as czi
+import xml.etree.ElementTree as ET
+
+
+class ZeissData:
+
+    def __init__(self, filename):
+
+        self.filename = filename
+        self._initialize()
+
+    def _initialize(self):
+        czi_obj = czi.CziFile(self.filename)
+        axes = czi_obj.axes
+        tmp = czi_obj.asarray()
+        self.axes = ""
+        # print(tmp.shape)
+        for i, size in enumerate(tmp.shape):
+            if size > 1:
+                self.axes += axes[i]
+
+        self.image = np.squeeze(tmp)
+        self.shape = self.image.shape
+        self.ndim = len(self.shape)
+        self.origin = np.array([[0, i1] for i1 in self.shape])
+
+        self.metadata = czi_obj.metadata()
+        root = ET.fromstring(self.metadata)
+        for d in root.findall("./Metadata/Scaling/Items/Distance"):
+            el = d.attrib["Id"]
+            if el in self.axes:
+                setattr(self, "p" + el.lower(), float(d[0].text) * 1e6)
+
+        # print(self.axes)
+        # print(self.shape)
+
+        # for k, v in kwargs.items():
+        #     if k in ImageJ.allowed_kwargs:
+        #         setattr(self, k, v)
+        #     else:
+        #         print(k, "is not allowed keyword argument!")
+
+    def get_channle_info(self, channelID):
+        #  print(self.metadata)
+        root = ET.fromstring(self.metadata)
+        # for child in root:
+        #     print(child.tag, child.attrib)
+        # print(type(root))
+
+        na = None
+        refractive_index = None
+        for _child in root.findall("./Metadata/Information/Instrument/Objectives/Objective"):
+            for _ch in _child:
+                if _ch.tag == "LensNA":
+                    na = _ch.text
+
+                if _ch.tag == "ImmersionRefractiveIndex":
+                    refractive_index = _ch.text
+            # print(_child.tag, _child.attrib, _child[1].tag, type(_child.tag), type(_child.attrib))
+
+        em, ex = None, None
+        for _child in root.findall("./Metadata/DisplaySetting/Channels"):
+
+            for _ch in _child.findall("./Channel"):
+                if _ch.attrib["Id"] == f"Channel:{channelID}":
+                    for _c in _ch:
+                        if _c.tag == "DyeMaxEmission":
+                            em = _c.text
+                        if _c.tag == "DyeMaxExcitation":
+                            ex = _c.text
+                        if ex is not None and em is not None:
+                            break
+
+            #             print(_c.tag)
+            #         print(_ch.tag, _ch.attrib["Id"], _ch.text)
+
+            # print()
+            # print(_child.tag, _child.attrib, _child[1].tag, type(_child.tag), type(_child.attrib))
+
+        info = {
+            "MainEmissionWavelength": float(em),
+            "MainExcitationWavelength": float(ex),
+            "ObjectiveNA": float(na),
+            "RefractiveIndex": float(refractive_index),
+        }
+        return info
+
+    def get_stack(self, channleID):
+        spacings = dict(X=self.px * 1e-6, Y=self.py * 1e-6, Z=self.pz * 1e-6)
+
+        return self.image[channleID], spacings, self.get_channle_info(channleID)

src/ploc/ploc_app.py

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+import argparse
+from ploc.io.image import Image
+
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument("image", type=str, help="Image file to process")
+    args = parser.parse_args()
+
+    print("Hello World")
+
+
+if __name__ == "__main__":
+    main()