Merge pull request #16 from rhoitink/develop

Pull request for v1.6.2

CITATION.cff

@@ -2,10 +2,10 @@
 # Visit https://bit.ly/cffinit to generate yours today!
 
 cff-version: 1.2.0
-title: Simulated Microscopy
-message: >-
-  If you use this software, please cite it using the
-  metadata from this file.
+title: >-
+  Simulated Microscopy: A Python Package for Simulation of
+  Confocal Microscopy Data based on Particle Coordinates
+message: 'If you use this software, please cite using the Zenodo DOI.'
 type: software
 authors:
   - given-names: Leroy Daniël
@@ -15,6 +15,10 @@ authors:
       Soft Condensed Matter & Biophysics, Debye Institute
       for Nanomaterials Science, Utrecht University
     orcid: 'https://orcid.org/0000-0002-3470-0078'
+identifiers:
+  - type: doi
+    value: 10.5281/zenodo.10678180
+    description: Zenodo
 repository-code: 'https://github.com/rhoitink/simulatedmicroscopy'
 url: 'https://rhoitink.github.io/simulatedmicroscopy/'
 abstract: >-
@@ -28,5 +32,5 @@ keywords:
   - point spread function
   - image generation
 license: MIT
-version: "v1.6.1"
+version: v1.6.1
 date-released: '2024-02-19'

src/simulatedmicroscopy/image.py

@@ -6,7 +6,6 @@
 
 import h5py
 import numpy as np
-import scipy.signal
 import skimage.measure
 
 from .input import Coordinates
@@ -162,7 +161,7 @@ def save_h5file(
 
     @classmethod
     def load_h5file(cls, filename: str) -> type[Image]:
-        """Load data from h5 file (custom format)
+        """Load data from h5 file (custom format or HuygensImage)
 
         Parameters
         ----------
@@ -176,19 +175,40 @@ def load_h5file(cls, filename: str) -> type[Image]:
         """
 
         with h5py.File(filename, "r") as f:
-            image = f["Image"][()]
-            pixel_sizes = [
-                float(f[f"Metadata/DimensionScale{dim.upper()}"][()])
-                for dim in list("zyx")
-            ]
-            if "PixelCoordinates" in f["Metadata"]:
-                pixel_coordinates = f["Metadata/PixelCoordinates"][()]
+            root_elements = list(f.keys())
+            if "Image" in root_elements and "Metadata" in root_elements:
+                return cls._load_h5file_custom(f)
             else:
-                pixel_coordinates = None
+                return HuygensImage(filename)
+
+    @staticmethod
+    def _load_h5file_custom(f: h5py.File) -> type[Image]:
+        """Load data from h5 file (custom format)
+
+        Parameters
+        ----------
+        f : h5py.File
+            File to load from
+
+        Returns
+        -------
+        Image
+            Resulting image with correct pixel sizes
+        """
 
-            metadata = dict(f["Metadata"].attrs)
+        image = f["Image"][()]
+        pixel_sizes = [
+            float(f[f"Metadata/DimensionScale{dim.upper()}"][()])
+            for dim in list("zyx")
+        ]
+        if "PixelCoordinates" in f["Metadata"]:
+            pixel_coordinates = f["Metadata/PixelCoordinates"][()]
+        else:
+            pixel_coordinates = None
+
+        metadata = dict(f["Metadata"].attrs)
 
-        im = cls(image=image, pixel_sizes=pixel_sizes, metadata=metadata)
+        im = Image(image=image, pixel_sizes=pixel_sizes, metadata=metadata)
         if pixel_coordinates is not None:
             im.pixel_coordinates = pixel_coordinates
         return im
@@ -398,9 +418,21 @@ def convolve(self, other: type[Image]) -> type[Image]:
                 "Cannot convolve images with different pixel sizes"
             )
 
-        self.image = scipy.signal.convolve(
-            self.image, other.image, mode="same"
-        )
+        try:
+            import cupy as cp
+            from cupyx.scipy import signal as cusignal
+
+            self.image = cusignal.fftconvolve(
+                cp.asarray(self.image), cp.asarray(other.image), mode="same"
+            ).get()
+        except ImportError:
+            # resort to scipy if cupy is not available
+
+            import scipy.signal
+
+            self.image = scipy.signal.convolve(
+                self.image, other.image, mode="same"
+            )
 
         self.is_convolved = True
         self.metadata["is_convolved"] = True
@@ -566,9 +598,23 @@ def __init__(self, filename: str | Path) -> None:
             raise FileNotFoundError("Requested file does not exist")
 
         with h5py.File(filepath, "r") as f:
-            image = np.squeeze(f[filepath.stem + "/ImageData/Image"][()])
+            root_elements = list(f.keys())
+            if len(root_elements) == 1:
+                root_element = root_elements[0]
+            else:
+                # find root element with ImageData
+                root_element = None
+                for re in root_elements:
+                    if "ImageData" in f[re].keys():
+                        root_element = re
+                        break
+                if root_element is None:
+                    raise ValueError(
+                        "No ImageData found in the file, cannot load image"
+                    )
+            image = np.squeeze(f[root_element + "/ImageData/Image"][()])
             pixel_sizes = [
-                float(f[filepath.stem + f"/ImageData/DimensionScale{dim}"][()])
+                float(f[root_element + f"/ImageData/DimensionScale{dim}"][()])
                 for dim in list("ZYX")
             ]
 

tests/test_image.py

@@ -1,6 +1,6 @@
 import numpy as np
 import pytest
-from simulatedmicroscopy import HuygensImage, Image
+from simulatedmicroscopy import HuygensImage, Image, HuygensPSF
 
 
 def create_demo_image():
@@ -40,6 +40,25 @@ def test_huygens_notexisting(tmp_path):
     with pytest.raises(FileNotFoundError):
         HuygensImage(tmp_path / "thisfiledoesnotexist.h5")
 
+def test_huygens_loading(tmp_path):
+    import h5py
+    im = create_demo_image()
+    pixel_sizes = im.get_pixel_sizes()
+    filename = tmp_path / "testfile.hdf5"
+    with h5py.File(filename, "w") as f:
+        root = f.create_group("testfile")
+        root.create_dataset("ImageData/Image", data=im.image)
+        [root.create_dataset(f"ImageData/DimensionScale{dim}", data=pixel_sizes[i]) for i,dim in enumerate(list("ZYX"))]
+
+
+    im_loaded = im.load_h5file(filename)
+    im_loaded_huygens_im = HuygensImage(filename)
+    im_loaded_huygens_psf = HuygensPSF(filename)
+
+
+    assert im_loaded == im
+    assert im_loaded_huygens_im == im
+    assert im_loaded_huygens_psf == im
 
 @pytest.mark.parametrize(
     "unit,conversionfactor",