impy-array 2.4.9__tar.gz → 2.4.10__tar.gz

{impy_array-2.4.9 → impy_array-2.4.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: impy-array
-Version: 2.4.9
+Version: 2.4.10
 Summary: Speed up coding/extending image analysis in Python.
 Project-URL: Download, https://github.com/hanjinliu/impy
 Author-email: Hanjin Liu <liuhanjin-sc@g.ecc.u-tokyo.ac.jp>

{impy_array-2.4.9 → impy_array-2.4.10}/impy/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "2.4.9"
+__version__ = "2.4.10"
 __author__ = "Hanjin Liu"
 __email__ = "liuhanjin-sc@g.ecc.u-tokyo.ac.jp"
 

{impy_array-2.4.9 → impy_array-2.4.10}/impy/arrays/_utils/_filters.py

@@ -155,7 +155,8 @@ def gabor_filter(img: np.ndarray, ker: np.ndarray, mode="reflect", cval=0.0):
 
 def skeletonize(img, selem):
     from skimage import morphology
-    skl = morphology.skeletonize_3d(img)
+
+    skl = morphology.skeletonize(img)
     if selem is not None:
         skl = morphology.binary_dilation(skl, selem)
     return skl

{impy_array-2.4.9 → impy_array-2.4.10}/impy/io/__init__.py

@@ -1,7 +1,7 @@
 from ._registry import imread, imread_dask, imsave, mark_reader, mark_writer, read_header
-from . import _tiff, _mrc, _npy, _zarr, _nd2
+from . import _tiff, _mrc, _npy, _zarr, _nd2, _czi
 
-del _tiff, _mrc, _npy, _zarr, _nd2
+del _tiff, _mrc, _npy, _zarr, _nd2, _czi
 
 __all__ = [
     "imread",

impy_array-2.4.10/impy/io/_czi.py

@@ -0,0 +1,52 @@
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+import numpy as np
+from impy.io._registry import IO
+from impy.io._utils import ImageData, ImageMetadata
+
+if TYPE_CHECKING:
+    from czifile import CziFile
+
+@IO.mark_reader(".czi")
+def _(path: str, memmap: bool = False) -> ImageData:
+    """The CZI format reader"""
+    import czifile
+
+    if memmap:
+        raise NotImplementedError("CZI reader does not support memmap mode yet.")
+    else:
+        out = None
+    with czifile.CziFile(path) as czi:
+        data = np.squeeze(czi.asarray(out=out))
+        meta = _parse_czi_meta(czi)
+
+    return ImageData.from_metadata(data, meta)
+
+def _parse_czi_meta(czi: CziFile) -> ImageMetadata:
+    """Parse metadata from a CZI file."""
+    axes_all: str = czi.axes
+    shape = czi.shape
+    axes = "".join(a.lower() for s, a in zip(shape, axes_all) if s > 1)
+    try:
+        img_meta = czi.metadata(raw=False)["ImageDocument"]["Metadata"]
+        scale = {}
+        for item in img_meta["Scaling"]["Items"]["Distance"]:
+            a = item["Id"].lower()
+            if a in axes:
+                scale[a] = item.get("Value", 1e-6) * 1e6  # as micron
+        try:
+            labels = [item["ImageChannelName"] for item in img_meta["Experiment"]["ExperimentBlocks"]["AcquisitionBlock"]["MultiTrackSetup"]["TrackSetup"]["Detectors"]["Detector"]]
+        except Exception:
+            labels = None
+    except KeyError:
+        scale = None
+        labels = None
+
+    return ImageMetadata(
+        axes=axes,
+        scale=scale,
+        unit="μm",
+        metadata=img_meta,
+        labels=labels,
+    )

{impy_array-2.4.9 → impy_array-2.4.10}/impy/io/_mrc.py

@@ -3,7 +3,6 @@ from __future__ import annotations
 from pathlib import Path
 from typing import TYPE_CHECKING
 import warnings
-import os
 import numpy as np
 from impy.io._registry import IO
 from impy.io._utils import rechunk_to_ones, MemmapArrayWriter, ImpyArray, ImageData, ImageMetadata
@@ -113,14 +112,23 @@ def _parse_mrcfile(mrc: MrcObject) -> ImageMetadata:
     else:
         axes = "zyx"
 
+    metadata = {}
     scale = dict.fromkeys(axes, 1.0)
     for a in axes:
         scale[a] = mrc.voxel_size[a] / 10
+    try:
+        orig_x, orig_y, orig_z = mrc.header["origin"].item()
+    except Exception:
+        pass
+    else:
+        metadata["origin_nm"] = np.array([orig_z, orig_y, orig_x], dtype=np.float32) / 10
+
+    metadata["labels"] = mrc.get_labels()
 
     return ImageMetadata(
         axes=axes,
         scale=scale,
         unit={a: "nm" for a in axes},
-        metadata={},
+        metadata=metadata,
         labels=None,
     )

{impy_array-2.4.9 → impy_array-2.4.10}/impy/io/_utils.py

@@ -40,7 +40,7 @@ class MemmapArrayWriter:
         chunksize: tuple[int, ...],
     ):
         self._path = path
-        self._offset = offset
+        self._offset = int(offset)
         self._shape = shape  # original shape
         self._chunksize = chunksize  # chunk size
         # shape = (33, 160, 1000, 1000)
@@ -56,7 +56,9 @@ class MemmapArrayWriter:
         # efficient: shape = (10, 100, 150) and sl = (3:5, 0:100, 0:150)
         # sl = (0:1, 16:32, 0:1000, 0:1000)
 
-        offset = np.sum([sl[i].start * arr.strides[i] for i in range(self._border + 1)])
+        # if input array is e.g. flipped, we need to make it contiguous
+        arr = np.ascontiguousarray(arr)
+        offset = sum(int(sl[i].start * arr.strides[i]) for i in range(self._border + 1))
         arr_ravel = arr.ravel()
         mmap = np.memmap(
             self._path,